Citrus Sinensis ID: 000887

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110------1120------1130------1140------1150------1160------1170------1180------1190------1200------1210------1220------1230------124
Protein Sequence
MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVYFDGPQEEE
Secondary Structure (PSIPRED)
cccccccccccccEEEEEEEccccHHHHHHHHHHccccccccccEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccEEEEEEcccccccHHHHHHHHHHccccccccEEEEEcccHHHHHHccccccEEcccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHcccccHHHHHHHccccccccHHHHHHHHccccccccccccccHHHHccccccccccHHHcccccccccccEEcHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHccccEEEccccccEEEcHHHHHHHHHHHHccEEEEEcccccccccccccccEEEEEEEccccccccccccccccccccEEccccccccccccccccHHHHHHHccccccccEEEcccccccccccccccccccccccccccccccccHHHHccccccEEEcccccccccccccccccccccEEEEccccccccccccccccccccccccEEEcccccccHHHcccccccccEEEEccccccccHHHHHHccccccccccEEEEEEccccccccccHHHHHHHHccccccccccEEEEEEcccccccccccccccccEEEEEEEcccccccccccccccccccEEEccccccEEEcccccccccccccccccEEEcccccccccccccccccccccccccccEEEEccccccccccccccccccEEEEcccccccccccccccccEEEEccccccccccccccccccccEEccccccccccccccccccEEEEEcccccccccccccccccccccccccEEEEEccccccccccccccccccEEEEEccccccccccccccccccccEEEEcccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccEEEEEcccccccccccccccccccEEEEEcccccccccccccccccccEEEEEcccccccccccccccccccEEEEEEcccccccccccccccccEEEEEEcccccccccccccccccEEEEEccccccccccccccccccEEEEEccccccccccccccccccccEEEEEcccccEEcccccccccccccccEEEEEccccccccccccccccccccEEEEEccccccccccccccccccEEEEEcccccccccccccccccccccccEEEEccEEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEEccccccHHHHHHHHHcHHHHHHccEEEEEEEcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccEEEEEEEccccccHHHHHHHHHHHHccccccEEEEEEccHHHHHHHccccccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHccccHHHHHHHHHcHHccccccccccHHEEEEHcccccHHHHHHHEHHcccccccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHcccccccccEEHHHHHHHHHHHHcccEEEEEcccccccccccccccEEEEEEEEcccccccccccHHHHHHHccEEccccccccccccccccHHHHHHHHHHcccEEEEEccccccccccccccccHHHEEEEccccccccccccccccHHHHHEEHcccccHHHccHcccccccccEEEccccccHccccccccccccccEEcEEEEcccccccHHHHHcHHHcccEEEEccccccccHHHHHHHHHHccccccEEEEEEcccccccccccHcHHHHHHHcccccccEEEEEEcccccccccccccccccccEEEEEcccccccccccccccccccEEEEcccccEEEccHHHccccccccccccEEEEEcccHHHHHcccccccHHHccccccccEEEEccccHHcccccHHcccHcHEEHcccHHHcccccccccccEEEEccccccccccccccccccccccccccccccccccccccccEEEEcccHHcccccccccccccccccccccEEEEcccccccccccccccccccEEEEccccccccccHHHcccccccEEEEEcccccccccccccccccccEEEEcccccHcccccHHccHcccccccccccccccccccccEEEEEccccccccccHcccccccccEEEEcccccHccccccccccccccEEEEccccccccccccccccccccEEEEcccccHHcccccccccccccEEEEcccccccccccccccccccEEEEcccHHHcccccccccccccEEEEcccccccccccccccccccEEEEccccccccccHHcccccccccEEEEcccccccccccccccccccccccEEEEcccHcHHcccHHHHHccccHHEEEEcccccccccccccccccccEEEEcccHHHHHcccccccccccEccccEEEEcccEEEEEccccccHcc
Coil and Loop (DISEMBL)
mvlkndpsdaanfrviplvgmggigkTTLAQEVYNdklteafepkawvcvsddfdVLRISKAILDSIkrssckledLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQAlkspfmagapgsriIVTTRSMDVALTmgsgknyelkllsdddcwSVFVAHAfegrdagthgnfeSTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIwnlqdkteipsvlklsyhhlpshlkRCFAYCAvlpkdyefkEKELVLLWIAEGLvqqsednkqledlgsgyfhdllsrslfqkssntesKYVMHDLVHDLaqwasgetcfrlddqfsvdrqsnvfekvrhfsylrsydcdgmdkFKVLDKVVNLRTFLPiffkqwriyppnispmvlsdllpqckklrvlslgsycitevpisiGCLKqlrylnfsrseiqclpdAICSLFNLEILILRNCWcllklpsrignlvnlHYLNIEGASALRELPLGMKELKCLRTLTnfivgkdsgcalrdlknwkfLRGRLCISGLENVIDSQEANEAMLRVKEGLtdlkldwrprrdgdsvdEAREKNILDMlkphsnikrleihsyggtrfpswvgdpsfsNVAVLILKncrrstslpslgqlcslkdlTIVGMSELKSIGseiygegcskpfqslQTLYFEDLQewehwepnrdndehvqAFPRLrklsikkcpklsgrlpnhlpslEEIVIAGCMHLAvslpslpalctmeidgckrlvcdgpseskspnkmtlcnisefenwssekFQKVEQLMIVGCEGFvneiclekplqglqRLTCLkdlligncptvvslpkacflpnlseitIQDCNALasltdgmiynnaRLEVLRIKRCdsltsisrehlpsslqaieirdcETLQCVLddreksctsssvtekninsssstyldleslfvyrcpsltclwsggrlpvtlkrlriedcsnfkvltsecqlpvevEELTIYGCSNLESIAErfhddaclrsIWISScenlkslpkglsnlshlhEIRIVrchnlvslpedalpsnvVDVLIEDCDKLkaliptgtlsSLRELalsecpgivvfpeeglstnltdleisgdnmykplvkwGFHKLTSLRKLyidgcsdavsfpdvgkgvilptsltsitisdfpklkrlsskgFQYLVSLEHlsvfscpnftsfpeagfpssllsleiqrcpllekckmrkgqewpkiahipltlinqerkhkvyfdgpqeee
Flexible Loop (DISEMBL)
mvlkndpsdaanfrVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILdsikrssckledlNSVQLElketvfkkKFLIVLDDVWSERYDLWQAlkspfmagapgSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGrdagthgnfeSTRQRVVEKCKGLPLAARALggllrskqgvDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNfivgkdsgcalRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKegltdlkldwrprrdgdsvdeAREKnildmlkphsnikRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRrstslpslgqlcslkDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCdgpseskspnkMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTsisrehlpsslqaieiRDCETLQCVLDDreksctsssvtekninsssstyldLESLFVYRCPSLTCLWSGGRLPVTLKRLRiedcsnfkvltsecqlpvEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTsltsitisdfpklkrLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIahipltlinqerkHKVYFDGPQEEE
Low Complexity Region (SEG)
MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKglplaaralggllrSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVYFDGPQEEE
Disordered region (IsUnstruct)
***********NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQ********DLGSGYFHDLLSRSLFQ*****ESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDW*****************LDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPN*****HVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCD***********TLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLD**********************YLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVYF*******
Disordered Region (DISOPRED)
MVL******AA**RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR**********VQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFE********NFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFS*****NVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRD*******REKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLD**********VTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAE*FHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKV**D******
Disordered Region (DISEMBL)
********DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDR***************SSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVY********
Disordered Region (DISPRO)
******PSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVYF*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQERKHKVYFDGPQEEE
Positional Conservation
no confident homologs detected

---

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	1237	2.2.26 [Sep-21-2011]
Q9LRR4	1054	Putative disease resistan	yes	no	0.636	0.746	0.381	1e-153
Q9LRR5	1424	Putative disease resistan	no	no	0.578	0.502	0.406	1e-144
Q7XBQ9	970	Disease resistance protei	N/A	no	0.619	0.789	0.339	1e-113
Q7XA39	988	Putative disease resistan	N/A	no	0.617	0.773	0.338	1e-112
Q7XA40	992	Putative disease resistan	N/A	no	0.636	0.793	0.342	1e-112
Q7XA42	979	Putative disease resistan	N/A	no	0.616	0.779	0.336	1e-111
P0DI18	1049	Probable disease resistan	no	no	0.576	0.679	0.290	9e-55
P0DI17	1049	Probable disease resistan	no	no	0.576	0.679	0.290	9e-55
Q39214	926	Disease resistance protei	no	no	0.381	0.509	0.292	2e-50
Q38834	852	Disease resistance RPP13-	no	no	0.453	0.658	0.299	2e-48

>sp|Q9LRR4|R13L1_ARATH Putative disease resistance RPP13-like protein 1 OS=Arabidopsis thaliana GN=RPPL1 PE=3 SV=1

 Score =  542 bits (1396), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 326/855 (38%), Positives = 487/855 (56%), Gaps = 68/855 (7%)

Query: 15   VIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIKRSSCK 73
            V+ +VG+GG+GKTTL+Q +YND+   + F  K W  VS++FDV +I+K + +S+    C+
Sbjct: 198  VVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPCE 257

Query: 74   LEDLNSVQLELKE--TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM 131
              DL+ +Q++LKE  T     FL+VLDD+W+E +  W  L+ PF+  A GS+I+VTTRS 
Sbjct: 258  FTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQ 317

Query: 132  DVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA 191
             VA  M +   + L+ LSD DCWS+F+   F  ++   +       +R+V KC+GLPLA 
Sbjct: 318  RVASIMCAVHVHNLQPLSDGDCWSLFMKTVFGNQEPCLNREIGDLAERIVHKCRGLPLAV 377

Query: 192  RALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLP 250
            + LGG+LR +  V EW  +L S+IW+L  DK+ +  VL++SY++LP+HLKRCFAYC++ P
Sbjct: 378  KTLGGVLRFEGKVIEWERVLSSRIWDLPADKSNLLPVLRVSYYYLPAHLKRCFAYCSIFP 437

Query: 251  KDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHD 310
            K + F++ ++VLLW+AEG +QQ+  +K LE+LG+ YF +L SRSL QK   T+++Y+MHD
Sbjct: 438  KGHAFEKDKVVLLWMAEGFLQQTRSSKNLEELGNEYFSELESRSLLQK---TKTRYIMHD 494

Query: 311  LVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLR 370
             +++LAQ+ASGE   + +D   +     V E+ R+ SYLR    + M+ F+ L +V  LR
Sbjct: 495  FINELAQFASGEFSSKFEDGCKL----QVSERTRYLSYLRDNYAEPME-FEALREVKFLR 549

Query: 371  TFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS-IGCLKQLRYLN 429
            TFLP+           +  MV   LLP   +LRVLSL  Y I  +P      +   R+L+
Sbjct: 550  TFLPLSLTN-SSRSCCLDQMVSEKLLPTLTRLRVLSLSHYKIARLPPDFFKNISHARFLD 608

Query: 430  FSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG 489
             SR+E++ LP ++C ++NL+ L+L  C  L +LP+ I NL+NL YL++ G + LR++P  
Sbjct: 609  LSRTELEKLPKSLCYMYNLQTLLLSYCSSLKELPTDISNLINLRYLDLIG-TKLRQMPRR 667

Query: 490  MKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEG 549
               LK L+TLT F V    G  + +L     L G+L I  L+ V+D  +A EA L  K+ 
Sbjct: 668  FGRLKSLQTLTTFFVSASDGSRISELGGLHDLHGKLKIVELQRVVDVADAAEANLNSKKH 727

Query: 550  LTDLKLDWRPRRDGDSVDE--------AREKNILDMLKPHSNIKRLEIHSYGGTRFPSWV 601
            L ++   W   R G S  E          E  + + L+PH +I++L I  Y G RFP W+
Sbjct: 728  LREIDFVW---RTGSSSSENNTNPHRTQNEAEVFEKLRPHRHIEKLAIERYKGRRFPDWL 784

Query: 602  GDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIY------GEGC 655
             DPSFS +  + L+ C+  TSLPSLGQL  LK+L I GM  L+SIG + Y       +  
Sbjct: 785  SDPSFSRIVCIRLRECQYCTSLPSLGQLPCLKELHISGMVGLQSIGRKFYFSDQQLRDQD 844

Query: 656  SKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLE 715
             +PF+SL+TL F++L +W+ W   R     +  FP L+KL I +CP+L+G LP  LPSL 
Sbjct: 845  QQPFRSLETLRFDNLPDWQEWLDVRVTRGDL--FPSLKKLFILRCPELTGTLPTFLPSLI 902

Query: 716  EIVIAGCM-------HLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEF 768
             + I  C        H   S  +L  L       C  LV                     
Sbjct: 903  SLHIYKCGLLDFQPDHHEYSYRNLQTLSIK--SSCDTLV--------------------- 939

Query: 769  ENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF 828
              +    F  +++L +  C    +   LE   + L+    L++L I +C  +  LPK   
Sbjct: 940  -KFPLNHFANLDKLEVDQCTSLYS---LELSNEHLRGPNALRNLRINDCQNLQLLPKLNA 995

Query: 829  LPNLSEITIQDCNAL 843
            LP   ++TI +C  L
Sbjct: 996  LPQNLQVTITNCRYL 1010

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

>sp|Q9LRR5|DRL21_ARATH Putative disease resistance protein At3g14460 OS=Arabidopsis thaliana GN=At3g14460 PE=3 SV=1

 Score =  513 bits (1320), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 300/738 (40%), Positives = 438/738 (59%), Gaps = 23/738 (3%)

Query: 1   MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRI 59
           ++L +D        VI +VGM G+GKTTL + V+ND ++TE FE K W+    +F+V  +
Sbjct: 181 LLLSDDEISIGKPAVISVVGMPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTV 240

Query: 60  SKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
           +KA+L  I  S+   EDL S+Q++LK+T+  K+FL+VLDD WSE    W++ +  F    
Sbjct: 241 TKAVLQDITSSAVNTEDLPSLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAE 300

Query: 120 PGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGT-HGNFESTRQ 178
            GS+I++TTRS  V+    + K Y++KL+++++CW +    AF     G+ +   E   +
Sbjct: 301 EGSKIVLTTRSEIVSTVAKAEKIYQMKLMTNEECWELISRFAFGNISVGSINQELEGIGK 360

Query: 179 RVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSH 238
           R+ E+CKGLPLAARA+   LRSK   D+W A+  SK ++    + +P VLKLSY  LP  
Sbjct: 361 RIAEQCKGLPLAARAIASHLRSKPNPDDWYAV--SKNFSSYTNSILP-VLKLSYDSLPPQ 417

Query: 239 LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK 298
           LKRCFA C++ PK + F  +ELVLLW+A  L+ Q   +++LED+G+ Y  DL+++S FQ+
Sbjct: 418 LKRCFALCSIFPKGHVFDREELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQR 477

Query: 299 SSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMD 358
              T + +VMHDL++DLA+  SG+ CFRL+D    D    +    RHFS+ RS  CD   
Sbjct: 478 LDITMTSFVMHDLMNDLAKAVSGDFCFRLED----DNIPEIPSTTRHFSFSRS-QCDASV 532

Query: 359 KFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS 418
            F+ +     LRT LP F     +    ++  VL+ LL     LR+LSL  Y IT +P S
Sbjct: 533 AFRSICGAEFLRTILP-FNSPTSLESLQLTEKVLNPLLNALSGLRILSLSHYQITNLPKS 591

Query: 419 IGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE 478
           +  LK LRYL+ S ++I+ LP+ +C+L NL+ L+L NC  L  LP  I  L+NL  L++ 
Sbjct: 592 LKGLKLLRYLDLSSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDLV 651

Query: 479 GASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQE 538
           G + L E+P G+K+L+ L+ L+NF++G+ SG  L +LK    LRG L IS L+NV  + E
Sbjct: 652 G-TPLVEMPPGIKKLRSLQKLSNFVIGRLSGAGLHELKELSHLRGTLRISELQNVAFASE 710

Query: 539 ANEAMLRVKEGLTDLKLDWRPRRDG-----DSVDEAREKNILDMLKPHSNIKRLEIHSYG 593
           A +A L+ K  L  L L W  +  G      +     +K +L ML+PH ++K   I SY 
Sbjct: 711 AKDAGLKRKPFLDGLILKWTVKGSGFVPGSFNALACDQKEVLRMLEPHPHLKTFCIESYQ 770

Query: 594 GTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSE-IYG 652
           G  FP W+GD SF  +  + L +C    SLP +GQL SLK L+I   + L+ +G +  +G
Sbjct: 771 GGAFPKWLGDSSFFGITSVTLSSCNLCISLPPVGQLPSLKYLSIEKFNILQKVGLDFFFG 830

Query: 653 EGCSK--PFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNH 710
           E  S+  PFQSLQ L F  +  W+ W      D     FP L+KL I++CP L  + P  
Sbjct: 831 ENNSRGVPFQSLQILKFYGMPRWDEWICPELED---GIFPCLQKLIIQRCPSLRKKFPEG 887

Query: 711 LPSLEEIVIAGCMHLAVS 728
           LPS  E+ I+ C   AVS
Sbjct: 888 LPSSTEVTISDCPLRAVS 905

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score =  410 bits (1054), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 300/883 (33%), Positives = 441/883 (49%), Gaps = 117/883 (13%)

Query: 2   VLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRIS 60
           +L N+ SDA +  V+P++GMGG+GKTTLAQ V+ND ++TE F  K W+CVS+DFD  R+ 
Sbjct: 164 ILINNVSDAQHLSVLPILGMGGLGKTTLAQMVFNDQRVTEHFHSKIWICVSEDFDEKRLI 223

Query: 61  KAILDSIK-RSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
           KAI++SI+ R      DL  +Q +L+E +  K++L+VLDDVW+E    W  L++    GA
Sbjct: 224 KAIVESIEGRPLLGEMDLAPLQKKLQELLNGKRYLLVLDDVWNEDQQKWANLRAVLKVGA 283

Query: 120 PGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR 179
            G+ ++ TTR   V   MG+ + YEL  LS +DCW +F+  AF G     + N  +  + 
Sbjct: 284 SGASVLTTTRLEKVGSIMGTLQPYELSNLSQEDCWLLFMQRAF-GHQEEINPNLVAIGKE 342

Query: 180 VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSH 238
           +V+K  G+PLAA+ LGG+L  K+    W  + DS IWNL QD++ I   L+LSYH LP  
Sbjct: 343 IVKKSGGVPLAAKTLGGILCFKREERAWEHVRDSPIWNLPQDESSILPALRLSYHQLPLD 402

Query: 239 LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK 298
           LK+CFAYCAV PKD + ++++L+ LW+A G +  S+ N +LED+G   + +L  RS FQ+
Sbjct: 403 LKQCFAYCAVFPKDAKMEKEKLISLWMAHGFL-LSKGNMELEDVGDEVWKELYLRSFFQE 461

Query: 299 SSNTESK--YVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDG 356
               + K  + MHDL+HDLA              FS +  S+   ++   SY        
Sbjct: 462 IEVKDGKTYFKMHDLIHDLA-----------TSLFSANTSSSNIREINKHSYTHMMSIG- 509

Query: 357 MDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVP 416
                          F  + F  +   PP          L +   LRVL+LG     ++P
Sbjct: 510 ---------------FAEVVF--FYTLPP----------LEKFISLRVLNLGDSTFNKLP 542

Query: 417 ISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN 476
            SIG L  LRYLN   S ++ LP  +C L NL+ L L+ C  L  LP     L +L  L 
Sbjct: 543 SSIGDLVHLRYLNLYGSGMRSLPKQLCKLQNLQTLDLQYCTKLCCLPKETSKLGSLRNLL 602

Query: 477 IEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDS 536
           ++G+ +L  +P  +  L CL+TL  F+VG+  G  L +L N   L G + IS LE V + 
Sbjct: 603 LDGSQSLTCMPPRIGSLTCLKTLGQFVVGRKKGYQLGELGNLN-LYGSIKISHLERVKND 661

Query: 537 QEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTR 596
           ++A EA L  K  L  L + W     G  + E+ E  +L+ LKPHSN+  L+I+ + G  
Sbjct: 662 KDAKEANLSAKGNLHSLSMSW--NNFGPHIYESEEVKVLEALKPHSNLTSLKIYGFRGIH 719

Query: 597 FPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCS 656
            P W+      N+  +++ N R  + LP  G L  L+ L +                   
Sbjct: 720 LPEWMNHSVLKNIVSILISNFRNCSCLPPFGDLPCLESLEL------------------- 760

Query: 657 KPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQ-----AFPRLRKLSIKKCPKLSGRLPN-- 709
             + S    Y E++          D D H        FP LRKL I     L G L    
Sbjct: 761 -HWGSADVEYVEEV----------DIDVHSGFPTRIRFPSLRKLDIWDFGSLKGLLKKEG 809

Query: 710 --HLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE 767
               P LEE++I  C  L +S  +L AL ++ I       C     +  P +M       
Sbjct: 810 EEQFPVLEEMIIHECPFLTLS-SNLRALTSLRI-------CYNKVATSFPEEM------- 854

Query: 768 FENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKAC 827
           F+N ++ K+     L I  C        L++    L  L  LK L I  C  + SLP+  
Sbjct: 855 FKNLANLKY-----LTISRCNN------LKELPTSLASLNALKSLKIQLCCALESLPEEG 903

Query: 828 F--LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSL 868
              L +L+E+ ++ CN L  L +G+ +    L  L+I+ C  L
Sbjct: 904 LEGLSSLTELFVEHCNMLKCLPEGLQHLTT-LTSLKIRGCPQL 945

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA39|RGA4_SOLBU Putative disease resistance protein RGA4 OS=Solanum bulbocastanum GN=RGA4 PE=2 SV=1

 Score =  407 bits (1045), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 307/907 (33%), Positives = 454/907 (50%), Gaps = 143/907 (15%)

Query: 2   VLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRIS 60
           +L N+ + A    V P++GMGG+GKTTLAQ ++ND ++T+ F PK WVCVSDDFD  R+ 
Sbjct: 166 ILINNVNVAEELPVFPIIGMGGLGKTTLAQMIFNDERVTKHFNPKIWVCVSDDFDEKRLI 225

Query: 61  KAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
           K I+ +I+RSS  +EDL S Q +L+E +  K++L+VLDDVW++  + W  L++    GA 
Sbjct: 226 KTIIGNIERSSPHVEDLASFQKKLQELLNGKRYLLVLDDVWNDDLEKWAKLRAVLTVGAR 285

Query: 121 GSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRV 180
           G+ I+ TTR   V   MG+ + Y L  LS  D   +F+  AF G+    + N  +  + +
Sbjct: 286 GASILATTRLEKVGSIMGTLQPYHLSNLSPHDSLLLFMQRAF-GQQKEANPNLVAIGKEI 344

Query: 181 VEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHL 239
           V+KC G+PLAA+ LGGLLR K+   EW  + D++IW+L QD++ I   L+LSYHHLP  L
Sbjct: 345 VKKCGGVPLAAKTLGGLLRFKREESEWEHVRDNEIWSLPQDESSILPALRLSYHHLPLDL 404

Query: 240 KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ-- 297
           ++CFAYCAV PKD +  ++ L+ LW+A G +  S+ N +LED+G+  +++L  RS FQ  
Sbjct: 405 RQCFAYCAVFPKDTKMIKENLITLWMAHGFL-LSKGNLELEDVGNEVWNELYLRSFFQEI 463

Query: 298 --KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCD 355
             KS NT  K  +HDL+HDLA                    +++F          S  C 
Sbjct: 464 EAKSGNTYFK--IHDLIHDLA--------------------TSLFSA--------SASCG 493

Query: 356 GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEV 415
            + +  V D      T    F      Y P+        LL +   LRVL+L    + ++
Sbjct: 494 NIREINVKDYK---HTVSIGFAAVVSSYSPS--------LLKKFVSLRVLNLSYSKLEQL 542

Query: 416 PISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYL 475
           P SIG L  LRYL+ S +  + LP+ +C L NL+ L + NC+ L  LP +   L +L +L
Sbjct: 543 PSSIGDLLHLRYLDLSCNNFRSLPERLCKLQNLQTLDVHNCYSLNCLPKQTSKLSSLRHL 602

Query: 476 NIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVID 535
            ++G   L   P  +  L CL+TL  FIVG   G  L +LKN   L G + I+ LE V +
Sbjct: 603 VVDGC-PLTSTPPRIGLLTCLKTLGFFIVGSKKGYQLGELKNLN-LCGSISITHLERVKN 660

Query: 536 SQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGT 595
             +A EA L  K  L  L + W    DG +  E++E  +L+ LKPH N+K LEI ++GG 
Sbjct: 661 DTDA-EANLSAKANLQSLSMSW--DNDGPNRYESKEVKVLEALKPHPNLKYLEIIAFGGF 717

Query: 596 RFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGC 655
           RFPSW+       V  + +K+C+    LP  G+L  L++L      EL++  +E+     
Sbjct: 718 RFPSWINHSVLEKVISVRIKSCKNCLCLPPFGELPCLENL------ELQNGSAEVE---- 767

Query: 656 SKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNH----L 711
                     Y E+      +   R       +FP L+KL I     L G +        
Sbjct: 768 ----------YVEEDDVHSRFSTRR-------SFPSLKKLRIWFFRSLKGLMKEEGEEKF 810

Query: 712 PSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENW 771
           P LEE+ I  C       P+L ++  +E+ G             + N   L +IS     
Sbjct: 811 PMLEEMAILYCPLFV--FPTLSSVKKLEVHG-------------NTNTRGLSSIS----- 850

Query: 772 SSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF--L 829
                                             L+ L  L IG      SLP+  F  L
Sbjct: 851 ---------------------------------NLSTLTSLRIGANYRATSLPEEMFTSL 877

Query: 830 PNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLP--SSLQAIEIRD 887
            NL  ++  D   L  L   +   NA L+ L+I+ CDSL S   + L   +SL  + ++ 
Sbjct: 878 TNLEFLSFFDFKNLKDLPTSLTSLNA-LKRLQIESCDSLESFPEQGLEGLTSLTQLFVKY 936

Query: 888 CETLQCV 894
           C+ L+C+
Sbjct: 937 CKMLKCL 943

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA40|RGA3_SOLBU Putative disease resistance protein RGA3 OS=Solanum bulbocastanum GN=RGA3 PE=2 SV=2

 Score =  405 bits (1042), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 303/884 (34%), Positives = 446/884 (50%), Gaps = 97/884 (10%)

Query: 2   VLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRIS 60
           +L N+ S +    V+P++GMGG+GKTTLAQ V+ND ++TE F  K WVCVSDDFD  R+ 
Sbjct: 164 ILINNVSYSEEVPVLPILGMGGLGKTTLAQMVFNDQRITEHFNLKIWVCVSDDFDEKRLI 223

Query: 61  KAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
           KAI++SI+  S    DL  +Q +L+E +  K++ +VLDDVW+E  + W  L++    GA 
Sbjct: 224 KAIVESIEGKSLGDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQEKWDNLRAVLKIGAS 283

Query: 121 GSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRV 180
           G+ I++TTR   +   MG+ + Y+L  LS +DCW +F   AF      T        + +
Sbjct: 284 GASILITTRLEKIGSIMGTLQLYQLSNLSQEDCWLLFKQRAF-CHQTETSPKLMEIGKEI 342

Query: 181 VEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHL 239
           V+KC G+PLAA+ LGGLLR K+   EW  + DS+IWNL QD+  +   L+LSYHHLP  L
Sbjct: 343 VKKCGGVPLAAKTLGGLLRFKREESEWEHVRDSEIWNLPQDENSVLPALRLSYHHLPLDL 402

Query: 240 KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ-- 297
           ++CFAYCAV PKD + +++ L+ LW+A   +  S+ N +LED+G+  +++L  RS FQ  
Sbjct: 403 RQCFAYCAVFPKDTKIEKEYLIALWMAHSFL-LSKGNMELEDVGNEVWNELYLRSFFQEI 461

Query: 298 KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGM 357
           +  + ++ + MHDL+HDLA      +           RQ NV                  
Sbjct: 462 EVKSGKTYFKMHDLIHDLATSMFSAS-----ASSRSIRQINV-----------------K 499

Query: 358 DKFKVLDKVVNLRTFLPIFFKQ-WRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVP 416
           D   ++  V N +  + I F +    Y P++    +S        LRVL+L +    ++P
Sbjct: 500 DDEDMMFIVTNYKDMMSIGFSEVVSSYSPSLFKRFVS--------LRVLNLSNSEFEQLP 551

Query: 417 ISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN 476
            S+G L  LRYL+ S ++I  LP  +C L NL+ L L NC  L  LP +   L +L  L 
Sbjct: 552 SSVGDLVHLRYLDLSGNKICSLPKRLCKLQNLQTLDLYNCQSLSCLPKQTSKLCSLRNLV 611

Query: 477 IEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDS 536
           ++    L  +P  +  L CL+TL  F+VG+  G  L +L+N   LRG + I+ LE V + 
Sbjct: 612 LDHC-PLTSMPPRIGLLTCLKTLGYFVVGERKGYQLGELRNLN-LRGAISITHLERVKND 669

Query: 537 QEANEAMLRVKEGLTDLKLDW-RPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGT 595
            EA EA L  K  L  L + W RP R      E+ E  +L+ LKPH N+K LEI  + G 
Sbjct: 670 MEAKEANLSAKANLHSLSMSWDRPNR-----YESEEVKVLEALKPHPNLKYLEIIDFCGF 724

Query: 596 RFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGC 655
             P W+      NV  +++  C   + LP  G+L  L+ L      EL+           
Sbjct: 725 CLPDWMNHSVLKNVVSILISGCENCSCLPPFGELPCLESL------ELQD---------- 768

Query: 656 SKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSG----RLPNHL 711
                S++  Y ED                 + FP LRKL I     L G    +     
Sbjct: 769 ----GSVEVEYVEDSGFLTR-----------RRFPSLRKLHIGGFCNLKGLQRMKGAEQF 813

Query: 712 PSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENW 771
           P LEE+ I+ C       P+L ++  +EI G      D    S   N  TL ++  F N 
Sbjct: 814 PVLEEMKISDCPMFV--FPTLSSVKKLEIWG----EADAGGLSSISNLSTLTSLKIFSNH 867

Query: 772 S-----SEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKA 826
           +      E F+ +E L+ +      N   L   L  L  L CL    I  C  + SLP+ 
Sbjct: 868 TVTSLLEEMFKNLENLIYLSVSFLENLKELPTSLASLNNLKCLD---IRYCYALESLPEE 924

Query: 827 CF--LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSL 868
               L +L+E+ ++ CN L  L +G+ +    L  L+I+ C  L
Sbjct: 925 GLEGLSSLTELFVEHCNMLKCLPEGLQHLTT-LTSLKIRGCPQL 967

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA42|RGA1_SOLBU Putative disease resistance protein RGA1 OS=Solanum bulbocastanum GN=RGA1 PE=2 SV=2

 Score =  404 bits (1038), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 289/860 (33%), Positives = 439/860 (51%), Gaps = 97/860 (11%)

Query: 2   VLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRIS 60
           +L N  SDA    V+P++GMGG+GKTTL+Q V+ND ++TE F PK W+C+SDDF+  R+ 
Sbjct: 164 ILINTASDAQKLSVLPILGMGGLGKTTLSQMVFNDQRVTERFYPKIWICISDDFNEKRLI 223

Query: 61  KAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
           KAI++SI+  S    DL  +Q +L+E +  K++ +VLDDVW+E    W  L++    GA 
Sbjct: 224 KAIVESIEGKSLSDMDLAPLQKKLQELLNGKRYFLVLDDVWNEDQHKWANLRAVLKVGAS 283

Query: 121 GSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRV 180
           G+ ++ TTR   V   MG+ + YEL  LS +DCW +F+  AF G     + N  +  + +
Sbjct: 284 GAFVLTTTRLEKVGSIMGTLQPYELSNLSPEDCWFLFMQRAF-GHQEEINPNLMAIGKEI 342

Query: 181 VEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHL 239
           V+KC G+PLAA+ LGG+LR K+   EW  + DS IWNL QD++ I   L+LSYHHLP  L
Sbjct: 343 VKKCGGVPLAAKTLGGILRFKREEREWEHVRDSPIWNLPQDESSILPALRLSYHHLPLDL 402

Query: 240 KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ-- 297
           ++CF YCAV PKD +  ++ L+  W+A G +  S+ N +LED+G+  +++L  RS FQ  
Sbjct: 403 RQCFVYCAVFPKDTKMAKENLIAFWMAHGFL-LSKGNLELEDVGNEVWNELYLRSFFQEI 461

Query: 298 KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGM 357
           +  + ++ + MHDL+HDLA              FS +  S+   ++       + + DG 
Sbjct: 462 EVESGKTYFKMHDLIHDLAT-----------SLFSANTSSSNIREI-------NANYDGY 503

Query: 358 DKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPI 417
                  +VV+              Y P+        LL +   LRVL+L +  + ++P 
Sbjct: 504 MMSIGFAEVVS-------------SYSPS--------LLQKFVSLRVLNLRNSNLNQLPS 542

Query: 418 SIGCLKQLRYLNFSRS-EIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN 476
           SIG L  LRYL+ S +  I+ LP  +C L NL+ L L  C  L  LP +   L +L  L 
Sbjct: 543 SIGDLVHLRYLDLSGNFRIRNLPKRLCKLQNLQTLDLHYCDSLSCLPKQTSKLGSLRNLL 602

Query: 477 IEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDS 536
           ++G S L   P  +  L CL++L+ F++GK  G  L +LKN   L G + I+ L+ V   
Sbjct: 603 LDGCS-LTSTPPRIGLLTCLKSLSCFVIGKRKGHQLGELKNLN-LYGSISITKLDRVKKD 660

Query: 537 QEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTR 596
            +A EA L  K  L  L L W    D D      +  +L+ LKPHSN+K LEI+ +GG R
Sbjct: 661 TDAKEANLSAKANLHSLCLSW----DLDG-KHRYDSEVLEALKPHSNLKYLEINGFGGIR 715

Query: 597 FPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCS 656
            P W+      NV  + ++ C   + LP  G+L  L+ L      EL +  +++      
Sbjct: 716 LPDWMNQSVLKNVVSIRIRGCENCSCLPPFGELPCLESL------ELHTGSADVE----- 764

Query: 657 KPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLP----NHLP 712
                    Y ED             + H   FP LRKL I     L G L        P
Sbjct: 765 ---------YVED-------------NVHPGRFPSLRKLVIWDFSNLKGLLKMEGEKQFP 802

Query: 713 SLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWS 772
            LEE+    C    +  P+L ++ T+++      V    S  ++   + + +  E  +  
Sbjct: 803 VLEEMTFYWCPMFVI--PTLSSVKTLKVIVTDATVLRSISNLRALTSLDISDNVEATSLP 860

Query: 773 SEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF--LP 830
            E F+ +  L  +    F N   L++    L  L  LK L    C  + SLP+     L 
Sbjct: 861 EEMFKSLANLKYLKISFFRN---LKELPTSLASLNALKSLKFEFCDALESLPEEGVKGLT 917

Query: 831 NLSEITIQDCNALASLTDGM 850
           +L+E+++ +C  L  L +G+
Sbjct: 918 SLTELSVSNCMMLKCLPEGL 937

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

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

 Score =  216 bits (550), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 237/816 (29%), Positives = 376/816 (46%), Gaps = 103/816 (12%)

Query: 9   DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
           D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct: 179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query: 68  K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
           K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct: 239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query: 124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHG---NFESTRQR 179
           +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA         E   + 
Sbjct: 296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query: 180 VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL---------QDKTEIPSVLKL 230
           +++ C GLPLA R LGG+L  K    +WR + ++   +L          +      VL L
Sbjct: 356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSL 415

Query: 231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQ-QSEDNKQLEDLGSGYFHD 289
           S+  LPS+LK CF Y A  P DYE   K L   W AEG+ Q +  D + + D+G  Y  +
Sbjct: 416 SFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEIIRDVGDVYIEE 475

Query: 290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSN------ 338
           L+ R++       K+S  E+ + +HD++ ++    + E  F    Q +  R S       
Sbjct: 476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENFL---QITSSRTSTGNSLSI 531

Query: 339 VFEKVRHFSYLRSYDCD-GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLP 397
           V  +   + Y  + D +  ++  K+   VV   T++  F+  W       S M+L     
Sbjct: 532 VTSRRLVYQYPITLDVEKDINDPKLRSLVVVANTYM--FWGGW-------SWMLLGSSFI 582

Query: 398 QCKKLRVLSLGSYCIT--EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           + + LRVL +    +   ++  SIG L  LRYLN   +E+  +P    SL NL++LI  N
Sbjct: 583 RLELLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLKHAEVTHIP---YSLGNLKLLIYLN 639

Query: 456 CWCLLK----LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCA 511
              L+     +P+ +  +  L YL +      R+  L +  L  L TL NF       C+
Sbjct: 640 LVILVSGSTLVPNVLKEMQQLRYLALPKDMG-RKTKLELSNLVKLETLKNF---STKNCS 695

Query: 512 LRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGL--TDLKLDWRPRRDGDSVDEA 569
           L DL+    LR        E  +++  A+   L+  E L  TDL  + R +  G   D  
Sbjct: 696 LEDLRGMVRLRTLTIELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFV 755

Query: 570 REKNI-LDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCR-RSTSLPSLG 627
             K + L +  P     RL    +    FP        S++  L L++CR     +P L 
Sbjct: 756 YLKTLTLKLYMP-----RLSKEQH----FP--------SHLTTLYLQHCRLEEDPMPILE 798

Query: 628 QLCSLKDLTIVGMSELKSIGSEIYGEGCSK-PFQSLQTLYFEDLQEWEHWEPNRDNDEHV 686
           +L  LK+L +   S     G E+    CS   F  LQ L  + L+EWE W+         
Sbjct: 799 KLHQLKELELRRKS---FSGKEMV---CSSGGFPQLQKLSIKGLEEWEDWKVEES----- 847

Query: 687 QAFPRLRKLSIKKCPKLSGRLPNHLPS-LEEIVIAGCMHLAVSLPSLPALCTM-EIDGCK 744
            + P L  L I+ C KL      HLPS L  I +  C      +P+L  L  + E+    
Sbjct: 848 -SMPVLHTLDIRDCRKLKQLPDEHLPSHLTSISLFFCCLEEDPMPTLERLVHLKELQLLF 906

Query: 745 R------LVCDGPSESKSPNKMTLCNISEFENWSSE 774
           R      +VC G S     +K+ L  +   E W  E
Sbjct: 907 RSFSGRIMVCAG-SGFPQLHKLKLSELDGLEEWIVE 941

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  216 bits (550), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 237/816 (29%), Positives = 376/816 (46%), Gaps = 103/816 (12%)

Query: 9   DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
           D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct: 179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query: 68  K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
           K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct: 239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query: 124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHG---NFESTRQR 179
           +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA         E   + 
Sbjct: 296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query: 180 VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL---------QDKTEIPSVLKL 230
           +++ C GLPLA R LGG+L  K    +WR + ++   +L          +      VL L
Sbjct: 356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSL 415

Query: 231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQ-QSEDNKQLEDLGSGYFHD 289
           S+  LPS+LK CF Y A  P DYE   K L   W AEG+ Q +  D + + D+G  Y  +
Sbjct: 416 SFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEIIRDVGDVYIEE 475

Query: 290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSN------ 338
           L+ R++       K+S  E+ + +HD++ ++    + E  F    Q +  R S       
Sbjct: 476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENFL---QITSSRTSTGNSLSI 531

Query: 339 VFEKVRHFSYLRSYDCD-GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLP 397
           V  +   + Y  + D +  ++  K+   VV   T++  F+  W       S M+L     
Sbjct: 532 VTSRRLVYQYPITLDVEKDINDPKLRSLVVVANTYM--FWGGW-------SWMLLGSSFI 582

Query: 398 QCKKLRVLSLGSYCIT--EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           + + LRVL +    +   ++  SIG L  LRYLN   +E+  +P    SL NL++LI  N
Sbjct: 583 RLELLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLKHAEVTHIP---YSLGNLKLLIYLN 639

Query: 456 CWCLLK----LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCA 511
              L+     +P+ +  +  L YL +      R+  L +  L  L TL NF       C+
Sbjct: 640 LVILVSGSTLVPNVLKEMQQLRYLALPKDMG-RKTKLELSNLVKLETLKNF---STKNCS 695

Query: 512 LRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGL--TDLKLDWRPRRDGDSVDEA 569
           L DL+    LR        E  +++  A+   L+  E L  TDL  + R +  G   D  
Sbjct: 696 LEDLRGMVRLRTLTIELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFV 755

Query: 570 REKNI-LDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCR-RSTSLPSLG 627
             K + L +  P     RL    +    FP        S++  L L++CR     +P L 
Sbjct: 756 YLKTLTLKLYMP-----RLSKEQH----FP--------SHLTTLYLQHCRLEEDPMPILE 798

Query: 628 QLCSLKDLTIVGMSELKSIGSEIYGEGCSK-PFQSLQTLYFEDLQEWEHWEPNRDNDEHV 686
           +L  LK+L +   S     G E+    CS   F  LQ L  + L+EWE W+         
Sbjct: 799 KLHQLKELELRRKS---FSGKEMV---CSSGGFPQLQKLSIKGLEEWEDWKVEES----- 847

Query: 687 QAFPRLRKLSIKKCPKLSGRLPNHLPS-LEEIVIAGCMHLAVSLPSLPALCTM-EIDGCK 744
            + P L  L I+ C KL      HLPS L  I +  C      +P+L  L  + E+    
Sbjct: 848 -SMPVLHTLDIRDCRKLKQLPDEHLPSHLTSISLFFCCLEEDPMPTLERLVHLKELQLLF 906

Query: 745 R------LVCDGPSESKSPNKMTLCNISEFENWSSE 774
           R      +VC G S     +K+ L  +   E W  E
Sbjct: 907 RSFSGRIMVCAG-SGFPQLHKLKLSELDGLEEWIVE 941

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  202 bits (513), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 159/544 (29%), Positives = 265/544 (48%), Gaps = 72/544 (13%)

Query: 15  VIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS-- 71
           V+ +VGMGG GKTTL+  ++  + +   FE  AWV +S  + +  + + ++    + +  
Sbjct: 195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query: 72  ---CKLEDLNSVQL--ELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV 126
               +L  L   +L  +L E +  K++++VLDDVW+    LW+ +      G  GSR+++
Sbjct: 255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTT--GLWREISIALPDGIYGSRVMM 312

Query: 127 TTRSMDVA---LTMGSGKNYELKLLSDDDCWSVFVAHAFEGR-DAGTHGNFESTRQRVVE 182
           TTR M+VA     +GS K +E++LL +D+ W +F   AF    +     N E   +++VE
Sbjct: 313 TTRDMNVASFPYGIGSTK-HEIELLKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVE 371

Query: 183 KCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTE---IPSVLKLSYHHLPSHL 239
           +C+GLPLA  +LG ++ +K+   EW+ +  +  W L +  E   + S++ LS++ LP  L
Sbjct: 372 RCQGLPLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYPL 431

Query: 240 KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ-- 297
           KRCF YC++ P +Y  K K L+ +W+A+  V+     K  E++   Y ++L+ R++ Q  
Sbjct: 432 KRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKA-EEVADSYLNELVYRNMLQVI 490

Query: 298 --KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCD 355
                     + MHD++ ++A   S                     K+  F  + + D D
Sbjct: 491 LWNPFGRPKAFKMHDVIWEIALSVS---------------------KLERFCDVYNDDSD 529

Query: 356 GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEV 415
           G D  + ++   +    +     Q  + P +I    L  LL       V S   + +  +
Sbjct: 530 GDDAAETMENYGSRHLCI-----QKEMTPDSIRATNLHSLL-------VCSSAKHKMELL 577

Query: 416 PISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYL 475
           P     L  LR L+   S I  LPD + ++FNL+ L L     + +LP     LVNL  L
Sbjct: 578 P----SLNLLRALDLEDSSISKLPDCLVTMFNLKYLNLSKT-QVKELPKNFHKLVNLETL 632

Query: 476 NIEGASALRELPLGMKELKCLRTLTNFIV--GKDSGCALRDLKNWKFLRGRLCISGLENV 533
           N +  S + ELPLGM +LK LR L  F    G DS        NW ++ G   +  +  +
Sbjct: 633 NTK-HSKIEELPLGMWKLKKLRYLITFRRNEGHDS--------NWNYVLGTRVVPKIWQL 683

Query: 534 IDSQ 537
            D Q
Sbjct: 684 KDLQ 687

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q38834|R13L4_ARATH Disease resistance RPP13-like protein 4 OS=Arabidopsis thaliana GN=RPP13L4 PE=2 SV=2

 Score =  195 bits (496), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 184/615 (29%), Positives = 280/615 (45%), Gaps = 54/615 (8%)

Query: 8   SDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDS 66
           S+ +   ++  VGMGG+GKTT+AQEV+NDK  E  FE + WV VS  F   +I ++IL +
Sbjct: 177 SNDSQLLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRN 236

Query: 67  IKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV 126
           +  +S   +D+ ++  ++++ +  K++LIV+DDVW +    W  +      G  GS +IV
Sbjct: 237 LGDASVG-DDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGS-VIV 294

Query: 127 TTRSMDVA--LTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAG-THGNFESTRQRVVEK 183
           TTRS  VA  +     K +  +LLS D+ W +F   AF   D        E   + +V K
Sbjct: 295 TTRSESVAKRVQARDDKTHRPELLSPDNSWLLFCNVAFAANDGTCERPELEDVGKEIVTK 354

Query: 184 CKGLPLAARALGGLLRSKQGV-DEWRAIL----DSKIWNLQDKTEIPSVLKLSYHHLPSH 238
           CKGLPL  +A+GGLL  K  V  EWR I     D    N  +   + S L+LSY  LPSH
Sbjct: 355 CKGLPLTIKAVGGLLLCKDHVYHEWRRIAEHFQDELRGNTSETDNVMSSLQLSYDELPSH 414

Query: 239 LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK 298
           LK C    ++ P+D    +++LV  WI EG V         E  G   F  L +R L + 
Sbjct: 415 LKSCILTLSLYPEDCVIPKQQLVHGWIGEGFVMWRNGRSATES-GEDCFSGLTNRCLIEV 473

Query: 299 SSNTESKYV----MHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDC 354
              T S  +    +HD+V DL             D FS     N     RH     ++D 
Sbjct: 474 VDKTYSGTIITCKIHDMVRDLV------IDIAKKDSFSNPEGLN----CRHLGISGNFD- 522

Query: 355 DGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITE 414
                    +K + +   L       +    N     L+     CK LRVL + S  I +
Sbjct: 523 ---------EKQIKVNHKLRGVVSTTKTGEVNKLNSDLAKKFTDCKYLRVLDI-SKSIFD 572

Query: 415 VPIS-----IGCLKQLRYLNFSRSE--IQCLPDAICSLFNLEILILRNCWCLLKLPSRIG 467
            P+S     I  L+ L  L+ S +   IQ  P ++  L NL+IL    C  L +L   I 
Sbjct: 573 APLSEILDEIASLQHLACLSLSNTHPLIQ-FPRSMEDLHNLQILDASYCQNLKQLQPCIV 631

Query: 468 NLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGK-DSGCALRDLKNWKFLRGRLC 526
               L  L++    +L   P G+  L  L  L  F   + ++GC L ++KN   LR +L 
Sbjct: 632 LFKKLLVLDMTNCGSLECFPKGIGSLVKLEVLLGFKPARSNNGCKLSEVKNLTNLR-KLG 690

Query: 527 ISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKR 586
           +S        +E  ++++ + + L  + ++       D + +      +D L P   +  
Sbjct: 691 LSLTRGDQIEEEELDSLINLSK-LMSISINCYDSYGDDLITK------IDALTPPHQLHE 743

Query: 587 LEIHSYGGTRFPSWV 601
           L +  Y G   PSW+
Sbjct: 744 LSLQFYPGKSSPSWL 758

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	1237
284026888	1424	CC-NBS-LRR protein [Quercus suber]	0.981	0.852	0.463	0.0
356554923	1399	PREDICTED: putative disease resistance R	0.953	0.842	0.434	0.0
225449649	1418	PREDICTED: putative disease resistance p	0.921	0.803	0.416	0.0
359495024	1390	PREDICTED: putative disease resistance p	0.910	0.810	0.412	0.0
359487065	1424	PREDICTED: putative disease resistance p	0.941	0.818	0.401	0.0
359487225	1373	PREDICTED: putative disease resistance R	0.926	0.834	0.422	0.0
147860511	1406	hypothetical protein VITISV_014536 [Viti	0.874	0.769	0.412	0.0
359495026	2204	PREDICTED: uncharacterized protein LOC10	0.897	0.503	0.406	0.0
359487069	1436	PREDICTED: putative disease resistance p	0.940	0.810	0.410	0.0
359487424	1453	PREDICTED: putative disease resistance R	0.950	0.809	0.395	0.0

>gi|284026888|gb|ADB66335.1| CC-NBS-LRR protein [Quercus suber]

 Score = 1043 bits (2698), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 576/1243 (46%), Positives = 811/1243 (65%), Gaps = 29/1243 (2%)

Query: 1    MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRIS 60
            ++LK++ +D +N+ VI +VGM G+GKTTLA+ VYND   + F P+AW+CVSDDFDV+ ++
Sbjct: 184  LILKDEQTDDSNYHVISIVGMAGVGKTTLARLVYNDDAVKHFNPRAWICVSDDFDVMMVT 243

Query: 61   KAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
            KA+L+S+    C L++LN VQ++L   +  KKFL+VLDD+W+E Y LW+AL  PF AGA 
Sbjct: 244  KALLESVTSQPCHLKELNEVQVKLASELEGKKFLLVLDDLWNENYGLWEALLPPFRAGAA 303

Query: 121  GSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRV 180
            GSRIIVTTR+  V   MG+ ++Y L  +S++DCW++FV H+    + G  GN    R+R+
Sbjct: 304  GSRIIVTTRNASVGKVMGAVQSYNLDFISNNDCWAIFVQHSLMNENFGRPGNSGLIRERI 363

Query: 181  VEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQD-KTEIPSVLKLSYHHLPSHL 239
            +E+C+GLPLAAR LGGL R K+ +DEW  I++SK+W+  +  ++I  +L+LSYHHLP HL
Sbjct: 364  LERCRGLPLAARTLGGLFRGKE-LDEWEDIMNSKLWSSSNMGSDIFPILRLSYHHLPHHL 422

Query: 240  KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKS 299
            KRCFAYC++ P+DYEF+EK+L+LLW+AEGL+ Q+E +K +EDLG  YF DLLSRS FQ+S
Sbjct: 423  KRCFAYCSLFPRDYEFEEKQLILLWMAEGLIYQAEGDKPMEDLGGEYFRDLLSRSFFQQS 482

Query: 300  SNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDK 359
            S+ +S++VMHDL+ DLAQW +G + FRL+ +   + QS V  K RH S++ S   DG  K
Sbjct: 483  SSNKSRFVMHDLITDLAQWVAGISYFRLETKLKGNEQSKVSSKARHLSFVGS-RYDGAKK 541

Query: 360  FKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI 419
            F+ + +  +LRTFLP+      +    +S  +++ LLP+ + LRVLSL  Y I  +P +I
Sbjct: 542  FEAISEFKHLRTFLPLMAPY--VGYSYLSYHIINQLLPKLQNLRVLSLSGYRIVYLPQTI 599

Query: 420  GCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
            G LK LRYL+ S ++++ LP +I +L+NL+ L+L NC  L  LP   G L NL +LNI G
Sbjct: 600  GDLKHLRYLDLSCTQLRSLPTSISTLYNLQTLLLENCTSLKFLPPDFGKLFNLRHLNIFG 659

Query: 480  ASALRELPLGMKELKCLRTLTNFIVGK-DSGCALRDLKNWKFLRGRLCISGLENVIDSQE 538
            ++ L  +PL +  L  L+TL+NF+VGK DS C +R+L     LRG LCIS LENV  +QE
Sbjct: 660  SNLLEGMPLSIGNLSSLQTLSNFVVGKADSFCVIRELGPLVHLRGTLCISKLENVTKAQE 719

Query: 539  ANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFP 598
            A ++ L  K+ L ++ ++W    + +S DE  +  +L+ML+P+  +K L +  YGGT+FP
Sbjct: 720  ARDSYLYGKQDLNEVVMEWSSNLN-ESQDEETQLEVLNMLQPNVKLKELTVKCYGGTKFP 778

Query: 599  SWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKP 658
            +W+GDPSFSN+ +L  +NC    SLP +GQL  LKDL I GM+ +KS+G E YGE CS+P
Sbjct: 779  TWIGDPSFSNLVLLRFENCDNCNSLPPVGQLPFLKDLLIKGMAGVKSVGREFYGESCSRP 838

Query: 659  FQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIV 718
            FQSL+TL+FED+  W +W P   N    +AF  L KLSI +C  L  +LP+HLPSL+++V
Sbjct: 839  FQSLETLHFEDMPRWVNWIPLGVN----EAFACLHKLSIIRCHNLVRKLPDHLPSLKKLV 894

Query: 719  IAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSS---EK 775
            I GC ++ VS+ +LP LC + I+GCKR+ C+      SP  M    ISEF N ++     
Sbjct: 895  IHGCWNMVVSVSNLPMLCVLVIEGCKRVECESSVGFGSPYSMAFSKISEFGNATAGLMHG 954

Query: 776  FQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEI 835
              KVE L IV  E        EK  +GL RL  L++L I +CPT+VS P + F   L  I
Sbjct: 955  VSKVEYLKIVDSEKLTT--LWEKIPEGLHRLKFLRELSIEDCPTLVSFPASGFPSMLKVI 1012

Query: 836  TIQDCNALAS-LTDGMIYN--NARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQ 892
             I+ C+ L S L +G +++  NA LE L + RCDS+ SI+R  LP++L+ +EI  C  LQ
Sbjct: 1013 QIKSCSGLKSLLPEGTLHSRENACLERLCVVRCDSMKSIARGQLPTTLKKLEISHCMNLQ 1072

Query: 893  CVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIE 952
            CVLD+ E S +SS + +++IN+ S T+  L+ L +  CPSLT L S G+LP TL  L + 
Sbjct: 1073 CVLDEGEGSSSSSGMHDEDINNRSKTH--LQYLDIKSCPSLTTLTSSGKLPATLTHLLLR 1130

Query: 953  DCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGL 1012
            +C     L+S  +LP  ++ L I   S L+ IAER H +  L  I I +C  LKSLP+ L
Sbjct: 1131 ECPKLMCLSSTGKLPAALQYLEIQSISKLQKIAERLHQNTSLECIKIWNCHGLKSLPEDL 1190

Query: 1013 SNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTG--TLSSLRELALS 1070
             NLS L +  I  C +  S P   LPSN+  + I++C  LKAL P G   L+SL++L +S
Sbjct: 1191 HNLSKLRQFLIFWCQSFSSFPAAGLPSNLRVLGIKNCKNLKAL-PNGMRNLTSLQKLDIS 1249

Query: 1071 ECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDG-CSDAVSFP-- 1127
                 +  P+EGL TNL +L +     YKP+ +WG  + TSL KL I G C D  S+P  
Sbjct: 1250 HRLDSLPSPQEGLPTNLIELNMHDLKFYKPMFEWGLQQPTSLIKLSIHGECLDVDSYPGE 1309

Query: 1128 -DVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSS 1186
             + G  ++LP SL+ + IS F  L+ LS KGFQ L SL  L +++C   TS P+ G P S
Sbjct: 1310 RENGVMMLLPNSLSILCISYFQNLECLSPKGFQNLTSLNQLKIYNCLKLTSLPKEGLPPS 1369

Query: 1187 LLSLEIQRCPLL-EKCKMRKGQEWPKIAHIPLTLINQERKHKV 1228
            L  LEI+ CPLL + C   KGQEW KIAHIP  LI+ +  H+ 
Sbjct: 1370 LTQLEIRNCPLLSQHCNNEKGQEWSKIAHIPCVLIDNKFIHET 1412

Source: Quercus suber

Species: Quercus suber

Genus: Quercus

Family: Fagaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356554923|ref|XP_003545790.1| PREDICTED: putative disease resistance RPP13-like protein 1-like [Glycine max]

 Score =  946 bits (2444), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 543/1251 (43%), Positives = 780/1251 (62%), Gaps = 72/1251 (5%)

Query: 1    MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRI 59
             +++N PS      VIP+VGM GIGKTTLAQ V+ND ++   FE KAWV V  DFDV  +
Sbjct: 180  FLMENRPSHGDEVLVIPIVGMPGIGKTTLAQVVFNDDEVNTHFELKAWVSVPYDFDVKVV 239

Query: 60   SKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
            ++ IL+S+   +C   +L+ +Q++L+  +  KKFLIVLDDVW++ Y+ W  L +PF   A
Sbjct: 240  TRKILESVTCVTCDFNNLHQLQVKLRAVLSGKKFLIVLDDVWNKNYNEWIKLVAPFRGAA 299

Query: 120  PGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTH------GNF 173
             GS +IVTTRS +VA  MG+ +++ +  LSD DCWSVFV HAF  +    +      GNF
Sbjct: 300  RGSSVIVTTRSAEVANMMGTVESHHVNQLSDKDCWSVFVQHAFRSKTIDANQAFAEIGNF 359

Query: 174  ESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSY 232
                +++ EKCKG PL A   GG+L S++   +W  ++D +IW+L ++++ I   L+LSY
Sbjct: 360  -LIGKKIAEKCKGSPLMATTFGGILSSQKDARDWENVMDFEIWDLAEEESNILQTLRLSY 418

Query: 233  HHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLS 292
            + LPS+LKRCFAYC++LPK +EF+EKE+VLLW+AEGL++Q +  KQ+ED+G  YF +LLS
Sbjct: 419  NQLPSYLKRCFAYCSILPKGFEFEEKEIVLLWMAEGLLEQ-KSQKQMEDVGHEYFQELLS 477

Query: 293  RSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEK--VRHFSYLR 350
             SLFQKSS+  S YVMHDL++DLAQW +GE+CF+LD+ F   +Q         R+ SY+ 
Sbjct: 478  ASLFQKSSSNRSLYVMHDLINDLAQWVAGESCFKLDNNFQSHKQKKKKISKMTRYASYVG 537

Query: 351  SYDCDGMDKFKVLDKVVNLRTFLPI---FFKQWRIYPPNISPMVLSDLLPQCKKLRVLSL 407
              + DG+  F+   +  +LRTFLP+     ++W  Y  N  P    +LLP+ + LR LSL
Sbjct: 538  G-EYDGIQMFQAFKEAKSLRTFLPLKHRRLEEWS-YITNHVPF---ELLPELRCLRALSL 592

Query: 408  GSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIG 467
              Y I+++P S+  L  LRYLN S ++++ LP++ICSL NL+ L+LR+C+ L +LPS + 
Sbjct: 593  SGYFISKLPNSVSNLNLLRYLNLSSTDLRQLPESICSLCNLQTLLLRDCFNLEELPSNMS 652

Query: 468  NLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCI 527
            +L+NL +L+I  + +L  +P G+ +L  L+TL+NF+VG      L  L N   +RG L +
Sbjct: 653  DLINLRHLDITRSHSLTRMPHGIGKLTHLQTLSNFVVGSSGIGELMKLSN---IRGVLSV 709

Query: 528  SGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRL 587
            S LE+V D++EA+EAM+  K G+  LKL W    +  S  E R K +L ML+PH N+ +L
Sbjct: 710  SRLEHVTDTREASEAMINKKVGIDVLKLKWTSCMNNQSHTE-RAKEVLQMLQPHKNLAKL 768

Query: 588  EIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIG 647
             I  YGGT FP W+GDPS+ ++  L LK+C   TSLP+LG L +LK+L I+GM E+  I 
Sbjct: 769  TIKCYGGTSFPKWIGDPSYKSLVFLKLKDCAHCTSLPALGNLHALKELYIIGMKEVCCID 828

Query: 648  SEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRL 707
             E  G  C +PF SL+ LYF D+++WE+W  + DN+E    F  L++L I KCPKL G+L
Sbjct: 829  GEFCGNACLRPFPSLERLYFMDMEKWENWFLS-DNNEQNDMFSSLQQLFIVKCPKLLGKL 887

Query: 708  PNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE 767
            P +LPSL+ +++  C  L V++ SLP L  +EI+GCK LV +  +E  S N M++  I E
Sbjct: 888  PENLPSLKHVIVKECEQLLVTISSLPVLYKLEIEGCKGLVLNCANEFNSLNSMSVSRILE 947

Query: 768  FENWSS---EKFQKVEQLMIVGC--------EGFVNEICLEKPLQGLQRLTCLKDLLIGN 816
            F        + F+ VE+L IV C        + +VNE+ LEK   GL  +          
Sbjct: 948  FTFLMERLVQAFKTVEELKIVSCALDETVLNDLWVNEVWLEKNPHGLSSI---------- 997

Query: 817  CPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHL 876
                           L  I I++CN + S+   ++ N+  LE L I  CDS+  ++ + L
Sbjct: 998  ---------------LRLIEIRNCNIMKSIPKVLMVNSHFLERLYICHCDSIVFVTMDQL 1042

Query: 877  PSSLQAIEIRDCETLQCVLDDREKSCTSSSVT--EKNINSSSSTYLDLESLFVYRCPSLT 934
            P SL+++EI +C+ L+C+LD+   +CTSSS+   + N+   S+    LE +++  CPSLT
Sbjct: 1043 PHSLKSLEISNCKNLRCLLDN--GTCTSSSIIMHDDNVQHGSTIISHLEYVYIGWCPSLT 1100

Query: 935  CLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACL 994
            C+   G LP ++K L I +CS    L+ + QLP  +E L I  C  LESIA R H +  L
Sbjct: 1101 CISRSGELPESVKHLFIWNCSELSCLSMKGQLPKSIERLEIQSCPKLESIANRLHRNTSL 1160

Query: 995  RSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALP-SNVVDVLIEDCDKLK 1053
             SI I +CENLKSLP+GL  L +L EI+I+ C NLVS PE+ LP S++ ++ I  C+KL 
Sbjct: 1161 ESIQIWNCENLKSLPEGLHFLVNLKEIKIIGCPNLVSFPEEGLPASSLSELSIMSCEKLV 1220

Query: 1054 ALIPTG--TLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTS 1111
            AL P     L SL+EL +  CP I  FPE     NLT L I+  N  + +  WG +KL+ 
Sbjct: 1221 AL-PNSMYNLDSLKELEIGYCPSIQYFPEINFPDNLTSLWINDHNACEAMFNWGLYKLSF 1279

Query: 1112 LRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFS 1171
            LR L I G +  +  P    G +LP++LTS+T+  FP L+ LSS+GF  L SL  LS+++
Sbjct: 1280 LRDLTIIGGN--LFMPLEKLGTMLPSTLTSLTVQGFPHLENLSSEGFHKLTSLSKLSIYN 1337

Query: 1172 CPNFTSFPEAGFPSSLLSLEIQRCPLL-EKCKMRKGQEWPKIAHIPLTLIN 1221
            CP     PE G PSSLL L IQ CP L E+C+  KG++W KIA +P   I+
Sbjct: 1338 CPKLLCLPEKGLPSSLLELYIQDCPFLKEQCRKDKGRDWLKIADVPYVEID 1388

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225449649|ref|XP_002262753.1| PREDICTED: putative disease resistance protein At3g14460 [Vitis vinifera]

 Score =  877 bits (2266), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 542/1300 (41%), Positives = 730/1300 (56%), Gaps = 160/1300 (12%)

Query: 2    VLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRIS 60
            +L  D    +   V+P+VGMGG+GKTTLA+ V+ND+ + + F  ++WVCVSD+FD++RI+
Sbjct: 189  LLLRDGGSESKVGVVPIVGMGGVGKTTLARLVFNDETIKQYFTLRSWVCVSDEFDIIRIT 248

Query: 61   KAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
            KAILDSI   +  L DLN +Q++L + +  K+FL+VLDDVW++ Y  W  L+SPF  GA 
Sbjct: 249  KAILDSITSQTTALSDLNQLQVKLSDALAGKRFLLVLDDVWNKNYGDWVLLRSPFSTGAA 308

Query: 121  GSRIIVTTRSMDVALTMGSGKNYE-LKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR 179
            GS+IIVTTR  +VA  M    NY  +K LS DDCWSVFV HAFE R+   H + E   ++
Sbjct: 309  GSKIIVTTRDAEVARMMAGSDNYHYVKALSYDDCWSVFVQHAFENRNICAHPSLEVIGKK 368

Query: 180  VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDK-TEIPSVLKLSYHHLPSH 238
            +V+KC GLPLAA+ LGGLLRSK   DEW  +L SKIWN  DK ++I   L+LSYH+LPSH
Sbjct: 369  IVQKCGGLPLAAKTLGGLLRSKSKDDEWEDVLYSKIWNFPDKESDILPALRLSYHYLPSH 428

Query: 239  LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQS-EDNKQLEDLGSGYFHDLLSRSLFQ 297
            LKRCFAYC++ PKDYEF +KELVLLW+AEGL+QQS +  KQ+ED+GS YF +LLSRS FQ
Sbjct: 429  LKRCFAYCSIFPKDYEFDKKELVLLWMAEGLIQQSPKGKKQMEDMGSDYFCELLSRSFFQ 488

Query: 298  KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLR-SYDCDG 356
             SS   S++VMHDL++DLAQ+ S E CF L+D    +++      VRH S+ R  Y+   
Sbjct: 489  LSSCNGSRFVMHDLINDLAQYVSEEICFHLEDSLDSNQKHTFSGSVRHSSFARCKYEV-- 546

Query: 357  MDKFKVLDKVVNLRTFL--PIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITE 414
              KF+   K  NLRTFL  PI  + +  +  +++  V  DLLP+ + LRVLSL  Y I E
Sbjct: 547  FRKFEDFYKAKNLRTFLALPIHMQYYDFF--HLTDKVSHDLLPKLRYLRVLSLSHYEIRE 604

Query: 415  VPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY 474
            +P SIG LK LRYLN S + IQ LPD++  L NL+ L+L  C  L +LP    NL+NL +
Sbjct: 605  LPNSIGDLKHLRYLNLSCTIIQELPDSLSDLHNLQTLVLFRCRRLNRLPRGFKNLINLRH 664

Query: 475  LNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVI 534
            L+I     L  +P  M +LK L+TL+ FIVGK     +++L +   LRG+L I  L+NV+
Sbjct: 665  LDIAHTHQLEVMPPQMGKLKSLQTLSKFIVGKSKELGIKELGDLLHLRGKLSILDLQNVV 724

Query: 535  DSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGG 594
            D Q+A +A L+ K  L +L ++W      DS +E  E N+L  L+P++N+K+L I SYGG
Sbjct: 725  DIQDARDANLKDKHHLEELLMEWSSNMFDDSQNETIELNVLHFLQPNTNLKKLTIQSYGG 784

Query: 595  TRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEG 654
              FP W+GDPSFS +  L L  CR+ T LPSLG+L SLK L + GM  +KS+G E YGE 
Sbjct: 785  LTFPYWIGDPSFSKMVCLELNYCRKCTLLPSLGRLSSLKKLCVKGMQGVKSVGIEFYGEP 844

Query: 655  --CSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLP 712
              C KPF SL+ L FED+ EWE W  +       +++PRLR+L I  CPKL  +LP+HLP
Sbjct: 845  SLCVKPFPSLEFLRFEDMPEWEEWCSS-------ESYPRLRELEIHHCPKLIQKLPSHLP 897

Query: 713  SLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE--FEN 770
            SL ++ I  C  L   LPSLP L  + +  C   +     +  S   + L NIS   F N
Sbjct: 898  SLVKLDIIDCPKLVAPLPSLPFLRDLIVAECNEAMLRSGGDLTSLITLRLENISNLTFLN 957

Query: 771  WSSEKF-QKVEQLMIVGCE----------GFVNEIC------------------------ 795
                +F   +E L I  C           GF N  C                        
Sbjct: 958  EGLVRFLGALEVLEICNCSELKFLLQSGVGFENLSCIRHLVIVMCPKLVLLAEDQPLPCN 1017

Query: 796  -----------LEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALA 844
                       LEK   GLQ LT L++L I  CP + SL +  F P L  + + DC  L 
Sbjct: 1018 LEYLEINKCASLEKLPIGLQSLTSLRELSIQKCPKLCSLAEMDFPPMLISLELYDCEGLE 1077

Query: 845  SLTDGMIYNNAR-----LEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDRE 899
            SL DGM+ N        LE L+I  C SL    R  LPS L+ +EI DC  LQ       
Sbjct: 1078 SLPDGMMINGENRNFCLLECLKIVHCPSLICFPRGELPSKLKELEIIDCAKLQ------- 1130

Query: 900  KSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSN--- 956
                  S+ E  I    + +  LE L ++RCP L+  +  G LP T+KRL I +C     
Sbjct: 1131 ------SLPEGLILGDHTCH--LEFLRIHRCPLLSS-FPRGLLPSTMKRLEIRNCKQLES 1181

Query: 957  -----------------FKVLTSECQLPVE-VEELTIYGCSNLESIAERFHDDACLRSIW 998
                              K+  S C   ++ + EL IY CS LES  ER      L+ + 
Sbjct: 1182 ISLLSHSTTLEYLRIDRLKINFSGCLHSLKHLIELHIYSCSGLESFPERGFSSPNLKMLH 1241

Query: 999  ISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPT 1058
            I  C+NLKSLP  + + + L ++RI  C NLVS  E+ L  N+    I +C  LK     
Sbjct: 1242 IDDCKNLKSLPLQMQSFTSLRDLRIYDCPNLVSFAEEGLSLNLTSFWIRNCKNLKM---- 1297

Query: 1059 GTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYID 1118
                                                     PL +WG H LTSL+   I+
Sbjct: 1298 -----------------------------------------PLYQWGLHGLTSLQTFVIN 1316

Query: 1119 GCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSF 1178
               +   F D     +LP +LT ++IS F  L+ LSS G Q L SLE L ++SCP   +F
Sbjct: 1317 ---NVAPFCDHDSLPLLPRTLTYLSISKFHNLESLSSMGLQNLTSLEILEIYSCPKLQTF 1373

Query: 1179 -PEAGFPSSLLSLEIQRCPLLE-KCKMRKGQEWPKIAHIP 1216
             P+ G  ++L +L I+ CP++E +C+  KG++WP I+HIP
Sbjct: 1374 LPKEGLSATLSNLRIKFCPIIEARCRKNKGEDWPMISHIP 1413

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495024|ref|XP_002267933.2| PREDICTED: putative disease resistance protein At3g14460-like [Vitis vinifera]

 Score =  848 bits (2191), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/1240 (41%), Positives = 729/1240 (58%), Gaps = 114/1240 (9%)

Query: 15   VIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK 73
            VIP+VGMGG+GKTTLAQ  YND ++   F+ +AWVCVSDDFDVLRI+K +L SI   + +
Sbjct: 206  VIPIVGMGGVGKTTLAQLAYNDDRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYTRE 265

Query: 74   LEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV 133
            + DLN +Q+++KE +  KKFL+VLDDVW+E YD W +L +P  AG PGS++I+TTR+M V
Sbjct: 266  INDLNLLQVKMKEKLSGKKFLLVLDDVWNENYDKWDSLCTPLRAGGPGSKVIITTRNMGV 325

Query: 134  ALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA 193
            A    +   Y L+ LS+DDC +VF  HA   R+   H + +   + +V +C+GLPL A+A
Sbjct: 326  ATLTRTVSPYLLQELSNDDCRAVFAQHALGARNFEAHPHLKIIGEEMVNRCRGLPLVAKA 385

Query: 194  LGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKD 252
            LGG+LR++   + W  IL SKIW+L ++K+ +   LKLSYHHLPSHLK+CFAYCA+ PK 
Sbjct: 386  LGGILRNELNHEAWDDILKSKIWDLPEEKSGVLPALKLSYHHLPSHLKQCFAYCAIFPKG 445

Query: 253  YEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLV 312
            YEFK+ EL+LLW+ EG +QQ++  K++EDLGS YF +LLSRS FQ+SSN   +++MHDL+
Sbjct: 446  YEFKKDELILLWMGEGFLQQTKGKKRMEDLGSKYFSELLSRSFFQQSSNIMPRFMMHDLI 505

Query: 313  HDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTF 372
            HDLAQ  +G  C  L+D+  ++   N+F+K RH S++R  + +   KF+V+DK   LRTF
Sbjct: 506  HDLAQSIAGNVCLNLEDK--LENNENIFQKARHLSFIRQAN-EIFKKFEVVDKGKYLRTF 562

Query: 373  LPI-----FFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRY 427
            L +     F K        I+  V  DLL + K LRVLSL  Y ++++P SI  L  LRY
Sbjct: 563  LALPISVSFMKSLSF----ITTKVTHDLLMEMKCLRVLSLSGYKMSDLPSSIDNLSHLRY 618

Query: 428  LNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELP 487
            LN  RS I+ LP+++  L+NL+ LILR+CW L ++P  +GNL+NL +L+I G S L E+P
Sbjct: 619  LNLCRSSIKRLPNSVGHLYNLQTLILRDCWSLTEMPVGMGNLINLRHLDIAGTSQLEEMP 678

Query: 488  LGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVK 547
              M  L  L+TL+ FIVGK +G ++++LK+   L+G L I GL NV ++++A +A L+ K
Sbjct: 679  PRMGSLTNLQTLSKFIVGKGNGSSIQELKHLLDLQGELSIQGLHNVRNTRDAMDACLKNK 738

Query: 548  EGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFS 607
              + +L + W    D DS +E  E  +L++L+P  N+K+L +  YGG +FPSW+G+PSFS
Sbjct: 739  CHIEELTMGWSGDFD-DSRNELNEMLVLELLQPQRNLKKLTVEFYGGPKFPSWIGNPSFS 797

Query: 608  NVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGE-GCSKPFQSLQTLY 666
             +  L LKNC + TSLP LG+L  LK L I GM ++K+IG E +GE    +PF  L++L 
Sbjct: 798  KMESLTLKNCGKCTSLPCLGRLSLLKALRIQGMCKVKTIGDEFFGEVSLFQPFPCLESLR 857

Query: 667  FEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLA 726
            FED+ EWE W  +   +E    F  LR+L I++CPKL+G LPN LPSL E+ I  C  L 
Sbjct: 858  FEDMPEWEDWCFSDMVEECEGLFSCLRELRIRECPKLTGSLPNCLPSLAELEIFECPKLK 917

Query: 727  VSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE------------------- 767
             +LP L  +C++ +  C  +V     +  S   + +  IS                    
Sbjct: 918  AALPRLAYVCSLNVVECNEVVLRNGVDLSSLTTLNIQRISRLTCLREGFTQLLAALQKLV 977

Query: 768  ----------FEN-WSSEKFQKVEQLMIVGCEGFVN---------------EIC--LEKP 799
                      +EN +  E  + +E + I  C G V+               E C  L++ 
Sbjct: 978  IRGCGEMTSLWENRFGLECLRGLESIDIWQCHGLVSLEEQRLPCNLKHLKIENCANLQRL 1037

Query: 800  LQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEV 859
              GLQRLTCL++L + +CP + S P+    P L  + +Q CN L  L     YN+  LE 
Sbjct: 1038 PNGLQRLTCLEELSLQSCPKLESFPEMGLPPMLRSLVLQKCNTLKLLPHN--YNSGFLEY 1095

Query: 860  LRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTY 919
            L I+ C  L S     LP+SL+ ++I+DC  LQ +            +T  N   S+++ 
Sbjct: 1096 LEIEHCPCLISFPEGELPASLKQLKIKDCANLQTL---------PEGMTHHNSMVSNNSC 1146

Query: 920  LDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCS 979
              LE L + +C SL  L +G  LP TLKRL I DC  F+ ++ +                
Sbjct: 1147 C-LEVLEIRKCSSLPSLPTG-ELPSTLKRLEIWDCRQFQPISEK---------------- 1188

Query: 980  NLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPS 1039
                     H +  L  + IS+  N+K LP  L +L++L+   I  C  LVS PE  LP+
Sbjct: 1189 -------MLHSNTALEHLSISNYPNMKILPGFLHSLTYLY---IYGCQGLVSFPERGLPT 1238

Query: 1040 -NVVDVLIEDCDKLKALI-PTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISG-DN 1096
             N+ D+ I +C+ LK+L      L SL+EL +  C G+  FPE GL+ NLT L I    N
Sbjct: 1239 PNLRDLYINNCENLKSLPHQMQNLLSLQELNIRNCQGLESFPECGLAPNLTSLSIRDCVN 1298

Query: 1097 MYKPLVKWGFHKLTSLRKLYIDG-CSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSS 1155
            +  PL +WG H+LTSL  LYI G C    S  D     +LPT+L+ + IS   KL  L  
Sbjct: 1299 LKVPLSEWGLHRLTSLSSLYISGVCPSLASLSD--DECLLPTTLSKLFIS---KLDSLVC 1353

Query: 1156 KGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRC 1195
               + L SLE +S++ CP   S    G P +L  LEI+ C
Sbjct: 1354 LALKNLSSLERISIYRCPKLRSI---GLPETLSRLEIRDC 1390

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487065|ref|XP_002270668.2| PREDICTED: putative disease resistance protein At3g14460-like [Vitis vinifera]

 Score =  845 bits (2183), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 517/1288 (40%), Positives = 738/1288 (57%), Gaps = 123/1288 (9%)

Query: 1    MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAWVCVSDDFDVLRI 59
            + + ND S   N  V+ +V MGG+GKTTLA  VY+D+ T + F  K WVCVSD F V  I
Sbjct: 192  LAMLNDESLGGNLSVVSIVAMGGMGKTTLAGLVYDDEETSKHFALKVWVCVSDQFHVETI 251

Query: 60   SKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
            ++A+L  I   +    D + +Q +L++    K+FLIVLDD+W+E+YD W +L+SP + GA
Sbjct: 252  TRAVLRDIAAGNNDSLDFHQIQRKLRDETKGKRFLIVLDDLWNEKYDQWDSLRSPLLEGA 311

Query: 120  PGSRIIVTTRSMDVALTMGSGKN-YELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQ 178
            PGS+I+VTTR+ +VA  MG  KN YELK LSD+DCW +F  HAFE R+   H +     +
Sbjct: 312  PGSKILVTTRNKNVATMMGGDKNFYELKHLSDNDCWELFKKHAFENRNTNEHPDLALIGR 371

Query: 179  RVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPS 237
             +V+KC GLPLAA+ALGGLLR +   D+W  IL SKIWNL  DK  I   L+LSY+HLPS
Sbjct: 372  EIVKKCGGLPLAAKALGGLLRHEHREDKWNIILASKIWNLPGDKCGILPALRLSYNHLPS 431

Query: 238  HLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ 297
            HLKRCFAYCA+ P+DYEFK++EL+LLW+AEGL+QQS +++++EDLG  YF +LLSRS FQ
Sbjct: 432  HLKRCFAYCALFPQDYEFKKEELILLWMAEGLIQQSNEDEKMEDLGDDYFCELLSRSFFQ 491

Query: 298  KSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGM 357
             S++ +S++VMHDL++DLA+  +G+TC  LDD    D Q +V E  RH S++R +D D  
Sbjct: 492  SSNSNKSRFVMHDLINDLAKSIAGDTCLHLDDGLWNDLQRSVPESTRHSSFIR-HDYDIF 550

Query: 358  DKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPI 417
             KF+  DK   L TF+ +   +   +   IS  VL +L+P+   LRVLSL  Y I+E+P 
Sbjct: 551  KKFERFDKKECLHTFIALPIDEPHSF---ISNKVLEELIPRLGHLRVLSLAHYMISEIPD 607

Query: 418  SIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI 477
            S G LK LRYL+ S + I+ LPD+I +LF L+ L L  C  L++LP  IGNL+NL +L++
Sbjct: 608  SFGKLKHLRYLDLSYTSIKWLPDSIGNLFYLQTLKLSCCEELIRLPISIGNLINLRHLDV 667

Query: 478  EGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQ 537
             GA  L+E+P+ + +LK LR L+NFIV K++G  +++L     LR +LCIS LENV++ Q
Sbjct: 668  AGAIRLQEMPVQIGKLKDLRILSNFIVDKNNGLTIKELTGMSHLRRQLCISKLENVVNIQ 727

Query: 538  EANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRF 597
            +A +A L++K  L  L + W    DG S +E  + ++LD L+P  N+ +L I  YGG  F
Sbjct: 728  DARDADLKLKRNLESLIMQWSSELDG-SGNERNQMDVLDSLQPCLNLNKLCIQLYGGPEF 786

Query: 598  PSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGE---G 654
            P W+GD  FS +  L L +CR+ TSLP LGQL SLK L I GM  +K +G+E YGE    
Sbjct: 787  PRWIGDALFSKMVDLSLIDCRKCTSLPCLGQLPSLKQLRIQGMVGVKKVGAEFYGETRVS 846

Query: 655  CSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSL 714
              K F SL++L+F  + EWEHWE    + E +  FP L +L+I+ CPKL  +LP +LPSL
Sbjct: 847  AGKFFPSLESLHFNSMSEWEHWEDWSSSTESL--FPCLHELTIEDCPKLIMKLPTYLPSL 904

Query: 715  EEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE------- 767
             E+ +  C  L   L  LP L  + +      V    ++  S  K+T+  IS        
Sbjct: 905  TELSVHFCPKLESPLSRLPLLKELHVGEFNEAVLSSGNDLTSLTKLTISRISGLIKLHEG 964

Query: 768  ----------FENWSSEKFQKV------------------EQLMIVGC--EGFVNEIC-- 795
                       E W  E+ + +                  +QL+ +GC  +      C  
Sbjct: 965  FMQFLQGLRVLEVWECEELEYLWEDGFGSENSLSLEIRDCDQLVSLGCNLQSLAISGCAK 1024

Query: 796  LEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIY--- 852
            LE+   G Q LTCL++L I +CP + S P   F P L  +T+ +C  + SL DGM+    
Sbjct: 1025 LERLPNGWQSLTCLEELTIRDCPKLASFPDVGFPPKLRSLTVGNCKGIKSLPDGMMLKMR 1084

Query: 853  -------NNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSS 905
                   N+  LE L I++C SL    +  LP++L+++ I  CE L+ + ++    C   
Sbjct: 1085 NDTTDSNNSCVLESLEIEQCPSLICFPKGQLPTTLKSLRILACENLKSLPEEMMGMCA-- 1142

Query: 906  SVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFK-----VL 960
                            LE   + RC SL  L  GG LP TLKRL I DC   +     ++
Sbjct: 1143 ----------------LEDFLIVRCHSLIGLPKGG-LPATLKRLTISDCRRLESLPEGIM 1185

Query: 961  TSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGL--SNLSHL 1018
                     ++EL I  C +L S   R    + L  + I +CE+L+S+ + +  S  + L
Sbjct: 1186 HHHSTNAAALKELEISVCPSLTSFP-RGKFPSTLERLHIENCEHLESISEEMFHSTNNSL 1244

Query: 1019 HEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIP-TGTLSSLRELALSECPGIVV 1077
              + + R  NL +LP+    + +VD      + L+ L+P    L+ L  L +  C     
Sbjct: 1245 QFLTLRRYPNLKTLPDKK--AGIVDF-----ENLELLLPQIKKLTRLTALVIRNC----- 1292

Query: 1078 FPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGC-SDAVSFPDVGKGVILP 1136
                             +N+  PL +WG  +LTSL+ L+I G   DA SF D    ++ P
Sbjct: 1293 -----------------ENIKTPLSQWGLSRLTSLKDLWIGGMFPDATSFSDDPHSILFP 1335

Query: 1137 TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTS-FPEAG-FPSSLLSLEIQR 1194
            T+LTS+ +SDF  L+ L+S   Q L SLE L+++SCP   S  P  G  P +L  L +  
Sbjct: 1336 TTLTSLYLSDFQNLESLASLSLQTLTSLEILAIYSCPKLRSILPREGLLPDTLSRLYVWC 1395

Query: 1195 CPLL-EKCKMRKGQEWPKIAHIPLTLIN 1221
            CP L ++    +G +WPKIAHIP  +IN
Sbjct: 1396 CPHLKQRYSKWEGDDWPKIAHIPRVVIN 1423

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487225|ref|XP_002268551.2| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  843 bits (2178), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 534/1265 (42%), Positives = 738/1265 (58%), Gaps = 119/1265 (9%)

Query: 1    MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRI 59
            M+LK+DPS      VIP+VGMGGIGKTTLAQ  +ND ++   F+ +AWVCVSDDFDV +I
Sbjct: 189  MLLKHDPSSDDEVSVIPIVGMGGIGKTTLAQLAFNDDEVKGRFDLRAWVCVSDDFDVSKI 248

Query: 60   SKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
            +K IL S+   +  + DLN +Q++LKE    KKFL+VLDDVW+E    W  L  P  AGA
Sbjct: 249  TKTILQSVDPGTHDVNDLNLLQVKLKEKFSGKKFLLVLDDVWNENCHEWDTLCMPMRAGA 308

Query: 120  PGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR 179
            PGS++IVTTR+  VA    +   Y L+ LS++DC S+F   A   R+   H + +   + 
Sbjct: 309  PGSKLIVTTRNEGVAAVTRTCPAYPLRELSNNDCLSLFTQQALRTRNFDAHPHLKEVGEE 368

Query: 180  VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSH 238
            +V +CKGLPLAA+ALGG+LR++   D W  IL S+IW+L +DK+ I   L LSYHHLPSH
Sbjct: 369  IVRRCKGLPLAAKALGGMLRNQLSRDAWANILTSRIWDLPEDKSHILPALMLSYHHLPSH 428

Query: 239  LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK 298
            LK+CFAYC++ PKDYEF + +LVLLW+AEG +Q++++  + EDLGS YF+DL SRS FQ 
Sbjct: 429  LKQCFAYCSMFPKDYEFNKDDLVLLWMAEGFLQKTKEAARPEDLGSKYFNDLFSRSFFQH 488

Query: 299  SSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMD 358
            SS   S+YVMHDL++DLAQ  +GE  F LD  +  ++QS + EK RH S+ R +  +   
Sbjct: 489  SSRNSSRYVMHDLINDLAQSVAGEIYFHLDGAWENNKQSTISEKTRHSSFNRQHS-ETQR 547

Query: 359  KFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS 418
            KF+   KV  LRT + +   Q       IS  VL DLL + K LRVLSL  Y I  +P S
Sbjct: 548  KFEPFHKVKCLRTLVALPMDQPVFSSGYISSKVLDDLLKEVKYLRVLSLSGYKIYGLPDS 607

Query: 419  IGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE 478
            IG LK LRYLN S S I+ LPD++C L+NL+ LIL +C  L  LP  IGNL+NL +L+I 
Sbjct: 608  IGNLKYLRYLNLSGSSIRRLPDSVCHLYNLQALILSDCKDLTTLPVGIGNLINLRHLHIF 667

Query: 479  GASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQE 538
                L+E+P     L  L+TL+ FIVG+ +   LR+LKN   LRG+L I GL NV++ ++
Sbjct: 668  DTWKLQEMPSQTGNLTKLQTLSKFIVGEGNNLGLRELKNLFDLRGQLSILGLHNVMNIRD 727

Query: 539  ANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFP 598
              +A L  K G+ +L ++W     G S +E  E+N+L+ L+PH N+K+L I SYGG+ FP
Sbjct: 728  GRDANLESKHGIEELTMEWSDDF-GASRNEMHERNVLEQLRPHRNLKKLTIASYGGSGFP 786

Query: 599  SWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKP 658
            +W+ DPSF  +  LILK+C+R TSLP+LGQ+ SLK L I GMSE+++I  E YG G  KP
Sbjct: 787  NWMKDPSFPIMTHLILKDCKRCTSLPALGQISSLKVLHIKGMSEVRTINEEFYG-GIVKP 845

Query: 659  FQSLQTLYFEDLQEWEHWE-PNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEI 717
            F SL++L FE + EWE+W  P+  N+  +  FP LR L+I+ C KL  +LPN LPS  ++
Sbjct: 846  FPSLESLTFEVMAEWEYWFCPDAVNEGEL--FPCLRLLTIRDCRKLQ-QLPNCLPSQVKL 902

Query: 718  VIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQ 777
             I+ C +L  +     +L      G +RL C+          + +  I +  N       
Sbjct: 903  DISCCPNLGFASSRFASL------GEQRLPCN----------LKMLRIHDDAN------- 939

Query: 778  KVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLP-NLSEIT 836
                              LEK   GLQ LTCL+ L I  CP++   P  C LP  L  + 
Sbjct: 940  ------------------LEKLPNGLQTLTCLEQLDITGCPSLRCFPN-CELPTTLKSLC 980

Query: 837  IQDCNALASLTDGMIYNNAR--LEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCV 894
            I+DC  L +L +GM+++++   LE L+I+ C  L S     LP  L+ +E+ +C+ L+  
Sbjct: 981  IKDCKNLEALPEGMMHHDSTCCLEELKIEGCPRLESFPDTGLPPLLRRLEVSECKGLKS- 1039

Query: 895  LDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDC 954
            L     SC                   LESL +  CPSL C +  G LP TLK + I+DC
Sbjct: 1040 LPHNYSSCA------------------LESLEISDCPSLRC-FPNGELPTTLKSIWIQDC 1080

Query: 955  SNFKVL-------TSEC--------------------QLPVEVEELTIYGCSNLESIAER 987
             N + L        S C                    +LP  +++L I GC +LES++E 
Sbjct: 1081 ENLESLPEGMMHHDSTCCLEEVIIMGCPRLESFPDTGELPSTLKKLEICGCPDLESMSEN 1140

Query: 988  F-HDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVL- 1045
               +++ L ++ +    NLK LP+ L +L  L   +I+ C  L   P   L +  +  L 
Sbjct: 1141 MCPNNSALDNLVLEGYPNLKILPECLHSLKSL---QIINCEGLECFPARGLSTPTLTSLR 1197

Query: 1046 IEDCDKLKALI-PTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISG-DNMYKPLVK 1103
            IE C+ LK+L      L SLR+L +  CPG+  FPE+G+  NL  LEIS  +N+ KP+  
Sbjct: 1198 IEGCENLKSLPHQMRDLKSLRDLTILFCPGVESFPEDGMPPNLISLEISYCENLKKPIS- 1256

Query: 1104 WGFHKLTSLRKLYIDGC-SDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLV 1162
              FH LTSL  L I+    D VSF D  +  +LP SLTS+ I+    L  LS    Q L+
Sbjct: 1257 -AFHTLTSLFSLTIENVFPDMVSFRD--EECLLPISLTSLRITAMESLAYLS---LQNLI 1310

Query: 1163 SLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLL-EKCKMRKGQEWPKIAHIPLTLIN 1221
            SL++L V +CPN  S      P++L  LEI  CP+L E+    KG+ WPKIAHIP   + 
Sbjct: 1311 SLQYLEVATCPNLGSL--GSMPATLEKLEIWCCPILEERYSKEKGEYWPKIAHIPCIAMR 1368

Query: 1222 QERKH 1226
             +  H
Sbjct: 1369 GQFIH 1373

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860511|emb|CAN79726.1| hypothetical protein VITISV_014536 [Vitis vinifera]

 Score =  823 bits (2127), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 491/1190 (41%), Positives = 704/1190 (59%), Gaps = 108/1190 (9%)

Query: 15   VIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK 73
            VIP+VGMGG+GKTTLAQ  YND ++   F+ +AWVCVSDDFDVLRI+K +L SI   + +
Sbjct: 206  VIPIVGMGGVGKTTLAQLAYNDDRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYTRE 265

Query: 74   LEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV 133
            + DLN +Q+++KE +  KKFL+VLDDVW+E YD W +L +P  AG PGS++I+TTR+M V
Sbjct: 266  INDLNLLQVKMKEKLSGKKFLLVLDDVWNENYDKWDSLCTPLRAGGPGSKVIITTRNMGV 325

Query: 134  ALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA 193
            A    +   Y L+ LS+DDC +VF  HA   R+   H + +   + +V +C+GLPL A+A
Sbjct: 326  ATLTRTVSPYLLQELSNDDCRAVFAQHALGARNFEAHPHLKIIGEEMVNRCRGLPLVAKA 385

Query: 194  LGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKD 252
            LGG+LR++   + W  IL SKIW+L ++K+ +   LKLSYHHLPSHLK+CFAYCA+ PK 
Sbjct: 386  LGGILRNELNHEAWDDILKSKIWDLPEEKSGVLPALKLSYHHLPSHLKQCFAYCAIFPKG 445

Query: 253  YEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLV 312
            YEFK+ EL+LLW+ EG +QQ++  K++EDLGS YF +LLSRS FQ+SSN   +++MHDL+
Sbjct: 446  YEFKKDELILLWMGEGFLQQTKGKKRMEDLGSKYFSELLSRSFFQQSSNIMPRFMMHDLI 505

Query: 313  HDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTF 372
            HDLAQ  +G  C  L+D+  ++   N+F+K RH S++R  + +   KF+V+DK   LRTF
Sbjct: 506  HDLAQSIAGNVCLNLEDK--LENNENIFQKARHLSFIRQAN-EIFKKFEVVDKGKYLRTF 562

Query: 373  LPI-----FFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRY 427
            L +     F K        I+  V  DLL + K LRVLSL  Y ++++P SI  L  LRY
Sbjct: 563  LALPISVSFMKSLSF----ITTKVTHDLLMEMKCLRVLSLSGYKMSDLPSSIDNLSHLRY 618

Query: 428  LNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELP 487
            LN  RS I+ LP+++  L+NL+ LILR+CW L ++P  +GNL+NL +L+I G S L E+P
Sbjct: 619  LNLCRSSIKRLPNSVGHLYNLQTLILRDCWSLTEMPVGMGNLINLRHLDIAGTSQLEEMP 678

Query: 488  LGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVK 547
              M  L  L+TL+ F VGK +G ++++LK+   L+G L I GL NV ++++A +A L+ K
Sbjct: 679  PRMGSLTNLQTLSKFXVGKGNGSSIQELKHLLDLQGELSIQGLHNVRNTRDAMDACLKNK 738

Query: 548  EGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFS 607
              + +L + W    D DS +E  E  +L++L+P  N+K+L +  YGG +FPSW+G+PSFS
Sbjct: 739  CHIEELTMGWSGDFD-DSRNELNEMLVLELLQPQRNLKKLTVEFYGGPKFPSWIGNPSFS 797

Query: 608  NVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGE-GCSKPFQSLQTLY 666
             +  L LKNC + TSLP LG+L  LK L I GM ++K+IG E +GE    +PF  L++L 
Sbjct: 798  KMESLTLKNCGKCTSLPCLGRLSLLKALRIQGMCKVKTIGDEFFGEVSLFQPFPCLESLR 857

Query: 667  FEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLA 726
            FED+ EWE W  +   +E    F  LR+L I++CPKL+G LPN LPSL E+ I  C  L 
Sbjct: 858  FEDMPEWEDWCFSDMVEECEGLFSCLRELRIRECPKLTGSLPNCLPSLAELEIFECPKLK 917

Query: 727  VSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISE------------------- 767
             +LP L  +C++ +  C  +V     +  S   + +  IS                    
Sbjct: 918  AALPRLAYVCSLNVVECNEVVLRNGVDLSSLTTLNIQRISRLTCLREGFTQLLAALQKLV 977

Query: 768  ----------FEN-WSSEKFQKVEQLMIVGCEGFVN---------------EIC--LEKP 799
                      +EN +  E  + +E + I  C G V+               E C  L++ 
Sbjct: 978  IRGCGEMTSLWENRFGLECLRGLESIDIWQCHGLVSLEEQRLPCNLKHLKIENCANLQRL 1037

Query: 800  LQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEV 859
              GLQRLTCL++L + +CP + S P+    P L  + +Q CN L  L     YN+  LE 
Sbjct: 1038 PNGLQRLTCLEELSLQSCPKLESFPEMGLPPMLRSLVLQKCNTLKLLPHN--YNSGFLEY 1095

Query: 860  LRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTY 919
            L I+ C  L S     LP+SL+ ++I+DC  LQ +            +   ++ S++S  
Sbjct: 1096 LEIEHCPCLISFPEGELPASLKQLKIKDCANLQTL--------PEGMMHHNSMVSNNSCC 1147

Query: 920  LDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCS 979
            L  E L + +C SL  L +G  LP TLKRL I DC  F+ ++ +                
Sbjct: 1148 L--EVLEIRKCSSLPSLPTG-ELPSTLKRLEIWDCRQFQPISEK---------------- 1188

Query: 980  NLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPS 1039
                     H +  L  + IS+  N+K LP  L +L++L+   I  C  LVS PE  LP+
Sbjct: 1189 -------MLHSNTALEHLSISNYPNMKILPGXLHSLTYLY---IYGCQGLVSFPERGLPT 1238

Query: 1040 -NVVDVLIEDCDKLKAL-IPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISG-DN 1096
             N+ D+ I +C+ LK+L      L SL+EL +  C G+  FPE GL+ NLT L I    N
Sbjct: 1239 PNLRDLYINNCENLKSLPHQMQNLLSLQELNIRNCQGLESFPECGLAPNLTSLSIRDCVN 1298

Query: 1097 MYKPLVKWGFHKLTSLRKLYIDG-CSDAVSFPDVGKGVILPTSLTSITIS 1145
            +  PL +WG H+LTSL  LYI G C    S  D     +LPT+L+ + I+
Sbjct: 1299 LKVPLSEWGLHRLTSLSSLYISGVCPSLASLSD--DECLLPTTLSKLFIN 1346

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495026|ref|XP_003634900.1| PREDICTED: uncharacterized protein LOC100854556 [Vitis vinifera]

 Score =  820 bits (2118), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 497/1222 (40%), Positives = 715/1222 (58%), Gaps = 112/1222 (9%)

Query: 15   VIPLVGMGGIGKTTLAQEVY-NDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK 73
            VIP+VGMGG+GKTTLAQ  Y +D++   F+ +AWVCVSDDFDVLRI+K +L SI   + +
Sbjct: 206  VIPIVGMGGVGKTTLAQLAYHDDRVKNHFDLRAWVCVSDDFDVLRITKTLLQSIASYARE 265

Query: 74   LEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV 133
            + DLN +Q++LKE +  KKFL+VLDDVW+E YD W  L +P  AG PGS++I+TTR+M V
Sbjct: 266  INDLNLLQVKLKEKLSGKKFLLVLDDVWNENYDKWDRLCTPLRAGGPGSKVIITTRNMGV 325

Query: 134  ALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA 193
            A    +   Y L+ LS+DDC +VF  HA   R+   H + +   + +V +C+GLPL A+A
Sbjct: 326  ASLTRTVSPYPLQELSNDDCRAVFAQHALGARNFEAHPHVKIIGEEMVNRCRGLPLVAKA 385

Query: 194  LGGLLRSKQGVDEWRAILDSKIWNL-QDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLPKD 252
            LGG+LR++   + W  IL SKIW+L ++K+ +   LKLSYHHLPSHLK+CFAYCA+ PK 
Sbjct: 386  LGGILRNELNHEAWDDILKSKIWDLPEEKSGVLPALKLSYHHLPSHLKQCFAYCAIFPKG 445

Query: 253  YEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLV 312
            YEFK+ EL+LLW+ EG +Q ++  K++EDLGS YF +LLSRS FQ+SS+   +++MHDL+
Sbjct: 446  YEFKKDELILLWMGEGFLQ-TKGKKRMEDLGSKYFSELLSRSFFQQSSDVMPRFMMHDLI 504

Query: 313  HDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTF 372
            HDLAQ  +G   F L+D+  ++   N+F+K RH S++R  + +   KF+V+DK   LRTF
Sbjct: 505  HDLAQSIAGNVSFNLEDK--LENNENIFQKARHLSFIRQAN-EIFKKFEVVDKGKYLRTF 561

Query: 373  LPI-----FFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRY 427
            L +     F K        I+  V  DLL + K LRVLSL  Y ++E+P SI  L  LRY
Sbjct: 562  LALPISVSFMKSLSF----ITTKVTHDLLMEMKCLRVLSLSGYKMSELPSSIDNLSHLRY 617

Query: 428  LNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELP 487
            LN  RS I+ LP+++  L+NL+ LILR+CW L ++P  +GNL+NL +L+I G S L E+P
Sbjct: 618  LNLCRSSIKRLPNSVGHLYNLQTLILRDCWSLTEMPVGMGNLINLRHLDIAGTSQLEEMP 677

Query: 488  LGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVK 547
              M  L  L+TL+ FIVGK +G ++++LK+   L+G L I GL NV ++++A +A L+ K
Sbjct: 678  PRMGCLTNLQTLSKFIVGKGNGSSIQELKHLLDLQGELSIQGLHNVRNTRDAVDACLKNK 737

Query: 548  EGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFS 607
              + +L + W    D DS +E  E  +L++L+P  N+K+L +  YGG +FPSW+G+PSFS
Sbjct: 738  CHIEELTMGWSGDFD-DSRNELNEMLVLELLQPQRNLKKLTVEFYGGPKFPSWIGNPSFS 796

Query: 608  NVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGE-GCSKPFQSLQTLY 666
             +  L LKNC + TSLP LG+L  LK L I GM ++K+IG E +GE    KPF  L++L 
Sbjct: 797  KMESLTLKNCGKCTSLPCLGRLSLLKALRIQGMCKVKTIGDEFFGEVSLFKPFPCLESLR 856

Query: 667  FEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLA 726
            FED+ EWE W  +   +E    F  LR+L I++CPKL+G LPN LPSL E+ I  C  L 
Sbjct: 857  FEDMPEWEDWCFSDMVEECEGLFSCLRELRIRECPKLTGSLPNCLPSLAELEIFECPKLK 916

Query: 727  VSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEF---ENWSSEKFQKVEQLM 783
             +LP L  +C++ +  C  +V     +  S   + +  IS         ++    +++L+
Sbjct: 917  AALPRLAYVCSLNVVECNEVVLRNGVDLSSLTTLNIQRISRLTCLREGFTQLLAALQKLV 976

Query: 784  IVGCEGFVN------------------------------------------EIC--LEKP 799
            I GC    +                                          E C  L++ 
Sbjct: 977  IRGCGEMTSLWENRFGLECLRGLESIDIWQCHGLESLEEQRLPCNLKHLKIENCANLQRL 1036

Query: 800  LQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEV 859
              GLQ LTCL++L + +CP + S P+    P L  + +Q CN L  L     YN+  LE 
Sbjct: 1037 PNGLQSLTCLEELSLQSCPKLESFPEMGLPPMLRSLVLQKCNTLKLLPHN--YNSGFLEY 1094

Query: 860  LRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTY 919
            L I+ C  L S     LP+SL+ ++I+DC  LQ +            +   ++ S++S  
Sbjct: 1095 LEIEHCPCLISFPEGELPASLKQLKIKDCANLQTL--------PEGMMHHNSMVSNNSCC 1146

Query: 920  LDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCS 979
            L  E L + +C SL  L +G  LP TLKRL I DC  F+ ++ +                
Sbjct: 1147 L--EVLEIRKCSSLPSLPTG-ELPSTLKRLEIWDCRQFQPISEK---------------- 1187

Query: 980  NLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPS 1039
                     H +  L  + IS+  N+K LP  L +L++L+   +  C  LVS PE  LP+
Sbjct: 1188 -------MLHSNTALEHLSISNYPNMKILPGFLHSLTYLY---MYGCQGLVSFPERGLPT 1237

Query: 1040 -NVVDVLIEDCDKLKALI-PTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISG-DN 1096
             N+ D+ I +C+ LK+L      L SL+EL +  C G+  FPE GL+ NLT L I    N
Sbjct: 1238 PNLRDLYINNCENLKSLPHQMQNLLSLQELNIRNCQGLESFPECGLAPNLTSLSIRDCVN 1297

Query: 1097 MYKPLVKWGFHKLTSLRKLYIDG-CSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSS 1155
            +  PL +WG H+LTSL  LYI G C    S  D     +LP++L+ + IS   KL  L+ 
Sbjct: 1298 LKVPLSEWGLHRLTSLSSLYISGVCPSLASLSD--DDCLLPSTLSKLFIS---KLDSLAC 1352

Query: 1156 KGFQYLVSLEHLSVFSCPNFTS 1177
               + L SLE +S++ CP   S
Sbjct: 1353 LALKNLSSLERISIYRCPKLRS 1374

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487069|ref|XP_003633511.1| PREDICTED: putative disease resistance protein At3g14460-like [Vitis vinifera]

 Score =  811 bits (2095), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 535/1302 (41%), Positives = 741/1302 (56%), Gaps = 138/1302 (10%)

Query: 1    MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND--KLTEAFEPKAWVCVSDDFDVLR 58
            M+L+N+P+   NF V+ +V  GG+GKTTLA+ VY+D   +T+ F+ KAWVCVSD FD +R
Sbjct: 192  MLLRNEPT-KTNFSVVSIVATGGMGKTTLARLVYDDDKTVTKHFDKKAWVCVSDQFDAVR 250

Query: 59   ISKAILDSIKRS-SCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMA 117
            I+K IL+S+  S S   +DL+ +Q  L++ +  KKFLIVLDD+W++ Y     L SPF  
Sbjct: 251  ITKTILNSVTNSQSSDSQDLHQIQENLRKELKGKKFLIVLDDLWNDDYFELDRLCSPFWV 310

Query: 118  GAPGSRIIVTTRSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFEST 176
            GA GS+I+VTTR+ +VA  M G    +ELK L  DDC  +F  HAFE  +   H N ES 
Sbjct: 311  GAQGSKILVTTRNNNVANKMRGRKILHELKQLPYDDCLKIFQTHAFEHMNIDEHPNLESI 370

Query: 177  RQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKT-EIPSVLKLSYHHL 235
             +R+VEKC G PLAARALGGLLRS+    EW  +L SK+WNL DK  +I   L+LSY+HL
Sbjct: 371  GRRIVEKCGGSPLAARALGGLLRSELRECEWERVLYSKVWNLTDKECDIIPALRLSYYHL 430

Query: 236  PSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSL 295
             SHLKRCF YCA  P+DYEF ++EL+LLWIAEGL+QQS+DN+++ED G  YF +LLSRS 
Sbjct: 431  SSHLKRCFTYCANFPQDYEFTKQELILLWIAEGLIQQSKDNRKMEDHGDKYFDELLSRSF 490

Query: 296  FQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCD 355
            FQ SS+  S++VMHDLVH LA+  +G+TC  LDD+   D Q ++ E  RH S+ R + CD
Sbjct: 491  FQSSSSNRSRFVMHDLVHALAKSIAGDTCLHLDDELWNDLQCSISENTRHSSFTRHF-CD 549

Query: 356  GMDKFKVLDKVVNLRTF--LPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCIT 413
               KF+   K  +LRTF  LPI     R +   IS  VL +L+P+   LRVLSL  Y I+
Sbjct: 550  IFKKFERFHKKEHLRTFIALPIDESTSRRH-SFISNKVLEELIPRLGHLRVLSLARYMIS 608

Query: 414  EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLH 473
            E+P S G LK LRYLN S + I+ LPD+I +LF L+ L L  C  L++LP  IGNL+NL 
Sbjct: 609  EIPDSFGELKHLRYLNLSYTNIKWLPDSIGNLFYLQTLKLSCCEKLIRLPISIGNLINLR 668

Query: 474  YLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENV 533
            +L++ GA  L+E+P+ + +LK LR L+NFIV K++G  ++ LK+   LR  LCIS LENV
Sbjct: 669  HLDVAGAKQLQEMPVQIGKLKDLRILSNFIVDKNNGLTIKGLKDMSHLR-ELCISKLENV 727

Query: 534  IDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYG 593
            ++ Q+A +A L++K  L  L + W    DG S +E  + ++LD L+P  N+ +L I  YG
Sbjct: 728  VNIQDARDADLKLKRNLESLIMQWSSELDG-SGNERNQMDVLDSLQPCLNLNKLCIKWYG 786

Query: 594  GTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGE 653
            G  FP W+GD  FS +  L L +CR  TSLP LGQL SLK L I GM  +K +G+E YGE
Sbjct: 787  GPEFPRWIGDALFSKMVDLSLIDCRECTSLPCLGQLPSLKQLRIQGMDGVKKVGAEFYGE 846

Query: 654  ---GCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNH 710
                  K F SL++L+F  + EWE WE    + E +  FP L +L+I+ CPKL  +LP +
Sbjct: 847  TRVSAGKFFPSLESLHFNRMSEWEQWEDWSSSTESL--FPCLHELTIEDCPKLIMKLPTY 904

Query: 711  LPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEF-- 768
            LPSL ++ +  C  L   L  LP L  +++  C   V    ++  S  K+T+  IS    
Sbjct: 905  LPSLTKLSVHFCPKLESPLSRLPLLKGLQVKECNEAVLSSGNDLTSLTKLTISGISGLIK 964

Query: 769  ---------------------------------ENWSSEKFQKVEQLMIVGCEGFVNEIC 795
                                             EN  S + +  +QL+ +GC     EI 
Sbjct: 965  LHEGFVQFLQGLRVLKVSECEELVYLWEDGFGSENSHSLEIRDCDQLVSLGCNLQSLEIS 1024

Query: 796  ----LEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMI 851
                LE+   G Q LTCL++L I +CP + S P   F P L  + +++C  L SL DGM+
Sbjct: 1025 GCDKLERLPNGWQSLTCLEELTIRDCPKLASFPDVGFPPMLRNLILENCEGLKSLPDGMM 1084

Query: 852  Y----------NNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKS 901
                       N   LE L I  C SL    +  LP++L+++ I  CE L+ + ++   +
Sbjct: 1085 LKMRNDSTDSNNLCLLECLSIWNCPSLICFPKGQLPTTLKSLHILHCENLKSLPEEMMGT 1144

Query: 902  CTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVL- 960
            C                   LE   +  CPSL  L  GG LP TLK+LRI  C   + L 
Sbjct: 1145 CA------------------LEDFSIEGCPSLIGLPKGG-LPATLKKLRIWSCGRLESLP 1185

Query: 961  --------TSECQLPV-EVEE---LTIYGCSNLESIAERFHDDACLRSIWISSCENLKSL 1008
                    T+   L V E+ E   LT +     +S  ER H         I  CE L+S+
Sbjct: 1186 EGIMHQHSTNAAALQVLEIGECPFLTSFPRGKFQSTLERLH---------IGDCERLESI 1236

Query: 1009 PKGL--SNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRE 1066
             + +  S  + L  + + R  NL +LP D L + + D+ IED + L+ L+P      +++
Sbjct: 1237 SEEMFHSTNNSLQSLTLRRYPNLKTLP-DCL-NTLTDLRIEDFENLELLLP-----QIKK 1289

Query: 1067 LALSECPGIVVFPEEGLSTNLTDLEIS-GDNMYKPLVKWGFHKLTSLRKLYIDGC-SDAV 1124
            L                 T LT LEIS  +N+  PL +WG  +LTSL+ L I G   DA 
Sbjct: 1290 L-----------------TRLTSLEISHSENIKTPLSQWGLSRLTSLKDLLISGMFPDAT 1332

Query: 1125 SFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTS-FPEAG- 1182
            SF D    +I PT+L+S+T+ +F  L+ L+S   Q L SLE L ++SCP   S  P  G 
Sbjct: 1333 SFSDDPHSIIFPTTLSSLTLLEFQNLESLASLSLQTLTSLEKLEIYSCPKLRSILPTEGL 1392

Query: 1183 FPSSLLSLEIQRCP-LLEKCKMRKGQEWPKIAHIPLTLINQE 1223
             P +L  L ++ CP L ++    +G +WPKIAHIP   I+ +
Sbjct: 1393 LPDTLSRLYVRDCPHLTQRYSKEEGDDWPKIAHIPYVDIDDQ 1434

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487424|ref|XP_002271822.2| PREDICTED: putative disease resistance RPP13-like protein 1-like [Vitis vinifera]

 Score =  811 bits (2094), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 506/1279 (39%), Positives = 742/1279 (58%), Gaps = 103/1279 (8%)

Query: 12   NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS 71
            N  VI +VGMGG+GKTTLA+ VYND++ + F+ KAWVCVSD FDV  I++A L+S++ S 
Sbjct: 202  NVGVISIVGMGGVGKTTLARLVYNDEMAKKFDLKAWVCVSDVFDVENITRAFLNSVENSD 261

Query: 72   CKLE-DLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS 130
                 D   VQ +L++ + ++KFLI+LDDVW+E +  W  L++P   GA GS++IVTTR+
Sbjct: 262  ASGSLDFQQVQKKLRDALTERKFLIILDDVWNENFGNWDRLRAPLSVGAKGSKLIVTTRN 321

Query: 131  MDVALTMGSGKN-YELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL 189
             +VAL MG+ +N +EL  LS+D CWSVF  HAFE R+   + N  S  +++V KC GLPL
Sbjct: 322  KNVALMMGAAENLHELNPLSEDACWSVFEKHAFEHRNMEDNPNLVSIGRKIVGKCGGLPL 381

Query: 190  AARALGGLLRSKQGVDEWRAILDSKIWNLQD-KTEIPSVLKLSYHHLPSHLKRCFAYCAV 248
            AA++LGGLLRSKQ  +EW  + +SKIW+L   + EI   L+LSYH++PS+LKRCFAYCA+
Sbjct: 382  AAKSLGGLLRSKQREEEWERVSNSKIWDLSSTECEILPALRLSYHYVPSYLKRCFAYCAM 441

Query: 249  LPKDYEFKEKELVLLWIAEGLVQQ-SEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYV 307
             PKD+EF  K LVLLW+AEGL+Q+ + DN  +EDLG  YF +LLSRS FQ S   E ++V
Sbjct: 442  FPKDFEFNSKTLVLLWMAEGLIQEPNADNLTMEDLGDDYFCELLSRSFFQSSGTDEFRFV 501

Query: 308  MHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVV 367
            MHDL+ DLA+ ASGE CF L+D    +RQS + ++ RH S++R    D   KF+    + 
Sbjct: 502  MHDLICDLARVASGEICFCLEDTLDSNRQSTISKETRHSSFIRG-KFDAFKKFEAFQGLE 560

Query: 368  NLRTF--LPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQL 425
            +LRTF  LPI   Q       ++ +V   L+P+ ++LRVLSL  Y I E+P SIG LK L
Sbjct: 561  HLRTFVALPI---QGTFTESFVTSLVCDHLVPKFRQLRVLSLSEYMIFELPDSIGGLKHL 617

Query: 426  RYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRE 485
            RYLN S ++I+ LPD++ +L+NL+ LIL NC  L +LPS IGNL++L +LN+ G S L++
Sbjct: 618  RYLNLSFTQIKLLPDSVTNLYNLQTLILSNCKHLTRLPSNIGNLISLRHLNVVGCS-LQD 676

Query: 486  LPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLR 545
            +P  + +LK L+TL++FIV K     +++LK+   LRG +CIS LENV+D Q+A +A L+
Sbjct: 677  MPQQIGKLKKLQTLSDFIVSKRGFLGIKELKDLSHLRGEICISKLENVVDVQDARDANLK 736

Query: 546  VKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPS 605
             K  +  L + W    DG S DE  E  +L  L+PH+++K+L I  YGG +FP+W+ DPS
Sbjct: 737  AKLNVERLSMIWSKELDG-SHDEDAEMEVLLSLQPHTSLKKLNIEGYGGRQFPNWICDPS 795

Query: 606  FSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGC--SKPFQSLQ 663
            +  +  L L  C R  S+PS+GQL  LK L I  M  +KS+G E  G+    +KPFQ L+
Sbjct: 796  YIKLVELSLIGCIRCISVPSVGQLPFLKKLVIKRMDGVKSVGLEFEGQVSLHAKPFQCLE 855

Query: 664  TLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCM 723
            +L+FED+ EWE W  ++      ++F  L +L IK CP+L  +LP HL SL ++ I  C 
Sbjct: 856  SLWFEDMMEWEEWCWSK------ESFSCLHQLEIKNCPRLIKKLPTHLTSLVKLNIGNCP 909

Query: 724  HLAVSLPS-LPALCTMEIDGCKRLVCDGPSE----------SKSPNKMT------LCNIS 766
             + V  P+ LP+L  + I  C  ++    +           S+S   +T      +  IS
Sbjct: 910  EIMVRRPTHLPSLKELNIYYCPEMMPQFENHEFFIMPLREASRSAIDITSHIYLDVSGIS 969

Query: 767  EFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDL-------LIGNCPT 819
            +      E  Q + +L ++  +      CL     GL  L+ L+ L       L G    
Sbjct: 970  QLSRLQPEFMQSLPRLELLEIDNSGQLQCLWLDGLGLGNLSRLRILSSDQLVSLGGEEEE 1029

Query: 820  VVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSS 879
            V  LP      NL  + I+ C+ L  L  G+    +  E++ I+ C  L S   +  P  
Sbjct: 1030 VQGLPY-----NLQHLEIRKCDKLEKLPHGLQSYTSLAELI-IEDCPKLVSFPEKGFPLM 1083

Query: 880  LQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSG 939
            L+ + I +CE+L  + D               + +SS+    LE L +  CPSL C +  
Sbjct: 1084 LRGLAISNCESLSSLPDGM------------MMRNSSNNMCHLEYLEIEECPSLIC-FPK 1130

Query: 940  GRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWI 999
            G+LP TL+RL I DC     L  +  +   +E+L +  C +L     +      L+ +WI
Sbjct: 1131 GQLPTTLRRLFISDCEKLVSLPEDIDV-CAIEQLIMKRCPSLTGFPGKL--PPTLKKLWI 1187

Query: 1000 SSCENLKSLPKGL-----SNLSH--LHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKL 1052
              CE L+SLP+G+     +N ++  L  + I +C +L S P    PS +  + I++C ++
Sbjct: 1188 WGCEKLQSLPEGIMHHHSNNTTNGGLQILDISQCSSLTSFPTGKFPSTLKSITIDNCAQM 1247

Query: 1053 KAL---IPTGTLSSLRELALSECPGIVVFPE-------------EGLS---------TNL 1087
            + +   +     ++L +L++S  P +   P+             E L          T+L
Sbjct: 1248 QPISEEMFHCNNNALEKLSISGHPNLKTIPDCLYNLKDLRIEKCENLDLQPHLLRNLTSL 1307

Query: 1088 TDLEISG-DNMYKPLVKWGFHKLTSLRKLYIDGCS-DAVSFPDVGKGV-ILPTSLTSITI 1144
            + L+I+  + +  PL +WG  +LTSLR L I G   +A SFP+    + +LPT+L  ++I
Sbjct: 1308 SSLQITNCETIKVPLSEWGLARLTSLRTLTIGGIFLEATSFPNHHHHLFLLPTTLVELSI 1367

Query: 1145 SDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSF-PEAGFPSSLLSLEIQRCPLL-EKCK 1202
            S+F  L+ L+    Q L SL  L VF CP   SF P  G P  L  L I+ CPLL ++C 
Sbjct: 1368 SNFQNLESLAFLSLQMLTSLRKLDVFQCPKLQSFIPREGLPDMLSELYIRDCPLLIQRCS 1427

Query: 1203 MRKGQEWPKIAHIPLTLIN 1221
              KG++WPKIAHIP   I+
Sbjct: 1428 KEKGEDWPKIAHIPCVKID 1446

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	1237
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.577	0.501	0.393	1.5e-171
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.562	0.660	0.397	1e-141
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.445	0.305	0.316	3.5e-73
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.629	0.742	0.265	2.1e-43
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.629	0.742	0.265	2.1e-43
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.392	0.476	0.276	2.9e-42
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.392	0.476	0.276	2.9e-42
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.354	0.474	0.277	3.4e-42
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.371	0.539	0.301	2.3e-37
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.379	0.527	0.272	6.1e-37

TAIR|locus:2091662 AT3G14460 [Arabidopsis thaliana (taxid:3702)]

 Score = 1278 (454.9 bits), Expect = 1.5e-171, Sum P(3) = 1.5e-171
 Identities = 291/739 (39%), Positives = 430/739 (58%)

Query:     1 MVLKNDPSDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEPKAWVCVSDDFDVLRI 59
             ++L +D        VI +VGM G+GKTTL + V+ND ++TE FE K W+    +F+V  +
Sbjct:   181 LLLSDDEISIGKPAVISVVGMPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTV 240

Query:    60 SKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGA 119
             +KA+L  I  S+   EDL S+Q++LK+T+  K+FL+VLDD WSE    W++ +  F    
Sbjct:   241 TKAVLQDITSSAVNTEDLPSLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAE 300

Query:   120 PGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGT-HGNFESTRQ 178
              GS+I++TTRS  V+    + K Y++KL+++++CW +    AF     G+ +   E   +
Sbjct:   301 EGSKIVLTTRSEIVSTVAKAEKIYQMKLMTNEECWELISRFAFGNISVGSINQELEGIGK 360

Query:   179 RVVEKCKXXXXXXXXXXXXXXSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSH 238
             R+ E+CK              SK   D+W A+  SK ++    + +P VLKLSY  LP  
Sbjct:   361 RIAEQCKGLPLAARAIASHLRSKPNPDDWYAV--SKNFSSYTNSILP-VLKLSYDSLPPQ 417

Query:   239 LKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK 298
             LKRCFA C++ PK + F  +ELVLLW+A  L+ Q   +++LED+G+ Y  DL+++S FQ+
Sbjct:   418 LKRCFALCSIFPKGHVFDREELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQR 477

Query:   299 SSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMD 358
                T + +VMHDL++DLA+  SG+ CFRL+D    D    +    RHFS+ RS  CD   
Sbjct:   478 LDITMTSFVMHDLMNDLAKAVSGDFCFRLED----DNIPEIPSTTRHFSFSRS-QCDASV 532

Query:   359 KFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS 418
              F+ +     LRT LP F     +    ++  VL+ LL     LR+LSL  Y IT +P S
Sbjct:   533 AFRSICGAEFLRTILP-FNSPTSLESLQLTEKVLNPLLNALSGLRILSLSHYQITNLPKS 591

Query:   419 IGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE 478
             +  LK LRYL+ S ++I+ LP+ +C+L NL+ L+L NC  L  LP  I  L+NL  L++ 
Sbjct:   592 LKGLKLLRYLDLSSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDLV 651

Query:   479 GASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQE 538
             G + L E+P G+K+L+ L+ L+NF++G+ SG  L +LK    LRG L IS L+NV  + E
Sbjct:   652 G-TPLVEMPPGIKKLRSLQKLSNFVIGRLSGAGLHELKELSHLRGTLRISELQNVAFASE 710

Query:   539 ANEAMLRVKEGLTDLKLDWRPRRDG---DSVDEAR--EKNILDMLKPHSNIKRLEIHSYG 593
             A +A L+ K  L  L L W  +  G    S +     +K +L ML+PH ++K   I SY 
Sbjct:   711 AKDAGLKRKPFLDGLILKWTVKGSGFVPGSFNALACDQKEVLRMLEPHPHLKTFCIESYQ 770

Query:   594 GTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIY-G 652
             G  FP W+GD SF  +  + L +C    SLP +GQL SLK L+I   + L+ +G + + G
Sbjct:   771 GGAFPKWLGDSSFFGITSVTLSSCNLCISLPPVGQLPSLKYLSIEKFNILQKVGLDFFFG 830

Query:   653 EGCSK--PFQSLQTLYFEDLQEWEHWE-PNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPN 709
             E  S+  PFQSLQ L F  +  W+ W  P  ++      FP L+KL I++CP L  + P 
Sbjct:   831 ENNSRGVPFQSLQILKFYGMPRWDEWICPELEDG----IFPCLQKLIIQRCPSLRKKFPE 886

Query:   710 HLPSLEEIVIAGCMHLAVS 728
              LPS  E+ I+ C   AVS
Sbjct:   887 GLPSSTEVTISDCPLRAVS 905

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2091672 AT3G14470 [Arabidopsis thaliana (taxid:3702)]

 Score = 1315 (468.0 bits), Expect = 1.0e-141, Sum P(2) = 1.0e-141
 Identities = 288/724 (39%), Positives = 434/724 (59%)

Query:    15 VIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIKRSSCK 73
             V+ +VG+GG+GKTTL+Q +YND+   + F  K W  VS++FDV +I+K + +S+    C+
Sbjct:   198 VVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPCE 257

Query:    74 LEDLNSVQLELKE--TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM 131
               DL+ +Q++LKE  T     FL+VLDD+W+E +  W  L+ PF+  A GS+I+VTTRS 
Sbjct:   258 FTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPFIHAAQGSQILVTTRSQ 317

Query:   132 DVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKXXXXXX 191
              VA  M +   + L+ LSD DCWS+F+   F  ++   +       +R+V KC+      
Sbjct:   318 RVASIMCAVHVHNLQPLSDGDCWSLFMKTVFGNQEPCLNREIGDLAERIVHKCRGLPLAV 377

Query:   192 XXXXXXXXSKQGVDEWRAILDSKIWNLQ-DKTEIPSVLKLSYHHLPSHLKRCFAYCAVLP 250
                      +  V EW  +L S+IW+L  DK+ +  VL++SY++LP+HLKRCFAYC++ P
Sbjct:   378 KTLGGVLRFEGKVIEWERVLSSRIWDLPADKSNLLPVLRVSYYYLPAHLKRCFAYCSIFP 437

Query:   251 KDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHD 310
             K + F++ ++VLLW+AEG +QQ+  +K LE+LG+ YF +L SRSL QK   T+++Y+MHD
Sbjct:   438 KGHAFEKDKVVLLWMAEGFLQQTRSSKNLEELGNEYFSELESRSLLQK---TKTRYIMHD 494

Query:   311 LVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLR 370
              +++LAQ+ASGE   + +D   +     V E+ R+ SYLR    + M+ F+ L +V  LR
Sbjct:   495 FINELAQFASGEFSSKFEDGCKLQ----VSERTRYLSYLRDNYAEPME-FEALREVKFLR 549

Query:   371 TFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLN 429
             TFLP+           +  MV   LLP   +LRVLSL  Y I  +P      +   R+L+
Sbjct:   550 TFLPLSLTN-SSRSCCLDQMVSEKLLPTLTRLRVLSLSHYKIARLPPDFFKNISHARFLD 608

Query:   430 FSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG 489
              SR+E++ LP ++C ++NL+ L+L  C  L +LP+ I NL+NL YL++ G   LR++P  
Sbjct:   609 LSRTELEKLPKSLCYMYNLQTLLLSYCSSLKELPTDISNLINLRYLDLIGTK-LRQMPRR 667

Query:   490 MKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEG 549
                LK L+TLT F V    G  + +L     L G+L I  L+ V+D  +A EA L  K+ 
Sbjct:   668 FGRLKSLQTLTTFFVSASDGSRISELGGLHDLHGKLKIVELQRVVDVADAAEANLNSKKH 727

Query:   550 LTDLKLDWRPRRDG--DSVDEAREKN---ILDMLKPHSNIKRLEIHSYGGTRFPSWVGDP 604
             L ++   WR       ++ +  R +N   + + L+PH +I++L I  Y G RFP W+ DP
Sbjct:   728 LREIDFVWRTGSSSSENNTNPHRTQNEAEVFEKLRPHRHIEKLAIERYKGRRFPDWLSDP 787

Query:   605 SFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIY------GEGCSKP 658
             SFS +  + L+ C+  TSLPSLGQL  LK+L I GM  L+SIG + Y       +   +P
Sbjct:   788 SFSRIVCIRLRECQYCTSLPSLGQLPCLKELHISGMVGLQSIGRKFYFSDQQLRDQDQQP 847

Query:   659 FQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIV 718
             F+SL+TL F++L +W+ W   R     +  FP L+KL I +CP+L+G LP  LPSL  + 
Sbjct:   848 FRSLETLRFDNLPDWQEWLDVRVTRGDL--FPSLKKLFILRCPELTGTLPTFLPSLISLH 905

Query:   719 IAGC 722
             I  C
Sbjct:   906 IYKC 909

GO:0005576 "extracellular region" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

UNIPROTKB|O48647 O48647 "XA1" [Oryza sativa (taxid:4530)]

 Score = 642 (231.1 bits), Expect = 3.5e-73, Sum P(2) = 3.5e-73
 Identities = 188/594 (31%), Positives = 310/594 (52%)

Query:     8 SDAAN-FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILD 65
             S+ +N   V+P+VG GGIGKTTLAQ V  D + ++ F  K WV VSD FDV++I++ ILD
Sbjct:   313 SNRSNGITVLPIVGNGGIGKTTLAQLVCKDLVIKSQFNVKIWVYVSDKFDVVKITRQILD 372

Query:    66 SIKRSSCK-LEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAG------ 118
              +   S + + +L+++Q +L+E +  KKFLIVLDDVW  R D W+ L +P          
Sbjct:   373 HVSNQSHEGISNLDTLQQDLEEQMKSKKFLIVLDDVWEIRTDDWKKLLAPLRPNDQVNSS 432

Query:   119 ---APGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFES 175
                A G+ II+TTR   +A ++G+ ++ +L+ L DDD WS+F  HAF      +    + 
Sbjct:   433 QEEATGNMIILTTRIQSIAKSLGTVQSIKLEALKDDDIWSLFKVHAFGNDKHDSSPGLQV 492

Query:   176 TRQRVVEKCKXXXXXXXXXXXXXXSKQGVDEWRAILDSKIW-NLQDKTEIPSVLKLSYHH 234
               +++  + K              +   +D W +I+ S+ W +LQ    I   LKLSY H
Sbjct:   493 LGKQIASELKGNPLAAKTVGSLLGTNLTIDHWDSIIKSEEWKSLQQAYGIMQALKLSYDH 552

Query:   235 LPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRS 294
             L + L++C +YC++ PK Y F + +L+ +WIA+G V++S +  +LE  G  Y  +L++  
Sbjct:   553 LSNPLQQCVSYCSLFPKGYSFSKAQLIQIWIAQGFVEESSE--KLEQKGWKYLAELVNSG 610

Query:   295 LFQKSSNTE--SKY-VMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYL-- 349
               Q+  +T   S+Y VMHDL+HDLAQ  S      +D     +    +   +RH S +  
Sbjct:   611 FLQQVESTRFSSEYFVMHDLMHDLAQKVSQTEYATIDGSECTE----LAPSIRHLSIVTD 666

Query:   350 ---RSYDCDGMDKFKVLDK---VVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLR 403
                R      + + +V +K    V  R+ L       + Y  +       D   + + LR
Sbjct:   667 SAYRKEKYRNISRNEVFEKRLMKVKSRSKLRSLVLIGQ-YDSHFFKY-FKDAFKEAQHLR 724

Query:   404 VLSL-GSYCITEVPIS-IGCLKQLRYLNFSRSEI-QCLPDAICSLFNLEILILRNCWCLL 460
             +L +  +Y  ++  +S +     LRYL     E  + LP ++   ++L++L +   + + 
Sbjct:   725 LLQITATYADSDSFLSSLVNSTHLRYLKIVTEESGRTLPRSLRKYYHLQVLDIGYRFGIP 784

Query:   461 KLPSRIGNLVNLHYLNI--EGASALRELPLGMKELKCLRTLTNFIVGKD-SGCALRDLKN 517
             ++ + I NL++L +L    E  S++  +  G  ++  L+ L NFIV  + SG  +  LK+
Sbjct:   785 RISNDINNLLSLRHLVAYDEVCSSIANI--G--KMTSLQELGNFIVQNNLSGFEVTQLKS 840

Query:   518 WKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEARE 571
                L  +L +S LENV   +EA  A L+ K+ L  L L W+   +G   DE+ E
Sbjct:   841 MNKLV-QLSVSQLENVRTQEEACGAKLKDKQHLEKLHLSWKDAWNGYDSDESYE 893

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

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

 Score = 494 (179.0 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 237/894 (26%), Positives = 393/894 (43%)

Query:     9 DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
             D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct:   179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query:    68 K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
             K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct:   239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query:   124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR--- 179
             +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA      E   +    
Sbjct:   296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query:   180 VVEKCKXXXXXXXXXXXXXXSKQGVDEWRAI---LDSKI------WNLQDKTEIPSVLKL 230
             +++ C                K    +WR +   + S +      +N  +      VL L
Sbjct:   356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSL 415

Query:   231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSE-DNKQLEDLGSGYFHD 289
             S+  LPS+LK CF Y A  P DYE   K L   W AEG+ Q    D + + D+G  Y  +
Sbjct:   416 SFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEIIRDVGDVYIEE 475

Query:   290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFR--LDDQFSVDRQSNVFEK 342
             L+ R++       K+S  E+ + +HD++ ++    + E  F      + S     ++   
Sbjct:   476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENFLQITSSRTSTGNSLSIVTS 534

Query:   343 VRH-FSYLRSYDCD-GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCK 400
              R  + Y  + D +  ++  K+   VV   T++  F+  W       S M+L     + +
Sbjct:   535 RRLVYQYPITLDVEKDINDPKLRSLVVVANTYM--FWGGW-------SWMLLGSSFIRLE 585

Query:   401 KLRVLSLGSYCIT--EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWC 458
              LRVL +    +   ++  SIG L  LRYLN   +E+  +P    SL NL++LI  N   
Sbjct:   586 LLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLKHAEVTHIP---YSLGNLKLLIYLNLVI 642

Query:   459 LLK----LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRD 514
             L+     +P+ +  +  L YL +      R+  L +  L  L TL NF       C+L D
Sbjct:   643 LVSGSTLVPNVLKEMQQLRYLALPKDMG-RKTKLELSNLVKLETLKNF---STKNCSLED 698

Query:   515 LKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLT--DLKLDWRPRRDGDSVDEAREK 572
             L+    LR        E  +++  A+   L+  E LT  DL  + R +  G   D    K
Sbjct:   699 LRGMVRLRTLTIELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFVYLK 758

Query:   573 NILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCR-RSTSLPSLGQLCS 631
              +   LK +  + RL    +    FPS        ++  L L++CR     +P L +L  
Sbjct:   759 TLT--LKLY--MPRLSKEQH----FPS--------HLTTLYLQHCRLEEDPMPILEKLHQ 802

Query:   632 LKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPN---------RD- 681
             LK+L +   S   S    +   G     Q L     E+ ++W+  E +         RD 
Sbjct:   803 LKELELRRKSF--SGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESSMPVLHTLDIRDC 860

Query:   682 ------NDEHVQAFPRLRKLSIKKCPKLSGRLPN-----HLPSLEEIV--IAG-CMHLAV 727
                    DEH+ +   L  +S+  C      +P      HL  L+ +    +G  M  A 
Sbjct:   861 RKLKQLPDEHLPS--HLTSISLFFCCLEEDPMPTLERLVHLKELQLLFRSFSGRIMVCAG 918

Query:   728 S-LPSLPALCTMEIDGCKR-LVCDGPSESKSPNKMTLC-NISEFENWSSEKFQKVEQLMI 784
             S  P L  L   E+DG +  +V DG        ++  C  + +  N     F +++ L +
Sbjct:   919 SGFPQLHKLKLSELDGLEEWIVEDGSMPQLHTLEIRRCPKLKKLPNG----FPQLQNLEL 974

Query:   785 VGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKAC-FLPNLSEITI 837
                E +  E  +E    G   L  L  L I NCP +  LP    F+ +L  +T+
Sbjct:   975 NELEEW-EEWIVE---DGSMPL--LHTLRIWNCPKLKQLPDGLRFIYSLKNLTV 1022

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 494 (179.0 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 237/894 (26%), Positives = 393/894 (43%)

Query:     9 DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
             D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct:   179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query:    68 K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
             K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct:   239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query:   124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR--- 179
             +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA      E   +    
Sbjct:   296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query:   180 VVEKCKXXXXXXXXXXXXXXSKQGVDEWRAI---LDSKI------WNLQDKTEIPSVLKL 230
             +++ C                K    +WR +   + S +      +N  +      VL L
Sbjct:   356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSL 415

Query:   231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSE-DNKQLEDLGSGYFHD 289
             S+  LPS+LK CF Y A  P DYE   K L   W AEG+ Q    D + + D+G  Y  +
Sbjct:   416 SFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEIIRDVGDVYIEE 475

Query:   290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFR--LDDQFSVDRQSNVFEK 342
             L+ R++       K+S  E+ + +HD++ ++    + E  F      + S     ++   
Sbjct:   476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENFLQITSSRTSTGNSLSIVTS 534

Query:   343 VRH-FSYLRSYDCD-GMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCK 400
              R  + Y  + D +  ++  K+   VV   T++  F+  W       S M+L     + +
Sbjct:   535 RRLVYQYPITLDVEKDINDPKLRSLVVVANTYM--FWGGW-------SWMLLGSSFIRLE 585

Query:   401 KLRVLSLGSYCIT--EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWC 458
              LRVL +    +   ++  SIG L  LRYLN   +E+  +P    SL NL++LI  N   
Sbjct:   586 LLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLKHAEVTHIP---YSLGNLKLLIYLNLVI 642

Query:   459 LLK----LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRD 514
             L+     +P+ +  +  L YL +      R+  L +  L  L TL NF       C+L D
Sbjct:   643 LVSGSTLVPNVLKEMQQLRYLALPKDMG-RKTKLELSNLVKLETLKNF---STKNCSLED 698

Query:   515 LKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLT--DLKLDWRPRRDGDSVDEAREK 572
             L+    LR        E  +++  A+   L+  E LT  DL  + R +  G   D    K
Sbjct:   699 LRGMVRLRTLTIELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFVYLK 758

Query:   573 NILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCR-RSTSLPSLGQLCS 631
              +   LK +  + RL    +    FPS        ++  L L++CR     +P L +L  
Sbjct:   759 TLT--LKLY--MPRLSKEQH----FPS--------HLTTLYLQHCRLEEDPMPILEKLHQ 802

Query:   632 LKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPN---------RD- 681
             LK+L +   S   S    +   G     Q L     E+ ++W+  E +         RD 
Sbjct:   803 LKELELRRKSF--SGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESSMPVLHTLDIRDC 860

Query:   682 ------NDEHVQAFPRLRKLSIKKCPKLSGRLPN-----HLPSLEEIV--IAG-CMHLAV 727
                    DEH+ +   L  +S+  C      +P      HL  L+ +    +G  M  A 
Sbjct:   861 RKLKQLPDEHLPS--HLTSISLFFCCLEEDPMPTLERLVHLKELQLLFRSFSGRIMVCAG 918

Query:   728 S-LPSLPALCTMEIDGCKR-LVCDGPSESKSPNKMTLC-NISEFENWSSEKFQKVEQLMI 784
             S  P L  L   E+DG +  +V DG        ++  C  + +  N     F +++ L +
Sbjct:   919 SGFPQLHKLKLSELDGLEEWIVEDGSMPQLHTLEIRRCPKLKKLPNG----FPQLQNLEL 974

Query:   785 VGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKAC-FLPNLSEITI 837
                E +  E  +E    G   L  L  L I NCP +  LP    F+ +L  +T+
Sbjct:   975 NELEEW-EEWIVE---DGSMPL--LHTLRIWNCPKLKQLPDGLRFIYSLKNLTV 1022

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 428 (155.7 bits), Expect = 2.9e-42, Sum P(2) = 2.9e-42
 Identities = 148/535 (27%), Positives = 253/535 (47%)

Query:     9 DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
             D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct:   179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query:    68 K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
             K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct:   239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query:   124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR--- 179
             +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA      E   +    
Sbjct:   296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query:   180 VVEKCKXXXXXXXXXXXXXXSKQGVDEWRAI---LDSKI------WNLQDKTEIPSVLKL 230
             +++ C                K    +WR +   + S +      +N  +     +VL L
Sbjct:   356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNNVLSL 415

Query:   231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSE-DNKQLEDLGSGYFHD 289
             S+  LPS+LK CF Y A  P+DYE K + L   W AEG+ Q    D + + D+G  Y  +
Sbjct:   416 SFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEGIFQPRHYDGETIRDVGDVYIEE 475

Query:   290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVR 344
             L+ R++       K+S  E+ + +HD++ ++    + E  F L    S    +N+   V 
Sbjct:   476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENF-LQITSSRPSTANLQSTVT 533

Query:   345 HFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCK-KLR 403
                ++  Y    +   K ++    LR  + +    W +   + + + L  +L   + K++
Sbjct:   534 SRRFVYQYPTT-LHVEKDINNP-KLRALVVVTLGSWNLAGSSFTRLELLRVLDLIEVKIK 591

Query:   404 VLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLK-- 461
                L S CI       G L  LRYL+   +E+  +P    SL NL++LI  N     +  
Sbjct:   592 GGKLAS-CI-------GKLIHLRYLSLEYAEVTHIP---YSLGNLKLLIYLNLASFGRST 640

Query:   462 -LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDL 515
              +P+ +  +  L YL +      R+  L +  L  L TL NF     S   L DL
Sbjct:   641 FVPNVLMGMQELRYLALPSDMG-RKTKLELSNLVKLETLENFSTENSS---LEDL 691

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 428 (155.7 bits), Expect = 2.9e-42, Sum P(2) = 2.9e-42
 Identities = 148/535 (27%), Positives = 253/535 (47%)

Query:     9 DAANFRVIPLVGMGGIGKTTLAQEVYN-DKLTEAFEPKAWVCVSDDFDVLRISKAILDSI 67
             D AN +V+ + GMGG+GKTTLA++V+N + +   F+  +WVCVS DF  + + + IL  +
Sbjct:   179 DEANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDL 238

Query:    68 K--RSSCKLEDL--NSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR 123
             K      K+ ++  +++Q EL   +   K LIVLDD+W E+ D W+ +K P      G +
Sbjct:   239 KPKEEEKKIMEMTQDTLQGELIRLLETSKSLIVLDDIW-EKED-WELIK-PIFPPTKGWK 295

Query:   124 IIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR--- 179
             +++T+R+  VA+   +   N++ + L+ +D W++F   A   +DA      E   +    
Sbjct:   296 VLLTSRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKL 355

Query:   180 VVEKCKXXXXXXXXXXXXXXSKQGVDEWRAI---LDSKI------WNLQDKTEIPSVLKL 230
             +++ C                K    +WR +   + S +      +N  +     +VL L
Sbjct:   356 MIKHCGGLPLAIRVLGGMLAEKYTSHDWRRLSENIGSHLVGGRTNFNDDNNNTCNNVLSL 415

Query:   231 SYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSE-DNKQLEDLGSGYFHD 289
             S+  LPS+LK CF Y A  P+DYE K + L   W AEG+ Q    D + + D+G  Y  +
Sbjct:   416 SFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEGIFQPRHYDGETIRDVGDVYIEE 475

Query:   290 LLSRSLF-----QKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVR 344
             L+ R++       K+S  E+ + +HD++ ++    + E  F L    S    +N+   V 
Sbjct:   476 LVRRNMVISERDVKTSRFETCH-LHDMMREVCLLKAKEENF-LQITSSRPSTANLQSTVT 533

Query:   345 HFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCK-KLR 403
                ++  Y    +   K ++    LR  + +    W +   + + + L  +L   + K++
Sbjct:   534 SRRFVYQYPTT-LHVEKDINNP-KLRALVVVTLGSWNLAGSSFTRLELLRVLDLIEVKIK 591

Query:   404 VLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLK-- 461
                L S CI       G L  LRYL+   +E+  +P    SL NL++LI  N     +  
Sbjct:   592 GGKLAS-CI-------GKLIHLRYLSLEYAEVTHIP---YSLGNLKLLIYLNLASFGRST 640

Query:   462 -LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDL 515
              +P+ +  +  L YL +      R+  L +  L  L TL NF     S   L DL
Sbjct:   641 FVPNVLMGMQELRYLALPSDMG-RKTKLELSNLVKLETLENFSTENSS---LEDL 691

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 456 (165.6 bits), Expect = 3.4e-42, Sum P(2) = 3.4e-42
 Identities = 134/483 (27%), Positives = 231/483 (47%)

Query:    15 VIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDF---DVLR--ISKAILDSIK 68
             V+ +VGMGG GKTTL+  ++  + +   FE  AWV +S  +   DV R  I +   ++  
Sbjct:   195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query:    69 RSSCKLEDLNSVQL--ELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV 126
             +   +L  L   +L  +L E +  K++++VLDDVW+    LW+ +      G  GSR+++
Sbjct:   255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVWTT--GLWREISIALPDGIYGSRVMM 312

Query:   127 TTRSMDVA-LTMGSGKN-YELKLLSDDDCWSVFVAHAFEGR-DAGTHGNFESTRQRVVEK 183
             TTR M+VA    G G   +E++LL +D+ W +F   AF    +     N E   +++VE+
Sbjct:   313 TTRDMNVASFPYGIGSTKHEIELLKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVER 372

Query:   184 CKXXXXXXXXXXXXXXSKQGVDEWRAILDSKIWNLQDKTEIP---SVLKLSYHHLPSHLK 240
             C+              +K+   EW+ +  +  W L +  E+    S++ LS++ LP  LK
Sbjct:   373 CQGLPLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYPLK 432

Query:   241 RCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ--- 297
             RCF YC++ P +Y  K K L+ +W+A+  V+     K  E++   Y ++L+ R++ Q   
Sbjct:   433 RCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKA-EEVADSYLNELVYRNMLQVIL 491

Query:   298 -KSSNTESKYVMHDLVHDLAQWASG--ETCFRLDDQFSVDRQSNVFEKV--RHFSYLRSY 352
                      + MHD++ ++A   S     C   +D    D  +   E    RH    +  
Sbjct:   492 WNPFGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRHLCIQKEM 551

Query:   353 DCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCI 412
               D +       +  NL + L     + ++           +LLP    LR L L    I
Sbjct:   552 TPDSI-------RATNLHSLLVCSSAKHKM-----------ELLPSLNLLRALDLEDSSI 593

Query:   413 TEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNL 472
             +++P  +  +  L+YLN S+++++ LP     L NLE L  ++   + +LP  +  L  L
Sbjct:   594 SKLPDCLVTMFNLKYLNLSKTQVKELPKNFHKLVNLETLNTKHSK-IEELPLGMWKLKKL 652

Query:   473 HYL 475
              YL
Sbjct:   653 RYL 655

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

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

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 436 (158.5 bits), Expect = 2.3e-37, P = 2.3e-37
 Identities = 149/495 (30%), Positives = 234/495 (47%)

Query:     8 SDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAILDS 66
             S+ +   ++  VGMGG+GKTT+AQEV+NDK  E  FE + WV VS  F   +I ++IL +
Sbjct:   177 SNDSQLLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRN 236

Query:    67 IKRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV 126
             +  +S   +D+ ++  ++++ +  K++LIV+DDVW +    W  +      G  GS +IV
Sbjct:   237 LGDASVG-DDIGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGS-VIV 294

Query:   127 TTRSMDVALTMGS--GKNYELKLLSDDDCWSVFVAHAFEGRDAGT--HGNFESTRQRVVE 182
             TTRS  VA  + +   K +  +LLS D+ W +F   AF   D GT      E   + +V 
Sbjct:   295 TTRSESVAKRVQARDDKTHRPELLSPDNSWLLFCNVAFAAND-GTCERPELEDVGKEIVT 353

Query:   183 KCKXXXXXXXXXXXXXXSKQGV-DEWRAIL----DSKIWNLQDKTEIPSVLKLSYHHLPS 237
             KCK               K  V  EWR I     D    N  +   + S L+LSY  LPS
Sbjct:   354 KCKGLPLTIKAVGGLLLCKDHVYHEWRRIAEHFQDELRGNTSETDNVMSSLQLSYDELPS 413

Query:   238 HLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQ 297
             HLK C    ++ P+D    +++LV  WI EG V         E  G   F  L +R L +
Sbjct:   414 HLKSCILTLSLYPEDCVIPKQQLVHGWIGEGFVMWRNGRSATES-GEDCFSGLTNRCLIE 472

Query:   298 KSSNTESKYVM----HDLVHDL----AQWAS-----GETCFRLDDQFSVD-RQSNVFEKV 343
                 T S  ++    HD+V DL    A+  S     G  C  L    + D +Q  V  K+
Sbjct:   473 VVDKTYSGTIITCKIHDMVRDLVIDIAKKDSFSNPEGLNCRHLGISGNFDEKQIKVNHKL 532

Query:   344 RHF-SYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKL 402
             R   S  ++ + + ++   +  K  + + +L +      I+   +S ++  D +   + L
Sbjct:   533 RGVVSTTKTGEVNKLNS-DLAKKFTDCK-YLRVLDISKSIFDAPLSEIL--DEIASLQHL 588

Query:   403 RVLSLGS-YCITEVPISIGCLKQLRYLNFSRSE-IQCLPDAICSLFNLEILILRNCWCLL 460
               LSL + + + + P S+  L  L+ L+ S  + ++ L   I     L +L + NC  L 
Sbjct:   589 ACLSLSNTHPLIQFPRSMEDLHNLQILDASYCQNLKQLQPCIVLFKKLLVLDMTNCGSLE 648

Query:   461 KLPSRIGNLVNLHYL 475
               P  IG+LV L  L
Sbjct:   649 CFPKGIGSLVKLEVL 663

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2201996 RPS5 "AT1G12220" [Arabidopsis thaliana (taxid:3702)]

 Score = 418 (152.2 bits), Expect = 6.1e-37, Sum P(2) = 6.1e-37
 Identities = 136/500 (27%), Positives = 233/500 (46%)

Query:    15 VIPLVGMGGIGKTTLAQEVYN--DKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC 72
             ++ L GMGG+GKTTL  ++ N   K+ + F+   WV VS    V +I + I + +     
Sbjct:   178 ILGLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGM 237

Query:    73 KLEDLNSVQL--ELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS 130
             +  + N  Q+  ++   + ++KF+++LDD+W E+ +L +A+  P+ +   G ++  TTRS
Sbjct:   238 EWSEKNDNQIAVDIHNVLRRRKFVLLLDDIW-EKVNL-KAVGVPYPSKDNGCKVAFTTRS 295

Query:   131 MDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDA-GTHGNFESTRQRVVEKCKXXXX 189
              DV   MG     E+  L  ++ W +F      G++  G+H +     ++V  KC+    
Sbjct:   296 RDVCGRMGVDDPMEVSCLQPEESWDLFQMKV--GKNTLGSHPDIPGLARKVARKCRGLPL 353

Query:   190 XXXXXXXXXXSKQGVDEWRAILDSKIWNLQD----KTEIPSVLKLSYHHLPSHL-KRCFA 244
                        K+ V EW   +D    +  D    + EI  VLK SY +L   L K CF 
Sbjct:   354 ALNVIGEAMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFL 413

Query:   245 YCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTES 304
             YC++ P+DY   ++ LV  WI+EG + + E  ++  + G      L+   L  +    +S
Sbjct:   414 YCSLFPEDYLIDKEGLVDYWISEGFINEKEGRERNINQGYEIIGTLVRACLLLEEERNKS 473

Query:   305 KYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFE--KVRHFSYLRSYDCDGMDKFKV 362
                MHD+V ++A W S +   +  ++  V     + E  KV+ ++ +R       +  ++
Sbjct:   474 NVKMHDVVREMALWISSDLG-KQKEKCIVRAGVGLREVPKVKDWNTVRKISLMNNEIEEI 532

Query:   363 LDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLG-SYCITEVPISIGC 421
              D          +F ++      N    + ++       L VL L  +  + E+P  I  
Sbjct:   533 FDSH-ECAALTTLFLQK------NDVVKISAEFFRCMPHLVVLDLSENQSLNELPEEISE 585

Query:   422 LKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIG--NLVNLHYLNIEG 479
             L  LRY N S + I  LP     L+ L+ LI  N   +  L S +G  NL NL  L +  
Sbjct:   586 LASLRYFNLSYTCIHQLP---VGLWTLKKLIHLNLEHMSSLGSILGISNLWNLRTLGLRD 642

Query:   480 ASALRELPLGMKELKCLRTL 499
             +  L ++ L +KEL+ L  L
Sbjct:   643 SRLLLDMSL-VKELQLLEHL 661

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

GO:0006952 "defense response" evidence=IMP;TAS

GO:0009816 "defense response to bacterium, incompatible interaction" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008219 "cell death" evidence=IMP

GO:0038023 "signaling receptor activity" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IMP

GO:0005622 "intracellular" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00010803001 SubName- Full=Chromosome chr13 scaffold_286, whole genome shotgun sequence; (1418 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	1237
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	7e-74
PLN03210	1153	PLN03210, PLN03210, Resistant to P	4e-14
PLN03210	1153	PLN03210, PLN03210, Resistant to P	1e-10
PLN03210	1153	PLN03210, PLN03210, Resistant to P	5e-10
PRK15386	426	PRK15386, PRK15386, type III secretion protein Gog	2e-05
PRK15386	426	PRK15386, PRK15386, type III secretion protein Gog	4e-04

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

 Score =  246 bits (631), Expect = 7e-74
 Identities = 111/270 (41%), Positives = 157/270 (58%), Gaps = 12/270 (4%)

Query: 12  NFRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAI---LDSI 67
           N  V+ +VGMGG+GKTTLA+++YND      F+  AWV VS  +   R+ K I   L   
Sbjct: 18  NLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLD 77

Query: 68  KRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVT 127
                +  + + + +++KE + +K+FL+VLDDVW +  + W  +  PF  G  GSR+IVT
Sbjct: 78  DSDWVEKNE-SELAVKIKEALLRKRFLLVLDDVWEK--NDWDKIGVPFPDGENGSRVIVT 134

Query: 128 TRSMDVALTMGSG-KNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKG 186
           TRS  VA  MG   K +E++ L  ++ W +F    FE          E   + +VEKCKG
Sbjct: 135 TRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKEL-PPCPELEEVAKEIVEKCKG 193

Query: 187 LPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKT---EIPSVLKLSYHHLPSHLKRCF 243
           LPLA + LGGLL  K  V EW  +L+     L  +    E+ S+L LSY +LP HLKRCF
Sbjct: 194 LPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNEVLSILSLSYDNLPMHLKRCF 253

Query: 244 AYCAVLPKDYEFKEKELVLLWIAEGLVQQS 273
            Y A+ P+DY  ++++L+ LWIAEG V  S
Sbjct: 254 LYLALFPEDYNIRKEQLIKLWIAEGFVIPS 283

Length = 285

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score = 77.2 bits (190), Expect = 4e-14
 Identities = 69/229 (30%), Positives = 105/229 (45%), Gaps = 20/229 (8%)

Query: 979  SNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALP 1038
            S LE + +  H    LR+I +   +NLK +P  LS  ++L  +++  C +LV LP     
Sbjct: 621  SKLEKLWDGVHSLTGLRNIDLRGSKNLKEIPD-LSMATNLETLKLSDCSSLVELPSSIQY 679

Query: 1039 SN-VVDVLIEDCDKLKALIPTG-TLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDN 1096
             N + D+ +  C+ L+ L PTG  L SL  L LS C  +  FP+  +STN++ L++    
Sbjct: 680  LNKLEDLDMSRCENLEIL-PTGINLKSLYRLNLSGCSRLKSFPD--ISTNISWLDLDETA 736

Query: 1097 MYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKG-------VILPTSLTSITISDFPK 1149
            + +      F     L  L      +  S     +         +L  SLT + +SD P 
Sbjct: 737  IEE------FPSNLRLENLDELILCEMKSEKLWERVQPLTPLMTMLSPSLTRLFLSDIPS 790

Query: 1150 LKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLL 1198
            L  L S   Q L  LEHL + +C N  + P      SL SL++  C  L
Sbjct: 791  LVELPSS-IQNLHKLEHLEIENCINLETLPTGINLESLESLDLSGCSRL 838

syringae 6; Provisional. Length = 1153

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score = 65.7 bits (160), Expect = 1e-10
 Identities = 191/805 (23%), Positives = 309/805 (38%), Gaps = 166/805 (20%)

Query: 14  RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-----KAWVCVS---------DDFDV-LR 58
           R++ + G  GIGKTT+A+ +++ +L+  F+      +A++  S         DD+++ L 
Sbjct: 208 RMVGIWGSSGIGKTTIARALFS-RLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLH 266

Query: 59  ISKAILDSI-KRSSCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMA 117
           + +A L  I  +   K+  L +++    E +  +K LI +DD+  +  D+  AL      
Sbjct: 267 LQRAFLSEILDKKDIKIYHLGAME----ERLKHRKVLIFIDDL--DDQDVLDALAGQTQW 320

Query: 118 GAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTR 177
              GSRIIV T+        G    YE+ L S++    +F   AF  +       F    
Sbjct: 321 FGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAF--KKNSPPDGFMELA 378

Query: 178 QRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPS 237
             V  +   LPL    LG  LR +   ++W  +L      L  K  I   L++SY  L +
Sbjct: 379 SEVALRAGNLPLGLNVLGSYLRGRD-KEDWMDMLPRLRNGLDGK--IEKTLRVSYDGLNN 435

Query: 238 HL-KRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLF 296
              K  F + A L      K  ++ LL     L           D+  G   +L+ +SL 
Sbjct: 436 KKDKAIFRHIACLFNGE--KVNDIKLLLANSDL-----------DVNIG-LKNLVDKSLI 481

Query: 297 QKSSNTESKYVMHDLVHDLAQWA----------------SGETCFRLDDQFSVDR----- 335
               +      MH L+ ++ +                  + + C  L+D     +     
Sbjct: 482 HVREDIVE---MHSLLQEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGIT 538

Query: 336 -----------QSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFK------ 378
                        N F+ +R+  +L+ Y        K  D+   +R  LP  F       
Sbjct: 539 LDIDEIDELHIHENAFKGMRNLLFLKFYT-------KKWDQKKEVRWHLPEGFDYLPPKL 591

Query: 379 ---QWRIY-----PPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNF 430
              +W  Y     P N  P  L  L  Q  KL  L  G          +  L  LR ++ 
Sbjct: 592 RLLRWDKYPLRCMPSNFRPENLVKLQMQGSKLEKLWDG----------VHSLTGLRNIDL 641

Query: 431 SRSE-IQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG 489
             S+ ++ +PD +    NLE L L +C  L++LPS I  L  L  L++     L  LP G
Sbjct: 642 RGSKNLKEIPD-LSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTG 700

Query: 490 --MKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVK 547
             +K L  L           SGC+   LK+  F      IS L+    + E   + LR+ 
Sbjct: 701 INLKSLYRLNL---------SGCS--RLKS--FPDISTNISWLDLDETAIEEFPSNLRL- 746

Query: 548 EGLTDLKL-DWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPS- 605
           E L +L L + +  +  + V       ++ ML P  ++ RL +     +  PS V  PS 
Sbjct: 747 ENLDELILCEMKSEKLWERVQPLTP--LMTMLSP--SLTRLFL-----SDIPSLVELPSS 797

Query: 606 ---FSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKS---IGSEIYGEGCSKPF 659
                 +  L ++NC    +LP+   L SL+ L + G S L++   I + I         
Sbjct: 798 IQNLHKLEHLEIENCINLETLPTGINLESLESLDLSGCSRLRTFPDISTNISD------- 850

Query: 660 QSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPN--HLPSLEEI 717
            +L     E++  W            ++ F  L  L +  C  L     N   L  LE +
Sbjct: 851 LNLSRTGIEEVPWW------------IEKFSNLSFLDMNGCNNLQRVSLNISKLKHLETV 898

Query: 718 VIAGCMHLA-VSLPSLPALCTMEID 741
             + C  L   S    P+   M  D
Sbjct: 899 DFSDCGALTEASWNGSPSEVAMATD 923

syringae 6; Provisional. Length = 1153

>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P

 Score = 63.7 bits (155), Expect = 5e-10
 Identities = 93/401 (23%), Positives = 152/401 (37%), Gaps = 101/401 (25%)

Query: 796  LEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNA 855
            LEK   G+  LT L+++ +     +  +P      NL  + + DC++L  L   + Y N 
Sbjct: 623  LEKLWDGVHSLTGLRNIDLRGSKNLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLN- 681

Query: 856  RLEVLRIKRCDSLTSISREHLPS-----SLQAIEIRDCETLQCVLDDREKSCTSSSVTEK 910
            +LE L + RC++L     E LP+     SL  + +  C  L+   D              
Sbjct: 682  KLEDLDMSRCENL-----EILPTGINLKSLYRLNLSGCSRLKSFPDI------------- 723

Query: 911  NINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEV 970
               S++ ++LDL+   +   PS                LR+E+     +   + +   E 
Sbjct: 724  ---STNISWLDLDETAIEEFPS---------------NLRLENLDELILCEMKSEKLWER 765

Query: 971  EELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLV 1030
             +      + L     R         +++S   +L  LP  + NL  L  + I  C NL 
Sbjct: 766  VQPLTPLMTMLSPSLTR---------LFLSDIPSLVELPSSIQNLHKLEHLEIENCINLE 816

Query: 1031 SLPEDALPSNVVDVLIEDCDKLKALIPTG-TLSSLRELALSECPGIVVFPEEGLSTNLTD 1089
            +L                        PTG  L SL  L LS C  +  FP+  +STN++D
Sbjct: 817  TL------------------------PTGINLESLESLDLSGCSRLRTFPD--ISTNISD 850

Query: 1090 LEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPK 1149
            L +S   + +  V W   K ++L  L ++GC++                  S+ IS   K
Sbjct: 851  LNLSRTGIEE--VPWWIEKFSNLSFLDMNGCNNLQR--------------VSLNIS---K 891

Query: 1150 LKRLSSKGFQYLVSLEHLSVFSCP----NFTSFPEAGFPSS 1186
            LK L +  F    +L   S    P      T    +  PS+
Sbjct: 892  LKHLETVDFSDCGALTEASWNGSPSEVAMATDNIHSKLPST 932

syringae 6; Provisional. Length = 1153

>gnl|CDD|237954 PRK15386, PRK15386, type III secretion protein GogB; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 42/143 (29%), Positives = 62/143 (43%), Gaps = 32/143 (22%)

Query: 1021 IRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSS-LRELALSECPGIVVFP 1079
            + I  C  + SLP   LP+ + ++ IE+C+ L  L   G++   L +L +  CP I   P
Sbjct: 57   LYIKDCD-IESLPV--LPNELTEITIENCNNLTTL--PGSIPEGLEKLTVCHCPEISGLP 111

Query: 1080 E---------------EGLSTNLTDLEISGDNMYKPLVKWGFHKLT--SLRKLYIDGCSD 1122
            E               + +   LT L I   N Y P  +     L   SL+ L + GCS+
Sbjct: 112  ESVRSLEIKGSATDSIKNVPNGLTSLSI---NSYNPENQARIDNLISPSLKTLSLTGCSN 168

Query: 1123 AVSFPDVGKGVILPTSLTSITIS 1145
             +  P       LP SL SIT+ 
Sbjct: 169  II-LP-----EKLPESLQSITLH 185

Length = 426

>gnl|CDD|237954 PRK15386, PRK15386, type III secretion protein GogB; Provisional

 Score = 44.1 bits (104), Expect = 4e-04
 Identities = 39/158 (24%), Positives = 69/158 (43%), Gaps = 22/158 (13%)

Query: 948  RLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKS 1007
            RL I+DC     + S   LP E+ E+TI  C+NL ++     +   L  + +  C  +  
Sbjct: 56   RLYIKDCD----IESLPVLPNELTEITIENCNNLTTLPGSIPEG--LEKLTVCHCPEISG 109

Query: 1008 LPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLREL 1067
            LP+ + +L    EI+     ++ ++P      ++     E+  ++  LI      SL+ L
Sbjct: 110  LPESVRSL----EIKGSATDSIKNVPNGLTSLSINSYNPENQARIDNLIS----PSLKTL 161

Query: 1068 ALSECPGIVV---FPEEGLSTNL-----TDLEISGDNM 1097
            +L+ C  I++    PE   S  L     T   IS +  
Sbjct: 162  SLTGCSNIILPEKLPESLQSITLHIEQKTTWNISFEGF 199

Length = 426

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	1237
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	100.0
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	100.0
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.89
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.88
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.87
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.86
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.85
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.84
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.8
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.8
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.7
PRK04841	903	transcriptional regulator MalT; Provisional	99.46
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.4
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.35
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.34
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.3
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.25
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.22
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.22
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.19
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.17
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.11
KOG4341	483	consensus F-box protein containing LRR [General fu	99.09
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.07
KOG4341	483	consensus F-box protein containing LRR [General fu	99.03
PF05729	166	NACHT: NACHT domain	99.01
COG3903	414	Predicted ATPase [General function prediction only	99.0
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.95
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.76
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.68
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.67
PRK06893	229	DNA replication initiation factor; Validated	98.64
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.64
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.62
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.58
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.58
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.57
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.53
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.52
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.5
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.49
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.45
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.44
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.43
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.42
PRK15386	426	type III secretion protein GogB; Provisional	98.42
PF13173	128	AAA_14: AAA domain	98.39
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.38
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.33
PRK09087	226	hypothetical protein; Validated	98.31
PRK08727	233	hypothetical protein; Validated	98.29
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.29
PRK08084	235	DNA replication initiation factor; Provisional	98.23
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.22
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.21
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.21
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.2
COG3899	849	Predicted ATPase [General function prediction only	98.19
PLN03025	319	replication factor C subunit; Provisional	98.18
PRK15386	426	type III secretion protein GogB; Provisional	98.17
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.16
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.15
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.15
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.14
PLN03150	623	hypothetical protein; Provisional	98.14
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.12
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.11
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.11
PRK13342	413	recombination factor protein RarA; Reviewed	98.1
PRK05642	234	DNA replication initiation factor; Validated	98.1
PRK12402	337	replication factor C small subunit 2; Reviewed	98.08
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.07
PRK04195	482	replication factor C large subunit; Provisional	98.07
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.07
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.07
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.05
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	98.02
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.01
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.0
cd01128	249	rho_factor Transcription termination factor rho is	98.0
PLN03150	623	hypothetical protein; Provisional	97.99
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.99
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.96
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.93
PRK09376	416	rho transcription termination factor Rho; Provisio	97.92
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.92
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.91
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.91
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.87
PRK06620	214	hypothetical protein; Validated	97.86
KOG2028	554	consensus ATPase related to the helicase subunit o	97.84
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.84
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.81
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.81
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.8
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.78
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.77
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.76
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.75
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.74
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.73
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.73
PRK13341	725	recombination factor protein RarA/unknown domain f	97.73
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.72
TIGR00767	415	rho transcription termination factor Rho. Members	97.71
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.7
PRK12422	445	chromosomal replication initiation protein; Provis	97.69
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.69
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.67
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.67
PF14516	331	AAA_35: AAA-like domain	97.67
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.67
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.67
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.65
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.65
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.65
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.64
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.64
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.64
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.64
CHL00181	287	cbbX CbbX; Provisional	97.62
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.62
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.6
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.6
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.6
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.57
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.57
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.55
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.54
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.5
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.5
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.49
smart00382	148	AAA ATPases associated with a variety of cellular	97.48
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.47
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.45
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.44
PF00004	132	AAA: ATPase family associated with various cellula	97.43
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.43
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.42
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.41
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.39
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.38
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.37
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.33
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.31
PHA02544	316	44 clamp loader, small subunit; Provisional	97.31
PRK08116	268	hypothetical protein; Validated	97.31
PTZ00202	550	tuzin; Provisional	97.3
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.26
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.15
PRK08181	269	transposase; Validated	97.15
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.14
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.11
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.11
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.08
KOG1947	482	consensus Leucine rich repeat proteins, some prote	97.05
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.04
PRK06526	254	transposase; Provisional	97.02
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.0
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.98
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.95
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.95
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.92
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.91
PRK08118	167	topology modulation protein; Reviewed	96.9
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.9
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.89
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.89
CHL00176	638	ftsH cell division protein; Validated	96.87
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.83
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.81
PRK06921	266	hypothetical protein; Provisional	96.81
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.8
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.8
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.8
PRK10536	262	hypothetical protein; Provisional	96.8
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.8
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.79
KOG1947	482	consensus Leucine rich repeat proteins, some prote	96.78
PRK12377	248	putative replication protein; Provisional	96.77
PRK07261	171	topology modulation protein; Provisional	96.75
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.74
PRK04296	190	thymidine kinase; Provisional	96.73
PRK12608	380	transcription termination factor Rho; Provisional	96.71
PRK04132	846	replication factor C small subunit; Provisional	96.69
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.69
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.69
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.67
PRK09183	259	transposase/IS protein; Provisional	96.65
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.63
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.59
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.58
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.58
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.58
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	96.57
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.55
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.53
CHL00095	821	clpC Clp protease ATP binding subunit	96.53
PRK08939	306	primosomal protein DnaI; Reviewed	96.51
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.49
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.45
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.44
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.43
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.43
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.41
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.39
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.38
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.38
PRK07952	244	DNA replication protein DnaC; Validated	96.37
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.34
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.34
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.34
CHL00195	489	ycf46 Ycf46; Provisional	96.33
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.32
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.31
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.31
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.3
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.3
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.28
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.28
KOG2982	418	consensus Uncharacterized conserved protein [Funct	96.27
PRK06835	329	DNA replication protein DnaC; Validated	96.27
PRK14974	336	cell division protein FtsY; Provisional	96.26
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.26
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.26
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.25
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	96.22
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.18
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.18
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.17
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.16
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.15
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.14
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.13
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.13
PHA00729	226	NTP-binding motif containing protein	96.12
PRK05541	176	adenylylsulfate kinase; Provisional	96.07
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.06
PRK10865	857	protein disaggregation chaperone; Provisional	96.04
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.03
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.03
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.0
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.99
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.99
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.99
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.95
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.93
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.93
PRK06067	234	flagellar accessory protein FlaH; Validated	95.93
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.92
PRK09354	349	recA recombinase A; Provisional	95.89
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.85
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.83
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.81
cd03216	163	ABC_Carb_Monos_I This family represents the domain	95.8
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.77
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.77
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	95.76
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.76
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.75
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.74
KOG2123	388	consensus Uncharacterized conserved protein [Funct	95.71
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.71
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.69
PRK10865	857	protein disaggregation chaperone; Provisional	95.68
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	95.68
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.68
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.66
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.65
COG2884	223	FtsE Predicted ATPase involved in cell division [C	95.65
PRK10867	433	signal recognition particle protein; Provisional	95.63
PRK08233	182	hypothetical protein; Provisional	95.63
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.62
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.6
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	95.56
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.56
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.55
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.5
cd03246	173	ABCC_Protease_Secretion This family represents the	95.49
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.49
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.44
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	95.44
TIGR00959	428	ffh signal recognition particle protein. This mode	95.43
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.42
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	95.41
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	95.39
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	95.39
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.36
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.36
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.34
KOG1514	767	consensus Origin recognition complex, subunit 1, a	95.31
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.28
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.24
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	95.23
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	95.21
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.19
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.18
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.16
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	95.13
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.11
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.09
CHL00095	821	clpC Clp protease ATP binding subunit	95.07
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.07
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.04
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.01
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	94.99
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	94.96
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	94.96
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.95
PTZ00301	210	uridine kinase; Provisional	94.95
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	94.89
PRK00889	175	adenylylsulfate kinase; Provisional	94.86
PRK13695	174	putative NTPase; Provisional	94.86
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	94.85
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.84
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.84
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.84
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	94.82
PHA02244	383	ATPase-like protein	94.82
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	94.81
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	94.81
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.8
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.77
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	94.74
COG4181	228	Predicted ABC-type transport system involved in ly	94.73
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	94.72
PF13245	76	AAA_19: Part of AAA domain	94.69
PRK06217	183	hypothetical protein; Validated	94.68
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	94.68
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	94.67
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	94.66
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.66
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	94.66
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	94.62
TIGR02236	310	recomb_radA DNA repair and recombination protein R	94.62
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	94.59
PRK05973	237	replicative DNA helicase; Provisional	94.59
PRK10416	318	signal recognition particle-docking protein FtsY;	94.58
PLN02924	220	thymidylate kinase	94.57
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.57
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.56
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	94.56
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.55
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	94.55
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	94.54
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.53
PRK06696	223	uridine kinase; Validated	94.51
COG4619	223	ABC-type uncharacterized transport system, ATPase	94.51
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	94.5
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	94.5
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	94.49
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	94.49
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	94.47
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	94.47
PRK05439	311	pantothenate kinase; Provisional	94.46
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.42
PRK07667	193	uridine kinase; Provisional	94.4
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	94.37
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	94.36
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	94.34
PRK06762	166	hypothetical protein; Provisional	94.34
PRK06547	172	hypothetical protein; Provisional	94.34
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.33
PRK05480	209	uridine/cytidine kinase; Provisional	94.32
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.32
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	94.31
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	94.29
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	94.28
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	94.28
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	94.28
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	94.26
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	94.26
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	94.25
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.24
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	94.18
PRK15453	290	phosphoribulokinase; Provisional	94.18
PRK03846	198	adenylylsulfate kinase; Provisional	94.18
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.17
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	94.15
CHL00206	2281	ycf2 Ycf2; Provisional	94.14
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.13
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.13
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.13
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	94.13
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.11
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	94.08
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	94.08
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	94.08
TIGR00235	207	udk uridine kinase. Model contains a number of lon	94.07
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	94.05
PRK07132	299	DNA polymerase III subunit delta'; Validated	94.05
PTZ00035	337	Rad51 protein; Provisional	94.05
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	94.03
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	94.03
PRK14527	191	adenylate kinase; Provisional	94.02
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	94.0
PRK04328	249	hypothetical protein; Provisional	93.99
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	93.97
PRK13948	182	shikimate kinase; Provisional	93.97
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	93.96
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	93.96
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	93.95
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	93.95
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	93.93
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.92
PTZ00088	229	adenylate kinase 1; Provisional	93.91
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	93.89
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	93.89
cd03269	210	ABC_putative_ATPase This subfamily is involved in	93.87
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.83
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.83
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	93.83
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	93.81
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	93.79
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	93.76
COG4133	209	CcmA ABC-type transport system involved in cytochr	93.76
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	93.76
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	93.74
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	93.73
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	93.73
PRK04040	188	adenylate kinase; Provisional	93.73
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.71
PRK03839	180	putative kinase; Provisional	93.7
KOG0473	326	consensus Leucine-rich repeat protein [Function un	93.7
cd03215	182	ABC_Carb_Monos_II This family represents domain II	93.7
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	93.67
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	93.66
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	93.66
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	93.64
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	93.6
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	93.58
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	93.56
COG5635	824	Predicted NTPase (NACHT family) [Signal transducti	93.55
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	93.54
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	93.53
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	93.51
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	93.5
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	93.49
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	93.47
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	93.46
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	93.45
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	93.43
PRK00625	173	shikimate kinase; Provisional	93.42
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	93.4
PRK10875	615	recD exonuclease V subunit alpha; Provisional	93.39
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	93.36
COG0488	530	Uup ATPase components of ABC transporters with dup	93.35
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.34
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	93.34
PRK00409	782	recombination and DNA strand exchange inhibitor pr	93.33
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	93.3
KOG0473	326	consensus Leucine-rich repeat protein [Function un	93.28
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	93.27
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.26
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	93.25
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	93.24
PF07726	131	AAA_3: ATPase family associated with various cellu	93.23
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	93.19
COG4240	300	Predicted kinase [General function prediction only	93.19
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	93.18
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	93.17
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	93.15
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	93.14
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	93.12
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	93.12
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	93.11
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	93.11
PRK00131	175	aroK shikimate kinase; Reviewed	93.1
KOG0736	953	consensus Peroxisome assembly factor 2 containing	93.1
KOG0927	614	consensus Predicted transporter (ABC superfamily)	93.08
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	93.07
PRK00279	215	adk adenylate kinase; Reviewed	93.07
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.07
PRK13531	498	regulatory ATPase RavA; Provisional	93.06
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	93.04
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	93.03
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	93.01
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	92.99
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	92.98
CHL00060	494	atpB ATP synthase CF1 beta subunit	92.97
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	92.95
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.95
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	92.94
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	92.93
PRK11823	446	DNA repair protein RadA; Provisional	92.93
COG0488	530	Uup ATPase components of ABC transporters with dup	92.92
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	92.84
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	92.83
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	92.81
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	92.8
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	92.8
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	92.79
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	92.79
PRK12339	197	2-phosphoglycerate kinase; Provisional	92.75
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	92.74

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=1.7e-65  Score=616.76  Aligned_cols=584  Identities=31%  Similarity=0.494  Sum_probs=456.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc--cccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC--ccCHHHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK--LTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK--LEDLNSVQLELKETVF   89 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~--~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~   89 (1237)
                      .+|+|+||||+||||||++++++.  ++.+||.++|+.++..++...++.+|+..++.....  ....++.+..+.+.|+
T Consensus       180 ~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~  259 (889)
T KOG4658|consen  180 GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLE  259 (889)
T ss_pred             CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhc
Confidence            899999999999999999999976  689999999999999999999999999999875443  2334788889999999


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHh-hcCCCeEeCCCCChhhhHHHHHHHhcCCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALT-MGSGKNYELKLLSDDDCWSVFVAHAFEGRDAG  168 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~-~~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~  168 (1237)
                      .+|++||+||||+.  .+|+.+..+++....|+||++|||+..++.. +++...++++.|+++|||+||.+.++..... 
T Consensus       260 ~krfllvLDDIW~~--~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~-  336 (889)
T KOG4658|consen  260 GKRFLLVLDDIWEE--VDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLG-  336 (889)
T ss_pred             cCceEEEEeccccc--ccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhcccccc-
Confidence            99999999999998  5699999999999899999999999999988 7777899999999999999999999765332 


Q ss_pred             CCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCHHHHHHHHhhcccccCC-----CCChhHHHHHHhhcChHHHHHHH
Q 000887          169 THGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQD-----KTEIPSVLKLSYHHLPSHLKRCF  243 (1237)
Q Consensus       169 ~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~~~~~~~l~~~~~~~~~-----~~~i~~~l~~s~~~L~~~~~~~~  243 (1237)
                      ..+.++++|++++++|+|+|||++++|+.|+.++...+|+++.+...+...+     ...+..++.+||+.|+++.|.||
T Consensus       337 ~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CF  416 (889)
T KOG4658|consen  337 SHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCF  416 (889)
T ss_pred             ccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHH
Confidence            2344899999999999999999999999999999999999999875444222     46788999999999998899999


Q ss_pred             hhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccccC--CCCCcchhhhHHHHHHhhhcc
Q 000887          244 AYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSS--NTESKYVMHDLVHDLAQWASG  321 (1237)
Q Consensus       244 ~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~~~--~~~~~~~~h~lv~~~~~~~~~  321 (1237)
                      +|||+||+|+.|+.+.++.+|+||||+.+..+...+++.+++++.+|++++|++..+  ....++.|||+||++|.|+++
T Consensus       417 LycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~~~~~~~kmHDvvRe~al~ias  496 (889)
T KOG4658|consen  417 LYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDEGRKETVKMHDVVREMALWIAS  496 (889)
T ss_pred             HhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccccceeEEEeeHHHHHHHHHHhc
Confidence            999999999999999999999999999998788899999999999999999999765  356789999999999999999


Q ss_pred             -----ceEEEecCc--cccccccCcccceeEEEEeeccCCCCCcccccccccccccccccccccccccCCCCCCcchhhh
Q 000887          322 -----ETCFRLDDQ--FSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSD  394 (1237)
Q Consensus       322 -----~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lr~l~~~~~~~~~~~~~~~~~~~~~~  394 (1237)
                           ++...+...  ....+....+..+|+++++.+..+.    ...-.+.+++++|.......       -...+...
T Consensus       497 ~~~~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~~~----~~~~~~~~~L~tLll~~n~~-------~l~~is~~  565 (889)
T KOG4658|consen  497 DFGKQEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKIEH----IAGSSENPKLRTLLLQRNSD-------WLLEISGE  565 (889)
T ss_pred             cccccccceEEECCcCccccccccchhheeEEEEeccchhh----ccCCCCCCccceEEEeecch-------hhhhcCHH
Confidence                 454444432  2223344556788999999876322    22223455799998775431       13466778


Q ss_pred             hcCCCCCccEEEccccc-cccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhccccccc
Q 000887          395 LLPQCKKLRVLSLGSYC-ITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLH  473 (1237)
Q Consensus       395 ~~~~~~~Lr~L~L~~~~-i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~  473 (1237)
                      +|..++.||||||++|. +.++|+++++|-+||||+|+++.|..+|..+++|++|.+||+..+.....+|..+..|.+||
T Consensus       566 ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr  645 (889)
T KOG4658|consen  566 FFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLR  645 (889)
T ss_pred             HHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccchhhhccccc
Confidence            89999999999999876 78999999999999999999999999999999999999999999977777777667799999


Q ss_pred             EEeccCCCccccCcccccccccccccceeeeccCCCcCcccccchHhcccceeecCccCCCChHHHHHHhhcCCCCCCee
Q 000887          474 YLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDL  553 (1237)
Q Consensus       474 ~L~l~~~~~l~~ip~~~~~L~~L~~L~~~~~~~~~~~~i~~l~~l~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L  553 (1237)
                      +|.+.... ...-...++.+.+|++|..+.....+...+..+..+..|+..                         .+.+
T Consensus       646 ~L~l~~s~-~~~~~~~l~el~~Le~L~~ls~~~~s~~~~e~l~~~~~L~~~-------------------------~~~l  699 (889)
T KOG4658|consen  646 VLRLPRSA-LSNDKLLLKELENLEHLENLSITISSVLLLEDLLGMTRLRSL-------------------------LQSL  699 (889)
T ss_pred             EEEeeccc-cccchhhHHhhhcccchhhheeecchhHhHhhhhhhHHHHHH-------------------------hHhh
Confidence            99998763 111122355556666665444332222112222222222210                         0000


Q ss_pred             EeeeCCCCCCCCcchHHHHhhhhcCCCCCCccEEEEeecCCCCCCC-CCCC---CC-CCCccEEEEccCCCCCcCCCCCC
Q 000887          554 KLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPS-WVGD---PS-FSNVAVLILKNCRRSTSLPSLGQ  628 (1237)
Q Consensus       554 ~l~~~~~~~~~~~~~~~~~~~l~~l~~~~~L~~L~l~~~~~~~~~~-~~~~---~~-~~~L~~L~L~~~~~~~~l~~l~~  628 (1237)
                      .+.+           .........+..+.+|+.|.+.++.+.+... |...   .. |+++.++.+.+|.....+.+..-
T Consensus       700 ~~~~-----------~~~~~~~~~~~~l~~L~~L~i~~~~~~e~~~~~~~~~~~~~~f~~l~~~~~~~~~~~r~l~~~~f  768 (889)
T KOG4658|consen  700 SIEG-----------CSKRTLISSLGSLGNLEELSILDCGISEIVIEWEESLIVLLCFPNLSKVSILNCHMLRDLTWLLF  768 (889)
T ss_pred             hhcc-----------cccceeecccccccCcceEEEEcCCCchhhcccccccchhhhHHHHHHHHhhccccccccchhhc
Confidence            0000           0011122335567788888887776654321 2111   12 56777778888877777777777


Q ss_pred             ccccceeEecCCCCceeecc
Q 000887          629 LCSLKDLTIVGMSELKSIGS  648 (1237)
Q Consensus       629 l~~L~~L~l~~~~~l~~i~~  648 (1237)
                      .|+|+.|++..|..++.+.+
T Consensus       769 ~~~L~~l~l~~~~~~e~~i~  788 (889)
T KOG4658|consen  769 APHLTSLSLVSCRLLEDIIP  788 (889)
T ss_pred             cCcccEEEEecccccccCCC
Confidence            89999999999888777643

>PLN03210 Resistant to P

Probab=100.00  E-value=2.8e-57  Score=582.16  Aligned_cols=453  Identities=23%  Similarity=0.292  Sum_probs=292.8

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEE---cCC-----------cC-HHHHHHHHHHHhhccCC-C
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV---SDD-----------FD-VLRISKAILDSIKRSSC-K   73 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~---~~~-----------~~-~~~~~~~i~~~l~~~~~-~   73 (1237)
                      ++++++|+|+||||+||||||+++|+ .....|++.+|+..   ...           .. ...++.+++.++..... .
T Consensus       204 ~~~~~vvgI~G~gGiGKTTLA~~l~~-~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~  282 (1153)
T PLN03210        204 SEEVRMVGIWGSSGIGKTTIARALFS-RLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIK  282 (1153)
T ss_pred             cCceEEEEEEcCCCCchHHHHHHHHH-HHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcc
Confidence            45789999999999999999999988 46678888887742   110           00 12344455554433221 1


Q ss_pred             ccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCeEeCCCCChhhh
Q 000887           74 LEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDC  153 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l~~l~~~ea  153 (1237)
                      ...    ...+++.++++|+|||+||||+.  .+++.+.....+.++|++||||||++.++...+..++++++.++++||
T Consensus       283 ~~~----~~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~~~~GsrIIiTTrd~~vl~~~~~~~~~~v~~l~~~ea  356 (1153)
T PLN03210        283 IYH----LGAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQWFGSGSRIIVITKDKHFLRAHGIDHIYEVCLPSNELA  356 (1153)
T ss_pred             cCC----HHHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCccCCCCcEEEEEeCcHHHHHhcCCCeEEEecCCCHHHH
Confidence            111    13567778899999999999764  677777766666789999999999999987766778999999999999


Q ss_pred             HHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCHHHHHHHHhhcccccCCCCChhHHHHHHhh
Q 000887          154 WSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYH  233 (1237)
Q Consensus       154 ~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~  233 (1237)
                      ++||.+.||+...  ++++..+++++|+++|+|+||||+++|++|+++ +..+|++++++.....  +..+.++|++||+
T Consensus       357 ~~LF~~~Af~~~~--~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k-~~~~W~~~l~~L~~~~--~~~I~~~L~~SYd  431 (1153)
T PLN03210        357 LEMFCRSAFKKNS--PPDGFMELASEVALRAGNLPLGLNVLGSYLRGR-DKEDWMDMLPRLRNGL--DGKIEKTLRVSYD  431 (1153)
T ss_pred             HHHHHHHhcCCCC--CcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCC-CHHHHHHHHHHHHhCc--cHHHHHHHHHhhh
Confidence            9999999986532  345678899999999999999999999999986 5789999998865433  3579999999999


Q ss_pred             cChH-HHHHHHhhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccccCCCCCcchhhhHH
Q 000887          234 HLPS-HLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSSNTESKYVMHDLV  312 (1237)
Q Consensus       234 ~L~~-~~~~~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~~~~~~~~~~~h~lv  312 (1237)
                      .|++ .+|.+|+++|+|+.+..++   .+..|.+.+....           ...++.|++++|++..   .++|.|||++
T Consensus       432 ~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~~-----------~~~l~~L~~ksLi~~~---~~~~~MHdLl  494 (1153)
T PLN03210        432 GLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLDV-----------NIGLKNLVDKSLIHVR---EDIVEMHSLL  494 (1153)
T ss_pred             ccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCCc-----------hhChHHHHhcCCEEEc---CCeEEhhhHH
Confidence            9986 5999999999999887653   3556666543321           2238899999999864   3579999999


Q ss_pred             HHHHhhhccceEE-------EecCc--cccccccCcccceeEEEEeeccCCCCCcccccccccccccccccccccccccC
Q 000887          313 HDLAQWASGETCF-------RLDDQ--FSVDRQSNVFEKVRHFSYLRSYDCDGMDKFKVLDKVVNLRTFLPIFFKQWRIY  383 (1237)
Q Consensus       313 ~~~~~~~~~~~~~-------~~~~~--~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lr~l~~~~~~~~~~~  383 (1237)
                      |++++++++++.-       .+...  ......+.....++++++.............++.+|.+|+.+....... . .
T Consensus       495 ~~~~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~~L~~L~~~~~~~-~-~  572 (1153)
T PLN03210        495 QEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFLKFYTKKW-D-Q  572 (1153)
T ss_pred             HHHHHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCccccEEEEecccc-c-c
Confidence            9999999876531       11100  0011123344556666554322111111223344555555554321110 0 0


Q ss_pred             CCCCCcchhhhhcCCC-CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccC
Q 000887          384 PPNISPMVLSDLLPQC-KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKL  462 (1237)
Q Consensus       384 ~~~~~~~~~~~~~~~~-~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~l  462 (1237)
                      ..+....++.. |..+ .+||.|.+.++.+..+|..| .+.+|+.|++++|.+..+|..+..+++|++|+|++|..+..+
T Consensus       573 ~~~~~~~lp~~-~~~lp~~Lr~L~~~~~~l~~lP~~f-~~~~L~~L~L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~i  650 (1153)
T PLN03210        573 KKEVRWHLPEG-FDYLPPKLRLLRWDKYPLRCMPSNF-RPENLVKLQMQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEI  650 (1153)
T ss_pred             cccceeecCcc-hhhcCcccEEEEecCCCCCCCCCcC-CccCCcEEECcCccccccccccccCCCCCEEECCCCCCcCcC
Confidence            00001111222 2222 34555555555555555544 345555555555555555555555555555555555445555


Q ss_pred             ChhhcccccccEEeccCCCccccCcccccccccc
Q 000887          463 PSRIGNLVNLHYLNIEGASALRELPLGMKELKCL  496 (1237)
Q Consensus       463 p~~i~~L~~L~~L~l~~~~~l~~ip~~~~~L~~L  496 (1237)
                      |. ++.+++|++|++++|..+..+|..++++++|
T Consensus       651 p~-ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L  683 (1153)
T PLN03210        651 PD-LSMATNLETLKLSDCSSLVELPSSIQYLNKL  683 (1153)
T ss_pred             Cc-cccCCcccEEEecCCCCccccchhhhccCCC
Confidence            53 5555555555555554444444444333333

syringae 6; Provisional

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

Probab=100.00  E-value=4.5e-37  Score=339.41  Aligned_cols=260  Identities=36%  Similarity=0.638  Sum_probs=208.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC---CccCHHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC---KLEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~   86 (1237)
                      ++.++|+|+||||+|||+||.+++++. .+..|+.++|+.++...+..+++..++.+++....   ...+.++....+.+
T Consensus        17 ~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~   96 (287)
T PF00931_consen   17 NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRE   96 (287)
T ss_dssp             TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHH
T ss_pred             CCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchh
Confidence            778999999999999999999999865 78899999999999998889999999999987743   45678889999999


Q ss_pred             HhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcC-CCeEeCCCCChhhhHHHHHHHhcCCC
Q 000887           87 TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGS-GKNYELKLLSDDDCWSVFVAHAFEGR  165 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~l~~~~~~~~~  165 (1237)
                      .++++++||||||||+.  ..|+.+...++....|++||||||+..++..+.. ...+++++|+++||++||.+.++...
T Consensus        97 ~L~~~~~LlVlDdv~~~--~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~  174 (287)
T PF00931_consen   97 LLKDKRCLLVLDDVWDE--EDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKE  174 (287)
T ss_dssp             HHCCTSEEEEEEEE-SH--HHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS
T ss_pred             hhccccceeeeeeeccc--ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999999999765  5777777777777789999999999988766554 57899999999999999999987554


Q ss_pred             CCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCHHHHHHHHhhcccccC----CCCChhHHHHHHhhcChHHHHH
Q 000887          166 DAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQ----DKTEIPSVLKLSYHHLPSHLKR  241 (1237)
Q Consensus       166 ~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~~~~~~~l~~~~~~~~----~~~~i~~~l~~s~~~L~~~~~~  241 (1237)
                       ....+..++.+++|+++|+|+||||+++|++++.+....+|.++++.......    ....+..++.+||+.|+++.|+
T Consensus       175 -~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~  253 (287)
T PF00931_consen  175 -SESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFSALELSYDSLPDELRR  253 (287)
T ss_dssp             -----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHHHHHHHHHSSHTCCHH
T ss_pred             -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccceechhcCCccHHH
Confidence             22334456789999999999999999999999765567889988876444432    2467999999999999999999


Q ss_pred             HHhhhccCCCCcccChHHHHHHHHHcCCCccC
Q 000887          242 CFAYCAVLPKDYEFKEKELVLLWIAEGLVQQS  273 (1237)
Q Consensus       242 ~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~  273 (1237)
                      ||.+||+||+++.|+.+.++++|+++|++...
T Consensus       254 ~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~~  285 (287)
T PF00931_consen  254 CFLYLSIFPEGVPIPRERLIRLWVAEGFISSK  285 (287)
T ss_dssp             HHHHGGGSGTTS-EEHHHHHHHHTT-HHTC--
T ss_pred             HHhhCcCCCCCceECHHHHHHHHHHCCCCccc
Confidence            99999999999999999999999999998753

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

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

Probab=100.00  E-value=1.2e-33  Score=367.02  Aligned_cols=229  Identities=14%  Similarity=0.087  Sum_probs=159.9

Q ss_pred             ccceeeeeeecCCCccccCcCCCCCCcccEEEEcCCCCccccccccCCcccccEEeeccccccccccccccCCCCCceee
Q 000887          943 PVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIR 1022 (1237)
Q Consensus       943 ~~~L~~L~l~~c~~l~~l~~~~~~~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~ 1022 (1237)
                      +++|+.|++.+|.....++.....+++|+.|++++|.....+|..+..+++|+.|++++|.....+|..+..+++|++|+
T Consensus       379 ~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~  458 (968)
T PLN00113        379 SGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDNSFSGELPSEFTKLPLVYFLDISNNNLQGRINSRKWDMPSLQMLS  458 (968)
T ss_pred             cCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCCEeeeECChhHhcCCCCCEEECcCCcccCccChhhccCCCCcEEE
Confidence            34555556655555455555555667777888877777667777777888888888888766666666667778888888


Q ss_pred             eccCCCcccCCCCCCCCcchhhhhhccccccccCCCCCCCcccEEeccCCCCccccCCC-CCCCCcCceEecCCCCcccc
Q 000887         1023 IVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEE-GLSTNLTDLEISGDNMYKPL 1101 (1237)
Q Consensus      1023 l~~c~~l~~l~~~~~~~~l~~l~l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~-~~~~~L~~L~l~~~~~~~~~ 1101 (1237)
                      +++|.....+|...                       ..++|+.|++++|.....+|.. ..+++|+.|++++|.....+
T Consensus       459 L~~n~~~~~~p~~~-----------------------~~~~L~~L~ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~  515 (968)
T PLN00113        459 LARNKFFGGLPDSF-----------------------GSKRLENLDLSRNQFSGAVPRKLGSLSELMQLKLSENKLSGEI  515 (968)
T ss_pred             CcCceeeeecCccc-----------------------ccccceEEECcCCccCCccChhhhhhhccCEEECcCCcceeeC
Confidence            88876555555432                       3457777777777544444443 34677888888887776666


Q ss_pred             cccccCCCCCCceEEEcCCCCceeccCCCCccccCCCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCCCcccCCCC
Q 000887         1102 VKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEA 1181 (1237)
Q Consensus      1102 ~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~ 1181 (1237)
                      |. .+..+++|+.|+|++|.....+|.   .+..+++|++|++++|.....+| ..+.++++|++|++++|+....+|..
T Consensus       516 p~-~~~~l~~L~~L~Ls~N~l~~~~p~---~~~~l~~L~~L~Ls~N~l~~~~p-~~l~~l~~L~~l~ls~N~l~~~~p~~  590 (968)
T PLN00113        516 PD-ELSSCKKLVSLDLSHNQLSGQIPA---SFSEMPVLSQLDLSQNQLSGEIP-KNLGNVESLVQVNISHNHLHGSLPST  590 (968)
T ss_pred             Ch-HHcCccCCCEEECCCCcccccCCh---hHhCcccCCEEECCCCcccccCC-hhHhcCcccCEEeccCCcceeeCCCc
Confidence            65 477788888888888765545554   23456788888888865544666 56788889999999998777788877


Q ss_pred             CCCCcccEeeecCCCCcc
Q 000887         1182 GFPSSLLSLEIQRCPLLE 1199 (1237)
Q Consensus      1182 ~~~~sL~~L~i~~cp~l~ 1199 (1237)
                      +.+.++....+.++|.+|
T Consensus       591 ~~~~~~~~~~~~~n~~lc  608 (968)
T PLN00113        591 GAFLAINASAVAGNIDLC  608 (968)
T ss_pred             chhcccChhhhcCCcccc
Confidence            666666667777888775

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

Probab=100.00  E-value=9.6e-32  Score=349.17  Aligned_cols=107  Identities=27%  Similarity=0.415  Sum_probs=72.7

Q ss_pred             hhhcCCCCCccEEEccccccc-cccccc-cCCCCCCeEEccCCCcc-ccchhhcccCCccEEEcCccccCccCChhhccc
Q 000887          393 SDLLPQCKKLRVLSLGSYCIT-EVPISI-GCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILILRNCWCLLKLPSRIGNL  469 (1237)
Q Consensus       393 ~~~~~~~~~Lr~L~L~~~~i~-~lp~~~-~~l~~Lr~L~L~~~~i~-~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L  469 (1237)
                      +..|..+++|++|+|++|.+. .+|..+ ..+++||+|+|++|.+. .+|.  +.+++|++|+|++|.....+|..++++
T Consensus        86 ~~~~~~l~~L~~L~Ls~n~~~~~ip~~~~~~l~~L~~L~Ls~n~l~~~~p~--~~l~~L~~L~Ls~n~~~~~~p~~~~~l  163 (968)
T PLN00113         86 SSAIFRLPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLSNNNFTGSIPR--GSIPNLETLDLSNNMLSGEIPNDIGSF  163 (968)
T ss_pred             ChHHhCCCCCCEEECCCCccCCcCChHHhccCCCCCEEECcCCccccccCc--cccCCCCEEECcCCcccccCChHHhcC
Confidence            445667777777777777775 566554 37777777777777765 3343  457777777777774445677777777


Q ss_pred             ccccEEeccCCCccccCcccccccccccccce
Q 000887          470 VNLHYLNIEGASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       470 ~~L~~L~l~~~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      ++|++|++++|.....+|..++++++|++|++
T Consensus       164 ~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L  195 (968)
T PLN00113        164 SSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTL  195 (968)
T ss_pred             CCCCEEECccCcccccCChhhhhCcCCCeeec
Confidence            77777777777444566766777777777755

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

Probab=99.89  E-value=3.9e-24  Score=229.06  Aligned_cols=384  Identities=17%  Similarity=0.205  Sum_probs=287.5

Q ss_pred             cceeEEEEecCCCccccccccccccccCCCCccceeEecCCCCceecCCCCC-CCCccEEEecCCcchhhhhhhccccCC
Q 000887          777 QKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF-LPNLSEITIQDCNALASLTDGMIYNNA  855 (1237)
Q Consensus       777 ~~L~~L~l~~c~~l~~~~~~~~~~~~~~~l~~L~~L~l~~~~~l~~~~~~~~-~~~L~~L~l~~c~~l~~~~~~~~~~~~  855 (1237)
                      +..+.|++++..- .     ..-+..+..+|+|+++++.+ +.++.+|..+. ..+|+.|.+.+|. +.++.......++
T Consensus        78 ~~t~~LdlsnNkl-~-----~id~~~f~nl~nLq~v~l~~-N~Lt~IP~f~~~sghl~~L~L~~N~-I~sv~se~L~~l~  149 (873)
T KOG4194|consen   78 SQTQTLDLSNNKL-S-----HIDFEFFYNLPNLQEVNLNK-NELTRIPRFGHESGHLEKLDLRHNL-ISSVTSEELSALP  149 (873)
T ss_pred             cceeeeecccccc-c-----cCcHHHHhcCCcceeeeecc-chhhhcccccccccceeEEeeeccc-cccccHHHHHhHh
Confidence            4677788887542 1     22355778899999999988 55999998777 4559999999964 7777766677789


Q ss_pred             ccceeeccCCCCcccccccCCC--CCccEEEEecCCCccccccccccccCCCCccccccCCCCCcccceeEEEEecCCCc
Q 000887          856 RLEVLRIKRCDSLTSISREHLP--SSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSL  933 (1237)
Q Consensus       856 ~L~~L~l~~c~~l~~~~~~~~~--~~L~~L~l~~c~~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l  933 (1237)
                      .|++|+++. +.+..++...+|  .++++|+++++.--+                  .....+..+.+|..|.++.. .+
T Consensus       150 alrslDLSr-N~is~i~~~sfp~~~ni~~L~La~N~It~------------------l~~~~F~~lnsL~tlkLsrN-ri  209 (873)
T KOG4194|consen  150 ALRSLDLSR-NLISEIPKPSFPAKVNIKKLNLASNRITT------------------LETGHFDSLNSLLTLKLSRN-RI  209 (873)
T ss_pred             hhhhhhhhh-chhhcccCCCCCCCCCceEEeeccccccc------------------cccccccccchheeeecccC-cc
Confidence            999999987 467777777777  579999998763221                  11234455667888888874 34


Q ss_pred             ccccCC-CCCccceeeeeeecCCCccccCcCCCCCCcccEEEEcCCCCccccccccCCcccccEEeecccccccccc-cc
Q 000887          934 TCLWSG-GRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLP-KG 1011 (1237)
Q Consensus       934 ~~~~~~-~~~~~~L~~L~l~~c~~l~~l~~~~~~~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~-~~ 1011 (1237)
                      +.+|.. +..+++|+.|++..+..-..-...+.++++|+.|.+..|...+--...|+.+.++++|+|..+ .+.... .+
T Consensus       210 ttLp~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~N-~l~~vn~g~  288 (873)
T KOG4194|consen  210 TTLPQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLETN-RLQAVNEGW  288 (873)
T ss_pred             cccCHHHhhhcchhhhhhccccceeeehhhhhcCchhhhhhhhhhcCcccccCcceeeecccceeecccc-hhhhhhccc
Confidence            444443 455778888888775432222445667788888888887666666677888888888888884 444443 36


Q ss_pred             ccCCCCCceeeeccCCCcccCCCCCCCCcchhhhhhccccccccCCCCCCCcccEEeccCCCCccccCCCCC--CCCcCc
Q 000887         1012 LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGL--STNLTD 1089 (1237)
Q Consensus      1012 l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~--~~~L~~ 1089 (1237)
                      +.++++|+.|++++ +.+..+....-                     ..+++|++|+++.+ .++.++++.+  +..|++
T Consensus       289 lfgLt~L~~L~lS~-NaI~rih~d~W---------------------sftqkL~~LdLs~N-~i~~l~~~sf~~L~~Le~  345 (873)
T KOG4194|consen  289 LFGLTSLEQLDLSY-NAIQRIHIDSW---------------------SFTQKLKELDLSSN-RITRLDEGSFRVLSQLEE  345 (873)
T ss_pred             ccccchhhhhccch-hhhheeecchh---------------------hhcccceeEecccc-ccccCChhHHHHHHHhhh
Confidence            77888888888887 45555533211                     36889999999998 5788888744  889999


Q ss_pred             eEecCCCCcccccccccCCCCCCceEEEcCCCCceeccCCCCccccCCCcCeeeecCCCCccccCcccCCCCCCCCeeee
Q 000887         1090 LEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSV 1169 (1237)
Q Consensus      1090 L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l 1169 (1237)
                      |.++.|. ++.+....|..+.+|++|+++.|.---.+.+...+|..+++|+.|++.+ |+++.|++..|.++++|+.|++
T Consensus       346 LnLs~Ns-i~~l~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~g-Nqlk~I~krAfsgl~~LE~LdL  423 (873)
T KOG4194|consen  346 LNLSHNS-IDHLAEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTG-NQLKSIPKRAFSGLEALEHLDL  423 (873)
T ss_pred             hcccccc-hHHHHhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecC-ceeeecchhhhccCcccceecC
Confidence            9999965 4555555788999999999999754444555556777889999999999 8999999999999999999999


Q ss_pred             cCCCCcccCCCCCC-CCcccEeeecCCCCcccccccCCccccccccC
Q 000887         1170 FSCPNFTSFPEAGF-PSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHI 1215 (1237)
Q Consensus      1170 ~~c~~l~~l~~~~~-~~sL~~L~i~~cp~l~~c~~~~~~~~~~~~~i 1215 (1237)
                      .+ +-+.++-...| +..|++|.+..-..+|.|+..|...|.+=..+
T Consensus       424 ~~-NaiaSIq~nAFe~m~Lk~Lv~nSssflCDCql~Wl~qWl~~~~l  469 (873)
T KOG4194|consen  424 GD-NAIASIQPNAFEPMELKELVMNSSSFLCDCQLKWLAQWLYRRKL  469 (873)
T ss_pred             CC-CcceeecccccccchhhhhhhcccceEEeccHHHHHHHHHhccc
Confidence            88 46777665555 56999999999999999999999999765333

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

Probab=99.88  E-value=1.2e-25  Score=230.02  Aligned_cols=174  Identities=20%  Similarity=0.286  Sum_probs=91.3

Q ss_pred             cccEEEEcCCCCccccccccCCccc---ccEEeeccccccccccccccCCCCCceeeeccCCCcccCCCCCCCCcchhhh
Q 000887          969 EVEELTIYGCSNLESIAERFHDDAC---LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVL 1045 (1237)
Q Consensus       969 ~L~~L~l~~c~~~~~~~~~~~~l~~---L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~ 1045 (1237)
                      +.+.|++++ ..+..+|...+...+   ....+++. +.+.++|..+..+..+.+.-+...+.+..+|...         
T Consensus       363 ~tkiL~~s~-~qlt~VPdEVfea~~~~~Vt~Vnfsk-NqL~elPk~L~~lkelvT~l~lsnn~isfv~~~l---------  431 (565)
T KOG0472|consen  363 TTKILDVSD-KQLTLVPDEVFEAAKSEIVTSVNFSK-NQLCELPKRLVELKELVTDLVLSNNKISFVPLEL---------  431 (565)
T ss_pred             hhhhhcccc-cccccCCHHHHHHhhhcceEEEeccc-chHhhhhhhhHHHHHHHHHHHhhcCccccchHHH---------
Confidence            344444444 334444443333322   45556665 4555566555554444444443433333332211         


Q ss_pred             hhccccccccCCCCCCCcccEEeccCCCCccccCCCCCCCCcCceEecCCCCcccccccccCCCCCCceEEEcCCCCcee
Q 000887         1046 IEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVS 1125 (1237)
Q Consensus      1046 l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~ 1125 (1237)
                                   ..+++|..|+++++. +..+|.                        .++.+..|+.|+|+.+ .+..
T Consensus       432 -------------~~l~kLt~L~L~NN~-Ln~LP~------------------------e~~~lv~Lq~LnlS~N-rFr~  472 (565)
T KOG0472|consen  432 -------------SQLQKLTFLDLSNNL-LNDLPE------------------------EMGSLVRLQTLNLSFN-RFRM  472 (565)
T ss_pred             -------------Hhhhcceeeecccch-hhhcch------------------------hhhhhhhhheeccccc-cccc
Confidence                         245555555555553 444444                        3455556666666664 4444


Q ss_pred             ccCCCCccccCCCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCCCcccCCCC-CCCCcccEeeecCCCC
Q 000887         1126 FPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEA-GFPSSLLSLEIQRCPL 1197 (1237)
Q Consensus      1126 l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~-~~~~sL~~L~i~~cp~ 1197 (1237)
                      +|+...   .+..|+.+-.++ +.++.+++.+++++.+|.+||+.+ +.++.+|.+ +..++|+.|+++|+|+
T Consensus       473 lP~~~y---~lq~lEtllas~-nqi~~vd~~~l~nm~nL~tLDL~n-Ndlq~IPp~LgnmtnL~hLeL~gNpf  540 (565)
T KOG0472|consen  473 LPECLY---ELQTLETLLASN-NQIGSVDPSGLKNMRNLTTLDLQN-NDLQQIPPILGNMTNLRHLELDGNPF  540 (565)
T ss_pred             chHHHh---hHHHHHHHHhcc-ccccccChHHhhhhhhcceeccCC-CchhhCChhhccccceeEEEecCCcc
Confidence            554321   112333333333 566677766677777777777766 567777665 5577777777777775

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

Probab=99.87  E-value=3.1e-24  Score=243.11  Aligned_cols=110  Identities=32%  Similarity=0.460  Sum_probs=93.0

Q ss_pred             chhhhhcCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhccc
Q 000887          390 MVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNL  469 (1237)
Q Consensus       390 ~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L  469 (1237)
                      ..|-++..+.-+|++|++++|.+..+|..+..+.+|+.|+++.|.|..+|.+++++.+|++|.|.+| .+..+|.++..+
T Consensus        35 ~~pl~~~~~~v~L~~l~lsnn~~~~fp~~it~l~~L~~ln~s~n~i~~vp~s~~~~~~l~~lnL~~n-~l~~lP~~~~~l  113 (1081)
T KOG0618|consen   35 SRPLEFVEKRVKLKSLDLSNNQISSFPIQITLLSHLRQLNLSRNYIRSVPSSCSNMRNLQYLNLKNN-RLQSLPASISEL  113 (1081)
T ss_pred             cCchHHhhheeeeEEeeccccccccCCchhhhHHHHhhcccchhhHhhCchhhhhhhcchhheeccc-hhhcCchhHHhh
Confidence            3344455555569999999999999999999999999999999999999999999999999999998 889999999999


Q ss_pred             ccccEEeccCCCccccCcccccccccccccce
Q 000887          470 VNLHYLNIEGASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       470 ~~L~~L~l~~~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      ++|++|+++.| ....+|..+..++.+..+..
T Consensus       114 knl~~LdlS~N-~f~~~Pl~i~~lt~~~~~~~  144 (1081)
T KOG0618|consen  114 KNLQYLDLSFN-HFGPIPLVIEVLTAEEELAA  144 (1081)
T ss_pred             hcccccccchh-ccCCCchhHHhhhHHHHHhh
Confidence            99999999998 67888887777777666643

>PLN03210 Resistant to P

Probab=99.86  E-value=8.8e-21  Score=245.14  Aligned_cols=341  Identities=19%  Similarity=0.289  Sum_probs=227.7

Q ss_pred             cccCCCCccceeEecCCC--C----ceecCCCC--CCCCccEEEecCCcchhhhhhhccccCCccceeeccCCCCccccc
Q 000887          801 QGLQRLTCLKDLLIGNCP--T----VVSLPKAC--FLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSIS  872 (1237)
Q Consensus       801 ~~~~~l~~L~~L~l~~~~--~----l~~~~~~~--~~~~L~~L~l~~c~~l~~~~~~~~~~~~~L~~L~l~~c~~l~~~~  872 (1237)
                      ..+.++++|+.|.+....  .    -..+|...  ..++|+.|++.+++ ++.+|...  .+.+|+.|++.++. +..++
T Consensus       552 ~aF~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~-l~~lP~~f--~~~~L~~L~L~~s~-l~~L~  627 (1153)
T PLN03210        552 NAFKGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYP-LRCMPSNF--RPENLVKLQMQGSK-LEKLW  627 (1153)
T ss_pred             HHHhcCccccEEEEecccccccccceeecCcchhhcCcccEEEEecCCC-CCCCCCcC--CccCCcEEECcCcc-ccccc
Confidence            457788999999886532  1    11233322  24579999999865 77787764  36889999998864 55554


Q ss_pred             cc-CCCCCccEEEEecCCCccccccccccccCCCCccccccCCCCCcccceeEEEEecCCCcccccCCCCCccceeeeee
Q 000887          873 RE-HLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRI  951 (1237)
Q Consensus       873 ~~-~~~~~L~~L~l~~c~~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~~L~~L~l  951 (1237)
                      .. ...++|+.+++++|..++.             ++      ....+++|+.|++.+|..+..+|.....+++|+.|++
T Consensus       628 ~~~~~l~~Lk~L~Ls~~~~l~~-------------ip------~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L  688 (1153)
T PLN03210        628 DGVHSLTGLRNIDLRGSKNLKE-------------IP------DLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDM  688 (1153)
T ss_pred             cccccCCCCCEEECCCCCCcCc-------------CC------ccccCCcccEEEecCCCCccccchhhhccCCCCEEeC
Confidence            32 2346788888888876652             22      2345678888999888888888888788888888888


Q ss_pred             ecCCCccccCcCCCCCCcccEEEEcCCCCccccccccCCcccccEEeeccccccccccccccCCCCCceeeeccCCCcc-
Q 000887          952 EDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLV- 1030 (1237)
Q Consensus       952 ~~c~~l~~l~~~~~~~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~- 1030 (1237)
                      ++|..++.+|... .+++|+.|++++|..+..+|..   .++|+.|+++++ .+..+|..+ .+++|++|.+.+|.... 
T Consensus       689 ~~c~~L~~Lp~~i-~l~sL~~L~Lsgc~~L~~~p~~---~~nL~~L~L~~n-~i~~lP~~~-~l~~L~~L~l~~~~~~~l  762 (1153)
T PLN03210        689 SRCENLEILPTGI-NLKSLYRLNLSGCSRLKSFPDI---STNISWLDLDET-AIEEFPSNL-RLENLDELILCEMKSEKL  762 (1153)
T ss_pred             CCCCCcCccCCcC-CCCCCCEEeCCCCCCccccccc---cCCcCeeecCCC-ccccccccc-cccccccccccccchhhc
Confidence            8888888887644 6678888888888887777653   357888888875 466777654 57888888887654211 


Q ss_pred             -----cCCC--CCCCCcchhhhhhccccccccCC-CCCCCcccEEeccCCCCccccCCCCCCCCcCceEecCCCCccccc
Q 000887         1031 -----SLPE--DALPSNVVDVLIEDCDKLKALIP-TGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLV 1102 (1237)
Q Consensus      1031 -----~l~~--~~~~~~l~~l~l~~~~~~~~~~~-~~~l~~L~~L~l~~c~~l~~~~~~~~~~~L~~L~l~~~~~~~~~~ 1102 (1237)
                           .++.  ...+++|+.|++++|..+..++. ++++++|+.|++++|..++.+|....+++|+.|++++|..+..++
T Consensus       763 ~~~~~~l~~~~~~~~~sL~~L~Ls~n~~l~~lP~si~~L~~L~~L~Ls~C~~L~~LP~~~~L~sL~~L~Ls~c~~L~~~p  842 (1153)
T PLN03210        763 WERVQPLTPLMTMLSPSLTRLFLSDIPSLVELPSSIQNLHKLEHLEIENCINLETLPTGINLESLESLDLSGCSRLRTFP  842 (1153)
T ss_pred             cccccccchhhhhccccchheeCCCCCCccccChhhhCCCCCCEEECCCCCCcCeeCCCCCccccCEEECCCCCcccccc
Confidence                 1110  11234567777777665554433 366777777777777777777665556677777777776665554


Q ss_pred             ccccCCCCCCceEEEcCCCCceeccCCCCccccCCCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCCCcccCC
Q 000887         1103 KWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFP 1179 (1237)
Q Consensus      1103 ~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~ 1179 (1237)
                      ..    .++|+.|+++++ .++.+|..   +..+++|+.|++.+|++++.++ ..+..+++|+.+++++|+.++.++
T Consensus       843 ~~----~~nL~~L~Ls~n-~i~~iP~s---i~~l~~L~~L~L~~C~~L~~l~-~~~~~L~~L~~L~l~~C~~L~~~~  910 (1153)
T PLN03210        843 DI----STNISDLNLSRT-GIEEVPWW---IEKFSNLSFLDMNGCNNLQRVS-LNISKLKHLETVDFSDCGALTEAS  910 (1153)
T ss_pred             cc----ccccCEeECCCC-CCccChHH---HhcCCCCCEEECCCCCCcCccC-cccccccCCCeeecCCCccccccc
Confidence            32    356777777764 45555542   2345677777777777777766 345566777777777777666543

syringae 6; Provisional

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

Probab=99.85  E-value=2.5e-23  Score=235.84  Aligned_cols=100  Identities=30%  Similarity=0.452  Sum_probs=85.9

Q ss_pred             CCccEEEccccccccccccc-cCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEecc
Q 000887          400 KKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~-~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      ..+..|+++.|.+-..|-.| .+..+|+.||+++|.+...|..|..+.+|+.|+++.| .+..+|.+++++.+|++|.|.
T Consensus        21 ~~~~~ln~~~N~~l~~pl~~~~~~v~L~~l~lsnn~~~~fp~~it~l~~L~~ln~s~n-~i~~vp~s~~~~~~l~~lnL~   99 (1081)
T KOG0618|consen   21 EALQILNLRRNSLLSRPLEFVEKRVKLKSLDLSNNQISSFPIQITLLSHLRQLNLSRN-YIRSVPSSCSNMRNLQYLNLK   99 (1081)
T ss_pred             HHHHhhhccccccccCchHHhhheeeeEEeeccccccccCCchhhhHHHHhhcccchh-hHhhCchhhhhhhcchhheec
Confidence            34888899888877766433 4445599999999999999999999999999999998 899999999999999999999


Q ss_pred             CCCccccCcccccccccccccce
Q 000887          479 GASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      +| .+..+|.+++.+++|+.|++
T Consensus       100 ~n-~l~~lP~~~~~lknl~~Ldl  121 (1081)
T KOG0618|consen  100 NN-RLQSLPASISELKNLQYLDL  121 (1081)
T ss_pred             cc-hhhcCchhHHhhhccccccc
Confidence            88 88999999988888888865

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

Probab=99.84  E-value=2.5e-21  Score=207.80  Aligned_cols=86  Identities=21%  Similarity=0.260  Sum_probs=62.4

Q ss_pred             CccEEEccccccccc-cccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCCh-hhcccccccEEecc
Q 000887          401 KLRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPS-RIGNLVNLHYLNIE  478 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~l-p~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~  478 (1237)
                      ..+.|++++|.+..+ +..|.++++|+.+++.+|.++.+|.......+|+.|+|.+| .|.++-. ++..+..|+.|||+
T Consensus        79 ~t~~LdlsnNkl~~id~~~f~nl~nLq~v~l~~N~Lt~IP~f~~~sghl~~L~L~~N-~I~sv~se~L~~l~alrslDLS  157 (873)
T KOG4194|consen   79 QTQTLDLSNNKLSHIDFEFFYNLPNLQEVNLNKNELTRIPRFGHESGHLEKLDLRHN-LISSVTSEELSALPALRSLDLS  157 (873)
T ss_pred             ceeeeeccccccccCcHHHHhcCCcceeeeeccchhhhcccccccccceeEEeeecc-ccccccHHHHHhHhhhhhhhhh
Confidence            446688888888776 45667888888888888888888776666777888888887 5655543 36777778888888


Q ss_pred             CCCccccCcc
Q 000887          479 GASALRELPL  488 (1237)
Q Consensus       479 ~~~~l~~ip~  488 (1237)
                      .| .+..+|.
T Consensus       158 rN-~is~i~~  166 (873)
T KOG4194|consen  158 RN-LISEIPK  166 (873)
T ss_pred             hc-hhhcccC
Confidence            77 5666654

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

Probab=99.80  E-value=2.7e-22  Score=205.59  Aligned_cols=205  Identities=24%  Similarity=0.201  Sum_probs=150.9

Q ss_pred             chhhhhcCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhccc
Q 000887          390 MVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNL  469 (1237)
Q Consensus       390 ~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L  469 (1237)
                      ..+|+.+.....++.|++++|.+.++|++++.+..|..|+..+|+|.++|..++.+.+|..|++.+| .+..+|+..-++
T Consensus       104 s~lp~~i~s~~~l~~l~~s~n~~~el~~~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l~~l~~~~n-~l~~l~~~~i~m  182 (565)
T KOG0472|consen  104 SELPEQIGSLISLVKLDCSSNELKELPDSIGRLLDLEDLDATNNQISSLPEDMVNLSKLSKLDLEGN-KLKALPENHIAM  182 (565)
T ss_pred             hhccHHHhhhhhhhhhhccccceeecCchHHHHhhhhhhhccccccccCchHHHHHHHHHHhhcccc-chhhCCHHHHHH
Confidence            4455566778888888888888888888888888888888888888888888888888888888887 788888877668


Q ss_pred             ccccEEeccCCCccccCcccccccccccccceeeeccCCCcCcccccchHhcccceeecCccCCCChHHHHHHhhcCCCC
Q 000887          470 VNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEG  549 (1237)
Q Consensus       470 ~~L~~L~l~~~~~l~~ip~~~~~L~~L~~L~~~~~~~~~~~~i~~l~~l~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~  549 (1237)
                      +.|++||...| .++.+|.+++.|.+|..|++-.+.......+.....|.++.                           
T Consensus       183 ~~L~~ld~~~N-~L~tlP~~lg~l~~L~~LyL~~Nki~~lPef~gcs~L~Elh---------------------------  234 (565)
T KOG0472|consen  183 KRLKHLDCNSN-LLETLPPELGGLESLELLYLRRNKIRFLPEFPGCSLLKELH---------------------------  234 (565)
T ss_pred             HHHHhcccchh-hhhcCChhhcchhhhHHHHhhhcccccCCCCCccHHHHHHH---------------------------
Confidence            88888888888 78888888888888888866444332222333333333333                           


Q ss_pred             CCeeEeeeCCCCCCCCcchHHHHhhhhcCCCCCCccEEEEeecCCCCCCCCCCCCCCCCccEEEEccCCCCCcCCCCCCc
Q 000887          550 LTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQL  629 (1237)
Q Consensus       550 L~~L~l~~~~~~~~~~~~~~~~~~~l~~l~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~~l~~l  629 (1237)
                           +.          ....+.---+..+.++++..|++.+++..++|..+.  -+++|++|++++|....-.+.++++
T Consensus       235 -----~g----------~N~i~~lpae~~~~L~~l~vLDLRdNklke~Pde~c--lLrsL~rLDlSNN~is~Lp~sLgnl  297 (565)
T KOG0472|consen  235 -----VG----------ENQIEMLPAEHLKHLNSLLVLDLRDNKLKEVPDEIC--LLRSLERLDLSNNDISSLPYSLGNL  297 (565)
T ss_pred             -----hc----------ccHHHhhHHHHhcccccceeeeccccccccCchHHH--HhhhhhhhcccCCccccCCcccccc
Confidence                 10          000001111234567888899999999988887654  5788999999999754444489999


Q ss_pred             cccceeEecCCC
Q 000887          630 CSLKDLTIVGMS  641 (1237)
Q Consensus       630 ~~L~~L~l~~~~  641 (1237)
                       .|+.|-+.|++
T Consensus       298 -hL~~L~leGNP  308 (565)
T KOG0472|consen  298 -HLKFLALEGNP  308 (565)
T ss_pred             -eeeehhhcCCc
Confidence             99999999975

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

Probab=99.80  E-value=1.1e-21  Score=211.32  Aligned_cols=75  Identities=20%  Similarity=0.277  Sum_probs=54.4

Q ss_pred             cCcCCCCCCcccEEEEcCCCCccccccccCCcccccEEeeccccccccccccccCCCCCceeeeccCCCcccCCCCC
Q 000887          960 LTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDA 1036 (1237)
Q Consensus       960 l~~~~~~~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~ 1036 (1237)
                      +|+.++.+.+|+.++..+ +.++-+|++++.+++|+.|.|+. +.+..+|+++.-++.|+.|+++.++++..-|...
T Consensus       308 iPSGIGKL~~Levf~aan-N~LElVPEglcRC~kL~kL~L~~-NrLiTLPeaIHlL~~l~vLDlreNpnLVMPPKP~  382 (1255)
T KOG0444|consen  308 IPSGIGKLIQLEVFHAAN-NKLELVPEGLCRCVKLQKLKLDH-NRLITLPEAIHLLPDLKVLDLRENPNLVMPPKPN  382 (1255)
T ss_pred             CccchhhhhhhHHHHhhc-cccccCchhhhhhHHHHHhcccc-cceeechhhhhhcCCcceeeccCCcCccCCCCcc
Confidence            334444455666666665 46777888888888888888876 5677788888888888888888888877665544

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

Probab=99.70  E-value=6.7e-19  Score=190.20  Aligned_cols=225  Identities=22%  Similarity=0.263  Sum_probs=146.8

Q ss_pred             hcCCCCCccEEEccccccc--cccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhh-ccccc
Q 000887          395 LLPQCKKLRVLSLGSYCIT--EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRI-GNLVN  471 (1237)
Q Consensus       395 ~~~~~~~Lr~L~L~~~~i~--~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i-~~L~~  471 (1237)
                      -++.++.||.+++..|++.  -+|+.+-.+..|.+||||+|++++.|..+..-+++-+|+||+| +|..||..+ -+|+-
T Consensus        73 ELs~Lp~LRsv~~R~N~LKnsGiP~diF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N-~IetIPn~lfinLtD  151 (1255)
T KOG0444|consen   73 ELSDLPRLRSVIVRDNNLKNSGIPTDIFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYN-NIETIPNSLFINLTD  151 (1255)
T ss_pred             hhccchhhHHHhhhccccccCCCCchhcccccceeeecchhhhhhcchhhhhhcCcEEEEcccC-ccccCCchHHHhhHh
Confidence            3567889999999999986  5798899999999999999999999999999999999999998 999999885 78999


Q ss_pred             ccEEeccCCCccccCcccccccccccccceeeeccCCCcCcccccchHhcccceeecCccCCCChHHHHHHhhcCCCCCC
Q 000887          472 LHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLT  551 (1237)
Q Consensus       472 L~~L~l~~~~~l~~ip~~~~~L~~L~~L~~~~~~~~~~~~i~~l~~l~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~L~  551 (1237)
                      |-+|||++| ++..+|+.+..|..|++|.+.++... ...+++|++++.|.    +..+.+......-.+..+..+.+|.
T Consensus       152 LLfLDLS~N-rLe~LPPQ~RRL~~LqtL~Ls~NPL~-hfQLrQLPsmtsL~----vLhms~TqRTl~N~Ptsld~l~NL~  225 (1255)
T KOG0444|consen  152 LLFLDLSNN-RLEMLPPQIRRLSMLQTLKLSNNPLN-HFQLRQLPSMTSLS----VLHMSNTQRTLDNIPTSLDDLHNLR  225 (1255)
T ss_pred             Hhhhccccc-hhhhcCHHHHHHhhhhhhhcCCChhh-HHHHhcCccchhhh----hhhcccccchhhcCCCchhhhhhhh
Confidence            999999999 89999999999999999987554321 22344455554444    1222222222222222333344444


Q ss_pred             eeEeeeCCCCCCCCcchHHHHhhhhcCCCCCCccEEEEeecCCCCCCCCCCCCCCCCccEEEEccCCCCCcCC-CCCCcc
Q 000887          552 DLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLP-SLGQLC  630 (1237)
Q Consensus       552 ~L~l~~~~~~~~~~~~~~~~~~~l~~l~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~-~l~~l~  630 (1237)
                      .++++.+..           ..+.+.+-.+.+|+.|+++++.++.+....+  ...+|+.|+++.|. +..+| .+..++
T Consensus       226 dvDlS~N~L-----------p~vPecly~l~~LrrLNLS~N~iteL~~~~~--~W~~lEtLNlSrNQ-Lt~LP~avcKL~  291 (1255)
T KOG0444|consen  226 DVDLSENNL-----------PIVPECLYKLRNLRRLNLSGNKITELNMTEG--EWENLETLNLSRNQ-LTVLPDAVCKLT  291 (1255)
T ss_pred             hccccccCC-----------CcchHHHhhhhhhheeccCcCceeeeeccHH--HHhhhhhhccccch-hccchHHHhhhH
Confidence            444433221           1122333344555555555555554432222  23455556666554 34444 455566


Q ss_pred             ccceeEecCC
Q 000887          631 SLKDLTIVGM  640 (1237)
Q Consensus       631 ~L~~L~l~~~  640 (1237)
                      +|+.|++.++
T Consensus       292 kL~kLy~n~N  301 (1255)
T KOG0444|consen  292 KLTKLYANNN  301 (1255)
T ss_pred             HHHHHHhccC
Confidence            6666655543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.46  E-value=5.5e-12  Score=163.94  Aligned_cols=277  Identities=13%  Similarity=0.194  Sum_probs=175.3

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcC-CcCHHHHHHHHHHHhhccCCC-------------ccC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSD-DFDVLRISKAILDSIKRSSCK-------------LED   76 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~-~~~~~~~~~~i~~~l~~~~~~-------------~~~   76 (1237)
                      ...+++.|+|++|.||||++.++++.     ++.++|+++.. +.+...+...++..+......             ..+
T Consensus        30 ~~~~~~~v~apaG~GKTtl~~~~~~~-----~~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~  104 (903)
T PRK04841         30 NNYRLVLVTSPAGYGKTTLISQWAAG-----KNNLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYAS  104 (903)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHh-----CCCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCC
Confidence            45789999999999999999997752     22688999864 446666667777766422111             012


Q ss_pred             HHHHHHHHHHHhc--CCcEEEEEeCCCCCChhhHHHhhcc-ccCCCCCcEEEEEeCchhHH--Hhhc-CCCeEeCC----
Q 000887           77 LNSVQLELKETVF--KKKFLIVLDDVWSERYDLWQALKSP-FMAGAPGSRIIVTTRSMDVA--LTMG-SGKNYELK----  146 (1237)
Q Consensus        77 ~~~~~~~l~~~l~--~~~~LlvlDdv~~~~~~~~~~~~~~-~~~~~~~~~iliTtR~~~~~--~~~~-~~~~~~l~----  146 (1237)
                      .......+...+.  +++++||+||+...+.......... +...+++.++|||||.....  .... .....+++    
T Consensus       105 ~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l  184 (903)
T PRK04841        105 LSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQL  184 (903)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHhC
Confidence            2233333333333  5799999999965432333333333 33346678899999984221  1111 12345556    


Q ss_pred             CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCC-HHHHHHHHhhcccccCCCCChh
Q 000887          147 LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQG-VDEWRAILDSKIWNLQDKTEIP  225 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~-~~~~~~~l~~~~~~~~~~~~i~  225 (1237)
                      +|+.+|+.++|....+..   .    ..+.+.+|.+.++|+|+++..++..++.... ....   .... .. .....+.
T Consensus       185 ~f~~~e~~~ll~~~~~~~---~----~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~~~~---~~~~-~~-~~~~~~~  252 (903)
T PRK04841        185 AFDHQEAQQFFDQRLSSP---I----EAAESSRLCDDVEGWATALQLIALSARQNNSSLHDS---ARRL-AG-INASHLS  252 (903)
T ss_pred             CCCHHHHHHHHHhccCCC---C----CHHHHHHHHHHhCChHHHHHHHHHHHhhCCCchhhh---hHhh-cC-CCchhHH
Confidence            999999999998765321   1    2556789999999999999999887765432 1111   1110 00 0113355


Q ss_pred             HHHH-HHhhcChHHHHHHHhhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccc-cCCCC
Q 000887          226 SVLK-LSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK-SSNTE  303 (1237)
Q Consensus       226 ~~l~-~s~~~L~~~~~~~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~-~~~~~  303 (1237)
                      ..+. ..++.||++.++++...|+++   .++.+..-.      +.+.        +.+...+..|.+.+++.. .+...
T Consensus       253 ~~l~~~v~~~l~~~~~~~l~~~a~~~---~~~~~l~~~------l~~~--------~~~~~~L~~l~~~~l~~~~~~~~~  315 (903)
T PRK04841        253 DYLVEEVLDNVDLETRHFLLRCSVLR---SMNDALIVR------VTGE--------ENGQMRLEELERQGLFIQRMDDSG  315 (903)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHhcccc---cCCHHHHHH------HcCC--------CcHHHHHHHHHHCCCeeEeecCCC
Confidence            5443 348999999999999999985   333332221      1111        113566899999999764 34445


Q ss_pred             CcchhhhHHHHHHhhhcc
Q 000887          304 SKYVMHDLVHDLAQWASG  321 (1237)
Q Consensus       304 ~~~~~h~lv~~~~~~~~~  321 (1237)
                      .+|+.|++++++++....
T Consensus       316 ~~yr~H~L~r~~l~~~l~  333 (903)
T PRK04841        316 EWFRYHPLFASFLRHRCQ  333 (903)
T ss_pred             CEEehhHHHHHHHHHHHH
Confidence            689999999999987753

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.40  E-value=1.8e-12  Score=154.48  Aligned_cols=155  Identities=27%  Similarity=0.398  Sum_probs=85.4

Q ss_pred             CcccEEEEcCCCCccccccccCCcccccEEeeccccccccccccccCCCCCceeeeccCCCcccCCCCCCCCcchhhhhh
Q 000887          968 VEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIE 1047 (1237)
Q Consensus       968 ~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~l~ 1047 (1237)
                      ++|+.|++++| .+..+|..   ..+|+.|++++| .++.+|..   ..+|+.|++++ +.++.+|..            
T Consensus       302 ~~L~~LdLS~N-~L~~Lp~l---p~~L~~L~Ls~N-~L~~LP~l---p~~Lq~LdLS~-N~Ls~LP~l------------  360 (788)
T PRK15387        302 PGLQELSVSDN-QLASLPAL---PSELCKLWAYNN-QLTSLPTL---PSGLQELSVSD-NQLASLPTL------------  360 (788)
T ss_pred             cccceeECCCC-ccccCCCC---cccccccccccC-cccccccc---ccccceEecCC-CccCCCCCC------------
Confidence            45555555554 23333321   124555566553 34444431   13566666665 345555431            


Q ss_pred             ccccccccCCCCCCCcccEEeccCCCCccccCCCCCCCCcCceEecCCCCcccccccccCCCCCCceEEEcCCCCceecc
Q 000887         1048 DCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFP 1127 (1237)
Q Consensus      1048 ~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l~ 1127 (1237)
                                   .++|+.|++++| .+..+|.  .+++|+.|++++|... .+|..    .++|+.|++++| .+..+|
T Consensus       361 -------------p~~L~~L~Ls~N-~L~~LP~--l~~~L~~LdLs~N~Lt-~LP~l----~s~L~~LdLS~N-~LssIP  418 (788)
T PRK15387        361 -------------PSELYKLWAYNN-RLTSLPA--LPSGLKELIVSGNRLT-SLPVL----PSELKELMVSGN-RLTSLP  418 (788)
T ss_pred             -------------Ccccceehhhcc-ccccCcc--cccccceEEecCCccc-CCCCc----ccCCCEEEccCC-cCCCCC
Confidence                         234555555555 2444443  2346667777665433 33321    246777777775 456666


Q ss_pred             CCCCccccCCCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCC
Q 000887         1128 DVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCP 1173 (1237)
Q Consensus      1128 ~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~ 1173 (1237)
                      .      .+.+|+.|++++ |.++.+| ..+.++++|+.|++++++
T Consensus       419 ~------l~~~L~~L~Ls~-NqLt~LP-~sl~~L~~L~~LdLs~N~  456 (788)
T PRK15387        419 M------LPSGLLSLSVYR-NQLTRLP-ESLIHLSSETTVNLEGNP  456 (788)
T ss_pred             c------chhhhhhhhhcc-CcccccC-hHHhhccCCCeEECCCCC
Confidence            4      345677777777 5677777 456677888888887754

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.35  E-value=7.1e-12  Score=149.52  Aligned_cols=80  Identities=24%  Similarity=0.250  Sum_probs=63.8

Q ss_pred             CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccC
Q 000887          400 KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG  479 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~  479 (1237)
                      ..-.+|+|+++.++.+|..+.  .+|+.|++++|.++.+|.   .+++|++|++++| .+..+|..   ..+|++|++++
T Consensus       201 ~~~~~LdLs~~~LtsLP~~l~--~~L~~L~L~~N~Lt~LP~---lp~~Lk~LdLs~N-~LtsLP~l---p~sL~~L~Ls~  271 (788)
T PRK15387        201 NGNAVLNVGESGLTTLPDCLP--AHITTLVIPDNNLTSLPA---LPPELRTLEVSGN-QLTSLPVL---PPGLLELSIFS  271 (788)
T ss_pred             CCCcEEEcCCCCCCcCCcchh--cCCCEEEccCCcCCCCCC---CCCCCcEEEecCC-ccCcccCc---ccccceeeccC
Confidence            446788999999999988775  489999999999998886   3578999999998 88888863   46788888988


Q ss_pred             CCccccCccc
Q 000887          480 ASALRELPLG  489 (1237)
Q Consensus       480 ~~~l~~ip~~  489 (1237)
                      | .+..+|..
T Consensus       272 N-~L~~Lp~l  280 (788)
T PRK15387        272 N-PLTHLPAL  280 (788)
T ss_pred             C-chhhhhhc
Confidence            8 57777653

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.34  E-value=5.8e-12  Score=144.53  Aligned_cols=283  Identities=17%  Similarity=0.209  Sum_probs=185.7

Q ss_pred             CCCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhccCC-------------Cc
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRSSC-------------KL   74 (1237)
Q Consensus         9 ~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~~~-------------~~   74 (1237)
                      ...+.|.+.|..++|.||||++.+++. . ...-..|.|++++.. .+.......++..++.-..             +.
T Consensus        33 ~~~~~RL~li~APAGfGKttl~aq~~~-~-~~~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~  110 (894)
T COG2909          33 RANDYRLILISAPAGFGKTTLLAQWRE-L-AADGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQY  110 (894)
T ss_pred             cCCCceEEEEeCCCCCcHHHHHHHHHH-h-cCcccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhccc
Confidence            345789999999999999999999875 2 222345889998755 4677777777777763221             23


Q ss_pred             cCHHHHHHHHHHHhc--CCcEEEEEeCCCCCChhhHH-HhhccccCCCCCcEEEEEeCchhHHHh--hcC-CCeEeCC--
Q 000887           75 EDLNSVQLELKETVF--KKKFLIVLDDVWSERYDLWQ-ALKSPFMAGAPGSRIIVTTRSMDVALT--MGS-GKNYELK--  146 (1237)
Q Consensus        75 ~~~~~~~~~l~~~l~--~~~~LlvlDdv~~~~~~~~~-~~~~~~~~~~~~~~iliTtR~~~~~~~--~~~-~~~~~l~--  146 (1237)
                      .+...+...+...+.  .++..+|+||..-....... .+...+...+.+-.++||||.+.....  +.. ...++++  
T Consensus       111 ~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~  190 (894)
T COG2909         111 VSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRDELLEIGSE  190 (894)
T ss_pred             ccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehhhHHhcChH
Confidence            444445555555444  47899999998544333333 344444556778999999998754421  111 1234444  


Q ss_pred             --CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCHHHHHHHHhhcccccCCCCCh
Q 000887          147 --LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEI  224 (1237)
Q Consensus       147 --~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~i  224 (1237)
                        .|+.+|+.++|....+..       -....+..+.+..+|.+-|+.+++-.++++.+.+.-...+.....     .-.
T Consensus       191 ~Lrf~~eE~~~fl~~~~~l~-------Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~LsG~~~-----~l~  258 (894)
T COG2909         191 ELRFDTEEAAAFLNDRGSLP-------LDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLSGAAS-----HLS  258 (894)
T ss_pred             hhcCChHHHHHHHHHcCCCC-------CChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhccchHH-----HHH
Confidence              489999999998765221       124567899999999999999999888854442222221111000     000


Q ss_pred             hHHHHHHhhcChHHHHHHHhhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccc-cCCCC
Q 000887          225 PSVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK-SSNTE  303 (1237)
Q Consensus       225 ~~~l~~s~~~L~~~~~~~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~-~~~~~  303 (1237)
                      .-..+--++.||++.|..++-+|+++.   +. ..+....             +-++.+..++++|.+++++.. -++..
T Consensus       259 dYL~eeVld~Lp~~l~~FLl~~svl~~---f~-~eL~~~L-------------tg~~ng~amLe~L~~~gLFl~~Ldd~~  321 (894)
T COG2909         259 DYLVEEVLDRLPPELRDFLLQTSVLSR---FN-DELCNAL-------------TGEENGQAMLEELERRGLFLQRLDDEG  321 (894)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhHHH---hh-HHHHHHH-------------hcCCcHHHHHHHHHhCCCceeeecCCC
Confidence            112234478999999999999999842   11 1222211             112335667999999998764 46678


Q ss_pred             CcchhhhHHHHHHhhhccc
Q 000887          304 SKYVMHDLVHDLAQWASGE  322 (1237)
Q Consensus       304 ~~~~~h~lv~~~~~~~~~~  322 (1237)
                      .||+.|++..+|.+.....
T Consensus       322 ~WfryH~LFaeFL~~r~~~  340 (894)
T COG2909         322 QWFRYHHLFAEFLRQRLQR  340 (894)
T ss_pred             ceeehhHHHHHHHHhhhcc
Confidence            9999999999999877654

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.30  E-value=1.5e-12  Score=159.01  Aligned_cols=290  Identities=27%  Similarity=0.363  Sum_probs=184.0

Q ss_pred             CCCccEEEccccc--ccccccc-ccCCCCCCeEEccCCC-ccccchhhcccCCccEEEcCccccCccCChhhcccccccE
Q 000887          399 CKKLRVLSLGSYC--ITEVPIS-IGCLKQLRYLNFSRSE-IQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY  474 (1237)
Q Consensus       399 ~~~Lr~L~L~~~~--i~~lp~~-~~~l~~Lr~L~L~~~~-i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~  474 (1237)
                      ++.|++|-+.+|.  +..++.. |..++.||+|||++|. +..+|++|+.|.+||||+++++ .+..+|.++++|+.|.+
T Consensus       544 ~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t-~I~~LP~~l~~Lk~L~~  622 (889)
T KOG4658|consen  544 NPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDT-GISHLPSGLGNLKKLIY  622 (889)
T ss_pred             CCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCC-CccccchHHHHHHhhhe
Confidence            4479999999997  6777654 6889999999999764 6799999999999999999998 89999999999999999


Q ss_pred             EeccCCCccccCcccccccccccccceeeec-cCCCcCcccccchHhcccceeecCccCCCChHHHHHHhhcCCCCCCee
Q 000887          475 LNIEGASALRELPLGMKELKCLRTLTNFIVG-KDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDL  553 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~~~~L~~L~~L~~~~~~-~~~~~~i~~l~~l~~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L  553 (1237)
                      |++..+..+..+|..+..|.+||+|.++... ..+...+.++.+|+.|+                             .+
T Consensus       623 Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~-----------------------------~l  673 (889)
T KOG4658|consen  623 LNLEVTGRLESIPGILLELQSLRVLRLPRSALSNDKLLLKELENLEHLE-----------------------------NL  673 (889)
T ss_pred             eccccccccccccchhhhcccccEEEeeccccccchhhHHhhhcccchh-----------------------------hh
Confidence            9999997777887767779999999886654 22233344444444444                             22


Q ss_pred             EeeeCCCCCCCCcchHHHHhhhhcCCCCCCcc----EEEEeecCCCCCCCCCCCCCCCCccEEEEccCCCCCcCC-C---
Q 000887          554 KLDWRPRRDGDSVDEAREKNILDMLKPHSNIK----RLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLP-S---  625 (1237)
Q Consensus       554 ~l~~~~~~~~~~~~~~~~~~~l~~l~~~~~L~----~L~l~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~-~---  625 (1237)
                      +..-..           . ..++.+.....|.    .+.+.+......+...  ..+.+|+.|.+.+|....... +   
T Consensus       674 s~~~~s-----------~-~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~--~~l~~L~~L~i~~~~~~e~~~~~~~~  739 (889)
T KOG4658|consen  674 SITISS-----------V-LLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSL--GSLGNLEELSILDCGISEIVIEWEES  739 (889)
T ss_pred             eeecch-----------h-HhHhhhhhhHHHHHHhHhhhhcccccceeeccc--ccccCcceEEEEcCCCchhhcccccc
Confidence            221000           0 0111111111111    1111111111111111  268899999999998653221 1   


Q ss_pred             --CCC-ccccceeEecCCCCceeecccccCCCcccCCcccceeeccccccccccccCCCCc----ccccccccccee-ec
Q 000887          626 --LGQ-LCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDND----EHVQAFPRLRKL-SI  697 (1237)
Q Consensus       626 --l~~-l~~L~~L~l~~~~~l~~i~~~~~~~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~----~~~~~~~~L~~L-~l  697 (1237)
                        ... ++++..+.+.+|..........+       .|+|+.|.+..+...++..+.....    .....|..+..+ .+
T Consensus       740 ~~~~~~f~~l~~~~~~~~~~~r~l~~~~f-------~~~L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~~  812 (889)
T KOG4658|consen  740 LIVLLCFPNLSKVSILNCHMLRDLTWLLF-------APHLTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRML  812 (889)
T ss_pred             cchhhhHHHHHHHHhhccccccccchhhc-------cCcccEEEEecccccccCCCHHHHhhhcccEEecccccccceee
Confidence              122 66788888888877776654332       6899999999998877765433211    012345555555 34


Q ss_pred             cCCCCccC--CCCCCCCCcceEEeccccCccccCCCCCcccEEEEcCC
Q 000887          698 KKCPKLSG--RLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGC  743 (1237)
Q Consensus       698 ~~~~~l~~--~~~~~l~~L~~L~l~~c~~l~~~~~~l~~L~~L~l~~~  743 (1237)
                      .+.+.+..  ..|-.++.|+++.+..|+.+.    .+|.+..+.+.+|
T Consensus       813 ~~l~~l~~i~~~~l~~~~l~~~~ve~~p~l~----~~P~~~~~~i~~~  856 (889)
T KOG4658|consen  813 CSLGGLPQLYWLPLSFLKLEELIVEECPKLG----KLPLLSTLTIVGC  856 (889)
T ss_pred             ecCCCCceeEecccCccchhheehhcCcccc----cCccccccceecc
Confidence            44333331  233445567888888776654    4566666666665

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

Probab=99.25  E-value=2.3e-13  Score=140.75  Aligned_cols=284  Identities=18%  Similarity=0.196  Sum_probs=169.2

Q ss_pred             eeEEEEecCCCcccccCC-CCCccceeeeeeecCCCccccCcCCCCCCcccEEEEcCCCCcccccc-ccCCcccccEEee
Q 000887          922 LESLFVYRCPSLTCLWSG-GRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAE-RFHDDACLRSIWI  999 (1237)
Q Consensus       922 L~~L~l~~~~~l~~~~~~-~~~~~~L~~L~l~~c~~l~~l~~~~~~~~~L~~L~l~~c~~~~~~~~-~~~~l~~L~~L~l  999 (1237)
                      ...+++.. +.++.+|.+ ++.+++|+.|+++++.....-+..+.++.+|.+|-+.+++++.+++. .|.++.+|+.|.+
T Consensus        69 tveirLdq-N~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLll  147 (498)
T KOG4237|consen   69 TVEIRLDQ-NQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQRLLL  147 (498)
T ss_pred             ceEEEecc-CCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHHHhc
Confidence            34455554 455555554 44566666666666544433444455556666666666556666553 4555666666666


Q ss_pred             ccccccccccccccCCCCCceeeeccCCCcccCCCCCCC--Ccchhhhh------hccccc-------cccCCCCCCCcc
Q 000887         1000 SSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALP--SNVVDVLI------EDCDKL-------KALIPTGTLSSL 1064 (1237)
Q Consensus      1000 ~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~~~--~~l~~l~l------~~~~~~-------~~~~~~~~l~~L 1064 (1237)
                      ..|..--.....+..+++|..|.++. +.+..++...+.  .+++.+.+      .+|+..       .....++.++-.
T Consensus       148 Nan~i~Cir~~al~dL~~l~lLslyD-n~~q~i~~~tf~~l~~i~tlhlA~np~icdCnL~wla~~~a~~~ietsgarc~  226 (498)
T KOG4237|consen  148 NANHINCIRQDALRDLPSLSLLSLYD-NKIQSICKGTFQGLAAIKTLHLAQNPFICDCNLPWLADDLAMNPIETSGARCV  226 (498)
T ss_pred             ChhhhcchhHHHHHHhhhcchhcccc-hhhhhhccccccchhccchHhhhcCccccccccchhhhHHhhchhhcccceec
Confidence            55432222333556666666666666 344444442221  12222221      111110       000000111111


Q ss_pred             cEEeccCCCCccccCCCCCC---CCcCceEecCCCCcccccccccCCCCCCceEEEcCCCCceeccCCCCccccCCCcCe
Q 000887         1065 RELALSECPGIVVFPEEGLS---TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTS 1141 (1237)
Q Consensus      1065 ~~L~l~~c~~l~~~~~~~~~---~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~ 1141 (1237)
                      ....+.+. .+..+....+.   ..+..=..+.|......|...|+.+++|++|++++| .++.+.+  ++|.....++.
T Consensus       227 ~p~rl~~~-Ri~q~~a~kf~c~~esl~s~~~~~d~~d~~cP~~cf~~L~~L~~lnlsnN-~i~~i~~--~aFe~~a~l~e  302 (498)
T KOG4237|consen  227 SPYRLYYK-RINQEDARKFLCSLESLPSRLSSEDFPDSICPAKCFKKLPNLRKLNLSNN-KITRIED--GAFEGAAELQE  302 (498)
T ss_pred             chHHHHHH-HhcccchhhhhhhHHhHHHhhccccCcCCcChHHHHhhcccceEeccCCC-ccchhhh--hhhcchhhhhh
Confidence            11111100 11112222221   122222344555556667777999999999999996 5666655  45656789999


Q ss_pred             eeecCCCCccccCcccCCCCCCCCeeeecCCCCcccCCCCCC--CCcccEeeecCCCCcccccccCCccccccc
Q 000887         1142 ITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF--PSSLLSLEIQRCPLLEKCKMRKGQEWPKIA 1213 (1237)
Q Consensus      1142 L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~--~~sL~~L~i~~cp~l~~c~~~~~~~~~~~~ 1213 (1237)
                      |.+.. +++..+....|.++..|+.|++++ ++++.+..+.|  +.+|.+|.+-++|..|+|...|..+|..-.
T Consensus       303 L~L~~-N~l~~v~~~~f~~ls~L~tL~L~~-N~it~~~~~aF~~~~~l~~l~l~~Np~~CnC~l~wl~~Wlr~~  374 (498)
T KOG4237|consen  303 LYLTR-NKLEFVSSGMFQGLSGLKTLSLYD-NQITTVAPGAFQTLFSLSTLNLLSNPFNCNCRLAWLGEWLRKK  374 (498)
T ss_pred             hhcCc-chHHHHHHHhhhccccceeeeecC-CeeEEEecccccccceeeeeehccCcccCccchHHHHHHHhhC
Confidence            99999 899999989999999999999999 68998887766  689999999999999999999999997653

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

Probab=99.22  E-value=2.8e-13  Score=123.10  Aligned_cols=101  Identities=32%  Similarity=0.384  Sum_probs=59.4

Q ss_pred             CCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEec
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI  477 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l  477 (1237)
                      .+.++..|.|++|.++.+|+.+..+.+|++|++++|+|+++|.+++.+++|+.|++.-| .+..+|.+||.++-|+.||+
T Consensus        31 ~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nnqie~lp~~issl~klr~lnvgmn-rl~~lprgfgs~p~levldl  109 (264)
T KOG0617|consen   31 NMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQIEELPTSISSLPKLRILNVGMN-RLNILPRGFGSFPALEVLDL  109 (264)
T ss_pred             chhhhhhhhcccCceeecCCcHHHhhhhhhhhcccchhhhcChhhhhchhhhheecchh-hhhcCccccCCCchhhhhhc
Confidence            34555556666666666666666666666666666666666666666666666666655 55566666666666666666


Q ss_pred             cCCCc-cccCccccccccccccc
Q 000887          478 EGASA-LRELPLGMKELKCLRTL  499 (1237)
Q Consensus       478 ~~~~~-l~~ip~~~~~L~~L~~L  499 (1237)
                      ..|+- -..+|..|-.|+.|+-|
T Consensus       110 tynnl~e~~lpgnff~m~tlral  132 (264)
T KOG0617|consen  110 TYNNLNENSLPGNFFYMTTLRAL  132 (264)
T ss_pred             cccccccccCCcchhHHHHHHHH
Confidence            65521 12345444444444444

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

Probab=99.22  E-value=7.9e-13  Score=120.19  Aligned_cols=90  Identities=29%  Similarity=0.396  Sum_probs=81.4

Q ss_pred             cccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccCCCccccCccccccc
Q 000887          414 EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKEL  493 (1237)
Q Consensus       414 ~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~~ip~~~~~L  493 (1237)
                      ++|. +-++.+...|.|++|.+..+|+.|..|.+|+.|++.+| .++++|.+|+.|++|++|+++-| ++..+|++|+.+
T Consensus        25 ~~~g-Lf~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nn-qie~lp~~issl~klr~lnvgmn-rl~~lprgfgs~  101 (264)
T KOG0617|consen   25 ELPG-LFNMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNN-QIEELPTSISSLPKLRILNVGMN-RLNILPRGFGSF  101 (264)
T ss_pred             hccc-ccchhhhhhhhcccCceeecCCcHHHhhhhhhhhcccc-hhhhcChhhhhchhhhheecchh-hhhcCccccCCC
Confidence            3444 45788899999999999999999999999999999998 99999999999999999999998 899999999999


Q ss_pred             ccccccceeeecc
Q 000887          494 KCLRTLTNFIVGK  506 (1237)
Q Consensus       494 ~~L~~L~~~~~~~  506 (1237)
                      +.|+.|++..+..
T Consensus       102 p~levldltynnl  114 (264)
T KOG0617|consen  102 PALEVLDLTYNNL  114 (264)
T ss_pred             chhhhhhcccccc
Confidence            9999998865543

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

Probab=99.19  E-value=1.2e-12  Score=135.54  Aligned_cols=113  Identities=21%  Similarity=0.270  Sum_probs=64.7

Q ss_pred             CCcchhhhhcCCCCCccEEEccccccccc-cccccCCCCCCeEEccC-CCccccch-hhcccCCccEEEcCccccCccCC
Q 000887          387 ISPMVLSDLLPQCKKLRVLSLGSYCITEV-PISIGCLKQLRYLNFSR-SEIQCLPD-AICSLFNLEILILRNCWCLLKLP  463 (1237)
Q Consensus       387 ~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~~~~l~~Lr~L~L~~-~~i~~lp~-~i~~L~~L~~L~L~~~~~l~~lp  463 (1237)
                      .+..+|+.+|+.+++||.|||+.|+|+.+ |+.|..+..|-.|-+.+ |.|+++|. .|++|..|+.|.+.-| .+.-++
T Consensus        78 ~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLllNan-~i~Cir  156 (498)
T KOG4237|consen   78 QISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQRLLLNAN-HINCIR  156 (498)
T ss_pred             CcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHHHhcChh-hhcchh
Confidence            34556666666666666666666666655 55565555555544444 56666655 5666666666666555 444443


Q ss_pred             hh-hcccccccEEeccCCCccccCccc-ccccccccccce
Q 000887          464 SR-IGNLVNLHYLNIEGASALRELPLG-MKELKCLRTLTN  501 (1237)
Q Consensus       464 ~~-i~~L~~L~~L~l~~~~~l~~ip~~-~~~L~~L~~L~~  501 (1237)
                      .. +..|++|..|.+.+| .++.++.+ +..+.+++++.+
T Consensus       157 ~~al~dL~~l~lLslyDn-~~q~i~~~tf~~l~~i~tlhl  195 (498)
T KOG4237|consen  157 QDALRDLPSLSLLSLYDN-KIQSICKGTFQGLAAIKTLHL  195 (498)
T ss_pred             HHHHHHhhhcchhcccch-hhhhhccccccchhccchHhh
Confidence            33 456666666666665 55556553 555556655544

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.17  E-value=8.4e-11  Score=141.72  Aligned_cols=83  Identities=20%  Similarity=0.336  Sum_probs=63.0

Q ss_pred             CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccC
Q 000887          400 KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG  479 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~  479 (1237)
                      .+..+|+++++.++.+|..+.  ++|+.|+|++|.++.+|..+.  .+|++|++++| .+..+|..+.  .+|+.|++++
T Consensus       178 ~~~~~L~L~~~~LtsLP~~Ip--~~L~~L~Ls~N~LtsLP~~l~--~nL~~L~Ls~N-~LtsLP~~l~--~~L~~L~Ls~  250 (754)
T PRK15370        178 NNKTELRLKILGLTTIPACIP--EQITTLILDNNELKSLPENLQ--GNIKTLYANSN-QLTSIPATLP--DTIQEMELSI  250 (754)
T ss_pred             cCceEEEeCCCCcCcCCcccc--cCCcEEEecCCCCCcCChhhc--cCCCEEECCCC-ccccCChhhh--ccccEEECcC
Confidence            356788888888888887664  578888888888888887654  48888888887 6778887653  4688888888


Q ss_pred             CCccccCcccc
Q 000887          480 ASALRELPLGM  490 (1237)
Q Consensus       480 ~~~l~~ip~~~  490 (1237)
                      | .+..+|..+
T Consensus       251 N-~L~~LP~~l  260 (754)
T PRK15370        251 N-RITELPERL  260 (754)
T ss_pred             C-ccCcCChhH
Confidence            8 566777654

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.11  E-value=1.6e-10  Score=139.45  Aligned_cols=92  Identities=17%  Similarity=0.292  Sum_probs=75.2

Q ss_pred             CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccC
Q 000887          400 KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG  479 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~  479 (1237)
                      ++|+.|+|++|.++.+|..+.  .+|++|++++|.++.+|..+.  .+|+.|+|++| .+..+|..+.  .+|+.|++++
T Consensus       199 ~~L~~L~Ls~N~LtsLP~~l~--~nL~~L~Ls~N~LtsLP~~l~--~~L~~L~Ls~N-~L~~LP~~l~--s~L~~L~Ls~  271 (754)
T PRK15370        199 EQITTLILDNNELKSLPENLQ--GNIKTLYANSNQLTSIPATLP--DTIQEMELSIN-RITELPERLP--SALQSLDLFH  271 (754)
T ss_pred             cCCcEEEecCCCCCcCChhhc--cCCCEEECCCCccccCChhhh--ccccEEECcCC-ccCcCChhHh--CCCCEEECcC
Confidence            478999999999999987664  589999999999999988664  47999999998 7888998775  5899999998


Q ss_pred             CCccccCcccccccccccccce
Q 000887          480 ASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       480 ~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      | .+..+|..+.  .+|+.|++
T Consensus       272 N-~L~~LP~~l~--~sL~~L~L  290 (754)
T PRK15370        272 N-KISCLPENLP--EELRYLSV  290 (754)
T ss_pred             C-ccCccccccC--CCCcEEEC
Confidence            8 7888887653  36666654

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

Probab=99.09  E-value=2.4e-12  Score=134.69  Aligned_cols=90  Identities=11%  Similarity=0.276  Sum_probs=58.9

Q ss_pred             cceeEEEEecCCCccccccccccccccCCCCccceeEecCCCCceecCCC---CCCCCccEEEecCCcchhhhh-hhccc
Q 000887          777 QKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKA---CFLPNLSEITIQDCNALASLT-DGMIY  852 (1237)
Q Consensus       777 ~~L~~L~l~~c~~l~~~~~~~~~~~~~~~l~~L~~L~l~~~~~l~~~~~~---~~~~~L~~L~l~~c~~l~~~~-~~~~~  852 (1237)
                      ..|+.|.+++|....    +..+......+|+++.|.+.+|.++++..-.   ..+++|+.|.+..|..++... .....
T Consensus       138 g~lk~LSlrG~r~v~----~sslrt~~~~CpnIehL~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~  213 (483)
T KOG4341|consen  138 GFLKELSLRGCRAVG----DSSLRTFASNCPNIEHLALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAE  213 (483)
T ss_pred             cccccccccccccCC----cchhhHHhhhCCchhhhhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHH
Confidence            356777777776543    2223334566778888888887766654322   237788888888887777633 23445


Q ss_pred             cCCccceeeccCCCCccc
Q 000887          853 NNARLEVLRIKRCDSLTS  870 (1237)
Q Consensus       853 ~~~~L~~L~l~~c~~l~~  870 (1237)
                      .+++|++|+++.|+.+..
T Consensus       214 gC~kL~~lNlSwc~qi~~  231 (483)
T KOG4341|consen  214 GCRKLKYLNLSWCPQISG  231 (483)
T ss_pred             hhhhHHHhhhccCchhhc
Confidence            678888888888877765

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

Probab=99.07  E-value=9.4e-09  Score=112.21  Aligned_cols=182  Identities=17%  Similarity=0.129  Sum_probs=114.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH-----
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET-----   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~-----   87 (1237)
                      .++++|+|++|+||||+++.++.......+ .++|+ +....+..+++..++..++.+... .+.......+.+.     
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~-~~~~~~~~~l~~~l~~~~  119 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERV-VAAKL-VNTRVDAEDLLRMVAADFGLETEG-RDKAALLRELEDFLIEQF  119 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCe-EEeee-eCCCCCHHHHHHHHHHHcCCCCCC-CCHHHHHHHHHHHHHHHH
Confidence            458999999999999999998875332211 12233 233446678888888888765332 2222233333322     


Q ss_pred             hcCCcEEEEEeCCCCCChhhHHHhhcccc---CCCCCcEEEEEeCchhHHHhh----------cCCCeEeCCCCChhhhH
Q 000887           88 VFKKKFLIVLDDVWSERYDLWQALKSPFM---AGAPGSRIIVTTRSMDVALTM----------GSGKNYELKLLSDDDCW  154 (1237)
Q Consensus        88 l~~~~~LlvlDdv~~~~~~~~~~~~~~~~---~~~~~~~iliTtR~~~~~~~~----------~~~~~~~l~~l~~~ea~  154 (1237)
                      ..+++.++|+||++......++.+.....   .......|++|.... ....+          .....+++++++.+|..
T Consensus       120 ~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~~~e~~  198 (269)
T TIGR03015       120 AAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLDREETR  198 (269)
T ss_pred             hCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCCHHHHH
Confidence            25678999999997765445555433221   112233455665432 21111          11246789999999999


Q ss_pred             HHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          155 SVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       155 ~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      +++...+...+......-.+++.+.|++.++|.|..|+.++..+
T Consensus       199 ~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       199 EYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            99987764332211122336889999999999999999888776

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

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

Probab=99.03  E-value=6.1e-12  Score=131.74  Aligned_cols=276  Identities=17%  Similarity=0.244  Sum_probs=140.1

Q ss_pred             CccceeEecCCCCceecCCC---CCCCCccEEEecCCcchhhhh-hhccccCCccceeeccCCCCccccccc---CCCCC
Q 000887          807 TCLKDLLIGNCPTVVSLPKA---CFLPNLSEITIQDCNALASLT-DGMIYNNARLEVLRIKRCDSLTSISRE---HLPSS  879 (1237)
Q Consensus       807 ~~L~~L~l~~~~~l~~~~~~---~~~~~L~~L~l~~c~~l~~~~-~~~~~~~~~L~~L~l~~c~~l~~~~~~---~~~~~  879 (1237)
                      ..|++|.+.+|.....-+..   ..+|++++|.+.+|..++... ..+...+++|++|++..|..+++....   ...++
T Consensus       138 g~lk~LSlrG~r~v~~sslrt~~~~CpnIehL~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~k  217 (483)
T KOG4341|consen  138 GFLKELSLRGCRAVGDSSLRTFASNCPNIEHLALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAEGCRK  217 (483)
T ss_pred             cccccccccccccCCcchhhHHhhhCCchhhhhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHHhhhh
Confidence            46899999999876654432   238999999999998877632 233446889999999999888775433   22356


Q ss_pred             ccEEEEecCCCccccccccccccCCCCccccccCCCCCcccceeEEEEecCCCcc--cccCCCCCccceeeeeeecCCCc
Q 000887          880 LQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLT--CLWSGGRLPVTLKRLRIEDCSNF  957 (1237)
Q Consensus       880 L~~L~l~~c~~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~--~~~~~~~~~~~L~~L~l~~c~~l  957 (1237)
                      |+.+.++.|+.++                ...+.....++..++.+...+|..+.  .+-......+-            
T Consensus       218 L~~lNlSwc~qi~----------------~~gv~~~~rG~~~l~~~~~kGC~e~~le~l~~~~~~~~~------------  269 (483)
T KOG4341|consen  218 LKYLNLSWCPQIS----------------GNGVQALQRGCKELEKLSLKGCLELELEALLKAAAYCLE------------  269 (483)
T ss_pred             HHHhhhccCchhh----------------cCcchHHhccchhhhhhhhcccccccHHHHHHHhccChH------------
Confidence            7777777776554                12233334444445555555554332  11111222233            


Q ss_pred             cccCcCCCCCCcccEEEEcCCCCccccc--cccCCcccccEEeecccccccccc--ccccCCCCCceeeeccCCCcccCC
Q 000887          958 KVLTSECQLPVEVEELTIYGCSNLESIA--ERFHDDACLRSIWISSCENLKSLP--KGLSNLSHLHEIRIVRCHNLVSLP 1033 (1237)
Q Consensus       958 ~~l~~~~~~~~~L~~L~l~~c~~~~~~~--~~~~~l~~L~~L~l~~~~~l~~l~--~~l~~l~~L~~L~l~~c~~l~~l~ 1033 (1237)
                                  +.++++..|..+.+..  ..-..+..|+.|..++|..++..+  .--+++.+|+.|.+.+|..+++..
T Consensus       270 ------------i~~lnl~~c~~lTD~~~~~i~~~c~~lq~l~~s~~t~~~d~~l~aLg~~~~~L~~l~l~~c~~fsd~~  337 (483)
T KOG4341|consen  270 ------------ILKLNLQHCNQLTDEDLWLIACGCHALQVLCYSSCTDITDEVLWALGQHCHNLQVLELSGCQQFSDRG  337 (483)
T ss_pred             ------------hhccchhhhccccchHHHHHhhhhhHhhhhcccCCCCCchHHHHHHhcCCCceEEEeccccchhhhhh
Confidence                        3344444444443322  222344555666666655544322  122445666666666666555433


Q ss_pred             CCCCC---Ccchhhhhhcccccccc---CCCCCCCcccEEeccCCCCccccCCC------CCCCCcCceEecCCCCcccc
Q 000887         1034 EDALP---SNVVDVLIEDCDKLKAL---IPTGTLSSLRELALSECPGIVVFPEE------GLSTNLTDLEISGDNMYKPL 1101 (1237)
Q Consensus      1034 ~~~~~---~~l~~l~l~~~~~~~~~---~~~~~l~~L~~L~l~~c~~l~~~~~~------~~~~~L~~L~l~~~~~~~~~ 1101 (1237)
                      .....   ..|+.+++..|......   ....+++.|+.|.+++|..++.-.+-      .....|+.+.+++|+.+++-
T Consensus       338 ft~l~rn~~~Le~l~~e~~~~~~d~tL~sls~~C~~lr~lslshce~itD~gi~~l~~~~c~~~~l~~lEL~n~p~i~d~  417 (483)
T KOG4341|consen  338 FTMLGRNCPHLERLDLEECGLITDGTLASLSRNCPRLRVLSLSHCELITDEGIRHLSSSSCSLEGLEVLELDNCPLITDA  417 (483)
T ss_pred             hhhhhcCChhhhhhcccccceehhhhHhhhccCCchhccCChhhhhhhhhhhhhhhhhccccccccceeeecCCCCchHH
Confidence            22211   22333333333322111   11135666666666666544433111      11334444444444444333


Q ss_pred             cccccCCCCCCceEEEcCCCC
Q 000887         1102 VKWGFHKLTSLRKLYIDGCSD 1122 (1237)
Q Consensus      1102 ~~~~~~~l~~L~~L~l~~c~~ 1122 (1237)
                      ....+..+++|+.+++.+|..
T Consensus       418 ~Le~l~~c~~Leri~l~~~q~  438 (483)
T KOG4341|consen  418 TLEHLSICRNLERIELIDCQD  438 (483)
T ss_pred             HHHHHhhCcccceeeeechhh
Confidence            222333444444444444443

>PF05729 NACHT: NACHT domain

Probab=99.01  E-value=1.8e-09  Score=108.43  Aligned_cols=143  Identities=22%  Similarity=0.292  Sum_probs=88.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccC-----CCCeEEEEEcCCcCHH---HHHHHHHHHhhccCCCccCHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEA-----FEPKAWVCVSDDFDVL---RISKAILDSIKRSSCKLEDLNSVQLELK   85 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~-----f~~~~w~~~~~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~~l~   85 (1237)
                      |++.|+|.+|+|||+++++++.+.....     +..++|+.........   .+...+.......   ..........+ 
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~---~~~~~~~~~~~-   76 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPES---IAPIEELLQEL-   76 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccc---hhhhHHHHHHH-
Confidence            5899999999999999999987653322     3445566665443322   3444444433221   11112211111 


Q ss_pred             HHhcCCcEEEEEeCCCCCChh-------hHHHhhccccC--CCCCcEEEEEeCchhHH---HhhcCCCeEeCCCCChhhh
Q 000887           86 ETVFKKKFLIVLDDVWSERYD-------LWQALKSPFMA--GAPGSRIIVTTRSMDVA---LTMGSGKNYELKLLSDDDC  153 (1237)
Q Consensus        86 ~~l~~~~~LlvlDdv~~~~~~-------~~~~~~~~~~~--~~~~~~iliTtR~~~~~---~~~~~~~~~~l~~l~~~ea  153 (1237)
                       ..+.++++||+|++++....       .+..+...+..  ..++++++||+|.....   ........+++++|++++.
T Consensus        77 -~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~~~~~  155 (166)
T PF05729_consen   77 -LEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFSEEDI  155 (166)
T ss_pred             -HHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCCHHHH
Confidence             12468999999999653221       12222222222  26789999999987662   2234446899999999999


Q ss_pred             HHHHHHHh
Q 000887          154 WSVFVAHA  161 (1237)
Q Consensus       154 ~~l~~~~~  161 (1237)
                      .+++.+..
T Consensus       156 ~~~~~~~f  163 (166)
T PF05729_consen  156 KQYLRKYF  163 (166)
T ss_pred             HHHHHHHh
Confidence            99998764

>COG3903 Predicted ATPase [General function prediction only]

Probab=99.00  E-value=1.2e-09  Score=116.33  Aligned_cols=294  Identities=19%  Similarity=0.199  Sum_probs=193.3

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ...|.+.++|.||||||+++.++++  .+..| +++.+++...-.+...+.-.+...++....   +.+.....+.....
T Consensus        12 ~~~RlvtL~g~ggvgkttl~~~~a~--~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~---~g~~~~~~~~~~~~   86 (414)
T COG3903          12 TALRLVTLTGAGGVGKTTLALQAAH--AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQ---PGDSAVDTLVRRIG   86 (414)
T ss_pred             hhhheeeeeccCccceehhhhhhHh--HhhhcccceeeeeccccCchhHhHHHHHhhcccccc---cchHHHHHHHHHHh
Confidence            3468899999999999999999877  44555 456677777777888888888888876642   22344445666777


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCeEeCCCCChh-hhHHHHHHHhcCCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDD-DCWSVFVAHAFEGRDAG  168 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l~~l~~~-ea~~l~~~~~~~~~~~~  168 (1237)
                      ++|.++|+||.... .+...+....+....+...++.|+|.....   ..+....+++++.- ++.++|...+.......
T Consensus        87 ~rr~llvldncehl-~~~~a~~i~all~~~~~~~~~atsre~~l~---~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f  162 (414)
T COG3903          87 DRRALLVLDNCEHL-LDACAALIVALLGACPRLAILATSREAILV---AGEVHRRVPSLSLFDEAIELFVCRAVLVALSF  162 (414)
T ss_pred             hhhHHHHhcCcHHH-HHHHHHHHHHHHccchhhhhHHHhHhhhcc---cccccccCCccccCCchhHHHHHHHHHhccce
Confidence            89999999998321 234445555566667778899999975432   34456777777764 79999877664333221


Q ss_pred             -CCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCC-------HHHHHHHHhhcccccCCCCChhHHHHHHhhcChHHHH
Q 000887          169 -THGNFESTRQRVVEKCKGLPLAARALGGLLRSKQG-------VDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLK  240 (1237)
Q Consensus       169 -~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~-------~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~~L~~~~~  240 (1237)
                       -.........+|+++.+|.|++|..+++..+.-..       .+.|..+-+........+......+.+||.-|..-++
T Consensus       163 ~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe~  242 (414)
T COG3903         163 WLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWER  242 (414)
T ss_pred             eecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHHH
Confidence             12334678899999999999999999999876532       1223222222111111245677899999999999999


Q ss_pred             HHHhhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccccC-CCCCcchhhhHHHHHHhhh
Q 000887          241 RCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSS-NTESKYVMHDLVHDLAQWA  319 (1237)
Q Consensus       241 ~~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~~~-~~~~~~~~h~lv~~~~~~~  319 (1237)
                      -.|..++.|...|.....    .|.+-|-......+     ..-..+-.+++++++.-.+ .+...|+.-+-++.|+-..
T Consensus       243 ~~~~rLa~~~g~f~~~l~----~~~a~g~~~~~~~y-----~~~~a~~ll~~kslv~a~~~~~~a~~Rl~eT~r~Yalae  313 (414)
T COG3903         243 ALFGRLAVFVGGFDLGLA----LAVAAGADVDVPRY-----LVLLALTLLVDKSLVVALDLLGRARYRLLETGRRYALAE  313 (414)
T ss_pred             HHhcchhhhhhhhcccHH----HHHhcCCccccchH-----HHHHHHHHHhhccchhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            999999999888775522    23322211100011     1122345677777765432 2345677777777776554


Q ss_pred             ccc
Q 000887          320 SGE  322 (1237)
Q Consensus       320 ~~~  322 (1237)
                      ..+
T Consensus       314 L~r  316 (414)
T COG3903         314 LHR  316 (414)
T ss_pred             HHh
Confidence            433

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.95  E-value=6.4e-08  Score=112.12  Aligned_cols=273  Identities=14%  Similarity=0.084  Sum_probs=156.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcCHHHHHHHHHHHhhcc-C-CCccCHHHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIKRS-S-CKLEDLNSVQLELKET   87 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~i~~~l~~~-~-~~~~~~~~~~~~l~~~   87 (1237)
                      +..+.+.|+|++|+|||++++++++...... ...++++++....+...++..++.++... . ....+.++....+.+.
T Consensus        53 ~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~  132 (394)
T PRK00411         53 SRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEY  132 (394)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHH
Confidence            3445678999999999999999988542222 23466777777777888888999988652 1 1233556677777777


Q ss_pred             hc--CCcEEEEEeCCCCCC----hhhHHHhhccccCC-CCCcEEEEEeCchhHHHhhc-------CCCeEeCCCCChhhh
Q 000887           88 VF--KKKFLIVLDDVWSER----YDLWQALKSPFMAG-APGSRIIVTTRSMDVALTMG-------SGKNYELKLLSDDDC  153 (1237)
Q Consensus        88 l~--~~~~LlvlDdv~~~~----~~~~~~~~~~~~~~-~~~~~iliTtR~~~~~~~~~-------~~~~~~l~~l~~~ea  153 (1237)
                      +.  +++.+||+|+++.-.    .+.+..+...+... +.+..+|.++....+.....       ....+.+++++.++.
T Consensus       133 l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~  212 (394)
T PRK00411        133 LDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEI  212 (394)
T ss_pred             HHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHH
Confidence            65  356899999995421    12233333222211 11333666666543322211       124688999999999


Q ss_pred             HHHHHHHhcCCCCCCCCCChHHHHHHHHHHc----cCCchHHHHHHhH--hh--c-CC--CHHHHHHHHhhcccccCCCC
Q 000887          154 WSVFVAHAFEGRDAGTHGNFESTRQRVVEKC----KGLPLAARALGGL--LR--S-KQ--GVDEWRAILDSKIWNLQDKT  222 (1237)
Q Consensus       154 ~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~----~g~PLal~~~~~~--l~--~-~~--~~~~~~~~l~~~~~~~~~~~  222 (1237)
                      .+++..++.......  .-..++++.+++.+    |..+.|+.++-..  .+  + ..  +.+.+..+.+..        
T Consensus       213 ~~il~~r~~~~~~~~--~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~--------  282 (394)
T PRK00411        213 FDILKDRVEEGFYPG--VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS--------  282 (394)
T ss_pred             HHHHHHHHHhhcccC--CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH--------
Confidence            999988764221111  11134445555544    5567776665322  11  1 11  245555554432        


Q ss_pred             ChhHHHHHHhhcChHHHHHHHhhhccCCC--CcccChHHHHHH--HHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccc
Q 000887          223 EIPSVLKLSYHHLPSHLKRCFAYCAVLPK--DYEFKEKELVLL--WIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQK  298 (1237)
Q Consensus       223 ~i~~~l~~s~~~L~~~~~~~~~~la~~~~--~~~~~~~~l~~~--w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~  298 (1237)
                       -.....-.++.||.++|..+..++..-+  ...+....+...  .+++.+-..    .........++.+|...+++..
T Consensus       283 -~~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~~~----~~~~~~~~~~l~~L~~~glI~~  357 (394)
T PRK00411        283 -EIVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELGYE----PRTHTRFYEYINKLDMLGIINT  357 (394)
T ss_pred             -HHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcCCC----cCcHHHHHHHHHHHHhcCCeEE
Confidence             1233455688999999988877764421  123444444321  222211111    0112335567888888888875

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.76  E-value=1.1e-06  Score=100.75  Aligned_cols=276  Identities=13%  Similarity=0.080  Sum_probs=151.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhccccc--CC---CCeEEEEEcCCcCHHHHHHHHHHHhh---ccCC-CccCHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTE--AF---EPKAWVCVSDDFDVLRISKAILDSIK---RSSC-KLEDLNSVQ   81 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~--~f---~~~~w~~~~~~~~~~~~~~~i~~~l~---~~~~-~~~~~~~~~   81 (1237)
                      +..+.+.|+|++|+|||++++++++.....  ..   -.++|+++....+...++..++.++.   .... ...+.++..
T Consensus        38 ~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  117 (365)
T TIGR02928        38 SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVF  117 (365)
T ss_pred             CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHH
Confidence            344678999999999999999998754211  11   13568887777777888899999884   2211 222345555


Q ss_pred             HHHHHHhc--CCcEEEEEeCCCCCC---hhhHHHhhccc-cCC--CCCcEEEEEeCchhHHHhh----cC---CCeEeCC
Q 000887           82 LELKETVF--KKKFLIVLDDVWSER---YDLWQALKSPF-MAG--APGSRIIVTTRSMDVALTM----GS---GKNYELK  146 (1237)
Q Consensus        82 ~~l~~~l~--~~~~LlvlDdv~~~~---~~~~~~~~~~~-~~~--~~~~~iliTtR~~~~~~~~----~~---~~~~~l~  146 (1237)
                      ..+.+.+.  +++++||+|+++.-.   .+....+.... ...  +.+..+|.++........+    ..   ...+.++
T Consensus       118 ~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~  197 (365)
T TIGR02928       118 RRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFP  197 (365)
T ss_pred             HHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeC
Confidence            56666553  467899999995431   11122222210 111  1334555555544332111    11   2468899


Q ss_pred             CCChhhhHHHHHHHhcCCC-CCCCCCChHHHHHHHHHHccCCchHH-HHHHh--Hhh--c-C--CCHHHHHHHHhhcccc
Q 000887          147 LLSDDDCWSVFVAHAFEGR-DAGTHGNFESTRQRVVEKCKGLPLAA-RALGG--LLR--S-K--QGVDEWRAILDSKIWN  217 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~-~~~~~~~~~~~~~~i~~~~~g~PLal-~~~~~--~l~--~-~--~~~~~~~~~l~~~~~~  217 (1237)
                      +.+.+|..+++..++.... ...-+++..+.+.+++....|-|..+ .++-.  .+.  + .  -+.+...++.+..   
T Consensus       198 p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~---  274 (365)
T TIGR02928       198 PYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI---  274 (365)
T ss_pred             CCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH---
Confidence            9999999999998874211 11112222334455666667877443 32211  111  1 1  1233444333321   


Q ss_pred             cCCCCChhHHHHHHhhcChHHHHHHHhhhccCC--CCcccChHHHHHHH--HHcCCCccCcchhhHHHHHHHHHHHHhhc
Q 000887          218 LQDKTEIPSVLKLSYHHLPSHLKRCFAYCAVLP--KDYEFKEKELVLLW--IAEGLVQQSEDNKQLEDLGSGYFHDLLSR  293 (1237)
Q Consensus       218 ~~~~~~i~~~l~~s~~~L~~~~~~~~~~la~~~--~~~~~~~~~l~~~w--~~~g~~~~~~~~~~~~~~~~~~l~~L~~~  293 (1237)
                            -.....-++..||.+++.++..++..-  ++..+....+...+  +++.+ +   .....+.....++..|...
T Consensus       275 ------~~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~-~---~~~~~~~~~~~~l~~l~~~  344 (365)
T TIGR02928       275 ------EKDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDI-G---VDPLTQRRISDLLNELDML  344 (365)
T ss_pred             ------HHHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhc-C---CCCCcHHHHHHHHHHHHhc
Confidence                  123344567888988887777665321  23334444444421  12211 1   1112234566778899999


Q ss_pred             Cccccc
Q 000887          294 SLFQKS  299 (1237)
Q Consensus       294 ~ll~~~  299 (1237)
                      |++...
T Consensus       345 gli~~~  350 (365)
T TIGR02928       345 GLVEAE  350 (365)
T ss_pred             CCeEEE
Confidence            998863

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

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

Probab=98.68  E-value=1.1e-08  Score=99.54  Aligned_cols=101  Identities=28%  Similarity=0.327  Sum_probs=31.0

Q ss_pred             CCCCccEEEcccccccccccccc-CCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhh-cccccccEE
Q 000887          398 QCKKLRVLSLGSYCITEVPISIG-CLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRI-GNLVNLHYL  475 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~-~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i-~~L~~L~~L  475 (1237)
                      +..++|.|+|.+|.|+.+.. ++ .+.+|+.|+|++|.|+.++ .+..+++|++|++++| .+..+++.+ ..+++|++|
T Consensus        17 n~~~~~~L~L~~n~I~~Ie~-L~~~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~N-~I~~i~~~l~~~lp~L~~L   93 (175)
T PF14580_consen   17 NPVKLRELNLRGNQISTIEN-LGATLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSNN-RISSISEGLDKNLPNLQEL   93 (175)
T ss_dssp             -------------------S---TT-TT--EEE-TTS--S--T-T----TT--EEE--SS----S-CHHHHHH-TT--EE
T ss_pred             cccccccccccccccccccc-hhhhhcCCCEEECCCCCCcccc-CccChhhhhhcccCCC-CCCccccchHHhCCcCCEE
Confidence            34456777777777777643 43 5677777777777777774 4777777777777777 677776555 357777777


Q ss_pred             eccCCCccccCcc--ccccccccccccee
Q 000887          476 NIEGASALRELPL--GMKELKCLRTLTNF  502 (1237)
Q Consensus       476 ~l~~~~~l~~ip~--~~~~L~~L~~L~~~  502 (1237)
                      ++++| .+..+..  .++.+++|++|++.
T Consensus        94 ~L~~N-~I~~l~~l~~L~~l~~L~~L~L~  121 (175)
T PF14580_consen   94 YLSNN-KISDLNELEPLSSLPKLRVLSLE  121 (175)
T ss_dssp             E-TTS----SCCCCGGGGG-TT--EEE-T
T ss_pred             ECcCC-cCCChHHhHHHHcCCCcceeecc
Confidence            77777 5555532  24455555555553

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.67  E-value=6e-07  Score=100.19  Aligned_cols=252  Identities=15%  Similarity=0.124  Sum_probs=127.9

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-CccCH----HHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-KLEDL----NSVQLELK   85 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~----~~~~~~l~   85 (1237)
                      ...+.+.++|++|+|||++|+.+++.. ...   ..++... .......+..++..+..... -..+.    ......+.
T Consensus        49 ~~~~~~ll~GppG~GKT~la~~ia~~l-~~~---~~~~~~~-~~~~~~~l~~~l~~l~~~~vl~IDEi~~l~~~~~e~l~  123 (328)
T PRK00080         49 EALDHVLLYGPPGLGKTTLANIIANEM-GVN---IRITSGP-ALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILY  123 (328)
T ss_pred             CCCCcEEEECCCCccHHHHHHHHHHHh-CCC---eEEEecc-cccChHHHHHHHHhcccCCEEEEecHhhcchHHHHHHH
Confidence            345678999999999999999998853 211   1122211 11111112222222221110 00000    11122233


Q ss_pred             HHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhc--CCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           86 ETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMG--SGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        86 ~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~--~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                      ..+.+.+..+|+|+.....     .+...+   .+.+-|..|+|...+...+.  ....+++++++.+|..+++.+.+..
T Consensus       124 ~~~e~~~~~~~l~~~~~~~-----~~~~~l---~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~  195 (328)
T PRK00080        124 PAMEDFRLDIMIGKGPAAR-----SIRLDL---PPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARI  195 (328)
T ss_pred             HHHHhcceeeeeccCcccc-----ceeecC---CCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHH
Confidence            3444445555555542211     000011   22345666777544433221  1246899999999999999988764


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCHHHHHHHHhhcccccCCCCChhHHHHHHhhcChHHHHHHH
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHLPSHLKRCF  243 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~~L~~~~~~~~  243 (1237)
                      .....    .++++..|++.|+|.|-.+..+...+.      .|.............-......+...+..|++..+..+
T Consensus       196 ~~~~~----~~~~~~~ia~~~~G~pR~a~~~l~~~~------~~a~~~~~~~I~~~~v~~~l~~~~~~~~~l~~~~~~~l  265 (328)
T PRK00080        196 LGVEI----DEEGALEIARRSRGTPRIANRLLRRVR------DFAQVKGDGVITKEIADKALDMLGVDELGLDEMDRKYL  265 (328)
T ss_pred             cCCCc----CHHHHHHHHHHcCCCchHHHHHHHHHH------HHHHHcCCCCCCHHHHHHHHHHhCCCcCCCCHHHHHHH
Confidence            33222    257789999999999965554444322      12211110000000001122334556778888888877


Q ss_pred             h-hhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHH-HHhhcCcccc
Q 000887          244 A-YCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFH-DLLSRSLFQK  298 (1237)
Q Consensus       244 ~-~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~-~L~~~~ll~~  298 (1237)
                      . ....|+++ .+..+.+....      +.  +    .+.+++.++ .|++.++++.
T Consensus       266 ~~~~~~~~~~-~~~~~~~a~~l------g~--~----~~~~~~~~e~~Li~~~li~~  309 (328)
T PRK00080        266 RTIIEKFGGG-PVGLDTLAAAL------GE--E----RDTIEDVYEPYLIQQGFIQR  309 (328)
T ss_pred             HHHHHHcCCC-ceeHHHHHHHH------CC--C----cchHHHHhhHHHHHcCCccc
Confidence            6 55666655 45544443321      11  1    123444566 8999999974

>PRK06893 DNA replication initiation factor; Validated

Probab=98.64  E-value=2.7e-07  Score=96.64  Aligned_cols=155  Identities=19%  Similarity=0.210  Sum_probs=96.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +.+.|+|++|+|||+||.++++...+. ...+.|+.+.....   ...                     .+.+.++ +.-
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~-~~~~~y~~~~~~~~---~~~---------------------~~~~~~~-~~d   93 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLN-QRTAIYIPLSKSQY---FSP---------------------AVLENLE-QQD   93 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc-CCCeEEeeHHHhhh---hhH---------------------HHHhhcc-cCC
Confidence            578999999999999999999865443 33567776531100   000                     1111112 335


Q ss_pred             EEEEeCCCCCC-hhhHH-HhhccccCC-CCCcEEE-EEeCc---------hhHHHhhcCCCeEeCCCCChhhhHHHHHHH
Q 000887           94 LIVLDDVWSER-YDLWQ-ALKSPFMAG-APGSRII-VTTRS---------MDVALTMGSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        94 LlvlDdv~~~~-~~~~~-~~~~~~~~~-~~~~~il-iTtR~---------~~~~~~~~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      +||+||+|... ...|. .+...+... ..|..++ +|++.         +.+..++.....+++++++.++.++++++.
T Consensus        94 lLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~  173 (229)
T PRK06893         94 LVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRN  173 (229)
T ss_pred             EEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHH
Confidence            89999997632 12333 222222221 2355554 55544         345555555678999999999999999988


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      +.......+    +++..-|++++.|-.-++..+-..+
T Consensus       174 a~~~~l~l~----~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        174 AYQRGIELS----DEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             HHHcCCCCC----HHHHHHHHHhccCCHHHHHHHHHHH
Confidence            864432222    6778899999988777666554443

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.64  E-value=9e-07  Score=98.38  Aligned_cols=243  Identities=17%  Similarity=0.100  Sum_probs=128.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC------CccCHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC------KLEDLNSVQLEL   84 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~------~~~~~~~~~~~l   84 (1237)
                      ..++.+.++|++|+|||+||+++++... ..   ...+..........+ ...+..++....      ...+ .+....+
T Consensus        28 ~~~~~~ll~Gp~G~GKT~la~~ia~~~~-~~---~~~~~~~~~~~~~~l-~~~l~~~~~~~vl~iDEi~~l~-~~~~e~l  101 (305)
T TIGR00635        28 EALDHLLLYGPPGLGKTTLAHIIANEMG-VN---LKITSGPALEKPGDL-AAILTNLEEGDVLFIDEIHRLS-PAVEELL  101 (305)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHhC-CC---EEEeccchhcCchhH-HHHHHhcccCCEEEEehHhhhC-HHHHHHh
Confidence            3456688999999999999999987532 11   112221111111111 122222221110      0001 1122334


Q ss_pred             HHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhc--CCCeEeCCCCChhhhHHHHHHHhc
Q 000887           85 KETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMG--SGKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~--~~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                      ...+.+.+..+|+|+.....     .+...+   .+.+-|..|+|...+...+.  ....+++++++.+|..+++.+.+.
T Consensus       102 ~~~~~~~~~~~v~~~~~~~~-----~~~~~~---~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~  173 (305)
T TIGR00635       102 YPAMEDFRLDIVIGKGPSAR-----SVRLDL---PPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAG  173 (305)
T ss_pred             hHHHhhhheeeeeccCcccc-----ceeecC---CCeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHH
Confidence            44555555566666553221     111111   23455667777654433221  124678999999999999998875


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhc------CC--CHHHHHHHHhhcccccCCCCChhHHHHHHhhc
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRS------KQ--GVDEWRAILDSKIWNLQDKTEIPSVLKLSYHH  234 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~------~~--~~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~~  234 (1237)
                      .....    -.++++..|++.++|.|-.+..++..+..      ..  +.+.....              ...+...+..
T Consensus       174 ~~~~~----~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~--------------l~~l~~~~~~  235 (305)
T TIGR00635       174 LLNVE----IEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKA--------------LEMLMIDELG  235 (305)
T ss_pred             HhCCC----cCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHH--------------HHHhCCCCCC
Confidence            43222    22667889999999999776555543211      00  11111111              1124455778


Q ss_pred             ChHHHHHHHh-hhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHH-HHhhcCcccc
Q 000887          235 LPSHLKRCFA-YCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFH-DLLSRSLFQK  298 (1237)
Q Consensus       235 L~~~~~~~~~-~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~-~L~~~~ll~~  298 (1237)
                      +++..+..+. .++.++++ .+....+....   |.         ....+...++ .|++++++..
T Consensus       236 l~~~~~~~L~al~~~~~~~-~~~~~~ia~~l---g~---------~~~~~~~~~e~~Li~~~li~~  288 (305)
T TIGR00635       236 LDEIDRKLLSVLIEQFQGG-PVGLKTLAAAL---GE---------DADTIEDVYEPYLLQIGFLQR  288 (305)
T ss_pred             CCHHHHHHHHHHHHHhCCC-cccHHHHHHHh---CC---------CcchHHHhhhHHHHHcCCccc
Confidence            8888877777 44666543 44443333221   11         1123455577 6999999964

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

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

Probab=98.62  E-value=4.1e-08  Score=95.62  Aligned_cols=105  Identities=28%  Similarity=0.332  Sum_probs=55.6

Q ss_pred             CCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhh-cccCCccEEEcCccccCccCCh--hhcccccccE
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAI-CSLFNLEILILRNCWCLLKLPS--RIGNLVNLHY  474 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i-~~L~~L~~L~L~~~~~l~~lp~--~i~~L~~L~~  474 (1237)
                      .+.+|++|+|++|.|+.++. +..++.|++|++++|.|.++++.+ ..+++|+.|++++| .+..+-.  .+..+++|++
T Consensus        40 ~l~~L~~L~Ls~N~I~~l~~-l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~L~~L~L~~N-~I~~l~~l~~L~~l~~L~~  117 (175)
T PF14580_consen   40 TLDKLEVLDLSNNQITKLEG-LPGLPRLKTLDLSNNRISSISEGLDKNLPNLQELYLSNN-KISDLNELEPLSSLPKLRV  117 (175)
T ss_dssp             T-TT--EEE-TTS--S--TT-----TT--EEE--SS---S-CHHHHHH-TT--EEE-TTS----SCCCCGGGGG-TT--E
T ss_pred             hhcCCCEEECCCCCCccccC-ccChhhhhhcccCCCCCCccccchHHhCCcCCEEECcCC-cCCChHHhHHHHcCCCcce
Confidence            67899999999999999975 888999999999999999997655 47999999999998 6665543  3678999999


Q ss_pred             EeccCCCccccCccc----ccccccccccceeeec
Q 000887          475 LNIEGASALRELPLG----MKELKCLRTLTNFIVG  505 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~----~~~L~~L~~L~~~~~~  505 (1237)
                      |++.+| .+...+..    +..+++|+.|+...+.
T Consensus       118 L~L~~N-Pv~~~~~YR~~vi~~lP~Lk~LD~~~V~  151 (175)
T PF14580_consen  118 LSLEGN-PVCEKKNYRLFVIYKLPSLKVLDGQDVT  151 (175)
T ss_dssp             EE-TT--GGGGSTTHHHHHHHH-TT-SEETTEETT
T ss_pred             eeccCC-cccchhhHHHHHHHHcChhheeCCEEcc
Confidence            999999 55555532    7788999999765544

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

Probab=98.58  E-value=2.3e-07  Score=99.32  Aligned_cols=177  Identities=20%  Similarity=0.175  Sum_probs=90.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHH---------HHHHHhhccCC----------C
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISK---------AILDSIKRSSC----------K   73 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~---------~i~~~l~~~~~----------~   73 (1237)
                      .+.+.|+|+.|+|||+|++++.+......+ .++|+.............         .+...+.....          .
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~-~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   98 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGY-KVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDL   98 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EE-CCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCC-cEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcc
Confidence            468999999999999999998875433333 455555544432221111         11222222111          1


Q ss_pred             ccCHHHHHHHHHHHhc--CCcEEEEEeCCCCCC------hhhHHHhhccccC--CCCCcEEEEEeCchhHHHh-------
Q 000887           74 LEDLNSVQLELKETVF--KKKFLIVLDDVWSER------YDLWQALKSPFMA--GAPGSRIIVTTRSMDVALT-------  136 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~l~--~~~~LlvlDdv~~~~------~~~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~-------  136 (1237)
                      .....+....+.+.+.  +++++||+|++....      ......+...+..  ...+..++++.........       
T Consensus        99 ~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~~~~~~~~~~  178 (234)
T PF01637_consen   99 SEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSSDSLMEEFLDDKSP  178 (234)
T ss_dssp             -GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESSHHHHHHTT-TTST
T ss_pred             hhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCchHHHHHhhcccCc
Confidence            1122333333333333  245999999995433      1112222222222  2334445555554444332       


Q ss_pred             -hcCCCeEeCCCCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          137 -MGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       137 -~~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                       ......+.+++|+.+|+++++....... ...  +...+..++|++.+||+|..|..
T Consensus       179 ~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~--~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  179 LFGRFSHIELKPLSKEEAREFLKELFKEL-IKL--PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             TTT---EEEE----HHHHHHHHHHHHHCC---------HHHHHHHHHHHTT-HHHHHH
T ss_pred             cccccceEEEeeCCHHHHHHHHHHHHHHh-hcc--cCCHHHHHHHHHHhCCCHHHHhc
Confidence             1222459999999999999999876433 111  12366779999999999998864

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

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

Probab=98.58  E-value=1.5e-07  Score=89.78  Aligned_cols=117  Identities=15%  Similarity=0.227  Sum_probs=81.4

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhccccc----CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTE----AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET   87 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~----~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~   87 (1237)
                      +-+++.|+|.+|+|||+++.+++......    .-..++|+.+....+...+...++.+++.........++....+.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDA   82 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHH
Confidence            34789999999999999999988754221    13457799998888999999999999998766656777888888888


Q ss_pred             hcCCc-EEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCc
Q 000887           88 VFKKK-FLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRS  130 (1237)
Q Consensus        88 l~~~~-~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~  130 (1237)
                      +.+.+ .+||+|+++.- ....++.+.....  ..+.++|+..+.
T Consensus        83 l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   83 LDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            77654 59999999543 3333334433222  667788887765

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

Probab=98.57  E-value=3.9e-09  Score=115.21  Aligned_cols=98  Identities=35%  Similarity=0.568  Sum_probs=50.8

Q ss_pred             CCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEecc
Q 000887          399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       399 ~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      +-.|..|.|..|.+..+|..++++..|.+|||+.|++..+|..++.|+ |+.|-+++| +++.+|++|+.+..|.+||.+
T Consensus        97 f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lp-Lkvli~sNN-kl~~lp~~ig~~~tl~~ld~s  174 (722)
T KOG0532|consen   97 FVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGLCDLP-LKVLIVSNN-KLTSLPEEIGLLPTLAHLDVS  174 (722)
T ss_pred             HHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhhhcCc-ceeEEEecC-ccccCCcccccchhHHHhhhh
Confidence            334444555555555555555555555555555555555555444443 455555554 555555555555555555555


Q ss_pred             CCCccccCccccccccccccc
Q 000887          479 GASALRELPLGMKELKCLRTL  499 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L~~L  499 (1237)
                      .| .+..+|..++.+.+|+.|
T Consensus       175 ~n-ei~slpsql~~l~slr~l  194 (722)
T KOG0532|consen  175 KN-EIQSLPSQLGYLTSLRDL  194 (722)
T ss_pred             hh-hhhhchHHhhhHHHHHHH
Confidence            55 455555555555555544

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

Probab=98.53  E-value=1.7e-08  Score=113.82  Aligned_cols=108  Identities=23%  Similarity=0.228  Sum_probs=71.7

Q ss_pred             hhhcCCCCCccEEEccccccc-----cccccccCCCCCCeEEccCCCccc-------cchhhcccCCccEEEcCccccCc
Q 000887          393 SDLLPQCKKLRVLSLGSYCIT-----EVPISIGCLKQLRYLNFSRSEIQC-------LPDAICSLFNLEILILRNCWCLL  460 (1237)
Q Consensus       393 ~~~~~~~~~Lr~L~L~~~~i~-----~lp~~~~~l~~Lr~L~L~~~~i~~-------lp~~i~~L~~L~~L~L~~~~~l~  460 (1237)
                      ...|..+..|++|+++++.++     .++..+...+.|+.|+++++.+..       ++..+..+.+|++|++++|....
T Consensus        16 ~~~~~~l~~L~~l~l~~~~l~~~~~~~i~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~   95 (319)
T cd00116          16 TELLPKLLCLQVLRLEGNTLGEEAAKALASALRPQPSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSDNALGP   95 (319)
T ss_pred             HHHHHHHhhccEEeecCCCCcHHHHHHHHHHHhhCCCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccCCCCCh
Confidence            455666777888888888873     355666777788888888876652       34467778888888888884444


Q ss_pred             cCChhhccccc---ccEEeccCCCccc-----cCccccccc-ccccccce
Q 000887          461 KLPSRIGNLVN---LHYLNIEGASALR-----ELPLGMKEL-KCLRTLTN  501 (1237)
Q Consensus       461 ~lp~~i~~L~~---L~~L~l~~~~~l~-----~ip~~~~~L-~~L~~L~~  501 (1237)
                      ..+..+..+.+   |++|++++|. +.     .+...+..+ ++|+.|++
T Consensus        96 ~~~~~~~~l~~~~~L~~L~ls~~~-~~~~~~~~l~~~l~~~~~~L~~L~L  144 (319)
T cd00116          96 DGCGVLESLLRSSSLQELKLNNNG-LGDRGLRLLAKGLKDLPPALEKLVL  144 (319)
T ss_pred             hHHHHHHHHhccCcccEEEeeCCc-cchHHHHHHHHHHHhCCCCceEEEc
Confidence            45555665555   8888888873 33     122234444 55666654

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

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

Probab=98.52  E-value=6.6e-08  Score=112.20  Aligned_cols=105  Identities=33%  Similarity=0.451  Sum_probs=93.9

Q ss_pred             CCCCCccEEEccccccccccccccCCC-CCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEE
Q 000887          397 PQCKKLRVLSLGSYCITEVPISIGCLK-QLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYL  475 (1237)
Q Consensus       397 ~~~~~Lr~L~L~~~~i~~lp~~~~~l~-~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L  475 (1237)
                      ...+.+..|++.+|.++++|+....+. +|+.|++++|.+..+|..++.+++|+.|++++| .+..+|...+.+.+|+.|
T Consensus       113 ~~~~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N-~l~~l~~~~~~~~~L~~L  191 (394)
T COG4886         113 LELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFN-DLSDLPKLLSNLSNLNNL  191 (394)
T ss_pred             hcccceeEEecCCcccccCccccccchhhcccccccccchhhhhhhhhccccccccccCCc-hhhhhhhhhhhhhhhhhe
Confidence            445789999999999999998888875 999999999999999988999999999999998 999999988899999999


Q ss_pred             eccCCCccccCcccccccccccccceee
Q 000887          476 NIEGASALRELPLGMKELKCLRTLTNFI  503 (1237)
Q Consensus       476 ~l~~~~~l~~ip~~~~~L~~L~~L~~~~  503 (1237)
                      ++++| .+..+|..++.+..|++|.+..
T Consensus       192 ~ls~N-~i~~l~~~~~~~~~L~~l~~~~  218 (394)
T COG4886         192 DLSGN-KISDLPPEIELLSALEELDLSN  218 (394)
T ss_pred             eccCC-ccccCchhhhhhhhhhhhhhcC
Confidence            99999 8999998877777788886633

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

Probab=98.50  E-value=2.7e-08  Score=112.23  Aligned_cols=109  Identities=21%  Similarity=0.154  Sum_probs=76.1

Q ss_pred             hhhhhcCCCCCccEEEcccccccc-------ccccccCCCCCCeEEccCCCcc-ccchhhcccCC---ccEEEcCccccC
Q 000887          391 VLSDLLPQCKKLRVLSLGSYCITE-------VPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFN---LEILILRNCWCL  459 (1237)
Q Consensus       391 ~~~~~~~~~~~Lr~L~L~~~~i~~-------lp~~~~~l~~Lr~L~L~~~~i~-~lp~~i~~L~~---L~~L~L~~~~~l  459 (1237)
                      .++..+...+.++.|+++++.+..       ++..+..+++|+.|++++|.+. ..+..+..+.+   |++|++++| .+
T Consensus        42 ~i~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~-~~  120 (319)
T cd00116          42 ALASALRPQPSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNN-GL  120 (319)
T ss_pred             HHHHHHhhCCCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCC-cc
Confidence            345567778889999999887763       3455677889999999999887 34555666655   999999998 44


Q ss_pred             c-----cCChhhccc-ccccEEeccCCCccc-----cCcccccccccccccce
Q 000887          460 L-----KLPSRIGNL-VNLHYLNIEGASALR-----ELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       460 ~-----~lp~~i~~L-~~L~~L~l~~~~~l~-----~ip~~~~~L~~L~~L~~  501 (1237)
                      .     .++..+..+ .+|+.|++++|. +.     .++..+..+++|++|++
T Consensus       121 ~~~~~~~l~~~l~~~~~~L~~L~L~~n~-l~~~~~~~~~~~~~~~~~L~~L~l  172 (319)
T cd00116         121 GDRGLRLLAKGLKDLPPALEKLVLGRNR-LEGASCEALAKALRANRDLKELNL  172 (319)
T ss_pred             chHHHHHHHHHHHhCCCCceEEEcCCCc-CCchHHHHHHHHHHhCCCcCEEEC
Confidence            3     233445666 889999999983 44     23334555566666654

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

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.49  E-value=9.3e-06  Score=95.26  Aligned_cols=151  Identities=11%  Similarity=0.041  Sum_probs=88.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc----ccCCC--CeEEEEEcCCcCHHHHHHHHHHHhhccC-CCccCHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL----TEAFE--PKAWVCVSDDFDVLRISKAILDSIKRSS-CKLEDLNSVQLELK   85 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~----~~~f~--~~~w~~~~~~~~~~~~~~~i~~~l~~~~-~~~~~~~~~~~~l~   85 (1237)
                      ..++.|+|++|+|||++++.|.....    +...+  .+++|++..-.+...++..|+.++.... .......+....+.
T Consensus       781 nnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF  860 (1164)
T PTZ00112        781 NQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLF  860 (1164)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHH
Confidence            36788999999999999999976541    11222  3678888777778888888888884332 22223344444555


Q ss_pred             HHhc---CCcEEEEEeCCCCCChhhHHHhhcccc-CCCCCcEEEE--EeCchhHH----HhhcC---CCeEeCCCCChhh
Q 000887           86 ETVF---KKKFLIVLDDVWSERYDLWQALKSPFM-AGAPGSRIIV--TTRSMDVA----LTMGS---GKNYELKLLSDDD  152 (1237)
Q Consensus        86 ~~l~---~~~~LlvlDdv~~~~~~~~~~~~~~~~-~~~~~~~ili--TtR~~~~~----~~~~~---~~~~~l~~l~~~e  152 (1237)
                      ..+.   +...+||||+++.-....-+.+...+. ....+++|+|  ++.+....    .++..   ...+..++.+.+|
T Consensus       861 ~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQ  940 (1164)
T PTZ00112        861 NQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDE  940 (1164)
T ss_pred             hhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhhhhhccccccccCCCCCHHH
Confidence            4442   234689999995321111112221111 1123455443  34322221    11111   1246779999999


Q ss_pred             hHHHHHHHhcC
Q 000887          153 CWSVFVAHAFE  163 (1237)
Q Consensus       153 a~~l~~~~~~~  163 (1237)
                      -.+++..++..
T Consensus       941 L~dILk~RAe~  951 (1164)
T PTZ00112        941 IEKIIKERLEN  951 (1164)
T ss_pred             HHHHHHHHHHh
Confidence            99999998854

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

Probab=98.45  E-value=2.9e-08  Score=105.36  Aligned_cols=181  Identities=18%  Similarity=0.161  Sum_probs=102.7

Q ss_pred             CccceeeeeeecCCCccccC--cCCCCCCcccEEEEcCCCCcc--ccccccCCcccccEEeeccccccccccc--cccCC
Q 000887          942 LPVTLKRLRIEDCSNFKVLT--SECQLPVEVEELTIYGCSNLE--SIAERFHDDACLRSIWISSCENLKSLPK--GLSNL 1015 (1237)
Q Consensus       942 ~~~~L~~L~l~~c~~l~~l~--~~~~~~~~L~~L~l~~c~~~~--~~~~~~~~l~~L~~L~l~~~~~l~~l~~--~l~~l 1015 (1237)
                      .+.+|+.+.+.+|+.- ..+  .....+++++.|+++.|-.-.  .+-.....+|+|+.|+|+.+ .+.....  .-..+
T Consensus       119 n~kkL~~IsLdn~~V~-~~~~~~~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~N-rl~~~~~s~~~~~l  196 (505)
T KOG3207|consen  119 NLKKLREISLDNYRVE-DAGIEEYSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSN-RLSNFISSNTTLLL  196 (505)
T ss_pred             hHHhhhheeecCcccc-ccchhhhhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccc-cccCCccccchhhh
Confidence            4456666666665421 111  234456778888887753221  22234556777888888773 3332221  12355


Q ss_pred             CCCceeeeccCCCcccCCCCCCCCcchhhhhhccccccccCCCCCCCcccEEeccCCCCccccCCC-CCCCCcCceEecC
Q 000887         1016 SHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEE-GLSTNLTDLEISG 1094 (1237)
Q Consensus      1016 ~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~-~~~~~L~~L~l~~ 1094 (1237)
                      ++|+.|.|++|..-.             -++..|        ...+|+|+.|.+.++..+...... ..+..|++|||++
T Consensus       197 ~~lK~L~l~~CGls~-------------k~V~~~--------~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~  255 (505)
T KOG3207|consen  197 SHLKQLVLNSCGLSW-------------KDVQWI--------LLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSN  255 (505)
T ss_pred             hhhheEEeccCCCCH-------------HHHHHH--------HHhCCcHHHhhhhcccccceecchhhhhhHHhhccccC
Confidence            777777777774210             000010        026788888888888533322222 4577888899998


Q ss_pred             CCCcccccccccCCCCCCceEEEcCCCCceec--cCCC--CccccCCCcCeeeecC
Q 000887         1095 DNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSF--PDVG--KGVILPTSLTSITISD 1146 (1237)
Q Consensus      1095 ~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l--~~~~--~~~~~~~~L~~L~l~~ 1146 (1237)
                      |+.+..-.....+.++.|+.|+++.| .+.++  |...  .-....++|++|.+..
T Consensus       256 N~li~~~~~~~~~~l~~L~~Lnls~t-gi~si~~~d~~s~~kt~~f~kL~~L~i~~  310 (505)
T KOG3207|consen  256 NNLIDFDQGYKVGTLPGLNQLNLSST-GIASIAEPDVESLDKTHTFPKLEYLNISE  310 (505)
T ss_pred             Ccccccccccccccccchhhhhcccc-CcchhcCCCccchhhhcccccceeeeccc
Confidence            88876554445788889999999886 34433  2210  0012445666666665

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

Probab=98.44  E-value=1.1e-08  Score=111.80  Aligned_cols=103  Identities=25%  Similarity=0.301  Sum_probs=93.3

Q ss_pred             CCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEec
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI  477 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l  477 (1237)
                      .+..-...||+.|++.++|..++.+..|..|.|.+|.|..+|..+++|..|.+|||+.| .+..+|..++.|. |+.|-+
T Consensus        73 ~ltdt~~aDlsrNR~~elp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~N-qlS~lp~~lC~lp-Lkvli~  150 (722)
T KOG0532|consen   73 DLTDTVFADLSRNRFSELPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSN-QLSHLPDGLCDLP-LKVLIV  150 (722)
T ss_pred             cccchhhhhccccccccCchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccc-hhhcCChhhhcCc-ceeEEE
Confidence            34556778999999999999999999999999999999999999999999999999998 9999999998874 899989


Q ss_pred             cCCCccccCcccccccccccccceee
Q 000887          478 EGASALRELPLGMKELKCLRTLTNFI  503 (1237)
Q Consensus       478 ~~~~~l~~ip~~~~~L~~L~~L~~~~  503 (1237)
                      ++| +++.+|.+++.+..|.+|+...
T Consensus       151 sNN-kl~~lp~~ig~~~tl~~ld~s~  175 (722)
T KOG0532|consen  151 SNN-KLTSLPEEIGLLPTLAHLDVSK  175 (722)
T ss_pred             ecC-ccccCCcccccchhHHHhhhhh
Confidence            988 8999999999888888887643

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.43  E-value=1.8e-06  Score=91.38  Aligned_cols=156  Identities=19%  Similarity=0.133  Sum_probs=93.3

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..+.|.|+|.+|+|||++|+.++....+. ....+++++..-.+      ..              .    .+...+.+ 
T Consensus        37 ~~~~lll~G~~G~GKT~la~~~~~~~~~~-~~~~~~i~~~~~~~------~~--------------~----~~~~~~~~-   90 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQAACAAAEER-GKSAIYLPLAELAQ------AD--------------P----EVLEGLEQ-   90 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhc-CCcEEEEeHHHHHH------hH--------------H----HHHhhccc-
Confidence            35689999999999999999988754322 33456665432211      00              0    01111222 


Q ss_pred             cEEEEEeCCCCCChh-h-HHHhhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSERYD-L-WQALKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~-~-~~~~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      .-+||+||++.-... . ...+...+.. ...+..+|+|++...         +..++.....+++.+++++|...+++.
T Consensus        91 ~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~  170 (226)
T TIGR03420        91 ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQS  170 (226)
T ss_pred             CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHH
Confidence            348999999543221 1 2233322221 123457999988532         122232235789999999999999887


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhH
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGL  197 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~  197 (1237)
                      .+......    -.+++++.|++.++|.|..+.-+...
T Consensus       171 ~~~~~~~~----~~~~~l~~L~~~~~gn~r~L~~~l~~  204 (226)
T TIGR03420       171 RAARRGLQ----LPDEVADYLLRHGSRDMGSLMALLDA  204 (226)
T ss_pred             HHHHcCCC----CCHHHHHHHHHhccCCHHHHHHHHHH
Confidence            65322221    22567788999999999887766443

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

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

Probab=98.42  E-value=6.8e-06  Score=87.48  Aligned_cols=205  Identities=17%  Similarity=0.171  Sum_probs=115.2

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      .+.+..+.+||++|+||||||+.++.. ....     |..++...+-.+-.+.++....                .....
T Consensus        45 ~~~l~SmIl~GPPG~GKTTlA~liA~~-~~~~-----f~~~sAv~~gvkdlr~i~e~a~----------------~~~~~  102 (436)
T COG2256          45 AGHLHSMILWGPPGTGKTTLARLIAGT-TNAA-----FEALSAVTSGVKDLREIIEEAR----------------KNRLL  102 (436)
T ss_pred             cCCCceeEEECCCCCCHHHHHHHHHHh-hCCc-----eEEeccccccHHHHHHHHHHHH----------------HHHhc
Confidence            356778899999999999999998873 2222     2333333222222222222110                11223


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEE--eCchhHHH---hhcCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVT--TRSMDVAL---TMGSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliT--tR~~~~~~---~~~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                      +++.+|++|.|..-+..+-+.   .++....|.-|+|-  |-++.+..   ......++++++|+.+|-.+++.+.+...
T Consensus       103 gr~tiLflDEIHRfnK~QQD~---lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~  179 (436)
T COG2256         103 GRRTILFLDEIHRFNKAQQDA---LLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDE  179 (436)
T ss_pred             CCceEEEEehhhhcChhhhhh---hhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhh
Confidence            789999999995533333222   34445667777764  44443221   11334689999999999999998844322


Q ss_pred             CCCCC---CCChHHHHHHHHHHccCCchH-HH---HHHhHhhcCC--CHHHHHHHHhhcccccCC----CCChhHHHHHH
Q 000887          165 RDAGT---HGNFESTRQRVVEKCKGLPLA-AR---ALGGLLRSKQ--GVDEWRAILDSKIWNLQD----KTEIPSVLKLS  231 (1237)
Q Consensus       165 ~~~~~---~~~~~~~~~~i~~~~~g~PLa-l~---~~~~~l~~~~--~~~~~~~~l~~~~~~~~~----~~~i~~~l~~s  231 (1237)
                      .....   ..-.+++...+++.++|=..+ +.   +++...+...  ..+..++.+++.......    ...+-++|.-|
T Consensus       180 ~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hYdliSA~hKS  259 (436)
T COG2256         180 ERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHYDLISALHKS  259 (436)
T ss_pred             hcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHHHHHHHHHHh
Confidence            22111   112255777888888884433 22   2332222221  245566666654333222    34566778777


Q ss_pred             hhcChHHH
Q 000887          232 YHHLPSHL  239 (1237)
Q Consensus       232 ~~~L~~~~  239 (1237)
                      ...=++++
T Consensus       260 vRGSD~dA  267 (436)
T COG2256         260 VRGSDPDA  267 (436)
T ss_pred             hccCCcCH
Confidence            77666554

>PRK15386 type III secretion protein GogB; Provisional

Probab=98.42  E-value=7.4e-07  Score=97.53  Aligned_cols=56  Identities=29%  Similarity=0.612  Sum_probs=36.6

Q ss_pred             CcccccEEeeccccccccccccccCCCCCceeeeccCCCcccCCCCCCCCcchhhhhhccc
Q 000887          990 DDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCD 1050 (1237)
Q Consensus       990 ~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~l~~~~ 1050 (1237)
                      .+.+++.|++++| .++.+|.   -.++|++|.+++|.+++.+|... +.+|+.|.+.+|.
T Consensus        50 ~~~~l~~L~Is~c-~L~sLP~---LP~sLtsL~Lsnc~nLtsLP~~L-P~nLe~L~Ls~Cs  105 (426)
T PRK15386         50 EARASGRLYIKDC-DIESLPV---LPNELTEITIENCNNLTTLPGSI-PEGLEKLTVCHCP  105 (426)
T ss_pred             HhcCCCEEEeCCC-CCcccCC---CCCCCcEEEccCCCCcccCCchh-hhhhhheEccCcc
Confidence            3577888888887 7777773   22468888888888887777532 3334444444443

>PF13173 AAA_14: AAA domain

Probab=98.39  E-value=1.4e-06  Score=82.05  Aligned_cols=120  Identities=24%  Similarity=0.255  Sum_probs=78.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      -+++.|.|+-|+||||++++++++..  ....++|+++.+.........                + ..+.+.+....++
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~--~~~~~~yi~~~~~~~~~~~~~----------------~-~~~~~~~~~~~~~   62 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL--PPENILYINFDDPRDRRLADP----------------D-LLEYFLELIKPGK   62 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc--ccccceeeccCCHHHHHHhhh----------------h-hHHHHHHhhccCC
Confidence            36899999999999999999887543  334577887655533110000                0 2223333333478


Q ss_pred             EEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhh------cCCCeEeCCCCChhhh
Q 000887           93 FLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTM------GSGKNYELKLLSDDDC  153 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~------~~~~~~~l~~l~~~ea  153 (1237)
                      .+|++|++..  ...|......+....++.+|++|+........-      +....+++.||+..|.
T Consensus        63 ~~i~iDEiq~--~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   63 KYIFIDEIQY--LPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             cEEEEehhhh--hccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            8999999944  356666666666656778999999977665321      1124678889987763

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.38  E-value=3.8e-07  Score=72.61  Aligned_cols=57  Identities=33%  Similarity=0.449  Sum_probs=41.4

Q ss_pred             CCccEEEcccccccccc-ccccCCCCCCeEEccCCCccccch-hhcccCCccEEEcCcc
Q 000887          400 KKLRVLSLGSYCITEVP-ISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNC  456 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp-~~~~~l~~Lr~L~L~~~~i~~lp~-~i~~L~~L~~L~L~~~  456 (1237)
                      ++|++|++++|.++.+| ..|..+++|++|++++|.+..+|+ .|.++++|++|++++|
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N   59 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNN   59 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSS
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCC
Confidence            35677777777777775 456777777777777777777754 6777777777777776

...

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

Probab=98.33  E-value=1.1e-07  Score=95.26  Aligned_cols=106  Identities=23%  Similarity=0.243  Sum_probs=80.3

Q ss_pred             hcCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccE
Q 000887          395 LLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY  474 (1237)
Q Consensus       395 ~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~  474 (1237)
                      .+..++.|..|||++|.|+.+.++..-++.+|+|++++|.|..+-. +..|.+|..|||++| .+.++...=.+|-|.++
T Consensus       279 ~~dTWq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~v~n-La~L~~L~~LDLS~N-~Ls~~~Gwh~KLGNIKt  356 (490)
T KOG1259|consen  279 SADTWQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRTVQN-LAELPQLQLLDLSGN-LLAECVGWHLKLGNIKT  356 (490)
T ss_pred             ecchHhhhhhccccccchhhhhhhhhhccceeEEeccccceeeehh-hhhcccceEeecccc-hhHhhhhhHhhhcCEee
Confidence            3456778888888888888888888888888888888888887744 888888888888887 66666654467777888


Q ss_pred             EeccCCCccccCcccccccccccccceeee
Q 000887          475 LNIEGASALRELPLGMKELKCLRTLTNFIV  504 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~~~~L~~L~~L~~~~~  504 (1237)
                      |.+.+| .++.+ .++++|.+|..|++..+
T Consensus       357 L~La~N-~iE~L-SGL~KLYSLvnLDl~~N  384 (490)
T KOG1259|consen  357 LKLAQN-KIETL-SGLRKLYSLVNLDLSSN  384 (490)
T ss_pred             eehhhh-hHhhh-hhhHhhhhheecccccc
Confidence            888877 56555 35667777777766443

>PRK09087 hypothetical protein; Validated

Probab=98.31  E-value=8.1e-06  Score=84.72  Aligned_cols=145  Identities=17%  Similarity=0.131  Sum_probs=90.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +.+.|+|++|+|||+|+..+++..      .+.|++..      ....++...+                     .+  -
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~~~------~~~~i~~~------~~~~~~~~~~---------------------~~--~   89 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWREKS------DALLIHPN------EIGSDAANAA---------------------AE--G   89 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhc------CCEEecHH------HcchHHHHhh---------------------hc--C
Confidence            568999999999999999887632      23345321      1111111111                     01  2


Q ss_pred             EEEEeCCCCCChhhHHHhhccccC-CCCCcEEEEEeCc---------hhHHHhhcCCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           94 LIVLDDVWSERYDLWQALKSPFMA-GAPGSRIIVTTRS---------MDVALTMGSGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~~~~~~~~~-~~~~~~iliTtR~---------~~~~~~~~~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                      +|++||++.....+ .++...+.. ...|..+|+|++.         ++...++....++++++++.++-.+++++.+..
T Consensus        90 ~l~iDDi~~~~~~~-~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~  168 (226)
T PRK09087         90 PVLIEDIDAGGFDE-TGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFAD  168 (226)
T ss_pred             eEEEECCCCCCCCH-HHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHH
Confidence            78889995422111 223322221 2346789999974         233444555678999999999999999988854


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      .....+    +++...|++++.|..-++..+-..+
T Consensus       169 ~~~~l~----~ev~~~La~~~~r~~~~l~~~l~~L  199 (226)
T PRK09087        169 RQLYVD----PHVVYYLVSRMERSLFAAQTIVDRL  199 (226)
T ss_pred             cCCCCC----HHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            332222    6778899999988877776544333

>PRK08727 hypothetical protein; Validated

Probab=98.29  E-value=8.7e-06  Score=85.45  Aligned_cols=148  Identities=20%  Similarity=0.126  Sum_probs=90.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      ..+.|+|.+|+|||+||.++++...+..+ .++|+++.+      ....+..                 .+. .+ .+.-
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~-~~~y~~~~~------~~~~~~~-----------------~~~-~l-~~~d   95 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGR-SSAYLPLQA------AAGRLRD-----------------ALE-AL-EGRS   95 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCC-cEEEEeHHH------hhhhHHH-----------------HHH-HH-hcCC
Confidence            45999999999999999999875544433 566776322      1111111                 111 11 2335


Q ss_pred             EEEEeCCCCCCh-hhHH-HhhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHHHh
Q 000887           94 LIVLDDVWSERY-DLWQ-ALKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        94 LlvlDdv~~~~~-~~~~-~~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                      +||+||++.... ..+. .+...+.. ...+..||+|++...         +..++.....+++++++.++-.+++++.+
T Consensus        96 lLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a  175 (233)
T PRK08727         96 LVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERA  175 (233)
T ss_pred             EEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHH
Confidence            899999953211 1122 22222211 234667999998542         22233344689999999999999999877


Q ss_pred             cCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          162 FEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ....-..    .+++...|++.++|-.-++
T Consensus       176 ~~~~l~l----~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        176 QRRGLAL----DEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHcCCCC----CHHHHHHHHHhCCCCHHHH
Confidence            5432222    2667788888888765554

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=98.29  E-value=1e-05  Score=83.78  Aligned_cols=165  Identities=18%  Similarity=0.181  Sum_probs=97.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ...+.|+|..|+|||.|..++++...+... ..++|++      ..+....++..+..     ...    ..+++.++ .
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~------~~~f~~~~~~~~~~-----~~~----~~~~~~~~-~   97 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS------AEEFIREFADALRD-----GEI----EEFKDRLR-S   97 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE------HHHHHHHHHHHHHT-----TSH----HHHHHHHC-T
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec------HHHHHHHHHHHHHc-----ccc----hhhhhhhh-c
Confidence            445789999999999999999986543322 2466774      34455555555533     112    23334444 4


Q ss_pred             cEEEEEeCCCCCCh-hhHHH-hhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSERY-DLWQA-LKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~-~~~~~-~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      -=+|++||++.-.. ..|.. +...+.. ...|.+||+|++...         ...++....++++++.+.++..+++++
T Consensus        98 ~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~  177 (219)
T PF00308_consen   98 ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQK  177 (219)
T ss_dssp             SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHH
T ss_pred             CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHH
Confidence            45778899955322 12222 2222221 135778999996442         333445557899999999999999999


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhH
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGL  197 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~  197 (1237)
                      .+.......+    ++++.-|++.+.+..-.|..+-..
T Consensus       178 ~a~~~~~~l~----~~v~~~l~~~~~~~~r~L~~~l~~  211 (219)
T PF00308_consen  178 KAKERGIELP----EEVIEYLARRFRRDVRELEGALNR  211 (219)
T ss_dssp             HHHHTT--S-----HHHHHHHHHHTTSSHHHHHHHHHH
T ss_pred             HHHHhCCCCc----HHHHHHHHHhhcCCHHHHHHHHHH
Confidence            8865444333    677788888887766665544433

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.23  E-value=1.4e-05  Score=84.10  Aligned_cols=156  Identities=16%  Similarity=0.117  Sum_probs=93.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .+.+.|+|++|+|||+|+.++++...+. ...+.|+.+.....                    ...+..    +.+.. -
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~~~-~~~v~y~~~~~~~~--------------------~~~~~~----~~~~~-~   98 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELSQR-GRAVGYVPLDKRAW--------------------FVPEVL----EGMEQ-L   98 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC-CCeEEEEEHHHHhh--------------------hhHHHH----HHhhh-C
Confidence            3578999999999999999988754332 23466776532110                    001111    11111 2


Q ss_pred             EEEEEeCCCCCCh-hhHHH-hhccccCC-CCC-cEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           93 FLIVLDDVWSERY-DLWQA-LKSPFMAG-APG-SRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        93 ~LlvlDdv~~~~~-~~~~~-~~~~~~~~-~~~-~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      -+||+||+..... ..|+. +...+... ..| .++|+||+...         +..++....++++++++.++-.+++++
T Consensus        99 dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~  178 (235)
T PRK08084         99 SLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQL  178 (235)
T ss_pred             CEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHH
Confidence            3788999954221 22322 22222221 123 47999998552         333445557899999999999999988


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      ++...+-..    .+++..-|++++.|-.-++..+-..+
T Consensus       179 ~a~~~~~~l----~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        179 RARLRGFEL----PEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             HHHHcCCCC----CHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence            664432222    26788889999988776665544443

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

Probab=98.22  E-value=2.8e-07  Score=92.49  Aligned_cols=110  Identities=25%  Similarity=0.243  Sum_probs=95.2

Q ss_pred             chhhhhcCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhccc
Q 000887          390 MVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNL  469 (1237)
Q Consensus       390 ~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L  469 (1237)
                      ...++...-.+.+|+|++++|.|..+-. +..+.+|..|||++|.+.++...-.+|-+.+.|.|++| .+..+.. +++|
T Consensus       297 ~~iDESvKL~Pkir~L~lS~N~i~~v~n-La~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKtL~La~N-~iE~LSG-L~KL  373 (490)
T KOG1259|consen  297 TQIDESVKLAPKLRRLILSQNRIRTVQN-LAELPQLQLLDLSGNLLAECVGWHLKLGNIKTLKLAQN-KIETLSG-LRKL  373 (490)
T ss_pred             hhhhhhhhhccceeEEeccccceeeehh-hhhcccceEeecccchhHhhhhhHhhhcCEeeeehhhh-hHhhhhh-hHhh
Confidence            4556677788999999999999998876 88999999999999999988777889999999999998 8877765 8999


Q ss_pred             ccccEEeccCCCccccCcc--cccccccccccceee
Q 000887          470 VNLHYLNIEGASALRELPL--GMKELKCLRTLTNFI  503 (1237)
Q Consensus       470 ~~L~~L~l~~~~~l~~ip~--~~~~L~~L~~L~~~~  503 (1237)
                      .+|..||+++| +++.+-.  .|++|+.|+++.+.+
T Consensus       374 YSLvnLDl~~N-~Ie~ldeV~~IG~LPCLE~l~L~~  408 (490)
T KOG1259|consen  374 YSLVNLDLSSN-QIEELDEVNHIGNLPCLETLRLTG  408 (490)
T ss_pred             hhheecccccc-chhhHHHhcccccccHHHHHhhcC
Confidence            99999999999 6777653  499999999987643

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.21  E-value=3.2e-05  Score=78.76  Aligned_cols=147  Identities=15%  Similarity=0.119  Sum_probs=90.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccccc--------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE--------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~--------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|+.|+|||++|+.++......                    .++...++.....                   
T Consensus        14 ~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~-------------------   74 (188)
T TIGR00678        14 AHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQ-------------------   74 (188)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccC-------------------
Confidence            3678999999999999999987754321                    1111222221111                   


Q ss_pred             CccCHHHHHHHHHHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCC
Q 000887           73 KLEDLNSVQLELKET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELK  146 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~  146 (1237)
                       ....++....+...    ..+.+-++|+||++.-.......+...+-...+.+.+|++|++. .+...+ .....+++.
T Consensus        75 -~~~~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~~~~~  153 (188)
T TIGR00678        75 -SIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFP  153 (188)
T ss_pred             -cCCHHHHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEEeeCC
Confidence             11222222222111    12456789999996554455556666665545566777777654 222222 223589999


Q ss_pred             CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCch
Q 000887          147 LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL  189 (1237)
                      +++.+|..+.+.+..      .    .++++..|++.++|.|.
T Consensus       154 ~~~~~~~~~~l~~~g------i----~~~~~~~i~~~~~g~~r  186 (188)
T TIGR00678       154 PLSEEALLQWLIRQG------I----SEEAAELLLALAGGSPG  186 (188)
T ss_pred             CCCHHHHHHHHHHcC------C----CHHHHHHHHHHcCCCcc
Confidence            999999999887761      1    15678999999999885

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.21  E-value=1.3e-05  Score=84.58  Aligned_cols=153  Identities=24%  Similarity=0.171  Sum_probs=91.7

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..+.+.|+|..|+|||+||.++++...+... .+++++.....      ..    +                  ... ..
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~-~~~~i~~~~~~------~~----~------------------~~~-~~   90 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVADASYGGR-NARYLDAASPL------LA----F------------------DFD-PE   90 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCC-cEEEEehHHhH------HH----H------------------hhc-cc
Confidence            3467899999999999999998875433332 35566543321      00    0                  011 23


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccccCC-CCCc-EEEEEeCchhHHH--------hhcCCCeEeCCCCChhhhHHHHHHHh
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPFMAG-APGS-RIIVTTRSMDVAL--------TMGSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~~~~-~~~~-~iliTtR~~~~~~--------~~~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                      .-+||+||++.........+...+... ..+. .+|+|++......        ++.....++++++++++-.+++.+.+
T Consensus        91 ~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~  170 (227)
T PRK08903         91 AELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAA  170 (227)
T ss_pred             CCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHH
Confidence            346888999543222223333333221 2233 4777776543211        22233688999999988777777654


Q ss_pred             cCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          162 FEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      ...+...    .+++.+.+++...|.+..+..+...+
T Consensus       171 ~~~~v~l----~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        171 AERGLQL----ADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HHcCCCC----CHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            3322222    26788899999999999887766554

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

Probab=98.20  E-value=3.2e-07  Score=97.64  Aligned_cols=91  Identities=15%  Similarity=0.107  Sum_probs=46.0

Q ss_pred             CCCCCCccEEEEeecCCCCCCCCCCCCCCCCccEEEEccCCCCCc--CCCCCCccccceeEecCCCCceeecccccCC-C
Q 000887          578 LKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTS--LPSLGQLCSLKDLTIVGMSELKSIGSEIYGE-G  654 (1237)
Q Consensus       578 l~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~~~~--l~~l~~l~~L~~L~l~~~~~l~~i~~~~~~~-~  654 (1237)
                      +..+++|+.|++..+.+.... -.....+..|+.|+|++|..+..  .+..+.||.|+.|.+..+ ++..+..--.+. .
T Consensus       218 ~~~fPsl~~L~L~~N~~~~~~-~~~~~i~~~L~~LdLs~N~li~~~~~~~~~~l~~L~~Lnls~t-gi~si~~~d~~s~~  295 (505)
T KOG3207|consen  218 LLTFPSLEVLYLEANEIILIK-ATSTKILQTLQELDLSNNNLIDFDQGYKVGTLPGLNQLNLSST-GIASIAEPDVESLD  295 (505)
T ss_pred             HHhCCcHHHhhhhccccccee-cchhhhhhHHhhccccCCcccccccccccccccchhhhhcccc-CcchhcCCCccchh
Confidence            344555555655554321111 11112466788888887775443  246777888888888764 333332100000 0


Q ss_pred             cccCCcccceeecccc
Q 000887          655 CSKPFQSLQTLYFEDL  670 (1237)
Q Consensus       655 ~~~~~~~L~~L~l~~~  670 (1237)
                      ....||+|++|.+..+
T Consensus       296 kt~~f~kL~~L~i~~N  311 (505)
T KOG3207|consen  296 KTHTFPKLEYLNISEN  311 (505)
T ss_pred             hhcccccceeeecccC
Confidence            1133556666655554

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.19  E-value=5.9e-05  Score=93.89  Aligned_cols=211  Identities=17%  Similarity=0.139  Sum_probs=120.8

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCC------CCcEEEEEeCch--hHHHhhcCCCeEeCCCCChhhhHHHHHHHh
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGA------PGSRIIVTTRSM--DVALTMGSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~------~~~~iliTtR~~--~~~~~~~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                      .++.++|+||+...+....+-+........      ...-.+.|.+..  .+.........+.|.||+..+...+.....
T Consensus       153 ~~plVi~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l  232 (849)
T COG3899         153 EHPLVIVLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATL  232 (849)
T ss_pred             cCCeEEEEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHh
Confidence            469999999995443333322221111111      122233344433  112222333689999999999999999887


Q ss_pred             cCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcC------CCHHHHHHHHhhcccccCCCCChhHHHHHHhhcC
Q 000887          162 FEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSK------QGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHL  235 (1237)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~------~~~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~~L  235 (1237)
                      ......     ..+.+..|.++..|+|+-+..+-..+.+.      .+...|..-.... .....-+.+-..+..-.+.|
T Consensus       233 ~~~~~~-----~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i-~~~~~~~~vv~~l~~rl~kL  306 (849)
T COG3899         233 GCTKLL-----PAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASL-GILATTDAVVEFLAARLQKL  306 (849)
T ss_pred             CCcccc-----cchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhc-CCchhhHHHHHHHHHHHhcC
Confidence            542221     14568899999999999999988888764      2234443222110 01111122445688889999


Q ss_pred             hHHHHHHHhhhccCCCCcccChHHHHHHHHHcCCCccCcchhhHHHHHHHHHHHHhhcCcccccC------CCCCc--c-
Q 000887          236 PSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLSRSLFQKSS------NTESK--Y-  306 (1237)
Q Consensus       236 ~~~~~~~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~~~~~~~~~~~~~~~l~~L~~~~ll~~~~------~~~~~--~-  306 (1237)
                      |...|+++...|++-..++  .+.+...+..           ...+++......| ..+++.+..      .....  | 
T Consensus       307 ~~~t~~Vl~~AA~iG~~F~--l~~La~l~~~-----------~~~~~a~~l~~al-~e~lI~~~~~~yr~~~~~~~~~Y~  372 (849)
T COG3899         307 PGTTREVLKAAACIGNRFD--LDTLAALAED-----------SPALEAAALLDAL-QEGLILPLSETYRFGSNVDIATYK  372 (849)
T ss_pred             CHHHHHHHHHHHHhCccCC--HHHHHHHHhh-----------chHHHHHHHHHHh-HhhceeccccccccccccchhhHH
Confidence            9999999999999976655  4444443311           1122333333443 344444311      11111  2 


Q ss_pred             hhhhHHHHHHhhhc
Q 000887          307 VMHDLVHDLAQWAS  320 (1237)
Q Consensus       307 ~~h~lv~~~~~~~~  320 (1237)
                      ..|+.||+.+-...
T Consensus       373 F~H~~vqqaaY~~i  386 (849)
T COG3899         373 FLHDRVQQAAYNLI  386 (849)
T ss_pred             hhHHHHHHHHhccC
Confidence            46999999886543

>PLN03025 replication factor C subunit; Provisional

Probab=98.18  E-value=2.5e-05  Score=86.79  Aligned_cols=162  Identities=15%  Similarity=0.129  Sum_probs=92.6

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCC-CeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ++.+.+.++|++|+|||++|..+++......|. .++-++.++......+ ++....+.......             -.
T Consensus        32 ~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~sd~~~~~~v-r~~i~~~~~~~~~~-------------~~   97 (319)
T PLN03025         32 GNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNASDDRGIDVV-RNKIKMFAQKKVTL-------------PP   97 (319)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecccccccHHHH-HHHHHHHHhccccC-------------CC
Confidence            344557799999999999999998754333332 2222333322222211 22221111100000             01


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      ++.-++|+|+++.-.......+...+-..+..+++++++... .+...+ .....+++.+++.++..+.+...+...+..
T Consensus        98 ~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~  177 (319)
T PLN03025         98 GRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP  177 (319)
T ss_pred             CCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCC
Confidence            346799999996654444444544443334567777766443 221111 122578999999999999998877543332


Q ss_pred             CCCCChHHHHHHHHHHccCCchH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      ..    ++.+..|++.++|-.-.
T Consensus       178 i~----~~~l~~i~~~~~gDlR~  196 (319)
T PLN03025        178 YV----PEGLEAIIFTADGDMRQ  196 (319)
T ss_pred             CC----HHHHHHHHHHcCCCHHH
Confidence            22    56788999999986543

>PRK15386 type III secretion protein GogB; Provisional

Probab=98.17  E-value=3.6e-06  Score=92.21  Aligned_cols=70  Identities=29%  Similarity=0.550  Sum_probs=44.4

Q ss_pred             ccceeEEEEecCCCcccccCCCCCccceeeeeeecCCCccccCcCCCCCCcccEEEEcCCCCccccccccCCcccccEEe
Q 000887          919 YLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIW  998 (1237)
Q Consensus       919 ~~~L~~L~l~~~~~l~~~~~~~~~~~~L~~L~l~~c~~l~~l~~~~~~~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~  998 (1237)
                      +.+++.|++++| .++.+|   ..+++|+.|.+.+|.+++.+|...  +++|+.|++++|..+..+|.      +|+.|+
T Consensus        51 ~~~l~~L~Is~c-~L~sLP---~LP~sLtsL~Lsnc~nLtsLP~~L--P~nLe~L~Ls~Cs~L~sLP~------sLe~L~  118 (426)
T PRK15386         51 ARASGRLYIKDC-DIESLP---VLPNELTEITIENCNNLTTLPGSI--PEGLEKLTVCHCPEISGLPE------SVRSLE  118 (426)
T ss_pred             hcCCCEEEeCCC-CCcccC---CCCCCCcEEEccCCCCcccCCchh--hhhhhheEccCccccccccc------ccceEE
Confidence            356777888877 666666   355667777777777776665422  35677777777766555543      355555


Q ss_pred             ec
Q 000887          999 IS 1000 (1237)
Q Consensus       999 l~ 1000 (1237)
                      +.
T Consensus       119 L~  120 (426)
T PRK15386        119 IK  120 (426)
T ss_pred             eC
Confidence            54

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

Probab=98.16  E-value=1e-06  Score=102.30  Aligned_cols=103  Identities=27%  Similarity=0.361  Sum_probs=91.1

Q ss_pred             cCCC-CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccE
Q 000887          396 LPQC-KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY  474 (1237)
Q Consensus       396 ~~~~-~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~  474 (1237)
                      .... .+|+.|++++|.+..+|..+..+++|+.|++++|.+.++|...+.+.+|+.|++++| .+..+|..++.+.+|++
T Consensus       135 ~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~L~ls~N-~i~~l~~~~~~~~~L~~  213 (394)
T COG4886         135 IGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNNLDLSGN-KISDLPPEIELLSALEE  213 (394)
T ss_pred             cccchhhcccccccccchhhhhhhhhccccccccccCCchhhhhhhhhhhhhhhhheeccCC-ccccCchhhhhhhhhhh
Confidence            3445 399999999999999998899999999999999999999998889999999999999 99999998889999999


Q ss_pred             EeccCCCccccCcccccccccccccc
Q 000887          475 LNIEGASALRELPLGMKELKCLRTLT  500 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~~~~L~~L~~L~  500 (1237)
                      |.+++| .+..++..++++.++..+.
T Consensus       214 l~~~~N-~~~~~~~~~~~~~~l~~l~  238 (394)
T COG4886         214 LDLSNN-SIIELLSSLSNLKNLSGLE  238 (394)
T ss_pred             hhhcCC-cceecchhhhhcccccccc
Confidence            999998 4566777777777777664

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.15  E-value=2.1e-06  Score=68.32  Aligned_cols=57  Identities=33%  Similarity=0.522  Sum_probs=51.4

Q ss_pred             CCCCeEEccCCCccccch-hhcccCCccEEEcCccccCccCCh-hhcccccccEEeccCC
Q 000887          423 KQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPS-RIGNLVNLHYLNIEGA  480 (1237)
Q Consensus       423 ~~Lr~L~L~~~~i~~lp~-~i~~L~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~~~  480 (1237)
                      ++|++|++++|.+..+|. .|.++++|++|++++| .+..+|+ .|.++++|++|++++|
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N   59 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNN-NLTSIPPDAFSNLPNLRYLDLSNN   59 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETSS-SESEEETTTTTTSTTESEEEETSS
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccCC-ccCccCHHHHcCCCCCCEEeCcCC
Confidence            579999999999999986 8899999999999998 7777765 5799999999999998

...

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.15  E-value=4.4e-05  Score=88.02  Aligned_cols=169  Identities=10%  Similarity=0.082  Sum_probs=103.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccccc-CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .-+.|+|..|+|||+|+.++++..... .-..+++++      ..++...+...+....       +....+++.++. .
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~~-------~~~~~~~~~~~~-~  207 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMS------GDEFARKAVDILQKTH-------KEIEQFKNEICQ-N  207 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEE------HHHHHHHHHHHHHHhh-------hHHHHHHHHhcc-C
Confidence            458999999999999999988744322 222355664      3455666666554311       122234444443 4


Q ss_pred             EEEEEeCCCCCC--hhhHHHhhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHHH
Q 000887           93 FLIVLDDVWSER--YDLWQALKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        93 ~LlvlDdv~~~~--~~~~~~~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      -+||+||+....  ....+.+...+.. ...|..||+|+....         +..++...-++.+++++.++..+++++.
T Consensus       208 dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~  287 (450)
T PRK14087        208 DVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKE  287 (450)
T ss_pred             CEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHH
Confidence            478889995422  1112223332222 133456888876432         2233444567889999999999999998


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      +...+..  ..-.++++..|++.++|.|-.+.-+...+
T Consensus       288 ~~~~gl~--~~l~~evl~~Ia~~~~gd~R~L~gaL~~l  323 (450)
T PRK14087        288 IKNQNIK--QEVTEEAINFISNYYSDDVRKIKGSVSRL  323 (450)
T ss_pred             HHhcCCC--CCCCHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            7543211  12236788999999999998887665443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.14  E-value=7.1e-05  Score=84.53  Aligned_cols=97  Identities=12%  Similarity=0.154  Sum_probs=64.0

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-....+..+...+-..+.++++|++|.+. .+...+ .....+++.+++.+|..+.+...+...+..
T Consensus       118 ~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~  197 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESID  197 (363)
T ss_pred             CCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            356799999996554445555655555445566667666543 333222 223689999999999999988866433221


Q ss_pred             CCCCChHHHHHHHHHHccCCchH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      .    .++++..|++.++|.|..
T Consensus       198 i----~~~al~~ia~~s~G~~R~  216 (363)
T PRK14961        198 T----DEYALKLIAYHAHGSMRD  216 (363)
T ss_pred             C----CHHHHHHHHHHcCCCHHH
Confidence            2    256788899999998754

>PLN03150 hypothetical protein; Provisional

Probab=98.14  E-value=2.9e-06  Score=102.79  Aligned_cols=93  Identities=26%  Similarity=0.376  Sum_probs=83.1

Q ss_pred             CccEEEccccccc-cccccccCCCCCCeEEccCCCcc-ccchhhcccCCccEEEcCccccCccCChhhcccccccEEecc
Q 000887          401 KLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~-~lp~~~~~l~~Lr~L~L~~~~i~-~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      .++.|+|++|.+. .+|..++++++|+.|+|++|.+. .+|..++.+++|++|+|++|.....+|..+++|++|++|+++
T Consensus       419 ~v~~L~L~~n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls  498 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLN  498 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECc
Confidence            4889999999987 67889999999999999999998 789999999999999999996667899999999999999999


Q ss_pred             CCCccccCccccccc
Q 000887          479 GASALRELPLGMKEL  493 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L  493 (1237)
                      +|.....+|..++.+
T Consensus       499 ~N~l~g~iP~~l~~~  513 (623)
T PLN03150        499 GNSLSGRVPAALGGR  513 (623)
T ss_pred             CCcccccCChHHhhc
Confidence            996666888877643

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

Probab=98.12  E-value=0.00023  Score=79.18  Aligned_cols=172  Identities=14%  Similarity=0.119  Sum_probs=107.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCC-eEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC--C
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK--K   91 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~--~   91 (1237)
                      -+.|+|.+|+|||+.++.++.......-.. +++|++....+..+++..++.+++..........+....+.+.+..  +
T Consensus        44 n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~  123 (366)
T COG1474          44 NIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGK  123 (366)
T ss_pred             cEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCC
Confidence            489999999999999999998654333333 7899999999999999999999975555556667777777777754  7


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccccCCC-CCcE--EEEEeCchhHHHhhcC-------CCeEeCCCCChhhhHHHHHHHh
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPFMAGA-PGSR--IIVTTRSMDVALTMGS-------GKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~~~~~-~~~~--iliTtR~~~~~~~~~~-------~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                      .+++|+|+++.-.....+.+-..+.... ..++  |+..+-+..+...+..       ...+..++-+.+|-.+++..++
T Consensus       124 ~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~  203 (366)
T COG1474         124 TVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERV  203 (366)
T ss_pred             eEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHH
Confidence            8999999994311110011212222211 1333  4444444433222211       1347788999999999998887


Q ss_pred             cCCC-CCCCCCChHHHHHHHHHHccC
Q 000887          162 FEGR-DAGTHGNFESTRQRVVEKCKG  186 (1237)
Q Consensus       162 ~~~~-~~~~~~~~~~~~~~i~~~~~g  186 (1237)
                      ...- ....++..-+.+..++..-+|
T Consensus       204 ~~~~~~~~~~~~vl~lia~~~a~~~G  229 (366)
T COG1474         204 EEGFSAGVIDDDVLKLIAALVAAESG  229 (366)
T ss_pred             HhhccCCCcCccHHHHHHHHHHHcCc
Confidence            4322 222233333444444444444

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.11  E-value=0.00027  Score=82.23  Aligned_cols=154  Identities=15%  Similarity=0.131  Sum_probs=94.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-c-------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-E-------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~-------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|+.|+||||+|+.++....- .                   .|..++.++....                   
T Consensus        37 ~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~-------------------   97 (702)
T PRK14960         37 HHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASR-------------------   97 (702)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEeccccc-------------------
Confidence            467799999999999999998775321 1                   1111222222111                   


Q ss_pred             CccCHHHHHHHHHHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHh-hcCCCeEeCC
Q 000887           73 KLEDLNSVQLELKET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALT-MGSGKNYELK  146 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~-~~~~~~~~l~  146 (1237)
                        ..+++.+..+...    ..++.-++|+|+|+.-.......+...+-....+.++|++|.+.. +... ......+++.
T Consensus        98 --~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq~feFk  175 (702)
T PRK14960         98 --TKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLR  175 (702)
T ss_pred             --CCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhheeecc
Confidence              1233332222211    134667899999965544555566655554455677777776542 2222 2233689999


Q ss_pred             CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          147 LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      +++.++..+.+...+...+...    ..+++..|++.++|-+..+
T Consensus       176 pLs~eEI~k~L~~Il~kEgI~i----d~eAL~~IA~~S~GdLRdA  216 (702)
T PRK14960        176 PLAVDEITKHLGAILEKEQIAA----DQDAIWQIAESAQGSLRDA  216 (702)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHHHH
Confidence            9999999999988775433222    2667889999999977543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.11  E-value=8.4e-05  Score=86.01  Aligned_cols=175  Identities=15%  Similarity=0.151  Sum_probs=96.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCC-eEEEEEcCCcCHHHHHHHHH-HHhhccCCCccCHHHHHHHHHHH--
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEP-KAWVCVSDDFDVLRISKAIL-DSIKRSSCKLEDLNSVQLELKET--   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~-~~w~~~~~~~~~~~~~~~i~-~~l~~~~~~~~~~~~~~~~l~~~--   87 (1237)
                      .+.+.++|+.|+||||+|+.++..... ..... --+..+....+...+....- ............++++...+...  
T Consensus        43 ~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~  122 (507)
T PRK06645         43 AGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEY  122 (507)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHh
Confidence            457889999999999999998875421 11100 00111111111111100000 00000000112233333332221  


Q ss_pred             --hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE-EeCchhHHHhhc-CCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           88 --VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV-TTRSMDVALTMG-SGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        88 --l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili-TtR~~~~~~~~~-~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                        ..+++-++|+|+++.-....+..+...+....+.+.+|+ |++...+...+. ....+++.+++.+|..+.+...+..
T Consensus       123 ~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~  202 (507)
T PRK06645        123 KPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQ  202 (507)
T ss_pred             ccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHH
Confidence              234677899999976555666677666655455666554 555444443332 2357899999999999999988754


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      .+...    ..+++..|++.++|.+--+
T Consensus       203 egi~i----e~eAL~~Ia~~s~GslR~a  226 (507)
T PRK06645        203 ENLKT----DIEALRIIAYKSEGSARDA  226 (507)
T ss_pred             cCCCC----CHHHHHHHHHHcCCCHHHH
Confidence            33222    2567788999999977443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.10  E-value=4.5e-05  Score=87.89  Aligned_cols=158  Identities=16%  Similarity=0.185  Sum_probs=89.9

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH-hc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET-VF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~-l~   89 (1237)
                      +..+.+.++|++|+||||+|+.+++.. ...|   +.++.... .... .+.+..                 ..... ..
T Consensus        34 ~~~~~ilL~GppGtGKTtLA~~ia~~~-~~~~---~~l~a~~~-~~~~-ir~ii~-----------------~~~~~~~~   90 (413)
T PRK13342         34 GRLSSMILWGPPGTGKTTLARIIAGAT-DAPF---EALSAVTS-GVKD-LREVIE-----------------EARQRRSA   90 (413)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHh-CCCE---EEEecccc-cHHH-HHHHHH-----------------HHHHhhhc
Confidence            345578899999999999999988743 2111   22222111 1111 111111                 11111 13


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEE--eCchhHH--Hh-hcCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVT--TRSMDVA--LT-MGSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliT--tR~~~~~--~~-~~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                      +++.+|++|+++.-.....+.+...+.   .+..++|.  |.+....  .. ......+.+.+++.++..+++.+.+...
T Consensus        91 g~~~vL~IDEi~~l~~~~q~~LL~~le---~~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~  167 (413)
T PRK13342         91 GRRTILFIDEIHRFNKAQQDALLPHVE---DGTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDK  167 (413)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhh---cCcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHh
Confidence            578899999997654444444443332   24445543  3333211  11 1223578999999999999998865321


Q ss_pred             CCCCCCCChHHHHHHHHHHccCCchHHHHHH
Q 000887          165 RDAGTHGNFESTRQRVVEKCKGLPLAARALG  195 (1237)
Q Consensus       165 ~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~  195 (1237)
                      .... ..-..++...|++.++|-+..+..+.
T Consensus       168 ~~~~-i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        168 ERGL-VELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             hcCC-CCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            1111 12236678899999999987765443

>PRK05642 DNA replication initiation factor; Validated

Probab=98.10  E-value=3.1e-05  Score=81.28  Aligned_cols=156  Identities=19%  Similarity=0.174  Sum_probs=94.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ...+.|+|..|+|||.||.++++..... -..++|++..+      +...              ..    .+.+.+++-.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~-~~~v~y~~~~~------~~~~--------------~~----~~~~~~~~~d   99 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQR-GEPAVYLPLAE------LLDR--------------GP----ELLDNLEQYE   99 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC-CCcEEEeeHHH------HHhh--------------hH----HHHHhhhhCC
Confidence            3678999999999999999988744332 24577876422      1111              01    1222233333


Q ss_pred             EEEEEeCCCCCC-hhhHHH-hhccccC-CCCCcEEEEEeCchhH---------HHhhcCCCeEeCCCCChhhhHHHHHHH
Q 000887           93 FLIVLDDVWSER-YDLWQA-LKSPFMA-GAPGSRIIVTTRSMDV---------ALTMGSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        93 ~LlvlDdv~~~~-~~~~~~-~~~~~~~-~~~~~~iliTtR~~~~---------~~~~~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                       +||+||+.... ...|.. +...+.. ...|..+|+|++....         ..++....++++++++.++-.++++.+
T Consensus       100 -~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~k  178 (234)
T PRK05642        100 -LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLR  178 (234)
T ss_pred             -EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHH
Confidence             67889995321 123322 3333322 2346789999885432         122333467899999999999999866


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHh
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLL  198 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l  198 (1237)
                      +.......+    +++..-|++.+.|-.-++..+-..+
T Consensus       179 a~~~~~~l~----~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        179 ASRRGLHLT----DEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             HHHcCCCCC----HHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            643322121    5778888888888776665554444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.08  E-value=8.4e-05  Score=84.28  Aligned_cols=178  Identities=18%  Similarity=0.117  Sum_probs=95.2

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCC-CeEEEEEcCCcCH--HHHHH--HHHHHhhcc-CCCccCHHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDV--LRISK--AILDSIKRS-SCKLEDLNSVQLELK   85 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~--~~~~~--~i~~~l~~~-~~~~~~~~~~~~~l~   85 (1237)
                      ..+.+.++|++|+|||++|+++++......+. ..+++++.+-...  ..+..  .....++.. .......+.....+.
T Consensus        35 ~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (337)
T PRK12402         35 NLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLK  114 (337)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHH
Confidence            44568899999999999999988754433322 2345554321100  00000  000000000 000011122221121


Q ss_pred             HHh-----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhh-cCCCeEeCCCCChhhhHHHHH
Q 000887           86 ETV-----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFV  158 (1237)
Q Consensus        86 ~~l-----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~  158 (1237)
                      ...     ...+-+||+||++.-.......+...+......+++|+|+..+. +...+ .....+++.+++.++..+++.
T Consensus       115 ~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~  194 (337)
T PRK12402        115 EYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLE  194 (337)
T ss_pred             HHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHH
Confidence            111     13455899999955433333344444433345677888775432 22222 222578899999999999998


Q ss_pred             HHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          159 AHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      ..+...+...    ..++++.+++.++|.+-.+..
T Consensus       195 ~~~~~~~~~~----~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        195 SIAEAEGVDY----DDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             HHHHHcCCCC----CHHHHHHHHHHcCCCHHHHHH
Confidence            8764333222    267888999999987666543

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

Probab=98.07  E-value=8.4e-08  Score=96.34  Aligned_cols=132  Identities=21%  Similarity=0.271  Sum_probs=67.8

Q ss_pred             CCcccEEEEcCCCCccccccccCCcccccEEeecccccccccc--ccccCCCCCceeeeccCCCcccCCCCCCCCcchhh
Q 000887          967 PVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLP--KGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDV 1044 (1237)
Q Consensus       967 ~~~L~~L~l~~c~~~~~~~~~~~~l~~L~~L~l~~~~~l~~l~--~~l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l 1044 (1237)
                      +.+|+.|.+.+...-..+...+..-.+|+.|+|+.|..+++..  -.+.+|+.|..|+++.|...++......       
T Consensus       209 C~kLk~lSlEg~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~ll~~scs~L~~LNlsWc~l~~~~Vtv~V-------  281 (419)
T KOG2120|consen  209 CSKLKNLSLEGLRLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQLLLSSCSRLDELNLSWCFLFTEKVTVAV-------  281 (419)
T ss_pred             HHhhhhccccccccCcHHHHHHhccccceeeccccccccchhHHHHHHHhhhhHhhcCchHhhccchhhhHHH-------
Confidence            3455555555554444444445555677777777777776532  2456777777777777754443211100       


Q ss_pred             hhhccccccccCCCCCCCcccEEeccCCCCccccCCC------CCCCCcCceEecCCCCcccccccccCCCCCCceEEEc
Q 000887         1045 LIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEE------GLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYID 1118 (1237)
Q Consensus      1045 ~l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~------~~~~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~ 1118 (1237)
                        .           .--+.|..|+++||..  .+...      ..+++|.+||+++|..++.-....|-.++.|++|.++
T Consensus       282 --~-----------hise~l~~LNlsG~rr--nl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSls  346 (419)
T KOG2120|consen  282 --A-----------HISETLTQLNLSGYRR--NLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLS  346 (419)
T ss_pred             --h-----------hhchhhhhhhhhhhHh--hhhhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchheeeehh
Confidence              0           0124566666666642  11111      2245555555555555433222233445555555555


Q ss_pred             CC
Q 000887         1119 GC 1120 (1237)
Q Consensus      1119 ~c 1120 (1237)
                      .|
T Consensus       347 RC  348 (419)
T KOG2120|consen  347 RC  348 (419)
T ss_pred             hh
Confidence            55

>PRK04195 replication factor C large subunit; Provisional

Probab=98.07  E-value=0.0003  Score=82.88  Aligned_cols=222  Identities=17%  Similarity=0.130  Sum_probs=121.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .+.+.|+|++|+|||++|.++++..   .++ ++-+++++..+...+ ..++.......              .....++
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~el---~~~-~ielnasd~r~~~~i-~~~i~~~~~~~--------------sl~~~~~   99 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALANDY---GWE-VIELNASDQRTADVI-ERVAGEAATSG--------------SLFGARR   99 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc---CCC-EEEEcccccccHHHH-HHHHHHhhccC--------------cccCCCC
Confidence            6789999999999999999998753   122 444555444333222 22222221110              0011367


Q ss_pred             EEEEEeCCCCCCh----hhHHHhhccccCCCCCcEEEEEeCchh-HHH-hh-cCCCeEeCCCCChhhhHHHHHHHhcCCC
Q 000887           93 FLIVLDDVWSERY----DLWQALKSPFMAGAPGSRIIVTTRSMD-VAL-TM-GSGKNYELKLLSDDDCWSVFVAHAFEGR  165 (1237)
Q Consensus        93 ~LlvlDdv~~~~~----~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~-~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~  165 (1237)
                      -+||+|+++.-..    ....++...+.  ..+..||+|+.+.. ... .+ .....+++.+++.++....+...+...+
T Consensus       100 kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~eg  177 (482)
T PRK04195        100 KLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEG  177 (482)
T ss_pred             eEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcC
Confidence            8999999965321    22344443333  23344666664332 111 11 2235789999999999999888775433


Q ss_pred             CCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcC-C--CHHHHHHHHhhcccccCCCCChhHHHHHHhh-cChHHHHH
Q 000887          166 DAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSK-Q--GVDEWRAILDSKIWNLQDKTEIPSVLKLSYH-HLPSHLKR  241 (1237)
Q Consensus       166 ~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~-~--~~~~~~~~l~~~~~~~~~~~~i~~~l~~s~~-~L~~~~~~  241 (1237)
                      ...    ..++...|++.++|-.-.+......+... .  +.+.......     ......++.++..-+. .-......
T Consensus       178 i~i----~~eaL~~Ia~~s~GDlR~ain~Lq~~a~~~~~it~~~v~~~~~-----~d~~~~if~~l~~i~~~k~~~~a~~  248 (482)
T PRK04195        178 IEC----DDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDVKTLGR-----RDREESIFDALDAVFKARNADQALE  248 (482)
T ss_pred             CCC----CHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCCcHHHHHHhhc-----CCCCCCHHHHHHHHHCCCCHHHHHH
Confidence            222    25778999999998666544333333322 1  1233322221     1113567777776665 33333433


Q ss_pred             HHhhhccCCCCcccChHHHHHHHHHcCCCcc
Q 000887          242 CFAYCAVLPKDYEFKEKELVLLWIAEGLVQQ  272 (1237)
Q Consensus       242 ~~~~la~~~~~~~~~~~~l~~~w~~~g~~~~  272 (1237)
                      .+..       ..++. ..+..|+.+.+...
T Consensus       249 ~~~~-------~~~~~-~~i~~~l~en~~~~  271 (482)
T PRK04195        249 ASYD-------VDEDP-DDLIEWIDENIPKE  271 (482)
T ss_pred             HHHc-------ccCCH-HHHHHHHHhccccc
Confidence            3322       12333 34667999988764

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

Probab=98.07  E-value=4.6e-08  Score=98.18  Aligned_cols=163  Identities=18%  Similarity=0.163  Sum_probs=91.7

Q ss_pred             cCCcccccEEeeccccccccccccccCCCCCceeeeccCCCcccCCCCCCCCcchhhhhhccccccccCCCCCCCcccEE
Q 000887          988 FHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLREL 1067 (1237)
Q Consensus       988 ~~~l~~L~~L~l~~~~~l~~l~~~l~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l~l~~~~~~~~~~~~~~l~~L~~L 1067 (1237)
                      +..+.+|+.|.|.+..--..+...+..=.+|+.|++++|..++.......                    +.+|+.|.+|
T Consensus       206 Ls~C~kLk~lSlEg~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~ll--------------------~~scs~L~~L  265 (419)
T KOG2120|consen  206 LSQCSKLKNLSLEGLRLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQLL--------------------LSSCSRLDEL  265 (419)
T ss_pred             HHHHHhhhhccccccccCcHHHHHHhccccceeeccccccccchhHHHHH--------------------HHhhhhHhhc
Confidence            44456666666666443334444555556677777777766654322110                    1367788888


Q ss_pred             eccCCCCccccCCC---CCCCCcCceEecCCCCc--ccccccccCCCCCCceEEEcCCCCceeccCCCCccccCCCcCee
Q 000887         1068 ALSECPGIVVFPEE---GLSTNLTDLEISGDNMY--KPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSI 1142 (1237)
Q Consensus      1068 ~l~~c~~l~~~~~~---~~~~~L~~L~l~~~~~~--~~~~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L 1142 (1237)
                      +++-|.........   ...++|+.|.++||...  ..-.+.....|++|.+|++++|..++.  ....++..++.|++|
T Consensus       266 NlsWc~l~~~~Vtv~V~hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~--~~~~~~~kf~~L~~l  343 (419)
T KOG2120|consen  266 NLSWCFLFTEKVTVAVAHISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDLSDSVMLKN--DCFQEFFKFNYLQHL  343 (419)
T ss_pred             CchHhhccchhhhHHHhhhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeeccccccccCc--hHHHHHHhcchheee
Confidence            88888543322111   23568888888887543  111121235688888888888766553  112233355667777


Q ss_pred             eecCCCCccccCcccCCCCCCCCeeeecCC
Q 000887         1143 TISDFPKLKRLSSKGFQYLVSLEHLSVFSC 1172 (1237)
Q Consensus      1143 ~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c 1172 (1237)
                      .++.|-.+.--..-.+...|+|.+|++.+|
T Consensus       344 SlsRCY~i~p~~~~~l~s~psl~yLdv~g~  373 (419)
T KOG2120|consen  344 SLSRCYDIIPETLLELNSKPSLVYLDVFGC  373 (419)
T ss_pred             ehhhhcCCChHHeeeeccCcceEEEEeccc
Confidence            777764332111123445666777777665

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.07  E-value=0.0001  Score=85.79  Aligned_cols=171  Identities=16%  Similarity=0.105  Sum_probs=95.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh---
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV---   88 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l---   88 (1237)
                      ...+.++|++|+||||+|+.+++... ...++..+|.+.+.. .+......-...+...  .....++... +.+.+   
T Consensus        36 ~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~-~i~~~~h~dv~el~~~--~~~~vd~iR~-l~~~~~~~  111 (504)
T PRK14963         36 GHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCL-AVRRGAHPDVLEIDAA--SNNSVEDVRD-LREKVLLA  111 (504)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhH-HHhcCCCCceEEeccc--ccCCHHHHHH-HHHHHhhc
Confidence            35669999999999999999887542 122222223221000 0000000000000000  1112222222 22211   


Q ss_pred             --cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           89 --FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        89 --~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                        .+++-++|+|+++......+..+...+-....++.+|+++... .+...+ .....+++.+++.++..+.+...+...
T Consensus       112 p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~e  191 (504)
T PRK14963        112 PLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAE  191 (504)
T ss_pred             cccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHHHHHHHc
Confidence              2466789999997655555666666665544555655555433 332222 223589999999999999998877543


Q ss_pred             CCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          165 RDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       165 ~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      +...    .++++..|++.++|.+--+
T Consensus       192 gi~i----~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        192 GREA----EPEALQLVARLADGAMRDA  214 (504)
T ss_pred             CCCC----CHHHHHHHHHHcCCCHHHH
Confidence            3222    2677899999999988644

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.05  E-value=0.00023  Score=83.71  Aligned_cols=175  Identities=15%  Similarity=0.113  Sum_probs=96.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcCHHHHHHH-HHHHhhccCCCccCHHHHHHHHHHH---
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFDVLRISKA-ILDSIKRSSCKLEDLNSVQLELKET---   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~~~~~~~~-i~~~l~~~~~~~~~~~~~~~~l~~~---   87 (1237)
                      ...+.++|..|+||||+|+.++.... ....+.   ..++...+...+... ..+.+..........++....+...   
T Consensus        38 ~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~---~PCG~C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~  114 (830)
T PRK07003         38 HHAYLFTGTRGVGKTTLSRIFAKALNCETGVTS---QPCGVCRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYA  114 (830)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCccCCCC---CCCcccHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhc
Confidence            45668999999999999999877542 111110   011111111111000 0000000000112223333222221   


Q ss_pred             -hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhH-HHhh-cCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           88 -VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV-ALTM-GSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        88 -l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~-~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                       ..++.-++|+|+++.-+...+..+...+-....++++|+||++..- ...+ .....+.+..++.++..+.+.+.+...
T Consensus       115 P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~E  194 (830)
T PRK07003        115 PVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEE  194 (830)
T ss_pred             cccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHc
Confidence             1235568999999665555566666655544567887777776532 2222 122579999999999999998876543


Q ss_pred             CCCCCCCChHHHHHHHHHHccCCc-hHHHHH
Q 000887          165 RDAGTHGNFESTRQRVVEKCKGLP-LAARAL  194 (1237)
Q Consensus       165 ~~~~~~~~~~~~~~~i~~~~~g~P-Lal~~~  194 (1237)
                      ....    ..+....|++.++|.. -|+.++
T Consensus       195 gI~i----d~eAL~lIA~~A~GsmRdALsLL  221 (830)
T PRK07003        195 RIAF----EPQALRLLARAAQGSMRDALSLT  221 (830)
T ss_pred             CCCC----CHHHHHHHHHHcCCCHHHHHHHH
Confidence            3222    2677889999998855 455553

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=98.02  E-value=5.2e-06  Score=59.90  Aligned_cols=38  Identities=32%  Similarity=0.440  Sum_probs=19.8

Q ss_pred             CccEEEccccccccccccccCCCCCCeEEccCCCcccc
Q 000887          401 KLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCL  438 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~l  438 (1237)
                      +|++|++++|.|+.+|..+++|++|++|++++|.|+++
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i   39 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDI   39 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBE
T ss_pred             cceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCC
Confidence            45555555555555555555555555555555555544

...

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.01  E-value=0.00022  Score=82.35  Aligned_cols=164  Identities=17%  Similarity=0.117  Sum_probs=91.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC--------------------CCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA--------------------FEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~--------------------f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|++|+||||+|+.+++......                    +..++.++.........+. .+......   
T Consensus        36 ~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~~~gid~iR-~i~~~~~~---  111 (472)
T PRK14962         36 SHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAASNRGIDEIR-KIRDAVGY---  111 (472)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcccCCHHHHH-HHHHHHhh---
Confidence            35678999999999999999887532110                    1112233222121121111 11111100   


Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCCh
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSD  150 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~  150 (1237)
                                   .-..+++-++|+|+++.-.....+.+...+-..+....+|++|.+ ..+...+ .....+++.+++.
T Consensus       112 -------------~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~  178 (472)
T PRK14962        112 -------------RPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISD  178 (472)
T ss_pred             -------------ChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccH
Confidence                         001246679999999543333444455444433344544444433 3333332 2235889999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccC-CchHHHHHHhH
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKG-LPLAARALGGL  197 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g-~PLal~~~~~~  197 (1237)
                      ++....+...+.......    .++++..|++.++| .+.|+..+...
T Consensus       179 ~el~~~L~~i~~~egi~i----~~eal~~Ia~~s~GdlR~aln~Le~l  222 (472)
T PRK14962        179 ELIIKRLQEVAEAEGIEI----DREALSFIAKRASGGLRDALTMLEQV  222 (472)
T ss_pred             HHHHHHHHHHHHHcCCCC----CHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            999999888774332222    25678889998765 56677666543

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.00  E-value=0.00015  Score=76.07  Aligned_cols=182  Identities=14%  Similarity=0.100  Sum_probs=112.5

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcc-ccc----CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHH
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK-LTE----AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLEL   84 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~-~~~----~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l   84 (1237)
                      ....+.+.|+|.+|.|||+++++++... ...    .--.|+.+.....++...++..|+.+++.+........+.....
T Consensus        58 ~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~  137 (302)
T PF05621_consen   58 RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQV  137 (302)
T ss_pred             ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHH
Confidence            3567789999999999999999987633 111    11147788888889999999999999998876666666666666


Q ss_pred             HHHhcC-CcEEEEEeCCCCC---ChhhHH---HhhccccCCCCCcEEEEEeCchhHHHhh-----cCCCeEeCCCCChhh
Q 000887           85 KETVFK-KKFLIVLDDVWSE---RYDLWQ---ALKSPFMAGAPGSRIIVTTRSMDVALTM-----GSGKNYELKLLSDDD  152 (1237)
Q Consensus        85 ~~~l~~-~~~LlvlDdv~~~---~~~~~~---~~~~~~~~~~~~~~iliTtR~~~~~~~~-----~~~~~~~l~~l~~~e  152 (1237)
                      .+.++. +.-+||+|++.+.   ....-.   .....+...-.=+-|.|-|++.--+...     .....+.++....++
T Consensus       138 ~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa~RF~~~~Lp~W~~d~  217 (302)
T PF05621_consen  138 LRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLASRFEPFELPRWELDE  217 (302)
T ss_pred             HHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHHhccCCccCCCCCCCc
Confidence            666665 5678999999441   011111   1222222222334566777654332211     112467788777655


Q ss_pred             h-HHHHHHHhcCCC-CCCCCCChHHHHHHHHHHccCCchHH
Q 000887          153 C-WSVFVAHAFEGR-DAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       153 a-~~l~~~~~~~~~-~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      . ..|+......-. .....-..++.++.|.+.++|+.=-+
T Consensus       218 ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l  258 (302)
T PF05621_consen  218 EFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGEL  258 (302)
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHH
Confidence            4 444433321111 11111234788999999999976443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

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

Probab=98.00  E-value=9.6e-06  Score=84.75  Aligned_cols=88  Identities=22%  Similarity=0.154  Sum_probs=59.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC--cCHHHHHHHHHHHhhccCCCccCHH------HHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD--FDVLRISKAILDSIKRSSCKLEDLN------SVQLELK   85 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~------~~~~~l~   85 (1237)
                      ..++|.|++|+|||||++++++.....+|+.++|+.+...  .++.++++.+...+-..........      .......
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~   96 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAK   96 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence            5789999999999999999998665558998889987666  6888999888333322211111111      1111122


Q ss_pred             HH-hcCCcEEEEEeCCC
Q 000887           86 ET-VFKKKFLIVLDDVW  101 (1237)
Q Consensus        86 ~~-l~~~~~LlvlDdv~  101 (1237)
                      .+ -.++++++++|++.
T Consensus        97 ~~~~~G~~vll~iDei~  113 (249)
T cd01128          97 RLVEHGKDVVILLDSIT  113 (249)
T ss_pred             HHHHCCCCEEEEEECHH
Confidence            11 24689999999993

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PLN03150 hypothetical protein; Provisional

Probab=97.99  E-value=1.1e-05  Score=97.73  Aligned_cols=97  Identities=22%  Similarity=0.431  Sum_probs=84.0

Q ss_pred             hhhhhcCCCCCccEEEccccccc-cccccccCCCCCCeEEccCCCcc-ccchhhcccCCccEEEcCccccCccCChhhcc
Q 000887          391 VLSDLLPQCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILILRNCWCLLKLPSRIGN  468 (1237)
Q Consensus       391 ~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~~~~l~~Lr~L~L~~~~i~-~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~  468 (1237)
                      .+|..+..+++|+.|+|++|.+. .+|..++.+++|++|+|++|.+. .+|..++++++|++|+|++|.....+|..++.
T Consensus       433 ~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls~N~l~g~iP~~l~~  512 (623)
T PLN03150        433 FIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLNGNSLSGRVPAALGG  512 (623)
T ss_pred             cCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECcCCcccccCChHHhh
Confidence            45666889999999999999997 78989999999999999999998 78999999999999999999666799999875


Q ss_pred             -cccccEEeccCCCccccCc
Q 000887          469 -LVNLHYLNIEGASALRELP  487 (1237)
Q Consensus       469 -L~~L~~L~l~~~~~l~~ip  487 (1237)
                       +.++..+++.+|..+...|
T Consensus       513 ~~~~~~~l~~~~N~~lc~~p  532 (623)
T PLN03150        513 RLLHRASFNFTDNAGLCGIP  532 (623)
T ss_pred             ccccCceEEecCCccccCCC
Confidence             4678899999885544444

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.99  E-value=0.00012  Score=84.87  Aligned_cols=175  Identities=15%  Similarity=0.112  Sum_probs=94.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCC---CCeEEEEEcCCcCHHHHHHH-HHHHhhccCCCccCHHHHHHHHHHH-
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAF---EPKAWVCVSDDFDVLRISKA-ILDSIKRSSCKLEDLNSVQLELKET-   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f---~~~~w~~~~~~~~~~~~~~~-i~~~l~~~~~~~~~~~~~~~~l~~~-   87 (1237)
                      ...+.++|..|+||||+|+.++....-..-   .+...-.++...+...+... ..+.+.........++++...+... 
T Consensus        38 pHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~  117 (700)
T PRK12323         38 HHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAV  117 (700)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHH
Confidence            356789999999999999998875421100   00000001111000000000 0000000101112334433333222 


Q ss_pred             ---hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcE-EEEEeCchhHHHhhcC-CCeEeCCCCChhhhHHHHHHHhc
Q 000887           88 ---VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR-IIVTTRSMDVALTMGS-GKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        88 ---l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iliTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                         ..++.-++|+|+++.-+......+...+-.-..+++ |++||....+...+.+ ...+.+..++.++..+.+.+.+.
T Consensus       118 ~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~  197 (700)
T PRK12323        118 YAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILG  197 (700)
T ss_pred             hchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHH
Confidence               134667999999976555566666665544445566 4555554455433322 25789999999999999887764


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ..+..    ...+....|++.++|.|...
T Consensus       198 ~Egi~----~d~eAL~~IA~~A~Gs~RdA  222 (700)
T PRK12323        198 EEGIA----HEVNALRLLAQAAQGSMRDA  222 (700)
T ss_pred             HcCCC----CCHHHHHHHHHHcCCCHHHH
Confidence            32221    12556788999999988643

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=6.3e-05  Score=84.93  Aligned_cols=171  Identities=15%  Similarity=0.058  Sum_probs=94.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc-cCCCccCHHHHHH---HHHH-Hh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR-SSCKLEDLNSVQL---ELKE-TV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~-~~~~~~~~~~~~~---~l~~-~l   88 (1237)
                      ..+.++|+.|+||||+|+.++..........  ...+....+...+.......+.. .......+++...   .+.. -.
T Consensus        41 ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~--~~pCg~C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~  118 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARILAKRLNCENPIG--NEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPM  118 (484)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCcccccC--ccccCCCcHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhh
Confidence            4579999999999999999887542221111  01111222222221111110000 0001112222222   2221 12


Q ss_pred             cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEE-EEeCchhHHHhhcC-CCeEeCCCCChhhhHHHHHHHhcCCCC
Q 000887           89 FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRII-VTTRSMDVALTMGS-GKNYELKLLSDDDCWSVFVAHAFEGRD  166 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~il-iTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~l~~~~~~~~~~  166 (1237)
                      .++.-++|+|+|+.-....+.++...+-.......+| .||....+...+.. ...+.+.+++.++..+.+.+.+...+.
T Consensus       119 ~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi  198 (484)
T PRK14956        119 GGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENV  198 (484)
T ss_pred             cCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCC
Confidence            3466799999997666566667666554434455544 45444444333322 257999999999999988887643322


Q ss_pred             CCCCCChHHHHHHHHHHccCCchH
Q 000887          167 AGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       167 ~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      .    -..+++..|++.++|.+.-
T Consensus       199 ~----~e~eAL~~Ia~~S~Gd~Rd  218 (484)
T PRK14956        199 Q----YDQEGLFWIAKKGDGSVRD  218 (484)
T ss_pred             C----CCHHHHHHHHHHcCChHHH
Confidence            2    2267789999999998743

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=0.00061  Score=79.48  Aligned_cols=161  Identities=16%  Similarity=0.106  Sum_probs=94.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-c-------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-E-------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~-------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|+.|+||||+|+.++..... .                   .|..+++++......+++              
T Consensus        38 ~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~~gvd~--------------  103 (546)
T PRK14957         38 HHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEE--------------  103 (546)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccccCHHH--------------
Confidence            355789999999999999998874321 1                   122233332211111111              


Q ss_pred             CccCHHHHHHHHHH-HhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEE-EEeCchhHHHhh-cCCCeEeCCCCC
Q 000887           73 KLEDLNSVQLELKE-TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRII-VTTRSMDVALTM-GSGKNYELKLLS  149 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~-~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~il-iTtR~~~~~~~~-~~~~~~~l~~l~  149 (1237)
                          ..++...+.. -..+++-++|+|+++.-.......+...+-..+..+++| +||....+...+ .....+++.+++
T Consensus       104 ----ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls  179 (546)
T PRK14957        104 ----TKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHIS  179 (546)
T ss_pred             ----HHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECChhhhhhhHHHheeeEEeCCCC
Confidence                1111111111 123567799999996655555666666655544566555 555444343222 223689999999


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCch-HHHHHH
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL-AARALG  195 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL-al~~~~  195 (1237)
                      .++..+.+...+...+.    ...++++..|++.++|-+- |+..+-
T Consensus       180 ~~eI~~~L~~il~~egi----~~e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        180 QADIKDQLKIILAKENI----NSDEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             HHHHHHHHHHHHHHcCC----CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            99998888876543221    1236677899999999664 555543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=0.00013  Score=87.67  Aligned_cols=100  Identities=12%  Similarity=0.076  Sum_probs=67.0

Q ss_pred             cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCC
Q 000887           89 FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRD  166 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~  166 (1237)
                      .+++-++|+|+++.-.......+...+-....++++|++|.+. .+...+ .....+++.+++.++..+.+.+.+.....
T Consensus       117 ~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI  196 (944)
T PRK14949        117 RGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL  196 (944)
T ss_pred             cCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC
Confidence            3567899999996655566666666554444566666555443 333222 22368999999999999999887643221


Q ss_pred             CCCCCChHHHHHHHHHHccCCchHHH
Q 000887          167 AGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       167 ~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                          ....+.+..|++.++|.|--+.
T Consensus       197 ----~~edeAL~lIA~~S~Gd~R~AL  218 (944)
T PRK14949        197 ----PFEAEALTLLAKAANGSMRDAL  218 (944)
T ss_pred             ----CCCHHHHHHHHHHcCCCHHHHH
Confidence                2236778899999999886443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.93  E-value=0.00027  Score=79.47  Aligned_cols=160  Identities=17%  Similarity=0.120  Sum_probs=91.8

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEE--cCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV--SDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~--~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ..+.+.++|.+|+|||++|+.+++......+.. .++.+  +.......+...+ ..+.....              ...
T Consensus        37 ~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~-~~i~~~~~~~~~~~~~~~~i-~~~~~~~~--------------~~~  100 (319)
T PRK00440         37 NMPHLLFAGPPGTGKTTAALALARELYGEDWRE-NFLELNASDERGIDVIRNKI-KEFARTAP--------------VGG  100 (319)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHcCCcccc-ceEEeccccccchHHHHHHH-HHHHhcCC--------------CCC
Confidence            345579999999999999999887544333322 22222  2222222111111 11111000              001


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      ..+-++|+|+++.-.......+...+......+++|+++.... +.... .....+++.++++++....+...+...+..
T Consensus       101 ~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~  180 (319)
T PRK00440        101 APFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIE  180 (319)
T ss_pred             CCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCC
Confidence            2456899999955433344445544444445677777764322 11111 122478999999999999988877543322


Q ss_pred             CCCCChHHHHHHHHHHccCCchHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      .    .++++..+++.++|.+.-+
T Consensus       181 i----~~~al~~l~~~~~gd~r~~  200 (319)
T PRK00440        181 I----TDDALEAIYYVSEGDMRKA  200 (319)
T ss_pred             C----CHHHHHHHHHHcCCCHHHH
Confidence            2    2667899999999987653

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.92  E-value=2.6e-05  Score=84.55  Aligned_cols=87  Identities=22%  Similarity=0.198  Sum_probs=59.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc--CHHHHHHHHHHHhhccCCCccCHHHHHH------HHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF--DVLRISKAILDSIKRSSCKLEDLNSVQL------ELK   85 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~~~~~~------~l~   85 (1237)
                      ...+|+|++|+||||||+++|+.....+|+.++|+.+.+..  .+.++++.+...+-..... ..++....      ...
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d-~~~~~~~~~a~~~ie~A  248 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFD-EPAERHVQVAEMVIEKA  248 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCC-CCHHHHHHHHHHHHHHH
Confidence            35689999999999999999987655589999999988776  7778888886433222211 11111111      111


Q ss_pred             HH--hcCCcEEEEEeCCC
Q 000887           86 ET--VFKKKFLIVLDDVW  101 (1237)
Q Consensus        86 ~~--l~~~~~LlvlDdv~  101 (1237)
                      ++  -.+++++|++|++.
T Consensus       249 e~~~e~G~dVlL~iDsIt  266 (416)
T PRK09376        249 KRLVEHGKDVVILLDSIT  266 (416)
T ss_pred             HHHHHcCCCEEEEEEChH
Confidence            22  24689999999993

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.92  E-value=1.1e-05  Score=58.29  Aligned_cols=41  Identities=34%  Similarity=0.441  Sum_probs=30.3

Q ss_pred             CCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCCh
Q 000887          423 KQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPS  464 (1237)
Q Consensus       423 ~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~  464 (1237)
                      ++|++|++++|.|+++|..+++|++|++|++++| .+..+|.
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N-~i~~i~~   41 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNN-PISDISP   41 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSS-CCSBEGG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCC-CCCCCcC
Confidence            4688888888888888777888888888888887 6665543

...

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.91  E-value=0.00017  Score=83.25  Aligned_cols=163  Identities=18%  Similarity=0.147  Sum_probs=96.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCC-CeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..-+.|+|.+|+|||+||.++++...+.... .++|++.      .++..++...+...     ..++    +++..+..
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~------~~f~~~~~~~~~~~-----~~~~----f~~~~~~~  194 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS------EKFLNDLVDSMKEG-----KLNE----FREKYRKK  194 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHhcc-----cHHH----HHHHHHhc
Confidence            4459999999999999999998865443333 4567753      34455555544321     1222    23333334


Q ss_pred             cEEEEEeCCCCCC-hhh-HHHhhccccC-CCCCcEEEEEeC-chhHH--------HhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSER-YDL-WQALKSPFMA-GAPGSRIIVTTR-SMDVA--------LTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~-~~~-~~~~~~~~~~-~~~~~~iliTtR-~~~~~--------~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      .-+||+||++... ... -..+...+.. ...|..||+||+ .+...        .++....++++++.+.++-.+++++
T Consensus       195 ~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~  274 (440)
T PRK14088        195 VDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARK  274 (440)
T ss_pred             CCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHH
Confidence            5688999995321 011 1122222211 123457888885 32221        1233345788999999999999998


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      .+.......+    ++++..|++...|..-.|.-+
T Consensus       275 ~~~~~~~~l~----~ev~~~Ia~~~~~~~R~L~g~  305 (440)
T PRK14088        275 MLEIEHGELP----EEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_pred             HHHhcCCCCC----HHHHHHHHhccccCHHHHHHH
Confidence            8754322222    677888999888866555443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.91  E-value=0.00027  Score=81.02  Aligned_cols=157  Identities=20%  Similarity=0.186  Sum_probs=96.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc--------------------ccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL--------------------TEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~--------------------~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|+.|+||||+|+.++....                    ...+..++.++......+.++. ++.......  
T Consensus        35 ~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~vddIR-~Iie~~~~~--  111 (491)
T PRK14964         35 PQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDDIK-VILENSCYL--  111 (491)
T ss_pred             CceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCCHHHHH-HHHHHHHhc--
Confidence            34788999999999999999876321                    0122334455443333332222 121111100  


Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeC-chhHHHhh-cCCCeEeCCCCCh
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTR-SMDVALTM-GSGKNYELKLLSD  150 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR-~~~~~~~~-~~~~~~~l~~l~~  150 (1237)
                                    -..++.-++|+|+++.-.......+...+-.-.+.+++|++|. ...+...+ .....+++.+++.
T Consensus       112 --------------P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~  177 (491)
T PRK14964        112 --------------PISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPT  177 (491)
T ss_pred             --------------cccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhheeeecccccH
Confidence                          0124667899999965554556666666655556676665554 34444333 2236789999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchH
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      ++..+.+...+...+...    .++++..|++.++|.+..
T Consensus       178 ~el~~~L~~ia~~Egi~i----~~eAL~lIa~~s~GslR~  213 (491)
T PRK14964        178 DKLVEHLVDIAKKENIEH----DEESLKLIAENSSGSMRN  213 (491)
T ss_pred             HHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHHH
Confidence            999999988775433322    266788999999997754

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.87  E-value=8e-05  Score=72.96  Aligned_cols=108  Identities=22%  Similarity=0.162  Sum_probs=58.8

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..+.+.|+|++|+|||++|++++..... ....++++..............+...            ............+
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~   84 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFR-PGAPFLYLNASDLLEGLVVAELFGHF------------LVRLLFELAEKAK   84 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhc-CCCCeEEEehhhhhhhhHHHHHhhhh------------hHhHHHHhhccCC
Confidence            3468999999999999999999875432 22346677654433222111111100            0111112222456


Q ss_pred             cEEEEEeCCCCCChhhHHHh---hccccCC---CCCcEEEEEeCchh
Q 000887           92 KFLIVLDDVWSERYDLWQAL---KSPFMAG---APGSRIIVTTRSMD  132 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~---~~~~~~~---~~~~~iliTtR~~~  132 (1237)
                      +.++|+||++.-.......+   .......   ..+..||+|+....
T Consensus        85 ~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          85 PGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             CeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence            89999999964211122222   2222221   36788888888643

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK06620 hypothetical protein; Validated

Probab=97.86  E-value=0.00015  Score=74.61  Aligned_cols=137  Identities=13%  Similarity=-0.008  Sum_probs=81.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +.+.|+|++|+|||+|+.++++.. .     ..++..  ...              .       +       +..+ ..-
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~-~-----~~~~~~--~~~--------------~-------~-------~~~~-~~d   87 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS-N-----AYIIKD--IFF--------------N-------E-------EILE-KYN   87 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc-C-----CEEcch--hhh--------------c-------h-------hHHh-cCC
Confidence            678999999999999999977642 1     122210  000              0       0       0111 234


Q ss_pred             EEEEeCCCCCChhhHHHhhccccC-CCCCcEEEEEeCchhH-------HHhhcCCCeEeCCCCChhhhHHHHHHHhcCCC
Q 000887           94 LIVLDDVWSERYDLWQALKSPFMA-GAPGSRIIVTTRSMDV-------ALTMGSGKNYELKLLSDDDCWSVFVAHAFEGR  165 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~-------~~~~~~~~~~~l~~l~~~ea~~l~~~~~~~~~  165 (1237)
                      ++++||++.-...   .+...+.. ...|..||+|++....       ..++....++++++++.++-.+++++.+...+
T Consensus        88 ~lliDdi~~~~~~---~lf~l~N~~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~  164 (214)
T PRK06620         88 AFIIEDIENWQEP---ALLHIFNIINEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             EEEEeccccchHH---HHHHHHHHHHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence            6788999532111   22222111 1346689999985432       23344445899999999998888887764322


Q ss_pred             CCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          166 DAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       166 ~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      -..+    ++++.-|++++.|---.+.-+
T Consensus       165 l~l~----~ev~~~L~~~~~~d~r~l~~~  189 (214)
T PRK06620        165 VTIS----RQIIDFLLVNLPREYSKIIEI  189 (214)
T ss_pred             CCCC----HHHHHHHHHHccCCHHHHHHH
Confidence            2222    667788888887765554433

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

Probab=97.84  E-value=0.00017  Score=75.29  Aligned_cols=158  Identities=15%  Similarity=0.160  Sum_probs=92.9

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ++..+.+.+||++|+|||+||+-++....+..   ..||..+....-..-.+.+..+...               ...+.
T Consensus       159 q~~ipSmIlWGppG~GKTtlArlia~tsk~~S---yrfvelSAt~a~t~dvR~ife~aq~---------------~~~l~  220 (554)
T KOG2028|consen  159 QNRIPSMILWGPPGTGKTTLARLIASTSKKHS---YRFVELSATNAKTNDVRDIFEQAQN---------------EKSLT  220 (554)
T ss_pred             cCCCCceEEecCCCCchHHHHHHHHhhcCCCc---eEEEEEeccccchHHHHHHHHHHHH---------------HHhhh
Confidence            36678899999999999999999887433332   4466655443222222223222110               11245


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE--EeCchhHHH---hhcCCCeEeCCCCChhhhHHHHHHHhc--
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV--TTRSMDVAL---TMGSGKNYELKLLSDDDCWSVFVAHAF--  162 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili--TtR~~~~~~---~~~~~~~~~l~~l~~~ea~~l~~~~~~--  162 (1237)
                      ++|.+|.+|.|..-+..+   .-..++....|.-++|  ||-++.+..   .+....++.|+.|..++-..++.+...  
T Consensus       221 krkTilFiDEiHRFNksQ---QD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l  297 (554)
T KOG2028|consen  221 KRKTILFIDEIHRFNKSQ---QDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASL  297 (554)
T ss_pred             cceeEEEeHHhhhhhhhh---hhcccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhh
Confidence            689999999994432222   2223455566776665  555554322   123336899999999999888877432  


Q ss_pred             -CCCC---CCCCC---ChHHHHHHHHHHccCCc
Q 000887          163 -EGRD---AGTHG---NFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       163 -~~~~---~~~~~---~~~~~~~~i~~~~~g~P  188 (1237)
                       +...   ..+.+   -...+.+-++..++|=.
T Consensus       298 ~dser~~~~l~n~s~~ve~siidyla~lsdGDa  330 (554)
T KOG2028|consen  298 GDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDA  330 (554)
T ss_pred             ccccccCCCCCCcchhhhHHHHHHHHHhcCchH
Confidence             2222   12221   23566777777888744

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.84  E-value=0.00069  Score=79.84  Aligned_cols=173  Identities=14%  Similarity=0.104  Sum_probs=92.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCeEEEEEcCCcCHHHHHHH-HHHHhhccCCCccCHHHHHHHHHHH---
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAWVCVSDDFDVLRISKA-ILDSIKRSSCKLEDLNSVQLELKET---   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~-i~~~l~~~~~~~~~~~~~~~~l~~~---   87 (1237)
                      ...+.++|+.|+||||+|+.++..... ....   +..++.......+... ..+-+.........++++...+...   
T Consensus        38 ~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~---~~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~  114 (709)
T PRK08691         38 HHAYLLTGTRGVGKTTIARILAKSLNCENAQH---GEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYA  114 (709)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhcccCCCC---CCCCcccHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhh
Confidence            456899999999999999998774321 1110   1111111100000000 0000000001112223333222211   


Q ss_pred             -hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           88 -VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        88 -l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                       ..+++-++|+|+++.-.......+...+-.....+++|++|.+. .+...+ +....+.+.+++.++..+.+.+.+...
T Consensus       115 P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kE  194 (709)
T PRK08691        115 PTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSE  194 (709)
T ss_pred             hhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHc
Confidence             12466789999996544444445555554444566777666543 222221 222467888999999999998877543


Q ss_pred             CCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          165 RDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       165 ~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      +...    ..+.+..|++.++|.+.-+.
T Consensus       195 gi~i----d~eAL~~Ia~~A~GslRdAl  218 (709)
T PRK08691        195 KIAY----EPPALQLLGRAAAGSMRDAL  218 (709)
T ss_pred             CCCc----CHHHHHHHHHHhCCCHHHHH
Confidence            3222    26678999999999885443

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.81  E-value=0.00024  Score=82.12  Aligned_cols=162  Identities=14%  Similarity=0.167  Sum_probs=94.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ...+.|+|..|+|||+||.++++...+... ..++|+++      .+....+...+...     ..+    .+.+.+++ 
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~------~~~~~~~~~~~~~~-----~~~----~~~~~~~~-  199 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS------EKFTNDFVNALRNN-----KME----EFKEKYRS-  199 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH------HHHHHHHHHHHHcC-----CHH----HHHHHHHh-
Confidence            356899999999999999999886543322 24567642      33344454444321     122    22333333 


Q ss_pred             cEEEEEeCCCCCChh-h-HHHhhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSERYD-L-WQALKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~-~-~~~~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      .-+||+||++..... . .+.+...+.. ...+..+|||+....         +..++.....+++++.+.++-.+++++
T Consensus       200 ~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~  279 (405)
T TIGR00362       200 VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQK  279 (405)
T ss_pred             CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHH
Confidence            347889999542111 1 1122222211 123556888886432         112222334789999999999999999


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      .+.......+    ++++..|++.+.|..-.+.-+
T Consensus       280 ~~~~~~~~l~----~e~l~~ia~~~~~~~r~l~~~  310 (405)
T TIGR00362       280 KAEEEGLELP----DEVLEFIAKNIRSNVRELEGA  310 (405)
T ss_pred             HHHHcCCCCC----HHHHHHHHHhcCCCHHHHHHH
Confidence            8854332222    677888999888877655443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.81  E-value=0.00068  Score=77.43  Aligned_cols=161  Identities=15%  Similarity=0.085  Sum_probs=92.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccccc---CC-----------------CCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE---AF-----------------EPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~---~f-----------------~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|++|+|||++|+.++......   .+                 ..+++++........ ..+++...+...  
T Consensus        36 ~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~--  112 (355)
T TIGR02397        36 AHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEIDAASNNGVD-DIREILDNVKYA--  112 (355)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeeccccCCHH-HHHHHHHHHhcC--
Confidence            3567899999999999999987754211   11                 112233222111111 111222221110  


Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhh-cCCCeEeCCCCCh
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSD  150 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~-~~~~~~~l~~l~~  150 (1237)
                                    -..+++-++|+|+++.-.......+...+......+.+|++|.+.. +...+ .....+++.++++
T Consensus       113 --------------p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~  178 (355)
T TIGR02397       113 --------------PSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPL  178 (355)
T ss_pred             --------------cccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCH
Confidence                          0123556899999955444445555555544445666666665443 22222 2235788999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      ++..+++...+...+...    .++++..+++.++|.|..+...
T Consensus       179 ~~l~~~l~~~~~~~g~~i----~~~a~~~l~~~~~g~~~~a~~~  218 (355)
T TIGR02397       179 EDIVERLKKILDKEGIKI----EDEALELIARAADGSLRDALSL  218 (355)
T ss_pred             HHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCChHHHHHH
Confidence            999999988764332222    2577889999999988655443

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=97.80  E-value=0.00025  Score=70.72  Aligned_cols=158  Identities=18%  Similarity=0.175  Sum_probs=80.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      +....+.++|++|+||||||.-+++.. ...|   .+.+...-...                     .+++..+.. + +
T Consensus        48 ~~l~h~lf~GPPG~GKTTLA~IIA~e~-~~~~---~~~sg~~i~k~---------------------~dl~~il~~-l-~  100 (233)
T PF05496_consen   48 EALDHMLFYGPPGLGKTTLARIIANEL-GVNF---KITSGPAIEKA---------------------GDLAAILTN-L-K  100 (233)
T ss_dssp             S---EEEEESSTTSSHHHHHHHHHHHC-T--E---EEEECCC--SC---------------------HHHHHHHHT----
T ss_pred             CCcceEEEECCCccchhHHHHHHHhcc-CCCe---EeccchhhhhH---------------------HHHHHHHHh-c-C
Confidence            456789999999999999999988842 3222   12322111111                     111111111 1 2


Q ss_pred             CcEEEEEeCCCCCChhhHHHhhccc--------cCCCCC-----------cEEEEEeCchhHHHhhcCC--CeEeCCCCC
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPF--------MAGAPG-----------SRIIVTTRSMDVALTMGSG--KNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~~~~~~--------~~~~~~-----------~~iliTtR~~~~~~~~~~~--~~~~l~~l~  149 (1237)
                      ++-+|++|++..-...+-+.+...+        ...+++           +-|=.|||...+...+...  ...+++..+
T Consensus       101 ~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~  180 (233)
T PF05496_consen  101 EGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYS  180 (233)
T ss_dssp             TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHCCCTTSSEEEE----T
T ss_pred             CCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchhHHhhcceecchhcCC
Confidence            3446677888543222222211111        111221           2344688876555444333  245799999


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhh
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLR  199 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~  199 (1237)
                      .+|-.++..+.+..-..    +-..+.+.+|++++.|-|--..-+-.+++
T Consensus       181 ~~el~~Iv~r~a~~l~i----~i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  181 EEELAKIVKRSARILNI----EIDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             HHHHHHHHHHCCHCTT-----EE-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhCC----CcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            99999999876643222    23378899999999999965444444433

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

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

Probab=97.78  E-value=5.2e-06  Score=96.21  Aligned_cols=102  Identities=23%  Similarity=0.280  Sum_probs=79.2

Q ss_pred             cCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEE
Q 000887          396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYL  475 (1237)
Q Consensus       396 ~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L  475 (1237)
                      +..+++|..|++.+|.|..+...+..+.+|++|++++|.|+.+. .+..+..|+.|++++| .+..++. +..+.+|+.+
T Consensus        91 l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N~I~~i~-~l~~l~~L~~L~l~~N-~i~~~~~-~~~l~~L~~l  167 (414)
T KOG0531|consen   91 LSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFNKITKLE-GLSTLTLLKELNLSGN-LISDISG-LESLKSLKLL  167 (414)
T ss_pred             cccccceeeeeccccchhhcccchhhhhcchheecccccccccc-chhhccchhhheeccC-cchhccC-Cccchhhhcc
Confidence            56778888888888888888776778888888888888888884 4777778888888888 7777765 6668888888


Q ss_pred             eccCCCccccCccc-ccccccccccce
Q 000887          476 NIEGASALRELPLG-MKELKCLRTLTN  501 (1237)
Q Consensus       476 ~l~~~~~l~~ip~~-~~~L~~L~~L~~  501 (1237)
                      ++++| .+..++.. ...+.+|+.+.+
T Consensus       168 ~l~~n-~i~~ie~~~~~~~~~l~~l~l  193 (414)
T KOG0531|consen  168 DLSYN-RIVDIENDELSELISLEELDL  193 (414)
T ss_pred             cCCcc-hhhhhhhhhhhhccchHHHhc
Confidence            88888 56666543 466677776655

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=0.0004  Score=81.24  Aligned_cols=158  Identities=15%  Similarity=0.102  Sum_probs=91.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-c-------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-E-------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~-------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ...+.++|+.|+||||+|+.++....- .                   .|..++.++......++++ +++...+...  
T Consensus        38 ~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~i-R~l~~~~~~~--  114 (509)
T PRK14958         38 HHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDT-RELLDNIPYA--  114 (509)
T ss_pred             CeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHH-HHHHHHHhhc--
Confidence            345789999999999999998875421 1                   1222333332222222221 1122111110  


Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCCh
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSD  150 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~  150 (1237)
                                    -..++.-++|+|+|+.-......++...+-.....+++|++|.+ ..+...+ .....+++.+++.
T Consensus       115 --------------p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~  180 (509)
T PRK14958        115 --------------PTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPP  180 (509)
T ss_pred             --------------cccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCH
Confidence                          01245668999999665555666666665554556766655544 3333222 2225788999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ++..+.+...+...+...    ..+.+..|++.++|.+.-+
T Consensus       181 ~~i~~~l~~il~~egi~~----~~~al~~ia~~s~GslR~a  217 (509)
T PRK14958        181 LQIAAHCQHLLKEENVEF----ENAALDLLARAANGSVRDA  217 (509)
T ss_pred             HHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCcHHHH
Confidence            998888777664332222    2566788999999977543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.76  E-value=0.00057  Score=76.95  Aligned_cols=150  Identities=15%  Similarity=0.051  Sum_probs=87.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccccc-------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE-------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK   73 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~-------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~   73 (1237)
                      .+-+.++|++|+|||++|+.++....-.                   .++.+.++...                    ..
T Consensus        36 ~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~~i~~~--------------------~~   95 (394)
T PRK07940         36 THAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVRVVAPE--------------------GL   95 (394)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEeccc--------------------cc
Confidence            4668899999999999999987743211                   11112222111                    01


Q ss_pred             ccCHHHHHHHHHHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhhc-CCCeEeCCC
Q 000887           74 LEDLNSVQLELKET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMG-SGKNYELKL  147 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~~-~~~~~~l~~  147 (1237)
                      ...++++...+...    ..+++-++|+|+++.-+......+...+-...+++.+|++|.+. .+...+. ....+.+.+
T Consensus        96 ~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~  175 (394)
T PRK07940         96 SIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRT  175 (394)
T ss_pred             cCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECChHHChHHHHhhCeEEECCC
Confidence            12233333222211    12355688889996654444444555554444556566555553 3333322 236899999


Q ss_pred             CChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          148 LSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       148 l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ++.++..+.+....+     .    ..+.+..+++.++|.|...
T Consensus       176 ~~~~~i~~~L~~~~~-----~----~~~~a~~la~~s~G~~~~A  210 (394)
T PRK07940        176 PSVEAVAEVLVRRDG-----V----DPETARRAARASQGHIGRA  210 (394)
T ss_pred             CCHHHHHHHHHHhcC-----C----CHHHHHHHHHHcCCCHHHH
Confidence            999999988874321     1    1456788999999998643

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.75  E-value=0.00057  Score=75.82  Aligned_cols=155  Identities=19%  Similarity=0.200  Sum_probs=94.1

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhccc-----ccCCCCeEEEEE-cCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKL-----TEAFEPKAWVCV-SDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELK   85 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~-----~~~f~~~~w~~~-~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~   85 (1237)
                      -.....++|+.|+|||++|.+++....     ..++|...|... +....++++. ++...+...               
T Consensus        25 ~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir-~~~~~~~~~---------------   88 (313)
T PRK05564         25 FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIR-NIIEEVNKK---------------   88 (313)
T ss_pred             CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHH-HHHHHHhcC---------------
Confidence            346678999999999999999887431     223342233321 1112222221 122222111               


Q ss_pred             HHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHH-Hhh-cCCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           86 ETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVA-LTM-GSGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        86 ~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~-~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                       -..+++-++|+|+++.-+...+..+...+-.-+.++.+|++|.+.... ..+ .....+++.++++++..+.+.+... 
T Consensus        89 -p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~-  166 (313)
T PRK05564         89 -PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYKYN-  166 (313)
T ss_pred             -cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHHhc-
Confidence             012456678888886555566777777776666788888888665322 111 2236889999999999888876541 


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                        .     ...+.++.++..++|.|..+
T Consensus       167 --~-----~~~~~~~~l~~~~~g~~~~a  187 (313)
T PRK05564        167 --D-----IKEEEKKSAIAFSDGIPGKV  187 (313)
T ss_pred             --C-----CCHHHHHHHHHHcCCCHHHH
Confidence              0     11445778899999988644

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.74  E-value=0.00044  Score=80.60  Aligned_cols=161  Identities=9%  Similarity=0.083  Sum_probs=95.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ..+.|+|..|+|||.|+.++++...+.. -..++|++      ..++..++...+...     ..+    .+++.+++ -
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit------aeef~~el~~al~~~-----~~~----~f~~~y~~-~  378 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS------SEEFTNEFINSIRDG-----KGD----SFRRRYRE-M  378 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee------HHHHHHHHHHHHHhc-----cHH----HHHHHhhc-C
Confidence            3489999999999999999988543321 22456774      333444444443211     111    23333333 3


Q ss_pred             EEEEEeCCCCCCh-hhH-HHhhccccC-CCCCcEEEEEeCch---------hHHHhhcCCCeEeCCCCChhhhHHHHHHH
Q 000887           93 FLIVLDDVWSERY-DLW-QALKSPFMA-GAPGSRIIVTTRSM---------DVALTMGSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        93 ~LlvlDdv~~~~~-~~~-~~~~~~~~~-~~~~~~iliTtR~~---------~~~~~~~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      =+||+||++.... ..+ ..+...+.. ...+..|||||+..         .+..++...-+++++..+.+.-.++++++
T Consensus       379 DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kk  458 (617)
T PRK14086        379 DILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKK  458 (617)
T ss_pred             CEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHH
Confidence            5788899954321 111 122222221 13356699998853         22334445568899999999999999988


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      +........    .+++.-|++++.+..-.|.-+
T Consensus       459 a~~r~l~l~----~eVi~yLa~r~~rnvR~Lega  488 (617)
T PRK14086        459 AVQEQLNAP----PEVLEFIASRISRNIRELEGA  488 (617)
T ss_pred             HHhcCCCCC----HHHHHHHHHhccCCHHHHHHH
Confidence            754433222    667788888877765555443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.73  E-value=0.0004  Score=81.26  Aligned_cols=162  Identities=14%  Similarity=0.145  Sum_probs=95.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..-+.|+|.+|+|||+||.++++...+.. -..++|++.      ..+...+...+...     ..+    .+.+.++ +
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~-----~~~----~~~~~~~-~  211 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS------EKFTNDFVNALRNN-----TME----EFKEKYR-S  211 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHHcC-----cHH----HHHHHHh-c
Confidence            35689999999999999999988543332 123556643      23334444444211     112    2333333 3


Q ss_pred             cEEEEEeCCCCCChh--hHHHhhccccC-CCCCcEEEEEeCchh---------HHHhhcCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSERYD--LWQALKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~--~~~~~~~~~~~-~~~~~~iliTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      .-+||+||++.....  ..+.+...+.. ...|..|++|+....         +..++....++++++.+.++-.+++++
T Consensus       212 ~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~  291 (450)
T PRK00149        212 VDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKK  291 (450)
T ss_pred             CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHH
Confidence            447889999542111  11222221111 123455888887542         122333345799999999999999999


Q ss_pred             HhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      .+.......    .++++..|++.++|..-.+.-+
T Consensus       292 ~~~~~~~~l----~~e~l~~ia~~~~~~~R~l~~~  322 (450)
T PRK00149        292 KAEEEGIDL----PDEVLEFIAKNITSNVRELEGA  322 (450)
T ss_pred             HHHHcCCCC----CHHHHHHHHcCcCCCHHHHHHH
Confidence            885432222    2677889999999877755433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.73  E-value=0.00082  Score=78.41  Aligned_cols=172  Identities=14%  Similarity=0.161  Sum_probs=91.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCeEEEEEcCCcCHHHHHHHHHHHhh-----ccCCCccCHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAWVCVSDDFDVLRISKAILDSIK-----RSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~i~~~l~-----~~~~~~~~~~~~~~~l~~   86 (1237)
                      .+.+.++|+.|+|||++|+.++..... ......   .++.....    +.+.....     ........+++....+..
T Consensus        38 ~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~---~Cg~C~sC----r~i~~~~h~DiieIdaas~igVd~IReIi~~  110 (605)
T PRK05896         38 THAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGD---CCNSCSVC----ESINTNQSVDIVELDAASNNGVDEIRNIIDN  110 (605)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC---CCcccHHH----HHHHcCCCCceEEeccccccCHHHHHHHHHH
Confidence            457889999999999999998875421 111100   01111100    11100000     000011222332222211


Q ss_pred             H----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhh-cCCCeEeCCCCChhhhHHHHHHH
Q 000887           87 T----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTM-GSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        87 ~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      .    ..+++-++|+|+++.-+......+...+-..+.++.+|++| ....+...+ .....+++.++++++....+...
T Consensus       111 ~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~i  190 (605)
T PRK05896        111 INYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSI  190 (605)
T ss_pred             HHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHH
Confidence            1    11244569999996544445555555554334455555444 433333222 23368999999999999998887


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCch-HHHHHH
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPL-AARALG  195 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PL-al~~~~  195 (1237)
                      +...+...    .++++..+++.++|-+. |+..+-
T Consensus       191 l~kegi~I----s~eal~~La~lS~GdlR~AlnlLe  222 (605)
T PRK05896        191 AKKEKIKI----EDNAIDKIADLADGSLRDGLSILD  222 (605)
T ss_pred             HHHcCCCC----CHHHHHHHHHHcCCcHHHHHHHHH
Confidence            64332222    25678899999999654 444443

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.73  E-value=0.00032  Score=85.12  Aligned_cols=154  Identities=21%  Similarity=0.209  Sum_probs=83.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh--
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV--   88 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l--   88 (1237)
                      +....+.++|++|+||||+|+.+++. ....|.   .++... ....                  +..+......+.+  
T Consensus        50 ~~~~slLL~GPpGtGKTTLA~aIA~~-~~~~f~---~lna~~-~~i~------------------dir~~i~~a~~~l~~  106 (725)
T PRK13341         50 DRVGSLILYGPPGVGKTTLARIIANH-TRAHFS---SLNAVL-AGVK------------------DLRAEVDRAKERLER  106 (725)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHH-hcCcce---eehhhh-hhhH------------------HHHHHHHHHHHHhhh
Confidence            34567789999999999999998874 333331   121110 0010                  0111111111111  


Q ss_pred             cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEE--eCchh--HHHhh-cCCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           89 FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVT--TRSMD--VALTM-GSGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliT--tR~~~--~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                      .+++.+||+|+++.-.....+.+...+   ..+..++|+  |.+..  +.... .....+.+++++.++...++...+..
T Consensus       107 ~~~~~IL~IDEIh~Ln~~qQdaLL~~l---E~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~  183 (725)
T PRK13341        107 HGKRTILFIDEVHRFNKAQQDALLPWV---ENGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQD  183 (725)
T ss_pred             cCCceEEEEeChhhCCHHHHHHHHHHh---cCceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHHHHH
Confidence            246789999999654444444444322   234555554  33321  11111 12357999999999999999877641


Q ss_pred             CCC---CCCCCChHHHHHHHHHHccCCchH
Q 000887          164 GRD---AGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       164 ~~~---~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      ...   .....-.+++...|++.+.|..-.
T Consensus       184 ~~~~~g~~~v~I~deaL~~La~~s~GD~R~  213 (725)
T PRK13341        184 KERGYGDRKVDLEPEAEKHLVDVANGDARS  213 (725)
T ss_pred             HHhhcCCcccCCCHHHHHHHHHhCCCCHHH
Confidence            000   011122366778888888886543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.72  E-value=0.00044  Score=76.73  Aligned_cols=170  Identities=17%  Similarity=0.191  Sum_probs=95.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC---CCCeEEEEEcCCcCHHHHHHHHHHH-------hhcc--C-----CCcc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA---FEPKAWVCVSDDFDVLRISKAILDS-------IKRS--S-----CKLE   75 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~---f~~~~w~~~~~~~~~~~~~~~i~~~-------l~~~--~-----~~~~   75 (1237)
                      ...+.|+|+.|+||||+|..++.......   +....   .......-...+.+...       +..+  .     ....
T Consensus        45 ~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~---~~~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I  121 (351)
T PRK09112         45 HHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPET---LADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAI  121 (351)
T ss_pred             CeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccc---cCCCCCCCHHHHHHHcCCCCCEEEeecccccccccccccC
Confidence            45689999999999999999887543211   11110   00011011122222211       1111  0     0122


Q ss_pred             CHHHHHHHHHHHhc-----CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcE-EEEEeCchhHHHhhc-CCCeEeCCCC
Q 000887           76 DLNSVQLELKETVF-----KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR-IIVTTRSMDVALTMG-SGKNYELKLL  148 (1237)
Q Consensus        76 ~~~~~~~~l~~~l~-----~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iliTtR~~~~~~~~~-~~~~~~l~~l  148 (1237)
                      .++++. .+.+++.     +++-++|+|+++.-+......+...+-....++. |++|++...+..... ....+.+.++
T Consensus       122 ~vd~iR-~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~~~~llptIrSRc~~i~l~pl  200 (351)
T PRK09112        122 TVDEIR-RVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPL  200 (351)
T ss_pred             CHHHHH-HHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECChhhccHHHHhhccEEEecCC
Confidence            345544 3344432     4667999999976555555555555544334444 455544433332222 2268999999


Q ss_pred             ChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          149 SDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      +.++..+++......   ..   ...+.+..+++.++|.|....
T Consensus       201 ~~~~~~~~L~~~~~~---~~---~~~~~~~~i~~~s~G~pr~Al  238 (351)
T PRK09112        201 DDDELKKALSHLGSS---QG---SDGEITEALLQRSKGSVRKAL  238 (351)
T ss_pred             CHHHHHHHHHHhhcc---cC---CCHHHHHHHHHHcCCCHHHHH
Confidence            999999999874311   11   224567889999999997543

>TIGR00767 rho transcription termination factor Rho

Probab=97.71  E-value=0.00014  Score=79.63  Aligned_cols=88  Identities=20%  Similarity=0.169  Sum_probs=59.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC--cCHHHHHHHHHHHhhccCCCccCHH------HHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD--FDVLRISKAILDSIKRSSCKLEDLN------SVQLELK   85 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~------~~~~~l~   85 (1237)
                      ..++|+|++|+|||||+..+++...+++|+..+|+.+.+.  .++.++++.+...+-..........      .......
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae  248 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAK  248 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHH
Confidence            3589999999999999999988655567998889998866  6888999988554433222111111      1111111


Q ss_pred             HH-hcCCcEEEEEeCCC
Q 000887           86 ET-VFKKKFLIVLDDVW  101 (1237)
Q Consensus        86 ~~-l~~~~~LlvlDdv~  101 (1237)
                      .. -.+++++|++|++.
T Consensus       249 ~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       249 RLVEHKKDVVILLDSIT  265 (415)
T ss_pred             HHHHcCCCeEEEEEChh
Confidence            11 24689999999994

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

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.70  E-value=0.001  Score=67.03  Aligned_cols=183  Identities=15%  Similarity=0.137  Sum_probs=105.7

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCH----HHHHHHHH
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDL----NSVQLELK   85 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~----~~~~~~l~   85 (1237)
                      .++.+++.++|.-|+|||.+++++.+. ..+.-..++.++ ....+...+...++..+..+  .....    ++....+.
T Consensus        48 ~d~qg~~~vtGevGsGKTv~~Ral~~s-~~~d~~~~v~i~-~~~~s~~~~~~ai~~~l~~~--p~~~~~~~~e~~~~~L~  123 (269)
T COG3267          48 ADGQGILAVTGEVGSGKTVLRRALLAS-LNEDQVAVVVID-KPTLSDATLLEAIVADLESQ--PKVNVNAVLEQIDRELA  123 (269)
T ss_pred             hcCCceEEEEecCCCchhHHHHHHHHh-cCCCceEEEEec-CcchhHHHHHHHHHHHhccC--ccchhHHHHHHHHHHHH
Confidence            355679999999999999999965542 221111222222 23345667777888777663  22222    23333333


Q ss_pred             HHh-cCCc-EEEEEeCCCCCChhhHHHhhccccC---CCCCcEEEEEeCch-------hHHHhhc--CCCeEeCCCCChh
Q 000887           86 ETV-FKKK-FLIVLDDVWSERYDLWQALKSPFMA---GAPGSRIIVTTRSM-------DVALTMG--SGKNYELKLLSDD  151 (1237)
Q Consensus        86 ~~l-~~~~-~LlvlDdv~~~~~~~~~~~~~~~~~---~~~~~~iliTtR~~-------~~~~~~~--~~~~~~l~~l~~~  151 (1237)
                      +.. +++| +.+++|++.+-..+..+.+......   ....-+|+..-.-.       .+.....  ..-.|++.|++.+
T Consensus       124 al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~  203 (269)
T COG3267         124 ALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEA  203 (269)
T ss_pred             HHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChH
Confidence            333 3456 9999999966555554443322211   11112233222111       0111111  1123899999999


Q ss_pred             hhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhH
Q 000887          152 DCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGL  197 (1237)
Q Consensus       152 ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~  197 (1237)
                      +...+++.+..+..... +--..++...|.+...|.|.+++.++..
T Consensus       204 ~t~~yl~~~Le~a~~~~-~l~~~~a~~~i~~~sqg~P~lin~~~~~  248 (269)
T COG3267         204 ETGLYLRHRLEGAGLPE-PLFSDDALLLIHEASQGIPRLINNLATL  248 (269)
T ss_pred             HHHHHHHHHHhccCCCc-ccCChhHHHHHHHHhccchHHHHHHHHH
Confidence            99999888875543222 2223677889999999999999987643

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.69  E-value=0.00076  Score=77.56  Aligned_cols=155  Identities=15%  Similarity=0.113  Sum_probs=89.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ..-+.|+|+.|+|||+||.++++..... ...+++++.      ..+...+...+...     .    ...+++..+ ..
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l~~~-~~~v~yi~~------~~f~~~~~~~l~~~-----~----~~~f~~~~~-~~  203 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHALRES-GGKILYVRS------ELFTEHLVSAIRSG-----E----MQRFRQFYR-NV  203 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHHHHc-CCCEEEeeH------HHHHHHHHHHHhcc-----h----HHHHHHHcc-cC
Confidence            3568899999999999999998854333 234667642      33444444444221     1    122333333 34


Q ss_pred             EEEEEeCCCCCChh--hHHHhhccccC-CCCCcEEEEEeCch-h--------HHHhhcCCCeEeCCCCChhhhHHHHHHH
Q 000887           93 FLIVLDDVWSERYD--LWQALKSPFMA-GAPGSRIIVTTRSM-D--------VALTMGSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~--~~~~~~~~~~~-~~~~~~iliTtR~~-~--------~~~~~~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      -+|++||+......  ..+++...+.. ...|..||+||... .        +..++.....+.+++++.++-.+++++.
T Consensus       204 dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k  283 (445)
T PRK12422        204 DALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERK  283 (445)
T ss_pred             CEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHH
Confidence            47888998442111  11122222211 12356788888642 1        1223333468899999999999999988


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      +.......+    ++++.-|++.+.|.-
T Consensus       284 ~~~~~~~l~----~evl~~la~~~~~di  307 (445)
T PRK12422        284 AEALSIRIE----ETALDFLIEALSSNV  307 (445)
T ss_pred             HHHcCCCCC----HHHHHHHHHhcCCCH
Confidence            754332222    566667777776544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.69  E-value=0.00062  Score=80.27  Aligned_cols=156  Identities=15%  Similarity=0.122  Sum_probs=91.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccc-c-------------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLT-E-------------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK   73 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~-~-------------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~   73 (1237)
                      ..+.++|+.|+||||+|+.++....- .                   .|..+++++....                    
T Consensus        39 ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~~--------------------   98 (527)
T PRK14969         39 HAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASN--------------------   98 (527)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeecccc--------------------
Confidence            45689999999999999998775421 1                   1112222221111                    


Q ss_pred             ccCHHHHHHHHHHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCC
Q 000887           74 LEDLNSVQLELKET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKL  147 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~  147 (1237)
                       ..+++....+...    ..+++-++|+|+++.-.......+...+-.....+.+|++|.+. .+...+ .....+++.+
T Consensus        99 -~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~  177 (527)
T PRK14969         99 -TQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQ  177 (527)
T ss_pred             -CCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhHHHHHHHHhcCC
Confidence             2223322222111    12467799999996554444555665555444566666555433 332111 1125788999


Q ss_pred             CChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCch-HHHHH
Q 000887          148 LSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL-AARAL  194 (1237)
Q Consensus       148 l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL-al~~~  194 (1237)
                      ++.++..+.+.+.+...+..    ..++++..|++.++|.+- |+..+
T Consensus       178 l~~~~i~~~L~~il~~egi~----~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        178 MPPPLIVSHLQHILEQENIP----FDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             CCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999998888766432221    225677899999999775 44444

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.00088  Score=78.63  Aligned_cols=105  Identities=10%  Similarity=0.109  Sum_probs=67.7

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-.......+...+-.......+|++|.. ..+...+ .....+++.+++.+|..+.+...+......
T Consensus       118 g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~  197 (624)
T PRK14959        118 GRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVD  197 (624)
T ss_pred             CCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCC
Confidence            46679999999665555556666655433345556655544 3443222 223578999999999999998866433222


Q ss_pred             CCCCChHHHHHHHHHHccCCc-hHHHHHHhHh
Q 000887          168 GTHGNFESTRQRVVEKCKGLP-LAARALGGLL  198 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~P-Lal~~~~~~l  198 (1237)
                      .    ..+.+..|++..+|-+ .|+..+...+
T Consensus       198 i----d~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        198 Y----DPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             C----CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            2    2567889999999855 5676665443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.67  E-value=0.00027  Score=72.60  Aligned_cols=162  Identities=17%  Similarity=0.150  Sum_probs=99.2

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeE-EEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKA-WVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~-w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      ...+....+|++|.|||+.|+++++.. -.+.|+.++ -.++++.....-+..           ...+.+.......+..
T Consensus        55 ~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~-----------Kik~fakl~~~~~~~~  123 (346)
T KOG0989|consen   55 RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVRE-----------KIKNFAKLTVLLKRSD  123 (346)
T ss_pred             cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhh-----------hhcCHHHHhhcccccc
Confidence            456788999999999999999988765 345665544 344444322110000           1111111111110000


Q ss_pred             c--CCc-EEEEEeCCCCCChhhHHHhhccccCCCCCcE-EEEEeCchhHHHhhcC-CCeEeCCCCChhhhHHHHHHHhcC
Q 000887           89 F--KKK-FLIVLDDVWSERYDLWQALKSPFMAGAPGSR-IIVTTRSMDVALTMGS-GKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        89 ~--~~~-~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iliTtR~~~~~~~~~~-~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                      .  -.+ =++|+|+++.-..+.|.++...+-.....++ |+||+--..+...+.. ..-+.-++|.+++..+-++..+..
T Consensus       124 ~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~  203 (346)
T KOG0989|consen  124 GYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASK  203 (346)
T ss_pred             CCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHHHH
Confidence            0  123 5889999988777889988887766666666 5566543333322211 246788899999999999888865


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCC
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGL  187 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~  187 (1237)
                      .+....    .++.+.|++.++|-
T Consensus       204 E~v~~d----~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  204 EGVDID----DDALKLIAKISDGD  223 (346)
T ss_pred             hCCCCC----HHHHHHHHHHcCCc
Confidence            444333    56778999999884

>PF14516 AAA_35: AAA-like domain

Probab=97.67  E-value=0.0038  Score=69.47  Aligned_cols=179  Identities=15%  Similarity=0.168  Sum_probs=105.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-----cCHHHHHHHHHHHhhccCC-----------CccCH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-----FDVLRISKAILDSIKRSSC-----------KLEDL   77 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-----~~~~~~~~~i~~~l~~~~~-----------~~~~~   77 (1237)
                      ..+.|.|+=.+|||+|..++.+...+..|. ++++++...     .+....++.++..+...-.           .....
T Consensus        32 ~~~~I~apRq~GKTSll~~l~~~l~~~~~~-~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~  110 (331)
T PF14516_consen   32 SYIRIKAPRQMGKTSLLLRLLERLQQQGYR-CVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSK  110 (331)
T ss_pred             CEEEEECcccCCHHHHHHHHHHHHHHCCCE-EEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCCh
Confidence            478999999999999999988765555554 567877542     2455555555544433211           11122


Q ss_pred             HHHHHHHHHHh-c--CCcEEEEEeCCCCCCh------hhHHHhhccccCCC-----CCcEEEEE-eCchhHHHh-----h
Q 000887           78 NSVQLELKETV-F--KKKFLIVLDDVWSERY------DLWQALKSPFMAGA-----PGSRIIVT-TRSMDVALT-----M  137 (1237)
Q Consensus        78 ~~~~~~l~~~l-~--~~~~LlvlDdv~~~~~------~~~~~~~~~~~~~~-----~~~~iliT-tR~~~~~~~-----~  137 (1237)
                      ......+.+.+ .  +++.+|++|+++..-.      +-+..+........     ..-++++. +........     +
T Consensus       111 ~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPF  190 (331)
T PF14516_consen  111 ISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPF  190 (331)
T ss_pred             hhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCc
Confidence            23333344432 2  5899999999954211      11122222111111     11222222 211111111     1


Q ss_pred             cCCCeEeCCCCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcC
Q 000887          138 GSGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSK  201 (1237)
Q Consensus       138 ~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~  201 (1237)
                      .....++|++|+.+|..+|.......    .    .....++|...+||+|.-+..++..+...
T Consensus       191 NIg~~i~L~~Ft~~ev~~L~~~~~~~----~----~~~~~~~l~~~tgGhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  191 NIGQPIELPDFTPEEVQELAQRYGLE----F----SQEQLEQLMDWTGGHPYLVQKACYLLVEE  246 (331)
T ss_pred             ccccceeCCCCCHHHHHHHHHhhhcc----C----CHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            22357999999999999998876421    1    13348999999999999999999999764

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

Probab=97.67  E-value=4.8e-06  Score=73.98  Aligned_cols=95  Identities=19%  Similarity=0.180  Sum_probs=46.8

Q ss_pred             cEEEccccccccccc---cccCCCCCCeEEccCCCccccchhhccc-CCccEEEcCccccCccCChhhcccccccEEecc
Q 000887          403 RVLSLGSYCITEVPI---SIGCLKQLRYLNFSRSEIQCLPDAICSL-FNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       403 r~L~L~~~~i~~lp~---~~~~l~~Lr~L~L~~~~i~~lp~~i~~L-~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      ..++|++|.+..+++   .+....+|...+|++|.+.++|+.|... +.+..|++++| .+..+|.++..++.|+.|+++
T Consensus        30 h~ldLssc~lm~i~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~n-eisdvPeE~Aam~aLr~lNl~  108 (177)
T KOG4579|consen   30 HFLDLSSCQLMYIADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANN-EISDVPEELAAMPALRSLNLR  108 (177)
T ss_pred             hhcccccchhhHHHHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchh-hhhhchHHHhhhHHhhhcccc
Confidence            344555555443332   2234444555555555555555544322 35555555554 555555555555555555555


Q ss_pred             CCCccccCccccccccccccc
Q 000887          479 GASALRELPLGMKELKCLRTL  499 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L~~L  499 (1237)
                      .| .+...|+-+..|.+|-.|
T Consensus       109 ~N-~l~~~p~vi~~L~~l~~L  128 (177)
T KOG4579|consen  109 FN-PLNAEPRVIAPLIKLDML  128 (177)
T ss_pred             cC-ccccchHHHHHHHhHHHh
Confidence            55 444445444444444444

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.67  E-value=0.0012  Score=78.22  Aligned_cols=176  Identities=12%  Similarity=0.101  Sum_probs=95.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC---CCCeEEEEEcCCcCHHHHHHHH-HHHhhccCCCccCHHHHHHHHHHH-
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA---FEPKAWVCVSDDFDVLRISKAI-LDSIKRSSCKLEDLNSVQLELKET-   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~---f~~~~w~~~~~~~~~~~~~~~i-~~~l~~~~~~~~~~~~~~~~l~~~-   87 (1237)
                      ...+.++|+.|+||||+|+.++....-..   ..+.-.-.++...+...+...- .+.+.........+++....+... 
T Consensus        38 ~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~  117 (618)
T PRK14951         38 HHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAV  117 (618)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHH
Confidence            45678999999999999999876432110   0111111111111111110000 000000000112333333333221 


Q ss_pred             ---hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhc
Q 000887           88 ---VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        88 ---l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                         ..++.-++|+|+|+.-.......+...+-.-...+++|++|.+ ..+...+ .....+++..++.++..+.+...+.
T Consensus       118 ~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~  197 (618)
T PRK14951        118 YKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLA  197 (618)
T ss_pred             hCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHH
Confidence               1234568999999766555666666665544556666655543 3333222 2336899999999999999988765


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      ..+...    ..+.+..|++.++|.+.-+.
T Consensus       198 ~egi~i----e~~AL~~La~~s~GslR~al  223 (618)
T PRK14951        198 AENVPA----EPQALRLLARAARGSMRDAL  223 (618)
T ss_pred             HcCCCC----CHHHHHHHHHHcCCCHHHHH
Confidence            433222    25678899999999775443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.65  E-value=0.00083  Score=79.69  Aligned_cols=172  Identities=14%  Similarity=0.113  Sum_probs=92.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccccc-CCCCeEEEEEcCCcCHHHHHHHH-HHHhhccCCCccCHHHHHHHHHHH----
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAI-LDSIKRSSCKLEDLNSVQLELKET----   87 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~i-~~~l~~~~~~~~~~~~~~~~l~~~----   87 (1237)
                      ..+.++|..|+||||+|+.++....-. .+..   ..++.......+...- .+-+.........+++....+...    
T Consensus        39 hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~---~pCg~C~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p  115 (647)
T PRK07994         39 HAYLFSGTRGVGKTTIARLLAKGLNCETGITA---TPCGECDNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAP  115 (647)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhhhhccCCCC---CCCCCCHHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhh
Confidence            446899999999999999988754221 1100   0011110000000000 000000000012233333222211    


Q ss_pred             hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCC
Q 000887           88 VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGR  165 (1237)
Q Consensus        88 l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~  165 (1237)
                      ..+++-++|+|+++.-.......+...+-.-..++++|.+|.+ ..+...+ .....+.+.+++.++..+.+...+....
T Consensus       116 ~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~  195 (647)
T PRK07994        116 ARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQ  195 (647)
T ss_pred             hcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcC
Confidence            2356779999999665555566666555444456655554444 3343222 2236899999999999999987663322


Q ss_pred             CCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          166 DAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       166 ~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      .    ....+....|++.++|.+-...
T Consensus       196 i----~~e~~aL~~Ia~~s~Gs~R~Al  218 (647)
T PRK07994        196 I----PFEPRALQLLARAADGSMRDAL  218 (647)
T ss_pred             C----CCCHHHHHHHHHHcCCCHHHHH
Confidence            1    1225677889999999776433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.65  E-value=0.00028  Score=80.68  Aligned_cols=174  Identities=12%  Similarity=0.097  Sum_probs=93.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCeEE-----EEEcCCcCHHHHHHHHHHHh-hccCCCccCHHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAW-----VCVSDDFDVLRISKAILDSI-KRSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~~w-----~~~~~~~~~~~~~~~i~~~l-~~~~~~~~~~~~~~~~l~~   86 (1237)
                      ..+.++|+.|+||||+|+.++....- ..+...-|     -.++...+...+....--.+ ..........+++......
T Consensus        39 ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~  118 (397)
T PRK14955         39 HGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLREN  118 (397)
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHH
Confidence            45789999999999999998875422 11111101     11111111111110000000 0000011223444332222


Q ss_pred             H----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhhc-CCCeEeCCCCChhhhHHHHHHH
Q 000887           87 T----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTMG-SGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        87 ~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~~-~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      .    ..+++-++|+|+++.-....+..+...+....+.+.+|++| +...+...+. ....+++.++++++..+.+...
T Consensus       119 ~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~  198 (397)
T PRK14955        119 VRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGI  198 (397)
T ss_pred             HhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Confidence            1    12456788999996554455666666655545566665555 4333332221 1257889999999999888877


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      +...+...    .++.+..|++.++|.+--+
T Consensus       199 ~~~~g~~i----~~~al~~l~~~s~g~lr~a  225 (397)
T PRK14955        199 CEAEGISV----DADALQLIGRKAQGSMRDA  225 (397)
T ss_pred             HHHcCCCC----CHHHHHHHHHHcCCCHHHH
Confidence            64322222    2678899999999977543

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

Probab=97.65  E-value=9e-06  Score=72.31  Aligned_cols=92  Identities=24%  Similarity=0.279  Sum_probs=76.9

Q ss_pred             cCCCCCccEEEccccccccccccc-cCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccE
Q 000887          396 LPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY  474 (1237)
Q Consensus       396 ~~~~~~Lr~L~L~~~~i~~lp~~~-~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~  474 (1237)
                      +....+|...+|++|.+.++|..| .+++.+..|+|++|.|.++|..+..++.|+.|+++.| .+...|..|..|.+|-.
T Consensus        49 l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N-~l~~~p~vi~~L~~l~~  127 (177)
T KOG4579|consen   49 LSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFN-PLNAEPRVIAPLIKLDM  127 (177)
T ss_pred             HhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccC-ccccchHHHHHHHhHHH
Confidence            455677888899999999998877 4556889999999999999998999999999999998 78888888888999999


Q ss_pred             EeccCCCccccCccc
Q 000887          475 LNIEGASALRELPLG  489 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~  489 (1237)
                      |+..+| ....+|..
T Consensus       128 Lds~~n-a~~eid~d  141 (177)
T KOG4579|consen  128 LDSPEN-ARAEIDVD  141 (177)
T ss_pred             hcCCCC-ccccCcHH
Confidence            988887 56777765

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.64  E-value=0.00099  Score=75.68  Aligned_cols=151  Identities=17%  Similarity=0.180  Sum_probs=80.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHH-HhcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKE-TVFKK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~-~l~~~   91 (1237)
                      ++-|.++|++|+|||++|+++++.. ...|     +.+..    ..+....   .+       ........+.+ .-...
T Consensus       156 p~gvLL~GppGtGKT~lakaia~~l-~~~~-----~~v~~----~~l~~~~---~g-------~~~~~i~~~f~~a~~~~  215 (364)
T TIGR01242       156 PKGVLLYGPPGTGKTLLAKAVAHET-NATF-----IRVVG----SELVRKY---IG-------EGARLVREIFELAKEKA  215 (364)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhC-CCCE-----Eecch----HHHHHHh---hh-------HHHHHHHHHHHHHHhcC
Confidence            4568999999999999999998743 2222     22211    1111111   00       01111112222 22346


Q ss_pred             cEEEEEeCCCCCC-----------hhh---HHHhhcccc--CCCCCcEEEEEeCchhHHH-hh----cCCCeEeCCCCCh
Q 000887           92 KFLIVLDDVWSER-----------YDL---WQALKSPFM--AGAPGSRIIVTTRSMDVAL-TM----GSGKNYELKLLSD  150 (1237)
Q Consensus        92 ~~LlvlDdv~~~~-----------~~~---~~~~~~~~~--~~~~~~~iliTtR~~~~~~-~~----~~~~~~~l~~l~~  150 (1237)
                      +.+|++|+++...           ...   +..+...+.  ....+..||.||....... .+    .....++++..+.
T Consensus       216 p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~  295 (364)
T TIGR01242       216 PSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDF  295 (364)
T ss_pred             CcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCH
Confidence            7899999985420           011   111211111  1134677888887543221 11    1235788999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      ++..++|+.++...... .+.    ....+++.+.|..
T Consensus       296 ~~r~~Il~~~~~~~~l~-~~~----~~~~la~~t~g~s  328 (364)
T TIGR01242       296 EGRLEILKIHTRKMKLA-EDV----DLEAIAKMTEGAS  328 (364)
T ss_pred             HHHHHHHHHHHhcCCCC-ccC----CHHHHHHHcCCCC
Confidence            99999999877432211 111    1467788887654

Many proteins may score above the trusted cutoff because an internal

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.64  E-value=0.0011  Score=78.72  Aligned_cols=173  Identities=14%  Similarity=0.134  Sum_probs=96.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-CC--CeEEEEEcCCcCHHHHHHHHHHHhhc-----cCCCccCHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FE--PKAWVCVSDDFDVLRISKAILDSIKR-----SSCKLEDLNSVQLEL   84 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~--~~~w~~~~~~~~~~~~~~~i~~~l~~-----~~~~~~~~~~~~~~l   84 (1237)
                      ..-+.++|+.|+||||+|+.++....-.. ..  +..+-.++...+.    +.+...-..     .......++++...+
T Consensus        46 ~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C----~~i~~g~h~Dv~e~~a~s~~gvd~IReIi  121 (598)
T PRK09111         46 AQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHC----QAIMEGRHVDVLEMDAASHTGVDDIREII  121 (598)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHH----HHHhcCCCCceEEecccccCCHHHHHHHH
Confidence            45688999999999999999887542111 10  1011111111111    111110000     001122334433322


Q ss_pred             HHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhh-cCCCeEeCCCCChhhhHHHHH
Q 000887           85 KET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTM-GSGKNYELKLLSDDDCWSVFV  158 (1237)
Q Consensus        85 ~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~  158 (1237)
                      ...    ..+++-++|+|+++.-.......+...+-.-..++++|++| ..+.+...+ .....+++..+++++..+.+.
T Consensus       122 e~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~  201 (598)
T PRK09111        122 ESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLS  201 (598)
T ss_pred             HHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHH
Confidence            211    12356689999996655455566666655445567665554 444443332 223588999999999999998


Q ss_pred             HHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          159 AHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      +.+.......    ..+.+..|++.++|.+.-+..
T Consensus       202 ~i~~kegi~i----~~eAl~lIa~~a~Gdlr~al~  232 (598)
T PRK09111        202 RIAAKEGVEV----EDEALALIARAAEGSVRDGLS  232 (598)
T ss_pred             HHHHHcCCCC----CHHHHHHHHHHcCCCHHHHHH
Confidence            8774333222    256788999999998865443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.64  E-value=0.0011  Score=74.01  Aligned_cols=96  Identities=13%  Similarity=0.100  Sum_probs=63.4

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++.++|+|+++.-+......+...+-.-..++.+|++|.... +.... .....+.+.+++.++..+++......    
T Consensus       140 ~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~----  215 (365)
T PRK07471        140 GGWRVVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPD----  215 (365)
T ss_pred             CCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhccc----
Confidence            4677999999976655555566666554445666666666543 32222 22368999999999999999875411    


Q ss_pred             CCCCChHHHHHHHHHHccCCchHHHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                       . .  .+....+++.++|.|.....
T Consensus       216 -~-~--~~~~~~l~~~s~Gsp~~Al~  237 (365)
T PRK07471        216 -L-P--DDPRAALAALAEGSVGRALR  237 (365)
T ss_pred             -C-C--HHHHHHHHHHcCCCHHHHHH
Confidence             1 1  22236889999999985433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.64  E-value=0.0017  Score=75.34  Aligned_cols=156  Identities=12%  Similarity=0.107  Sum_probs=94.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCC--------------------CCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAF--------------------EPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f--------------------~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      .....++|+.|+|||++|+.++........                    ..++.++....                   
T Consensus        36 ~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eldaas~-------------------   96 (535)
T PRK08451         36 AHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMDAASN-------------------   96 (535)
T ss_pred             CeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEeccccc-------------------
Confidence            346689999999999999998775421111                    11222221111                   


Q ss_pred             CccCHHHHHHHHHHH----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCC
Q 000887           73 KLEDLNSVQLELKET----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELK  146 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~  146 (1237)
                        ...++++..+...    ..+++-++|+|+++.-..+...++...+-..++.+++|++|.+. .+.... .....+++.
T Consensus        97 --~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~  174 (535)
T PRK08451         97 --RGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFK  174 (535)
T ss_pred             --cCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhceeEEcC
Confidence              1123333322211    11456789999996655555666666655445667777666653 222111 223689999


Q ss_pred             CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          147 LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      +++.++..+.+...+...+...    .++++..|++.++|-+.-+..
T Consensus       175 ~Ls~~ei~~~L~~Il~~EGi~i----~~~Al~~Ia~~s~GdlR~aln  217 (535)
T PRK08451        175 QIPQNSIISHLKTILEKEGVSY----EPEALEILARSGNGSLRDTLT  217 (535)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCcHHHHHH
Confidence            9999999999887764433222    267889999999998855443

>CHL00181 cbbX CbbX; Provisional

Probab=97.62  E-value=0.0013  Score=71.13  Aligned_cols=134  Identities=10%  Similarity=0.070  Sum_probs=72.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ..+.++|++|+|||++|+.+++......+ ...-|+.++    ..++    ...+...     ........+.+.   ..
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~----~~~l----~~~~~g~-----~~~~~~~~l~~a---~g  123 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVT----RDDL----VGQYIGH-----TAPKTKEVLKKA---MG  123 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEec----HHHH----HHHHhcc-----chHHHHHHHHHc---cC
Confidence            35889999999999999999775433222 111244333    1122    2222111     011122222222   34


Q ss_pred             EEEEEeCCCCC---------ChhhHHHhhccccCCCCCcEEEEEeCchhHHH--------hhcCCCeEeCCCCChhhhHH
Q 000887           93 FLIVLDDVWSE---------RYDLWQALKSPFMAGAPGSRIIVTTRSMDVAL--------TMGSGKNYELKLLSDDDCWS  155 (1237)
Q Consensus        93 ~LlvlDdv~~~---------~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~--------~~~~~~~~~l~~l~~~ea~~  155 (1237)
                      -+|++|+++.-         ..+....+...+.....+..||.++.......        .-.....+..++++.+|..+
T Consensus       124 gVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~  203 (287)
T CHL00181        124 GVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQ  203 (287)
T ss_pred             CEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHH
Confidence            59999999531         11222333333333345566777765333211        11123579999999999999


Q ss_pred             HHHHHhcC
Q 000887          156 VFVAHAFE  163 (1237)
Q Consensus       156 l~~~~~~~  163 (1237)
                      ++...+..
T Consensus       204 I~~~~l~~  211 (287)
T CHL00181        204 IAKIMLEE  211 (287)
T ss_pred             HHHHHHHH
Confidence            99888754

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.62  E-value=0.0014  Score=72.01  Aligned_cols=153  Identities=17%  Similarity=0.155  Sum_probs=90.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC--------------------CCCeEEEEEcCCcCHHHHHHHHHHHhhccCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA--------------------FEPKAWVCVSDDFDVLRISKAILDSIKRSSC   72 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~--------------------f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~   72 (1237)
                      ..-+.++|+.|+|||++|+.++....-..                    .+...|+.-...                  .
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~------------------~   83 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA------------------D   83 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC------------------C
Confidence            45678999999999999999887542111                    112222211100                  0


Q ss_pred             CccCHHHHHHHHHHHh----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhhc-CCCeEeCC
Q 000887           73 KLEDLNSVQLELKETV----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTMG-SGKNYELK  146 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~~-~~~~~~l~  146 (1237)
                      ....+++++..+...-    .+++-++|+|+++.-+......+...+-.-+.++.+|+||.+.. +...+. ....+.+.
T Consensus        84 ~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~  163 (328)
T PRK05707         84 KTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACP  163 (328)
T ss_pred             CCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCC
Confidence            1223444443322211    13444557799976665666666665554445677776666553 332322 23679999


Q ss_pred             CCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          147 LLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       147 ~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      +++.+++.+.+......        ...+.+..+++.++|.|...
T Consensus       164 ~~~~~~~~~~L~~~~~~--------~~~~~~~~~l~la~Gsp~~A  200 (328)
T PRK05707        164 LPSNEESLQWLQQALPE--------SDERERIELLTLAGGSPLRA  200 (328)
T ss_pred             CcCHHHHHHHHHHhccc--------CChHHHHHHHHHcCCCHHHH
Confidence            99999999999765310        11344567889999999643

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.60  E-value=0.00056  Score=73.61  Aligned_cols=137  Identities=11%  Similarity=0.037  Sum_probs=70.1

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      +...-+.++|++|+|||++|+.++....+... ....++.+...    ++.    ...     ...........+.+.  
T Consensus        40 ~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~----~l~----~~~-----~g~~~~~~~~~~~~a--  104 (261)
T TIGR02881        40 KQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA----DLV----GEY-----IGHTAQKTREVIKKA--  104 (261)
T ss_pred             CCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH----Hhh----hhh-----ccchHHHHHHHHHhc--
Confidence            34567889999999999999998774322111 11123322211    111    111     001111122222221  


Q ss_pred             CCcEEEEEeCCCCCC--------hhhHHHhhccccCCCCCcEEEEEeCchhHHH------hh--cCCCeEeCCCCChhhh
Q 000887           90 KKKFLIVLDDVWSER--------YDLWQALKSPFMAGAPGSRIIVTTRSMDVAL------TM--GSGKNYELKLLSDDDC  153 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~--------~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~------~~--~~~~~~~l~~l~~~ea  153 (1237)
                       ...+|++|+++.-.        .+..+.+...+........+++++.......      .+  .....+++++++.+|-
T Consensus       105 -~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el  183 (261)
T TIGR02881       105 -LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEEL  183 (261)
T ss_pred             -cCCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHH
Confidence             24588999995311        1223334433333333345555554332210      11  1124688999999999


Q ss_pred             HHHHHHHhcC
Q 000887          154 WSVFVAHAFE  163 (1237)
Q Consensus       154 ~~l~~~~~~~  163 (1237)
                      .+++...+..
T Consensus       184 ~~Il~~~~~~  193 (261)
T TIGR02881       184 MEIAERMVKE  193 (261)
T ss_pred             HHHHHHHHHH
Confidence            9999887743

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.60  E-value=0.0024  Score=74.31  Aligned_cols=100  Identities=12%  Similarity=0.091  Sum_probs=63.4

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-......++...+-..++.+.+|++| +...+...+ .....+.+.+++.++..+.+...+...+..
T Consensus       118 ~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~  197 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIE  197 (486)
T ss_pred             CCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCC
Confidence            466799999996544445555655554444455555544 433333222 223578999999999999888876433322


Q ss_pred             CCCCChHHHHHHHHHHccCCchHHHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                          ...+++..|++.++|.+..+..
T Consensus       198 ----id~~al~~La~~s~G~lr~al~  219 (486)
T PRK14953        198 ----YEEKALDLLAQASEGGMRDAAS  219 (486)
T ss_pred             ----CCHHHHHHHHHHcCCCHHHHHH
Confidence                2256788899999997654433

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.60  E-value=0.0019  Score=77.09  Aligned_cols=173  Identities=16%  Similarity=0.129  Sum_probs=91.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh----
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV----   88 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----   88 (1237)
                      .+.+.++|+.|+|||++|+.++....-.... ..+-.+.....   ....-...+.........++++.. +.+..    
T Consensus        40 ~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~-~~~~pC~~C~~---~~~~~~Dvieidaasn~~vd~IRe-Lie~~~~~P  114 (725)
T PRK07133         40 SHAYLFSGPRGTGKTSVAKIFANALNCSHKT-DLLEPCQECIE---NVNNSLDIIEMDAASNNGVDEIRE-LIENVKNLP  114 (725)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhcccccC-CCCCchhHHHH---hhcCCCcEEEEeccccCCHHHHHH-HHHHHHhch
Confidence            4566899999999999999988754211110 00000000000   000000000000001112222222 21211    


Q ss_pred             -cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcE-EEEEeCchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCC
Q 000887           89 -FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSR-IIVTTRSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGR  165 (1237)
Q Consensus        89 -~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~-iliTtR~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~  165 (1237)
                       .+++-++|+|+++.-....+.++...+-..+..+. |++|++...+...+ .....+++.+++.++..+.+...+...+
T Consensus       115 ~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~keg  194 (725)
T PRK07133        115 TQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKEN  194 (725)
T ss_pred             hcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcC
Confidence             24667999999965554555566555544344555 44555544444332 2236899999999999988887654332


Q ss_pred             CCCCCCChHHHHHHHHHHccCCch-HHHHH
Q 000887          166 DAGTHGNFESTRQRVVEKCKGLPL-AARAL  194 (1237)
Q Consensus       166 ~~~~~~~~~~~~~~i~~~~~g~PL-al~~~  194 (1237)
                      ..    ...+++..+++.++|-+. |+..+
T Consensus       195 I~----id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        195 IS----YEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             CC----CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            22    125678899999998664 44433

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

Probab=97.57  E-value=1e-05  Score=93.83  Aligned_cols=103  Identities=26%  Similarity=0.373  Sum_probs=86.0

Q ss_pred             CCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEe
Q 000887          397 PQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN  476 (1237)
Q Consensus       397 ~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~  476 (1237)
                      ..+..+..+.+..|.|.++-..++.++.|.+|++.+|.|+.+...+..+.+|++|++++| .|..+.. +..+..|+.|+
T Consensus        69 ~~l~~l~~l~l~~n~i~~~~~~l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N-~I~~i~~-l~~l~~L~~L~  146 (414)
T KOG0531|consen   69 ESLTSLKELNLRQNLIAKILNHLSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFN-KITKLEG-LSTLTLLKELN  146 (414)
T ss_pred             HHhHhHHhhccchhhhhhhhcccccccceeeeeccccchhhcccchhhhhcchheecccc-ccccccc-hhhccchhhhe
Confidence            356677777799999998777788999999999999999999776999999999999999 8888876 88899999999


Q ss_pred             ccCCCccccCcccccccccccccceee
Q 000887          477 IEGASALRELPLGMKELKCLRTLTNFI  503 (1237)
Q Consensus       477 l~~~~~l~~ip~~~~~L~~L~~L~~~~  503 (1237)
                      +.+| .+..++ .+..+++|+.+++..
T Consensus       147 l~~N-~i~~~~-~~~~l~~L~~l~l~~  171 (414)
T KOG0531|consen  147 LSGN-LISDIS-GLESLKSLKLLDLSY  171 (414)
T ss_pred             eccC-cchhcc-CCccchhhhcccCCc
Confidence            9999 676664 355577777776533

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.57  E-value=0.0012  Score=79.64  Aligned_cols=111  Identities=14%  Similarity=0.065  Sum_probs=58.2

Q ss_pred             HHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE--EeCchhH-HHhhc-CCCeEeCCCCChhhhHHH
Q 000887           81 QLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV--TTRSMDV-ALTMG-SGKNYELKLLSDDDCWSV  156 (1237)
Q Consensus        81 ~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili--TtR~~~~-~~~~~-~~~~~~l~~l~~~ea~~l  156 (1237)
                      ...+.+.++++++.++-|+.|..+...|+.+...+....+...++|  ||++... ...+. ....+.+.+++.+|.+++
T Consensus       282 Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~I  361 (615)
T TIGR02903       282 QNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALI  361 (615)
T ss_pred             HHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHH
Confidence            4455666666666666665554443444444433333344444555  5664432 11111 124678899999999999


Q ss_pred             HHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHH
Q 000887          157 FVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALG  195 (1237)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~  195 (1237)
                      +.+.+......    -.+++.+.|++....-+-|+..++
T Consensus       362 l~~~a~~~~v~----ls~eal~~L~~ys~~gRraln~L~  396 (615)
T TIGR02903       362 VLNAAEKINVH----LAAGVEELIARYTIEGRKAVNILA  396 (615)
T ss_pred             HHHHHHHcCCC----CCHHHHHHHHHCCCcHHHHHHHHH
Confidence            99876432111    113444555554433344444333

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

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.55  E-value=3.4e-05  Score=78.09  Aligned_cols=83  Identities=19%  Similarity=0.248  Sum_probs=44.9

Q ss_pred             CCCCccEEEcccccccc---ccccccCCCCCCeEEccCCCccccchhh-cccCCccEEEcCccccC-ccCChhhcccccc
Q 000887          398 QCKKLRVLSLGSYCITE---VPISIGCLKQLRYLNFSRSEIQCLPDAI-CSLFNLEILILRNCWCL-LKLPSRIGNLVNL  472 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~---lp~~~~~l~~Lr~L~L~~~~i~~lp~~i-~~L~~L~~L~L~~~~~l-~~lp~~i~~L~~L  472 (1237)
                      .+++++.|||.+|.|+.   +-..+.++++|++|+|+.|.+...-.+. -.+++|++|-|.++..- .........++.+
T Consensus        69 ~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~L~w~~~~s~l~~lP~v  148 (418)
T KOG2982|consen   69 SVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTGLSWTQSTSSLDDLPKV  148 (418)
T ss_pred             HhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCCCChhhhhhhhhcchhh
Confidence            45666677777777653   2333456677777777776554322222 34566666666665211 2222334555556


Q ss_pred             cEEeccCC
Q 000887          473 HYLNIEGA  480 (1237)
Q Consensus       473 ~~L~l~~~  480 (1237)
                      +.|.++.|
T Consensus       149 telHmS~N  156 (418)
T KOG2982|consen  149 TELHMSDN  156 (418)
T ss_pred             hhhhhccc
Confidence            66666555

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.54  E-value=0.00086  Score=74.21  Aligned_cols=154  Identities=15%  Similarity=0.181  Sum_probs=92.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCC-eEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ....+.|+|..|.|||.|+.++.+...+..... +++++      .+.....++.++..         .....+++..  
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~------se~f~~~~v~a~~~---------~~~~~Fk~~y--  174 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLT------SEDFTNDFVKALRD---------NEMEKFKEKY--  174 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEecc------HHHHHHHHHHHHHh---------hhHHHHHHhh--
Confidence            457899999999999999999988654444433 44553      33444445444432         1223444444  


Q ss_pred             CcEEEEEeCCCCCCh-hhH-HHhhccccC-CCCCcEEEEEeCch---------hHHHhhcCCCeEeCCCCChhhhHHHHH
Q 000887           91 KKFLIVLDDVWSERY-DLW-QALKSPFMA-GAPGSRIIVTTRSM---------DVALTMGSGKNYELKLLSDDDCWSVFV  158 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~-~~~-~~~~~~~~~-~~~~~~iliTtR~~---------~~~~~~~~~~~~~l~~l~~~ea~~l~~  158 (1237)
                      .-=++++||++--.. +.+ .++...+.. ...|..||+|++..         .+..++...-++++.+.+.+....++.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~  254 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILR  254 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHH
Confidence            334788999954211 111 222222222 13344899999743         233445555789999999999999999


Q ss_pred             HHhcCCCCCCCCCChHHHHHHHHHHccC
Q 000887          159 AHAFEGRDAGTHGNFESTRQRVVEKCKG  186 (1237)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~~~i~~~~~g  186 (1237)
                      +.+.......+    .+++.-|++....
T Consensus       255 kka~~~~~~i~----~ev~~~la~~~~~  278 (408)
T COG0593         255 KKAEDRGIEIP----DEVLEFLAKRLDR  278 (408)
T ss_pred             HHHHhcCCCCC----HHHHHHHHHHhhc
Confidence            97755544444    3445555554444

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.001  Score=79.14  Aligned_cols=172  Identities=12%  Similarity=0.095  Sum_probs=92.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEE-----EEcCCcCHHHHHHHHHHHhh-ccCCCccCHHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWV-----CVSDDFDVLRISKAILDSIK-RSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~-----~~~~~~~~~~~~~~i~~~l~-~~~~~~~~~~~~~~~l~~   86 (1237)
                      ..+.++|+.|+||||+|+.+++... ....+...|.     .++...+...+...---.+. ........++++...+..
T Consensus        39 ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~  118 (620)
T PRK14954         39 HGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLREN  118 (620)
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHH
Confidence            4578999999999999999887542 1211111111     11222111111100000000 000011224444433322


Q ss_pred             H----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhh-cCCCeEeCCCCChhhhHHHHHHH
Q 000887           87 T----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTM-GSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        87 ~----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      .    ..+++-++|+|+++.-.......+...+-.-...+.+|++| +...+...+ .....+++.+++.++....+...
T Consensus       119 ~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i  198 (620)
T PRK14954        119 VRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMI  198 (620)
T ss_pred             HHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHH
Confidence            2    23456688999996655455556666655444455555444 434443322 33468999999999998888876


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCch
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PL  189 (1237)
                      +...+...    ..+.++.|++.++|..-
T Consensus       199 ~~~egi~I----~~eal~~La~~s~Gdlr  223 (620)
T PRK14954        199 CRAEGIQI----DADALQLIARKAQGSMR  223 (620)
T ss_pred             HHHcCCCC----CHHHHHHHHHHhCCCHH
Confidence            64322222    26778899999999554

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.50  E-value=0.0022  Score=73.17  Aligned_cols=157  Identities=15%  Similarity=0.149  Sum_probs=86.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-------CCC-eEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-------FEP-KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLEL   84 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-------f~~-~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l   84 (1237)
                      .+.+.++|++|+|||++|.++++......       |.. ++.++........++ .++..++...              
T Consensus        39 ~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i-~~l~~~~~~~--------------  103 (367)
T PRK14970         39 AQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDI-RNLIDQVRIP--------------  103 (367)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHH-HHHHHHHhhc--------------
Confidence            46888999999999999999877432211       111 111111111111111 1111111100              


Q ss_pred             HHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhc
Q 000887           85 KETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                        -..+++-++|+|+++......+..+...+-.....+.+|+++.. ..+...+ .....++..++++++....+...+.
T Consensus       104 --p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~  181 (367)
T PRK14970        104 --PQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAV  181 (367)
T ss_pred             --cccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHHHHHHHH
Confidence              01235568999999554434455554444333344555555533 2222221 2235789999999999998888764


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCchH
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      ..+....    ++++..+++.++|-+-.
T Consensus       182 ~~g~~i~----~~al~~l~~~~~gdlr~  205 (367)
T PRK14970        182 KEGIKFE----DDALHIIAQKADGALRD  205 (367)
T ss_pred             HcCCCCC----HHHHHHHHHhCCCCHHH
Confidence            4332222    57788999999986553

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.49  E-value=0.0031  Score=76.03  Aligned_cols=173  Identities=14%  Similarity=0.138  Sum_probs=93.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc-----cCCCccCHHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR-----SSCKLEDLNSVQLELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~-----~~~~~~~~~~~~~~l~~~   87 (1237)
                      ...+.++|+.|+|||++|+.++....-...+.. +-.++..    ...+.+......     ........++....+...
T Consensus        38 ~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~-~~~c~~c----~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~  112 (585)
T PRK14950         38 AHAYLFTGPRGVGKTSTARILAKAVNCTTNDPK-GRPCGTC----EMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERV  112 (585)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC-CCCCccC----HHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHH
Confidence            355689999999999999998875321100000 0001111    111111111110     000112233322221111


Q ss_pred             ----hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHh
Q 000887           88 ----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        88 ----l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                          ..+++-++|+|+++.-.......+...+-.....+.+|+++.+. .+...+ .....+++..++.++..+.+...+
T Consensus       113 ~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a  192 (585)
T PRK14950        113 QFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIA  192 (585)
T ss_pred             hhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHH
Confidence                12456789999996544445555655554444566666655433 333222 223578899999999999888876


Q ss_pred             cCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          162 FEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      ...+...    ..+.+..|++.++|.+..+...
T Consensus       193 ~~egl~i----~~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        193 AAEGINL----EPGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             HHcCCCC----CHHHHHHHHHHcCCCHHHHHHH
Confidence            5433222    2567889999999988655443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.48  E-value=0.00054  Score=66.55  Aligned_cols=87  Identities=20%  Similarity=0.052  Sum_probs=48.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC-c
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK-K   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~-~   92 (1237)
                      +.+.|+|++|+||||+|++++....... ..++++..............  .....................+..+.. .
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG-GGVIYIDGEDILEEVLDQLL--LIIVGGKKASGSGELRLRLALALARKLKP   79 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC-CCEEEECCEEccccCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHHhcCC
Confidence            5789999999999999999987543322 34666665444322222111  111111112222233333344443433 4


Q ss_pred             EEEEEeCCCCC
Q 000887           93 FLIVLDDVWSE  103 (1237)
Q Consensus        93 ~LlvlDdv~~~  103 (1237)
                      .+|++|+++..
T Consensus        80 ~viiiDei~~~   90 (148)
T smart00382       80 DVLILDEITSL   90 (148)
T ss_pred             CEEEEECCccc
Confidence            99999999664

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.47  E-value=0.0018  Score=70.20  Aligned_cols=133  Identities=12%  Similarity=0.067  Sum_probs=71.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      -+.++|++|+|||++|+.++....+..+ ...-|+.+..    .++    ...+...     ........+.+.   ..-
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~~l----~~~~~g~-----~~~~~~~~~~~a---~~g  123 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DDL----VGQYIGH-----TAPKTKEILKRA---MGG  123 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----HHH----hHhhccc-----chHHHHHHHHHc---cCc
Confidence            5889999999999999988764433222 1112343332    112    2211111     111222222222   346


Q ss_pred             EEEEeCCCCC---------ChhhHHHhhccccCCCCCcEEEEEeCchhHHHhh--------cCCCeEeCCCCChhhhHHH
Q 000887           94 LIVLDDVWSE---------RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTM--------GSGKNYELKLLSDDDCWSV  156 (1237)
Q Consensus        94 LlvlDdv~~~---------~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~--------~~~~~~~l~~l~~~ea~~l  156 (1237)
                      +|++|++..-         .......+...+.....+.+||+++.......-.        .....+++++++.+|-.++
T Consensus       124 vL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I  203 (284)
T TIGR02880       124 VLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVI  203 (284)
T ss_pred             EEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHH
Confidence            8899999521         1112233344443344566676666433221110        1135789999999999999


Q ss_pred             HHHHhcC
Q 000887          157 FVAHAFE  163 (1237)
Q Consensus       157 ~~~~~~~  163 (1237)
                      +...+..
T Consensus       204 ~~~~l~~  210 (284)
T TIGR02880       204 AGLMLKE  210 (284)
T ss_pred             HHHHHHH
Confidence            9887643

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.45  E-value=0.0031  Score=72.94  Aligned_cols=101  Identities=10%  Similarity=0.100  Sum_probs=63.2

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-.......+...+-....++.+|++|.. ..+...+ .....+++.++++++..+.+...+...+..
T Consensus       120 ~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~  199 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIE  199 (451)
T ss_pred             CCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCC
Confidence            46778999999554434444555555444456666666543 2232222 223578999999999999888776432222


Q ss_pred             CCCCChHHHHHHHHHHccCCch-HHHHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPL-AARAL  194 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PL-al~~~  194 (1237)
                      .    .++++..|++.++|-+- |+..+
T Consensus       200 i----~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        200 T----SREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             C----CHHHHHHHHHHcCCCHHHHHHHH
Confidence            2    26678899999999664 44433

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0033  Score=74.29  Aligned_cols=177  Identities=12%  Similarity=0.067  Sum_probs=94.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCeEEEEEcCCcCHHHHHHH---HHHHhhccCCCccCHHHHHHHHHHH-
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAWVCVSDDFDVLRISKA---ILDSIKRSSCKLEDLNSVQLELKET-   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~~w~~~~~~~~~~~~~~~---i~~~l~~~~~~~~~~~~~~~~l~~~-   87 (1237)
                      ...+.++|+.|+||||+|+.++....- ...+   +..++...+...+...   -.+.+.........+++........ 
T Consensus        35 ~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~---~~pCg~C~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~  111 (584)
T PRK14952         35 NHAYLFSGPRGCGKTSSARILARSLNCAQGPT---ATPCGVCESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAF  111 (584)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccccCCC---CCcccccHHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHH
Confidence            345689999999999999998874321 1110   0111111111111000   0000000000111233332211111 


Q ss_pred             ---hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEe-CchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhc
Q 000887           88 ---VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTT-RSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        88 ---l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTt-R~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                         ..+++-++|+|+++.-.......+...+-....++.+|++| ....+...+ .....+++..++.++..+.+...+.
T Consensus       112 ~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~  191 (584)
T PRK14952        112 YAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICE  191 (584)
T ss_pred             hhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHH
Confidence               12456688999996655566666666665555566655544 444443332 2236899999999999988887664


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCch-HHHHHHh
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPL-AARALGG  196 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PL-al~~~~~  196 (1237)
                      ..+...    ..+.+..|++..+|-+- |+..+-.
T Consensus       192 ~egi~i----~~~al~~Ia~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        192 QEGVVV----DDAVYPLVIRAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HcCCCC----CHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            333222    25677889999999774 4444433

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.43  E-value=0.00035  Score=66.54  Aligned_cols=21  Identities=48%  Similarity=0.517  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhc
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |.|+|++|+|||++|+.+++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            579999999999999999885

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

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

Probab=97.43  E-value=1.8e-05  Score=82.36  Aligned_cols=90  Identities=19%  Similarity=0.170  Sum_probs=61.2

Q ss_pred             hhhhcCCCCCccEEEcccccccc-----ccccccCCCCCCeEEccCCC----ccccchh-------hcccCCccEEEcCc
Q 000887          392 LSDLLPQCKKLRVLSLGSYCITE-----VPISIGCLKQLRYLNFSRSE----IQCLPDA-------ICSLFNLEILILRN  455 (1237)
Q Consensus       392 ~~~~~~~~~~Lr~L~L~~~~i~~-----lp~~~~~l~~Lr~L~L~~~~----i~~lp~~-------i~~L~~L~~L~L~~  455 (1237)
                      +.+....+..+..++|+||.+..     +...+.+.++||.-++++-.    ..++|+.       +-+.++|++||||.
T Consensus        22 v~~~~~~~~s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSD  101 (382)
T KOG1909|consen   22 VEEELEPMDSLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSD  101 (382)
T ss_pred             HHHHhcccCceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeeccc
Confidence            34455678889999999999863     44556777899999988642    2345543       44566899999998


Q ss_pred             cccCccCChh----hcccccccEEeccCCC
Q 000887          456 CWCLLKLPSR----IGNLVNLHYLNIEGAS  481 (1237)
Q Consensus       456 ~~~l~~lp~~----i~~L~~L~~L~l~~~~  481 (1237)
                      |-.=..-++.    |..+..|++|+|.+|.
T Consensus       102 NA~G~~g~~~l~~ll~s~~~L~eL~L~N~G  131 (382)
T KOG1909|consen  102 NAFGPKGIRGLEELLSSCTDLEELYLNNCG  131 (382)
T ss_pred             cccCccchHHHHHHHHhccCHHHHhhhcCC
Confidence            8322222222    4567888888888884

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.42  E-value=0.0015  Score=78.36  Aligned_cols=171  Identities=12%  Similarity=0.075  Sum_probs=91.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc-----cCCCccCHHHHHHHHHHH-
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR-----SSCKLEDLNSVQLELKET-   87 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~-----~~~~~~~~~~~~~~l~~~-   87 (1237)
                      +.+.++|+.|+|||++|+.++........+....-.++..    ..-+.+......     .......++++...+... 
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C----~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~  114 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKC----ELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQ  114 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCccc----HHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHh
Confidence            5678999999999999999887543221111100111111    111111111100     001112233333333221 


Q ss_pred             ---hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhc
Q 000887           88 ---VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAF  162 (1237)
Q Consensus        88 ---l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~  162 (1237)
                         ..+++-++|+|+++.-.......+...+-.-...+.+|++|.+ ..+...+ .....+++..++.++..+.+.+.+.
T Consensus       115 ~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~  194 (620)
T PRK14948        115 FAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAE  194 (620)
T ss_pred             hChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHH
Confidence               1245678999999655445555665555443445555544443 3333222 2235788889999998888877664


Q ss_pred             CCCCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          163 EGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       163 ~~~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      ..+...    ..+++..|++.++|.+..+.
T Consensus       195 kegi~i----s~~al~~La~~s~G~lr~A~  220 (620)
T PRK14948        195 KESIEI----EPEALTLVAQRSQGGLRDAE  220 (620)
T ss_pred             HhCCCC----CHHHHHHHHHHcCCCHHHHH
Confidence            322222    14668899999999775443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.41  E-value=0.0049  Score=73.06  Aligned_cols=173  Identities=15%  Similarity=0.133  Sum_probs=93.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccccc-CCCCeEEEEEcCCcCHHHHHHHHHHH-hhccCCCccCHHHHHHHHHH----
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAILDS-IKRSSCKLEDLNSVQLELKE----   86 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~i~~~-l~~~~~~~~~~~~~~~~l~~----   86 (1237)
                      .+.+.++|+.|+|||++|+.++....-. ....   ..++...+...+.....-. ...........++.+.....    
T Consensus        38 ~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~---~pC~~C~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~  114 (563)
T PRK06647         38 ANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP---MPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFP  114 (563)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhhccccCCCC---CCCccchHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhc
Confidence            4568899999999999999988754211 1100   0111111111110000000 00000011223333322211    


Q ss_pred             HhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCC
Q 000887           87 TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEG  164 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~  164 (1237)
                      -..+++-++|+|+++.-.......+...+-..+..+.+|++|.. ..+...+ .....++..+++.++..+.+.+.+...
T Consensus       115 p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~e  194 (563)
T PRK06647        115 PASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLED  194 (563)
T ss_pred             hhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHc
Confidence            11346678999999665545566666665544456666655543 3333222 223578999999999998888876433


Q ss_pred             CCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          165 RDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       165 ~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      +..    -.++++..|++.++|.+..+.
T Consensus       195 gi~----id~eAl~lLa~~s~GdlR~al  218 (563)
T PRK06647        195 QIK----YEDEALKWIAYKSTGSVRDAY  218 (563)
T ss_pred             CCC----CCHHHHHHHHHHcCCCHHHHH
Confidence            222    226778889999999775443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=97.39  E-value=0.0011  Score=64.81  Aligned_cols=83  Identities=20%  Similarity=0.193  Sum_probs=51.4

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      +++++-+.|.||+|+||||-+..+++......| +++.-.++++...++.+...|-.-.....               .+
T Consensus        45 ~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv---------------~l  109 (333)
T KOG0991|consen   45 EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKV---------------TL  109 (333)
T ss_pred             cCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHHHHhhc---------------cC
Confidence            477888999999999999999998886654444 45556666665544444333322111000               01


Q ss_pred             -cCCcEEEEEeCCCCCChhh
Q 000887           89 -FKKKFLIVLDDVWSERYDL  107 (1237)
Q Consensus        89 -~~~~~LlvlDdv~~~~~~~  107 (1237)
                       .++.=++|+|.+++-+...
T Consensus       110 p~grhKIiILDEADSMT~gA  129 (333)
T KOG0991|consen  110 PPGRHKIIILDEADSMTAGA  129 (333)
T ss_pred             CCCceeEEEeeccchhhhHH
Confidence             1355688999996644333

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

Probab=97.38  E-value=0.00045  Score=70.45  Aligned_cols=44  Identities=20%  Similarity=0.221  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus         9 ~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      .....+.+.|+|.+|+|||+++++++....+.... ++.+.+...
T Consensus        20 ~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~-~~~~~~~~~   63 (185)
T PF13191_consen   20 QSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGY-VISINCDDS   63 (185)
T ss_dssp             SS-----EEE-B-TTSSHHHHHHHHHHHHHHHT---EEEEEEETT
T ss_pred             HcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCE-EEEEEEecc
Confidence            34556999999999999999999988755333222 444444433

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.37  E-value=0.0033  Score=75.38  Aligned_cols=97  Identities=12%  Similarity=0.073  Sum_probs=63.9

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE-EeCchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV-TTRSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili-TtR~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-.......+...+-.-..++.+|+ |++...+...+ .....+++.++++++..+.+...+...+..
T Consensus       120 ~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~  199 (614)
T PRK14971        120 GKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGIT  199 (614)
T ss_pred             CCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCC
Confidence            3566889999966555556666666655445666555 44444444332 223689999999999999998876443322


Q ss_pred             CCCCChHHHHHHHHHHccCCchH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      .    ..+++..|++.+||-.--
T Consensus       200 i----~~~al~~La~~s~gdlr~  218 (614)
T PRK14971        200 A----EPEALNVIAQKADGGMRD  218 (614)
T ss_pred             C----CHHHHHHHHHHcCCCHHH
Confidence            2    256788999999996643

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.33  E-value=0.0021  Score=73.23  Aligned_cols=151  Identities=18%  Similarity=0.186  Sum_probs=79.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH-hcC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET-VFK   90 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~-l~~   90 (1237)
                      .++-|.++|++|+|||++|+++++.. ...     |+.+..    ..+.    ....      .........+.+. -..
T Consensus       164 ~p~gvLL~GppGtGKT~lAkaia~~~-~~~-----~i~v~~----~~l~----~~~~------g~~~~~i~~~f~~a~~~  223 (389)
T PRK03992        164 PPKGVLLYGPPGTGKTLLAKAVAHET-NAT-----FIRVVG----SELV----QKFI------GEGARLVRELFELAREK  223 (389)
T ss_pred             CCCceEEECCCCCChHHHHHHHHHHh-CCC-----EEEeeh----HHHh----Hhhc------cchHHHHHHHHHHHHhc
Confidence            35668999999999999999998743 211     222211    1111    1110      0111122222222 234


Q ss_pred             CcEEEEEeCCCCC-----------ChhhHHHhhccc---cC--CCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCC
Q 000887           91 KKFLIVLDDVWSE-----------RYDLWQALKSPF---MA--GAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~-----------~~~~~~~~~~~~---~~--~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~  149 (1237)
                      .+.+|++|+++.-           .......+...+   ..  ...+..||.||........ +    .-...++++..+
T Consensus       224 ~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~  303 (389)
T PRK03992        224 APSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPD  303 (389)
T ss_pred             CCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCC
Confidence            6789999999531           001111122211   11  1235667777765432211 1    123578999999


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCC
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGL  187 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~  187 (1237)
                      .++..++|+.+....... .+..    ...+++.+.|.
T Consensus       304 ~~~R~~Il~~~~~~~~~~-~~~~----~~~la~~t~g~  336 (389)
T PRK03992        304 EEGRLEILKIHTRKMNLA-DDVD----LEELAELTEGA  336 (389)
T ss_pred             HHHHHHHHHHHhccCCCC-CcCC----HHHHHHHcCCC
Confidence            999999999876432211 1111    35666766664

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.31  E-value=0.0048  Score=76.15  Aligned_cols=171  Identities=12%  Similarity=0.058  Sum_probs=93.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcCHHHHHHH---HHHHhhccCCCccCHHHHHHHHHH---
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFDVLRISKA---ILDSIKRSSCKLEDLNSVQLELKE---   86 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~~~~~~~~---i~~~l~~~~~~~~~~~~~~~~l~~---   86 (1237)
                      ..+.++|+.|+||||+|+.++.... ......   -.++...+...+...   -.+.+.........+++++....+   
T Consensus        38 Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~---~pCg~C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~  114 (824)
T PRK07764         38 HAYLFSGPRGCGKTSSARILARSLNCVEGPTS---TPCGECDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFF  114 (824)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCcccCCCC---CCCcccHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHh
Confidence            4578999999999999999887542 111100   001111111110000   000000000011223333322111   


Q ss_pred             -HhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhhc-CCCeEeCCCCChhhhHHHHHHHhcC
Q 000887           87 -TVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTMG-SGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        87 -~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~~-~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                       -..++.-++|+|+++.-+......+...+-.-..++.+|++|.+ ..+...+. ....+++..++.++-.+++.+....
T Consensus       115 ~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~  194 (824)
T PRK07764        115 APAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQ  194 (824)
T ss_pred             chhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHH
Confidence             12345668999999766666666677666655566666655543 34433322 2368899999999998888876533


Q ss_pred             CCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ....    ...+.+..|++.++|.+..+
T Consensus       195 EGv~----id~eal~lLa~~sgGdlR~A  218 (824)
T PRK07764        195 EGVP----VEPGVLPLVIRAGGGSVRDS  218 (824)
T ss_pred             cCCC----CCHHHHHHHHHHcCCCHHHH
Confidence            2221    12556788999999987433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.31  E-value=0.0033  Score=70.32  Aligned_cols=127  Identities=14%  Similarity=0.105  Sum_probs=69.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      -..++.++|++|+|||++|+++++.. .   ..+..++.... ....+...+.... ..               ....+.
T Consensus        42 ~~~~lll~G~~G~GKT~la~~l~~~~-~---~~~~~i~~~~~-~~~~i~~~l~~~~-~~---------------~~~~~~  100 (316)
T PHA02544         42 IPNMLLHSPSPGTGKTTVAKALCNEV-G---AEVLFVNGSDC-RIDFVRNRLTRFA-ST---------------VSLTGG  100 (316)
T ss_pred             CCeEEEeeCcCCCCHHHHHHHHHHHh-C---ccceEeccCcc-cHHHHHHHHHHHH-Hh---------------hcccCC
Confidence            35677779999999999999988743 1   12345554442 2222211111110 00               001134


Q ss_pred             cEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHH-Hhh-cCCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVA-LTM-GSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~-~~~-~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      +-++|+|+++.. .......+...+.....++++|+||...... ..+ .....+.++..+.++..+++..
T Consensus       101 ~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544        101 GKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             CeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHH
Confidence            568999999543 2222233333333345677888888754321 111 1224677777888887766554

>PRK08116 hypothetical protein; Validated

Probab=97.31  E-value=0.00078  Score=72.04  Aligned_cols=104  Identities=29%  Similarity=0.311  Sum_probs=58.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .-+.++|.+|+|||.||.++++...+. ...+++++      ..++...+.......  ......    .+.+.+.+-. 
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~-~~~v~~~~------~~~ll~~i~~~~~~~--~~~~~~----~~~~~l~~~d-  180 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK-GVPVIFVN------FPQLLNRIKSTYKSS--GKEDEN----EIIRSLVNAD-  180 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc-CCeEEEEE------HHHHHHHHHHHHhcc--ccccHH----HHHHHhcCCC-
Confidence            358899999999999999999865444 33466765      334444444443221  111111    2333344444 


Q ss_pred             EEEEeCCCCCChhhHHH--hhccccC-CCCCcEEEEEeCch
Q 000887           94 LIVLDDVWSERYDLWQA--LKSPFMA-GAPGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~~--~~~~~~~-~~~~~~iliTtR~~  131 (1237)
                      |||+||+......+|..  +...+.. ...+..+||||...
T Consensus       181 lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        181 LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            89999995432233322  2222221 13456699999754

>PTZ00202 tuzin; Provisional

Probab=97.30  E-value=0.019  Score=63.27  Aligned_cols=140  Identities=11%  Similarity=0.181  Sum_probs=80.4

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh---
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV---   88 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l---   88 (1237)
                      .+++++|.|++|+|||||++.+.....   + ..++++. .  +..+++..++.+|+.+..  ....++...+.+.+   
T Consensus       285 ~privvLtG~~G~GKTTLlR~~~~~l~---~-~qL~vNp-r--g~eElLr~LL~ALGV~p~--~~k~dLLrqIqeaLl~~  355 (550)
T PTZ00202        285 HPRIVVFTGFRGCGKSSLCRSAVRKEG---M-PAVFVDV-R--GTEDTLRSVVKALGVPNV--EACGDLLDFISEACRRA  355 (550)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhcCC---c-eEEEECC-C--CHHHHHHHHHHHcCCCCc--ccHHHHHHHHHHHHHHH
Confidence            457999999999999999999886432   2 1333332 3  678999999999997432  22233333333332   


Q ss_pred             --c-CCcEEEEEeCCCCCChhh-HHHhhccccCCCCCcEEEEEeCchhHHHh---hcCCCeEeCCCCChhhhHHHHHHHh
Q 000887           89 --F-KKKFLIVLDDVWSERYDL-WQALKSPFMAGAPGSRIIVTTRSMDVALT---MGSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        89 --~-~~~~LlvlDdv~~~~~~~-~~~~~~~~~~~~~~~~iliTtR~~~~~~~---~~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                        . +++.+||+-==+...... +.+. ..+.-...-|+|++----+.+...   .+.-..+-++.|+.++|.+......
T Consensus       356 ~~e~GrtPVLII~lreg~~l~rvyne~-v~la~drr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        356 KKMNGETPLLVLKLREGSSLQRVYNEV-VALACDRRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             HHhCCCCEEEEEEecCCCcHHHHHHHH-HHHHccchhheeeeeehHhhcchhcccCccceeEecCCCCHHHHHHHHhhcc
Confidence              2 466666663321111111 1111 112223446777775543322111   1112468899999999998876553

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.26  E-value=0.018  Score=69.12  Aligned_cols=101  Identities=15%  Similarity=0.153  Sum_probs=63.5

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE-EeCchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV-TTRSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili-TtR~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-+......+...+-.-..++.+|+ |+....+...+ .....+++.+++.++..+.+...+...+..
T Consensus       118 ~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~  197 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGIS  197 (576)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCC
Confidence            3556899999965544555556655544445666554 44444444332 223578899999999988887765433222


Q ss_pred             CCCCChHHHHHHHHHHccCCc-hHHHHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLP-LAARAL  194 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~P-Lal~~~  194 (1237)
                      .    ..+.+..|++.++|.. .|+..+
T Consensus       198 i----~~~al~~la~~a~G~lr~al~~L  221 (576)
T PRK14965        198 I----SDAALALVARKGDGSMRDSLSTL  221 (576)
T ss_pred             C----CHHHHHHHHHHcCCCHHHHHHHH
Confidence            2    2567889999999965 444444

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

Probab=97.15  E-value=2.2e-05  Score=88.99  Aligned_cols=79  Identities=28%  Similarity=0.359  Sum_probs=34.2

Q ss_pred             CCCCccEEEccccccccccccccCCCCCCeEEccCCCccccch-hhcccCCccEEEcCccccCccCChhhcccccccEEe
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN  476 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~-~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~  476 (1237)
                      -++.|+.|+|++|.+++.. .+..+++|+.|||++|.+..+|. +-... +|+.|.+++| .++++-. |.+|++|+.||
T Consensus       185 ll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc-~L~~L~lrnN-~l~tL~g-ie~LksL~~LD  260 (1096)
T KOG1859|consen  185 LLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYNCLRHVPQLSMVGC-KLQLLNLRNN-ALTTLRG-IENLKSLYGLD  260 (1096)
T ss_pred             HHHHhhhhccchhhhhhhH-HHHhcccccccccccchhccccccchhhh-hheeeeeccc-HHHhhhh-HHhhhhhhccc
Confidence            3344444444444444443 23444444444444444444443 11111 2444444444 3333322 44444444444


Q ss_pred             ccCC
Q 000887          477 IEGA  480 (1237)
Q Consensus       477 l~~~  480 (1237)
                      ++.|
T Consensus       261 lsyN  264 (1096)
T KOG1859|consen  261 LSYN  264 (1096)
T ss_pred             hhHh
Confidence            4444

>PRK08181 transposase; Validated

Probab=97.15  E-value=0.0012  Score=70.16  Aligned_cols=101  Identities=19%  Similarity=0.146  Sum_probs=55.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .-+.++|++|+|||.||.++++...+..+ .++|++      ..++...+....     .....++..   . .+ .+.=
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~-~v~f~~------~~~L~~~l~~a~-----~~~~~~~~l---~-~l-~~~d  169 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGW-RVLFTR------TTDLVQKLQVAR-----RELQLESAI---A-KL-DKFD  169 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCC-ceeeee------HHHHHHHHHHHH-----hCCcHHHHH---H-HH-hcCC
Confidence            45899999999999999999875544433 456664      334444443321     111222222   2 22 2445


Q ss_pred             EEEEeCCCCCChhhH--HHhhccccCCCCCcEEEEEeCch
Q 000887           94 LIVLDDVWSERYDLW--QALKSPFMAGAPGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~--~~~~~~~~~~~~~~~iliTtR~~  131 (1237)
                      |||+||+.......+  ..+...+.....+..+||||...
T Consensus       170 LLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        170 LLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             EEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            999999954322222  12333222222234699999864

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.14  E-value=0.011  Score=64.80  Aligned_cols=173  Identities=16%  Similarity=0.123  Sum_probs=95.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc--------------cCCCCeEEEEEcCCcCHHHHHHHHHHHhh--ccCCCccC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT--------------EAFEPKAWVCVSDDFDVLRISKAILDSIK--RSSCKLED   76 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~--------------~~f~~~~w~~~~~~~~~~~~~~~i~~~l~--~~~~~~~~   76 (1237)
                      .....++|+.|+||+++|.+++.....              ..++...|+.-....+...+-...+...+  ........
T Consensus        26 ~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~  105 (314)
T PRK07399         26 APAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIR  105 (314)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccccccccchhhhhhccccccccccCc
Confidence            478899999999999999998775421              23344556542111000000011111221  11111233


Q ss_pred             HHHHHHHHHHHh-----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhc-CCCeEeCCCCCh
Q 000887           77 LNSVQLELKETV-----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMG-SGKNYELKLLSD  150 (1237)
Q Consensus        77 ~~~~~~~l~~~l-----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~-~~~~~~l~~l~~  150 (1237)
                      +++... +.+.+     .+++-++|+|+++.-+.....++...+-.-+...-|++|++...+...+. ....+.+.++++
T Consensus       106 id~ir~-i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~  184 (314)
T PRK07399        106 LEQIRE-IKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPSPESLLPTIVSRCQIIPFYRLSD  184 (314)
T ss_pred             HHHHHH-HHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCCCCeEEEEECChHhCcHHHHhhceEEecCCCCH
Confidence            444333 33333     24677899999965554455555555433232333455554444443332 236899999999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      ++..+.+.+.....   .    .......++..++|.|.....
T Consensus       185 ~~~~~~L~~~~~~~---~----~~~~~~~l~~~a~Gs~~~al~  220 (314)
T PRK07399        185 EQLEQVLKRLGDEE---I----LNINFPELLALAQGSPGAAIA  220 (314)
T ss_pred             HHHHHHHHHhhccc---c----chhHHHHHHHHcCCCHHHHHH
Confidence            99999998764211   1    111236889999999965543

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

Probab=97.11  E-value=3.3e-05  Score=87.72  Aligned_cols=118  Identities=25%  Similarity=0.242  Sum_probs=93.6

Q ss_pred             CCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChh-hcccccccEEec
Q 000887          399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSR-IGNLVNLHYLNI  477 (1237)
Q Consensus       399 ~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~-i~~L~~L~~L~l  477 (1237)
                      ...|.+.+.++|.+..+..++.-++.|+.|||++|.+...- .+..+.+|++|||++| .+..+|.- ...+. |+.|.+
T Consensus       163 Wn~L~~a~fsyN~L~~mD~SLqll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN-~L~~vp~l~~~gc~-L~~L~l  239 (1096)
T KOG1859|consen  163 WNKLATASFSYNRLVLMDESLQLLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYN-CLRHVPQLSMVGCK-LQLLNL  239 (1096)
T ss_pred             hhhHhhhhcchhhHHhHHHHHHHHHHhhhhccchhhhhhhH-HHHhcccccccccccc-hhccccccchhhhh-heeeee
Confidence            45788889999999999888999999999999999999885 7999999999999999 88888873 23344 999999


Q ss_pred             cCCCccccCcccccccccccccceeeeccCCCcCcccccchHhc
Q 000887          478 EGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFL  521 (1237)
Q Consensus       478 ~~~~~l~~ip~~~~~L~~L~~L~~~~~~~~~~~~i~~l~~l~~L  521 (1237)
                      ++| .++.+ .++.+|++|+.|++..+-......+.-|..|..|
T Consensus       240 rnN-~l~tL-~gie~LksL~~LDlsyNll~~hseL~pLwsLs~L  281 (1096)
T KOG1859|consen  240 RNN-ALTTL-RGIENLKSLYGLDLSYNLLSEHSELEPLWSLSSL  281 (1096)
T ss_pred             ccc-HHHhh-hhHHhhhhhhccchhHhhhhcchhhhHHHHHHHH
Confidence            998 67777 5689999999998866544444333333333333

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.11  E-value=0.0007  Score=67.35  Aligned_cols=101  Identities=23%  Similarity=0.304  Sum_probs=52.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .-+.++|.+|+|||.||.+++....+..+. +.|++      ..+++..+    .... .....++.   +. .+. +-=
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~-v~f~~------~~~L~~~l----~~~~-~~~~~~~~---~~-~l~-~~d  110 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYS-VLFIT------ASDLLDEL----KQSR-SDGSYEEL---LK-RLK-RVD  110 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT---EEEEE------HHHHHHHH----HCCH-CCTTHCHH---HH-HHH-TSS
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcc-eeEee------cCceeccc----cccc-cccchhhh---cC-ccc-ccc
Confidence            468999999999999999998866554443 66774      33344433    2221 11122222   22 223 345


Q ss_pred             EEEEeCCCCCChhhHHH--hhccccCCCCCcEEEEEeCch
Q 000887           94 LIVLDDVWSERYDLWQA--LKSPFMAGAPGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~~--~~~~~~~~~~~~~iliTtR~~  131 (1237)
                      |||+||+-......|..  +...+.....+..+||||...
T Consensus       111 lLilDDlG~~~~~~~~~~~l~~ii~~R~~~~~tIiTSN~~  150 (178)
T PF01695_consen  111 LLILDDLGYEPLSEWEAELLFEIIDERYERKPTIITSNLS  150 (178)
T ss_dssp             CEEEETCTSS---HHHHHCTHHHHHHHHHT-EEEEEESS-
T ss_pred             EecccccceeeecccccccchhhhhHhhcccCeEeeCCCc
Confidence            77799995543333322  111111111123588898754

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.08  E-value=0.015  Score=69.31  Aligned_cols=97  Identities=13%  Similarity=0.086  Sum_probs=61.1

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEE-EeCchhHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIV-TTRSMDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~ili-TtR~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      ++.-++|+|+++.-.......+...+-....++.+|+ ||....+...+ .....++..+++.++..+.+...+...+..
T Consensus       118 ~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~  197 (559)
T PRK05563        118 AKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIE  197 (559)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCC
Confidence            4667889999965554556666655544344555454 44433333222 223578899999999998888876433222


Q ss_pred             CCCCChHHHHHHHHHHccCCchH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      .    ..+++..|++.++|-+..
T Consensus       198 i----~~~al~~ia~~s~G~~R~  216 (559)
T PRK05563        198 Y----EDEALRLIARAAEGGMRD  216 (559)
T ss_pred             C----CHHHHHHHHHHcCCCHHH
Confidence            2    256788899999987654

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=97.05  E-value=5.4e-05  Score=91.24  Aligned_cols=111  Identities=21%  Similarity=0.281  Sum_probs=72.1

Q ss_pred             ccceeEEEEecCCCccc--ccCCCCCccceeeeeeecC-CCccccC----cCCCCCCcccEEEEcCCCCccccc--cccC
Q 000887          919 YLDLESLFVYRCPSLTC--LWSGGRLPVTLKRLRIEDC-SNFKVLT----SECQLPVEVEELTIYGCSNLESIA--ERFH  989 (1237)
Q Consensus       919 ~~~L~~L~l~~~~~l~~--~~~~~~~~~~L~~L~l~~c-~~l~~l~----~~~~~~~~L~~L~l~~c~~~~~~~--~~~~  989 (1237)
                      ++.|+.+.+.+|..+..  +......++.|+.|++.+| ......+    .....+.+|+.|++++|..+.+..  ....
T Consensus       187 ~~~L~~l~l~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~L~~l~l~~~~~isd~~l~~l~~  266 (482)
T KOG1947|consen  187 CPLLKRLSLSGCSKITDDSLDALALKCPNLEELDLSGCCLLITLSPLLLLLLLSICRKLKSLDLSGCGLVTDIGLSALAS  266 (482)
T ss_pred             CchhhHhhhcccccCChhhHHHHHhhCchhheecccCcccccccchhHhhhhhhhcCCcCccchhhhhccCchhHHHHHh
Confidence            67788888888888776  3344566778888888874 2222221    222334778888888877544432  1222


Q ss_pred             CcccccEEeeccccccc--cccccccCCCCCceeeeccCCCc
Q 000887          990 DDACLRSIWISSCENLK--SLPKGLSNLSHLHEIRIVRCHNL 1029 (1237)
Q Consensus       990 ~l~~L~~L~l~~~~~l~--~l~~~l~~l~~L~~L~l~~c~~l 1029 (1237)
                      .+++|++|.+.+|..++  .+-.....+++|++|++++|..+
T Consensus       267 ~c~~L~~L~l~~c~~lt~~gl~~i~~~~~~L~~L~l~~c~~~  308 (482)
T KOG1947|consen  267 RCPNLETLSLSNCSNLTDEGLVSIAERCPSLRELDLSGCHGL  308 (482)
T ss_pred             hCCCcceEccCCCCccchhHHHHHHHhcCcccEEeeecCccc
Confidence            36788888888887654  23344567788888888888766

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.04  E-value=0.0072  Score=68.44  Aligned_cols=153  Identities=18%  Similarity=0.169  Sum_probs=80.1

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      .++-|.++|++|+|||++|+++++.. ...|   +.+.  .    ..+....   .+      .........+.......
T Consensus       178 ~pkgvLL~GppGTGKT~LAkalA~~l-~~~f---i~i~--~----s~l~~k~---~g------e~~~~lr~lf~~A~~~~  238 (398)
T PTZ00454        178 PPRGVLLYGPPGTGKTMLAKAVAHHT-TATF---IRVV--G----SEFVQKY---LG------EGPRMVRDVFRLARENA  238 (398)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHhc-CCCE---EEEe--h----HHHHHHh---cc------hhHHHHHHHHHHHHhcC
Confidence            45678999999999999999998742 2111   2221  1    1111111   11      11111222222333457


Q ss_pred             cEEEEEeCCCCCC-----------hh---hHHHhhccccC--CCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCCh
Q 000887           92 KFLIVLDDVWSER-----------YD---LWQALKSPFMA--GAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLSD  150 (1237)
Q Consensus        92 ~~LlvlDdv~~~~-----------~~---~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~  150 (1237)
                      +.+|++|+++..-           ..   .+..+...+..  ...+..||+||........ +    .-...++++..+.
T Consensus       239 P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~  318 (398)
T PTZ00454        239 PSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDR  318 (398)
T ss_pred             CeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCH
Confidence            8999999985310           00   01112211111  2245678888875543321 1    1235688998999


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      ++..++|+....... ...+..    ..++++...|.-
T Consensus       319 ~~R~~Il~~~~~~~~-l~~dvd----~~~la~~t~g~s  351 (398)
T PTZ00454        319 RQKRLIFQTITSKMN-LSEEVD----LEDFVSRPEKIS  351 (398)
T ss_pred             HHHHHHHHHHHhcCC-CCcccC----HHHHHHHcCCCC
Confidence            998889987763221 112112    356667665543

>PRK06526 transposase; Provisional

Probab=97.02  E-value=0.0011  Score=69.91  Aligned_cols=101  Identities=16%  Similarity=0.138  Sum_probs=53.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +-+.++|++|+|||+||.+++....+..+. +.|+      +..++...+.....    . ..   ....+.+.  .+.-
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~-v~f~------t~~~l~~~l~~~~~----~-~~---~~~~l~~l--~~~d  161 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHR-VLFA------TAAQWVARLAAAHH----A-GR---LQAELVKL--GRYP  161 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCc-hhhh------hHHHHHHHHHHHHh----c-Cc---HHHHHHHh--ccCC
Confidence            468999999999999999998755544443 4443      23334444432210    1 11   11223322  2456


Q ss_pred             EEEEeCCCCCChhhH--HHhhccccCCCCCcEEEEEeCch
Q 000887           94 LIVLDDVWSERYDLW--QALKSPFMAGAPGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~--~~~~~~~~~~~~~~~iliTtR~~  131 (1237)
                      +||+||+.....+.+  ..+...+........+||||..+
T Consensus       162 lLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~  201 (254)
T PRK06526        162 LLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKP  201 (254)
T ss_pred             EEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCC
Confidence            899999954321121  12222221111122488888864

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

Probab=97.00  E-value=4.4e-05  Score=79.57  Aligned_cols=90  Identities=14%  Similarity=0.098  Sum_probs=63.9

Q ss_pred             ccccCCCCCCeEEccCCCcc-----ccchhhcccCCccEEEcCcc---ccCccCChhh-------cccccccEEeccCCC
Q 000887          417 ISIGCLKQLRYLNFSRSEIQ-----CLPDAICSLFNLEILILRNC---WCLLKLPSRI-------GNLVNLHYLNIEGAS  481 (1237)
Q Consensus       417 ~~~~~l~~Lr~L~L~~~~i~-----~lp~~i~~L~~L~~L~L~~~---~~l~~lp~~i-------~~L~~L~~L~l~~~~  481 (1237)
                      +.+..+..+..|+|++|.+.     .+.+.+.+.++|+..++++=   ....++|+.+       -..++|++|+|++|-
T Consensus        24 ~~~~~~~s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSDNA  103 (382)
T KOG1909|consen   24 EELEPMDSLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSDNA  103 (382)
T ss_pred             HHhcccCceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeeccccc
Confidence            33567789999999999876     34557888899999998863   1234556543       355699999999995


Q ss_pred             ccccCccc----ccccccccccceeeecc
Q 000887          482 ALRELPLG----MKELKCLRTLTNFIVGK  506 (1237)
Q Consensus       482 ~l~~ip~~----~~~L~~L~~L~~~~~~~  506 (1237)
                      .-..-++.    +++.+.|++|.+.+++.
T Consensus       104 ~G~~g~~~l~~ll~s~~~L~eL~L~N~Gl  132 (382)
T KOG1909|consen  104 FGPKGIRGLEELLSSCTDLEELYLNNCGL  132 (382)
T ss_pred             cCccchHHHHHHHHhccCHHHHhhhcCCC
Confidence            44444443    56678888887765543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.98  E-value=0.02  Score=62.42  Aligned_cols=158  Identities=15%  Similarity=0.168  Sum_probs=89.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-----------------CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCcc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-----------------FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLE   75 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-----------------f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~   75 (1237)
                      ...+.++|+.|+||+++|.++++...-..                 ++...|+.......            +.......
T Consensus        26 ~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~------------~~k~~~~I   93 (319)
T PRK08769         26 GHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRT------------GDKLRTEI   93 (319)
T ss_pred             ceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcc------------cccccccc
Confidence            45688999999999999999887542111                 11122221000000            00000112


Q ss_pred             CHHHHHHHHHHHh----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhhcC-CCeEeCCCCC
Q 000887           76 DLNSVQLELKETV----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTMGS-GKNYELKLLS  149 (1237)
Q Consensus        76 ~~~~~~~~l~~~l----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~~~-~~~~~l~~l~  149 (1237)
                      .++++.......-    .+++-++|+|+++.-+.....++...+-.-+.++.+|++|.. ..+...+.+ ...+.+.+++
T Consensus        94 ~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~  173 (319)
T PRK08769         94 VIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLPP  173 (319)
T ss_pred             cHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEeeCCCcC
Confidence            2444333322111    235679999999655544555565555444556766666554 334333322 3578899999


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHH
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~  192 (1237)
                      .+++.+.+....      ..    ...+..++..++|.|+...
T Consensus       174 ~~~~~~~L~~~~------~~----~~~a~~~~~l~~G~p~~A~  206 (319)
T PRK08769        174 AHEALAWLLAQG------VS----ERAAQEALDAARGHPGLAA  206 (319)
T ss_pred             HHHHHHHHHHcC------CC----hHHHHHHHHHcCCCHHHHH
Confidence            999998887531      11    2336678999999997543

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

Probab=96.95  E-value=0.00042  Score=83.68  Aligned_cols=109  Identities=20%  Similarity=0.180  Sum_probs=78.9

Q ss_pred             ccccccccccccccccccccCCCCCCcchhhhhcCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccc--h
Q 000887          363 LDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLP--D  440 (1237)
Q Consensus       363 ~~~~~~lr~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp--~  440 (1237)
                      ...+|.||+|...+...        ...-+...+..+++|++||+++++++.+ ..++.|++|++|.+.+-.++.-.  .
T Consensus       144 g~~LPsL~sL~i~~~~~--------~~~dF~~lc~sFpNL~sLDIS~TnI~nl-~GIS~LknLq~L~mrnLe~e~~~~l~  214 (699)
T KOG3665|consen  144 GTMLPSLRSLVISGRQF--------DNDDFSQLCASFPNLRSLDISGTNISNL-SGISRLKNLQVLSMRNLEFESYQDLI  214 (699)
T ss_pred             hhhCcccceEEecCcee--------cchhHHHHhhccCccceeecCCCCccCc-HHHhccccHHHHhccCCCCCchhhHH
Confidence            34567777776544221        1122567788999999999999999988 56899999999999888777543  3


Q ss_pred             hhcccCCccEEEcCccccCccCChhh-------cccccccEEeccCCC
Q 000887          441 AICSLFNLEILILRNCWCLLKLPSRI-------GNLVNLHYLNIEGAS  481 (1237)
Q Consensus       441 ~i~~L~~L~~L~L~~~~~l~~lp~~i-------~~L~~L~~L~l~~~~  481 (1237)
                      .+.+|++|++||+|..... ..+.-+       ..|++||.||.+++.
T Consensus       215 ~LF~L~~L~vLDIS~~~~~-~~~~ii~qYlec~~~LpeLrfLDcSgTd  261 (699)
T KOG3665|consen  215 DLFNLKKLRVLDISRDKNN-DDTKIIEQYLECGMVLPELRFLDCSGTD  261 (699)
T ss_pred             HHhcccCCCeeeccccccc-cchHHHHHHHHhcccCccccEEecCCcc
Confidence            6889999999999986332 222211       248899999998773

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.95  E-value=0.0031  Score=72.68  Aligned_cols=80  Identities=20%  Similarity=0.281  Sum_probs=60.2

Q ss_pred             CCCCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH
Q 000887            8 SDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET   87 (1237)
Q Consensus         8 ~~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~   87 (1237)
                      .+-+.-+|.-++|++|.||||||.-++++   ..| .|+-+++++..+...+-+.|..++.......+            
T Consensus       321 s~RP~kKilLL~GppGlGKTTLAHViAkq---aGY-sVvEINASDeRt~~~v~~kI~~avq~~s~l~a------------  384 (877)
T KOG1969|consen  321 SKRPPKKILLLCGPPGLGKTTLAHVIAKQ---AGY-SVVEINASDERTAPMVKEKIENAVQNHSVLDA------------  384 (877)
T ss_pred             cCCCccceEEeecCCCCChhHHHHHHHHh---cCc-eEEEecccccccHHHHHHHHHHHHhhcccccc------------
Confidence            33455689999999999999999988763   344 38899999999988888888777654432211            


Q ss_pred             hcCCcEEEEEeCCCCCC
Q 000887           88 VFKKKFLIVLDDVWSER  104 (1237)
Q Consensus        88 l~~~~~LlvlDdv~~~~  104 (1237)
                       ..++.-||+|.++...
T Consensus       385 -dsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  385 -DSRPVCLVIDEIDGAP  400 (877)
T ss_pred             -CCCcceEEEecccCCc
Confidence             1588899999996544

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=96.92  E-value=0.023  Score=58.25  Aligned_cols=71  Identities=18%  Similarity=0.106  Sum_probs=46.8

Q ss_pred             EEEEeCchhHHHhhcC--CCeEeCCCCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcC
Q 000887          124 IIVTTRSMDVALTMGS--GKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSK  201 (1237)
Q Consensus       124 iliTtR~~~~~~~~~~--~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~  201 (1237)
                      |=-|||--.+...+..  ..+.+++-.+.+|-.++..+.+..-..    +-..+.+.+|+++..|-|-   ++.+.+++.
T Consensus       155 IGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i----~i~~~~a~eIA~rSRGTPR---IAnRLLrRV  227 (332)
T COG2255         155 IGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI----EIDEEAALEIARRSRGTPR---IANRLLRRV  227 (332)
T ss_pred             eeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC----CCChHHHHHHHHhccCCcH---HHHHHHHHH
Confidence            3368886544332222  246788889999999998887743222    2236789999999999995   444555543

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.91  E-value=0.0013  Score=66.50  Aligned_cols=88  Identities=19%  Similarity=0.113  Sum_probs=54.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCC---CccCHHHHH-HHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSC---KLEDLNSVQ-LELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~---~~~~~~~~~-~~l~~~   87 (1237)
                      ++++.++|+.|+||||.+.++++....+ -..+..++.+...- ..+-++..++.++.+..   ...+..+.. +.+.+.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~   79 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKF   79 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHH
Confidence            5799999999999999999998865444 44577888765543 44566677888876532   222333333 333333


Q ss_pred             hcCCcEEEEEeCCC
Q 000887           88 VFKKKFLIVLDDVW  101 (1237)
Q Consensus        88 l~~~~~LlvlDdv~  101 (1237)
                      -.++-=+|++|=.-
T Consensus        80 ~~~~~D~vlIDT~G   93 (196)
T PF00448_consen   80 RKKGYDLVLIDTAG   93 (196)
T ss_dssp             HHTTSSEEEEEE-S
T ss_pred             hhcCCCEEEEecCC
Confidence            22334577788774

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK08118 topology modulation protein; Reviewed

Probab=96.90  E-value=0.002  Score=63.55  Aligned_cols=34  Identities=32%  Similarity=0.626  Sum_probs=27.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-c-ccCCCCeEE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-L-TEAFEPKAW   47 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~-~~~f~~~~w   47 (1237)
                      +.|.|+|++|+||||+|+++++.. . --.||..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            468999999999999999998865 2 245676666

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.90  E-value=0.015  Score=64.76  Aligned_cols=144  Identities=12%  Similarity=0.052  Sum_probs=76.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcCHHHHHHHHHHHhh--ccCCCccCHHHHHHHHHHH--
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFDVLRISKAILDSIK--RSSCKLEDLNSVQLELKET--   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~~~~~~~~i~~~l~--~~~~~~~~~~~~~~~l~~~--   87 (1237)
                      .....++|+.|+|||++|..+++...-.. ....   .++...+...+....-..+.  .........++++..+...  
T Consensus        28 ~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~---~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~  104 (329)
T PRK08058         28 SHAYLFEGAKGTGKKATALWLAKSLFCLERNGVE---PCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSK  104 (329)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCC---CCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhh
Confidence            45678999999999999999877542211 1100   01111000000000000000  0001112334443333221  


Q ss_pred             --hcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhh-cCCCeEeCCCCChhhhHHHHHH
Q 000887           88 --VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        88 --l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                        ..+++-++|+|+++.-+......+...+-.-+.++.+|++|..+. +...+ .....+++.++++++..+.+..
T Consensus       105 ~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        105 SGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             CCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHH
Confidence              124566799999966555555566666665556777777776543 32222 2236899999999999888864

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=96.89  E-value=0.0036  Score=64.32  Aligned_cols=36  Identities=25%  Similarity=0.346  Sum_probs=28.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV   50 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~   50 (1237)
                      -.++|.|..|+|||+++..+... ..+.|+.+++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~-~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYY-LRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHh-hcccCCEEEEEec
Confidence            36789999999999999998864 5667777766643

This is thought to be an ATPase involved in viral DNA packaging [].

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

Probab=96.89  E-value=0.015  Score=62.09  Aligned_cols=142  Identities=14%  Similarity=0.152  Sum_probs=85.4

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCcc-------CHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLE-------DLNSVQLEL   84 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~-------~~~~~~~~l   84 (1237)
                      -+.+|.|+|-+|.|||.+.+++....    -...+|+++.+.++.+.+...|+...+..+..+.       +..+....+
T Consensus        29 ~PS~~~iyG~sgTGKT~~~r~~l~~~----n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l  104 (438)
T KOG2543|consen   29 IPSIVHIYGHSGTGKTYLVRQLLRKL----NLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLL  104 (438)
T ss_pred             cceeEEEeccCCCchhHHHHHHHhhc----CCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHH
Confidence            35567999999999999999988753    2236799999999999999999999863222211       122222233


Q ss_pred             HHH--hc--CCcEEEEEeCCCCCChhhHHH-----hhccccCCCCCcEEEEEeCchhHHH---hhcCC--CeEeCCCCCh
Q 000887           85 KET--VF--KKKFLIVLDDVWSERYDLWQA-----LKSPFMAGAPGSRIIVTTRSMDVAL---TMGSG--KNYELKLLSD  150 (1237)
Q Consensus        85 ~~~--l~--~~~~LlvlDdv~~~~~~~~~~-----~~~~~~~~~~~~~iliTtR~~~~~~---~~~~~--~~~~l~~l~~  150 (1237)
                      .++  ..  ++.+.||+||++.-.  +.++     +....--.....-+|+++-......   +++..  .++..+.-+.
T Consensus       105 ~q~~~~t~~d~~~~liLDnad~lr--D~~a~ll~~l~~L~el~~~~~i~iils~~~~e~~y~~n~g~~~i~~l~fP~Ys~  182 (438)
T KOG2543|consen  105 VQWPAATNRDQKVFLILDNADALR--DMDAILLQCLFRLYELLNEPTIVIILSAPSCEKQYLINTGTLEIVVLHFPQYSV  182 (438)
T ss_pred             HhhHHhhccCceEEEEEcCHHhhh--ccchHHHHHHHHHHHHhCCCceEEEEeccccHHHhhcccCCCCceEEecCCCCH
Confidence            331  12  358999999995421  1111     1111111122334555554332221   12332  3566788899


Q ss_pred             hhhHHHHHH
Q 000887          151 DDCWSVFVA  159 (1237)
Q Consensus       151 ~ea~~l~~~  159 (1237)
                      +|..+++.+
T Consensus       183 ~e~~~Il~~  191 (438)
T KOG2543|consen  183 EETQVILSR  191 (438)
T ss_pred             HHHHHHHhc
Confidence            999998864

>CHL00176 ftsH cell division protein; Validated

Probab=96.87  E-value=0.019  Score=69.05  Aligned_cols=156  Identities=15%  Similarity=0.204  Sum_probs=84.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ++-|.++|++|+|||++|++++... .     +-|+.++..    ++.....   +      .........+.......+
T Consensus       216 p~gVLL~GPpGTGKT~LAralA~e~-~-----~p~i~is~s----~f~~~~~---g------~~~~~vr~lF~~A~~~~P  276 (638)
T CHL00176        216 PKGVLLVGPPGTGKTLLAKAIAGEA-E-----VPFFSISGS----EFVEMFV---G------VGAARVRDLFKKAKENSP  276 (638)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh-C-----CCeeeccHH----HHHHHhh---h------hhHHHHHHHHHHHhcCCC
Confidence            4568999999999999999998742 1     112322211    1111100   0      111223334444555678


Q ss_pred             EEEEEeCCCCCC----------hhh----HHHhhcccc--CCCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCChh
Q 000887           93 FLIVLDDVWSER----------YDL----WQALKSPFM--AGAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLSDD  151 (1237)
Q Consensus        93 ~LlvlDdv~~~~----------~~~----~~~~~~~~~--~~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~~  151 (1237)
                      ++|++|+++.-.          .+.    +..+...+.  ....+..||.||........ +    .-...+.++..+.+
T Consensus       277 ~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~  356 (638)
T CHL00176        277 CIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDRE  356 (638)
T ss_pred             cEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHH
Confidence            999999995320          011    111221111  12345566666665443221 1    12357888889999


Q ss_pred             hhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccC-CchHHH
Q 000887          152 DCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKG-LPLAAR  192 (1237)
Q Consensus       152 ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g-~PLal~  192 (1237)
                      +-.++++.++.....     ........+++.+.| .+-.|.
T Consensus       357 ~R~~IL~~~l~~~~~-----~~d~~l~~lA~~t~G~sgaDL~  393 (638)
T CHL00176        357 GRLDILKVHARNKKL-----SPDVSLELIARRTPGFSGADLA  393 (638)
T ss_pred             HHHHHHHHHHhhccc-----chhHHHHHHHhcCCCCCHHHHH
Confidence            999999988743111     113345678887776 333343

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.83  E-value=0.003  Score=70.74  Aligned_cols=88  Identities=15%  Similarity=0.152  Sum_probs=54.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCH-HHHHHHHHHHhc--
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDL-NSVQLELKETVF--   89 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~-~~~~~~l~~~l~--   89 (1237)
                      +.|.++|++|+|||++|++++... ....++.+.|+.+....+..+....+    ........-. .-..+.+....+  
T Consensus       195 ~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~----rP~~vgy~~~~G~f~~~~~~A~~~p  270 (459)
T PRK11331        195 KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY----RPNGVGFRRKDGIFYNFCQQAKEQP  270 (459)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhccc----CCCCCCeEecCchHHHHHHHHHhcc
Confidence            468889999999999999998865 34466777799998877765554322    1111111000 111122222222  


Q ss_pred             CCcEEEEEeCCCCCCh
Q 000887           90 KKKFLIVLDDVWSERY  105 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~  105 (1237)
                      ++++++|+|++...+.
T Consensus       271 ~~~~vliIDEINRani  286 (459)
T PRK11331        271 EKKYVFIIDEINRANL  286 (459)
T ss_pred             cCCcEEEEehhhccCH
Confidence            3689999999966543

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.81  E-value=0.014  Score=67.52  Aligned_cols=140  Identities=12%  Similarity=0.081  Sum_probs=72.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC----CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA----FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~----f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      ++-+.++|++|+|||++|+++++......    .....|+.+....    +....   .+.   ............++..
T Consensus       216 p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~~~e----Ll~ky---vGe---te~~ir~iF~~Ar~~a  285 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIKGPE----LLNKY---VGE---TERQIRLIFQRAREKA  285 (512)
T ss_pred             CcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEeccchh----hcccc---cch---HHHHHHHHHHHHHHHh
Confidence            45689999999999999999988542221    2234455443221    11000   000   0001111222222211


Q ss_pred             -cCCcEEEEEeCCCCCC-------hhh-----HHHhhccccC--CCCCcEEEEEeCchhHHH-hh----cCCCeEeCCCC
Q 000887           89 -FKKKFLIVLDDVWSER-------YDL-----WQALKSPFMA--GAPGSRIIVTTRSMDVAL-TM----GSGKNYELKLL  148 (1237)
Q Consensus        89 -~~~~~LlvlDdv~~~~-------~~~-----~~~~~~~~~~--~~~~~~iliTtR~~~~~~-~~----~~~~~~~l~~l  148 (1237)
                       .+++++|+||+++..-       ..+     ...+...+..  ...+..||.||....... .+    .-+..++++..
T Consensus       286 ~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~P  365 (512)
T TIGR03689       286 SDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERP  365 (512)
T ss_pred             hcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCC
Confidence             2468999999995310       001     1122222211  123444555665443221 11    12346899999


Q ss_pred             ChhhhHHHHHHHhc
Q 000887          149 SDDDCWSVFVAHAF  162 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~  162 (1237)
                      +.++..++|+.+..
T Consensus       366 d~e~r~~Il~~~l~  379 (512)
T TIGR03689       366 DAEAAADIFSKYLT  379 (512)
T ss_pred             CHHHHHHHHHHHhh
Confidence            99999999998863

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK06921 hypothetical protein; Provisional

Probab=96.81  E-value=0.0047  Score=65.94  Aligned_cols=38  Identities=26%  Similarity=0.301  Sum_probs=29.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEE
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV   50 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~   50 (1237)
                      ..-+.++|..|+|||.||.++++...+.....++|++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH
Confidence            45789999999999999999988655442345677764

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.80  E-value=0.025  Score=62.82  Aligned_cols=150  Identities=19%  Similarity=0.141  Sum_probs=84.8

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ......|.+.|++|+|||+||..++.   ...|+-+=-++   ..+   +       .+..  +......+...+.+..+
T Consensus       535 ~s~lvSvLl~Gp~~sGKTaLAA~iA~---~S~FPFvKiiS---pe~---m-------iG~s--EsaKc~~i~k~F~DAYk  596 (744)
T KOG0741|consen  535 RSPLVSVLLEGPPGSGKTALAAKIAL---SSDFPFVKIIS---PED---M-------IGLS--ESAKCAHIKKIFEDAYK  596 (744)
T ss_pred             cCcceEEEEecCCCCChHHHHHHHHh---hcCCCeEEEeC---hHH---c-------cCcc--HHHHHHHHHHHHHHhhc
Confidence            34566778999999999999999876   45676333332   111   0       0111  11222333344455556


Q ss_pred             CCcEEEEEeCCCCCChhhH------------HHhhcc---ccCCCCCcEEEEEeCchhHHHhhcCC----CeEeCCCCCh
Q 000887           90 KKKFLIVLDDVWSERYDLW------------QALKSP---FMAGAPGSRIIVTTRSMDVALTMGSG----KNYELKLLSD  150 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~------------~~~~~~---~~~~~~~~~iliTtR~~~~~~~~~~~----~~~~l~~l~~  150 (1237)
                      ..--.||+||+..  ..+|            .++...   .++.+..--|+-||..+.+...|+-.    ..+.++.++.
T Consensus       597 S~lsiivvDdiEr--LiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~  674 (744)
T KOG0741|consen  597 SPLSIIVVDDIER--LLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTT  674 (744)
T ss_pred             CcceEEEEcchhh--hhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCc
Confidence            6778999999933  2222            222222   23333333355577777777766432    4788888877


Q ss_pred             -hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHc
Q 000887          151 -DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKC  184 (1237)
Q Consensus       151 -~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~  184 (1237)
                       ++..+.+...-     .-.+.+.+.++.+...++
T Consensus       675 ~~~~~~vl~~~n-----~fsd~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  675 GEQLLEVLEELN-----IFSDDEVRAIAEQLLSKK  704 (744)
T ss_pred             hHHHHHHHHHcc-----CCCcchhHHHHHHHhccc
Confidence             77777776542     222334455555555555

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=96.80  E-value=0.023  Score=58.04  Aligned_cols=24  Identities=29%  Similarity=0.498  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .-|-++|..|+|||++++++.+..
T Consensus        53 nnvLL~G~rGtGKSSlVkall~~y   76 (249)
T PF05673_consen   53 NNVLLWGARGTGKSSLVKALLNEY   76 (249)
T ss_pred             cceEEecCCCCCHHHHHHHHHHHH
Confidence            467889999999999999988753

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.80  E-value=0.0088  Score=74.46  Aligned_cols=134  Identities=13%  Similarity=0.090  Sum_probs=69.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCC-----CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAF-----EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f-----~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .-+.++|++|+|||++|..+++.......     +..+|..     +...+.    .    ......+.++..+.+.+.+
T Consensus       204 ~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~-----~~~~l~----a----~~~~~g~~e~~l~~i~~~~  270 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSL-----DMGSLL----A----GTKYRGDFEERLKAVVSEI  270 (731)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEe-----cHHHHh----h----hccccchHHHHHHHHHHHH
Confidence            34679999999999999999885432211     2233331     111111    0    0001123333333334333


Q ss_pred             -cCCcEEEEEeCCCCCC--------hhhHHHhhccccCCCCCcEEEEEeCchhHHH------h-hcCCCeEeCCCCChhh
Q 000887           89 -FKKKFLIVLDDVWSER--------YDLWQALKSPFMAGAPGSRIIVTTRSMDVAL------T-MGSGKNYELKLLSDDD  152 (1237)
Q Consensus        89 -~~~~~LlvlDdv~~~~--------~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~------~-~~~~~~~~l~~l~~~e  152 (1237)
                       +.++.+|++|+++.-.        ..+...+..+....+ .-++|-+|...+...      . ......+++++++.++
T Consensus       271 ~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~g-~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~  349 (731)
T TIGR02639       271 EKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSG-KLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEE  349 (731)
T ss_pred             hccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhCC-CeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHH
Confidence             3468999999995210        011122222222221 234555544322110      1 1123578999999999


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      ..++++...
T Consensus       350 ~~~il~~~~  358 (731)
T TIGR02639       350 TVKILKGLK  358 (731)
T ss_pred             HHHHHHHHH
Confidence            999998654

>PRK10536 hypothetical protein; Provisional

Probab=96.80  E-value=0.0074  Score=62.31  Aligned_cols=116  Identities=12%  Similarity=0.098  Sum_probs=61.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEE--EcCCc-------CH----HHHHHHHHHHhhccCCCccCHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVC--VSDDF-------DV----LRISKAILDSIKRSSCKLEDLNS   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~--~~~~~-------~~----~~~~~~i~~~l~~~~~~~~~~~~   79 (1237)
                      .+|.+.|.+|+|||+||.+++.+. ....|+.++...  +....       +.    .-.+.-+.+.+..-- .....+.
T Consensus        75 ~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~~~pi~D~L~~~~-~~~~~~~  153 (262)
T PRK10536         75 QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIAEKFAPYFRPVYDVLVRRL-GASFMQY  153 (262)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCCHHHHHHHHHHHHHHHHHHHh-ChHHHHH
Confidence            489999999999999999987754 344455333321  10000       11    112222222222110 0011111


Q ss_pred             HHH--------HHHHHhcCCc---EEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhH
Q 000887           80 VQL--------ELKETVFKKK---FLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        80 ~~~--------~l~~~l~~~~---~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~  133 (1237)
                      ...        .-..+++++.   -+||+|++..-+..+...+.   -..+.++++|+|--..++
T Consensus       154 ~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~l---tR~g~~sk~v~~GD~~Qi  215 (262)
T PRK10536        154 CLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFL---TRLGENVTVIVNGDITQC  215 (262)
T ss_pred             HHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHH---hhcCCCCEEEEeCChhhc
Confidence            100        0123556654   59999999766554444444   344679999999765433

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=96.80  E-value=0.0064  Score=69.28  Aligned_cols=132  Identities=15%  Similarity=0.201  Sum_probs=71.4

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ..+-|.++|++|+|||++|+++++.. ...|     +.+... +   +....   .+      .........+.......
T Consensus       216 ~p~gVLL~GPPGTGKT~LAraIA~el-~~~f-----i~V~~s-e---L~~k~---~G------e~~~~vr~lF~~A~~~~  276 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLAKAVANET-SATF-----LRVVGS-E---LIQKY---LG------DGPKLVRELFRVAEENA  276 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh-CCCE-----EEEecc-h---hhhhh---cc------hHHHHHHHHHHHHHhCC
Confidence            34568899999999999999998743 2222     222111 1   11110   00      11111222222233456


Q ss_pred             cEEEEEeCCCCCC-----------hhh---HHHhhccccC--CCCCcEEEEEeCchhHHHhh-----cCCCeEeCCCCCh
Q 000887           92 KFLIVLDDVWSER-----------YDL---WQALKSPFMA--GAPGSRIIVTTRSMDVALTM-----GSGKNYELKLLSD  150 (1237)
Q Consensus        92 ~~LlvlDdv~~~~-----------~~~---~~~~~~~~~~--~~~~~~iliTtR~~~~~~~~-----~~~~~~~l~~l~~  150 (1237)
                      +.+|++|+++...           ...   ...+...+..  ...+.+||+||.........     .....++++..+.
T Consensus       277 P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~  356 (438)
T PTZ00361        277 PSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDE  356 (438)
T ss_pred             CcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCH
Confidence            8899999984210           000   1111111111  13456788888765443321     1235789999999


Q ss_pred             hhhHHHHHHHhc
Q 000887          151 DDCWSVFVAHAF  162 (1237)
Q Consensus       151 ~ea~~l~~~~~~  162 (1237)
                      ++..++|..+..
T Consensus       357 ~~R~~Il~~~~~  368 (438)
T PTZ00361        357 KTKRRIFEIHTS  368 (438)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998764

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.041  Score=60.15  Aligned_cols=160  Identities=10%  Similarity=0.045  Sum_probs=91.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCe--------EEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPK--------AWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLE   83 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~--------~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~   83 (1237)
                      ..-..++|+.|+||+++|++++.... .......        -++..+..+|+..+        .........+++++..
T Consensus        24 ~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i--------~p~~~~~I~id~iR~l   95 (325)
T PRK06871         24 HHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHIL--------EPIDNKDIGVDQVREI   95 (325)
T ss_pred             ceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEE--------ccccCCCCCHHHHHHH
Confidence            45667899999999999999887542 1111000        01111111111100        0001122345555443


Q ss_pred             HHHHh----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhhcC-CCeEeCCCCChhhhHHHH
Q 000887           84 LKETV----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMGS-GKNYELKLLSDDDCWSVF  157 (1237)
Q Consensus        84 l~~~l----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~~~-~~~~~l~~l~~~ea~~l~  157 (1237)
                      ....-    .+++=++|+|+++.-+.....++...+-.-++++.+|.+|... .+...+.+ ...+.+.+++++++.+.+
T Consensus        96 ~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L  175 (325)
T PRK06871         96 NEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWL  175 (325)
T ss_pred             HHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHH
Confidence            22221    2456788899996655555556666665555566666666554 34333322 368999999999999998


Q ss_pred             HHHhcCCCCCCCCCChHHHHHHHHHHccCCch
Q 000887          158 VAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       158 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL  189 (1237)
                      .....     ..    ...+...++.++|.|.
T Consensus       176 ~~~~~-----~~----~~~~~~~~~l~~g~p~  198 (325)
T PRK06871        176 QAQSS-----AE----ISEILTALRINYGRPL  198 (325)
T ss_pred             HHHhc-----cC----hHHHHHHHHHcCCCHH
Confidence            87541     11    2235677888999995

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=96.78  E-value=8e-05  Score=89.72  Aligned_cols=14  Identities=29%  Similarity=0.627  Sum_probs=6.3

Q ss_pred             CCccceeeccCCCC
Q 000887          854 NARLEVLRIKRCDS  867 (1237)
Q Consensus       854 ~~~L~~L~l~~c~~  867 (1237)
                      +++|+.|.+.+|..
T Consensus       268 c~~L~~L~l~~c~~  281 (482)
T KOG1947|consen  268 CPNLETLSLSNCSN  281 (482)
T ss_pred             CCCcceEccCCCCc
Confidence            44444444444443

>PRK12377 putative replication protein; Provisional

Probab=96.77  E-value=0.0028  Score=66.35  Aligned_cols=101  Identities=20%  Similarity=0.169  Sum_probs=55.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      ..+.++|.+|+|||+||.++++...+.. ..++++++      .++...+-......    ....    .+.+.+ .+-=
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g-~~v~~i~~------~~l~~~l~~~~~~~----~~~~----~~l~~l-~~~d  165 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKG-RSVIVVTV------PDVMSRLHESYDNG----QSGE----KFLQEL-CKVD  165 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcC-CCeEEEEH------HHHHHHHHHHHhcc----chHH----HHHHHh-cCCC
Confidence            5789999999999999999998655443 34677754      23444443332111    1111    122222 3567


Q ss_pred             EEEEeCCCCCChhhHH--HhhccccCC-CCCcEEEEEeCc
Q 000887           94 LIVLDDVWSERYDLWQ--ALKSPFMAG-APGSRIIVTTRS  130 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~--~~~~~~~~~-~~~~~iliTtR~  130 (1237)
                      |||+||+.......|.  .+...+... ....-+||||-.
T Consensus       166 LLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        166 LLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             EEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            8999999443323332  222222221 223347888864

>PRK07261 topology modulation protein; Provisional

Probab=96.75  E-value=0.0045  Score=61.42  Aligned_cols=64  Identities=17%  Similarity=0.307  Sum_probs=39.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc-c-ccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK-L-TEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~-~-~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .|+|+|++|+||||||++++... . .-..|...|-..                     ....+.++....+.+.+.+.+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~~~   60 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPN---------------------WQERDDDDMIADISNFLLKHD   60 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccc---------------------cccCCHHHHHHHHHHHHhCCC
Confidence            58999999999999999987643 1 123344444211                     112233445555556666666


Q ss_pred             EEEEEeCCC
Q 000887           93 FLIVLDDVW  101 (1237)
Q Consensus        93 ~LlvlDdv~  101 (1237)
                        .|+|+..
T Consensus        61 --wIidg~~   67 (171)
T PRK07261         61 --WIIDGNY   67 (171)
T ss_pred             --EEEcCcc
Confidence              5778873

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.74  E-value=0.043  Score=59.83  Aligned_cols=166  Identities=13%  Similarity=0.090  Sum_probs=90.2

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHH---Hhhcc-CCCccCHHHHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILD---SIKRS-SCKLEDLNSVQLELKET   87 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~---~l~~~-~~~~~~~~~~~~~l~~~   87 (1237)
                      -...+-++|+.|+||+++|.+++....-......   .++...+-..+...---   .+... ......+++++.. .+.
T Consensus        24 l~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~---~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l-~~~   99 (319)
T PRK06090         24 IPGALLLQSDEGLGVESLVELFSRALLCQNYQSE---ACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQC-NRL   99 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCC---CCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHH-HHH
Confidence            3457889999999999999998775421111000   11111110000000000   00000 0122344554432 222


Q ss_pred             h-----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhhcC-CCeEeCCCCChhhhHHHHHHH
Q 000887           88 V-----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTMGS-GKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        88 l-----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~~~-~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      +     .++.-++|+|+++.-+.....++...+-.-++++.+|.+|.+ ..+...+.+ ...+.+.+++++++.+.+...
T Consensus       100 ~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~  179 (319)
T PRK06090        100 AQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQ  179 (319)
T ss_pred             HhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHc
Confidence            2     235668899999665555555566655544556665555544 444444333 358899999999999988653


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      .       .+     .+..+++.++|.|+....
T Consensus       180 ~-------~~-----~~~~~l~l~~G~p~~A~~  200 (319)
T PRK06090        180 G-------IT-----VPAYALKLNMGSPLKTLA  200 (319)
T ss_pred             C-------Cc-----hHHHHHHHcCCCHHHHHH
Confidence            2       00     135678899999986543

>PRK04296 thymidine kinase; Provisional

Probab=96.73  E-value=0.0043  Score=62.84  Aligned_cols=114  Identities=12%  Similarity=-0.014  Sum_probs=62.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC--ccCHHHHHHHHHHHhcCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK--LEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~~~   91 (1237)
                      .++.|+|..|.||||+|..++.+..... ..++.+. + ..+.......++.+++.....  ....++....+.+ ..++
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g-~~v~i~k-~-~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~-~~~~   78 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERG-MKVLVFK-P-AIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE-EGEK   78 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcC-CeEEEEe-c-cccccccCCcEecCCCCcccceEeCChHHHHHHHHh-hCCC
Confidence            4788999999999999999877543332 2334342 1 111111123344444432111  2334555555554 2334


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhH
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~  133 (1237)
                      .-+||+|.+.--..++..++...+  ...|..|++|.++...
T Consensus        79 ~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~~  118 (190)
T PRK04296         79 IDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTDF  118 (190)
T ss_pred             CCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCccc
Confidence            568999999432223233333332  2457889999998543

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.71  E-value=0.0077  Score=65.92  Aligned_cols=87  Identities=17%  Similarity=0.182  Sum_probs=55.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCC-eEEEEEcCC-cCHHHHHHHHHHHhhccCCCccC-----HHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDD-FDVLRISKAILDSIKRSSCKLED-----LNSVQLELKE   86 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~-~~~~~~~~~i~~~l~~~~~~~~~-----~~~~~~~l~~   86 (1237)
                      ..+.|+|.+|+|||||++++++.....+-+. ++|+.+++. .++.++.+.+...+.........     +.+....+.+
T Consensus       134 QR~LIvG~pGtGKTTLl~~la~~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae  213 (380)
T PRK12608        134 QRGLIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAK  213 (380)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHH
Confidence            3569999999999999999887544433344 356666544 57888888888776654321111     1111112222


Q ss_pred             Hh--cCCcEEEEEeCC
Q 000887           87 TV--FKKKFLIVLDDV  100 (1237)
Q Consensus        87 ~l--~~~~~LlvlDdv  100 (1237)
                      ++  ++++++||+|++
T Consensus       214 ~f~~~GkdVVLvlDsl  229 (380)
T PRK12608        214 RLVEQGKDVVILLDSL  229 (380)
T ss_pred             HHHHcCCCEEEEEeCc
Confidence            22  468999999999

>PRK04132 replication factor C small subunit; Provisional

Probab=96.69  E-value=0.04  Score=67.74  Aligned_cols=153  Identities=16%  Similarity=0.058  Sum_probs=95.7

Q ss_pred             Ec--CCCCcHHHHHHHHHhcccccCCC-CeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEEE
Q 000887           19 VG--MGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLI   95 (1237)
Q Consensus        19 ~G--~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~Ll   95 (1237)
                      .|  |.|+||||+|.++++....+.++ .++-+++++......+...+ ..+......              -..+.-++
T Consensus       570 ~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iI-k~~a~~~~~--------------~~~~~KVv  634 (846)
T PRK04132        570 GGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKV-KEFARTKPI--------------GGASFKII  634 (846)
T ss_pred             cCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHH-HHHHhcCCc--------------CCCCCEEE
Confidence            36  67999999999998865443332 36677777655555444333 322211000              01245799


Q ss_pred             EEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhhc-CCCeEeCCCCChhhhHHHHHHHhcCCCCCCCCCCh
Q 000887           96 VLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMG-SGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNF  173 (1237)
Q Consensus        96 vlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~~-~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~  173 (1237)
                      |+|+++.-+.++..++...+-.....+++|.++.+. .+..... ....+.+.+++.++-.+.+...+.......    .
T Consensus       635 IIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi~i----~  710 (846)
T PRK04132        635 FLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLEL----T  710 (846)
T ss_pred             EEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCCCC----C
Confidence            999997766566666666655445567766665544 3322222 236899999999999888877664322111    2


Q ss_pred             HHHHHHHHHHccCCchH
Q 000887          174 ESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       174 ~~~~~~i~~~~~g~PLa  190 (1237)
                      .+.+..|++.++|-+..
T Consensus       711 ~e~L~~Ia~~s~GDlR~  727 (846)
T PRK04132        711 EEGLQAILYIAEGDMRR  727 (846)
T ss_pred             HHHHHHHHHHcCCCHHH
Confidence            56788999999997744

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.69  E-value=0.0089  Score=74.89  Aligned_cols=159  Identities=11%  Similarity=0.012  Sum_probs=78.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccC-----CCCeEE-EEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEA-----FEPKAW-VCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~-----f~~~~w-~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      -+.++|.+|+|||++|..++.......     ....+| ++++.-              ........+.++....+.+..
T Consensus       210 n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l--------------~ag~~~~ge~e~~lk~ii~e~  275 (852)
T TIGR03345       210 NPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLL--------------QAGASVKGEFENRLKSVIDEV  275 (852)
T ss_pred             ceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhh--------------hcccccchHHHHHHHHHHHHH
Confidence            467999999999999999887542221     112232 222110              000001112222222222222


Q ss_pred             c--CCcEEEEEeCCCCCC-------hhhHHHhhccccCCCCCcEEEEEeCchhHHH-------hhcCCCeEeCCCCChhh
Q 000887           89 F--KKKFLIVLDDVWSER-------YDLWQALKSPFMAGAPGSRIIVTTRSMDVAL-------TMGSGKNYELKLLSDDD  152 (1237)
Q Consensus        89 ~--~~~~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~-------~~~~~~~~~l~~l~~~e  152 (1237)
                      .  +++++|++|++....       ..+...+..+.... ..-++|-||...+...       -......+.+++++.++
T Consensus       276 ~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~-G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~  354 (852)
T TIGR03345       276 KASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALAR-GELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEET  354 (852)
T ss_pred             HhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhhC-CCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHH
Confidence            2  468999999994321       11112233332222 2355666665432211       11223589999999999


Q ss_pred             hHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          153 CWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       153 a~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      +.++++.....-.......-..++...+++.+.++.
T Consensus       355 ~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       355 AIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             HHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence            999976544211110111112455666666665543

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.69  E-value=0.04  Score=58.59  Aligned_cols=154  Identities=17%  Similarity=0.177  Sum_probs=85.1

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-C
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-K   90 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~   90 (1237)
                      .++=|.++|++|.|||-||++|++.. .     .-|+.+...        ++.+..-.      +.....+.+.+.-+ .
T Consensus       184 PPKGVLLYGPPGTGKTLLAkAVA~~T-~-----AtFIrvvgS--------ElVqKYiG------EGaRlVRelF~lArek  243 (406)
T COG1222         184 PPKGVLLYGPPGTGKTLLAKAVANQT-D-----ATFIRVVGS--------ELVQKYIG------EGARLVRELFELAREK  243 (406)
T ss_pred             CCCceEeeCCCCCcHHHHHHHHHhcc-C-----ceEEEeccH--------HHHHHHhc------cchHHHHHHHHHHhhc
Confidence            34568899999999999999999842 2     223443222        22222211      11223333333333 3


Q ss_pred             CcEEEEEeCCCCC-----------ChhhHH---HhhccccCC--CCCcEEEEEeCchhHHHhh-----cCCCeEeCCCCC
Q 000887           91 KKFLIVLDDVWSE-----------RYDLWQ---ALKSPFMAG--APGSRIIVTTRSMDVALTM-----GSGKNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~-----------~~~~~~---~~~~~~~~~--~~~~~iliTtR~~~~~~~~-----~~~~~~~l~~l~  149 (1237)
                      .+.+|.+|.++..           +.+.-.   ++...+-.+  ..+.|||..|-..++....     .-+..++++.-+
T Consensus       244 aPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd  323 (406)
T COG1222         244 APSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPD  323 (406)
T ss_pred             CCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCC
Confidence            6899999999531           001111   122222222  3567899888765544221     223578888666


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchH
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      .+.-.++|+-++.+ .....+-+    .+.+++.+.|.-=|
T Consensus       324 ~~gR~~Il~IHtrk-M~l~~dvd----~e~la~~~~g~sGA  359 (406)
T COG1222         324 EEGRAEILKIHTRK-MNLADDVD----LELLARLTEGFSGA  359 (406)
T ss_pred             HHHHHHHHHHHhhh-ccCccCcC----HHHHHHhcCCCchH
Confidence            67777888887632 22222222    35778888776533

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.67  E-value=0.0034  Score=63.07  Aligned_cols=116  Identities=16%  Similarity=0.143  Sum_probs=55.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcC--CcCHHH-----------HHHHHHHHhhccCCCccCHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSD--DFDVLR-----------ISKAILDSIKRSSCKLEDLNS   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~--~~~~~~-----------~~~~i~~~l~~~~~~~~~~~~   79 (1237)
                      .+|.+.|++|.|||.||.+.+.+. ....|+.++++.-.-  +.+.-.           ...-+.+.+..-. .....++
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~-~~~~~~~   98 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELF-GKEKLEE   98 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS--TTCHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHh-ChHhHHH
Confidence            589999999999999999987765 567788777775321  111111           1111122221110 1112222


Q ss_pred             HHHH------HHHHhcC---CcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhH
Q 000887           80 VQLE------LKETVFK---KKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        80 ~~~~------l~~~l~~---~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~  133 (1237)
                      ....      -..++++   ....||+|++.+....++..+.   -..+.|||++++--..+.
T Consensus        99 ~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~il---TR~g~~skii~~GD~~Q~  158 (205)
T PF02562_consen   99 LIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMIL---TRIGEGSKIIITGDPSQI  158 (205)
T ss_dssp             HHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHH---TTB-TT-EEEEEE-----
T ss_pred             HhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHH---cccCCCcEEEEecCceee
Confidence            2110      0123344   3679999999776555555554   445779999999865433

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK09183 transposase/IS protein; Provisional

Probab=96.65  E-value=0.005  Score=65.59  Aligned_cols=101  Identities=15%  Similarity=0.203  Sum_probs=52.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      ..+.|+|++|+|||+||.+++.......+ .+.+++      ..++...+......     ..   ....+.+. ....-
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~-~v~~~~------~~~l~~~l~~a~~~-----~~---~~~~~~~~-~~~~d  166 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGI-KVRFTT------AADLLLQLSTAQRQ-----GR---YKTTLQRG-VMAPR  166 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCC-eEEEEe------HHHHHHHHHHHHHC-----Cc---HHHHHHHH-hcCCC
Confidence            46789999999999999999764433333 344553      22333333222111     11   11222222 23556


Q ss_pred             EEEEeCCCCCChhhHH--HhhccccCC-CCCcEEEEEeCch
Q 000887           94 LIVLDDVWSERYDLWQ--ALKSPFMAG-APGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~--~~~~~~~~~-~~~~~iliTtR~~  131 (1237)
                      ++|+||+.-.......  .+...+... ..+ .+||||...
T Consensus       167 lLiiDdlg~~~~~~~~~~~lf~li~~r~~~~-s~iiTsn~~  206 (259)
T PRK09183        167 LLIIDEIGYLPFSQEEANLFFQVIAKRYEKG-SMILTSNLP  206 (259)
T ss_pred             EEEEcccccCCCChHHHHHHHHHHHHHHhcC-cEEEecCCC
Confidence            9999999543222221  222222211 223 488888753

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.63  E-value=0.0063  Score=58.34  Aligned_cols=118  Identities=18%  Similarity=0.126  Sum_probs=64.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC---cCHHHHHHHHHHHh-----hccC-CCccCHHH-----
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD---FDVLRISKAILDSI-----KRSS-CKLEDLNS-----   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~---~~~~~~~~~i~~~l-----~~~~-~~~~~~~~-----   79 (1237)
                      .+|-|++..|.|||++|...+-+.....+. +.++-+-..   ......++.+ ..+     +... ....+.++     
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~-v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~a   80 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRALGHGYR-VGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAAA   80 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCe-EEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHHH
Confidence            478899999999999999987755555554 444433332   2222222222 000     0000 00011111     


Q ss_pred             --HHHHHHHHhcC-CcEEEEEeCCCC---CChhhHHHhhccccCCCCCcEEEEEeCchhH
Q 000887           80 --VQLELKETVFK-KKFLIVLDDVWS---ERYDLWQALKSPFMAGAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        80 --~~~~l~~~l~~-~~~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~  133 (1237)
                        .....++.+.. .-=|+|+|++--   -.....+++...+...+.+..||+|.|+..-
T Consensus        81 ~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~  140 (159)
T cd00561          81 AEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPK  140 (159)
T ss_pred             HHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCH
Confidence              22223333333 456999999832   1223345566666667778899999998654

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.59  E-value=0.052  Score=59.81  Aligned_cols=90  Identities=17%  Similarity=0.196  Sum_probs=58.1

Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEE-EEeCchhHHHhhc-CCCeEeCCCCChhhhHHHHHHHhcCCCCC
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRII-VTTRSMDVALTMG-SGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~il-iTtR~~~~~~~~~-~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      +++-++|+|+++.-+......+...+-.-++++.+| +|++...+...+. ....+.+.+++.++..+.+....      
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~------  204 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG------  204 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC------
Confidence            356688899997666566666666665545566554 5555444443332 23688999999999999987641      


Q ss_pred             CCCCChHHHHHHHHHHccCCchHH
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      .. +     ...++..++|.|...
T Consensus       205 ~~-~-----~~~~l~~~~Gsp~~A  222 (342)
T PRK06964        205 VA-D-----ADALLAEAGGAPLAA  222 (342)
T ss_pred             CC-h-----HHHHHHHcCCCHHHH
Confidence            11 1     224577889999643

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.58  E-value=0.025  Score=60.70  Aligned_cols=41  Identities=27%  Similarity=0.339  Sum_probs=27.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHH
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRI   59 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~   59 (1237)
                      -|.+.|++|+|||++|++++.. ..   ...+++++....+..++
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~-lg---~~~~~i~~~~~~~~~dl   63 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARK-RD---RPVMLINGDAELTTSDL   63 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHH-hC---CCEEEEeCCccCCHHHH
Confidence            4678999999999999998763 21   12445555554444433

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=96.58  E-value=0.0089  Score=68.86  Aligned_cols=138  Identities=19%  Similarity=0.149  Sum_probs=79.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      =++++.+|++|||||.+|+.++....+++|    .++++.-.|+.++-..      +..-...-+...+..++.. +-..
T Consensus       438 GkIlCf~GPPGVGKTSI~kSIA~ALnRkFf----RfSvGG~tDvAeIkGH------RRTYVGAMPGkiIq~LK~v-~t~N  506 (906)
T KOG2004|consen  438 GKILCFVGPPGVGKTSIAKSIARALNRKFF----RFSVGGMTDVAEIKGH------RRTYVGAMPGKIIQCLKKV-KTEN  506 (906)
T ss_pred             CcEEEEeCCCCCCcccHHHHHHHHhCCceE----EEeccccccHHhhccc------ceeeeccCChHHHHHHHhh-CCCC
Confidence            389999999999999999999986555554    3566666665544311      1111233445555555544 3356


Q ss_pred             EEEEEeCCCC----CChhhHHHhhccccCCCC-------------CcEEEEE-eCch--hHH-HhhcCCCeEeCCCCChh
Q 000887           93 FLIVLDDVWS----ERYDLWQALKSPFMAGAP-------------GSRIIVT-TRSM--DVA-LTMGSGKNYELKLLSDD  151 (1237)
Q Consensus        93 ~LlvlDdv~~----~~~~~~~~~~~~~~~~~~-------------~~~iliT-tR~~--~~~-~~~~~~~~~~l~~l~~~  151 (1237)
                      =|+.+|.|+.    .+.+..+++...+.+..+             =|||++. |-+.  .+. .......+|++.+...+
T Consensus       507 PliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN~idtIP~pLlDRMEvIelsGYv~e  586 (906)
T KOG2004|consen  507 PLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVIDTIPPPLLDRMEVIELSGYVAE  586 (906)
T ss_pred             ceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhheEEEEeccccccCChhhhhhhheeeccCccHH
Confidence            6778899853    222344455444433221             2566643 3321  011 11122357888888888


Q ss_pred             hhHHHHHHHh
Q 000887          152 DCWSVFVAHA  161 (1237)
Q Consensus       152 ea~~l~~~~~  161 (1237)
                      |-+++-.++.
T Consensus       587 EKv~IA~~yL  596 (906)
T KOG2004|consen  587 EKVKIAERYL  596 (906)
T ss_pred             HHHHHHHHhh
Confidence            8777665544

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.58  E-value=0.054  Score=59.94  Aligned_cols=161  Identities=9%  Similarity=0.029  Sum_probs=90.3

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCe--------EEEEEcCCcCHHHHHHHHHHHhhccCC-CccCHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPK--------AWVCVSDDFDVLRISKAILDSIKRSSC-KLEDLNSVQ   81 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~--------~w~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~   81 (1237)
                      -..-..++|+.|+||+++|.+++....- ..-+..        -++..+..+|+..+        .+... ....+++++
T Consensus        23 l~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i--------~p~~~~~~I~idqiR   94 (334)
T PRK07993         23 GHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTL--------TPEKGKSSLGVDAVR   94 (334)
T ss_pred             cceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEE--------ecccccccCCHHHHH
Confidence            3456779999999999999998775421 111000        01111111111100        00000 123455554


Q ss_pred             HHHHHHh----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCc-hhHHHhhc-CCCeEeCCCCChhhhHH
Q 000887           82 LELKETV----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRS-MDVALTMG-SGKNYELKLLSDDDCWS  155 (1237)
Q Consensus        82 ~~l~~~l----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~-~~~~~~~~-~~~~~~l~~l~~~ea~~  155 (1237)
                      ......-    .+++-++|+|+++.-+......+...+-.-+.++.+|.+|.. ..+...+. ....+.+.+++++++.+
T Consensus        95 ~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~  174 (334)
T PRK07993         95 EVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALT  174 (334)
T ss_pred             HHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHH
Confidence            4333221    246778999999665555555566655444456655555544 44443432 23578899999999998


Q ss_pred             HHHHHhcCCCCCCCCCChHHHHHHHHHHccCCch
Q 000887          156 VFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       156 l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL  189 (1237)
                      .+....+     .    ..+.+..+++.++|.|.
T Consensus       175 ~L~~~~~-----~----~~~~a~~~~~la~G~~~  199 (334)
T PRK07993        175 WLSREVT-----M----SQDALLAALRLSAGAPG  199 (334)
T ss_pred             HHHHccC-----C----CHHHHHHHHHHcCCCHH
Confidence            8865321     1    13346788999999995

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

Probab=96.57  E-value=0.00078  Score=67.65  Aligned_cols=84  Identities=20%  Similarity=0.185  Sum_probs=62.0

Q ss_pred             CCCCccEEEcccccccc-----ccccccCCCCCCeEEccCCCcc----ccc-------hhhcccCCccEEEcCccccCcc
Q 000887          398 QCKKLRVLSLGSYCITE-----VPISIGCLKQLRYLNFSRSEIQ----CLP-------DAICSLFNLEILILRNCWCLLK  461 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~-----lp~~~~~l~~Lr~L~L~~~~i~----~lp-------~~i~~L~~L~~L~L~~~~~l~~  461 (1237)
                      .+..+..++||||.|..     +...+.+-.+|++-+++.-...    .+|       +.+-++++|+..+||.|-.-..
T Consensus        28 ~~d~~~evdLSGNtigtEA~e~l~~~ia~~~~L~vvnfsd~ftgr~kde~~~~L~~Ll~aLlkcp~l~~v~LSDNAfg~~  107 (388)
T COG5238          28 MMDELVEVDLSGNTIGTEAMEELCNVIANVRNLRVVNFSDAFTGRDKDELYSNLVMLLKALLKCPRLQKVDLSDNAFGSE  107 (388)
T ss_pred             hhcceeEEeccCCcccHHHHHHHHHHHhhhcceeEeehhhhhhcccHHHHHHHHHHHHHHHhcCCcceeeeccccccCcc
Confidence            48889999999999873     4455677788999998864221    333       3467889999999999844444


Q ss_pred             CChh----hcccccccEEeccCCC
Q 000887          462 LPSR----IGNLVNLHYLNIEGAS  481 (1237)
Q Consensus       462 lp~~----i~~L~~L~~L~l~~~~  481 (1237)
                      .|+.    |++-+.|.||.+.+|.
T Consensus       108 ~~e~L~d~is~~t~l~HL~l~NnG  131 (388)
T COG5238         108 FPEELGDLISSSTDLVHLKLNNNG  131 (388)
T ss_pred             cchHHHHHHhcCCCceeEEeecCC
Confidence            5544    4677889999999884

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.55  E-value=0.024  Score=62.50  Aligned_cols=147  Identities=15%  Similarity=0.073  Sum_probs=72.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc--ccCC---CC-----eEEEEEcCCcCHHHHHHHHH-HHhhccCCCccCHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL--TEAF---EP-----KAWVCVSDDFDVLRISKAIL-DSIKRSSCKLEDLNSVQ   81 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~--~~~f---~~-----~~w~~~~~~~~~~~~~~~i~-~~l~~~~~~~~~~~~~~   81 (1237)
                      ..-+.++|+.|+|||++|..++....  ...-   .+     +.++..+..+|+..+.-+-. ..-+ .......+++++
T Consensus        21 ~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g-~~~~~I~id~iR   99 (325)
T PRK08699         21 PNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENG-RKLLQIKIDAVR   99 (325)
T ss_pred             ceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEeccccccccc-ccCCCcCHHHHH
Confidence            45678999999999999999877542  1100   00     00111111111110000000 0000 000112455555


Q ss_pred             HHHHHHh----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhhc-CCCeEeCCCCChhhhHH
Q 000887           82 LELKETV----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTMG-SGKNYELKLLSDDDCWS  155 (1237)
Q Consensus        82 ~~l~~~l----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~~-~~~~~~l~~l~~~ea~~  155 (1237)
                      ......-    .+++-++|+|+++.-+......+...+-....++.+|++|.+.. +..... ....+.+.+++.+++.+
T Consensus       100 ~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~  179 (325)
T PRK08699        100 EIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALA  179 (325)
T ss_pred             HHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHH
Confidence            4332221    13444556688855444444444444433334566777777654 332222 22578899999999998


Q ss_pred             HHHHH
Q 000887          156 VFVAH  160 (1237)
Q Consensus       156 l~~~~  160 (1237)
                      .+...
T Consensus       180 ~L~~~  184 (325)
T PRK08699        180 YLRER  184 (325)
T ss_pred             HHHhc
Confidence            88653

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.53  E-value=0.016  Score=63.63  Aligned_cols=91  Identities=14%  Similarity=0.138  Sum_probs=53.9

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      .++++|+++|++|+||||++..++.......+ .+..++.+... ....-+...+..++.+.....+.++....+...-.
T Consensus       239 ~~~~vI~LVGptGvGKTTTiaKLA~~L~~~Gk-kVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~  317 (436)
T PRK11889        239 KEVQTIALIGPTGVGKTTTLAKMAWQFHGKKK-TVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKE  317 (436)
T ss_pred             cCCcEEEEECCCCCcHHHHHHHHHHHHHHcCC-cEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHh
Confidence            34689999999999999999999875443333 35566654433 11222233444444433233455666655554422


Q ss_pred             C-CcEEEEEeCCCC
Q 000887           90 K-KKFLIVLDDVWS  102 (1237)
Q Consensus        90 ~-~~~LlvlDdv~~  102 (1237)
                      . +-=+|++|-.-.
T Consensus       318 ~~~~DvVLIDTaGR  331 (436)
T PRK11889        318 EARVDYILIDTAGK  331 (436)
T ss_pred             ccCCCEEEEeCccc
Confidence            1 345778888744

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.53  E-value=0.012  Score=74.39  Aligned_cols=132  Identities=12%  Similarity=0.071  Sum_probs=69.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCC-----CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh-
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAF-----EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV-   88 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f-----~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-   88 (1237)
                      -+.++|++|+|||++|..++.......-     +..+|.-     +...+.       ... .-..+.++....+.+.+ 
T Consensus       202 n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l-----~~~~l~-------ag~-~~~ge~e~rl~~i~~~~~  268 (821)
T CHL00095        202 NPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITL-----DIGLLL-------AGT-KYRGEFEERLKRIFDEIQ  268 (821)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEe-----eHHHHh-------ccC-CCccHHHHHHHHHHHHHH
Confidence            4679999999999999998875432211     2334431     111111       111 11123333333333333 


Q ss_pred             cCCcEEEEEeCCCCC-------ChhhHHHhhccccCCCCCcEEEEEeCchhHHHh-------hcCCCeEeCCCCChhhhH
Q 000887           89 FKKKFLIVLDDVWSE-------RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALT-------MGSGKNYELKLLSDDDCW  154 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~-------~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~-------~~~~~~~~l~~l~~~ea~  154 (1237)
                      ..++.+|++|+++.-       .......+..+.... ..-++|.+|...+....       ......+.++..+.+|+.
T Consensus       269 ~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~r-g~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~  347 (821)
T CHL00095        269 ENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALAR-GELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETI  347 (821)
T ss_pred             hcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhC-CCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHH
Confidence            346899999999421       001122233222222 23456666665543211       122256888899999988


Q ss_pred             HHHHHH
Q 000887          155 SVFVAH  160 (1237)
Q Consensus       155 ~l~~~~  160 (1237)
                      .+++..
T Consensus       348 aILr~l  353 (821)
T CHL00095        348 EILFGL  353 (821)
T ss_pred             HHHHHH
Confidence            888654

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.51  E-value=0.008  Score=65.49  Aligned_cols=101  Identities=17%  Similarity=0.266  Sum_probs=60.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .+-+.++|..|+|||.||.++++...+..+. +.++++      ..+...+......     ....+   .+.. + .+-
T Consensus       156 ~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~-v~~~~~------~~l~~~lk~~~~~-----~~~~~---~l~~-l-~~~  218 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLAAIANELAKKGVS-STLLHF------PEFIRELKNSISD-----GSVKE---KIDA-V-KEA  218 (306)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCC-EEEEEH------HHHHHHHHHHHhc-----CcHHH---HHHH-h-cCC
Confidence            4568999999999999999999866554444 566654      2344444444321     11222   2222 2 256


Q ss_pred             EEEEEeCCCCCChhhHHH--hhcccc-CC-CCCcEEEEEeCc
Q 000887           93 FLIVLDDVWSERYDLWQA--LKSPFM-AG-APGSRIIVTTRS  130 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~--~~~~~~-~~-~~~~~iliTtR~  130 (1237)
                      =|||+||+.......|..  +...+. .. ..+-.++|||-.
T Consensus       219 dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        219 PVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             CEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            689999996554455542  333332 12 245568888864

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.49  E-value=0.0079  Score=63.73  Aligned_cols=120  Identities=18%  Similarity=0.191  Sum_probs=67.1

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcc--cccCCCCeEEE----EEcCC---------cCHHHHHHHHHHHhhccCCCc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK--LTEAFEPKAWV----CVSDD---------FDVLRISKAILDSIKRSSCKL   74 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~--~~~~f~~~~w~----~~~~~---------~~~~~~~~~i~~~l~~~~~~~   74 (1237)
                      ++++..|.+.|.+|.|||.||.++.-..  .++.|..++-.    .++++         ..+.-..+.|.+-+..-....
T Consensus       242 d~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG~eEeKm~PWmq~i~DnLE~L~~~~  321 (436)
T COG1875         242 DDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPGTEEEKMGPWMQAIFDNLEVLFSPN  321 (436)
T ss_pred             CCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCCchhhhccchHHHHHhHHHHHhccc
Confidence            3567899999999999999998864332  56667655422    12211         112233344444333221111


Q ss_pred             cCHHHHHHHHH----------HHhcC---CcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh
Q 000887           75 EDLNSVQLELK----------ETVFK---KKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD  132 (1237)
Q Consensus        75 ~~~~~~~~~l~----------~~l~~---~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~  132 (1237)
                      ...++....+.          .+.++   .+.++|+|.+.+-+..+...+   +-..+.|+||+.|---.+
T Consensus       322 ~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTpheikTi---ltR~G~GsKIVl~gd~aQ  389 (436)
T COG1875         322 EPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPHELKTI---LTRAGEGSKIVLTGDPAQ  389 (436)
T ss_pred             ccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHHHHHHH---HHhccCCCEEEEcCCHHH
Confidence            11122222221          12234   367999999977655554444   344688999999876443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.45  E-value=0.0099  Score=61.77  Aligned_cols=47  Identities=13%  Similarity=0.139  Sum_probs=35.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISK   61 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~   61 (1237)
                      =+++.|+|.+|+|||++|.+++....+ ....++|++... .+...+.+
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~-~g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAAR-QGKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh-CCCeEEEEECCC-CCHHHHHH
Confidence            478999999999999999998764333 345688998865 45544443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.44  E-value=0.031  Score=66.43  Aligned_cols=158  Identities=18%  Similarity=0.168  Sum_probs=82.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ++-+.++|++|+|||++|++++... ...     ++.++    ...+....   .+      .........+.......+
T Consensus        88 ~~giLL~GppGtGKT~la~alA~~~-~~~-----~~~i~----~~~~~~~~---~g------~~~~~l~~~f~~a~~~~p  148 (495)
T TIGR01241        88 PKGVLLVGPPGTGKTLLAKAVAGEA-GVP-----FFSIS----GSDFVEMF---VG------VGASRVRDLFEQAKKNAP  148 (495)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHc-CCC-----eeecc----HHHHHHHH---hc------ccHHHHHHHHHHHHhcCC
Confidence            4558899999999999999998742 111     22221    11111111   00      111223333444444578


Q ss_pred             EEEEEeCCCCCC----------hhhHH----Hhhcccc--CCCCCcEEEEEeCchhHHH-hh----cCCCeEeCCCCChh
Q 000887           93 FLIVLDDVWSER----------YDLWQ----ALKSPFM--AGAPGSRIIVTTRSMDVAL-TM----GSGKNYELKLLSDD  151 (1237)
Q Consensus        93 ~LlvlDdv~~~~----------~~~~~----~~~~~~~--~~~~~~~iliTtR~~~~~~-~~----~~~~~~~l~~l~~~  151 (1237)
                      .+|++|+++.-.          .....    .+...+.  ....+..||.||....... .+    .-...+.++..+.+
T Consensus       149 ~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~  228 (495)
T TIGR01241       149 CIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIK  228 (495)
T ss_pred             CEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHH
Confidence            999999994310          00111    1111111  1223445666665543211 11    12357889999999


Q ss_pred             hhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCC-chHHHHH
Q 000887          152 DCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGL-PLAARAL  194 (1237)
Q Consensus       152 ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~-PLal~~~  194 (1237)
                      +-.++++.+....... .    ......+++.+.|. +-.|..+
T Consensus       229 ~R~~il~~~l~~~~~~-~----~~~l~~la~~t~G~sgadl~~l  267 (495)
T TIGR01241       229 GREEILKVHAKNKKLA-P----DVDLKAVARRTPGFSGADLANL  267 (495)
T ss_pred             HHHHHHHHHHhcCCCC-c----chhHHHHHHhCCCCCHHHHHHH
Confidence            9999998876432211 1    12245788888764 4445444

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.43  E-value=0.0049  Score=65.24  Aligned_cols=80  Identities=23%  Similarity=0.272  Sum_probs=48.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ..-+.++|.+|+|||.||.+++++.. ..-..+.+++      ..++..++......        ......+.+.+ .+-
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv~f~~------~~el~~~Lk~~~~~--------~~~~~~l~~~l-~~~  168 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFIT------APDLLSKLKAAFDE--------GRLEEKLLREL-KKV  168 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEE------HHHHHHHHHHHHhc--------CchHHHHHHHh-hcC
Confidence            34689999999999999999998766 3333466774      33445555544432        11111222222 244


Q ss_pred             EEEEEeCCCCCChhhH
Q 000887           93 FLIVLDDVWSERYDLW  108 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~  108 (1237)
                      =|||+||+--.....|
T Consensus       169 dlLIiDDlG~~~~~~~  184 (254)
T COG1484         169 DLLIIDDIGYEPFSQE  184 (254)
T ss_pred             CEEEEecccCccCCHH
Confidence            5889999955433433

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

Probab=96.43  E-value=0.0011  Score=80.06  Aligned_cols=132  Identities=16%  Similarity=0.097  Sum_probs=81.3

Q ss_pred             CCCcccEEeccCCCCccccCCC---CCCCCcCceEecCCCCcccccccccCCCCCCceEEEcCCCCceeccCCCCccccC
Q 000887         1060 TLSSLRELALSECPGIVVFPEE---GLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILP 1136 (1237)
Q Consensus      1060 ~l~~L~~L~l~~c~~l~~~~~~---~~~~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~ 1136 (1237)
                      .-.+|++|+++|...+..-+..   ..+|+|+.|.+.+-....+-......++++|..||||++ +++.+.    +...+
T Consensus       120 sr~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~T-nI~nl~----GIS~L  194 (699)
T KOG3665|consen  120 SRQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGT-NISNLS----GISRL  194 (699)
T ss_pred             HHHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCC-CccCcH----HHhcc
Confidence            3457888888875433222211   347888888888855543222224667888888888885 566553    33467


Q ss_pred             CCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCCCccc-------CCCCCCCCcccEeeecCCC
Q 000887         1137 TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTS-------FPEAGFPSSLLSLEIQRCP 1196 (1237)
Q Consensus      1137 ~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~-------l~~~~~~~sL~~L~i~~cp 1196 (1237)
                      ++|+.|.+.+.+....-....+-+|++|+.||++.-.....       +.-+..+|.|+.||.++..
T Consensus       195 knLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLDcSgTd  261 (699)
T KOG3665|consen  195 KNLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLDCSGTD  261 (699)
T ss_pred             ccHHHHhccCCCCCchhhHHHHhcccCCCeeeccccccccchHHHHHHHHhcccCccccEEecCCcc
Confidence            78888888775433322223455688888888886332221       1112347888888888754

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.41  E-value=0.03  Score=63.83  Aligned_cols=119  Identities=22%  Similarity=0.218  Sum_probs=75.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFL   94 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~L   94 (1237)
                      ++.|.|+=++||||+++.+.......    .+++...+......-..+....+                 .+.-..++..
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~----~iy~~~~d~~~~~~~l~d~~~~~-----------------~~~~~~~~~y   97 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE----IIYINFDDLRLDRIELLDLLRAY-----------------IELKEREKSY   97 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcc----eEEEEecchhcchhhHHHHHHHH-----------------HHhhccCCce
Confidence            99999999999999997655532232    56665444322111111221111                 1111127789


Q ss_pred             EEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHh-----h-cCCCeEeCCCCChhhhHHHH
Q 000887           95 IVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALT-----M-GSGKNYELKLLSDDDCWSVF  157 (1237)
Q Consensus        95 lvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~-----~-~~~~~~~l~~l~~~ea~~l~  157 (1237)
                      +++|.|..  ...|......+...++. +|+||+-+......     . +....+++-||+..|-..+-
T Consensus        98 ifLDEIq~--v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~~~  163 (398)
T COG1373          98 IFLDEIQN--VPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLKLK  163 (398)
T ss_pred             EEEecccC--chhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHhhc
Confidence            99999944  47788877777776666 89999887654321     1 22357899999998887654

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.39  E-value=0.004  Score=60.21  Aligned_cols=99  Identities=22%  Similarity=0.293  Sum_probs=60.1

Q ss_pred             CCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcc-cCCccEEEcCccccCccCChh--hcccccccEEe
Q 000887          400 KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICS-LFNLEILILRNCWCLLKLPSR--IGNLVNLHYLN  476 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~-L~~L~~L~L~~~~~l~~lp~~--i~~L~~L~~L~  476 (1237)
                      ...-.+||++|.+..++. |..+..|..|.|.+|+|..+.+.+.. +++|..|.|.+| ++..+.+-  +..+++|++|.
T Consensus        42 d~~d~iDLtdNdl~~l~~-lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnN-si~~l~dl~pLa~~p~L~~Lt  119 (233)
T KOG1644|consen   42 DQFDAIDLTDNDLRKLDN-LPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNN-SIQELGDLDPLASCPKLEYLT  119 (233)
T ss_pred             cccceecccccchhhccc-CCCccccceEEecCCcceeeccchhhhccccceEEecCc-chhhhhhcchhccCCccceee
Confidence            344567777777766665 56677777777777777777444433 456777777776 55444321  45566777777


Q ss_pred             ccCCCccccCcc----cccccccccccce
Q 000887          477 IEGASALRELPL----GMKELKCLRTLTN  501 (1237)
Q Consensus       477 l~~~~~l~~ip~----~~~~L~~L~~L~~  501 (1237)
                      +-+| ....-+.    -+-++++|++|+.
T Consensus       120 ll~N-pv~~k~~YR~yvl~klp~l~~LDF  147 (233)
T KOG1644|consen  120 LLGN-PVEHKKNYRLYVLYKLPSLRTLDF  147 (233)
T ss_pred             ecCC-chhcccCceeEEEEecCcceEeeh
Confidence            7666 3333322    1456666666654

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.38  E-value=0.029  Score=64.70  Aligned_cols=161  Identities=16%  Similarity=0.078  Sum_probs=89.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC--cCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD--FDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      .-|.|.|+.|+|||+||++++....++.+-.+.+++++.-  .+.+.+++.+..                 .+.+.+...
T Consensus       432 ~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~-----------------vfse~~~~~  494 (952)
T KOG0735|consen  432 GNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSLEKIQKFLNN-----------------VFSEALWYA  494 (952)
T ss_pred             ccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhHHHHHHHHHH-----------------HHHHHHhhC
Confidence            4578999999999999999988656665555667776533  344445444332                 233455668


Q ss_pred             cEEEEEeCCCCC------ChhhHH-----------HhhccccCCCCCcEEEEEeCchhHHH-hhcC----CCeEeCCCCC
Q 000887           92 KFLIVLDDVWSE------RYDLWQ-----------ALKSPFMAGAPGSRIIVTTRSMDVAL-TMGS----GKNYELKLLS  149 (1237)
Q Consensus        92 ~~LlvlDdv~~~------~~~~~~-----------~~~~~~~~~~~~~~iliTtR~~~~~~-~~~~----~~~~~l~~l~  149 (1237)
                      +-+||+||++..      +-.+++           ++...+...+..-++|.|........ ....    ..+..++.+.
T Consensus       495 PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~  574 (952)
T KOG0735|consen  495 PSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPA  574 (952)
T ss_pred             CcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcc
Confidence            999999999421      001111           11111111222223455554432221 1111    1367788888


Q ss_pred             hhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccC-CchHHHHHH
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKG-LPLAARALG  195 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g-~PLal~~~~  195 (1237)
                      ..+-.++++......-    .....+...-++.+++| .|.-+.+..
T Consensus       575 ~~~R~~IL~~~~s~~~----~~~~~~dLd~ls~~TEGy~~~DL~ifV  617 (952)
T KOG0735|consen  575 VTRRKEILTTIFSKNL----SDITMDDLDFLSVKTEGYLATDLVIFV  617 (952)
T ss_pred             hhHHHHHHHHHHHhhh----hhhhhHHHHHHHHhcCCccchhHHHHH
Confidence            8888888876543211    11112333447777766 455555543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.38  E-value=0.088  Score=65.71  Aligned_cols=93  Identities=17%  Similarity=0.191  Sum_probs=51.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-CC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-KK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~   91 (1237)
                      ..++.++|+.|+|||.+|+.+++..    +...+.++.+...+.    ..+...++.+.. ....++ ...+.+.++ ..
T Consensus       484 ~~~~lf~Gp~GvGKT~lA~~la~~l----~~~~~~~d~se~~~~----~~~~~lig~~~g-yvg~~~-~~~l~~~~~~~p  553 (731)
T TIGR02639       484 VGSFLFTGPTGVGKTELAKQLAEAL----GVHLERFDMSEYMEK----HTVSRLIGAPPG-YVGFEQ-GGLLTEAVRKHP  553 (731)
T ss_pred             ceeEEEECCCCccHHHHHHHHHHHh----cCCeEEEeCchhhhc----ccHHHHhcCCCC-Ccccch-hhHHHHHHHhCC
Confidence            3468899999999999999998743    233456655442221    112222232221 111111 112233333 34


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccc
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPF  115 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~  115 (1237)
                      ..+++||+++..+.+....+...+
T Consensus       554 ~~VvllDEieka~~~~~~~Ll~~l  577 (731)
T TIGR02639       554 HCVLLLDEIEKAHPDIYNILLQVM  577 (731)
T ss_pred             CeEEEEechhhcCHHHHHHHHHhh
Confidence            579999999776666555555544

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.37  E-value=0.0086  Score=62.58  Aligned_cols=103  Identities=17%  Similarity=0.199  Sum_probs=56.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ...+.++|.+|+|||+||.++++...+.. ..+++++      ..++...+-.....   .....+    .+.+.+. +.
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~g-~~v~~it------~~~l~~~l~~~~~~---~~~~~~----~~l~~l~-~~  163 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLRG-KSVLIIT------VADIMSAMKDTFSN---SETSEE----QLLNDLS-NV  163 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhcC-CeEEEEE------HHHHHHHHHHHHhh---ccccHH----HHHHHhc-cC
Confidence            35789999999999999999988654433 3466664      34444444333321   111112    2333344 34


Q ss_pred             EEEEEeCCCCCChhhHHH--hhccccCC-CCCcEEEEEeCc
Q 000887           93 FLIVLDDVWSERYDLWQA--LKSPFMAG-APGSRIIVTTRS  130 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~--~~~~~~~~-~~~~~iliTtR~  130 (1237)
                      =+||+||+.......|..  +...+... .....+||||-.
T Consensus       164 dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        164 DLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             CEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence            478889996544444442  21111111 223457788764

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.34  E-value=0.00026  Score=71.26  Aligned_cols=101  Identities=22%  Similarity=0.295  Sum_probs=74.3

Q ss_pred             CCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChh--hcccccccEE
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSR--IGNLVNLHYL  475 (1237)
Q Consensus       398 ~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~--i~~L~~L~~L  475 (1237)
                      .+.+.+.|++.||.++.+.- ..+++.|++|.|+-|.|+.+. .+..+++|+.|.|+.| .|..+.+-  +.+|++|+.|
T Consensus        17 dl~~vkKLNcwg~~L~DIsi-c~kMp~lEVLsLSvNkIssL~-pl~rCtrLkElYLRkN-~I~sldEL~YLknlpsLr~L   93 (388)
T KOG2123|consen   17 DLENVKKLNCWGCGLDDISI-CEKMPLLEVLSLSVNKISSLA-PLQRCTRLKELYLRKN-CIESLDELEYLKNLPSLRTL   93 (388)
T ss_pred             HHHHhhhhcccCCCccHHHH-HHhcccceeEEeeccccccch-hHHHHHHHHHHHHHhc-ccccHHHHHHHhcCchhhhH
Confidence            35567788888888887754 357888999999999988884 4888889999999888 66666553  3678888888


Q ss_pred             eccCCCccccCccc-----ccccccccccce
Q 000887          476 NIEGASALRELPLG-----MKELKCLRTLTN  501 (1237)
Q Consensus       476 ~l~~~~~l~~ip~~-----~~~L~~L~~L~~  501 (1237)
                      .|..|.....-+..     +..|++|++|+.
T Consensus        94 WL~ENPCc~~ag~nYR~~VLR~LPnLkKLDn  124 (388)
T KOG2123|consen   94 WLDENPCCGEAGQNYRRKVLRVLPNLKKLDN  124 (388)
T ss_pred             hhccCCcccccchhHHHHHHHHcccchhccC
Confidence            88877544444432     556677777754

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.34  E-value=0.022  Score=69.93  Aligned_cols=133  Identities=14%  Similarity=0.132  Sum_probs=70.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccC-----CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh-
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEA-----FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV-   88 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~-----f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-   88 (1237)
                      -+.++|++|+|||++|+.++.......     .+..+|..     +...+    ..    ...-..+.++....+.+.+ 
T Consensus       209 n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l-----~~~~l----la----G~~~~Ge~e~rl~~l~~~l~  275 (758)
T PRK11034        209 NPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL-----DIGSL----LA----GTKYRGDFEKRFKALLKQLE  275 (758)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec-----cHHHH----hc----ccchhhhHHHHHHHHHHHHH
Confidence            456899999999999999887543222     12333321     11111    10    1001123333333333333 


Q ss_pred             cCCcEEEEEeCCCCC--------ChhhHHHhhccccCCCCCcEEEEEeCchhHHH-------hhcCCCeEeCCCCChhhh
Q 000887           89 FKKKFLIVLDDVWSE--------RYDLWQALKSPFMAGAPGSRIIVTTRSMDVAL-------TMGSGKNYELKLLSDDDC  153 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~--------~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~-------~~~~~~~~~l~~l~~~ea  153 (1237)
                      +.++.+|++|+++.-        ...+...+..++... ..-++|-+|...+...       .......+.+++.+.+++
T Consensus       276 ~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~-g~i~vIgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~  354 (758)
T PRK11034        276 QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS-GKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEET  354 (758)
T ss_pred             hcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhC-CCeEEEecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHH
Confidence            346789999999421        111222233333322 2344555554433211       112235799999999999


Q ss_pred             HHHHHHHh
Q 000887          154 WSVFVAHA  161 (1237)
Q Consensus       154 ~~l~~~~~  161 (1237)
                      .++++...
T Consensus       355 ~~IL~~~~  362 (758)
T PRK11034        355 VQIINGLK  362 (758)
T ss_pred             HHHHHHHH
Confidence            99998654

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.34  E-value=0.0021  Score=61.75  Aligned_cols=83  Identities=25%  Similarity=0.213  Sum_probs=44.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEEE
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLI   95 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~Ll   95 (1237)
                      |.|+|++|+|||++|+.+++..    -...+-+.+....+..++....--.-+.........-+   .+     .+..++
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~----~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~---a~-----~~~~il   69 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL----GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVR---AM-----RKGGIL   69 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH----TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCT---TH-----HEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHh----hcceEEEEeccccccccceeeeeecccccccccccccc---cc-----cceeEE
Confidence            6799999999999999998753    11233566677667665553221110000000000000   00     178999


Q ss_pred             EEeCCCCCChhhHHH
Q 000887           96 VLDDVWSERYDLWQA  110 (1237)
Q Consensus        96 vlDdv~~~~~~~~~~  110 (1237)
                      |+|++.......+..
T Consensus        70 ~lDEin~a~~~v~~~   84 (139)
T PF07728_consen   70 VLDEINRAPPEVLES   84 (139)
T ss_dssp             EESSCGG--HHHHHT
T ss_pred             EECCcccCCHHHHHH
Confidence            999996544333333

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.33  E-value=0.031  Score=64.89  Aligned_cols=155  Identities=14%  Similarity=0.110  Sum_probs=79.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      .++-|.++|++|+|||.+|+++++.. ...   .+-++.+      .+..    ..     ...........+...-...
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~e~-~~~---~~~l~~~------~l~~----~~-----vGese~~l~~~f~~A~~~~  318 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIANDW-QLP---LLRLDVG------KLFG----GI-----VGESESRMRQMIRIAEALS  318 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHHHh-CCC---EEEEEhH------Hhcc----cc-----cChHHHHHHHHHHHHHhcC
Confidence            45678999999999999999998742 111   1222211      1110    00     0011112222222222347


Q ss_pred             cEEEEEeCCCCCC-------hh-hH----HHhhccccCCCCCcEEEEEeCchhHHH-hh----cCCCeEeCCCCChhhhH
Q 000887           92 KFLIVLDDVWSER-------YD-LW----QALKSPFMAGAPGSRIIVTTRSMDVAL-TM----GSGKNYELKLLSDDDCW  154 (1237)
Q Consensus        92 ~~LlvlDdv~~~~-------~~-~~----~~~~~~~~~~~~~~~iliTtR~~~~~~-~~----~~~~~~~l~~l~~~ea~  154 (1237)
                      +++|++|+++..-       .. ..    ..+...+.....+.-||.||....... .+    .-+..+.++.-+.++-.
T Consensus       319 P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~  398 (489)
T CHL00195        319 PCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEERE  398 (489)
T ss_pred             CcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHH
Confidence            8999999995310       00 00    111111222233445666776543211 11    22357888888999999


Q ss_pred             HHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          155 SVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       155 ~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      ++|+.+..+.......   ......+++.+.|.-
T Consensus       399 ~Il~~~l~~~~~~~~~---~~dl~~La~~T~GfS  429 (489)
T CHL00195        399 KIFKIHLQKFRPKSWK---KYDIKKLSKLSNKFS  429 (489)
T ss_pred             HHHHHHHhhcCCCccc---ccCHHHHHhhcCCCC
Confidence            9999887543211110   112456777766543

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.32  E-value=0.0046  Score=59.77  Aligned_cols=86  Identities=27%  Similarity=0.293  Sum_probs=69.6

Q ss_pred             hhcCCCCCccEEEccccccccccccc-cCCCCCCeEEccCCCccccch--hhcccCCccEEEcCccccCccCCh----hh
Q 000887          394 DLLPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQCLPD--AICSLFNLEILILRNCWCLLKLPS----RI  466 (1237)
Q Consensus       394 ~~~~~~~~Lr~L~L~~~~i~~lp~~~-~~l~~Lr~L~L~~~~i~~lp~--~i~~L~~L~~L~L~~~~~l~~lp~----~i  466 (1237)
                      +-|+.++.|.+|.|.+|+|+.+.+.+ .-+++|..|.|.+|.|.++-+  .+..+++|++|.+-+| .+..-+.    -+
T Consensus        58 ~~lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll~N-pv~~k~~YR~yvl  136 (233)
T KOG1644|consen   58 DNLPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLLGN-PVEHKKNYRLYVL  136 (233)
T ss_pred             ccCCCccccceEEecCCcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceeeecCC-chhcccCceeEEE
Confidence            44788999999999999999996555 456779999999999987744  5788899999999998 4444332    26


Q ss_pred             cccccccEEeccCC
Q 000887          467 GNLVNLHYLNIEGA  480 (1237)
Q Consensus       467 ~~L~~L~~L~l~~~  480 (1237)
                      .++++|++||..+-
T Consensus       137 ~klp~l~~LDF~kV  150 (233)
T KOG1644|consen  137 YKLPSLRTLDFQKV  150 (233)
T ss_pred             EecCcceEeehhhh
Confidence            88999999999865

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=96.31  E-value=0.017  Score=67.13  Aligned_cols=137  Identities=18%  Similarity=0.179  Sum_probs=79.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      ++++++|++|||||.|++.++....+.+|    .+.++.-.|...+...      +..--.+-+..+.+.+++. +.+.=
T Consensus       351 pILcLVGPPGVGKTSLgkSIA~al~Rkfv----R~sLGGvrDEAEIRGH------RRTYIGamPGrIiQ~mkka-~~~NP  419 (782)
T COG0466         351 PILCLVGPPGVGKTSLGKSIAKALGRKFV----RISLGGVRDEAEIRGH------RRTYIGAMPGKIIQGMKKA-GVKNP  419 (782)
T ss_pred             cEEEEECCCCCCchhHHHHHHHHhCCCEE----EEecCccccHHHhccc------cccccccCChHHHHHHHHh-CCcCC
Confidence            79999999999999999999985444332    4566666565444311      1111223344555555544 44677


Q ss_pred             EEEEeCCCCC----ChhhHHHhhccccCCCCC-------------cEEE-EEeCch-h-HH-HhhcCCCeEeCCCCChhh
Q 000887           94 LIVLDDVWSE----RYDLWQALKSPFMAGAPG-------------SRII-VTTRSM-D-VA-LTMGSGKNYELKLLSDDD  152 (1237)
Q Consensus        94 LlvlDdv~~~----~~~~~~~~~~~~~~~~~~-------------~~il-iTtR~~-~-~~-~~~~~~~~~~l~~l~~~e  152 (1237)
                      ++++|.++.-    ..+..+++...+.+..+.             |+|+ |||-+. + +. ..+....++++.+.+++|
T Consensus       420 v~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~E  499 (782)
T COG0466         420 VFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLSGYTEDE  499 (782)
T ss_pred             eEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeecCCChHH
Confidence            8889999531    223344444444332111             3444 444432 1 11 122334689999999999


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      -.++-+++.
T Consensus       500 Kl~IAk~~L  508 (782)
T COG0466         500 KLEIAKRHL  508 (782)
T ss_pred             HHHHHHHhc
Confidence            888776654

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.31  E-value=0.13  Score=56.96  Aligned_cols=152  Identities=16%  Similarity=0.112  Sum_probs=88.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ...+.+-|.|-+|.|||.+...++.+.....- ..++++++..-....+++..|...+...........+....+.....
T Consensus       173 ~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~  252 (529)
T KOG2227|consen  173 NTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTK  252 (529)
T ss_pred             ccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHh
Confidence            34567899999999999999998876432222 24578888776667777777777763222122222444445555544


Q ss_pred             C--CcEEEEEeCCCCCChhhHHHhhccc-cCCCCCcEEEEEeC-ch-----hHHHhhc-----CCCeEeCCCCChhhhHH
Q 000887           90 K--KKFLIVLDDVWSERYDLWQALKSPF-MAGAPGSRIIVTTR-SM-----DVALTMG-----SGKNYELKLLSDDDCWS  155 (1237)
Q Consensus        90 ~--~~~LlvlDdv~~~~~~~~~~~~~~~-~~~~~~~~iliTtR-~~-----~~~~~~~-----~~~~~~l~~l~~~ea~~  155 (1237)
                      +  ..+|+|+|..+.-.......+...+ ++.-+++++|+.-- +.     ....++.     ....+..++.+.++-.+
T Consensus       253 q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~  332 (529)
T KOG2227|consen  253 QSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVE  332 (529)
T ss_pred             cccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHH
Confidence            4  3689999998321101111122222 23345666543321 10     1111111     12577888999999999


Q ss_pred             HHHHHhc
Q 000887          156 VFVAHAF  162 (1237)
Q Consensus       156 l~~~~~~  162 (1237)
                      +|..+..
T Consensus       333 Il~~rl~  339 (529)
T KOG2227|consen  333 ILQQRLS  339 (529)
T ss_pred             HHHHHHh
Confidence            9998874

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.30  E-value=0.052  Score=53.26  Aligned_cols=117  Identities=18%  Similarity=0.147  Sum_probs=65.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cC------------------CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EA------------------FEPKAWVCVSDDFDVLRISKAILDSIKRSSCK   73 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~------------------f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~   73 (1237)
                      +..+.++|+.|+||+++|.+++..... ..                  ++.+.|+.-....                  .
T Consensus        19 ~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~------------------~   80 (162)
T PF13177_consen   19 PHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKK------------------K   80 (162)
T ss_dssp             -SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSS------------------S
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEeccccc------------------c
Confidence            346789999999999999998875422 11                  2233343222110                  0


Q ss_pred             ccCHHHHHHHHHHHh-----cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh-HHHhhcC-CCeEeCC
Q 000887           74 LEDLNSVQLELKETV-----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTMGS-GKNYELK  146 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~l-----~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~-~~~~~~~-~~~~~l~  146 (1237)
                      ....++.. .+.+.+     .++.=++|+||++.-+.....++...+-.-+.++.+|++|++.. +...... ...+.+.
T Consensus        81 ~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc~~i~~~  159 (162)
T PF13177_consen   81 SIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRCQVIRFR  159 (162)
T ss_dssp             SBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTSEEEEE-
T ss_pred             hhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhceEEecC
Confidence            12334433 222222     23577899999977666777777777766667888888887664 3322222 2455555


Q ss_pred             CC
Q 000887          147 LL  148 (1237)
Q Consensus       147 ~l  148 (1237)
                      ++
T Consensus       160 ~l  161 (162)
T PF13177_consen  160 PL  161 (162)
T ss_dssp             --
T ss_pred             CC
Confidence            44

...

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.30  E-value=0.019  Score=68.43  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=21.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .++++|+|++|+||||+++.++..
T Consensus       110 ~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602       110 KRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999998874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.28  E-value=0.013  Score=61.65  Aligned_cols=44  Identities=14%  Similarity=0.156  Sum_probs=33.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLR   58 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~   58 (1237)
                      =.++.|+|.+|+|||++|.+++....+ ....++|++.. ..+...
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~-~~~~v~yi~~e-~~~~~r   66 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAK-NGKKVIYIDTE-GLSPER   66 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEECC-CCCHHH
Confidence            368999999999999999998774433 34568899877 444443

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.28  E-value=0.018  Score=60.72  Aligned_cols=87  Identities=16%  Similarity=0.117  Sum_probs=53.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-----CCCeEEEEEcCCcCHHHHHHHHHHHhhccC---------CCccCHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-----FEPKAWVCVSDDFDVLRISKAILDSIKRSS---------CKLEDLN   78 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-----f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~---------~~~~~~~   78 (1237)
                      -.++.|+|.+|+|||++|.+++.......     -..++|++.....+...+. +++.......         ....+.+
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~~~~~~~~~~~~i~~~~~~~~~   97 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVRFGLDPEEVLDNIYVARPYNGE   97 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHHhccchhhhhccEEEEeCCCHH
Confidence            36899999999999999999876432222     1467899877665554433 2222221110         0223455


Q ss_pred             HHHHHHHHHhc----CCcEEEEEeCC
Q 000887           79 SVQLELKETVF----KKKFLIVLDDV  100 (1237)
Q Consensus        79 ~~~~~l~~~l~----~~~~LlvlDdv  100 (1237)
                      +....+.+...    .+.-++|+|.+
T Consensus        98 ~~~~~l~~~~~~~~~~~~~lvVIDsi  123 (226)
T cd01393          98 QQLEIVEELERIMSSGRVDLVVVDSV  123 (226)
T ss_pred             HHHHHHHHHHHHhhcCCeeEEEEcCc
Confidence            55555555432    34568999998

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.27  E-value=0.0014  Score=66.76  Aligned_cols=65  Identities=20%  Similarity=0.210  Sum_probs=50.8

Q ss_pred             hhhhcCCCCCccEEEccccccccccccc-cCCCCCCeEEccCCCcc--ccchhhcccCCccEEEcCcc
Q 000887          392 LSDLLPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQ--CLPDAICSLFNLEILILRNC  456 (1237)
Q Consensus       392 ~~~~~~~~~~Lr~L~L~~~~i~~lp~~~-~~l~~Lr~L~L~~~~i~--~lp~~i~~L~~L~~L~L~~~  456 (1237)
                      ...++.++++|++|+|+.|.+..--..+ ..+.+|++|-|.++++.  ..-.....++.++.|.++.|
T Consensus        89 I~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~L~w~~~~s~l~~lP~vtelHmS~N  156 (418)
T KOG2982|consen   89 IGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTGLSWTQSTSSLDDLPKVTELHMSDN  156 (418)
T ss_pred             HHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCCCChhhhhhhhhcchhhhhhhhccc
Confidence            4456789999999999999865322222 35689999999999876  45557888999999999987

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.27  E-value=0.013  Score=64.24  Aligned_cols=102  Identities=15%  Similarity=0.183  Sum_probs=55.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .-+.++|.+|+|||.||.++++...+..+ .|+|+++      .++...+...-. .  ...+..+   . .+.+. .-=
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~-~V~y~t~------~~l~~~l~~~~~-~--~~~~~~~---~-~~~l~-~~D  248 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGK-SVIYRTA------DELIEILREIRF-N--NDKELEE---V-YDLLI-NCD  248 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCC-eEEEEEH------HHHHHHHHHHHh-c--cchhHHH---H-HHHhc-cCC
Confidence            56899999999999999999986655544 4677753      223333322111 1  1111111   1 22233 224


Q ss_pred             EEEEeCCCCCChhhH--HHhhccccCC-CCCcEEEEEeCc
Q 000887           94 LIVLDDVWSERYDLW--QALKSPFMAG-APGSRIIVTTRS  130 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~--~~~~~~~~~~-~~~~~iliTtR~  130 (1237)
                      |||+||+.......|  ..+...+... ..+..+||||..
T Consensus       249 LLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl  288 (329)
T PRK06835        249 LLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNL  288 (329)
T ss_pred             EEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            799999955432232  2233222221 234568888875

>PRK14974 cell division protein FtsY; Provisional

Probab=96.26  E-value=0.024  Score=62.21  Aligned_cols=91  Identities=14%  Similarity=0.074  Sum_probs=50.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCC---CccCHHHH-HHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSC---KLEDLNSV-QLELK   85 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~---~~~~~~~~-~~~l~   85 (1237)
                      .++++|+++|++|+||||++..+++......+ .++.+...... ....-++..+..++.+..   ...++... ...+.
T Consensus       138 ~~~~vi~~~G~~GvGKTTtiakLA~~l~~~g~-~V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~ai~  216 (336)
T PRK14974        138 GKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGF-SVVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDAIE  216 (336)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCC-eEEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHHHH
Confidence            45789999999999999999998875444334 34455433221 122233445566654322   12233222 23333


Q ss_pred             HHhcCCcEEEEEeCCCC
Q 000887           86 ETVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        86 ~~l~~~~~LlvlDdv~~  102 (1237)
                      .......-+|++|-+-.
T Consensus       217 ~~~~~~~DvVLIDTaGr  233 (336)
T PRK14974        217 HAKARGIDVVLIDTAGR  233 (336)
T ss_pred             HHHhCCCCEEEEECCCc
Confidence            22222333999999854

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.26  E-value=0.018  Score=62.28  Aligned_cols=87  Identities=22%  Similarity=0.159  Sum_probs=51.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhccccc-CCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ..++++++|++|+||||++..++...... .-..+..++...... ....+...+..++.+.....+..+....+... .
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~-~  271 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRL-R  271 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHc-c
Confidence            46799999999999999999988755333 223466776654332 12222333444444433344555555454443 3


Q ss_pred             CCcEEEEEeCC
Q 000887           90 KKKFLIVLDDV  100 (1237)
Q Consensus        90 ~~~~LlvlDdv  100 (1237)
                      + .=+|++|.+
T Consensus       272 ~-~d~vliDt~  281 (282)
T TIGR03499       272 D-KDLILIDTA  281 (282)
T ss_pred             C-CCEEEEeCC
Confidence            3 457777754

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.26  E-value=0.015  Score=57.73  Aligned_cols=39  Identities=28%  Similarity=0.326  Sum_probs=28.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF   54 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~   54 (1237)
                      ++.|+|.+|+|||++|..++..... .-..++|++.....
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~-~~~~v~~~~~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIAT-KGGKVVYVDIEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHh-cCCEEEEEECCcch
Confidence            4789999999999999998775433 33446788765553

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.25  E-value=0.0027  Score=64.38  Aligned_cols=107  Identities=23%  Similarity=0.208  Sum_probs=67.7

Q ss_pred             hcCCCCCccEEEccccccccccccccCCCCCCeEEccCC--Ccc-ccchhhcccCCccEEEcCccccCcc---CChhhcc
Q 000887          395 LLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRS--EIQ-CLPDAICSLFNLEILILRNCWCLLK---LPSRIGN  468 (1237)
Q Consensus       395 ~~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~--~i~-~lp~~i~~L~~L~~L~L~~~~~l~~---lp~~i~~  468 (1237)
                      ....+..|..|++.+..++.+.. +..|++|++|.++.|  ++. .++-...++++|++|++++| .+..   +++ ...
T Consensus        38 l~d~~~~le~ls~~n~gltt~~~-~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~N-ki~~lstl~p-l~~  114 (260)
T KOG2739|consen   38 LTDEFVELELLSVINVGLTTLTN-FPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGN-KIKDLSTLRP-LKE  114 (260)
T ss_pred             ccccccchhhhhhhccceeeccc-CCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCC-ccccccccch-hhh
Confidence            34455666666676666665544 556778888888888  444 44444556688888888887 5543   222 456


Q ss_pred             cccccEEeccCCCccccCcc----cccccccccccceeeec
Q 000887          469 LVNLHYLNIEGASALRELPL----GMKELKCLRTLTNFIVG  505 (1237)
Q Consensus       469 L~~L~~L~l~~~~~l~~ip~----~~~~L~~L~~L~~~~~~  505 (1237)
                      +.+|..|++..|. ...+-.    .+.-+++|..|+.+.+.
T Consensus       115 l~nL~~Ldl~n~~-~~~l~dyre~vf~ll~~L~~LD~~dv~  154 (260)
T KOG2739|consen  115 LENLKSLDLFNCS-VTNLDDYREKVFLLLPSLKYLDGCDVD  154 (260)
T ss_pred             hcchhhhhcccCC-ccccccHHHHHHHHhhhhccccccccC
Confidence            7777888888773 333322    15566777777665544

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.22  E-value=0.023  Score=57.88  Aligned_cols=190  Identities=15%  Similarity=0.167  Sum_probs=104.6

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccc-----cCCCCeEEEEEcCC---------------------cCHHHHHHHH
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLT-----EAFEPKAWVCVSDD---------------------FDVLRISKAI   63 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~-----~~f~~~~w~~~~~~---------------------~~~~~~~~~i   63 (1237)
                      .++.+-..++|++|.||-|.+..+.+....     -.-+..-|.+-+..                     ..-+.+.+++
T Consensus        31 ~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQel  110 (351)
T KOG2035|consen   31 TGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQEL  110 (351)
T ss_pred             cCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHH
Confidence            366788999999999999988887664311     11112223321111                     0112334444


Q ss_pred             HHHhhccCCCccCHHHHHHHHHHHhcCCcE-EEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhhcC-C
Q 000887           64 LDSIKRSSCKLEDLNSVQLELKETVFKKKF-LIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMGS-G  140 (1237)
Q Consensus        64 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~-LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~~~-~  140 (1237)
                      +..++-...    .+        .-..+.+ ++|+-.+++-+.+.-.++....-.....+|+|+..-+- .+...... .
T Consensus       111 lKevAQt~q----ie--------~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~RlIl~cns~SriIepIrSRC  178 (351)
T KOG2035|consen  111 LKEVAQTQQ----IE--------TQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNCRLILVCNSTSRIIEPIRSRC  178 (351)
T ss_pred             HHHHHhhcc----hh--------hccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCceEEEEecCcccchhHHhhhe
Confidence            444432210    00        0012333 45556665444555556666555556788887654321 11111222 2


Q ss_pred             CeEeCCCCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCch-HHHHHHhH-hhcCC--------CHHHHHHH
Q 000887          141 KNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL-AARALGGL-LRSKQ--------GVDEWRAI  210 (1237)
Q Consensus       141 ~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PL-al~~~~~~-l~~~~--------~~~~~~~~  210 (1237)
                      -.+.+...+++|-...+.+.+...+-..+    .+.+.+|+++++|.-. ||-+.-+. +...+        ..-+|+-+
T Consensus       179 l~iRvpaps~eeI~~vl~~v~~kE~l~lp----~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~  254 (351)
T KOG2035|consen  179 LFIRVPAPSDEEITSVLSKVLKKEGLQLP----KELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIY  254 (351)
T ss_pred             eEEeCCCCCHHHHHHHHHHHHHHhcccCc----HHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHHHH
Confidence            46889999999999999988755444443    7889999999988643 43332211 11111        14578877


Q ss_pred             Hhhcc
Q 000887          211 LDSKI  215 (1237)
Q Consensus       211 l~~~~  215 (1237)
                      +.+..
T Consensus       255 i~e~a  259 (351)
T KOG2035|consen  255 IQEIA  259 (351)
T ss_pred             HHHHH
Confidence            76543

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.18  E-value=0.049  Score=54.84  Aligned_cols=121  Identities=12%  Similarity=0.166  Sum_probs=65.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEc--CCcCHHHHHH------HHHHHhhccC------CCccCHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVS--DDFDVLRISK------AILDSIKRSS------CKLEDLNS   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~--~~~~~~~~~~------~i~~~l~~~~------~~~~~~~~   79 (1237)
                      .+++|.|..|+|||||++.++...  ....+.+++.-.  ...+......      +++..++...      ......+.
T Consensus        26 ~~~~l~G~nGsGKStLl~~i~G~~--~~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~~  103 (180)
T cd03214          26 EIVGILGPNGAGKSTLLKTLAGLL--KPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGGER  103 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--CCCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHHH
Confidence            489999999999999999987632  223444544211  1112211111      1334443221      12233344


Q ss_pred             HHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCC-CC-CcEEEEEeCchhHHHh
Q 000887           80 VQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAG-AP-GSRIIVTTRSMDVALT  136 (1237)
Q Consensus        80 ~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~-~~~iliTtR~~~~~~~  136 (1237)
                      ..-.+.+.+-..+-++++|+-... +......+...+... .. +..||++|.+......
T Consensus       104 qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~~~  163 (180)
T cd03214         104 QRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLAAR  163 (180)
T ss_pred             HHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            444566667778899999998432 112222333333221 12 5678899888766533

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.18  E-value=0.004  Score=58.07  Aligned_cols=22  Identities=45%  Similarity=0.599  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +|+|.|++|+||||+|+++++.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999874

...

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.17  E-value=0.02  Score=60.86  Aligned_cols=47  Identities=19%  Similarity=0.206  Sum_probs=34.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc-cccC----CCCeEEEEEcCCcCHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK-LTEA----FEPKAWVCVSDDFDVLRI   59 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~-~~~~----f~~~~w~~~~~~~~~~~~   59 (1237)
                      -.++.|+|.+|+|||++|.+++... ....    ...++|++.....+...+
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl   70 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL   70 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH
Confidence            4789999999999999999987543 2221    357889988776554433

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.16  E-value=0.035  Score=55.36  Aligned_cols=117  Identities=15%  Similarity=0.205  Sum_probs=60.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHH-HHHHHHHhhccCCC------------ccCHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRI-SKAILDSIKRSSCK------------LEDLNSV   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~-~~~i~~~l~~~~~~------------~~~~~~~   80 (1237)
                      .+++|.|+.|.|||||.+.++.-.  ....+.+++.-.   +.... .......++.-...            ....+..
T Consensus        29 ~~~~l~G~nGsGKstLl~~i~G~~--~~~~G~i~~~g~---~~~~~~~~~~~~~i~~~~~~~~~~~~t~~e~lLS~G~~~  103 (171)
T cd03228          29 EKVAIVGPSGSGKSTLLKLLLRLY--DPTSGEILIDGV---DLRDLDLESLRKNIAYVPQDPFLFSGTIRENILSGGQRQ  103 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC--CCCCCEEEECCE---EhhhcCHHHHHhhEEEEcCCchhccchHHHHhhCHHHHH
Confidence            478999999999999999987732  223444444211   11000 00111111110000            1112233


Q ss_pred             HHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHHH
Q 000887           81 QLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVAL  135 (1237)
Q Consensus        81 ~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~  135 (1237)
                      .-.+.+.+-.++-++++|+-... +......+...+.....+..||++|.+.....
T Consensus       104 rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  159 (171)
T cd03228         104 RIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIR  159 (171)
T ss_pred             HHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHHH
Confidence            33455666678889999997542 11222223332222223567889998877654

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.15  E-value=0.027  Score=64.32  Aligned_cols=90  Identities=21%  Similarity=0.133  Sum_probs=52.2

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCC---ccCHHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCK---LEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~---~~~~~~~~~~l~~   86 (1237)
                      ..+.+|.++|.+|+||||+|..++....+..+ .+..+++.... ...+.+..++.+++.+...   ..+..+......+
T Consensus        93 ~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~-kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~  171 (437)
T PRK00771         93 LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGL-KVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLE  171 (437)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCC-eEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHH
Confidence            45789999999999999999999875444333 35555544322 2233445556665543221   1233333333333


Q ss_pred             HhcCCcEEEEEeCCCC
Q 000887           87 TVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv~~  102 (1237)
                      ..++. -+||+|-.-.
T Consensus       172 ~~~~~-DvVIIDTAGr  186 (437)
T PRK00771        172 KFKKA-DVIIVDTAGR  186 (437)
T ss_pred             HhhcC-CEEEEECCCc
Confidence            33333 5688888843

>TIGR02012 tigrfam_recA protein RecA

Probab=96.14  E-value=0.011  Score=64.16  Aligned_cols=83  Identities=20%  Similarity=0.142  Sum_probs=54.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccC-----CCccCHHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS-----CKLEDLNSVQLELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~-----~~~~~~~~~~~~l~~~   87 (1237)
                      =+++-|+|++|+|||+||.+++....+ .-..++|++.....+..     .+.+++...     ..+...++....+...
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~-~g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~~l  128 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAETL  128 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHH
Confidence            378999999999999999998764433 23457799776655442     344443221     1334566666666555


Q ss_pred             hc-CCcEEEEEeCCC
Q 000887           88 VF-KKKFLIVLDDVW  101 (1237)
Q Consensus        88 l~-~~~~LlvlDdv~  101 (1237)
                      .+ ...-+||+|.|-
T Consensus       129 i~~~~~~lIVIDSv~  143 (321)
T TIGR02012       129 VRSGAVDIIVVDSVA  143 (321)
T ss_pred             hhccCCcEEEEcchh
Confidence            54 357799999983

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.13  E-value=0.065  Score=53.84  Aligned_cols=117  Identities=19%  Similarity=0.146  Sum_probs=61.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc--c-------------CCCccCHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR--S-------------SCKLEDLN   78 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~--~-------------~~~~~~~~   78 (1237)
                      .+++|.|..|+|||||++.++...  ....+.+++.-   .+.......+...++.  +             .......+
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g---~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~LS~G~  103 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGDL--KPQQGEITLDG---VPVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRRFSGGE  103 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhccC--CCCCCEEEECC---EEHHHHHHHHHhhEEEEccCCeeecccHHHhhcccCCHHH
Confidence            378999999999999999987632  12234444421   1111111111111110  0             00112223


Q ss_pred             HHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHHH
Q 000887           79 SVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVAL  135 (1237)
Q Consensus        79 ~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~  135 (1237)
                      ...-.+.+.+-.++=++++|+.... +......+...+.....+..||++|.+.....
T Consensus       104 ~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  161 (178)
T cd03247         104 RQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIE  161 (178)
T ss_pred             HHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHH
Confidence            3334455666678889999998542 11222222222222223677899998877654

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.13  E-value=0.011  Score=64.11  Aligned_cols=82  Identities=21%  Similarity=0.149  Sum_probs=54.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccC-----CCccCHHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS-----CKLEDLNSVQLELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~-----~~~~~~~~~~~~l~~~   87 (1237)
                      =+++-|+|++|+|||+||.+++....+ .-..++|++.....+..     .+.+++...     ..+.+.++....+...
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~-~g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~~l  128 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQK-LGGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIADSL  128 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-cCCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHHHH
Confidence            468899999999999999998764322 34567899876665542     333333221     1344566666666555


Q ss_pred             hcC-CcEEEEEeCC
Q 000887           88 VFK-KKFLIVLDDV  100 (1237)
Q Consensus        88 l~~-~~~LlvlDdv  100 (1237)
                      .+. ..-+||+|.|
T Consensus       129 i~s~~~~lIVIDSv  142 (325)
T cd00983         129 VRSGAVDLIVVDSV  142 (325)
T ss_pred             HhccCCCEEEEcch
Confidence            543 5779999998

RecA couples ATP hydrolysis to DNA strand exchange.

>PHA00729 NTP-binding motif containing protein

Probab=96.12  E-value=0.011  Score=60.13  Aligned_cols=26  Identities=38%  Similarity=0.468  Sum_probs=22.6

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+...|+|+|.+|+|||+||.++++.
T Consensus        15 ~~f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         15 NGFVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34567999999999999999999875

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.07  E-value=0.021  Score=57.36  Aligned_cols=37  Identities=30%  Similarity=0.432  Sum_probs=28.2

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEE
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      ...+|++.|++|+||||+|++++... ...+..+++++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l-~~~~~~~~~~~   42 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERL-KLKYSNVIYLD   42 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH-HHcCCcEEEEe
Confidence            44699999999999999999988743 33455566653

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.06  E-value=0.06  Score=68.28  Aligned_cols=134  Identities=11%  Similarity=0.045  Sum_probs=68.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccC-----CCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEA-----FEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~-----f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .-+.++|++|+|||++|..++.......     ....+|..     +...+.   +     ......+.++....+.+.+
T Consensus       195 ~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l-----~~~~l~---a-----~~~~~g~~e~~l~~~l~~~  261 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLAL-----DMGALI---A-----GAKYRGEFEERLKAVLNEV  261 (852)
T ss_pred             CceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEe-----eHHHHh---h-----cchhhhhHHHHHHHHHHHH
Confidence            3567899999999999999887542211     11222221     111111   0     0001112233333333333


Q ss_pred             c--CCcEEEEEeCCCCCC-------hhhHHHhhccccCCCCCcEEEEEeCchhHHH-------hhcCCCeEeCCCCChhh
Q 000887           89 F--KKKFLIVLDDVWSER-------YDLWQALKSPFMAGAPGSRIIVTTRSMDVAL-------TMGSGKNYELKLLSDDD  152 (1237)
Q Consensus        89 ~--~~~~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~-------~~~~~~~~~l~~l~~~e  152 (1237)
                      .  +++.+|++|++..-.       ..+...+..+.... ..-++|-+|...+...       .......+.++..+.++
T Consensus       262 ~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~-g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~  340 (852)
T TIGR03346       262 TKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALAR-GELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVED  340 (852)
T ss_pred             HhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhc-CceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHH
Confidence            2  368999999994311       01122233332222 2245555555443311       11223568899999999


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      ..++++...
T Consensus       341 ~~~iL~~~~  349 (852)
T TIGR03346       341 TISILRGLK  349 (852)
T ss_pred             HHHHHHHHH
Confidence            999987654

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.04  E-value=0.098  Score=66.06  Aligned_cols=110  Identities=18%  Similarity=0.207  Sum_probs=56.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC-Cc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK-KK   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~-~~   92 (1237)
                      .++.++|+.|+|||++|+.++...... ....+.++++.-...    .....-++.+.. ....++ ...+.+.++. ..
T Consensus       599 ~~~Lf~Gp~G~GKT~lA~aLa~~l~~~-~~~~i~id~se~~~~----~~~~~LiG~~pg-y~g~~~-~g~l~~~v~~~p~  671 (857)
T PRK10865        599 GSFLFLGPTGVGKTELCKALANFMFDS-DDAMVRIDMSEFMEK----HSVSRLVGAPPG-YVGYEE-GGYLTEAVRRRPY  671 (857)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhhcC-CCcEEEEEhHHhhhh----hhHHHHhCCCCc-ccccch-hHHHHHHHHhCCC
Confidence            578899999999999999988643322 223445544322110    111222232211 111111 1122333333 34


Q ss_pred             EEEEEeCCCCCChhhHHHhhccccCC-----------CCCcEEEEEeCc
Q 000887           93 FLIVLDDVWSERYDLWQALKSPFMAG-----------APGSRIIVTTRS  130 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~~~~~~~~~-----------~~~~~iliTtR~  130 (1237)
                      .+|+||++...+.+.+..+...+..+           ..++-||+||..
T Consensus       672 ~vLllDEieka~~~v~~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~  720 (857)
T PRK10865        672 SVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNL  720 (857)
T ss_pred             CeEEEeehhhCCHHHHHHHHHHHhhCceecCCceEEeecccEEEEeCCc
Confidence            79999999765555555554433221           123447778765

>cd01394 radB RadB

Probab=96.03  E-value=0.02  Score=59.91  Aligned_cols=41  Identities=20%  Similarity=0.144  Sum_probs=30.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF   54 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~   54 (1237)
                      -+++.|.|.+|+|||++|.+++....+. -..++|++.....
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~~-g~~v~yi~~e~~~   59 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQ-GKKVAYIDTEGLS   59 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEECCCCC
Confidence            4789999999999999999987744333 3357788754443

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=96.03  E-value=0.015  Score=69.76  Aligned_cols=98  Identities=18%  Similarity=0.261  Sum_probs=59.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ..+....|+.|||||.||++++...+... +..+.++.+.-.    --..+.+-+|.+.. -..-++ .-.+-+..++++
T Consensus       521 igsFlF~GPTGVGKTELAkaLA~~Lfg~e-~aliR~DMSEy~----EkHsVSrLIGaPPG-YVGyee-GG~LTEaVRr~P  593 (786)
T COG0542         521 IGSFLFLGPTGVGKTELAKALAEALFGDE-QALIRIDMSEYM----EKHSVSRLIGAPPG-YVGYEE-GGQLTEAVRRKP  593 (786)
T ss_pred             ceEEEeeCCCcccHHHHHHHHHHHhcCCC-ccceeechHHHH----HHHHHHHHhCCCCC-Cceecc-ccchhHhhhcCC
Confidence            46778899999999999999988543222 344555544332    12334444454432 111122 223444556676


Q ss_pred             E-EEEEeCCCCCChhhHHHhhccccC
Q 000887           93 F-LIVLDDVWSERYDLWQALKSPFMA  117 (1237)
Q Consensus        93 ~-LlvlDdv~~~~~~~~~~~~~~~~~  117 (1237)
                      + +|.||++...+.+....+.+.+-.
T Consensus       594 ySViLlDEIEKAHpdV~nilLQVlDd  619 (786)
T COG0542         594 YSVILLDEIEKAHPDVFNLLLQVLDD  619 (786)
T ss_pred             CeEEEechhhhcCHHHHHHHHHHhcC
Confidence            5 888999988777777766666554

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.00  E-value=0.036  Score=53.83  Aligned_cols=121  Identities=14%  Similarity=0.033  Sum_probs=64.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeE--EEEEcCCcCHHHHHHHHHHH---hhcc-CCCccC-------HHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKA--WVCVSDDFDVLRISKAILDS---IKRS-SCKLED-------LNS   79 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~--w~~~~~~~~~~~~~~~i~~~---l~~~-~~~~~~-------~~~   79 (1237)
                      ..+|-|++..|.||||.|..++.+.....+...+  |+--.........+....-.   .+.. .....+       ..+
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra~~~g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~   84 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRALGHGKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAKA   84 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHHH
Confidence            3688899999999999999987755555554322  22222112222233222000   0110 001111       112


Q ss_pred             HHHHHHHHhcC-CcEEEEEeCCCC---CChhhHHHhhccccCCCCCcEEEEEeCchhH
Q 000887           80 VQLELKETVFK-KKFLIVLDDVWS---ERYDLWQALKSPFMAGAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        80 ~~~~l~~~l~~-~~~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~  133 (1237)
                      .....++.+.. .-=+||+|.+-.   -.....+++...+...+.+..||+|-|+...
T Consensus        85 ~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~  142 (173)
T TIGR00708        85 AWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQ  142 (173)
T ss_pred             HHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCH
Confidence            22233344433 456999999821   1223344555666667778899999998744

Alternate name: corrinoid adenosyltransferase.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.052  Score=59.53  Aligned_cols=91  Identities=16%  Similarity=0.191  Sum_probs=58.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      .+.++++++|+.|+||||++..++....+.. ..+.+++.+.... ...-++..+..++.+.....++++....+...-.
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA~~l~~~g-~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~~l~~  282 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQLLKQN-RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQYMTY  282 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHHcC-CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHHHHHh
Confidence            4568999999999999999999887543333 3466777765543 2233444555555443334566666665554421


Q ss_pred             -CCcEEEEEeCCCC
Q 000887           90 -KKKFLIVLDDVWS  102 (1237)
Q Consensus        90 -~~~~LlvlDdv~~  102 (1237)
                       +..=+|++|-+-.
T Consensus       283 ~~~~D~VLIDTAGr  296 (407)
T PRK12726        283 VNCVDHILIDTVGR  296 (407)
T ss_pred             cCCCCEEEEECCCC
Confidence             3457888898844

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.99  E-value=0.094  Score=66.54  Aligned_cols=111  Identities=19%  Similarity=0.220  Sum_probs=58.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-CC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-KK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~   91 (1237)
                      ...+.+.|+.|+|||++|+.++...... -...+.++++.-....    .....++.+.. ....++. ..+.+.++ ..
T Consensus       595 ~~~~Lf~Gp~GvGKt~lA~~La~~l~~~-~~~~i~~d~s~~~~~~----~~~~l~g~~~g-~~g~~~~-g~l~~~v~~~p  667 (852)
T TIGR03346       595 IGSFLFLGPTGVGKTELAKALAEFLFDD-EDAMVRIDMSEYMEKH----SVARLIGAPPG-YVGYEEG-GQLTEAVRRKP  667 (852)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhcCC-CCcEEEEechhhcccc----hHHHhcCCCCC-ccCcccc-cHHHHHHHcCC
Confidence            3578899999999999999988743322 2234555554332211    11122222211 1111111 12222222 34


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccccCC-----------CCCcEEEEEeCc
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPFMAG-----------APGSRIIVTTRS  130 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~~~~-----------~~~~~iliTtR~  130 (1237)
                      ..+|+||++...+.+.+..+...+-.+           ..++-||+||..
T Consensus       668 ~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       668 YSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             CcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            468999999776666666555544322           134447777764

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.021  Score=63.39  Aligned_cols=88  Identities=18%  Similarity=0.158  Sum_probs=52.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -++++++|+.|+||||++.+++.... +.....+..++..... ...+-++..++.++.+.....+..+....+.+ +.+
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~-l~~  215 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAE-LRN  215 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHH-hcC
Confidence            46999999999999999999987543 2223446666644332 23344445555565544333333444444443 344


Q ss_pred             CcEEEEEeCCCC
Q 000887           91 KKFLIVLDDVWS  102 (1237)
Q Consensus        91 ~~~LlvlDdv~~  102 (1237)
                      + -+|++|.+-.
T Consensus       216 ~-DlVLIDTaG~  226 (374)
T PRK14722        216 K-HMVLIDTIGM  226 (374)
T ss_pred             C-CEEEEcCCCC
Confidence            4 5566899843

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=95.95  E-value=0.051  Score=53.88  Aligned_cols=120  Identities=17%  Similarity=0.205  Sum_probs=63.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc--c--cc---CCC--CeEEEEEcCCcCHHHHHHHHHHHhhccCC-------CccCH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK--L--TE---AFE--PKAWVCVSDDFDVLRISKAILDSIKRSSC-------KLEDL   77 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~--~--~~---~f~--~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-------~~~~~   77 (1237)
                      .+++|.|+.|+|||||.+.+..+.  +  ..   .|.  .+.|+.  +        .+.+..++....       .....
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~~--q--------~~~l~~~~L~~~~~~~~~~~LSgG   91 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFID--Q--------LQFLIDVGLGYLTLGQKLSTLSGG   91 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEEh--H--------HHHHHHcCCCccccCCCcCcCCHH
Confidence            489999999999999999886321  1  00   010  122321  1        345555553321       11122


Q ss_pred             HHHHHHHHHHhcCC--cEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchhHHHhhcCCCeEeC
Q 000887           78 NSVQLELKETVFKK--KFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMDVALTMGSGKNYEL  145 (1237)
Q Consensus        78 ~~~~~~l~~~l~~~--~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~~~~~~~~~~~~l  145 (1237)
                      +...-.+.+.+-.+  +=++++|+-... +......+...+.. ...|..||++|.+..... . .+.++.+
T Consensus        92 q~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~-~-~d~i~~l  161 (176)
T cd03238          92 ELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLS-S-ADWIIDF  161 (176)
T ss_pred             HHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH-h-CCEEEEE
Confidence            33333455555566  788889997442 11222222222222 124677999998887653 2 3344444

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.93  E-value=0.028  Score=58.56  Aligned_cols=78  Identities=17%  Similarity=0.279  Sum_probs=46.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cc--cCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LT--EAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~--~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      |+|.++|++|.|||+|++++++.. ++  ..|....-+-+...    .++.....    .  ...-+....+.+.+...+
T Consensus       178 RliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinsh----sLFSKWFs----E--SgKlV~kmF~kI~ELv~d  247 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSH----SLFSKWFS----E--SGKLVAKMFQKIQELVED  247 (423)
T ss_pred             eEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehh----HHHHHHHh----h--hhhHHHHHHHHHHHHHhC
Confidence            789999999999999999999976 32  33444444433222    12211111    1  223445555666666666


Q ss_pred             Cc--EEEEEeCCC
Q 000887           91 KK--FLIVLDDVW  101 (1237)
Q Consensus        91 ~~--~LlvlDdv~  101 (1237)
                      +.  +.+.+|.|.
T Consensus       248 ~~~lVfvLIDEVE  260 (423)
T KOG0744|consen  248 RGNLVFVLIDEVE  260 (423)
T ss_pred             CCcEEEEEeHHHH
Confidence            54  344568884

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.93  E-value=0.046  Score=62.65  Aligned_cols=87  Identities=17%  Similarity=0.079  Sum_probs=52.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -++++++|++|+||||++..++.... ......+..++...... ...-+...++.++.+.....+.++....+.+. . 
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~-~-  298 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQL-R-  298 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHh-C-
Confidence            36999999999999999999877543 33334567777654322 11223333444444433334455555555543 2 


Q ss_pred             CcEEEEEeCCC
Q 000887           91 KKFLIVLDDVW  101 (1237)
Q Consensus        91 ~~~LlvlDdv~  101 (1237)
                      ..=+||+|..-
T Consensus       299 ~~DlVlIDt~G  309 (424)
T PRK05703        299 DCDVILIDTAG  309 (424)
T ss_pred             CCCEEEEeCCC
Confidence            45778889763

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.93  E-value=0.029  Score=59.38  Aligned_cols=86  Identities=17%  Similarity=0.148  Sum_probs=53.3

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccC--------------------
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS--------------------   71 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~--------------------   71 (1237)
                      .-.++.|.|.+|+|||++|.+++....++ -..++|++....  ...+.+++ .+++...                    
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~-g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~~   99 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ-GKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGFE   99 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC-CCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEeccccccc
Confidence            34789999999999999999986643333 345788887644  33444432 2222110                    


Q ss_pred             CCccCHHHHHHHHHHHhcC-CcEEEEEeCCC
Q 000887           72 CKLEDLNSVQLELKETVFK-KKFLIVLDDVW  101 (1237)
Q Consensus        72 ~~~~~~~~~~~~l~~~l~~-~~~LlvlDdv~  101 (1237)
                      ......++....+.+.... +.-++|+|.+.
T Consensus       100 ~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067        100 WNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             cCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence            0112335566666666654 56689999984

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.92  E-value=0.015  Score=57.13  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=43.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccC--CCc-cCHHHHHHHHHHHhcCC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSS--CKL-EDLNSVQLELKETVFKK   91 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~--~~~-~~~~~~~~~l~~~l~~~   91 (1237)
                      ++.|.|.+|+|||++|.+++..    ....++|+.-....+.+ +.+.|.+--....  ... ....++...+.+. . +
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~----~~~~~~y~at~~~~d~e-m~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~-~-~   73 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE----LGGPVTYIATAEAFDDE-MAERIARHRKRRPAHWRTIETPRDLVSALKEL-D-P   73 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh----cCCCeEEEEccCcCCHH-HHHHHHHHHHhCCCCceEeecHHHHHHHHHhc-C-C
Confidence            3679999999999999998753    22356677555554432 3333333221111  111 2222333333221 2 3


Q ss_pred             cEEEEEeCC
Q 000887           92 KFLIVLDDV  100 (1237)
Q Consensus        92 ~~LlvlDdv  100 (1237)
                      .-.+++|.+
T Consensus        74 ~~~VLIDcl   82 (169)
T cd00544          74 GDVVLIDCL   82 (169)
T ss_pred             CCEEEEEcH
Confidence            447999997

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK09354 recA recombinase A; Provisional

Probab=95.89  E-value=0.018  Score=63.00  Aligned_cols=83  Identities=20%  Similarity=0.152  Sum_probs=55.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhcc-----CCCccCHHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRS-----SCKLEDLNSVQLELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~-----~~~~~~~~~~~~~l~~~   87 (1237)
                      =+++-|+|++|+|||+||.+++....+ .-..++|++.....+..     .+..++..     ...+...++....+...
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~-~G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~~l  133 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQK-AGGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIADTL  133 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHHHH
Confidence            468889999999999999998764333 33567899887766642     34444322     11344566666666655


Q ss_pred             hcC-CcEEEEEeCCC
Q 000887           88 VFK-KKFLIVLDDVW  101 (1237)
Q Consensus        88 l~~-~~~LlvlDdv~  101 (1237)
                      .+. ..-+||+|.|-
T Consensus       134 i~s~~~~lIVIDSva  148 (349)
T PRK09354        134 VRSGAVDLIVVDSVA  148 (349)
T ss_pred             hhcCCCCEEEEeChh
Confidence            544 56799999983

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.85  E-value=0.052  Score=54.31  Aligned_cols=86  Identities=17%  Similarity=0.144  Sum_probs=45.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhcc---CCCccCHHHHH-HHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRS---SCKLEDLNSVQ-LELKETVF   89 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~---~~~~~~~~~~~-~~l~~~l~   89 (1237)
                      ++.+.|++|+||||++..++....+..+ .++.++.+... ...+.+...+.+.+.+   .....++.+.. +.+.....
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~g~-~v~~i~~D~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGK-KVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHARE   80 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC-cEEEEEcCCCChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHHHh
Confidence            6889999999999999998874433322 35556544322 2222333334443321   11223444333 23333334


Q ss_pred             CCcEEEEEeCCC
Q 000887           90 KKKFLIVLDDVW  101 (1237)
Q Consensus        90 ~~~~LlvlDdv~  101 (1237)
                      +..-++|+|-.-
T Consensus        81 ~~~d~viiDt~g   92 (173)
T cd03115          81 ENFDVVIVDTAG   92 (173)
T ss_pred             CCCCEEEEECcc
Confidence            444466688763

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.83  E-value=0.057  Score=61.34  Aligned_cols=151  Identities=15%  Similarity=0.158  Sum_probs=78.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      +|=|.+||++|+|||.||.+++... .     +=++.++..        ++...+     .....+.+.+.+.+..+.-+
T Consensus       223 prGvLlHGPPGCGKT~lA~AiAgel-~-----vPf~~isAp--------eivSGv-----SGESEkkiRelF~~A~~~aP  283 (802)
T KOG0733|consen  223 PRGVLLHGPPGCGKTSLANAIAGEL-G-----VPFLSISAP--------EIVSGV-----SGESEKKIRELFDQAKSNAP  283 (802)
T ss_pred             CCceeeeCCCCccHHHHHHHHhhhc-C-----CceEeecch--------hhhccc-----CcccHHHHHHHHHHHhccCC
Confidence            3558899999999999999998853 1     223333222        111111     22333344444455556689


Q ss_pred             EEEEEeCCCCCCh------h-----hHHHhhccc---cCC---CCCcEEEE-EeCchhHHHh---hc-CCCeEeCCCCCh
Q 000887           93 FLIVLDDVWSERY------D-----LWQALKSPF---MAG---APGSRIIV-TTRSMDVALT---MG-SGKNYELKLLSD  150 (1237)
Q Consensus        93 ~LlvlDdv~~~~~------~-----~~~~~~~~~---~~~---~~~~~ili-TtR~~~~~~~---~~-~~~~~~l~~l~~  150 (1237)
                      +++++|+++....      .     .+.++...+   ...   +.+.-||= |+|-..+...   .+ -+..|.+.--++
T Consensus       284 civFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e  363 (802)
T KOG0733|consen  284 CIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSE  363 (802)
T ss_pred             eEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCHHHhccccccceeeecCCch
Confidence            9999999954211      0     011222111   111   22222222 3343222211   11 235688888888


Q ss_pred             hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCC
Q 000887          151 DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGL  187 (1237)
Q Consensus       151 ~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~  187 (1237)
                      ++-.++++..+.+-.... +-.    .++|++..-|.
T Consensus       364 ~aR~~IL~~~~~~lrl~g-~~d----~~qlA~lTPGf  395 (802)
T KOG0733|consen  364 TAREEILRIICRGLRLSG-DFD----FKQLAKLTPGF  395 (802)
T ss_pred             HHHHHHHHHHHhhCCCCC-CcC----HHHHHhcCCCc
Confidence            888888887774333322 222    35666666554

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=95.81  E-value=0.084  Score=52.21  Aligned_cols=114  Identities=12%  Similarity=0.060  Sum_probs=60.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEE-------EcCCcCH--HHHHHHHHHHhhccCCCccCHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC-------VSDDFDV--LRISKAILDSIKRSSCKLEDLNSVQLEL   84 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~-------~~~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~l   84 (1237)
                      .+++|.|..|.|||||++.++... . ...+.+++.       +.+....  ..+.+.+...   ........+..+-.+
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~-~-~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~---~~~~LS~G~~~rv~l  102 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLW-P-WGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYP---WDDVLSGGEQQRLAF  102 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC-C-CCCceEEECCCceEEEECCCCccccccHHHHhhcc---CCCCCCHHHHHHHHH
Confidence            378999999999999999987742 1 112222211       1122111  1233332211   122333344455556


Q ss_pred             HHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHH
Q 000887           85 KETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~  134 (1237)
                      .+.+-.++=++++|+-... +......+...+...  +..||++|.+....
T Consensus       103 aral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223         103 ARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             HHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            6667778888999997432 112222222222222  35688888876654

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.80  E-value=0.036  Score=54.67  Aligned_cols=117  Identities=17%  Similarity=0.113  Sum_probs=63.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC--cCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD--FDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      .+++|.|..|+|||||.+.++...  ....+.+++.-..-  .+..+.   ....++... +....+...-.+.+.+-..
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~~--~~~~G~v~~~g~~~~~~~~~~~---~~~~i~~~~-qLS~G~~qrl~laral~~~  100 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGLY--KPDSGEILVDGKEVSFASPRDA---RRAGIAMVY-QLSVGERQMVEIARALARN  100 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--CCCCeEEEECCEECCcCCHHHH---HhcCeEEEE-ecCHHHHHHHHHHHHHhcC
Confidence            379999999999999999987632  23345555532111  111111   111111111 1233344444566666778


Q ss_pred             cEEEEEeCCCCC-ChhhHHHhhccccCC-CCCcEEEEEeCchhHHHh
Q 000887           92 KFLIVLDDVWSE-RYDLWQALKSPFMAG-APGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        92 ~~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iliTtR~~~~~~~  136 (1237)
                      +-++++|+-... +......+...+... ..+..||++|.+......
T Consensus       101 p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~~  147 (163)
T cd03216         101 ARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEVFE  147 (163)
T ss_pred             CCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            889999998542 112222333333221 236678899988765433

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.77  E-value=0.12  Score=64.81  Aligned_cols=152  Identities=16%  Similarity=0.164  Sum_probs=78.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ++-|.++|++|+|||++|++++... ...     ++.+...        ++....     .......+...+...-...+
T Consensus       487 ~~giLL~GppGtGKT~lakalA~e~-~~~-----fi~v~~~--------~l~~~~-----vGese~~i~~~f~~A~~~~p  547 (733)
T TIGR01243       487 PKGVLLFGPPGTGKTLLAKAVATES-GAN-----FIAVRGP--------EILSKW-----VGESEKAIREIFRKARQAAP  547 (733)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhc-CCC-----EEEEehH--------HHhhcc-----cCcHHHHHHHHHHHHHhcCC
Confidence            4558899999999999999998742 211     2222111        111111     11111122222233334568


Q ss_pred             EEEEEeCCCCC------C--hh----hHHHhhccccC--CCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCChhhh
Q 000887           93 FLIVLDDVWSE------R--YD----LWQALKSPFMA--GAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLSDDDC  153 (1237)
Q Consensus        93 ~LlvlDdv~~~------~--~~----~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~~ea  153 (1237)
                      .+|++|+++.-      .  ..    ....+...+..  ...+.-||.||..+..... +    .-...+.++..+.++.
T Consensus       548 ~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R  627 (733)
T TIGR01243       548 AIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEAR  627 (733)
T ss_pred             EEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHH
Confidence            99999998431      0  00    11122222221  1234456666655433221 1    1235788999999999


Q ss_pred             HHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          154 WSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       154 ~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      .++|+.+..+.. ...+.    ....+++.+.|.-
T Consensus       628 ~~i~~~~~~~~~-~~~~~----~l~~la~~t~g~s  657 (733)
T TIGR01243       628 KEIFKIHTRSMP-LAEDV----DLEELAEMTEGYT  657 (733)
T ss_pred             HHHHHHHhcCCC-CCccC----CHHHHHHHcCCCC
Confidence            999987653221 11111    2457777777644

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.77  E-value=0.037  Score=62.35  Aligned_cols=118  Identities=19%  Similarity=0.164  Sum_probs=69.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccC--------------------CCCeEEEEEcCCcC---HHHHHHHHHHHhhcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEA--------------------FEPKAWVCVSDDFD---VLRISKAILDSIKRS   70 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~--------------------f~~~~w~~~~~~~~---~~~~~~~i~~~l~~~   70 (1237)
                      ..+-++|++|+|||++|.++++......                    ++.+..++.++...   ..+..+++.......
T Consensus        25 halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~  104 (325)
T COG0470          25 HALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSES  104 (325)
T ss_pred             ceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhccC
Confidence            3489999999999999999988543221                    24455555554443   223333333332221


Q ss_pred             CCCccCHHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhhcC-CCeEeCCC
Q 000887           71 SCKLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMGS-GKNYELKL  147 (1237)
Q Consensus        71 ~~~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~~~-~~~~~l~~  147 (1237)
                      ..                .++.-++|+|+++.-+.+...++...+-....++.++++|... .+...+.. ...+++.+
T Consensus       105 ~~----------------~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~~~~il~tI~SRc~~i~f~~  167 (325)
T COG0470         105 PL----------------EGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITNDPSKILPTIRSRCQRIRFKP  167 (325)
T ss_pred             CC----------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCChhhccchhhhcceeeecCC
Confidence            10                2567899999996655555555665555556677777777633 22222221 24566666

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=95.76  E-value=0.013  Score=57.69  Aligned_cols=80  Identities=13%  Similarity=0.124  Sum_probs=43.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC---CccCHHHHHHHHHHHhcCC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC---KLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ++.|.|.+|+|||++|..++....    ..++++.-... .-.+..+.+.........   ..+...++...+..... +
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~----~~~~~iat~~~-~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~-~   76 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSG----LQVLYIATAQP-FDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAA-P   76 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcC----CCcEeCcCCCC-ChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcC-C
Confidence            689999999999999999876421    12444433332 233444555443332221   11222234444444333 2


Q ss_pred             cEEEEEeCC
Q 000887           92 KFLIVLDDV  100 (1237)
Q Consensus        92 ~~LlvlDdv  100 (1237)
                      .-++++|.+
T Consensus        77 ~~~VlID~L   85 (170)
T PRK05800         77 GRCVLVDCL   85 (170)
T ss_pred             CCEEEehhH
Confidence            337888987

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=95.76  E-value=0.2  Score=56.30  Aligned_cols=27  Identities=26%  Similarity=0.279  Sum_probs=24.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ....+|+|.|.=|+|||++...+.+..
T Consensus        18 ~~~~~IgL~G~WGsGKSs~l~~l~~~L   44 (325)
T PF07693_consen   18 DDPFVIGLYGEWGSGKSSFLNMLKEEL   44 (325)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            667899999999999999999987754

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.75  E-value=0.08  Score=50.86  Aligned_cols=105  Identities=20%  Similarity=0.192  Sum_probs=58.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .+++|.|..|.|||||++.++...  ....+.+|++-..             .++.-. +....+...-.+.+.+..++-
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~~~~-------------~i~~~~-~lS~G~~~rv~laral~~~p~   90 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGEL--EPDEGIVTWGSTV-------------KIGYFE-QLSGGEKMRLALAKLLLENPN   90 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCC--CCCceEEEECCeE-------------EEEEEc-cCCHHHHHHHHHHHHHhcCCC
Confidence            488999999999999999987632  2233444442100             000000 022223334445566667778


Q ss_pred             EEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHHHh
Q 000887           94 LIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        94 LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~  136 (1237)
                      ++++|+-... +......+...+...  +..|+++|.+......
T Consensus        91 illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~~  132 (144)
T cd03221          91 LLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLDQ  132 (144)
T ss_pred             EEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHHH
Confidence            9999998432 222223333333222  3468888887766543

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.74  E-value=0.084  Score=57.47  Aligned_cols=50  Identities=26%  Similarity=0.337  Sum_probs=34.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILD   65 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~   65 (1237)
                      .++.|.|.+|+|||+++.+++.......-..++|++....  ..++...+..
T Consensus        31 ~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~E~~--~~~~~~r~~~   80 (271)
T cd01122          31 ELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEP--VVRTARRLLG   80 (271)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEcccC--HHHHHHHHHH
Confidence            5889999999999999999877544442345889887553  3444444433

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.71  E-value=0.0017  Score=65.49  Aligned_cols=98  Identities=24%  Similarity=0.162  Sum_probs=75.7

Q ss_pred             CCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccCCCccccCccc--ccccccccc
Q 000887          421 CLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG--MKELKCLRT  498 (1237)
Q Consensus       421 ~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~~ip~~--~~~L~~L~~  498 (1237)
                      .+.+.+.|+..+|++.++ .-..+++.|++|.|+-| .|..+.. +..+++|++|+|+.| .+..+-+-  +.++++|+.
T Consensus        17 dl~~vkKLNcwg~~L~DI-sic~kMp~lEVLsLSvN-kIssL~p-l~rCtrLkElYLRkN-~I~sldEL~YLknlpsLr~   92 (388)
T KOG2123|consen   17 DLENVKKLNCWGCGLDDI-SICEKMPLLEVLSLSVN-KISSLAP-LQRCTRLKELYLRKN-CIESLDELEYLKNLPSLRT   92 (388)
T ss_pred             HHHHhhhhcccCCCccHH-HHHHhcccceeEEeecc-ccccchh-HHHHHHHHHHHHHhc-ccccHHHHHHHhcCchhhh
Confidence            466788999999999988 44779999999999998 8888866 899999999999999 66666432  778889999


Q ss_pred             cceeeeccCC--C-----cCcccccchHhcc
Q 000887          499 LTNFIVGKDS--G-----CALRDLKNWKFLR  522 (1237)
Q Consensus       499 L~~~~~~~~~--~-----~~i~~l~~l~~L~  522 (1237)
                      |++..+....  +     ..++.|++|++|.
T Consensus        93 LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   93 LWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             HhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            9876554322  1     1255566666665

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.71  E-value=0.063  Score=60.28  Aligned_cols=90  Identities=18%  Similarity=0.144  Sum_probs=55.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccc---cCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLT---EAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~---~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~   86 (1237)
                      ...++|.++|+.|+||||.+..+++....   ..-..+..++...... ...-++..+..++.+.......++....+.+
T Consensus       172 ~~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~  251 (388)
T PRK12723        172 LKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ  251 (388)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH
Confidence            34689999999999999999998875421   1223455666554322 2222445555565543344455555555554


Q ss_pred             HhcCCcEEEEEeCCCC
Q 000887           87 TVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv~~  102 (1237)
                      .  ++.-+||+|-+..
T Consensus       252 ~--~~~DlVLIDTaGr  265 (388)
T PRK12723        252 S--KDFDLVLVDTIGK  265 (388)
T ss_pred             h--CCCCEEEEcCCCC
Confidence            3  4567889999854

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.69  E-value=0.01  Score=55.21  Aligned_cols=35  Identities=23%  Similarity=0.289  Sum_probs=26.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCC-CeEEE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWV   48 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~   48 (1237)
                      -.|+|+|++|+||||++..+++....+.|. +.+|.
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t   41 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFIT   41 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEe
Confidence            468999999999999999998765555464 33444

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.68  E-value=0.1  Score=65.97  Aligned_cols=132  Identities=9%  Similarity=0.036  Sum_probs=67.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCC-----CCe-EEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAF-----EPK-AWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f-----~~~-~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      -+.++|.+|+|||++|..++.......-     ... ++++++.      +..       .. ....+.++....+.+.+
T Consensus       201 n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~------l~a-------g~-~~~g~~e~~lk~~~~~~  266 (857)
T PRK10865        201 NPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------LVA-------GA-KYRGEFEERLKGVLNDL  266 (857)
T ss_pred             ceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhh------hhh-------cc-chhhhhHHHHHHHHHHH
Confidence            5679999999999999998875432211     122 2222211      110       00 01112223222222222


Q ss_pred             --cCCcEEEEEeCCCCCC-------hhhHHHhhccccCCCCCcEEEEEeCchhHHHh-------hcCCCeEeCCCCChhh
Q 000887           89 --FKKKFLIVLDDVWSER-------YDLWQALKSPFMAGAPGSRIIVTTRSMDVALT-------MGSGKNYELKLLSDDD  152 (1237)
Q Consensus        89 --~~~~~LlvlDdv~~~~-------~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~-------~~~~~~~~l~~l~~~e  152 (1237)
                        .+++++|++|+++.-.       ..+...+..+.... ..-++|-+|...+....       ......+.+..-+.++
T Consensus       267 ~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~-g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~  345 (857)
T PRK10865        267 AKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR-GELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVED  345 (857)
T ss_pred             HHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhhc-CCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHH
Confidence              2468999999994321       01122333333222 23456656555443111       1122366777778899


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      +.++++...
T Consensus       346 ~~~iL~~l~  354 (857)
T PRK10865        346 TIAILRGLK  354 (857)
T ss_pred             HHHHHHHHh
Confidence            999887654

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=95.68  E-value=0.052  Score=57.47  Aligned_cols=89  Identities=20%  Similarity=0.171  Sum_probs=56.1

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc-cCCCccCHHHHHHH---HHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR-SSCKLEDLNSVQLE---LKE   86 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~-~~~~~~~~~~~~~~---l~~   86 (1237)
                      +.-+++=|+|+.|+|||++|.+++... +..-..++|++.....+...+..-....+.. ...++.+.++....   +..
T Consensus        58 ~~g~ItEiyG~~gsGKT~lal~~~~~a-q~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~~  136 (279)
T COG0468          58 PRGRITEIYGPESSGKTTLALQLVANA-QKPGGKAAFIDTEHALDPERAKQLGVDLLDNLLVSQPDTGEQQLEIAEKLAR  136 (279)
T ss_pred             ccceEEEEecCCCcchhhHHHHHHHHh-hcCCCeEEEEeCCCCCCHHHHHHHHHhhhcceeEecCCCHHHHHHHHHHHHH
Confidence            344788999999999999999987643 3333478999998888876554333331211 11133444443333   333


Q ss_pred             HhcCCcEEEEEeCC
Q 000887           87 TVFKKKFLIVLDDV  100 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv  100 (1237)
                      ...++--|+|+|.+
T Consensus       137 ~~~~~i~LvVVDSv  150 (279)
T COG0468         137 SGAEKIDLLVVDSV  150 (279)
T ss_pred             hccCCCCEEEEecC
Confidence            33334679999998

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.68  E-value=0.031  Score=70.14  Aligned_cols=110  Identities=17%  Similarity=0.157  Sum_probs=57.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-Cc-cCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-KL-EDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-~~-~~~~~~~~~l~~~l~~   90 (1237)
                      ..++.++|++|+|||.+|++++...... ....+-++++...+    ...+..-++.+.. .. .....+...++   +.
T Consensus       596 ~~~~lf~Gp~GvGKT~lA~~La~~l~~~-~~~~~~~dmse~~~----~~~~~~l~g~~~gyvg~~~~g~L~~~v~---~~  667 (852)
T TIGR03345       596 LGVFLLVGPSGVGKTETALALAELLYGG-EQNLITINMSEFQE----AHTVSRLKGSPPGYVGYGEGGVLTEAVR---RK  667 (852)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhCC-CcceEEEeHHHhhh----hhhhccccCCCCCcccccccchHHHHHH---hC
Confidence            4578999999999999999988753321 22233333222111    1122222232211 11 11112222332   24


Q ss_pred             CcEEEEEeCCCCCChhhHHHhhccccCCC-----------CCcEEEEEeCc
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPFMAGA-----------PGSRIIVTTRS  130 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~~~~~~~~~~-----------~~~~iliTtR~  130 (1237)
                      ...+|+||+++..+.+.+..+...+..+.           .++-||+||.-
T Consensus       668 p~svvllDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNl  718 (852)
T TIGR03345       668 PYSVVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNA  718 (852)
T ss_pred             CCcEEEEechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCCC
Confidence            56899999997666555555544443321           44556677653

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.66  E-value=0.0056  Score=36.50  Aligned_cols=18  Identities=28%  Similarity=0.728  Sum_probs=7.6

Q ss_pred             CCeEEccCCCccccchhh
Q 000887          425 LRYLNFSRSEIQCLPDAI  442 (1237)
Q Consensus       425 Lr~L~L~~~~i~~lp~~i  442 (1237)
                      |++|||++|.++.+|++|
T Consensus         2 L~~Ldls~n~l~~ip~~~   19 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSSF   19 (22)
T ss_dssp             ESEEEETSSEESEEGTTT
T ss_pred             ccEEECCCCcCEeCChhh
Confidence            344444444444444433

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.65  E-value=0.047  Score=60.94  Aligned_cols=85  Identities=19%  Similarity=0.167  Sum_probs=44.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ..++++++|++|+||||+|..++... ....+ .+..++...... ....+...+..++.+.....+.......+.   +
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~-~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~~~~~~l~~~l~---~  297 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGK-SVSLYTTDNYRIAAIEQLKRYADTMGMPFYPVKDIKKFKETLA---R  297 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCC-eEEEecccchhhhHHHHHHHHHHhcCCCeeehHHHHHHHHHHH---h
Confidence            45789999999999999999998643 23222 344554433222 122233333444433222222222222222   2


Q ss_pred             CCcEEEEEeCC
Q 000887           90 KKKFLIVLDDV  100 (1237)
Q Consensus        90 ~~~~LlvlDdv  100 (1237)
                      +..=+||+|-.
T Consensus       298 ~~~D~VLIDTa  308 (432)
T PRK12724        298 DGSELILIDTA  308 (432)
T ss_pred             CCCCEEEEeCC
Confidence            33455888954

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=95.65  E-value=0.1  Score=50.40  Aligned_cols=66  Identities=12%  Similarity=0.238  Sum_probs=41.9

Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchhHHHhhc
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMDVALTMG  138 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~~~~~~  138 (1237)
                      +....++..-.+.+.+-+++-+++=|.=... +.+-...+...+.. ...|+.||++|-+..+...+.
T Consensus       137 ~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         137 QLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             ccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhcc
Confidence            3455666667777888889999999875321 11111222222222 356899999999998887664

>PRK10867 signal recognition particle protein; Provisional

Probab=95.63  E-value=0.067  Score=60.97  Aligned_cols=91  Identities=18%  Similarity=0.095  Sum_probs=50.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCH-HHHHHHHHHHhhccCC---CccCHHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDV-LRISKAILDSIKRSSC---KLEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~-~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~   86 (1237)
                      ..+.+|.++|++|+||||+|..++....+..-..+..+++...... .+-++..+.+.+.+..   ...++.+......+
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~~~~~~dp~~i~~~a~~  177 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSGDGQDPVDIAKAALE  177 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcCCeEEecCCCCCHHHHHHHHHH
Confidence            4578999999999999999999887543331234556655433221 1223334455443211   22344454443333


Q ss_pred             HhcCC-cEEEEEeCCC
Q 000887           87 TVFKK-KFLIVLDDVW  101 (1237)
Q Consensus        87 ~l~~~-~~LlvlDdv~  101 (1237)
                      ..+.+ .-++|+|-.-
T Consensus       178 ~a~~~~~DvVIIDTaG  193 (433)
T PRK10867        178 EAKENGYDVVIVDTAG  193 (433)
T ss_pred             HHHhcCCCEEEEeCCC
Confidence            33333 3377777764

>PRK08233 hypothetical protein; Provisional

Probab=95.63  E-value=0.03  Score=56.73  Aligned_cols=25  Identities=28%  Similarity=0.484  Sum_probs=22.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ..+|+|.|.+|+||||+|..++...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            4799999999999999999998743

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.62  E-value=0.093  Score=51.94  Aligned_cols=123  Identities=17%  Similarity=0.230  Sum_probs=70.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEc---C----------------Cc--------------------
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVS---D----------------DF--------------------   54 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~---~----------------~~--------------------   54 (1237)
                      .+|+|+|++|+|||||.+-+.. . ...-.+.+|++-.   .                .+                    
T Consensus        29 evv~iiGpSGSGKSTlLRclN~-L-E~~~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~~v~  106 (240)
T COG1126          29 EVVVIIGPSGSGKSTLLRCLNG-L-EEPDSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVKVK  106 (240)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC-C-cCCCCceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhHHHc
Confidence            4899999999999999998654 2 2222234454321   0                00                    


Q ss_pred             -----CHHHHHHHHHHHhhccC------CCccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCC
Q 000887           55 -----DVLRISKAILDSIKRSS------CKLEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPG  121 (1237)
Q Consensus        55 -----~~~~~~~~i~~~l~~~~------~~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~  121 (1237)
                           ...+...+++..++...      .+.....+-+-.|.+.|.-++=++.||...+. +.+-..++...... ...|
T Consensus       107 ~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~eG  186 (240)
T COG1126         107 KLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEEG  186 (240)
T ss_pred             CCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHcC
Confidence                 11223333333333221      13344555566778888888999999998653 22222333222222 2346


Q ss_pred             cEEEEEeCchhHHHhhc
Q 000887          122 SRIIVTTRSMDVALTMG  138 (1237)
Q Consensus       122 ~~iliTtR~~~~~~~~~  138 (1237)
                      -..++.|-+..++....
T Consensus       187 mTMivVTHEM~FAr~Va  203 (240)
T COG1126         187 MTMIIVTHEMGFAREVA  203 (240)
T ss_pred             CeEEEEechhHHHHHhh
Confidence            67888888888776653

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=95.60  E-value=0.045  Score=55.86  Aligned_cols=80  Identities=19%  Similarity=0.164  Sum_probs=44.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCC---CeEEEEEcCCcCHHHHHHHHHHHhh----ccCCCccCHHHHHHHHHHH
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFE---PKAWVCVSDDFDVLRISKAILDSIK----RSSCKLEDLNSVQLELKET   87 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~---~~~w~~~~~~~~~~~~~~~i~~~l~----~~~~~~~~~~~~~~~l~~~   87 (1237)
                      ||+|.|++|+||||+|++++....+....   .+..+.............. .....    .......+.+.....+...
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~~p~a~d~~~l~~~l~~L   79 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNKRGIPAMEMDIILSLDDFYDDYHLRDR-KGRGENRYNFDHPDAFDFDLLKEDLKAL   79 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTTCTTTCCCSEEEEEGGGGBHHHHHHHH-HHHCTTTSSTTSGGGBSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCccCcCccceeEEEeecccccccchhhH-hhccccccCCCCccccCHHHHHHHHHHH
Confidence            79999999999999999988754444444   2334433332222121111 11111    1112345677777777766


Q ss_pred             hcCCcEEE
Q 000887           88 VFKKKFLI   95 (1237)
Q Consensus        88 l~~~~~Ll   95 (1237)
                      .+++.+-+
T Consensus        80 ~~g~~i~~   87 (194)
T PF00485_consen   80 KNGGSIEI   87 (194)
T ss_dssp             HTTSCEEE
T ss_pred             hCCCcccc
Confidence            55555444

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=95.56  E-value=0.069  Score=56.31  Aligned_cols=86  Identities=22%  Similarity=0.245  Sum_probs=49.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCC-eEEEEEcCCc-CHHHHHHHHHHHhhcc------CCCccCHH-H-----
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDF-DVLRISKAILDSIKRS------SCKLEDLN-S-----   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~-~~~~~~~~i~~~l~~~------~~~~~~~~-~-----   79 (1237)
                      ..++|.|.+|+|||+||.+++... +..|.. ++++-++... .+.++.+++...-...      ......+. +     
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~~i-~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~  148 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELINNI-AKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVAL  148 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHHHH-HhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            467999999999999999998753 334443 4455555443 4445555554321111      00111111 1     


Q ss_pred             HHHHHHHHh--c-CCcEEEEEeCC
Q 000887           80 VQLELKETV--F-KKKFLIVLDDV  100 (1237)
Q Consensus        80 ~~~~l~~~l--~-~~~~LlvlDdv  100 (1237)
                      ..-.+.+++  + ++++|+++||+
T Consensus       149 ~a~~~AEyfr~~~g~~Vl~~~Dsl  172 (274)
T cd01133         149 TGLTMAEYFRDEEGQDVLLFIDNI  172 (274)
T ss_pred             HHHHHHHHHHHhcCCeEEEEEeCh
Confidence            112244555  2 78999999999

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.56  E-value=0.17  Score=57.68  Aligned_cols=131  Identities=16%  Similarity=0.174  Sum_probs=73.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      +.=|.++|++|+|||-||++|++. -+..     |+.+-..    .++...   .|.      ....++..+.+.-..-+
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANE-ag~N-----FisVKGP----ELlNkY---VGE------SErAVR~vFqRAR~saP  605 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANE-AGAN-----FISVKGP----ELLNKY---VGE------SERAVRQVFQRARASAP  605 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhh-ccCc-----eEeecCH----HHHHHH---hhh------HHHHHHHHHHHhhcCCC
Confidence            345789999999999999999984 2222     4555333    122221   111      11222222333333479


Q ss_pred             EEEEEeCCCCC------C-hhh----HHHhhccccC--CCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCChhhhH
Q 000887           93 FLIVLDDVWSE------R-YDL----WQALKSPFMA--GAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLSDDDCW  154 (1237)
Q Consensus        93 ~LlvlDdv~~~------~-~~~----~~~~~~~~~~--~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~~ea~  154 (1237)
                      ++|.||.++.-      . ...    +.++..-+..  ...|..||-.|-.+++... +    .-+..+-++.-+.+|-.
T Consensus       606 CVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~  685 (802)
T KOG0733|consen  606 CVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERV  685 (802)
T ss_pred             eEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHH
Confidence            99999999531      0 011    1122222221  2356667766655544321 1    12356778888889999


Q ss_pred             HHHHHHhc
Q 000887          155 SVFVAHAF  162 (1237)
Q Consensus       155 ~l~~~~~~  162 (1237)
                      ++++....
T Consensus       686 ~ILK~~tk  693 (802)
T KOG0733|consen  686 AILKTITK  693 (802)
T ss_pred             HHHHHHhc
Confidence            99998874

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.55  E-value=0.075  Score=55.04  Aligned_cols=123  Identities=15%  Similarity=0.112  Sum_probs=70.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcC-----CcCHHHHHHHHHHHhhccCC-------CccCHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSD-----DFDVLRISKAILDSIKRSSC-------KLEDLNSVQ   81 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~-----~~~~~~~~~~i~~~l~~~~~-------~~~~~~~~~   81 (1237)
                      .+++|+|-+|+||||+++.+.. ..+-.. +.+++.-.+     .....+...+++...+....       +......-+
T Consensus        40 e~~glVGESG~GKSTlgr~i~~-L~~pt~-G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQR  117 (268)
T COG4608          40 ETLGLVGESGCGKSTLGRLILG-LEEPTS-GEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQR  117 (268)
T ss_pred             CEEEEEecCCCCHHHHHHHHHc-CcCCCC-ceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhh
Confidence            4789999999999999999876 333333 334332111     11233344555555554321       223333334


Q ss_pred             HHHHHHhcCCcEEEEEeCCCCCChhhH-HHhhcccc--CCCCCcEEEEEeCchhHHHhhc
Q 000887           82 LELKETVFKKKFLIVLDDVWSERYDLW-QALKSPFM--AGAPGSRIIVTTRSMDVALTMG  138 (1237)
Q Consensus        82 ~~l~~~l~~~~~LlvlDdv~~~~~~~~-~~~~~~~~--~~~~~~~iliTtR~~~~~~~~~  138 (1237)
                      -.+.+.+.-++-++|.|...+.-+... +++...+.  ....|...++.|-+-.+...+.
T Consensus       118 i~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~is  177 (268)
T COG4608         118 IGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYIS  177 (268)
T ss_pred             HHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhhc
Confidence            456777788999999999744321111 11222121  1234677888888877776554

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=95.50  E-value=0.025  Score=60.34  Aligned_cols=34  Identities=26%  Similarity=0.205  Sum_probs=22.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWV   48 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~   48 (1237)
                      +.|.|+|.+|+||||+|+++......... .+.++
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~~~~-~v~~i   35 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEEKGK-EVVII   35 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHHTT---EEEE
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHhcCC-EEEEE
Confidence            57999999999999999998875433222 24455

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=95.49  E-value=0.069  Score=53.37  Aligned_cols=115  Identities=21%  Similarity=0.247  Sum_probs=59.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcC--CcCHHHHHHHHHHHhhccCCC------------ccCHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSD--DFDVLRISKAILDSIKRSSCK------------LEDLNS   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~--~~~~~~~~~~i~~~l~~~~~~------------~~~~~~   79 (1237)
                      .+++|.|..|+|||||++.++...  ....+.++++-..  .......    ...++.-...            ....+.
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g~~~~~~~~~~~----~~~i~~~~q~~~~~~~tv~~~lLS~G~~  102 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILGLL--RPTSGRVRLDGADISQWDPNEL----GDHVGYLPQDDELFSGSIAENILSGGQR  102 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcc--CCCCCeEEECCEEcccCCHHHH----HhheEEECCCCccccCcHHHHCcCHHHH
Confidence            379999999999999999987632  2223444432111  0111111    1111110000            122233


Q ss_pred             HHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchhHH
Q 000887           80 VQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        80 ~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~~  134 (1237)
                      ..-.+.+.+-.++=++++|+.... +......+...+.. ...|..||++|.+....
T Consensus       103 qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~  159 (173)
T cd03246         103 QRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPETL  159 (173)
T ss_pred             HHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHH
Confidence            344455666667789999998542 11222222222222 12366788888887665

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.49  E-value=0.067  Score=57.40  Aligned_cols=92  Identities=13%  Similarity=0.097  Sum_probs=51.8

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCH-HHHHHHHHHHhhccC---CCccCHHH-HHHHH
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDV-LRISKAILDSIKRSS---CKLEDLNS-VQLEL   84 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~-~~~~~~i~~~l~~~~---~~~~~~~~-~~~~l   84 (1237)
                      ....++++++|++|+||||++..++....+.. ..+.+++....... ..-+...+...+.+.   ....++.. ....+
T Consensus        69 ~~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g-~~V~li~~D~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~l  147 (272)
T TIGR00064        69 ENKPNVILFVGVNGVGKTTTIAKLANKLKKQG-KSVLLAAGDTFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDAI  147 (272)
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHHHhcC-CEEEEEeCCCCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHH
Confidence            35578999999999999999999887543332 34666765432221 122233444444221   11223322 22334


Q ss_pred             HHHhcCCcEEEEEeCCCC
Q 000887           85 KETVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~~  102 (1237)
                      .....+..=++|+|-.-.
T Consensus       148 ~~~~~~~~D~ViIDT~G~  165 (272)
T TIGR00064       148 QKAKARNIDVVLIDTAGR  165 (272)
T ss_pred             HHHHHCCCCEEEEeCCCC
Confidence            444344556788898843

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.44  E-value=0.046  Score=55.63  Aligned_cols=38  Identities=32%  Similarity=0.388  Sum_probs=28.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      ++.|.|.+|+|||++|.+++....+. -..++|++....
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~-g~~v~~~s~e~~   38 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR-GEPGLYVTLEES   38 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC-CCcEEEEECCCC
Confidence            36899999999999999987654333 245778876543

A related protein is found in archaea.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.44  E-value=0.13  Score=51.49  Aligned_cols=66  Identities=14%  Similarity=0.113  Sum_probs=39.8

Q ss_pred             cCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchhHHHhhcCC
Q 000887           75 EDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMDVALTMGSG  140 (1237)
Q Consensus        75 ~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~~~~~~~~  140 (1237)
                      ...+..+..+.+.+--++-+.|+|.-++- +.+.+..+...... ..+++.+||.|-.+.+......+
T Consensus       146 SGGEkKR~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~liITHy~rll~~i~pD  213 (251)
T COG0396         146 SGGEKKRNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVLIITHYQRLLDYIKPD  213 (251)
T ss_pred             CcchHHHHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHhhcCCC
Confidence            34455666677777778899999998652 23333333322221 23466677777777777655444

>TIGR00959 ffh signal recognition particle protein

Probab=95.43  E-value=0.096  Score=59.72  Aligned_cols=91  Identities=15%  Similarity=0.052  Sum_probs=51.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcC-HHHHHHHHHHHhhccCC---CccCHHHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSC---KLEDLNSVQLELK   85 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~   85 (1237)
                      ..+.++.++|.+|+||||+|..++.... +..+ .+..+++..... ..+-+...+.+.+.+..   ...++.+......
T Consensus        97 ~~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~-kV~lV~~D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959        97 KPPTVILMVGLQGSGKTTTCGKLAYYLKKKQGK-KVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHHhCCC-eEEEEeccccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHH
Confidence            3478999999999999999999887533 2333 355665543322 22233344454443321   2234444443333


Q ss_pred             HHhcCCc-EEEEEeCCCC
Q 000887           86 ETVFKKK-FLIVLDDVWS  102 (1237)
Q Consensus        86 ~~l~~~~-~LlvlDdv~~  102 (1237)
                      +....+. =++|+|-.-.
T Consensus       176 ~~~~~~~~DvVIIDTaGr  193 (428)
T TIGR00959       176 EYAKENGFDVVIVDTAGR  193 (428)
T ss_pred             HHHHhcCCCEEEEeCCCc
Confidence            3333333 4888888743

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=95.42  E-value=0.074  Score=56.61  Aligned_cols=53  Identities=23%  Similarity=0.335  Sum_probs=37.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cccC----CCCeEEEEEcCCcCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTEA----FEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~~~----f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      .+.=|+|.+|+|||+||.+++-.. ....    -..++|++-...++...+. +|+++.
T Consensus        39 ~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~   96 (256)
T PF08423_consen   39 SITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERF   96 (256)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHT
T ss_pred             cEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhcc
Confidence            477899999999999999876533 2221    2347899988888877665 455544

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=95.41  E-value=0.098  Score=52.91  Aligned_cols=64  Identities=9%  Similarity=0.152  Sum_probs=36.9

Q ss_pred             cCHHHHHHHHHHHhcCCcEEEEEeCCCCCCh-hhHHHhhccccC--CCCCcEEEEEeCchhHHHhhc
Q 000887           75 EDLNSVQLELKETVFKKKFLIVLDDVWSERY-DLWQALKSPFMA--GAPGSRIIVTTRSMDVALTMG  138 (1237)
Q Consensus        75 ~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~~-~~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~~~  138 (1237)
                      ...+..+-.+.+.+--++=+||+|..-+.-+ ..-+.+...+..  ...+-.+|+.|-+-.+...+.
T Consensus       143 SGGQ~QRiaIARAL~~~PklLIlDEptSaLD~siQa~IlnlL~~l~~~~~lt~l~IsHdl~~v~~~c  209 (252)
T COG1124         143 SGGQRQRIAIARALIPEPKLLILDEPTSALDVSVQAQILNLLLELKKERGLTYLFISHDLALVEHMC  209 (252)
T ss_pred             ChhHHHHHHHHHHhccCCCEEEecCchhhhcHHHHHHHHHHHHHHHHhcCceEEEEeCcHHHHHHHh
Confidence            3334444456777778899999999844211 111122222221  245667888888877766553

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.39  E-value=0.015  Score=57.30  Aligned_cols=43  Identities=23%  Similarity=0.244  Sum_probs=30.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD   55 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~   55 (1237)
                      ...+.+.|+.|+|||.+|++++...........+-++++.-..
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~   45 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSE   45 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccc
Confidence            4678999999999999999988743213444566666655444

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=95.39  E-value=0.53  Score=52.48  Aligned_cols=112  Identities=12%  Similarity=0.095  Sum_probs=71.9

Q ss_pred             cEEEEEeCCCCCC---hhhHHHh---hccccCCCCCcEEEEEeCchhHHHhh----c--CCCeEeCCCCChhhhHHHHHH
Q 000887           92 KFLIVLDDVWSER---YDLWQAL---KSPFMAGAPGSRIIVTTRSMDVALTM----G--SGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        92 ~~LlvlDdv~~~~---~~~~~~~---~~~~~~~~~~~~iliTtR~~~~~~~~----~--~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      +=+||+||.-...   ...++.+   ...+. ..+-.+||++|-+......+    +  ..+.+.|.-.+++.|.++...
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv-~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~  227 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLV-QNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLS  227 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHH-hcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHH
Confidence            5689999984311   1111111   11111 23456799999876554322    2  235788999999999999988


Q ss_pred             HhcCCCCCC------------C----CCChHHHHHHHHHHccCCchHHHHHHhHhhcCCCH
Q 000887          160 HAFEGRDAG------------T----HGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGV  204 (1237)
Q Consensus       160 ~~~~~~~~~------------~----~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~~~~  204 (1237)
                      +........            .    .....+.....++.+||=-.-|..++++++...++
T Consensus       228 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p  288 (431)
T PF10443_consen  228 QLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESP  288 (431)
T ss_pred             HhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCH
Confidence            875431110            0    01345566788899999999999999999987653

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.36  E-value=0.089  Score=50.85  Aligned_cols=23  Identities=39%  Similarity=0.579  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +|.|.|.+|+||||+|+.+....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l   23 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKL   23 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            57899999999999999987743

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.36  E-value=0.029  Score=55.66  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .|.|.|++|+||||+|+.+++..
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998863

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.34  E-value=0.14  Score=54.44  Aligned_cols=22  Identities=36%  Similarity=0.431  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +..|+|++|+|||+||..++..
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHH
Confidence            5678999999999999998764

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=95.31  E-value=0.55  Score=54.90  Aligned_cols=176  Identities=13%  Similarity=0.066  Sum_probs=97.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhccc----c---cCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKL----T---EAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLEL   84 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~----~---~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l   84 (1237)
                      .-+.+-|.|.+|+|||+.+.+|.....    +   ..|+ .+.++...-.+..+++..|..++....   .........+
T Consensus       421 ~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~~~~~Y~~I~~~lsg~~---~~~~~al~~L  496 (767)
T KOG1514|consen  421 LGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLASPREIYEKIWEALSGER---VTWDAALEAL  496 (767)
T ss_pred             CceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecCHHHHHHHHHHhcccCc---ccHHHHHHHH
Confidence            335999999999999999999987432    1   2233 345555555678899999988886542   2333344444


Q ss_pred             HHHhc-----CCcEEEEEeCCCCCChhhHHHhhccc--cCCCCCcEEEEEeC--chhHHHhh-c-------CCCeEeCCC
Q 000887           85 KETVF-----KKKFLIVLDDVWSERYDLWQALKSPF--MAGAPGSRIIVTTR--SMDVALTM-G-------SGKNYELKL  147 (1237)
Q Consensus        85 ~~~l~-----~~~~LlvlDdv~~~~~~~~~~~~~~~--~~~~~~~~iliTtR--~~~~~~~~-~-------~~~~~~l~~  147 (1237)
                      ..+..     .+.++|++|+++.-- ..-.++...+  ++..+++|++|-+=  ..+...++ .       ....+..++
T Consensus       497 ~~~f~~~k~~~~~~VvLiDElD~Lv-tr~QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg~tRi~F~p  575 (767)
T KOG1514|consen  497 NFRFTVPKPKRSTTVVLIDELDILV-TRSQDVLYNIFDWPTLKNSKLVVIAIANTMDLPERLLMNRVSSRLGLTRICFQP  575 (767)
T ss_pred             HHhhccCCCCCCCEEEEeccHHHHh-cccHHHHHHHhcCCcCCCCceEEEEecccccCHHHHhccchhhhccceeeecCC
Confidence            44443     357899999983210 0001222222  23457787665432  11111111 0       114667777


Q ss_pred             CChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHH
Q 000887          148 LSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARA  193 (1237)
Q Consensus       148 l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~  193 (1237)
                      .+.++-.++...+..+. ........+-+|+.++...|-.-.|+.+
T Consensus       576 Yth~qLq~Ii~~RL~~~-~~f~~~aielvarkVAavSGDaRraldi  620 (767)
T KOG1514|consen  576 YTHEQLQEIISARLKGL-DAFENKAIELVARKVAAVSGDARRALDI  620 (767)
T ss_pred             CCHHHHHHHHHHhhcch-hhcchhHHHHHHHHHHhccccHHHHHHH
Confidence            78777777777665433 2222223333444444444444444433

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=95.28  E-value=0.041  Score=59.57  Aligned_cols=26  Identities=19%  Similarity=0.249  Sum_probs=23.5

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..++.++|+|++|+|||.+|++++..
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999885

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=95.24  E-value=0.0085  Score=57.16  Aligned_cols=36  Identities=31%  Similarity=0.194  Sum_probs=27.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEE
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      ..+|.|+|.+|+||||||+++.+..... -..+++++
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~-g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFAR-GIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHT-TS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHc-CCcEEEec
Confidence            3689999999999999999988754433 34566665

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=95.23  E-value=0.24  Score=51.40  Aligned_cols=60  Identities=12%  Similarity=0.211  Sum_probs=37.2

Q ss_pred             cCHHHHHHHHHHHhcCCcEEEEEeCCCCC----ChhhHHHhhccccCCCCCcEEEEEeCchhHHHh
Q 000887           75 EDLNSVQLELKETVFKKKFLIVLDDVWSE----RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        75 ~~~~~~~~~l~~~l~~~~~LlvlDdv~~~----~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~  136 (1237)
                      ...+..+..+.+.|...+=|+++|.-...    .....-++...+..  .|+.||++|-|-.....
T Consensus       141 SGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~--eg~tIl~vtHDL~~v~~  204 (254)
T COG1121         141 SGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQ--EGKTVLMVTHDLGLVMA  204 (254)
T ss_pred             CcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHH--CCCEEEEEeCCcHHhHh
Confidence            34445555677888889999999985331    11222223333333  28899999998766543

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.34  Score=48.50  Aligned_cols=132  Identities=17%  Similarity=0.199  Sum_probs=72.7

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      .+++=|.++|++|.|||-||++||++      ..+.|+.++...   -+++-|    +.   ...-+.++.-+-+   ..
T Consensus       179 aQPKGvlLygppgtGktLlaraVahh------t~c~firvsgse---lvqk~i----ge---gsrmvrelfvmar---eh  239 (404)
T KOG0728|consen  179 AQPKGVLLYGPPGTGKTLLARAVAHH------TDCTFIRVSGSE---LVQKYI----GE---GSRMVRELFVMAR---EH  239 (404)
T ss_pred             CCCcceEEecCCCCchhHHHHHHHhh------cceEEEEechHH---HHHHHh----hh---hHHHHHHHHHHHH---hc
Confidence            45667889999999999999999984      234456665431   112111    11   1111122221212   23


Q ss_pred             CcEEEEEeCCCCCCh-----------hhHH---HhhccccC--CCCCcEEEEEeCchhHHHh-----hcCCCeEeCCCCC
Q 000887           91 KKFLIVLDDVWSERY-----------DLWQ---ALKSPFMA--GAPGSRIIVTTRSMDVALT-----MGSGKNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~-----------~~~~---~~~~~~~~--~~~~~~iliTtR~~~~~~~-----~~~~~~~~l~~l~  149 (1237)
                      -+.+|.+|.+++...           +.-.   ++...+..  ..++-|||..|..-++...     ...+..++.++-+
T Consensus       240 apsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatknikvimatnridild~allrpgridrkiefp~p~  319 (404)
T KOG0728|consen  240 APSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPN  319 (404)
T ss_pred             CCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccceEEEEeccccccccHhhcCCCcccccccCCCCC
Confidence            588899998854211           1111   11112221  2456788877764444321     1233568888888


Q ss_pred             hhhhHHHHHHHh
Q 000887          150 DDDCWSVFVAHA  161 (1237)
Q Consensus       150 ~~ea~~l~~~~~  161 (1237)
                      ++...++++-+.
T Consensus       320 e~ar~~ilkihs  331 (404)
T KOG0728|consen  320 EEARLDILKIHS  331 (404)
T ss_pred             HHHHHHHHHHhh
Confidence            887788887665

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.19  E-value=0.04  Score=51.48  Aligned_cols=44  Identities=30%  Similarity=0.313  Sum_probs=32.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRS   70 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~   70 (1237)
                      +|+|.|++|+||||+|+.++++.--.      .+      +.-.+++++++..+.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~------~v------saG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK------LV------SAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc------ee------eccHHHHHHHHHcCCC
Confidence            68999999999999999998853110      11      2335778888887754

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=95.18  E-value=0.12  Score=51.41  Aligned_cols=118  Identities=11%  Similarity=0.036  Sum_probs=60.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .+++|.|+.|+|||||++.++.-.  ....+.+++.-..   +..+         .+.......+...-.+.+.+..++-
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~Gl~--~p~~G~i~~~g~~---i~~~---------~q~~~LSgGq~qrv~laral~~~p~   91 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAGQL--IPNGDNDEWDGIT---PVYK---------PQYIDLSGGELQRVAIAAALLRNAT   91 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHcCC--CCCCcEEEECCEE---EEEE---------cccCCCCHHHHHHHHHHHHHhcCCC
Confidence            489999999999999999987632  1223333331100   0000         0000022233344455566667888


Q ss_pred             EEEEeCCCCCC-hhhHHHhhccccCC--CCCcEEEEEeCchhHHHhhcCCCeEeCC
Q 000887           94 LIVLDDVWSER-YDLWQALKSPFMAG--APGSRIIVTTRSMDVALTMGSGKNYELK  146 (1237)
Q Consensus        94 LlvlDdv~~~~-~~~~~~~~~~~~~~--~~~~~iliTtR~~~~~~~~~~~~~~~l~  146 (1237)
                      ++++|+-...- ......+...+...  ..+..||++|.+........ ...+.++
T Consensus        92 lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~~~~~-d~i~~l~  146 (177)
T cd03222          92 FYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLDYLS-DRIHVFE  146 (177)
T ss_pred             EEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHHHHhC-CEEEEEc
Confidence            99999974321 11122222222211  12356888888876654432 2344444

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=95.16  E-value=0.079  Score=61.04  Aligned_cols=166  Identities=13%  Similarity=0.124  Sum_probs=91.6

Q ss_pred             EEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCcCHHHHHHH-HHHHhhccCCCccCHHHHHHHHHHHh----cC
Q 000887           17 PLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRISKA-ILDSIKRSSCKLEDLNSVQLELKETV----FK   90 (1237)
Q Consensus        17 ~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~~~~~~~~~-i~~~l~~~~~~~~~~~~~~~~l~~~l----~~   90 (1237)
                      ...|+=|+||||+|+-++... -...-+   .-.++....-..+... ..+-+.........+++.+..+.+..    ++
T Consensus        42 lfsG~RGvGKTt~Ari~AkalNC~~~~~---~ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~  118 (515)
T COG2812          42 LFSGPRGVGKTTIARILAKALNCENGPT---AEPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEG  118 (515)
T ss_pred             hhcCCCCcCchhHHHHHHHHhcCCCCCC---CCcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccc
Confidence            468999999999999987744 111100   0011111111111111 11111111112233444443333222    24


Q ss_pred             CcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCch-hHHHhh-cCCCeEeCCCCChhhhHHHHHHHhcCCCCCC
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDAG  168 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~  168 (1237)
                      +-=+.|+|.|.--....+.++...+-.-+.+.+.|..|++. .+.... .....+.+..++.++-...+...+.......
T Consensus       119 ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~  198 (515)
T COG2812         119 RYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINI  198 (515)
T ss_pred             cceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCcc
Confidence            55688999995444455666666665555666655555544 444332 2336899999999999999988875443332


Q ss_pred             CCCChHHHHHHHHHHccCCch
Q 000887          169 THGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       169 ~~~~~~~~~~~i~~~~~g~PL  189 (1237)
                          .+++..-|++..+|...
T Consensus       199 ----e~~aL~~ia~~a~Gs~R  215 (515)
T COG2812         199 ----EEDALSLIARAAEGSLR  215 (515)
T ss_pred             ----CHHHHHHHHHHcCCChh
Confidence                36677788888888654

>TIGR00763 lon ATP-dependent protease La

Probab=95.13  E-value=0.15  Score=64.12  Aligned_cols=137  Identities=20%  Similarity=0.175  Sum_probs=67.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +++.++|++|+|||++|+.++... ...|   +-+.++...+..++..    .  ...............+...- ..+-
T Consensus       348 ~~lll~GppG~GKT~lAk~iA~~l-~~~~---~~i~~~~~~~~~~i~g----~--~~~~~g~~~g~i~~~l~~~~-~~~~  416 (775)
T TIGR00763       348 PILCLVGPPGVGKTSLGKSIAKAL-NRKF---VRFSLGGVRDEAEIRG----H--RRTYVGAMPGRIIQGLKKAK-TKNP  416 (775)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh-cCCe---EEEeCCCcccHHHHcC----C--CCceeCCCCchHHHHHHHhC-cCCC
Confidence            579999999999999999998753 2222   2233333223222211    0  01011111223333344332 2334


Q ss_pred             EEEEeCCCCCCh----hhHHHhhcccc--------CC-------CCCcEEEEEeCchhH-HHhh-cCCCeEeCCCCChhh
Q 000887           94 LIVLDDVWSERY----DLWQALKSPFM--------AG-------APGSRIIVTTRSMDV-ALTM-GSGKNYELKLLSDDD  152 (1237)
Q Consensus        94 LlvlDdv~~~~~----~~~~~~~~~~~--------~~-------~~~~~iliTtR~~~~-~~~~-~~~~~~~l~~l~~~e  152 (1237)
                      +|++|+++....    +....+...+-        ..       ..+.-+|.||..... ...+ .....+++.+++.+|
T Consensus       417 villDEidk~~~~~~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~R~~vi~~~~~~~~e  496 (775)
T TIGR00763       417 LFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPLLDRMEVIELSGYTEEE  496 (775)
T ss_pred             EEEEechhhcCCccCCCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCCchhCCHHHhCCeeEEecCCCCHHH
Confidence            789999954311    11122222111        10       123334444443221 1111 222578899999988


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      -.+++....
T Consensus       497 ~~~I~~~~l  505 (775)
T TIGR00763       497 KLEIAKKYL  505 (775)
T ss_pred             HHHHHHHHH
Confidence            888876654

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=95.11  E-value=0.033  Score=60.19  Aligned_cols=81  Identities=19%  Similarity=0.152  Sum_probs=51.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      +++-|+|+.|+||||||..+.....+ .-..++|++.....+..     .+.+++....     .+...++..+...+.+
T Consensus        54 ~ivEi~G~~ssGKttLaL~~ia~~q~-~g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e~li  127 (322)
T PF00154_consen   54 RIVEIYGPESSGKTTLALHAIAEAQK-QGGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAEQLI  127 (322)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHH-TT-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHHHHH
T ss_pred             ceEEEeCCCCCchhhhHHHHHHhhhc-ccceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHHHHh
Confidence            68999999999999999998774333 33457799887776543     3344443221     3455677766666666


Q ss_pred             cCC-cEEEEEeCC
Q 000887           89 FKK-KFLIVLDDV  100 (1237)
Q Consensus        89 ~~~-~~LlvlDdv  100 (1237)
                      +.. --++|+|.|
T Consensus       128 rsg~~~lVVvDSv  140 (322)
T PF00154_consen  128 RSGAVDLVVVDSV  140 (322)
T ss_dssp             HTTSESEEEEE-C
T ss_pred             hcccccEEEEecC
Confidence            653 458899998

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.09  E-value=0.036  Score=56.45  Aligned_cols=110  Identities=15%  Similarity=0.156  Sum_probs=53.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHH-h----
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET-V----   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~-l----   88 (1237)
                      ++++|.|++|+|||++++.+........+ .++++ .........+.+.    .+...   ............. .    
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~-~v~~~-apT~~Aa~~L~~~----~~~~a---~Ti~~~l~~~~~~~~~~~~   89 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGK-RVIGL-APTNKAAKELREK----TGIEA---QTIHSFLYRIPNGDDEGRP   89 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEE-ESSHHHHHHHHHH----HTS-E---EEHHHHTTEECCEECCSSC
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCC-eEEEE-CCcHHHHHHHHHh----hCcch---hhHHHHHhcCCcccccccc
Confidence            58899999999999999997764333332 23333 3333222233222    22110   0000000000000 0    


Q ss_pred             -cCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHH
Q 000887           89 -FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        89 -~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~  134 (1237)
                       ..+.-+||+|++.-.+...+..+......  .++|+|+.--..+..
T Consensus        90 ~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klilvGD~~QL~  134 (196)
T PF13604_consen   90 ELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLILVGDPNQLP  134 (196)
T ss_dssp             C-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEEEE-TTSHH
T ss_pred             cCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEEECCcchhc
Confidence             12345999999966555555555554433  478888877655443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=95.07  E-value=0.085  Score=66.73  Aligned_cols=110  Identities=19%  Similarity=0.219  Sum_probs=58.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCC-c
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK-K   92 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~-~   92 (1237)
                      ..+.++|+.|+|||++|+.+++...... ...+.++.+.-.+..    .+...++.+.. -...++. ..+.+.++.+ .
T Consensus       540 ~~~lf~Gp~GvGKt~lA~~LA~~l~~~~-~~~~~~d~s~~~~~~----~~~~l~g~~~g-yvg~~~~-~~l~~~~~~~p~  612 (821)
T CHL00095        540 ASFLFSGPTGVGKTELTKALASYFFGSE-DAMIRLDMSEYMEKH----TVSKLIGSPPG-YVGYNEG-GQLTEAVRKKPY  612 (821)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHhcCCc-cceEEEEchhccccc----cHHHhcCCCCc-ccCcCcc-chHHHHHHhCCC
Confidence            4677899999999999999987543221 234455544322211    11122222211 1111111 1233334444 4


Q ss_pred             EEEEEeCCCCCChhhHHHhhccccCC-----------CCCcEEEEEeCc
Q 000887           93 FLIVLDDVWSERYDLWQALKSPFMAG-----------APGSRIIVTTRS  130 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~~~~~~~~~-----------~~~~~iliTtR~  130 (1237)
                      .+++||+++..+.+.+..+...+-.+           ..++-+|+||..
T Consensus       613 ~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~  661 (821)
T CHL00095        613 TVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNL  661 (821)
T ss_pred             eEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCCc
Confidence            79999999776666666555544332           234556666654

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.07  E-value=0.012  Score=35.04  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=18.7

Q ss_pred             CccEEEccccccccccccccCC
Q 000887          401 KLRVLSLGSYCITEVPISIGCL  422 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~lp~~~~~l  422 (1237)
                      +|++|+|++|+++.+|++|++|
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT-
T ss_pred             CccEEECCCCcCEeCChhhcCC
Confidence            5899999999999999887654

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=95.04  E-value=0.073  Score=53.18  Aligned_cols=118  Identities=18%  Similarity=0.149  Sum_probs=61.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc--cCC---C---------ccCHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR--SSC---K---------LEDLNS   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~--~~~---~---------~~~~~~   79 (1237)
                      .+++|.|..|.|||||++.++...  ....+.++++-....+..   ......++.  +..   .         ....+.
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g~~~~~~~---~~~~~~i~~~~q~~~~~~~~tv~~~~~LS~G~~  101 (173)
T cd03230          27 EIYGLLGPNGAGKTTLIKIILGLL--KPDSGEIKVLGKDIKKEP---EEVKRRIGYLPEEPSLYENLTVRENLKLSGGMK  101 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC--CCCCeEEEECCEEcccch---HhhhccEEEEecCCccccCCcHHHHhhcCHHHH
Confidence            489999999999999999987632  123344444211100000   111111110  000   0         122233


Q ss_pred             HHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCC-CCCcEEEEEeCchhHHHh
Q 000887           80 VQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAG-APGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        80 ~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iliTtR~~~~~~~  136 (1237)
                      ..-.+...+..++-++++|+-... +......+...+... ..|..||++|.+......
T Consensus       102 qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~~~~~  160 (173)
T cd03230         102 QRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILEEAER  160 (173)
T ss_pred             HHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHH
Confidence            344566677778899999998442 112222233322221 236779999988776543

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.01  E-value=0.093  Score=51.87  Aligned_cols=122  Identities=14%  Similarity=0.027  Sum_probs=66.8

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC---cCHHHHHHHHH--H--Hhhcc-CCCccCHH-----
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD---FDVLRISKAIL--D--SIKRS-SCKLEDLN-----   78 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~---~~~~~~~~~i~--~--~l~~~-~~~~~~~~-----   78 (1237)
                      ....|.|+|..|-||||.|..++.+.....+. |..+-+-.+   ......++.+-  .  +.+.. .....+.+     
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~-V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~~   99 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGHGKK-VGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIAA   99 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHCCCe-EEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHHH
Confidence            34789999999999999999987755555554 333333222   22222222210  0  00111 00111111     


Q ss_pred             --HHHHHHHHHhcC-CcEEEEEeCCCC---CChhhHHHhhccccCCCCCcEEEEEeCchhHH
Q 000887           79 --SVQLELKETVFK-KKFLIVLDDVWS---ERYDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        79 --~~~~~l~~~l~~-~~~LlvlDdv~~---~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~  134 (1237)
                        +.....++.+.. +-=+||||.+-.   -.....+++...+...+.+..||+|-|+....
T Consensus       100 ~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~  161 (191)
T PRK05986        100 AREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRE  161 (191)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHH
Confidence              122233344433 456999999822   12233455666666677788999999986443

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=94.99  E-value=0.092  Score=57.78  Aligned_cols=88  Identities=18%  Similarity=0.068  Sum_probs=56.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCcCHHH-HHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDFDVLR-ISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~~~~~-~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -++|+++|+.||||||....+++... ...-..|..++.+.-.-... -++..++-++.+-....++.+....+... ++
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l-~~  281 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEAL-RD  281 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHh-hc
Confidence            58999999999999988777777553 34445677887766554333 33445555666655556666666666544 33


Q ss_pred             CcEEEEEeCCCC
Q 000887           91 KKFLIVLDDVWS  102 (1237)
Q Consensus        91 ~~~LlvlDdv~~  102 (1237)
                      . =+|.+|=+..
T Consensus       282 ~-d~ILVDTaGr  292 (407)
T COG1419         282 C-DVILVDTAGR  292 (407)
T ss_pred             C-CEEEEeCCCC
Confidence            3 4555677643

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=94.96  E-value=0.04  Score=56.89  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=20.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++.|+|+.|.||||+.+.++.
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            48999999999999999999864

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=94.96  E-value=0.25  Score=50.44  Aligned_cols=64  Identities=13%  Similarity=0.146  Sum_probs=40.9

Q ss_pred             ccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC--CCCCcEEEEEeCchhHHHhh
Q 000887           74 LEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA--GAPGSRIIVTTRSMDVALTM  137 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~~  137 (1237)
                      ....++.+-++.+.+-..+-+|+-|+=... +...-..+...+..  ...|..||+.|-++.++..+
T Consensus       143 LSGGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~~  209 (226)
T COG1136         143 LSGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKYA  209 (226)
T ss_pred             cCHHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHhC
Confidence            344566666788888889999999985321 11222233333332  24477899999999988643

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.95  E-value=0.25  Score=52.30  Aligned_cols=147  Identities=20%  Similarity=0.147  Sum_probs=79.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCC-eEEEEEcCCcC-----HHHHHHHHHHHhhccCCCccCHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDFD-----VLRISKAILDSIKRSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~~-----~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~   86 (1237)
                      ..-|.|+|+.|.|||.|......+  .+.|.- .+-+......-     +..+.+++..++........+..+....+.+
T Consensus        49 snsviiigprgsgkT~li~~~Ls~--~q~~~E~~l~v~Lng~~~~dk~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~  126 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTILIDTRLSD--IQENGENFLLVRLNGELQTDKIALKGITRQLALELNRIVKSFGSFTENLSKLLE  126 (408)
T ss_pred             CCceEEEccCCCCceEeeHHHHhh--HHhcCCeEEEEEECccchhhHHHHHHHHHHHHHHHhhhheeecccchhHHHHHH
Confidence            346889999999999998887665  222322 22333332221     2233333443433332233444454555555


Q ss_pred             HhcC------CcEEEEEeCCCCCChhhHHHhhccc-----cCCCCCcEEEEEeCchhHH---Hh----hcCCCeEeCCCC
Q 000887           87 TVFK------KKFLIVLDDVWSERYDLWQALKSPF-----MAGAPGSRIIVTTRSMDVA---LT----MGSGKNYELKLL  148 (1237)
Q Consensus        87 ~l~~------~~~LlvlDdv~~~~~~~~~~~~~~~-----~~~~~~~~iliTtR~~~~~---~~----~~~~~~~~l~~l  148 (1237)
                      .|+.      .++++|+|.++--.......+.-.+     ....|=|-|-+|||-.-..   .+    +.-..++-++.+
T Consensus       127 ~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKSRFshr~I~m~~~~  206 (408)
T KOG2228|consen  127 ALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKSRFSHRVIFMLPSL  206 (408)
T ss_pred             HHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHhhcccceeeccCCC
Confidence            5542      4689999988432111111111111     1235667788999965332   12    222234556678


Q ss_pred             ChhhhHHHHHHHh
Q 000887          149 SDDDCWSVFVAHA  161 (1237)
Q Consensus       149 ~~~ea~~l~~~~~  161 (1237)
                      ..++..++++...
T Consensus       207 ~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  207 PLGDYVDLYRKLL  219 (408)
T ss_pred             ChHHHHHHHHHHh
Confidence            8888888888776

>PTZ00301 uridine kinase; Provisional

Probab=94.95  E-value=0.048  Score=55.76  Aligned_cols=24  Identities=29%  Similarity=0.585  Sum_probs=21.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..+|+|.|.+|+||||+|.++...
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHH
Confidence            479999999999999999988764

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=94.89  E-value=0.1  Score=54.14  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +|+|.|.+|+||||+|+.++...
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l   23 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALL   23 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHH
Confidence            58999999999999999988743

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=94.86  E-value=0.053  Score=54.39  Aligned_cols=25  Identities=28%  Similarity=0.387  Sum_probs=22.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -.+|+|.|++|+||||+|++++...
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l   28 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKL   28 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3599999999999999999988754

>PRK13695 putative NTPase; Provisional

Probab=94.86  E-value=0.034  Score=55.63  Aligned_cols=23  Identities=35%  Similarity=0.436  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .|+|.|.+|+||||++..+++..
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999987643

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=94.85  E-value=0.019  Score=58.38  Aligned_cols=93  Identities=27%  Similarity=0.301  Sum_probs=66.6

Q ss_pred             cCCCCCccEEEcccc--ccc-cccccccCCCCCCeEEccCCCccccc--hhhcccCCccEEEcCccccCccCCh---h-h
Q 000887          396 LPQCKKLRVLSLGSY--CIT-EVPISIGCLKQLRYLNFSRSEIQCLP--DAICSLFNLEILILRNCWCLLKLPS---R-I  466 (1237)
Q Consensus       396 ~~~~~~Lr~L~L~~~--~i~-~lp~~~~~l~~Lr~L~L~~~~i~~lp--~~i~~L~~L~~L~L~~~~~l~~lp~---~-i  466 (1237)
                      |..+++|+.|.++.|  ++. .++-...++++|++|+|++|+|..+.  .....+.+|..|++.+|... .+-.   . +
T Consensus        61 ~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~pl~~l~nL~~Ldl~n~~~~-~l~dyre~vf  139 (260)
T KOG2739|consen   61 FPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRPLKELENLKSLDLFNCSVT-NLDDYREKVF  139 (260)
T ss_pred             CCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccchhhhhcchhhhhcccCCcc-ccccHHHHHH
Confidence            567889999999999  444 34443456699999999999988542  24778888999999999433 3321   1 4


Q ss_pred             cccccccEEeccCCCccccCcccc
Q 000887          467 GNLVNLHYLNIEGASALRELPLGM  490 (1237)
Q Consensus       467 ~~L~~L~~L~l~~~~~l~~ip~~~  490 (1237)
                      .-|++|.+||-... .-...|...
T Consensus       140 ~ll~~L~~LD~~dv-~~~Ea~~~~  162 (260)
T KOG2739|consen  140 LLLPSLKYLDGCDV-DGEEAPEAD  162 (260)
T ss_pred             HHhhhhcccccccc-CCccccccc
Confidence            67899999987766 445566544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.84  E-value=0.054  Score=55.34  Aligned_cols=109  Identities=13%  Similarity=0.121  Sum_probs=56.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .+|.|.|+.|+||||++..++... .....+.++.. .+....  ..... ..+-.......+.......++..++..+=
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~-~~~~~~~i~t~-e~~~E~--~~~~~-~~~i~q~~vg~~~~~~~~~i~~aLr~~pd   76 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYI-NKNKTHHILTI-EDPIEF--VHESK-RSLINQREVGLDTLSFENALKAALRQDPD   76 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh-hhcCCcEEEEE-cCCccc--cccCc-cceeeecccCCCccCHHHHHHHHhcCCcC
Confidence            479999999999999999877643 22233344332 222111  10000 00000101111223455567777777788


Q ss_pred             EEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchh
Q 000887           94 LIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD  132 (1237)
Q Consensus        94 LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~  132 (1237)
                      ++++|++.+.  +.........   ..|..++.|+-...
T Consensus        77 ~ii~gEird~--e~~~~~l~~a---~~G~~v~~t~Ha~~  110 (198)
T cd01131          77 VILVGEMRDL--ETIRLALTAA---ETGHLVMSTLHTNS  110 (198)
T ss_pred             EEEEcCCCCH--HHHHHHHHHH---HcCCEEEEEecCCc
Confidence            9999999543  3333222221   23455666665443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.84  E-value=0.13  Score=54.43  Aligned_cols=40  Identities=28%  Similarity=0.416  Sum_probs=30.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      -.++.|.|.+|+|||++|.+++.... ..-..++|++....
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~lyvs~ee~   60 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPGIYVALEEH   60 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcEEEEEeeCC
Confidence            47899999999999999999766433 23456888887553

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=94.84  E-value=0.091  Score=52.80  Aligned_cols=121  Identities=17%  Similarity=0.151  Sum_probs=60.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc--cCC---C-----------ccCH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR--SSC---K-----------LEDL   77 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~--~~~---~-----------~~~~   77 (1237)
                      .+++|.|..|+|||||++.++...  ....+.+++.-........-.......++.  +..   .           ....
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~~--~~~~G~i~~~g~~~~~~~~~~~~~~~~i~~~~q~~~~~~~~t~~~~l~~~lS~G  104 (178)
T cd03229          27 EIVALLGPSGSGKSTLLRCIAGLE--EPDSGSILIDGEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVLENIALGLSGG  104 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--CCCceEEEECCEEccccchhHHHHhhcEEEEecCCccCCCCCHHHheeecCCHH
Confidence            489999999999999999987632  223344443211100000000011111110  000   0           1112


Q ss_pred             HHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCC--CCCcEEEEEeCchhHHHh
Q 000887           78 NSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAG--APGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        78 ~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~--~~~~~iliTtR~~~~~~~  136 (1237)
                      +...-.+...+..++=++|+|+-... +......+...+...  ..+..||++|.+......
T Consensus       105 ~~qr~~la~al~~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~~~~~~  166 (178)
T cd03229         105 QQQRVALARALAMDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDLDEAAR  166 (178)
T ss_pred             HHHHHHHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            33334456666678889999997432 122222233323221  225678888888766543

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=94.82  E-value=0.085  Score=59.65  Aligned_cols=41  Identities=29%  Similarity=0.425  Sum_probs=30.6

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSD   52 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~   52 (1237)
                      ..+++|.++|+.|+||||+|..++....+..+ .++.++...
T Consensus        98 ~~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~-kV~lV~~D~  138 (429)
T TIGR01425        98 GKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGF-KPCLVCADT  138 (429)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEcCcc
Confidence            44789999999999999999998875433333 466665543

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PHA02244 ATPase-like protein

Probab=94.82  E-value=0.11  Score=56.80  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|.|+|++|+|||++|+++++.
T Consensus       121 PVLL~GppGtGKTtLA~aLA~~  142 (383)
T PHA02244        121 PVFLKGGAGSGKNHIAEQIAEA  142 (383)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999998874

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=94.81  E-value=0.021  Score=53.87  Aligned_cols=21  Identities=43%  Similarity=0.664  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhc
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |+|.|++|+||||+|+++...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            789999999999999998875

...

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=94.81  E-value=0.023  Score=46.24  Aligned_cols=22  Identities=32%  Similarity=0.616  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +|+|.|.+|+||||+|+++.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998875

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.80  E-value=0.088  Score=60.48  Aligned_cols=87  Identities=18%  Similarity=0.061  Sum_probs=48.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcC-HHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFD-VLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -++|+|+|++|+||||++..++......+ ...+..++...... ....+......++.......+..+....+.+. . 
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l-~-  427 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERL-R-  427 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHh-c-
Confidence            47999999999999999999877543322 34466665543222 11222222333333222233444444444433 3 


Q ss_pred             CcEEEEEeCCC
Q 000887           91 KKFLIVLDDVW  101 (1237)
Q Consensus        91 ~~~LlvlDdv~  101 (1237)
                      ..=+||+|..-
T Consensus       428 ~~DLVLIDTaG  438 (559)
T PRK12727        428 DYKLVLIDTAG  438 (559)
T ss_pred             cCCEEEecCCC
Confidence            35588888874

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.77  E-value=0.21  Score=62.61  Aligned_cols=154  Identities=16%  Similarity=0.123  Sum_probs=77.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .+-|.++|++|+|||++|+++++.. ...   .+.++..      .+.    ...     ...........+.......+
T Consensus       212 ~~giLL~GppGtGKT~laraia~~~-~~~---~i~i~~~------~i~----~~~-----~g~~~~~l~~lf~~a~~~~p  272 (733)
T TIGR01243       212 PKGVLLYGPPGTGKTLLAKAVANEA-GAY---FISINGP------EIM----SKY-----YGESEERLREIFKEAEENAP  272 (733)
T ss_pred             CceEEEECCCCCChHHHHHHHHHHh-CCe---EEEEecH------HHh----ccc-----ccHHHHHHHHHHHHHHhcCC
Confidence            3568899999999999999988743 111   1223211      111    000     00111222223333334567


Q ss_pred             EEEEEeCCCCCC-----------hhhHHHhhccccCC-CCCcEEEE-EeCchhH-HHhhc----CCCeEeCCCCChhhhH
Q 000887           93 FLIVLDDVWSER-----------YDLWQALKSPFMAG-APGSRIIV-TTRSMDV-ALTMG----SGKNYELKLLSDDDCW  154 (1237)
Q Consensus        93 ~LlvlDdv~~~~-----------~~~~~~~~~~~~~~-~~~~~ili-TtR~~~~-~~~~~----~~~~~~l~~l~~~ea~  154 (1237)
                      .+|++|+++...           ......+...+... ..+..++| ||..... ...+.    -...+.++..+.++..
T Consensus       273 ~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~  352 (733)
T TIGR01243       273 SIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARK  352 (733)
T ss_pred             cEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHH
Confidence            899999984310           00111222222211 22334444 4443321 11111    1246778888888888


Q ss_pred             HHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchH
Q 000887          155 SVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       155 ~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      ++++....... ...    ......+++.+.|.--+
T Consensus       353 ~Il~~~~~~~~-l~~----d~~l~~la~~t~G~~ga  383 (733)
T TIGR01243       353 EILKVHTRNMP-LAE----DVDLDKLAEVTHGFVGA  383 (733)
T ss_pred             HHHHHHhcCCC-Ccc----ccCHHHHHHhCCCCCHH
Confidence            88886542211 111    12256788888876543

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.74  E-value=0.29  Score=56.72  Aligned_cols=154  Identities=12%  Similarity=0.095  Sum_probs=75.3

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..++=|-++|++|+|||++|++++.. -+..|     +.+...    +++...         .......+...+++.-+.
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAne-~~~nF-----lsvkgp----EL~sk~---------vGeSEr~ir~iF~kAR~~  526 (693)
T KOG0730|consen  466 SPPKGVLLYGPPGCGKTLLAKALANE-AGMNF-----LSVKGP----ELFSKY---------VGESERAIREVFRKARQV  526 (693)
T ss_pred             CCCceEEEECCCCcchHHHHHHHhhh-hcCCe-----eeccCH----HHHHHh---------cCchHHHHHHHHHHHhhc
Confidence            34577899999999999999998874 23333     322211    111111         111112222222222233


Q ss_pred             CcEEEEEeCCCCCCh-----------hhHHHhhccccCCCCC-cEEEEEeCchh--HHH-hhc---CCCeEeCCCCChhh
Q 000887           91 KKFLIVLDDVWSERY-----------DLWQALKSPFMAGAPG-SRIIVTTRSMD--VAL-TMG---SGKNYELKLLSDDD  152 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~-----------~~~~~~~~~~~~~~~~-~~iliTtR~~~--~~~-~~~---~~~~~~l~~l~~~e  152 (1237)
                      -+++|.||.++....           -.+..+..-+...... .-+||...++.  +.. -+.   -+..+.++.-+.+.
T Consensus       527 aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~a  606 (693)
T KOG0730|consen  527 APCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEA  606 (693)
T ss_pred             CCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHH
Confidence            578999998843110           0111222222222222 22333333322  211 122   33567777777777


Q ss_pred             hHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCc
Q 000887          153 CWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       153 a~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~P  188 (1237)
                      -.++|+.++.+-... ++    -...+|+++..|.-
T Consensus       607 R~~Ilk~~~kkmp~~-~~----vdl~~La~~T~g~S  637 (693)
T KOG0730|consen  607 RLEILKQCAKKMPFS-ED----VDLEELAQATEGYS  637 (693)
T ss_pred             HHHHHHHHHhcCCCC-cc----ccHHHHHHHhccCC
Confidence            788999887432221 11    12456776666544

>COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=94.73  E-value=0.57  Score=44.45  Aligned_cols=83  Identities=14%  Similarity=0.155  Sum_probs=54.0

Q ss_pred             CHHHHHHHHHHHhhccC------CCccCHHHHHHHHHHHhcCCcEEEEEeCCC----CCChhhHHHhhccccCCCCCcEE
Q 000887           55 DVLRISKAILDSIKRSS------CKLEDLNSVQLELKETVFKKKFLIVLDDVW----SERYDLWQALKSPFMAGAPGSRI  124 (1237)
Q Consensus        55 ~~~~~~~~i~~~l~~~~------~~~~~~~~~~~~l~~~l~~~~~LlvlDdv~----~~~~~~~~~~~~~~~~~~~~~~i  124 (1237)
                      +.....+..+.+++...      .+....++.+-.+.+.+..++-+++-|.-.    ..+.+...++...+ ....|..+
T Consensus       122 ~~~~~A~~lL~~vGLg~Rl~HyP~qLSGGEQQRVAiARAfa~~P~vLfADEPTGNLD~~Tg~~iaDLlF~l-nre~G~Tl  200 (228)
T COG4181         122 DSRAGAKALLEAVGLGKRLTHYPAQLSGGEQQRVALARAFAGRPDVLFADEPTGNLDRATGDKIADLLFAL-NRERGTTL  200 (228)
T ss_pred             cHHHHHHHHHHHhCcccccccCccccCchHHHHHHHHHHhcCCCCEEeccCCCCCcchhHHHHHHHHHHHH-hhhcCceE
Confidence            45555666777766542      244566777778888889999999988752    22333333443333 23568888


Q ss_pred             EEEeCchhHHHhhc
Q 000887          125 IVTTRSMDVALTMG  138 (1237)
Q Consensus       125 liTtR~~~~~~~~~  138 (1237)
                      +..|-++.++.++.
T Consensus       201 VlVTHD~~LA~Rc~  214 (228)
T COG4181         201 VLVTHDPQLAARCD  214 (228)
T ss_pred             EEEeCCHHHHHhhh
Confidence            88888988887654

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=94.72  E-value=0.14  Score=52.03  Aligned_cols=85  Identities=15%  Similarity=0.173  Sum_probs=47.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccc-cCCCCeEEE-------EEcCCcCHHH--HHHHHHHHhhccCCC-------
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLT-EAFEPKAWV-------CVSDDFDVLR--ISKAILDSIKRSSCK-------   73 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~-~~f~~~~w~-------~~~~~~~~~~--~~~~i~~~l~~~~~~-------   73 (1237)
                      ..+.+|.++||+|+||||..++++.+.+. ...+.++=+       ......++++  -+++.+.+.+....+       
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPNGgI~TsLN   96 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHLHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPNGGIVTSLN   96 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHHhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCCcchhhhHH
Confidence            45678899999999999999998875532 222222221       1122234443  245566665544332       


Q ss_pred             --ccCHHHHHHHHHHHhcCCcEEE
Q 000887           74 --LEDLNSVQLELKETVFKKKFLI   95 (1237)
Q Consensus        74 --~~~~~~~~~~l~~~l~~~~~Ll   95 (1237)
                        ....++.+..+.+.-...++.|
T Consensus        97 LF~tk~dqv~~~iek~~~~~~~~l  120 (366)
T KOG1532|consen   97 LFATKFDQVIELIEKRAEEFDYVL  120 (366)
T ss_pred             HHHHHHHHHHHHHHHhhcccCEEE
Confidence              1345566666665544434443

>PF13245 AAA_19: Part of AAA domain

Probab=94.69  E-value=0.055  Score=44.80  Aligned_cols=26  Identities=27%  Similarity=0.257  Sum_probs=19.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL   38 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~   38 (1237)
                      -+++.|.|++|.|||+++.+.+....
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            45788999999999977776655443

>PRK06217 hypothetical protein; Validated

Probab=94.68  E-value=0.11  Score=52.43  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ..|+|.|.+|+||||+|+++++..
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999998754

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=94.68  E-value=0.16  Score=56.09  Aligned_cols=56  Identities=21%  Similarity=0.162  Sum_probs=39.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc-cc----cCCCCeEEEEEcCCcCHHHHHHHHHHHhhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK-LT----EAFEPKAWVCVSDDFDVLRISKAILDSIKR   69 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~-~~----~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~   69 (1237)
                      -+++-|+|.+|+|||+|+.+++-.. ..    ..-..++|++....++..++.+ ++.+++.
T Consensus       126 G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~  186 (344)
T PLN03187        126 RCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGM  186 (344)
T ss_pred             CeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            3677899999999999999976422 21    1124678999888777776654 4555543

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.67  E-value=0.022  Score=55.27  Aligned_cols=24  Identities=42%  Similarity=0.573  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +.|.+.|.+|+||||+|++++...
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L   25 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKEL   25 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHH
Confidence            578899999999999999988743

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.66  E-value=0.74  Score=50.59  Aligned_cols=49  Identities=18%  Similarity=0.123  Sum_probs=35.1

Q ss_pred             eEeCCCCChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHH
Q 000887          142 NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       142 ~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal  191 (1237)
                      ++++++++.+|+..++.-......-.. ....+...+++.-..+|+|--+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~-~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRS-RVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCcccc-CCCCHHHHHHHHHhcCCCHHHh
Confidence            789999999999999988774333222 1334556777777779999654

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.66  E-value=0.16  Score=57.47  Aligned_cols=87  Identities=21%  Similarity=0.234  Sum_probs=49.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      .-.+++++|+.|+||||++..++.... ....+.+..+...... ...+-+...++.++.+.....+..+....+.. ++
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al~~-l~  268 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLMLHE-LR  268 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHHHHHHHHH-hc
Confidence            347999999999999999999877432 2233444555443322 22223444555555544444444554444333 33


Q ss_pred             CCcEEEEEeCC
Q 000887           90 KKKFLIVLDDV  100 (1237)
Q Consensus        90 ~~~~LlvlDdv  100 (1237)
                      + .-++++|-+
T Consensus       269 ~-~d~VLIDTa  278 (420)
T PRK14721        269 G-KHMVLIDTV  278 (420)
T ss_pred             C-CCEEEecCC
Confidence            3 345667776

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=94.66  E-value=0.13  Score=56.87  Aligned_cols=55  Identities=16%  Similarity=0.147  Sum_probs=38.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc-ccc----CCCCeEEEEEcCCcCHHHHHHHHHHHhh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK-LTE----AFEPKAWVCVSDDFDVLRISKAILDSIK   68 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~-~~~----~f~~~~w~~~~~~~~~~~~~~~i~~~l~   68 (1237)
                      -.++-|+|.+|+|||++|..++... ...    .-..++|++....++.+++. +++..++
T Consensus       123 g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~  182 (342)
T PLN03186        123 GSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFG  182 (342)
T ss_pred             ceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcC
Confidence            4678899999999999999876432 111    11258899988887776654 4555554

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=94.62  E-value=0.2  Score=50.99  Aligned_cols=22  Identities=36%  Similarity=0.521  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        34 e~~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          34 TLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999885

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=94.62  E-value=0.13  Score=56.96  Aligned_cols=54  Identities=17%  Similarity=0.201  Sum_probs=37.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-c----CCCCeEEEEEcCCcCHHHHHHHHHHHh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-E----AFEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~----~f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      -+++-|+|.+|+|||++|.+++..... .    .-..++|++....++...+. +++..+
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~  153 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEAR  153 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHc
Confidence            478899999999999999998764321 1    11268899988777766554 334443

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=94.59  E-value=0.14  Score=55.84  Aligned_cols=80  Identities=26%  Similarity=0.324  Sum_probs=52.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      .+|.|-|-+|||||||..+++++..+..  .+.||+-...  ..++ +--+.+++....     ...+.+++...+.+  
T Consensus        94 s~iLIgGdPGIGKSTLLLQva~~lA~~~--~vLYVsGEES--~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~~--  166 (456)
T COG1066          94 SVILIGGDPGIGKSTLLLQVAARLAKRG--KVLYVSGEES--LQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELEQ--  166 (456)
T ss_pred             cEEEEccCCCCCHHHHHHHHHHHHHhcC--cEEEEeCCcC--HHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHHh--
Confidence            5789999999999999999988654333  6888864333  3222 223445553322     23456665555554  


Q ss_pred             cCCcEEEEEeCCC
Q 000887           89 FKKKFLIVLDDVW  101 (1237)
Q Consensus        89 ~~~~~LlvlDdv~  101 (1237)
                       .++-++|+|.+.
T Consensus       167 -~~p~lvVIDSIQ  178 (456)
T COG1066         167 -EKPDLVVIDSIQ  178 (456)
T ss_pred             -cCCCEEEEeccc
Confidence             589999999983

>PRK05973 replicative DNA helicase; Provisional

Probab=94.59  E-value=0.11  Score=53.78  Aligned_cols=39  Identities=18%  Similarity=0.187  Sum_probs=29.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      .++.|.|.+|+|||++|.+++....++ -..++|++....
T Consensus        65 sl~LIaG~PG~GKT~lalqfa~~~a~~-Ge~vlyfSlEes  103 (237)
T PRK05973         65 DLVLLGARPGHGKTLLGLELAVEAMKS-GRTGVFFTLEYT  103 (237)
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEEEEeCC
Confidence            588999999999999999987644443 345777776554

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.58  E-value=0.15  Score=55.90  Aligned_cols=90  Identities=12%  Similarity=0.038  Sum_probs=48.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcC--HHHHHHHHHHHhhccC---CCccCHH-HHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD--VLRISKAILDSIKRSS---CKLEDLN-SVQLEL   84 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~--~~~~~~~i~~~l~~~~---~~~~~~~-~~~~~l   84 (1237)
                      ....+++++|++|+||||++..++........ .+..++......  ..+ +...+...+.+.   ....++. .....+
T Consensus       112 ~~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~-~V~Li~~D~~r~~a~eq-l~~~a~~~~i~~~~~~~~~dpa~~v~~~l  189 (318)
T PRK10416        112 KKPFVILVVGVNGVGKTTTIGKLAHKYKAQGK-KVLLAAGDTFRAAAIEQ-LQVWGERVGVPVIAQKEGADPASVAFDAI  189 (318)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhcCC-eEEEEecCccchhhHHH-HHHHHHHcCceEEEeCCCCCHHHHHHHHH
Confidence            45689999999999999999999875433322 355554432211  111 112233333221   1112222 223344


Q ss_pred             HHHhcCCcEEEEEeCCCC
Q 000887           85 KETVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~~  102 (1237)
                      .....+.-=++|+|-.-.
T Consensus       190 ~~~~~~~~D~ViIDTaGr  207 (318)
T PRK10416        190 QAAKARGIDVLIIDTAGR  207 (318)
T ss_pred             HHHHhCCCCEEEEeCCCC
Confidence            444445556888898843

>PLN02924 thymidylate kinase

Probab=94.57  E-value=0.14  Score=53.00  Aligned_cols=33  Identities=18%  Similarity=0.112  Sum_probs=26.5

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP   44 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~   44 (1237)
                      .-..|+|-|..|+||||+|..+++......+..
T Consensus        15 ~g~~IviEGiDGsGKsTq~~~L~~~l~~~g~~v   47 (220)
T PLN02924         15 RGALIVLEGLDRSGKSTQCAKLVSFLKGLGVAA   47 (220)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCCc
Confidence            346899999999999999999988655555553

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.57  E-value=0.069  Score=57.09  Aligned_cols=23  Identities=35%  Similarity=0.660  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +|.++|++|+||||+|++++...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l   23 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKL   23 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            47899999999999999988754

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.56  E-value=0.11  Score=56.87  Aligned_cols=55  Identities=20%  Similarity=0.212  Sum_probs=38.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc-cc----cCCCCeEEEEEcCCcCHHHHHHHHHHHhhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LT----EAFEPKAWVCVSDDFDVLRISKAILDSIKR   69 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~-~~----~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~   69 (1237)
                      +++-|+|.+|+|||++|.+++... ..    ..-..++|++....++.+++.+ ++.+++.
T Consensus        97 ~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~  156 (313)
T TIGR02238        97 SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGV  156 (313)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            678899999999999999876422 11    1124688999888777776653 4555543

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=94.56  E-value=0.067  Score=54.56  Aligned_cols=22  Identities=23%  Similarity=0.225  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      ++++|.|+.|.||||+.+.++.
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            7999999999999999999865

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.55  E-value=0.11  Score=63.96  Aligned_cols=93  Identities=14%  Similarity=0.177  Sum_probs=49.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-CC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-KK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~   91 (1237)
                      ...+.++|++|+|||.+|+.++... .   ...+.++++......    .+..-++.+.... ..++ ...+.+.++ ..
T Consensus       488 ~~~~Lf~GP~GvGKT~lAk~LA~~l-~---~~~i~id~se~~~~~----~~~~LiG~~~gyv-g~~~-~g~L~~~v~~~p  557 (758)
T PRK11034        488 VGSFLFAGPTGVGKTEVTVQLSKAL-G---IELLRFDMSEYMERH----TVSRLIGAPPGYV-GFDQ-GGLLTDAVIKHP  557 (758)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHh-C---CCcEEeechhhcccc----cHHHHcCCCCCcc-cccc-cchHHHHHHhCC
Confidence            4578999999999999999987743 2   233455544322111    1222223221110 0010 112223333 34


Q ss_pred             cEEEEEeCCCCCChhhHHHhhccc
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPF  115 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~~~~~~  115 (1237)
                      ..+|+||+++..+.+.+..+...+
T Consensus       558 ~sVlllDEieka~~~v~~~LLq~l  581 (758)
T PRK11034        558 HAVLLLDEIEKAHPDVFNLLLQVM  581 (758)
T ss_pred             CcEEEeccHhhhhHHHHHHHHHHH
Confidence            579999999766555555554433

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=94.55  E-value=0.093  Score=57.58  Aligned_cols=35  Identities=23%  Similarity=0.305  Sum_probs=24.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCV   50 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~   50 (1237)
                      ++++.|++|+||||+++.+++... ...+ .+.+++.
T Consensus         1 ~~~l~Gl~GaGKST~~~~l~~~l~~~~g~-~v~~~~~   36 (340)
T TIGR03575         1 LCVLCGLPAAGKSTLARSLSATLRRERGW-AVAVITY   36 (340)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHhccCC-eEEEEcc
Confidence            368999999999999999887543 3333 3445544

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=94.54  E-value=0.15  Score=47.97  Aligned_cols=109  Identities=20%  Similarity=0.298  Sum_probs=57.1

Q ss_pred             CCCCcccEEeccCCCCccccCCCCC--CCCcCceEecCCCCcccccccccCCCCCCceEEEcCCCCceeccCCCCccccC
Q 000887         1059 GTLSSLRELALSECPGIVVFPEEGL--STNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILP 1136 (1237)
Q Consensus      1059 ~~l~~L~~L~l~~c~~l~~~~~~~~--~~~L~~L~l~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~ 1136 (1237)
                      ..+++|+.+.+..  .+..++...+  +++|+.+.+.+.  +..+....|.++++|+.+.+.+  .+..++.  ..+...
T Consensus         9 ~~~~~l~~i~~~~--~~~~I~~~~F~~~~~l~~i~~~~~--~~~i~~~~F~~~~~l~~i~~~~--~~~~i~~--~~F~~~   80 (129)
T PF13306_consen    9 YNCSNLESITFPN--TIKKIGENAFSNCTSLKSINFPNN--LTSIGDNAFSNCKSLESITFPN--NLKSIGD--NAFSNC   80 (129)
T ss_dssp             TT-TT--EEEETS--T--EE-TTTTTT-TT-SEEEESST--TSCE-TTTTTT-TT-EEEEETS--TT-EE-T--TTTTT-
T ss_pred             hCCCCCCEEEECC--CeeEeChhhccccccccccccccc--ccccceeeeecccccccccccc--ccccccc--cccccc
Confidence            4667788888764  4566666633  567888888763  6666666788887888888865  4555554  344456


Q ss_pred             CCcCeeeecCCCCccccCcccCCCCCCCCeeeecCCCCcccCCC
Q 000887         1137 TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPE 1180 (1237)
Q Consensus      1137 ~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~ 1180 (1237)
                      ++|+.+++..  .+..++...|.++ .|+.+.+..  .++.++.
T Consensus        81 ~~l~~i~~~~--~~~~i~~~~f~~~-~l~~i~~~~--~~~~i~~  119 (129)
T PF13306_consen   81 TNLKNIDIPS--NITEIGSSSFSNC-NLKEINIPS--NITKIEE  119 (129)
T ss_dssp             TTECEEEETT--T-BEEHTTTTTT--T--EEE-TT--B-SS---
T ss_pred             ccccccccCc--cccEEchhhhcCC-CceEEEECC--CccEECC
Confidence            7788888754  3666776777776 777777654  4444444

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.53  E-value=0.056  Score=54.72  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +|.|.|++|+||||+|+.++..
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999999998874

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK06696 uridine kinase; Validated

Probab=94.51  E-value=0.033  Score=58.33  Aligned_cols=28  Identities=25%  Similarity=0.317  Sum_probs=24.6

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+++.+|+|.|.+|+||||+|.++++..
T Consensus        19 ~~~~~iI~I~G~sgsGKSTlA~~L~~~l   46 (223)
T PRK06696         19 LTRPLRVAIDGITASGKTTFADELAEEI   46 (223)
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            3568899999999999999999998753

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=94.51  E-value=0.37  Score=45.49  Aligned_cols=21  Identities=38%  Similarity=0.553  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+.|.|++|+|||||.++++.
T Consensus        31 ~iaitGPSG~GKStllk~va~   51 (223)
T COG4619          31 FIAITGPSGCGKSTLLKIVAS   51 (223)
T ss_pred             eEEEeCCCCccHHHHHHHHHh
Confidence            589999999999999999886

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=94.50  E-value=0.093  Score=54.85  Aligned_cols=57  Identities=25%  Similarity=0.197  Sum_probs=38.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc--cccCCC-------CeEEEEEcCC-cCHHHHHHHHHHHhhccC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK--LTEAFE-------PKAWVCVSDD-FDVLRISKAILDSIKRSS   71 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~--~~~~f~-------~~~w~~~~~~-~~~~~~~~~i~~~l~~~~   71 (1237)
                      ++.|+|.||+|||+++...+=..  -++.|.       .++++++... .++..-++.+..+++.+.
T Consensus        91 ~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~mgLsP  157 (402)
T COG3598          91 VSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRARMGLSP  157 (402)
T ss_pred             eEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHHcCCCh
Confidence            34567999999999998854322  234443       5678887654 356666677777777654

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=94.50  E-value=0.13  Score=55.41  Aligned_cols=80  Identities=15%  Similarity=0.028  Sum_probs=42.2

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCC--CCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF--EPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f--~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      ..+.+|||.|..|+||||+|+.+.. ......  ..+..+....-....+........-........+.+.....+.+..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~-ll~~~~~~g~V~vi~~D~f~~~~~~l~~~g~~~~~g~P~s~D~~~l~~~L~~Lk  138 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA-LLSRWPEHRKVELITTDGFLHPNQVLKERNLMKKKGFPESYDMHRLVKFLSDLK  138 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH-HHhhcCCCCceEEEecccccccHHHHHHcCCccccCCChhccHHHHHHHHHHHH
Confidence            5678999999999999999987654 322222  1244454433322222222211000011124456666666666654


Q ss_pred             cCC
Q 000887           89 FKK   91 (1237)
Q Consensus        89 ~~~   91 (1237)
                      .++
T Consensus       139 ~g~  141 (290)
T TIGR00554       139 SGK  141 (290)
T ss_pred             CCC
Confidence            443

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.49  E-value=0.78  Score=53.63  Aligned_cols=152  Identities=18%  Similarity=0.156  Sum_probs=79.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFL   94 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~L   94 (1237)
                      =|.++|++|.|||-||.+++...      ..-++++-..       +-+.+.+|..      .+..+..+.+.-..++|+
T Consensus       703 giLLyGppGcGKT~la~a~a~~~------~~~fisvKGP-------ElL~KyIGaS------Eq~vR~lF~rA~~a~PCi  763 (952)
T KOG0735|consen  703 GILLYGPPGCGKTLLASAIASNS------NLRFISVKGP-------ELLSKYIGAS------EQNVRDLFERAQSAKPCI  763 (952)
T ss_pred             ceEEECCCCCcHHHHHHHHHhhC------CeeEEEecCH-------HHHHHHhccc------HHHHHHHHHHhhccCCeE
Confidence            47899999999999999988742      1225655443       2222333322      122233333333469999


Q ss_pred             EEEeCCCCCC-------hh----hHHHhhccccC--CCCCcEEEE-EeCchhHHHhh-c---CCCeEeCCCCChhhhHHH
Q 000887           95 IVLDDVWSER-------YD----LWQALKSPFMA--GAPGSRIIV-TTRSMDVALTM-G---SGKNYELKLLSDDDCWSV  156 (1237)
Q Consensus        95 lvlDdv~~~~-------~~----~~~~~~~~~~~--~~~~~~ili-TtR~~~~~~~~-~---~~~~~~l~~l~~~ea~~l  156 (1237)
                      +.||..++..       ..    .+.++...+..  +-.|..|+- |||-..+.... +   -++.+.=+.-++.|-.++
T Consensus       764 LFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~i  843 (952)
T KOG0735|consen  764 LFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEI  843 (952)
T ss_pred             EEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHH
Confidence            9999996521       11    11222222211  124555554 55543322211 1   123444455567788888


Q ss_pred             HHHHhcCCCCCCCCCChHHHHHHHHHHccCCchH
Q 000887          157 FVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLa  190 (1237)
                      |+..+..-....     ....+.++.+.+|.--|
T Consensus       844 l~~ls~s~~~~~-----~vdl~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  844 LQVLSNSLLKDT-----DVDLECLAQKTDGFTGA  872 (952)
T ss_pred             HHHHhhccCCcc-----ccchHHHhhhcCCCchh
Confidence            887663211111     12245777777776543

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=94.49  E-value=0.13  Score=50.44  Aligned_cols=119  Identities=18%  Similarity=0.164  Sum_probs=63.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .+++|.|..|.|||||++.++...  ....+.+++.-......  ........+.... +....+...-.+...+...+=
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~~--~~~~G~i~~~~~~~~~~--~~~~~~~~i~~~~-qlS~G~~~r~~l~~~l~~~~~  100 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGLL--KPTSGEILIDGKDIAKL--PLEELRRRIGYVP-QLSGGQRQRVALARALLLNPD  100 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC--CCCccEEEECCEEcccC--CHHHHHhceEEEe-eCCHHHHHHHHHHHHHhcCCC
Confidence            589999999999999999987632  23445555532211110  0111111122111 122334444455666666788


Q ss_pred             EEEEeCCCCCC-hhhHHHhhccccCC-CCCcEEEEEeCchhHHHhh
Q 000887           94 LIVLDDVWSER-YDLWQALKSPFMAG-APGSRIIVTTRSMDVALTM  137 (1237)
Q Consensus        94 LlvlDdv~~~~-~~~~~~~~~~~~~~-~~~~~iliTtR~~~~~~~~  137 (1237)
                      ++++|+....- ......+...+... ..+..++++|.+.......
T Consensus       101 i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~~~  146 (157)
T cd00267         101 LLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAELA  146 (157)
T ss_pred             EEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHh
Confidence            99999985421 11222222222211 1256788888887766543

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=94.47  E-value=0.47  Score=49.08  Aligned_cols=22  Identities=36%  Similarity=0.599  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        35 ~~~~i~G~nGsGKSTLl~~l~G   56 (207)
T cd03369          35 EKIGIVGRTGAGKSTLILALFR   56 (207)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4799999999999999999875

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=94.47  E-value=0.22  Score=61.97  Aligned_cols=138  Identities=17%  Similarity=0.151  Sum_probs=70.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      -.++.++|++|+|||++|+.++... ...|   +-+.++...+...+...-...      ...........+... ....
T Consensus       349 g~~i~l~GppG~GKTtl~~~ia~~l-~~~~---~~i~~~~~~d~~~i~g~~~~~------~g~~~G~~~~~l~~~-~~~~  417 (784)
T PRK10787        349 GPILCLVGPPGVGKTSLGQSIAKAT-GRKY---VRMALGGVRDEAEIRGHRRTY------IGSMPGKLIQKMAKV-GVKN  417 (784)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh-CCCE---EEEEcCCCCCHHHhccchhcc------CCCCCcHHHHHHHhc-CCCC
Confidence            3579999999999999999988743 2222   234444444432222111001      111122233333322 2234


Q ss_pred             EEEEEeCCCCCChh----hHHHhhccccC---------------CCCCcEEEEEeCchhHHHhh-cCCCeEeCCCCChhh
Q 000887           93 FLIVLDDVWSERYD----LWQALKSPFMA---------------GAPGSRIIVTTRSMDVALTM-GSGKNYELKLLSDDD  152 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~----~~~~~~~~~~~---------------~~~~~~iliTtR~~~~~~~~-~~~~~~~l~~l~~~e  152 (1237)
                      -++++|.++....+    ..+++...+-+               .-.+.-+|.|+....+...+ +...++++.+++++|
T Consensus       418 ~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~ee  497 (784)
T PRK10787        418 PLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLSGYTEDE  497 (784)
T ss_pred             CEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCCCCCHHHhcceeeeecCCCCHHH
Confidence            47889999543211    12333332221               11334455555543332222 222578899999998


Q ss_pred             hHHHHHHHh
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      -.++.+.+.
T Consensus       498 k~~Ia~~~L  506 (784)
T PRK10787        498 KLNIAKRHL  506 (784)
T ss_pred             HHHHHHHhh
Confidence            888877665

>PRK05439 pantothenate kinase; Provisional

Probab=94.46  E-value=0.2  Score=54.21  Aligned_cols=83  Identities=13%  Similarity=-0.005  Sum_probs=44.1

Q ss_pred             CCCCcEEEEEEcCCCCcHHHHHHHHHhccccc-CCCCeEEEEEcCCcCHHHHHHHHHHHhh-ccCCCccCHHHHHHHHHH
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAILDSIK-RSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus         9 ~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~i~~~l~-~~~~~~~~~~~~~~~l~~   86 (1237)
                      ..+.+-+|+|.|.+|+||||+|+.+.....+. ....+.-++..+-....+.+..- ..+. ......-+.+.....+..
T Consensus        82 ~~~~~~iIgIaG~~gsGKSTla~~L~~~l~~~~~~~~v~vi~~DdFy~~~~~l~~~-~l~~~kg~Pes~D~~~l~~~L~~  160 (311)
T PRK05439         82 GQKVPFIIGIAGSVAVGKSTTARLLQALLSRWPEHPKVELVTTDGFLYPNAVLEER-GLMKRKGFPESYDMRALLRFLSD  160 (311)
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHhhCCCCceEEEeccccccCHHHHhhh-hccccCCCcccccHHHHHHHHHH
Confidence            34567899999999999999999987632221 11234444433322222221110 1111 111234566666666666


Q ss_pred             HhcCCc
Q 000887           87 TVFKKK   92 (1237)
Q Consensus        87 ~l~~~~   92 (1237)
                      ...++.
T Consensus       161 Lk~G~~  166 (311)
T PRK05439        161 VKSGKP  166 (311)
T ss_pred             HHcCCC
Confidence            655554

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.42  E-value=0.17  Score=54.08  Aligned_cols=41  Identities=20%  Similarity=0.379  Sum_probs=31.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      .-+++.|.|.+|+|||++|.+++....+. -..++|++....
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~-Ge~vlyis~Ee~   75 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR-GNPVLFVTVESP   75 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC-CCcEEEEEecCC
Confidence            34789999999999999999986643333 346788887643

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK07667 uridine kinase; Provisional

Probab=94.40  E-value=0.046  Score=55.59  Aligned_cols=27  Identities=22%  Similarity=0.342  Sum_probs=23.5

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ++..+|+|.|.+|+||||+|..+++..
T Consensus        15 ~~~~iIgI~G~~gsGKStla~~L~~~l   41 (193)
T PRK07667         15 ENRFILGIDGLSRSGKTTFVANLKENM   41 (193)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            455899999999999999999988743

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=94.37  E-value=0.34  Score=52.55  Aligned_cols=42  Identities=19%  Similarity=0.284  Sum_probs=29.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRI   59 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~   59 (1237)
                      +.|.|.|++|+|||++|+.+++.. ..   ..+.+.+....+..++
T Consensus        65 ~~ilL~G~pGtGKTtla~~lA~~l-~~---~~~rV~~~~~l~~~Dl  106 (327)
T TIGR01650        65 RRVMVQGYHGTGKSTHIEQIAARL-NW---PCVRVNLDSHVSRIDL  106 (327)
T ss_pred             CcEEEEeCCCChHHHHHHHHHHHH-CC---CeEEEEecCCCChhhc
Confidence            458999999999999999998743 21   2345655555444333

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=94.36  E-value=0.32  Score=59.56  Aligned_cols=130  Identities=17%  Similarity=0.144  Sum_probs=68.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +-|.++|++|+|||++|+.++... ...|   +.++.++      +....   .      ..........+.......++
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~-~~~f---~~is~~~------~~~~~---~------g~~~~~~~~~f~~a~~~~P~  246 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEA-KVPF---FTISGSD------FVEMF---V------GVGASRVRDMFEQAKKAAPC  246 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc-CCCE---EEEehHH------hHHhh---h------cccHHHHHHHHHHHHhcCCc
Confidence            348999999999999999987742 2111   2222111      11100   0      01112223333333345789


Q ss_pred             EEEEeCCCCCC----------hhhH----HHhhccccCC--CCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCChhh
Q 000887           94 LIVLDDVWSER----------YDLW----QALKSPFMAG--APGSRIIVTTRSMDVALT-M----GSGKNYELKLLSDDD  152 (1237)
Q Consensus        94 LlvlDdv~~~~----------~~~~----~~~~~~~~~~--~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~~e  152 (1237)
                      +|++|+++.-.          ....    ..+...+...  ..+.-+|.||..++.... .    .-+..+.++..+.++
T Consensus       247 IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~  326 (644)
T PRK10733        247 IIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRG  326 (644)
T ss_pred             EEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHH
Confidence            99999994420          0011    1111111111  234445556766543221 1    123578888888888


Q ss_pred             hHHHHHHHhc
Q 000887          153 CWSVFVAHAF  162 (1237)
Q Consensus       153 a~~l~~~~~~  162 (1237)
                      ..++++.+..
T Consensus       327 R~~Il~~~~~  336 (644)
T PRK10733        327 REQILKVHMR  336 (644)
T ss_pred             HHHHHHHHhh
Confidence            8888888764

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=94.34  E-value=0.038  Score=55.44  Aligned_cols=26  Identities=35%  Similarity=0.526  Sum_probs=23.6

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..+.+|||.|.+|+||||+|++++..
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~~   31 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHHH
Confidence            56789999999999999999998874

>PRK06762 hypothetical protein; Provisional

Probab=94.34  E-value=0.036  Score=55.08  Aligned_cols=24  Identities=33%  Similarity=0.488  Sum_probs=21.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +++|+|.|++|+||||+|++++..
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998764

>PRK06547 hypothetical protein; Provisional

Probab=94.34  E-value=0.042  Score=54.31  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=23.3

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ....+|+|.|++|+||||+|..+++.
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            56789999999999999999998874

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.33  E-value=0.18  Score=56.69  Aligned_cols=80  Identities=23%  Similarity=0.221  Sum_probs=48.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      .++.|.|.+|+|||+|+.+++....+. -..++|++....  ..++. .-+.+++....     ...+.+++...+.   
T Consensus        83 slvLI~G~pG~GKStLllq~a~~~a~~-g~~VlYvs~EEs--~~qi~-~Ra~rlg~~~~~l~l~~e~~le~I~~~i~---  155 (372)
T cd01121          83 SVILIGGDPGIGKSTLLLQVAARLAKR-GGKVLYVSGEES--PEQIK-LRADRLGISTENLYLLAETNLEDILASIE---  155 (372)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhc-CCeEEEEECCcC--HHHHH-HHHHHcCCCcccEEEEccCcHHHHHHHHH---
Confidence            689999999999999999988744332 245778875432  33322 22334443221     1233444444443   


Q ss_pred             cCCcEEEEEeCC
Q 000887           89 FKKKFLIVLDDV  100 (1237)
Q Consensus        89 ~~~~~LlvlDdv  100 (1237)
                      ..+.-+||+|.+
T Consensus       156 ~~~~~lVVIDSI  167 (372)
T cd01121         156 ELKPDLVIIDSI  167 (372)
T ss_pred             hcCCcEEEEcch
Confidence            236778999998

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=94.32  E-value=0.04  Score=57.17  Aligned_cols=26  Identities=35%  Similarity=0.571  Sum_probs=23.2

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+..+|+|.|.+|+||||||+.++..
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            35689999999999999999998874

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.32  E-value=0.25  Score=58.94  Aligned_cols=22  Identities=32%  Similarity=0.472  Sum_probs=19.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .-|.|+|.+|+|||++|+.+++
T Consensus        87 ~~vLi~Ge~GtGKt~lAr~i~~  108 (531)
T TIGR02902        87 QHVIIYGPPGVGKTAAARLVLE  108 (531)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999865

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=94.31  E-value=0.13  Score=51.51  Aligned_cols=26  Identities=42%  Similarity=0.433  Sum_probs=22.5

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.++=|.++|++|.|||.||++|+++
T Consensus       187 dpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  187 DPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             CCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            44566889999999999999999884

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=94.29  E-value=0.28  Score=50.75  Aligned_cols=65  Identities=14%  Similarity=0.086  Sum_probs=37.0

Q ss_pred             HHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchhHHHhhcCCCeEeCCCCCh
Q 000887           83 ELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMDVALTMGSGKNYELKLLSD  150 (1237)
Q Consensus        83 ~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~~~~~~~~~~~~l~~l~~  150 (1237)
                      .+...+-.++-++++|+-... +......+...+.. ...|..||++|.+......   ..++.++.+..
T Consensus       137 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~~~~~~---~~~~~~~~~~~  203 (207)
T PRK13539        137 ALARLLVSNRPIWILDEPTAALDAAAVALFAELIRAHLAQGGIVIAATHIPLGLPG---ARELDLGPFAA  203 (207)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCchhhcc---CcEEeecCccC
Confidence            345555667889999997442 11222233333322 1236678999888765533   55677666443

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=94.28  E-value=0.24  Score=51.87  Aligned_cols=22  Identities=32%  Similarity=0.490  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|+|||||++.++.
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~G   50 (220)
T cd03263          29 EIFGLLGHNGAGKTTTLKMLTG   50 (220)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            3899999999999999999876

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=94.28  E-value=0.15  Score=57.78  Aligned_cols=85  Identities=15%  Similarity=0.110  Sum_probs=47.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhcc-----CCCccCHH------HHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRS-----SCKLEDLN------SVQL   82 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~-----~~~~~~~~------~~~~   82 (1237)
                      ..++|+|.+|+|||||+..++...  ....++++..-.+..++..+...........     ........      ...-
T Consensus       166 qri~I~G~SGsGKTTLL~~Ia~l~--~pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~~a~  243 (450)
T PRK06002        166 QRIGIFAGSGVGKSTLLAMLARAD--AFDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPLTAT  243 (450)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC--CCCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHHHHH
Confidence            478999999999999999876532  1122344443334555555444433332111     11111111      1112


Q ss_pred             HHHHHh--cCCcEEEEEeCC
Q 000887           83 ELKETV--FKKKFLIVLDDV  100 (1237)
Q Consensus        83 ~l~~~l--~~~~~LlvlDdv  100 (1237)
                      .+.+++  +++++|+++||+
T Consensus       244 ~iAEyfrd~G~~Vll~~Dsl  263 (450)
T PRK06002        244 AIAEYFRDRGENVLLIVDSV  263 (450)
T ss_pred             HHHHHHHHcCCCEEEeccch
Confidence            234444  368999999999

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=94.28  E-value=0.052  Score=51.51  Aligned_cols=39  Identities=23%  Similarity=0.314  Sum_probs=30.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSD   52 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~   52 (1237)
                      ++|.|+|..|+|||||++.+.+...++.+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRRGYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHcCCceEEEEEccC
Confidence            589999999999999999999876667777666777655

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.26  E-value=0.23  Score=50.84  Aligned_cols=21  Identities=29%  Similarity=0.553  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .|+|.|++|+|||||.+.++.
T Consensus        31 fvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            799999999999999999876

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=94.26  E-value=0.037  Score=53.35  Aligned_cols=22  Identities=41%  Similarity=0.558  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +|.+.|++|+||||+|++++..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~   22 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKR   22 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6889999999999999998753

...

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=94.25  E-value=0.27  Score=50.51  Aligned_cols=120  Identities=17%  Similarity=0.083  Sum_probs=60.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEE-------------------cCCcCH--HHHHHHHHHHhhccCC
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV-------------------SDDFDV--LRISKAILDSIKRSSC   72 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~-------------------~~~~~~--~~~~~~i~~~l~~~~~   72 (1237)
                      .+++|.|..|.|||||++.++.......-.+.+.++-                   .+....  .....+++..   ...
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~~~~p~~G~i~~~g~~~~~~~~~~~~~~~i~~v~q~~~~~~~~~~~~~l~~---~~~  103 (200)
T cd03217          27 EVHALMGPNGSGKSTLAKTIMGHPKYEVTEGEILFKGEDITDLPPEERARLGIFLAFQYPPEIPGVKNADFLRY---VNE  103 (200)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCCCccEEEECCEECCcCCHHHHhhCcEEEeecChhhccCccHHHHHhh---ccc
Confidence            4899999999999999999877410011112222210                   111000  0001111111   111


Q ss_pred             CccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCC-CCCcEEEEEeCchhHHHh
Q 000887           73 KLEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAG-APGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        73 ~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~-~~~~~iliTtR~~~~~~~  136 (1237)
                      .....+...-.+.+.+-.++=++++|+.... +......+...+... ..+..||++|.+......
T Consensus       104 ~LS~G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~L~~~~~~~~tiii~sh~~~~~~~  169 (200)
T cd03217         104 GFSGGEKKRNEILQLLLLEPDLAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQRLLDY  169 (200)
T ss_pred             cCCHHHHHHHHHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCHHHHHH
Confidence            2223334444566666678889999998442 112222233322221 236678999988776543

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.24  E-value=0.25  Score=52.63  Aligned_cols=90  Identities=14%  Similarity=0.151  Sum_probs=50.2

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-   89 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-   89 (1237)
                      ...+++++|.+|+||||++..++....... ..+.+++..... ....-++..+..++.+.....+.++....+...-+ 
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~~-~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~  152 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGKK-KTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEE  152 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHcC-CeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHHHhc
Confidence            346999999999999999999876433222 235566654332 11111222333333222223445555544443322 


Q ss_pred             CCcEEEEEeCCCC
Q 000887           90 KKKFLIVLDDVWS  102 (1237)
Q Consensus        90 ~~~~LlvlDdv~~  102 (1237)
                      ++.-++|+|-.-.
T Consensus       153 ~~~D~ViIDt~Gr  165 (270)
T PRK06731        153 ARVDYILIDTAGK  165 (270)
T ss_pred             CCCCEEEEECCCC
Confidence            2467889999854

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=94.18  E-value=0.18  Score=55.53  Aligned_cols=55  Identities=18%  Similarity=0.148  Sum_probs=36.8

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcc-ccc----CCCCeEEEEEcCCcCHHHHHHHHHHHh
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK-LTE----AFEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~-~~~----~f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      .-.++.|+|.+|+|||++|..++... ...    .-..++|++....++...+ .+++..+
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~  154 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERY  154 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHc
Confidence            34789999999999999999986522 111    1135789987776666543 3344444

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PRK15453 phosphoribulokinase; Provisional

Probab=94.18  E-value=0.27  Score=51.74  Aligned_cols=79  Identities=18%  Similarity=0.093  Sum_probs=43.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc--CHHHHHHHHHH--Hhhc--cC--CCccCHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF--DVLRISKAILD--SIKR--SS--CKLEDLNSVQL   82 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~--~~~~~~~~i~~--~l~~--~~--~~~~~~~~~~~   82 (1237)
                      ....+|+|.|.+|+||||+|+++++.. +..-..++.+....-.  +.......+..  +-+.  .-  ....+.+.+..
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if-~~~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~~   81 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIF-RRENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELEQ   81 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH-hhcCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHHH
Confidence            456899999999999999999987632 2211223444433222  32222222211  1111  11  24566777777


Q ss_pred             HHHHHhcC
Q 000887           83 ELKETVFK   90 (1237)
Q Consensus        83 ~l~~~l~~   90 (1237)
                      .+++..++
T Consensus        82 ~l~~l~~~   89 (290)
T PRK15453         82 LFREYGET   89 (290)
T ss_pred             HHHHHhcC
Confidence            77766543

>PRK03846 adenylylsulfate kinase; Provisional

Probab=94.18  E-value=0.098  Score=53.59  Aligned_cols=27  Identities=26%  Similarity=0.313  Sum_probs=23.3

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ....+|+|+|++|+||||+|+.+....
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l   48 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEAL   48 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            456799999999999999999987743

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.17  E-value=0.16  Score=56.33  Aligned_cols=54  Identities=17%  Similarity=0.252  Sum_probs=38.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc-cC----CCCeEEEEEcCCcCHHHHHHHHHHHh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT-EA----FEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~-~~----f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      -.++-|+|.+|+|||++|.+++..... ..    -..++|++....++...+.+ ++..+
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~  160 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEAL  160 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHc
Confidence            468889999999999999998764321 11    13688999888777666543 33443

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=94.15  E-value=0.12  Score=52.88  Aligned_cols=117  Identities=15%  Similarity=0.169  Sum_probs=58.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCcc-------CHHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLE-------DLNSVQLELKE   86 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~-------~~~~~~~~l~~   86 (1237)
                      ++++|.|+.|.||||+.+.++......+.  .+++.+...  ...+...+...++..+....       +..+.. .+.+
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~~~~la~~--G~~vpa~~~--~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~-~il~  104 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIALLAIMAQI--GCFVPAEYA--TLPIFNRLLSRLSNDDSMERNLSTFASEMSETA-YILD  104 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHHHc--CCCcchhhc--CccChhheeEecCCccccchhhhHHHHHHHHHH-HHHH
Confidence            78999999999999999987643211111  111111110  01122222222222211100       111111 1111


Q ss_pred             HhcCCcEEEEEeCCCCCC-hhh----HHHhhccccCCCCCcEEEEEeCchhHHHhhc
Q 000887           87 TVFKKKFLIVLDDVWSER-YDL----WQALKSPFMAGAPGSRIIVTTRSMDVALTMG  138 (1237)
Q Consensus        87 ~l~~~~~LlvlDdv~~~~-~~~----~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~  138 (1237)
                       +..++-|+++|...... ..+    ..++...+..  .+..+|++|-+..+.....
T Consensus       105 -~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~--~~~~~i~~TH~~~l~~~~~  158 (204)
T cd03282         105 -YADGDSLVLIDELGRGTSSADGFAISLAILECLIK--KESTVFFATHFRDIAAILG  158 (204)
T ss_pred             -hcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHh--cCCEEEEECChHHHHHHhh
Confidence             23568899999974321 111    1223333332  3788999999988876554

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>CHL00206 ycf2 Ycf2; Provisional

Probab=94.14  E-value=0.39  Score=62.97  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=21.9

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .++=|.++|++|+|||-||+++|.+
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~e 1653 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATN 1653 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHh
Confidence            3556889999999999999999885

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.13  E-value=0.15  Score=58.24  Aligned_cols=88  Identities=18%  Similarity=0.201  Sum_probs=53.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhcc------CCCccCHH------HH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRS------SCKLEDLN------SV   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~------~~~~~~~~------~~   80 (1237)
                      ..++|.|.+|+|||+|+.++++...+.+-+.++++-++.. ..+.++..++...-...      ......+.      ..
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~  223 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNISKQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLT  223 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHH
Confidence            4689999999999999999887554445566667766543 34555555554322111      00111111      12


Q ss_pred             HHHHHHHhc---CCcEEEEEeCCC
Q 000887           81 QLELKETVF---KKKFLIVLDDVW  101 (1237)
Q Consensus        81 ~~~l~~~l~---~~~~LlvlDdv~  101 (1237)
                      +..+.++++   ++++|+++|++.
T Consensus       224 a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        224 GLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHhcCCceEEEeccch
Confidence            223445552   689999999993

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.13  E-value=0.46  Score=50.72  Aligned_cols=114  Identities=17%  Similarity=0.122  Sum_probs=59.7

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhc-cC-------CCccCHHHHHHH
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR-SS-------CKLEDLNSVQLE   83 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~-~~-------~~~~~~~~~~~~   83 (1237)
                      ..+-++|.|+.|+||||+.+.++.. .. ...+.+++.-.+ ....+...+++..... +.       +...+... ...
T Consensus       110 ~~~~~~i~g~~g~GKttl~~~l~~~-~~-~~~G~i~~~g~~-v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k-~~~  185 (270)
T TIGR02858       110 RVLNTLIISPPQCGKTTLLRDLARI-LS-TGISQLGLRGKK-VGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPK-AEG  185 (270)
T ss_pred             CeeEEEEEcCCCCCHHHHHHHHhCc-cC-CCCceEEECCEE-eecchhHHHHHHHhcccccccccccccccccchH-HHH
Confidence            3578999999999999999998863 22 223344442111 1111111233322211 10       01111111 112


Q ss_pred             HHHHhc-CCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHH
Q 000887           84 LKETVF-KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        84 l~~~l~-~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~  134 (1237)
                      +...++ ..+=++|+|.+..  ...+.++...+.   .|..||+||-+..+.
T Consensus       186 ~~~~i~~~~P~villDE~~~--~e~~~~l~~~~~---~G~~vI~ttH~~~~~  232 (270)
T TIGR02858       186 MMMLIRSMSPDVIVVDEIGR--EEDVEALLEALH---AGVSIIATAHGRDVE  232 (270)
T ss_pred             HHHHHHhCCCCEEEEeCCCc--HHHHHHHHHHHh---CCCEEEEEechhHHH
Confidence            333333 5788999999843  344444444432   477899999876553

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.13  E-value=0.32  Score=47.25  Aligned_cols=22  Identities=27%  Similarity=0.605  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++.|.|++|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            4789999999999999998774

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=94.13  E-value=0.14  Score=52.46  Aligned_cols=83  Identities=20%  Similarity=0.291  Sum_probs=48.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhccC------CCccCH-HHHH-----
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRSS------CKLEDL-NSVQ-----   81 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~~------~~~~~~-~~~~-----   81 (1237)
                      .++|.|.+|+|||+|+.++++..   .-+.++++.++.. ..+.++.+++...-....      ...... .+..     
T Consensus        17 r~~I~g~~g~GKt~Ll~~i~~~~---~~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a   93 (215)
T PF00006_consen   17 RIGIFGGAGVGKTVLLQEIANNQ---DADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTA   93 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHC---TTTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHH
T ss_pred             EEEEEcCcccccchhhHHHHhcc---cccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhccc
Confidence            68899999999999999998753   2333477777644 455556665543311110      011111 1111     


Q ss_pred             HHHHHHh--cCCcEEEEEeCC
Q 000887           82 LELKETV--FKKKFLIVLDDV  100 (1237)
Q Consensus        82 ~~l~~~l--~~~~~LlvlDdv  100 (1237)
                      -.+.+++  +++++|+|+||.
T Consensus        94 ~t~AEyfrd~G~dVlli~Dsl  114 (215)
T PF00006_consen   94 LTIAEYFRDQGKDVLLIIDSL  114 (215)
T ss_dssp             HHHHHHHHHTTSEEEEEEETH
T ss_pred             hhhhHHHhhcCCceeehhhhh
Confidence            1122333  578999999998

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=94.11  E-value=0.52  Score=56.35  Aligned_cols=133  Identities=18%  Similarity=0.145  Sum_probs=72.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ...+.+-++|++|.|||.||++++.. .+..|     +.+... +   +.    ...     .......+...+....+.
T Consensus       274 ~~~~giLl~GpPGtGKT~lAkava~~-~~~~f-----i~v~~~-~---l~----sk~-----vGesek~ir~~F~~A~~~  334 (494)
T COG0464         274 RPPKGVLLYGPPGTGKTLLAKAVALE-SRSRF-----ISVKGS-E---LL----SKW-----VGESEKNIRELFEKARKL  334 (494)
T ss_pred             CCCCeeEEECCCCCCHHHHHHHHHhh-CCCeE-----EEeeCH-H---Hh----ccc-----cchHHHHHHHHHHHHHcC
Confidence            44568999999999999999999883 22222     222221 1   11    100     111112222333334456


Q ss_pred             CcEEEEEeCCCCC------Ch-----hhHHHhhccccC--CCCCcEEEEEeCchhHHHh-h----cCCCeEeCCCCChhh
Q 000887           91 KKFLIVLDDVWSE------RY-----DLWQALKSPFMA--GAPGSRIIVTTRSMDVALT-M----GSGKNYELKLLSDDD  152 (1237)
Q Consensus        91 ~~~LlvlDdv~~~------~~-----~~~~~~~~~~~~--~~~~~~iliTtR~~~~~~~-~----~~~~~~~l~~l~~~e  152 (1237)
                      .++.|.+|+++.-      ..     .....+...+..  ...+..||-||-.+..... +    .-...+.++.-+.++
T Consensus       335 ~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~  414 (494)
T COG0464         335 APSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEE  414 (494)
T ss_pred             CCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCCCHHH
Confidence            8999999999431      10     122233333322  2233334444443332221 1    123578899999999


Q ss_pred             hHHHHHHHhc
Q 000887          153 CWSVFVAHAF  162 (1237)
Q Consensus       153 a~~l~~~~~~  162 (1237)
                      ..+.|..+..
T Consensus       415 r~~i~~~~~~  424 (494)
T COG0464         415 RLEIFKIHLR  424 (494)
T ss_pred             HHHHHHHHhc
Confidence            9999999875

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=94.08  E-value=0.039  Score=54.47  Aligned_cols=47  Identities=30%  Similarity=0.253  Sum_probs=31.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAI   63 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i   63 (1237)
                      -.+|+|-||-|+||||||.+++++. +  +. +++-.+.+.+=.+...++.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l-~--~~-~~~E~vednp~L~~FY~d~   50 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHL-G--FK-VFYELVEDNPFLDLFYEDP   50 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHh-C--Cc-eeeecccCChHHHHHHHhH
Confidence            4689999999999999999988753 2  22 4444455554344444433

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=94.08  E-value=0.44  Score=49.94  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        31 e~~~i~G~nGsGKSTLl~~l~G~   53 (221)
T cd03244          31 EKVGIVGRTGSGKSSLLLALFRL   53 (221)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            48999999999999999998763

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=94.08  E-value=0.42  Score=48.75  Aligned_cols=117  Identities=16%  Similarity=0.184  Sum_probs=58.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEE---------------EcCCcC---HHHHHHHHHHHhhccCCCcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC---------------VSDDFD---VLRISKAILDSIKRSSCKLE   75 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~---------------~~~~~~---~~~~~~~i~~~l~~~~~~~~   75 (1237)
                      .+++|.|+.|.|||||.+.++.-.......+.++++               +.+...   ...+.+.+.......  ...
T Consensus        36 e~~~l~G~nGsGKStLl~~i~Gl~~~~~~~G~i~~~g~~~~~~~~~~~i~~~~q~~~~~~~~t~~~~i~~~~~~~--~LS  113 (194)
T cd03213          36 ELTAIMGPSGAGKSTLLNALAGRRTGLGVSGEVLINGRPLDKRSFRKIIGYVPQDDILHPTLTVRETLMFAAKLR--GLS  113 (194)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCCCCCCceEEEECCEeCchHhhhheEEEccCcccCCCCCcHHHHHHHHHHhc--cCC
Confidence            479999999999999999987632002222322221               011110   012222221110000  122


Q ss_pred             CHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccC-CCCCcEEEEEeCchh
Q 000887           76 DLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMA-GAPGSRIIVTTRSMD  132 (1237)
Q Consensus        76 ~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~-~~~~~~iliTtR~~~  132 (1237)
                      ..+...-.+.+.+-.++-++++|+.... +......+...+.. ...+..||++|.+..
T Consensus       114 ~G~~qrv~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  172 (194)
T cd03213         114 GGERKRVSIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLADTGRTIICSIHQPS  172 (194)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEecCch
Confidence            2333344555666677789999998442 11222223222222 123667888888764

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>TIGR00235 udk uridine kinase

Probab=94.07  E-value=0.049  Score=56.31  Aligned_cols=26  Identities=35%  Similarity=0.529  Sum_probs=22.7

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..-.+|+|.|++|+||||||+.++..
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999999998763

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=94.05  E-value=0.19  Score=49.65  Aligned_cols=21  Identities=33%  Similarity=0.604  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHhc
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |+|.|++|+||||+|+++.+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999998874

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=94.05  E-value=1.5  Score=47.69  Aligned_cols=156  Identities=10%  Similarity=0.036  Sum_probs=86.5

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccc--------c-CCCCeEEEEE-cCCcCHHHHHHHHHHHhhccCCCccCHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT--------E-AFEPKAWVCV-SDDFDVLRISKAILDSIKRSSCKLEDLNSVQL   82 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~--------~-~f~~~~w~~~-~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~   82 (1237)
                      .++..++|..|+||+++|.++++...-        . +-+.+.+++. +....++++. ++...+...+           
T Consensus        18 ~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~~~-----------   85 (299)
T PRK07132         18 SHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYFSS-----------   85 (299)
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhccCC-----------
Confidence            456679999999999999998775411        1 1112333321 1111222222 1222221110           


Q ss_pred             HHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeC-chhHHHhh-cCCCeEeCCCCChhhhHHHHHHH
Q 000887           83 ELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTR-SMDVALTM-GSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        83 ~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR-~~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                          .-.+++-++|+|+++.-+.....++...+-.-++++.+|++|. ...+...+ .....+++.++++++..+.+...
T Consensus        86 ----~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~~l~~~  161 (299)
T PRK07132         86 ----FVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILAKLLSK  161 (299)
T ss_pred             ----cccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHHHHHHc
Confidence                0014677888999855544455556666655556676665554 33343332 23468999999999998877653


Q ss_pred             hcCCCCCCCCCChHHHHHHHHHHccCCchHHHHH
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPLAARAL  194 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~  194 (1237)
                      .      .+    ++.+..++...+|.--|+..+
T Consensus       162 ~------~~----~~~a~~~a~~~~~~~~a~~~~  185 (299)
T PRK07132        162 N------KE----KEYNWFYAYIFSNFEQAEKYI  185 (299)
T ss_pred             C------CC----hhHHHHHHHHcCCHHHHHHHH
Confidence            1      11    334666677777633555553

>PTZ00035 Rad51 protein; Provisional

Probab=94.05  E-value=0.29  Score=54.38  Aligned_cols=55  Identities=18%  Similarity=0.130  Sum_probs=36.1

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-c----cCCCCeEEEEEcCCcCHHHHHHHHHHHhh
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-T----EAFEPKAWVCVSDDFDVLRISKAILDSIK   68 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~----~~f~~~~w~~~~~~~~~~~~~~~i~~~l~   68 (1237)
                      -.++.|+|.+|+|||+++..++.... .    ..-..++|++....++..++ .++++.++
T Consensus       118 G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g  177 (337)
T PTZ00035        118 GSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFG  177 (337)
T ss_pred             CeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhC
Confidence            46889999999999999998764321 1    12235679987666665553 33444443

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=94.03  E-value=0.098  Score=49.82  Aligned_cols=31  Identities=26%  Similarity=0.447  Sum_probs=25.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcccccCC
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF   42 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f   42 (1237)
                      +..+|-++|.+|+||||+|.+++.......+
T Consensus        22 ~~~viW~TGLSGsGKSTiA~ale~~L~~~G~   52 (197)
T COG0529          22 KGAVIWFTGLSGSGKSTIANALEEKLFAKGY   52 (197)
T ss_pred             CCeEEEeecCCCCCHHHHHHHHHHHHHHcCC
Confidence            3568999999999999999998875544443

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=94.03  E-value=0.3  Score=51.22  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        49 e~~~i~G~nGsGKSTLl~~l~G~   71 (224)
T cd03220          49 ERIGLIGRNGAGKSTLLRLLAGI   71 (224)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999998763

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>PRK14527 adenylate kinase; Provisional

Probab=94.02  E-value=0.11  Score=53.01  Aligned_cols=25  Identities=28%  Similarity=0.449  Sum_probs=22.1

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...+|.|.|++|+||||+|+.+++.
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3478999999999999999998764

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=94.00  E-value=0.23  Score=51.96  Aligned_cols=94  Identities=16%  Similarity=0.175  Sum_probs=61.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFL   94 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~L   94 (1237)
                      .+.++|.+|+|||+-++.+++.     .+..+.+..+...+...+...+.......  ......+....+...+++..-+
T Consensus        96 l~~vyg~~g~gKt~a~~~y~~s-----~p~~~l~~~~p~~~a~~~i~~i~~~~~~~--~~~~~~d~~~~~~~~l~~~~~~  168 (297)
T COG2842          96 LVVVYGYAGLGKTQAAKNYAPS-----NPNALLIEADPSYTALVLILIICAAAFGA--TDGTINDLTERLMIRLRDTVRL  168 (297)
T ss_pred             eEEEeccccchhHHHHHhhccc-----CccceeecCChhhHHHHHHHHHHHHHhcc--cchhHHHHHHHHHHHHccCcce
Confidence            8899999999999999998763     33344444555555555555555544433  2234445555666666889999


Q ss_pred             EEEeCCCCCChhhHHHhhccc
Q 000887           95 IVLDDVWSERYDLWQALKSPF  115 (1237)
Q Consensus        95 lvlDdv~~~~~~~~~~~~~~~  115 (1237)
                      +++|+++.-....++.+....
T Consensus       169 iivDEA~~L~~~ale~lr~i~  189 (297)
T COG2842         169 IIVDEADRLPYRALEELRRIH  189 (297)
T ss_pred             eeeehhhccChHHHHHHHHHH
Confidence            999999665455555554443

>PRK04328 hypothetical protein; Provisional

Probab=93.99  E-value=0.22  Score=52.94  Aligned_cols=40  Identities=28%  Similarity=0.399  Sum_probs=30.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      =.++.|.|.+|+|||++|.+++....++ -..++|++....
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~~~~~-ge~~lyis~ee~   62 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWNGLQM-GEPGVYVALEEH   62 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhc-CCcEEEEEeeCC
Confidence            3688999999999999999987643333 456888887654

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=93.97  E-value=0.45  Score=53.50  Aligned_cols=21  Identities=33%  Similarity=0.581  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .++|+|++|+||||||+.+..
T Consensus       364 ~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         364 ALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             eEEEECCCCccHHHHHHHHHc
Confidence            689999999999999999765

>PRK13948 shikimate kinase; Provisional

Probab=93.97  E-value=0.6  Score=46.57  Aligned_cols=26  Identities=23%  Similarity=0.376  Sum_probs=22.8

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...+.|+++|+.|+||||+++.+++.
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            34578999999999999999998874

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=93.96  E-value=0.21  Score=57.00  Aligned_cols=87  Identities=22%  Similarity=0.200  Sum_probs=51.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhccC------CCcc-CHHH-----H
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRSS------CKLE-DLNS-----V   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~~------~~~~-~~~~-----~   80 (1237)
                      ..++|.|.+|+|||+|+.+++....+++-+.++++-++.. ..+.++.+++...-....      .... ...+     .
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~~~~~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~  224 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALT  224 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            4689999999999999999876433222234567766544 345555555554321110      0111 1111     1


Q ss_pred             HHHHHHHh---cCCcEEEEEeCC
Q 000887           81 QLELKETV---FKKKFLIVLDDV  100 (1237)
Q Consensus        81 ~~~l~~~l---~~~~~LlvlDdv  100 (1237)
                      .-.+.+++   +++++|+++|++
T Consensus       225 a~tiAEyfrd~~G~~VLll~Dsl  247 (463)
T PRK09280        225 GLTMAEYFRDVEGQDVLLFIDNI  247 (463)
T ss_pred             HHHHHHHHHHhcCCceEEEecch
Confidence            22345555   468999999999

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=93.96  E-value=0.16  Score=57.81  Aligned_cols=88  Identities=15%  Similarity=0.227  Sum_probs=52.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhcc-------CCCccCHHH-----H
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRS-------SCKLEDLNS-----V   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~~-----~   80 (1237)
                      ..++|.|.+|+|||+|+.+++....+.+-+.++|+-++... .+.++.+++...-...       ........+     .
T Consensus       139 Qr~~Ifg~~G~GKt~l~~~~~~~~~~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~~  218 (449)
T TIGR03305       139 GKAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHT  218 (449)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHHH
Confidence            46899999999999999998775433334667788776543 4455555554321111       001111111     2


Q ss_pred             HHHHHHHhc---CCcEEEEEeCCC
Q 000887           81 QLELKETVF---KKKFLIVLDDVW  101 (1237)
Q Consensus        81 ~~~l~~~l~---~~~~LlvlDdv~  101 (1237)
                      +-.+.++++   ++++|+++||+.
T Consensus       219 a~tiAEyfrd~~G~~VLl~~DslT  242 (449)
T TIGR03305       219 ALTMAEYFRDDEKQDVLLLIDNIF  242 (449)
T ss_pred             HHHHHHHHHHhcCCceEEEecChH
Confidence            223455554   489999999993

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=93.95  E-value=0.29  Score=51.87  Aligned_cols=22  Identities=32%  Similarity=0.504  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G   49 (236)
T TIGR03864        28 EFVALLGPNGAGKSTLFSLLTR   49 (236)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999875

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=93.95  E-value=0.21  Score=52.53  Aligned_cols=28  Identities=25%  Similarity=0.282  Sum_probs=24.4

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+...+|+|.|++|+|||||++.++...
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~~l   57 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEALL   57 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4668899999999999999999988743

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.93  E-value=0.25  Score=59.95  Aligned_cols=87  Identities=21%  Similarity=0.217  Sum_probs=54.3

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhccc-ccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-TEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~-~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -++++++|+.|+||||++..++.... ......+..++.+... ...+-++..+..++.+.....+.++....+.+ +++
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~-~~~  263 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAA-LGD  263 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHH-hcC
Confidence            47999999999999999999887542 2222345566544322 12344455556666554444566666655554 344


Q ss_pred             CcEEEEEeCCC
Q 000887           91 KKFLIVLDDVW  101 (1237)
Q Consensus        91 ~~~LlvlDdv~  101 (1237)
                      + =+|++|=+-
T Consensus       264 ~-D~VLIDTAG  273 (767)
T PRK14723        264 K-HLVLIDTVG  273 (767)
T ss_pred             C-CEEEEeCCC
Confidence            4 477888874

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.92  E-value=0.29  Score=50.08  Aligned_cols=39  Identities=26%  Similarity=0.366  Sum_probs=27.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhccc-ccCC--------CCeEEEEEcCC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL-TEAF--------EPKAWVCVSDD   53 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~-~~~f--------~~~~w~~~~~~   53 (1237)
                      ++.|.|++|+|||+++.+++.... ...|        ..++|++....
T Consensus        34 l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   34 LTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             EEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            789999999999999999877552 2222        35778876555

>PTZ00088 adenylate kinase 1; Provisional

Probab=93.91  E-value=0.061  Score=55.90  Aligned_cols=22  Identities=36%  Similarity=0.522  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|+|.|++|+||||+|+.+++.
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3889999999999999998874

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.89  E-value=0.93  Score=46.11  Aligned_cols=153  Identities=18%  Similarity=0.169  Sum_probs=76.4

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHh-
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV-   88 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-   88 (1237)
                      +=.++-|..+|++|.|||.+|+++++.. +-.     ++.+-..    .+   |....       .+....+..+.+.- 
T Consensus       148 ~WAPknVLFyGppGTGKTm~Akalane~-kvp-----~l~vkat----~l---iGehV-------Gdgar~Ihely~rA~  207 (368)
T COG1223         148 DWAPKNVLFYGPPGTGKTMMAKALANEA-KVP-----LLLVKAT----EL---IGEHV-------GDGARRIHELYERAR  207 (368)
T ss_pred             ccCcceeEEECCCCccHHHHHHHHhccc-CCc-----eEEechH----HH---HHHHh-------hhHHHHHHHHHHHHH
Confidence            3457889999999999999999998742 211     2222111    11   11111       11122223333322 


Q ss_pred             cCCcEEEEEeCCCCCCh--------hh----HHHhhccccC--CCCCcEEEEEeCchhHHH-hhcC--CCeEeCCCCChh
Q 000887           89 FKKKFLIVLDDVWSERY--------DL----WQALKSPFMA--GAPGSRIIVTTRSMDVAL-TMGS--GKNYELKLLSDD  151 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~~~~--------~~----~~~~~~~~~~--~~~~~~iliTtR~~~~~~-~~~~--~~~~~l~~l~~~  151 (1237)
                      +.-+|++.+|..+....        .+    +.++...+..  .+-|..-|-.|....... .+..  ...++..--+.+
T Consensus       208 ~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~e  287 (368)
T COG1223         208 KAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDE  287 (368)
T ss_pred             hcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCceEEEeecCChhhcCHHHHhhhhheeeeeCCChH
Confidence            33699999999853211        11    2222222221  233443344444333322 1111  235566666788


Q ss_pred             hhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCC
Q 000887          152 DCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGL  187 (1237)
Q Consensus       152 ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~  187 (1237)
                      |-.+++...+..-.-..     ....+.++++.+|.
T Consensus       288 Er~~ile~y~k~~Plpv-----~~~~~~~~~~t~g~  318 (368)
T COG1223         288 ERLEILEYYAKKFPLPV-----DADLRYLAAKTKGM  318 (368)
T ss_pred             HHHHHHHHHHHhCCCcc-----ccCHHHHHHHhCCC
Confidence            88888887763222111     12246677776664

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=93.89  E-value=0.21  Score=60.88  Aligned_cols=55  Identities=16%  Similarity=0.187  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcCCcEEEEEeCCCCCChhhHH-HhhccccCC-CCCcEEEEEeCchhH
Q 000887           79 SVQLELKETVFKKKFLIVLDDVWSERYDLWQ-ALKSPFMAG-APGSRIIVTTRSMDV  133 (1237)
Q Consensus        79 ~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~-~~~~~~~~~-~~~~~iliTtR~~~~  133 (1237)
                      +-+-.+.+.+-.++-++|+|...+.-+...+ .+...+... ...+.|+||=|..-+
T Consensus       615 rQrlalARaLl~~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~~~~T~I~IaHRl~ti  671 (709)
T COG2274         615 RQRLALARALLSKPKILLLDEATSALDPETEAIILQNLLQILQGRTVIIIAHRLSTI  671 (709)
T ss_pred             HHHHHHHHHhccCCCEEEEeCcccccCHhHHHHHHHHHHHHhcCCeEEEEEccchHh
Confidence            3344566777789999999999653222222 233334333 335667777776544

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=93.87  E-value=0.33  Score=50.43  Aligned_cols=23  Identities=30%  Similarity=0.450  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          27 EIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998763

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.83  E-value=0.29  Score=56.51  Aligned_cols=87  Identities=16%  Similarity=0.172  Sum_probs=48.0

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      -+|++++|+.|+||||++..++... .+.....+..++..... ....-+...+..++.+.....+..+....+. .+++
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL~-~L~d  334 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLALS-ELRN  334 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhHHHHHH-hccC
Confidence            4799999999999999999998754 23222245566544321 1222333344554443322223333333332 2334


Q ss_pred             CcEEEEEeCCC
Q 000887           91 KKFLIVLDDVW  101 (1237)
Q Consensus        91 ~~~LlvlDdv~  101 (1237)
                      + -.+++|-.-
T Consensus       335 ~-d~VLIDTaG  344 (484)
T PRK06995        335 K-HIVLIDTIG  344 (484)
T ss_pred             C-CeEEeCCCC
Confidence            4 477778874

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.83  E-value=0.32  Score=51.87  Aligned_cols=49  Identities=14%  Similarity=0.231  Sum_probs=34.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAIL   64 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~   64 (1237)
                      .++.|.|.+|+|||++|.+++.+.....-..++|++....  ...+...++
T Consensus        14 ~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~--~~~~~~r~~   62 (242)
T cd00984          14 DLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMS--KEQLLQRLL   62 (242)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCC--HHHHHHHHH
Confidence            5899999999999999999877554442345788876554  344444443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=93.83  E-value=0.19  Score=45.57  Aligned_cols=31  Identities=16%  Similarity=0.257  Sum_probs=26.3

Q ss_pred             CCCCcEEEEEEcCCCCcHHHHHHHHHhcccc
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLT   39 (1237)
Q Consensus         9 ~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~   39 (1237)
                      .++.+-|+..+|++|+|||-+|+.+++...+
T Consensus        49 ~p~KpLVlSfHG~tGtGKn~v~~liA~~ly~   79 (127)
T PF06309_consen   49 NPRKPLVLSFHGWTGTGKNFVSRLIAEHLYK   79 (127)
T ss_pred             CCCCCEEEEeecCCCCcHHHHHHHHHHHHHh
Confidence            4577889999999999999999998886533

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=93.81  E-value=0.051  Score=55.38  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=22.4

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.++|+|.|++|+||||+|+.++..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999998864

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=93.79  E-value=0.44  Score=49.33  Aligned_cols=111  Identities=11%  Similarity=0.042  Sum_probs=57.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCC-------------eEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-------------KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNS   79 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~-------------~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~   79 (1237)
                      -++++|.|+.|.||||+.+.++.......-..             .++.......+...-.....          .+..+
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~----------~e~~~  100 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFM----------VELSE  100 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHH----------HHHHH
Confidence            36889999999999999998766221111111             22222222222211111111          11222


Q ss_pred             HHHHHHHHhcCCcEEEEEeCCCCCC--hhh---HHHhhccccCCCCCcEEEEEeCchhHHHh
Q 000887           80 VQLELKETVFKKKFLIVLDDVWSER--YDL---WQALKSPFMAGAPGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        80 ~~~~l~~~l~~~~~LlvlDdv~~~~--~~~---~~~~~~~~~~~~~~~~iliTtR~~~~~~~  136 (1237)
                      ....++.  ..++.|+++|......  .+.   ...+...+... .++.+|++|-+..+...
T Consensus       101 ~~~il~~--~~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~~  159 (222)
T cd03287         101 TSHILSN--CTSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGEI  159 (222)
T ss_pred             HHHHHHh--CCCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHHH
Confidence            2222222  2478999999973321  111   11233333322 57889999999887643

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=93.76  E-value=0.14  Score=53.93  Aligned_cols=84  Identities=23%  Similarity=0.256  Sum_probs=51.0

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhcc---------------CCC-----
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRS---------------SCK-----   73 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~---------------~~~-----   73 (1237)
                      .++.|.|.+|+|||++|.+++....++.-..++|++.....  ..+.+.+. .++..               ...     
T Consensus        20 s~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~~--~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~~~~   96 (226)
T PF06745_consen   20 SVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEPP--EELIENMK-SFGWDLEEYEDSGKLKIIDAFPERIGWS   96 (226)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS-H--HHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGST-T
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCCH--HHHHHHHH-HcCCcHHHHhhcCCEEEEeccccccccc
Confidence            58999999999999999998764434324458888865543  33333322 22210               001     


Q ss_pred             ccCHHHHHHHHHHHhcC-CcEEEEEeCC
Q 000887           74 LEDLNSVQLELKETVFK-KKFLIVLDDV  100 (1237)
Q Consensus        74 ~~~~~~~~~~l~~~l~~-~~~LlvlDdv  100 (1237)
                      ..+.++....+.+.+++ +...+|+|.+
T Consensus        97 ~~~~~~l~~~i~~~i~~~~~~~vVIDsl  124 (226)
T PF06745_consen   97 PNDLEELLSKIREAIEELKPDRVVIDSL  124 (226)
T ss_dssp             SCCHHHHHHHHHHHHHHHTSSEEEEETH
T ss_pred             ccCHHHHHHHHHHHHHhcCCCEEEEECH
Confidence            34566666666666554 4578888887

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=93.76  E-value=0.44  Score=46.17  Aligned_cols=33  Identities=27%  Similarity=0.389  Sum_probs=24.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEE
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWV   48 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~   48 (1237)
                      .+.|.|+.|+|||||.+.++. ..+..-..|.|-
T Consensus        30 ~~~i~G~NG~GKTtLLRilaG-Ll~p~~G~v~~~   62 (209)
T COG4133          30 ALQITGPNGAGKTTLLRILAG-LLRPDAGEVYWQ   62 (209)
T ss_pred             EEEEECCCCCcHHHHHHHHHc-ccCCCCCeEEec
Confidence            688999999999999999876 333333334454

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=93.76  E-value=0.18  Score=53.06  Aligned_cols=88  Identities=15%  Similarity=0.176  Sum_probs=52.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccc---ccCCCCeEEEEEcCCc-CHHHHHHHHHHHhhccC------CCccC-HHH---
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKL---TEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSS------CKLED-LNS---   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~---~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~------~~~~~-~~~---   79 (1237)
                      ..++|.|-+|+|||+|+.++++...   +..-+.++++-+++.. .+.++.+++...=....      ..... ..+   
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a  149 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIIT  149 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHH
Confidence            3679999999999999999876432   1234567788776553 45555555544321110      01111 111   


Q ss_pred             --HHHHHHHHhc---CCcEEEEEeCCC
Q 000887           80 --VQLELKETVF---KKKFLIVLDDVW  101 (1237)
Q Consensus        80 --~~~~l~~~l~---~~~~LlvlDdv~  101 (1237)
                        ..-.+.++++   ++++|+++||+.
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~lt  176 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMT  176 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChh
Confidence              1223445553   579999999993

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=93.74  E-value=0.34  Score=50.68  Aligned_cols=23  Identities=35%  Similarity=0.372  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++.-
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl   54 (218)
T cd03266          32 EVTGLLGPNGAGKTTTLRMLAGL   54 (218)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999998763

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=93.73  E-value=0.072  Score=56.78  Aligned_cols=89  Identities=20%  Similarity=0.216  Sum_probs=54.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhcc------------CCCccCHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRS------------SCKLEDLNSV   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~------------~~~~~~~~~~   80 (1237)
                      ..+++.|-+|+|||.+.+++.+...+.+-...+|.-++.. ..-.+++.++...-..+            ......+.-.
T Consensus       148 gKiGLFGGAGVGKTVl~~ELI~Nia~~h~g~SVFaGvGERtREGndLy~Em~es~vl~ktalv~gQMNEpPGaR~RValt  227 (468)
T COG0055         148 GKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRVALT  227 (468)
T ss_pred             ceeeeeccCCccceeeHHHHHHHHHHHcCCeEEEEeccccccchHHHHHHHHhcCCCCceeEEEeecCCCCcceeeehhh
Confidence            4689999999999999999988654544444567766543 34556776665542111            1111111111


Q ss_pred             HHHHHHHhc---CCcEEEEEeCCCC
Q 000887           81 QLELKETVF---KKKFLIVLDDVWS  102 (1237)
Q Consensus        81 ~~~l~~~l~---~~~~LlvlDdv~~  102 (1237)
                      .-.+.++++   ++.+|+.+||+..
T Consensus       228 GlT~AEyfRD~~gqdVLlFIDNIfR  252 (468)
T COG0055         228 GLTMAEYFRDEEGQDVLLFIDNIFR  252 (468)
T ss_pred             hhhHHHHhhcccCCeEEEEehhhhH
Confidence            222344554   4789999999965

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=93.73  E-value=0.094  Score=52.53  Aligned_cols=40  Identities=30%  Similarity=0.468  Sum_probs=29.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccC-CCCeEEEEEcCCcC
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEA-FEPKAWVCVSDDFD   55 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~-f~~~~w~~~~~~~~   55 (1237)
                      .|+|+|-||+||||+|..++.....+. |. +.-+++..+.+
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~~~-VLvVDaDpd~n   42 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGGYN-VLVVDADPDSN   42 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCCce-EEEEeCCCCCC
Confidence            589999999999999999666554444 43 66676666544

>PRK04040 adenylate kinase; Provisional

Probab=93.73  E-value=0.055  Score=54.46  Aligned_cols=24  Identities=29%  Similarity=0.638  Sum_probs=21.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..+|+|+|++|+||||+++.+++.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~   25 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEK   25 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            468999999999999999998774

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.71  E-value=0.23  Score=52.38  Aligned_cols=40  Identities=20%  Similarity=0.262  Sum_probs=29.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      =.++.|.|.+|+|||++|.+++....+ .-..++|++....
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~~~~-~g~~~~~is~e~~   59 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYKGLR-DGDPVIYVTTEES   59 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHHHHh-cCCeEEEEEccCC
Confidence            368999999999999999987653333 2346788876443

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK03839 putative kinase; Provisional

Probab=93.70  E-value=0.051  Score=54.81  Aligned_cols=22  Identities=32%  Similarity=0.632  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|.|.|++|+||||+|+++++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999875

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=93.70  E-value=0.0032  Score=61.90  Aligned_cols=84  Identities=15%  Similarity=0.133  Sum_probs=65.9

Q ss_pred             cCCCCCccEEEccccccccccccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEE
Q 000887          396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYL  475 (1237)
Q Consensus       396 ~~~~~~Lr~L~L~~~~i~~lp~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L  475 (1237)
                      +...+..++||++.|++..+-..|+.++.|.-||++.|.|..+|..++.+..++.+++..| .....|.+++.+++++++
T Consensus        38 i~~~kr~tvld~~s~r~vn~~~n~s~~t~~~rl~~sknq~~~~~~d~~q~~e~~~~~~~~n-~~~~~p~s~~k~~~~k~~  116 (326)
T KOG0473|consen   38 IASFKRVTVLDLSSNRLVNLGKNFSILTRLVRLDLSKNQIKFLPKDAKQQRETVNAASHKN-NHSQQPKSQKKEPHPKKN  116 (326)
T ss_pred             hhccceeeeehhhhhHHHhhccchHHHHHHHHHhccHhhHhhChhhHHHHHHHHHHHhhcc-chhhCCccccccCCcchh
Confidence            4456677888888888777766677778888888888888888888888888888887776 777788888888888888


Q ss_pred             eccCC
Q 000887          476 NIEGA  480 (1237)
Q Consensus       476 ~l~~~  480 (1237)
                      ++-++
T Consensus       117 e~k~~  121 (326)
T KOG0473|consen  117 EQKKT  121 (326)
T ss_pred             hhccC
Confidence            77776

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.70  E-value=0.66  Score=46.77  Aligned_cols=23  Identities=26%  Similarity=0.576  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          27 EIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999998763

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=93.67  E-value=0.28  Score=55.70  Aligned_cols=88  Identities=22%  Similarity=0.213  Sum_probs=52.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhccC------CCccC-HHH-----H
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRSS------CKLED-LNS-----V   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~~------~~~~~-~~~-----~   80 (1237)
                      ..++|.|.+|+|||+|+.+++....+++-+.++++-++.. ..+.++.+++...-....      ..... ..+     .
T Consensus       144 Qr~~If~~~G~GKt~L~~~~~~~~~~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~  223 (461)
T TIGR01039       144 GKIGLFGGAGVGKTVLIQELINNIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALT  223 (461)
T ss_pred             CEEEeecCCCCChHHHHHHHHHHHHhcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            4689999999999999999876443333345567766544 445556665543211110      11111 111     2


Q ss_pred             HHHHHHHhc---CCcEEEEEeCCC
Q 000887           81 QLELKETVF---KKKFLIVLDDVW  101 (1237)
Q Consensus        81 ~~~l~~~l~---~~~~LlvlDdv~  101 (1237)
                      +-.+.++++   ++++|+++||+.
T Consensus       224 a~tiAEyfrd~~G~~VLll~DslT  247 (461)
T TIGR01039       224 GLTMAEYFRDEQGQDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHhcCCeeEEEecchh
Confidence            223455553   579999999993

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=93.66  E-value=0.48  Score=52.22  Aligned_cols=23  Identities=26%  Similarity=0.478  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||.+.++..
T Consensus        29 ei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        29 RIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998763

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=93.66  E-value=0.53  Score=48.60  Aligned_cols=22  Identities=45%  Similarity=0.655  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|+|||||++.++.
T Consensus        27 e~~~i~G~nGsGKSTLl~~l~G   48 (205)
T cd03226          27 EIIALTGKNGAGKTTLAKILAG   48 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4899999999999999999876

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=93.64  E-value=0.067  Score=55.59  Aligned_cols=24  Identities=21%  Similarity=0.217  Sum_probs=21.0

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHh
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      ..+++.|+|+.|.||||+.+.++.
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~   52 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGV   52 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHH
Confidence            457999999999999999998764

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=93.60  E-value=0.053  Score=54.78  Aligned_cols=21  Identities=29%  Similarity=0.248  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      ++.|+|+.|.||||+.+.++.
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            478999999999999999874

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=93.58  E-value=0.08  Score=54.46  Aligned_cols=22  Identities=23%  Similarity=0.256  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|+|+.|.||||+.+.++.
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6899999999999999999884

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=93.56  E-value=0.42  Score=49.62  Aligned_cols=21  Identities=38%  Similarity=0.517  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 000887           15 VIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      +++|.|+.|+|||||++.++.
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~G   47 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILAT   47 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhC
Confidence            899999999999999999875

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG5635 Predicted NTPase (NACHT family) [Signal transduction mechanisms]

Probab=93.55  E-value=0.14  Score=64.79  Aligned_cols=135  Identities=13%  Similarity=0.097  Sum_probs=73.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcccccCC---CCeEEEEEcCCc----CHH--HHHHHHHHHhhccCCCccCHHHHHHHHH
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAF---EPKAWVCVSDDF----DVL--RISKAILDSIKRSSCKLEDLNSVQLELK   85 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~~f---~~~~w~~~~~~~----~~~--~~~~~i~~~l~~~~~~~~~~~~~~~~l~   85 (1237)
                      -+.|+|.+|+||||....++-....+.+   +..+++.+....    ...  .+..-+...+...    ....+......
T Consensus       224 ~~~Ilg~pGsGKTtfl~~lA~~~~~~~~~~~~vpi~~~l~~~~~~~~~~~q~~~~~~l~~~~~~~----~~~~~~~~~~~  299 (824)
T COG5635         224 KLLILGAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDYLAEELFSQ----GIAKQLIEAHQ  299 (824)
T ss_pred             heeeecCCCCCceehHHHHHHHhccCcCCcccCceeeechhHHHhhhhHhhccHHHHHHHHHhcc----CCcchhhHHHH
Confidence            6789999999999999998764433332   233455443111    111  1222222222222    12222222335


Q ss_pred             HHhcCCcEEEEEeCCCCCChhh----HHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCeEeCCCCChhhhH
Q 000887           86 ETVFKKKFLIVLDDVWSERYDL----WQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSDDDCW  154 (1237)
Q Consensus        86 ~~l~~~~~LlvlDdv~~~~~~~----~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l~~l~~~ea~  154 (1237)
                      ++++.+++++.+|.++......    ... ...+.+.-+.+++|+|+|....-........+++..+.++.-.
T Consensus       300 e~l~~g~~llLlDGlDe~~~~~~~~~~~~-i~~f~~~~~~~~~iltcR~~~~~~~~~~f~~~ei~~~~~~~i~  371 (824)
T COG5635         300 ELLKTGKLLLLLDGLDELEPKNQRALIRE-INKFLQEYPDAQVLLTCRPDTYKEEFKGFAVFEIYKFLDLQIN  371 (824)
T ss_pred             HHHhccchhhHhhccchhhhhhHHHHHHH-HHHHhhhccCCeEEEEeccchhhhhhhhhhhccchhhhHHHHH
Confidence            6778899999999985532211    112 2233344568899999987655433333345556666555443

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=93.54  E-value=0.048  Score=49.16  Aligned_cols=22  Identities=50%  Similarity=0.640  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhcc
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.|+|.+|+|||++|..++.+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l   22 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDL   22 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            5699999999999999988754

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=93.53  E-value=0.37  Score=49.49  Aligned_cols=21  Identities=33%  Similarity=0.544  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHH
Q 000887           14 RVIPLVGMGGIGKTTLAQEVY   34 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~   34 (1237)
                      .+++|.|..|+|||||..+++
T Consensus        23 g~~~i~G~NGsGKTTLl~ai~   43 (204)
T cd03240          23 PLTLIVGQNGAGKTTIIEALK   43 (204)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            499999999999999999984

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=93.51  E-value=0.42  Score=50.72  Aligned_cols=123  Identities=14%  Similarity=0.065  Sum_probs=63.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccc--c--CCCC--eEEEEEc----CCcCHHHHH--------------HHHHHHhhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLT--E--AFEP--KAWVCVS----DDFDVLRIS--------------KAILDSIKR   69 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~--~--~f~~--~~w~~~~----~~~~~~~~~--------------~~i~~~l~~   69 (1237)
                      .+++|.|..|+|||||++.++.....  .  .+++  +.++.-.    ...++.+..              .+++..++.
T Consensus        26 e~~~i~G~NGsGKSTLlk~L~G~~~p~~G~i~~~g~~i~~~~q~~~~~~~~tv~e~l~~~~~~~~~~~~~~~~~l~~l~l  105 (246)
T cd03237          26 EVIGILGPNGIGKTTFIKMLAGVLKPDEGDIEIELDTVSYKPQYIKADYEGTVRDLLSSITKDFYTHPYFKTEIAKPLQI  105 (246)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCCCCeEEECCceEEEecccccCCCCCCHHHHHHHHhhhccccHHHHHHHHHHcCC
Confidence            48999999999999999998774211  0  1121  2222111    011222221              122222222


Q ss_pred             cC------CCccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCC--CCCcEEEEEeCchhHHHh
Q 000887           70 SS------CKLEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAG--APGSRIIVTTRSMDVALT  136 (1237)
Q Consensus        70 ~~------~~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~--~~~~~iliTtR~~~~~~~  136 (1237)
                      ..      ......+...-.+...+...+=++++|+-... +......+...+...  ..+..||++|.+......
T Consensus       106 ~~~~~~~~~~LSgGe~qrv~iaraL~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tiiivsHd~~~~~~  181 (246)
T cd03237         106 EQILDREVPELSGGELQRVAIAACLSKDADIYLLDEPSAYLDVEQRLMASKVIRRFAENNEKTAFVVEHDIIMIDY  181 (246)
T ss_pred             HHHhhCChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            11      01222333444566677778899999998442 112222222222221  236679999988776544

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=93.50  E-value=0.085  Score=54.60  Aligned_cols=22  Identities=23%  Similarity=0.338  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      ++++|.|+.|.||||+.+.++.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999854

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=93.49  E-value=0.12  Score=56.27  Aligned_cols=49  Identities=20%  Similarity=0.265  Sum_probs=35.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKA   62 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~   62 (1237)
                      .+++.+.|-|||||||+|.+.+-..-... ..+.-++.....+..+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g-~kvLlvStDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESG-KKVLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcC-CcEEEEEeCCCCchHhhhcc
Confidence            48999999999999999999665433333 44777776666666655544

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.47  E-value=2.6  Score=47.14  Aligned_cols=152  Identities=11%  Similarity=0.035  Sum_probs=77.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEEE
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLI   95 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~Ll   95 (1237)
                      -.++|++|.|||++..++|+..   .|+ |+=+..+...+-.+ ++.++..                      ...+-+|
T Consensus       238 YLLYGPPGTGKSS~IaAmAn~L---~yd-IydLeLt~v~~n~d-Lr~LL~~----------------------t~~kSIi  290 (457)
T KOG0743|consen  238 YLLYGPPGTGKSSFIAAMANYL---NYD-IYDLELTEVKLDSD-LRHLLLA----------------------TPNKSIL  290 (457)
T ss_pred             ceeeCCCCCCHHHHHHHHHhhc---CCc-eEEeeeccccCcHH-HHHHHHh----------------------CCCCcEE
Confidence            3589999999999999998853   233 33333322222111 2222221                      1356667


Q ss_pred             EEeCCCCC------Ch------------hhHHHhh---ccccCCCCCcE-EEEEeCchhHHH--hh---cCCCeEeCCCC
Q 000887           96 VLDDVWSE------RY------------DLWQALK---SPFMAGAPGSR-IIVTTRSMDVAL--TM---GSGKNYELKLL  148 (1237)
Q Consensus        96 vlDdv~~~------~~------------~~~~~~~---~~~~~~~~~~~-iliTtR~~~~~~--~~---~~~~~~~l~~l  148 (1237)
                      |+.|++-.      ..            ..+..+.   ..++....+-| |++||-..+-..  .+   +-+..+.+.-=
T Consensus       291 vIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyC  370 (457)
T KOG0743|consen  291 LIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYC  370 (457)
T ss_pred             EEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCC
Confidence            77776321      00            0011111   11111122334 556776554321  11   22246777777


Q ss_pred             ChhhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhcC
Q 000887          149 SDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSK  201 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~~  201 (1237)
                      +.+.-..|+.+..+...   +    ...+.+|.+...|.-+.=..++..+-.+
T Consensus       371 tf~~fK~La~nYL~~~~---~----h~L~~eie~l~~~~~~tPA~V~e~lm~~  416 (457)
T KOG0743|consen  371 TFEAFKTLASNYLGIEE---D----HRLFDEIERLIEETEVTPAQVAEELMKN  416 (457)
T ss_pred             CHHHHHHHHHHhcCCCC---C----cchhHHHHHHhhcCccCHHHHHHHHhhc
Confidence            78777788887764322   1    2345677776667655555555555444

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=93.46  E-value=0.34  Score=48.97  Aligned_cols=26  Identities=35%  Similarity=0.413  Sum_probs=22.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ...+++|.|.+|+||||+|+.+....
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~~l   42 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEKKL   42 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34799999999999999999988743

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.45  E-value=0.55  Score=48.40  Aligned_cols=23  Identities=26%  Similarity=0.404  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        28 e~~~l~G~nGsGKSTLl~~l~G~   50 (204)
T PRK13538         28 ELVQIEGPNGAGKTSLLRILAGL   50 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998763

>TIGR01069 mutS2 MutS2 family protein

Probab=93.43  E-value=0.17  Score=62.88  Aligned_cols=25  Identities=24%  Similarity=0.170  Sum_probs=21.6

Q ss_pred             CcEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.++++|+|+.|.||||+.+.+...
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHH
Confidence            3478999999999999999998654

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK00625 shikimate kinase; Provisional

Probab=93.42  E-value=0.052  Score=53.62  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|.++|++|+||||+|+.++..
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999998774

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=93.40  E-value=0.46  Score=50.71  Aligned_cols=23  Identities=35%  Similarity=0.612  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|+|||||++.++..
T Consensus        31 e~~~I~G~NGsGKSTLl~~i~Gl   53 (251)
T PRK09544         31 KILTLLGPNGAGKSTLVRVVLGL   53 (251)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999998763

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=93.39  E-value=0.29  Score=58.72  Aligned_cols=118  Identities=14%  Similarity=0.175  Sum_probs=64.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhccccc--CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCC---ccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE--AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCK---LEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~--~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~---~~~~~~~~~~l~~~l   88 (1237)
                      +++.|.|.+|.||||+++++.....+.  .-...+.+......-...+.+.+...+......   .........-+.+.+
T Consensus       168 ~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiHrlL  247 (615)
T PRK10875        168 RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLHRLL  247 (615)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHHHHh
Confidence            588999999999999999987644221  112456666666655555665554433211000   000000112222222


Q ss_pred             cC------------Cc---EEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHH
Q 000887           89 FK------------KK---FLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        89 ~~------------~~---~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~  134 (1237)
                      ..            .+   -++|+|.+.-.+...+..+...+   .+++|+|+---..+.+
T Consensus       248 g~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al---~~~~rlIlvGD~~QL~  305 (615)
T PRK10875        248 GAQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDAL---PPHARVIFLGDRDQLA  305 (615)
T ss_pred             CcCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhc---ccCCEEEEecchhhcC
Confidence            11            11   38999998444444444555544   4578888877655443

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=93.36  E-value=0.042  Score=58.94  Aligned_cols=77  Identities=22%  Similarity=0.278  Sum_probs=41.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +-|.++|+.|+|||++++..........|- +.-+..+...+...+++.+-..+.......-.+          -.+++.
T Consensus        34 ~pvLl~G~~GtGKT~li~~~l~~l~~~~~~-~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP----------~~~k~l  102 (272)
T PF12775_consen   34 RPVLLVGPSGTGKTSLIQNFLSSLDSDKYL-VITINFSAQTTSNQLQKIIESKLEKRRGRVYGP----------PGGKKL  102 (272)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHCSTTCCEE-EEEEES-TTHHHHHHHHCCCTTECECTTEEEEE----------ESSSEE
T ss_pred             CcEEEECCCCCchhHHHHhhhccCCccccc-eeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCC----------CCCcEE
Confidence            457899999999999999977643332221 334455544443333322222211110000000          125889


Q ss_pred             EEEEeCCC
Q 000887           94 LIVLDDVW  101 (1237)
Q Consensus        94 LlvlDdv~  101 (1237)
                      ++.+||+.
T Consensus       103 v~fiDDlN  110 (272)
T PF12775_consen  103 VLFIDDLN  110 (272)
T ss_dssp             EEEEETTT
T ss_pred             EEEecccC
Confidence            99999993

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=93.35  E-value=0.56  Score=55.22  Aligned_cols=130  Identities=16%  Similarity=0.158  Sum_probs=73.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhccccc------CC-CCeEEEEEcC-----CcCH------------HHHHHHHHHHhhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTE------AF-EPKAWVCVSD-----DFDV------------LRISKAILDSIKRS   70 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~~~~------~f-~~~~w~~~~~-----~~~~------------~~~~~~i~~~l~~~   70 (1237)
                      .|+|+|+.|+|||||.+.++......      .- -.+.|++-..     ..++            ....+..+.+++-+
T Consensus       350 riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~F~  429 (530)
T COG0488         350 RIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFGFT  429 (530)
T ss_pred             EEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcCCC
Confidence            68999999999999999985432110      00 1122332111     0011            23334444444433


Q ss_pred             CC-------CccCHHHHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCe
Q 000887           71 SC-------KLEDLNSVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKN  142 (1237)
Q Consensus        71 ~~-------~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~  142 (1237)
                      ..       .....+..+-.+...+..++=++|+|.=.++ +.+..+++...+..+ +| .||+.|-++.+..... ..+
T Consensus       430 ~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f-~G-tvl~VSHDr~Fl~~va-~~i  506 (530)
T COG0488         430 GEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDF-EG-TVLLVSHDRYFLDRVA-TRI  506 (530)
T ss_pred             hHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhC-CC-eEEEEeCCHHHHHhhc-ceE
Confidence            22       1233444555566677789999999997543 234444455544433 34 4999999999887654 345


Q ss_pred             EeCCC
Q 000887          143 YELKL  147 (1237)
Q Consensus       143 ~~l~~  147 (1237)
                      +.+.+
T Consensus       507 ~~~~~  511 (530)
T COG0488         507 WLVED  511 (530)
T ss_pred             EEEcC
Confidence            55553

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.34  E-value=0.34  Score=50.74  Aligned_cols=48  Identities=19%  Similarity=0.180  Sum_probs=32.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAI   63 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i   63 (1237)
                      -.++.|.|.+|+|||++|.+++....+.. ..++|++...  +..++.+.+
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g-~~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNG-YSVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCC-CcEEEEeCCC--CHHHHHHHH
Confidence            35899999999999999988766443333 3467776333  344444444

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=93.34  E-value=0.52  Score=48.44  Aligned_cols=23  Identities=30%  Similarity=0.388  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|.|||||.+.++..
T Consensus        27 e~~~i~G~nGsGKSTLl~~l~G~   49 (201)
T cd03231          27 EALQVTGPNGSGKTTLLRILAGL   49 (201)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            48999999999999999998763

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=93.33  E-value=0.52  Score=58.83  Aligned_cols=167  Identities=16%  Similarity=0.138  Sum_probs=80.6

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc--ccc-------------CCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCcc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK--LTE-------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLE   75 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~--~~~-------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~   75 (1237)
                      ++.+++.|+|+.+.||||+.+.++-..  .+.             .|+ .++...++..++..-...+...+        
T Consensus       325 ~~~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~-~i~~~ig~~~si~~~lStfS~~m--------  395 (782)
T PRK00409        325 FDKTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFK-EIFADIGDEQSIEQSLSTFSGHM--------  395 (782)
T ss_pred             CCceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccc-eEEEecCCccchhhchhHHHHHH--------
Confidence            345789999999999999999875421  000             111 23344444333322222222111        


Q ss_pred             CHHHHHHHHHHHhcCCcEEEEEeCCCCCC-hhhHHHh----hccccCCCCCcEEEEEeCchhHHHhhcCCCeEeCCCCCh
Q 000887           76 DLNSVQLELKETVFKKKFLIVLDDVWSER-YDLWQAL----KSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELKLLSD  150 (1237)
Q Consensus        76 ~~~~~~~~l~~~l~~~~~LlvlDdv~~~~-~~~~~~~----~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l~~l~~  150 (1237)
                        .+....+. .+ ..+-|+++|...... ......+    ...+.  ..|+.+|+||-+..+.........+....+..
T Consensus       396 --~~~~~Il~-~~-~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~~~~~~~v~~~~~~~  469 (782)
T PRK00409        396 --TNIVRILE-KA-DKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALMYNREGVENASVEF  469 (782)
T ss_pred             --HHHHHHHH-hC-CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHHHhcCCCeEEEEEEE
Confidence              11222222 22 477899999985432 1222222    22222  24789999999987765433222111111111


Q ss_pred             -hhhHHHHHHHhcCCCCCCCCCChHHHHHHHHHHccCCchHHHHHHhHhhc
Q 000887          151 -DDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRS  200 (1237)
Q Consensus       151 -~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~PLal~~~~~~l~~  200 (1237)
                       ++......+..  .+...     ...|-+|++++ |+|-.+.--|..+..
T Consensus       470 d~~~l~~~Ykl~--~G~~g-----~S~a~~iA~~~-Glp~~ii~~A~~~~~  512 (782)
T PRK00409        470 DEETLRPTYRLL--IGIPG-----KSNAFEIAKRL-GLPENIIEEAKKLIG  512 (782)
T ss_pred             ecCcCcEEEEEe--eCCCC-----CcHHHHHHHHh-CcCHHHHHHHHHHHh
Confidence             11111111111  11111     34577888887 566666655555443

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.30  E-value=0.66  Score=48.25  Aligned_cols=23  Identities=30%  Similarity=0.354  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|.|||||++.++..
T Consensus        38 e~~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         38 EALLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            37999999999999999998763

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=93.28  E-value=0.0048  Score=60.67  Aligned_cols=88  Identities=17%  Similarity=0.153  Sum_probs=78.7

Q ss_pred             ccccc-ccccCCCCCCeEEccCCCccccchhhcccCCccEEEcCccccCccCChhhcccccccEEeccCCCccccCcccc
Q 000887          412 ITEVP-ISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGM  490 (1237)
Q Consensus       412 i~~lp-~~~~~l~~Lr~L~L~~~~i~~lp~~i~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~~ip~~~  490 (1237)
                      ++++| .++.....-++||++.|++-.+-..|+.+..|..||++.| .+..+|.+++.+..++++++..| .....|..+
T Consensus        30 ~s~~~v~ei~~~kr~tvld~~s~r~vn~~~n~s~~t~~~rl~~skn-q~~~~~~d~~q~~e~~~~~~~~n-~~~~~p~s~  107 (326)
T KOG0473|consen   30 LSEIPVREIASFKRVTVLDLSSNRLVNLGKNFSILTRLVRLDLSKN-QIKFLPKDAKQQRETVNAASHKN-NHSQQPKSQ  107 (326)
T ss_pred             hcccchhhhhccceeeeehhhhhHHHhhccchHHHHHHHHHhccHh-hHhhChhhHHHHHHHHHHHhhcc-chhhCCccc
Confidence            44555 4567788999999999999888889999999999999998 99999999999999999999888 789999999


Q ss_pred             cccccccccce
Q 000887          491 KELKCLRTLTN  501 (1237)
Q Consensus       491 ~~L~~L~~L~~  501 (1237)
                      ++++.++.++.
T Consensus       108 ~k~~~~k~~e~  118 (326)
T KOG0473|consen  108 KKEPHPKKNEQ  118 (326)
T ss_pred             cccCCcchhhh
Confidence            99999998865

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=93.27  E-value=0.058  Score=53.82  Aligned_cols=22  Identities=32%  Similarity=0.434  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +|+|.|.+|+||||+|++++..
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998874

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.26  E-value=0.25  Score=60.18  Aligned_cols=82  Identities=18%  Similarity=0.128  Sum_probs=55.4

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHH
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKET   87 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~   87 (1237)
                      -+++-|+|.+|+|||+||.+++....+ .-..++|++.....+.     ..+.+++....     .....++....+...
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~a~~-~G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~~l  133 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVANAQA-AGGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIADML  133 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH-cCCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHHHH
Confidence            478889999999999999987653322 2345789987666553     35566654322     344556666666665


Q ss_pred             hcC-CcEEEEEeCC
Q 000887           88 VFK-KKFLIVLDDV  100 (1237)
Q Consensus        88 l~~-~~~LlvlDdv  100 (1237)
                      .+. +.-+||+|.+
T Consensus       134 v~~~~~~LVVIDSI  147 (790)
T PRK09519        134 IRSGALDIVVIDSV  147 (790)
T ss_pred             hhcCCCeEEEEcch
Confidence            544 5778999998

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=93.25  E-value=0.7  Score=49.01  Aligned_cols=65  Identities=14%  Similarity=0.237  Sum_probs=36.2

Q ss_pred             HHHHHHHHHhcCCcEEEEEeCCCCC-ChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCeEeC
Q 000887           79 SVQLELKETVFKKKFLIVLDDVWSE-RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYEL  145 (1237)
Q Consensus        79 ~~~~~l~~~l~~~~~LlvlDdv~~~-~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l  145 (1237)
                      ...-.+.+.+-.++=++|+|+.... +......+...+.....|..||++|.+......  ....+.+
T Consensus       143 ~~rl~la~aL~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sh~~~~~~~--~d~~~~l  208 (236)
T cd03253         143 KQRVAIARAILKNPPILLLDEATSALDTHTEREIQAALRDVSKGRTTIVIAHRLSTIVN--ADKIIVL  208 (236)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCHHHHHh--CCEEEEE
Confidence            3334456666778899999998542 112222233333222226678888888776643  3444444

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=93.24  E-value=0.71  Score=48.69  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|+|||||++.++..
T Consensus        30 ~~~~i~G~nGsGKSTLl~~l~G~   52 (229)
T cd03254          30 ETVAIVGPTGAGKTTLINLLMRF   52 (229)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            37999999999999999998763

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=93.23  E-value=0.039  Score=50.07  Aligned_cols=27  Identities=41%  Similarity=0.639  Sum_probs=17.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHhcccccCCC
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDKLTEAFE   43 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~~~~~f~   43 (1237)
                      |-|.|.+|+|||++|++++.. ....|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~-~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARS-LGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHH-TT--EE
T ss_pred             EeeECCCccHHHHHHHHHHHH-cCCcee
Confidence            679999999999999998874 444453

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=93.19  E-value=0.18  Score=47.42  Aligned_cols=102  Identities=18%  Similarity=0.337  Sum_probs=52.6

Q ss_pred             hhhhhcCCCCCccEEEcccccccccc-ccccCCCCCCeEEccCCCccccch-hhcccCCccEEEcCccccCccCChh-hc
Q 000887          391 VLSDLLPQCKKLRVLSLGSYCITEVP-ISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPSR-IG  467 (1237)
Q Consensus       391 ~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~~~~l~~Lr~L~L~~~~i~~lp~-~i~~L~~L~~L~L~~~~~l~~lp~~-i~  467 (1237)
                      +.+..|.++++|+.+.+.. .+..++ ..|..++.|+.+++.++ +..++. .|.+..+|+.+.+.+  .+..++.. +.
T Consensus         3 i~~~~F~~~~~l~~i~~~~-~~~~I~~~~F~~~~~l~~i~~~~~-~~~i~~~~F~~~~~l~~i~~~~--~~~~i~~~~F~   78 (129)
T PF13306_consen    3 IGNNAFYNCSNLESITFPN-TIKKIGENAFSNCTSLKSINFPNN-LTSIGDNAFSNCKSLESITFPN--NLKSIGDNAFS   78 (129)
T ss_dssp             E-TTTTTT-TT--EEEETS-T--EE-TTTTTT-TT-SEEEESST-TSCE-TTTTTT-TT-EEEEETS--TT-EE-TTTTT
T ss_pred             ECHHHHhCCCCCCEEEECC-CeeEeChhhccccccccccccccc-ccccceeeeecccccccccccc--ccccccccccc
Confidence            3455677777777777764 466664 45677777888877764 666655 677777778877765  34444443 45


Q ss_pred             ccccccEEeccCCCccccCccc-cccccccccc
Q 000887          468 NLVNLHYLNIEGASALRELPLG-MKELKCLRTL  499 (1237)
Q Consensus       468 ~L~~L~~L~l~~~~~l~~ip~~-~~~L~~L~~L  499 (1237)
                      .+.+|+.+++..+  +..++.. +.+. +|+.+
T Consensus        79 ~~~~l~~i~~~~~--~~~i~~~~f~~~-~l~~i  108 (129)
T PF13306_consen   79 NCTNLKNIDIPSN--ITEIGSSSFSNC-NLKEI  108 (129)
T ss_dssp             T-TTECEEEETTT---BEEHTTTTTT--T--EE
T ss_pred             ccccccccccCcc--ccEEchhhhcCC-CceEE
Confidence            6777777777553  4455443 4444 55544

>COG4240 Predicted kinase [General function prediction only]

Probab=93.19  E-value=0.29  Score=48.51  Aligned_cols=84  Identities=14%  Similarity=0.072  Sum_probs=51.6

Q ss_pred             CCCCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhh-----ccCCCccCHHHHHHH
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIK-----RSSCKLEDLNSVQLE   83 (1237)
Q Consensus         9 ~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~-----~~~~~~~~~~~~~~~   83 (1237)
                      .-+++-+++|.|+-|+||||++..++.....+.-..++..+..+=.-..+-+..++++..     +......++.-....
T Consensus        46 e~grPli~gisGpQGSGKStls~~i~~~L~~kg~ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnV  125 (300)
T COG4240          46 ERGRPLIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNV  125 (300)
T ss_pred             hcCCceEEEeecCCCCchhhHHHHHHHHHHHhcccceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHH
Confidence            446688999999999999999999887553333236667765544333333344444432     122244555555566


Q ss_pred             HHHHhcCCc
Q 000887           84 LKETVFKKK   92 (1237)
Q Consensus        84 l~~~l~~~~   92 (1237)
                      +....+++.
T Consensus       126 Lnai~~g~~  134 (300)
T COG4240         126 LNAIARGGP  134 (300)
T ss_pred             HHHHhcCCC
Confidence            666656553

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=93.18  E-value=0.13  Score=50.23  Aligned_cols=32  Identities=19%  Similarity=0.328  Sum_probs=25.4

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCC
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF   42 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f   42 (1237)
                      ...++++|+|..|+|||||+.++........+
T Consensus         4 ~~~~ii~ivG~sgsGKTTLi~~li~~l~~~g~   35 (173)
T PRK10751          4 TMIPLLAIAAWSGTGKTTLLKKLIPALCARGI   35 (173)
T ss_pred             CCceEEEEECCCCChHHHHHHHHHHHHhhcCC
Confidence            35679999999999999999999875433333

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=93.17  E-value=0.3  Score=55.16  Aligned_cols=84  Identities=15%  Similarity=0.133  Sum_probs=47.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhhccC------CCccCHHH------H
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIKRSS------CKLEDLNS------V   80 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~~~~------~~~~~~~~------~   80 (1237)
                      ..++|.|..|+|||||+..++...   ..+.++..-++.. ..+.++.+.++..-+...      .....+.+      .
T Consensus       163 qrigI~G~sG~GKSTLL~~I~~~~---~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~  239 (444)
T PRK08972        163 QRMGLFAGSGVGKSVLLGMMTRGT---TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCET  239 (444)
T ss_pred             CEEEEECCCCCChhHHHHHhccCC---CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHH
Confidence            468999999999999999987531   2244555555443 334445555433321110      01111111      1


Q ss_pred             HHHHHHHh--cCCcEEEEEeCC
Q 000887           81 QLELKETV--FKKKFLIVLDDV  100 (1237)
Q Consensus        81 ~~~l~~~l--~~~~~LlvlDdv  100 (1237)
                      +-.+.+++  +++++|+++||+
T Consensus       240 A~tiAEyfrd~G~~VLl~~Dsl  261 (444)
T PRK08972        240 ATTIAEYFRDQGLNVLLLMDSL  261 (444)
T ss_pred             HHHHHHHHHHcCCCEEEEEcCh
Confidence            12244444  468999999999

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=93.15  E-value=0.32  Score=50.67  Aligned_cols=28  Identities=21%  Similarity=0.300  Sum_probs=24.8

Q ss_pred             CCCcEEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        10 ~~~~~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ...+-++..+|++|+||.-.|+.+++..
T Consensus       107 p~KPLvLSfHG~tGTGKN~Va~iiA~n~  134 (344)
T KOG2170|consen  107 PRKPLVLSFHGWTGTGKNYVAEIIAENL  134 (344)
T ss_pred             CCCCeEEEecCCCCCchhHHHHHHHHHH
Confidence            4677899999999999999999998864

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=93.14  E-value=0.16  Score=54.09  Aligned_cols=86  Identities=20%  Similarity=0.164  Sum_probs=47.7

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-------CccCHHHHHHH
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-------KLEDLNSVQLE   83 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-------~~~~~~~~~~~   83 (1237)
                      .+..+|.|.|.+|+|||||+.++.... +... .++.+. .+..+..+  .+.++..+.+..       .-.+.......
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~~l-~~~~-~~~VI~-gD~~t~~D--a~rI~~~g~pvvqi~tG~~Chl~a~mv~~A  176 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLMRL-KDSV-PCAVIE-GDQQTVND--AARIRATGTPAIQVNTGKGCHLDAQMIADA  176 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHh-ccCC-CEEEEC-CCcCcHHH--HHHHHhcCCcEEEecCCCCCcCcHHHHHHH
Confidence            457899999999999999999988743 2222 233332 22222221  122333332211       12334445555


Q ss_pred             HHHHhcCCcEEEEEeCCC
Q 000887           84 LKETVFKKKFLIVLDDVW  101 (1237)
Q Consensus        84 l~~~l~~~~~LlvlDdv~  101 (1237)
                      +........-++|++++-
T Consensus       177 l~~L~~~~~d~liIEnvG  194 (290)
T PRK10463        177 APRLPLDDNGILFIENVG  194 (290)
T ss_pred             HHHHhhcCCcEEEEECCC
Confidence            555444455778899983

>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D

Probab=93.12  E-value=0.45  Score=50.27  Aligned_cols=23  Identities=35%  Similarity=0.444  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|..|.|||||.+.++..
T Consensus        27 e~~~i~G~nGsGKSTLl~~l~g~   49 (232)
T cd03300          27 EFFTLLGPSGCGKTTLLRLIAGF   49 (232)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998774

PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.12  E-value=0.37  Score=48.51  Aligned_cols=94  Identities=26%  Similarity=0.357  Sum_probs=50.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcE
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      .-|-++|.=|.|||.|++++.+.. .......+-|  ... ++.+                  ...+...++.  +..|+
T Consensus        86 NnVLLwGaRGtGKSSLVKA~~~e~-~~~glrLVEV--~k~-dl~~------------------Lp~l~~~Lr~--~~~kF  141 (287)
T COG2607          86 NNVLLWGARGTGKSSLVKALLNEY-ADEGLRLVEV--DKE-DLAT------------------LPDLVELLRA--RPEKF  141 (287)
T ss_pred             cceEEecCCCCChHHHHHHHHHHH-HhcCCeEEEE--cHH-HHhh------------------HHHHHHHHhc--CCceE
Confidence            358899999999999999987743 3333222222  111 1111                  1111112221  25799


Q ss_pred             EEEEeCCC-CCChhhHHHhhccccC---CCCCcEEEEEeCch
Q 000887           94 LIVLDDVW-SERYDLWQALKSPFMA---GAPGSRIIVTTRSM  131 (1237)
Q Consensus        94 LlvlDdv~-~~~~~~~~~~~~~~~~---~~~~~~iliTtR~~  131 (1237)
                      +|..||.. ++..+.+..+...+-.   ..+...++..|.++
T Consensus       142 IlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNR  183 (287)
T COG2607         142 ILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNR  183 (287)
T ss_pred             EEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCC
Confidence            99999982 3333455555444433   24455555555544

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=93.11  E-value=0.2  Score=56.05  Aligned_cols=71  Identities=20%  Similarity=0.189  Sum_probs=41.6

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      ++=|.++|++|.|||-||++++......     +|...+..+  +.++    -        ......++..+.+.-..-+
T Consensus       337 PKGVLLvGPPGTGKTlLARAvAGEA~VP-----FF~~sGSEF--dEm~----V--------GvGArRVRdLF~aAk~~AP  397 (752)
T KOG0734|consen  337 PKGVLLVGPPGTGKTLLARAVAGEAGVP-----FFYASGSEF--DEMF----V--------GVGARRVRDLFAAAKARAP  397 (752)
T ss_pred             CCceEEeCCCCCchhHHHHHhhcccCCC-----eEeccccch--hhhh----h--------cccHHHHHHHHHHHHhcCC
Confidence            4568899999999999999998753211     222223332  2222    1        1112223333333334569


Q ss_pred             EEEEEeCCCC
Q 000887           93 FLIVLDDVWS  102 (1237)
Q Consensus        93 ~LlvlDdv~~  102 (1237)
                      ++|.+|.++.
T Consensus       398 cIIFIDEiDa  407 (752)
T KOG0734|consen  398 CIIFIDEIDA  407 (752)
T ss_pred             eEEEEechhh
Confidence            9999999854

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=93.11  E-value=0.7  Score=48.38  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|+|||||++.++..
T Consensus        31 ~~~~i~G~nGsGKSTLl~~i~G~   53 (220)
T cd03245          31 EKVAIIGRVGSGKSTLLKLLAGL   53 (220)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            48999999999999999998763

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=93.10  E-value=0.074  Score=53.41  Aligned_cols=24  Identities=29%  Similarity=0.382  Sum_probs=21.7

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...|.|+|++|+||||+|++++..
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999999999875

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=93.10  E-value=0.97  Score=53.45  Aligned_cols=145  Identities=14%  Similarity=0.044  Sum_probs=0.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhcCCcEEE
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKFLI   95 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~Ll   95 (1237)
                      |.++|++|.|||-+|++|+-.       .-.=+-.-.++.....+            .....+.+++.+.+.-..++|+|
T Consensus       708 ILLYGPPGTGKTLlAKAVATE-------csL~FlSVKGPELLNMY------------VGqSE~NVR~VFerAR~A~PCVI  768 (953)
T KOG0736|consen  708 ILLYGPPGTGKTLLAKAVATE-------CSLNFLSVKGPELLNMY------------VGQSEENVREVFERARSAAPCVI  768 (953)
T ss_pred             eEEECCCCCchHHHHHHHHhh-------ceeeEEeecCHHHHHHH------------hcchHHHHHHHHHHhhccCCeEE


Q ss_pred             EEeCC-----------------CCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhh-----cCCCeEeCCCCChhhh
Q 000887           96 VLDDV-----------------WSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTM-----GSGKNYELKLLSDDDC  153 (1237)
Q Consensus        96 vlDdv-----------------~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~-----~~~~~~~l~~l~~~ea  153 (1237)
                      .||.+                 +..-..-++++-........+.-||=.|-.++.....     +-++-+.+++=+.+|.
T Consensus       769 FFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~es  848 (953)
T KOG0736|consen  769 FFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAES  848 (953)
T ss_pred             EeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHH


Q ss_pred             HHHHHHHhcCCCCCCCCCChHHHHHH
Q 000887          154 WSVFVAHAFEGRDAGTHGNFESTRQR  179 (1237)
Q Consensus       154 ~~l~~~~~~~~~~~~~~~~~~~~~~~  179 (1237)
                      ..=..+..-+.-.-.++-.+.++|+.
T Consensus       849 k~~vL~AlTrkFkLdedVdL~eiAk~  874 (953)
T KOG0736|consen  849 KLRVLEALTRKFKLDEDVDLVEIAKK  874 (953)
T ss_pred             HHHHHHHHHHHccCCCCcCHHHHHhh

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=93.08  E-value=0.51  Score=53.40  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +..||+|.+|.||||+.+.++...
T Consensus       102 ~rygLiG~nG~Gkst~L~~i~~~e  125 (614)
T KOG0927|consen  102 RRYGLIGPNGSGKSTFLRAIAGRE  125 (614)
T ss_pred             ceEEEEcCCCCcHhHHHHHHhcCC
Confidence            468999999999999999998764

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=93.07  E-value=1.1  Score=46.11  Aligned_cols=59  Identities=14%  Similarity=0.137  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHhcCCcEEEEEeCCCCCC-hhhHHHhhcc-cc-CCCCCcEEEEEeCchhHHH
Q 000887           77 LNSVQLELKETVFKKKFLIVLDDVWSER-YDLWQALKSP-FM-AGAPGSRIIVTTRSMDVAL  135 (1237)
Q Consensus        77 ~~~~~~~l~~~l~~~~~LlvlDdv~~~~-~~~~~~~~~~-~~-~~~~~~~iliTtR~~~~~~  135 (1237)
                      .+...-.+.+.+..++=++++|+-...- ....+.+... +. ....|..||++|.+.....
T Consensus       131 G~~qrv~laral~~~p~llllDEP~~~LD~~~~~~l~~~ll~~~~~~~~tvi~~sh~~~~~~  192 (204)
T cd03250         131 GQKQRISLARAVYSDADIYLLDDPLSAVDAHVGRHIFENCILGLLLNNKTRILVTHQLQLLP  192 (204)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHHhccCCCEEEEEeCCHHHHh
Confidence            4444445667777889999999974421 1222233331 21 1223677888888776654

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK00279 adk adenylate kinase; Reviewed

Probab=93.07  E-value=0.17  Score=52.75  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|.|.|++|+||||+|+.++..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~   23 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEK   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999998764

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=93.07  E-value=0.35  Score=52.13  Aligned_cols=52  Identities=13%  Similarity=0.219  Sum_probs=35.8

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      .+++|.|.+|+|||++|.+++.+.....-..++|++...  +..++...++...
T Consensus        20 ~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlEm--~~~~l~~R~la~~   71 (259)
T PF03796_consen   20 ELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSLEM--SEEELAARLLARL   71 (259)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESSS---HHHHHHHHHHHH
T ss_pred             cEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCCC--CHHHHHHHHHHHh
Confidence            489999999999999999998866443335577776543  3445555555544

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK13531 regulatory ATPase RavA; Provisional

Probab=93.06  E-value=0.67  Score=53.06  Aligned_cols=23  Identities=26%  Similarity=0.364  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .-|.|.|++|+|||++|+.++..
T Consensus        40 ~hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         40 ESVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             CCEEEECCCChhHHHHHHHHHHH
Confidence            35889999999999999998774

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=93.04  E-value=0.74  Score=48.75  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|+|||||++.++.-
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~Gl   51 (234)
T cd03251          29 ETVALVGPSGSGKSTLVNLIPRF   51 (234)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            37999999999999999998763

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=93.03  E-value=0.074  Score=53.27  Aligned_cols=23  Identities=30%  Similarity=0.460  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++|.+.|++|+||||+|+++...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999998764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.01  E-value=0.98  Score=46.84  Aligned_cols=70  Identities=27%  Similarity=0.339  Sum_probs=41.9

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc-CC
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF-KK   91 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~   91 (1237)
                      -+-|.++|++|.|||-||++|+.... ..|     ++++..        ++......      +-+.+...+.+.-+ .+
T Consensus       166 wrgiLLyGPPGTGKSYLAKAVATEAn-STF-----FSvSSS--------DLvSKWmG------ESEkLVknLFemARe~k  225 (439)
T KOG0739|consen  166 WRGILLYGPPGTGKSYLAKAVATEAN-STF-----FSVSSS--------DLVSKWMG------ESEKLVKNLFEMARENK  225 (439)
T ss_pred             ceeEEEeCCCCCcHHHHHHHHHhhcC-Cce-----EEeehH--------HHHHHHhc------cHHHHHHHHHHHHHhcC
Confidence            36688999999999999999987433 222     233322        11111111      11344444444433 47


Q ss_pred             cEEEEEeCCCC
Q 000887           92 KFLIVLDDVWS  102 (1237)
Q Consensus        92 ~~LlvlDdv~~  102 (1237)
                      +-+|.+|.++.
T Consensus       226 PSIIFiDEiDs  236 (439)
T KOG0739|consen  226 PSIIFIDEIDS  236 (439)
T ss_pred             CcEEEeehhhh
Confidence            89999999953

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=92.99  E-value=0.52  Score=49.85  Aligned_cols=22  Identities=32%  Similarity=0.472  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        27 e~~~l~G~nGsGKSTLl~~l~G   48 (232)
T cd03218          27 EIVGLLGPNGAGKTTTFYMIVG   48 (232)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999876

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=92.98  E-value=1.3  Score=46.89  Aligned_cols=22  Identities=36%  Similarity=0.613  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~G   50 (237)
T cd03252          29 EVVGIVGRSGSGKSTLTKLIQR   50 (237)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3799999999999999999875

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=92.97  E-value=0.3  Score=55.93  Aligned_cols=88  Identities=19%  Similarity=0.190  Sum_probs=52.3

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCC-cCHHHHHHHHHHHhh--cc-----------CCCccCH-H
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-FDVLRISKAILDSIK--RS-----------SCKLEDL-N   78 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-~~~~~~~~~i~~~l~--~~-----------~~~~~~~-~   78 (1237)
                      ..++|.|.+|+|||+|+.+++....+.+-+.++++-++.. ..+.++...+...-.  ..           ......+ .
T Consensus       162 QR~gIfgg~GvGKs~L~~~~~~~~~~~~~dv~V~~lIGERgrEv~efi~~~~~~~~~~~~~~~~~rsvvv~atsd~p~~~  241 (494)
T CHL00060        162 GKIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVALVYGQMNEPPGA  241 (494)
T ss_pred             CEEeeecCCCCChhHHHHHHHHHHHHhcCCeEEEEEeccCchHHHHHHHHHHhcCccccCcccccceEEEEECCCCCHHH
Confidence            4689999999999999999876422222266778777654 345566665554110  00           0011111 1


Q ss_pred             -----HHHHHHHHHhcC---CcEEEEEeCCC
Q 000887           79 -----SVQLELKETVFK---KKFLIVLDDVW  101 (1237)
Q Consensus        79 -----~~~~~l~~~l~~---~~~LlvlDdv~  101 (1237)
                           ..+-.+.+++++   +++||++||+.
T Consensus       242 R~~a~~~A~tiAEyfrd~g~~~VLll~DslT  272 (494)
T CHL00060        242 RMRVGLTALTMAEYFRDVNKQDVLLFIDNIF  272 (494)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCEEEEcccch
Confidence                 222235566643   49999999993

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=92.95  E-value=0.066  Score=29.49  Aligned_cols=14  Identities=36%  Similarity=0.612  Sum_probs=4.7

Q ss_pred             CCeEEccCCCcccc
Q 000887          425 LRYLNFSRSEIQCL  438 (1237)
Q Consensus       425 Lr~L~L~~~~i~~l  438 (1237)
                      ||.|++++|.++++
T Consensus         3 L~~L~l~~n~L~~l   16 (17)
T PF13504_consen    3 LRTLDLSNNRLTSL   16 (17)
T ss_dssp             -SEEEETSS--SSE
T ss_pred             cCEEECCCCCCCCC
Confidence            44444444444433

...

>TIGR00416 sms DNA repair protein RadA

Probab=92.95  E-value=0.39  Score=55.82  Aligned_cols=80  Identities=18%  Similarity=0.188  Sum_probs=46.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      .++.|.|.+|+|||||+.+++....+.. ..++|++....  ..++.. -+.+++....     ...+.+++...+.+  
T Consensus        95 svilI~G~pGsGKTTL~lq~a~~~a~~g-~kvlYvs~EEs--~~qi~~-ra~rlg~~~~~l~~~~e~~~~~I~~~i~~--  168 (454)
T TIGR00416        95 SLILIGGDPGIGKSTLLLQVACQLAKNQ-MKVLYVSGEES--LQQIKM-RAIRLGLPEPNLYVLSETNWEQICANIEE--  168 (454)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHhcC-CcEEEEECcCC--HHHHHH-HHHHcCCChHHeEEcCCCCHHHHHHHHHh--
Confidence            6889999999999999999876443322 35788875433  333221 1223332111     12334444433332  


Q ss_pred             cCCcEEEEEeCC
Q 000887           89 FKKKFLIVLDDV  100 (1237)
Q Consensus        89 ~~~~~LlvlDdv  100 (1237)
                       .+.-++|+|.+
T Consensus       169 -~~~~~vVIDSI  179 (454)
T TIGR00416       169 -ENPQACVIDSI  179 (454)
T ss_pred             -cCCcEEEEecc
Confidence             25567888887

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=92.94  E-value=0.72  Score=47.81  Aligned_cols=23  Identities=30%  Similarity=0.352  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|+|||||++.++.-
T Consensus        14 e~~~l~G~NGsGKSTLlk~i~Gl   36 (213)
T PRK15177         14 EHIGILAAPGSGKTTLTRLLCGL   36 (213)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998863

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=92.93  E-value=0.16  Score=53.51  Aligned_cols=84  Identities=18%  Similarity=0.219  Sum_probs=45.5

Q ss_pred             EEEEEEcCCCCcHHHHHHH-HHhcccccCCCCe-EEEEEcCC-cCHHHHHHHHHHHhhcc------CCCccCHHH-----
Q 000887           14 RVIPLVGMGGIGKTTLAQE-VYNDKLTEAFEPK-AWVCVSDD-FDVLRISKAILDSIKRS------SCKLEDLNS-----   79 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~-~~~~~~~~~f~~~-~w~~~~~~-~~~~~~~~~i~~~l~~~------~~~~~~~~~-----   79 (1237)
                      ..++|.|.+|+|||+||.. +++.   ..-+.+ +++-++.. ..+.++.+++...-...      ......+..     
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~---~~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~  146 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQ---KGKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAP  146 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHh---cCCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHH
Confidence            4689999999999999744 4432   223444 55555544 34555555554322111      001111111     


Q ss_pred             -HHHHHHHHh--cCCcEEEEEeCC
Q 000887           80 -VQLELKETV--FKKKFLIVLDDV  100 (1237)
Q Consensus        80 -~~~~l~~~l--~~~~~LlvlDdv  100 (1237)
                       ..-.+.+++  +++.+|+|+||+
T Consensus       147 ~~a~aiAE~fr~~G~~Vlvl~Dsl  170 (274)
T cd01132         147 YTGCAMGEYFMDNGKHALIIYDDL  170 (274)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcCh
Confidence             112233333  468999999999

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.93  E-value=0.33  Score=56.38  Aligned_cols=80  Identities=23%  Similarity=0.267  Sum_probs=47.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhcccccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCC-----CccCHHHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      .++.|.|.+|+|||||+.+++....+. -..++|++....  ..++... +.+++....     ...+.+++...+.+  
T Consensus        81 s~~lI~G~pG~GKTtL~lq~a~~~a~~-g~~vlYvs~Ees--~~qi~~r-a~rlg~~~~~l~~~~e~~l~~i~~~i~~--  154 (446)
T PRK11823         81 SVVLIGGDPGIGKSTLLLQVAARLAAA-GGKVLYVSGEES--ASQIKLR-AERLGLPSDNLYLLAETNLEAILATIEE--  154 (446)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEEEcccc--HHHHHHH-HHHcCCChhcEEEeCCCCHHHHHHHHHh--
Confidence            588999999999999999987744322 235788875433  3333222 344432111     12334444444332  


Q ss_pred             cCCcEEEEEeCC
Q 000887           89 FKKKFLIVLDDV  100 (1237)
Q Consensus        89 ~~~~~LlvlDdv  100 (1237)
                       .+.-++|+|.+
T Consensus       155 -~~~~lVVIDSI  165 (446)
T PRK11823        155 -EKPDLVVIDSI  165 (446)
T ss_pred             -hCCCEEEEech
Confidence             35567888887

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=92.92  E-value=0.62  Score=54.86  Aligned_cols=68  Identities=15%  Similarity=0.131  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHhcCCcEEEEEeCCCCCChhhHHHhhccccCCCCCcEEEEEeCchhHHHhhcCCCeEeCC
Q 000887           77 LNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSGKNYELK  146 (1237)
Q Consensus        77 ~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~~~~~~~~~~~~~~iliTtR~~~~~~~~~~~~~~~l~  146 (1237)
                      ....+..+.+.|-.++=++++|.=.++-....-.....+....+| .+||.|-|+.+...+.+ .+++++
T Consensus       157 G~r~Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~~~g-tviiVSHDR~FLd~V~t-~I~~ld  224 (530)
T COG0488         157 GWRRRVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKRYPG-TVIVVSHDRYFLDNVAT-HILELD  224 (530)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHhCCC-cEEEEeCCHHHHHHHhh-heEEec
Confidence            344445566677778889999987543211111122222223455 79999999998876543 445544

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=92.84  E-value=0.78  Score=47.14  Aligned_cols=22  Identities=27%  Similarity=0.456  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|..|+|||||++.++.
T Consensus        34 e~~~i~G~nGsGKSTLl~~l~G   55 (202)
T cd03233          34 EMVLVLGRPGSGCSTLLKALAN   55 (202)
T ss_pred             cEEEEECCCCCCHHHHHHHhcc
Confidence            4899999999999999999866

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=92.83  E-value=0.84  Score=49.27  Aligned_cols=22  Identities=32%  Similarity=0.495  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHh
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|+|..|.|||||++.++.
T Consensus        31 e~~~IvG~nGsGKSTLl~~L~g   52 (275)
T cd03289          31 QRVGLLGRTGSGKSTLLSAFLR   52 (275)
T ss_pred             CEEEEECCCCCCHHHHHHHHhh
Confidence            3799999999999999999876

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=92.81  E-value=0.088  Score=50.14  Aligned_cols=20  Identities=35%  Similarity=0.647  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 000887           15 VIPLVGMGGIGKTTLAQEVY   34 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~   34 (1237)
                      .|+|+|.+|+||||+|..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999976

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=92.80  E-value=0.1  Score=49.12  Aligned_cols=24  Identities=29%  Similarity=0.571  Sum_probs=21.2

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .++|+|+|.+|+||||+...+...
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~   27 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE   27 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH
Confidence            689999999999999999986553

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=92.80  E-value=0.062  Score=55.95  Aligned_cols=51  Identities=24%  Similarity=0.208  Sum_probs=35.7

Q ss_pred             CCCCCcEEEEEEcCCCCcHHHHHHHHHhcccccCC-CCeEEEEEcCCcCHHH
Q 000887            8 SDAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF-EPKAWVCVSDDFDVLR   58 (1237)
Q Consensus         8 ~~~~~~~~v~i~G~~G~GKT~La~~~~~~~~~~~f-~~~~w~~~~~~~~~~~   58 (1237)
                      ...++..+|+|+|.||+|||||.-++......+.. -+|+-|+-+.+++--.
T Consensus        46 p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGs   97 (323)
T COG1703          46 PRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGS   97 (323)
T ss_pred             hcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCcc
Confidence            34567889999999999999999998775533333 3455665555554333

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=92.79  E-value=0.098  Score=52.35  Aligned_cols=23  Identities=39%  Similarity=0.603  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhcc
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 ~v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +|+|.|.+|+||||+|..++...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l   23 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQL   23 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999988743

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=92.79  E-value=0.35  Score=54.06  Aligned_cols=108  Identities=18%  Similarity=0.166  Sum_probs=56.0

Q ss_pred             CCcEEEEEEcCCCCcHHHHHHHHHhcc-cccCCCCeEEEEEcCCcCHHHHHHHHHHHhhccCCCccCHHHHHHHHHHHhc
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK-LTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~~v~i~G~~G~GKT~La~~~~~~~-~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ..++=+-|+|..|.|||.|.-.+|+.. .+..-  ++        -.-....++-..+............    +.+.+.
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~--R~--------HFh~Fm~~vh~~l~~~~~~~~~l~~----va~~l~  125 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKR--RV--------HFHEFMLDVHSRLHQLRGQDDPLPQ----VADELA  125 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCccccc--cc--------cccHHHHHHHHHHHHHhCCCccHHH----HHHHHH
Confidence            456779999999999999999998854 22111  01        1112223333333222122223333    334445


Q ss_pred             CCcEEEEEeCCCCCChhhHHHhhccccC-CCCCcEEEEEeCchhH
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMA-GAPGSRIIVTTRSMDV  133 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~~~~~~~~-~~~~~~iliTtR~~~~  133 (1237)
                      ++..||.||.+.-++..+..-+...+.. ...|. |||+|.+...
T Consensus       126 ~~~~lLcfDEF~V~DiaDAmil~rLf~~l~~~gv-vlVaTSN~~P  169 (362)
T PF03969_consen  126 KESRLLCFDEFQVTDIADAMILKRLFEALFKRGV-VLVATSNRPP  169 (362)
T ss_pred             hcCCEEEEeeeeccchhHHHHHHHHHHHHHHCCC-EEEecCCCCh
Confidence            6777999999855433332222222221 23466 5555555433

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=92.75  E-value=0.1  Score=52.86  Aligned_cols=24  Identities=21%  Similarity=0.368  Sum_probs=21.8

Q ss_pred             cEEEEEEcCCCCcHHHHHHHHHhc
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..+|.|.|.+|+||||+|..++..
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            468999999999999999998874

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=92.74  E-value=0.089  Score=52.99  Aligned_cols=23  Identities=39%  Similarity=0.494  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCCcHHHHHHHHHhc
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~~v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++++|.|++|+||||+++.++..
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999998774

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	1237
4fcg_A	328	Structure Of The Leucine-Rich Repeat Domain Of The		1e-04
4b8c_D	727	Nuclease Module Of The Yeast Ccr4-Not Complex Lengt		1e-04

>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type Iii Effector Xcv3220 (Xopl) Length = 328

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/120 (30%), Positives = 59/120 (49%), Gaps = 10/120 (8%)
Query: 932  SLTCLWSGGR-LPVT------LKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESI 984
            SL   W+G R LP +      LK L+I +     +  +   LP ++EEL + GC+ L + 
Sbjct: 187  SLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLP-KLEELDLRGCTALRNY 245
Query: 985  AERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPE--DALPSNVV 1042
               F   A L+ + +  C NL +LP  +  L+ L ++ +  C NL  LP     LP+N +
Sbjct: 246  PPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCI 305

>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex Length = 727

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 49/104 (47%), Gaps = 9/104 (8%)
Query: 402 LRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLK 461
           L  L L    +TE+P  I  L  LR L+ S + +  LP  + S F L+     +   +  
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDN-MVTT 307
Query: 462 LPSRIGNLVNLHYLNIEGASALRELPLGMKELKCL--RTLTNFI 503
           LP   GNL NL +L +EG       PL  + LK L  +++T  I
Sbjct: 308 LPWEFGNLCNLQFLGVEGN------PLEKQFLKILTEKSVTGLI 345

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	1237
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	1e-109
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	4e-85
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-49
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-23
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	6e-19
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	8e-19
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-18
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	1e-14
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-11
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	7e-05
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	2e-18
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	1e-17
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	3e-17
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-17
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	3e-15
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	1e-12
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-11
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	7e-12
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	3e-06
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	3e-05
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	8e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	7e-12
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-06
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	3e-06
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	8e-05
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-04
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	1e-10
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-09
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	3e-04
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	7e-10
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	1e-08
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	2e-06
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	1e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-08
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	7e-04
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	4e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	4e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	5e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-05
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-09
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-05
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-05
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	5e-04
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	8e-04
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-08
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-08
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	5e-07
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	2e-04
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	5e-04
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-08
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-06
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-06
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-05
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	1e-08
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	1e-08
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-08
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	4e-08
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	5e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	9e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	3e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	3e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	7e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	7e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	1e-04
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-04
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	3e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	7e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-07
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-07
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	6e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-04
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-04
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	7e-04
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	8e-04
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	3e-08
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-07
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-06
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	4e-08
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	2e-05
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	3e-05
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	8e-05
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	2e-04
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	9e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-07
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	9e-06
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	5e-05
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	2e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	6e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	6e-04
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	5e-07
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	6e-07
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	3e-06
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	6e-07
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	6e-05
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	5e-04
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	7e-07
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	5e-06
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-04
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	6e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	9e-07
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	9e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	9e-07
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	4e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	6e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-05
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	1e-06
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	3e-06
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	1e-06
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	6e-06
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	5e-06
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	5e-06
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	7e-06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-04
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	5e-06
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	7e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	7e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	6e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	8e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	8e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	8e-05
1o6v_A	466	Internalin A; bacterial infection, extracellular r	1e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-04
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	6e-06
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	7e-06
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	7e-06
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	1e-05
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	2e-05
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	4e-05
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	2e-05
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	8e-04
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	3e-05
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	2e-04
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	4e-05
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	9e-05
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	5e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	9e-05
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	5e-04
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	1e-04
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	3e-04
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	8e-04
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	1e-04
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	4e-04
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	2e-04
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	2e-04
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	2e-04
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	3e-04
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	3e-04
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	3e-04
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	6e-04
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	8e-04

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  354 bits (910), Expect = e-109
 Identities = 76/462 (16%), Positives = 143/462 (30%), Gaps = 66/462 (14%)

Query: 8   SDAANFRVIPLVGMGGIGKTTLAQEVYND-KLTEAFEP--KAWVCVSDDFDVLRISK--- 61
                   + + GM G GK+ LA E   D  L E   P    WV V        + K   
Sbjct: 142 KLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQN 201

Query: 62  ---AILDSIKRSSCKLEDLNSVQLELKETVFKK--KFLIVLDDVWSERYDLWQALKSPFM 116
               +      S     ++   +  L+  + +K  + L++LDDVW               
Sbjct: 202 LCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWV---------LK 252

Query: 117 AGAPGSRIIVTTRSMDVALTMGSGKN--YELKLLSDDDCWSVFVAHAFEGRDAGTHGNFE 174
           A     +I++TTR   V  ++   K        L  +    +               +  
Sbjct: 253 AFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM-----KKADLP 307

Query: 175 STRQRVVEKCKGLPLAARALGGLLRSKQG-VDEWRAILDSKIWNLQDKTEIPS------V 227
                ++++CKG PL    +G LLR      + +   L +K +    K+           
Sbjct: 308 EQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEA 367

Query: 228 LKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYF 287
           + +S   L   +K  +   ++L KD +   K L +LW  E             +      
Sbjct: 368 MSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME------------TEEVEDIL 415

Query: 288 HDLLSRSLFQKSSNTESK-YVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHF 346
            + +++SL     N +S  Y +HDL  D       + C +L D      +  + +  R+ 
Sbjct: 416 QEFVNKSLLFCDRNGKSFRYYLHDLQVDFLT---EKNCSQLQD----LHKKIITQFQRYH 468

Query: 347 SYLRSYDCDGMDKF------KVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCK 400
                        +        +      +    + F            +  + L+ +  
Sbjct: 469 QPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALMF-SLDWIKAKTELVGPAHLIHEFV 527

Query: 401 KLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAI 442
           + R          +        ++   LN      Q  P+ +
Sbjct: 528 EYR-----HILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIV 564

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  287 bits (735), Expect = 4e-85
 Identities = 61/388 (15%), Positives = 117/388 (30%), Gaps = 50/388 (12%)

Query: 14  RVIPLVGMGGIGKTTLAQEVYND---KLTEAFEPKAWVCVSDDF---------DVLRISK 61
             + L G  G GK+ +A +  +     +   ++   W+  S            D+L + K
Sbjct: 153 FFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLK 212

Query: 62  AILDSIKRSSC-KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAP 120
           +  D +   S   +  +   ++     + +   L V DDV  E    W        A   
Sbjct: 213 SEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRW--------AQEL 264

Query: 121 GSRIIVTTRSMDVALTMGSGK-NYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR 179
             R +VTTR ++++          E+  L  D+C+    A+             E    +
Sbjct: 265 RLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV---GEKEEDVLNK 321

Query: 180 VVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNL----------QDKTEIPSVLK 229
            +E   G P            K    E  A L++K+ +                +   L+
Sbjct: 322 TIELSSGNPATLMMFFKSCEPKT--FEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQ 379

Query: 230 LSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHD 289
                L    +   A+  V+P   +   K    +   +     S + +QL+D  +     
Sbjct: 380 RCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDI---CSNEEEQLDDEVADRLKR 436

Query: 290 LLSRSLFQKSSNTESK-YVMHDLVHDLAQWASGETCFR-----LDDQFSVDRQSNVFEKV 343
           L  R             + +  ++H   +              L+ +      +NV    
Sbjct: 437 LSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQTIANGISILEQRLLEIGNNNVSVPE 496

Query: 344 RHFSY----LRSYDCDGMDKFKVLDKVV 367
           RH        R      M      + V+
Sbjct: 497 RHIPSHFQKFRRSSASEMYPKTTEETVI 524

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score =  192 bits (488), Expect = 1e-49
 Identities = 81/469 (17%), Positives = 167/469 (35%), Gaps = 99/469 (21%)

Query: 16  IPLVGMGGIGKTTLAQEVYND-KLTEAFEPKA-WV----CVSDDFDVLRISKAILDSIKR 69
           + + G+ G GKT +A +V    K+    + K  W+    C S +  VL + + +L  I  
Sbjct: 153 VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE-TVLEMLQKLLYQIDP 211

Query: 70  SSCKLED--------LNSVQLELKETVFKKKF---LIVLDDVWSERYDLWQALKSPFMAG 118
           +     D        ++S+Q EL+  +  K +   L+VL +V + +   W A        
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK--AWNAFN------ 263

Query: 119 APGSRIIVTTRSMDVALTMGSGKNYELKL------LSDDDCWSVFVAHAFEGRDAGTHGN 172
               +I++TTR   V   + +     + L      L+ D+  S+      + R       
Sbjct: 264 -LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL-LKYLDCR------- 314

Query: 173 FESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSY 232
            +   +   E     P     +   +R   G+  W        W   +  ++ ++++ S 
Sbjct: 315 PQDLPR---EVLTTNPRRLSIIAESIR--DGLATW------DNWKHVNCDKLTTIIESSL 363

Query: 233 HHL-PSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLL 291
           + L P+  ++ F   +V P         L L+W           +  +  +     + L 
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW------FDVIKSDVMVVV-----NKLH 412

Query: 292 SRSLFQKSSNTESKYVMHDLVHDLAQWASGETCF--RLDDQFSVDR--QSNVFEKVRHFS 347
             SL +K    ES   +  +  +L      E      + D +++ +   S+         
Sbjct: 413 KYSLVEKQPK-ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

Query: 348 YLRSY------DCDGMDKFKVLDKV-VNLRTFLPIFFKQWRI---YPPNISPMVLSDLLP 397
           Y  S+      + +  ++  +   V ++ R     F +Q +I        +   + + L 
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFR-----FLEQ-KIRHDSTAWNASGSILNTLQ 525

Query: 398 QCKKLRVLSLGSYCITEVPISIGCLKQL--RYLNFSRSEIQCLPDAICS 444
           Q K  +      Y I +   +    ++L    L+F     +   + ICS
Sbjct: 526 QLKFYK-----PY-ICD---NDPKYERLVNAILDFLP---KIEENLICS 562

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 65.3 bits (158), Expect = 1e-10
 Identities = 99/651 (15%), Positives = 200/651 (30%), Gaps = 197/651 (30%)

Query: 663  QTLYFEDLQEWEHWEPN--RDND-EHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVI 719
                ++D+     +E     + D + VQ  P+   LS ++   +     + +     +  
Sbjct: 14   HQYQYKDI--LSVFEDAFVDNFDCKDVQDMPK-SILSKEEIDHIIM-SKDAVSGTLRLFW 69

Query: 720  AGCMHLAVSLPSLPALCTMEIDGCKRLVCDG------------PSESKSPNKMT------ 761
                           L + + +  ++ V +              +E + P+ MT      
Sbjct: 70   T--------------LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ 115

Query: 762  ---LCNISE-FENWSSEKFQKVEQL-------------MIVGCEGF-----VNEICLEKP 799
               L N ++ F  ++  + Q   +L             +I G  G        ++CL   
Sbjct: 116  RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175

Query: 800  LQGLQRLTCLKD-----LLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIY-- 852
            +Q      C  D     L + NC +  ++ +   L  L      +  + +  +  +    
Sbjct: 176  VQ------CKMDFKIFWLNLKNCNSPETVLEM--LQKLLYQIDPNWTSRSDHSSNIKLRI 227

Query: 853  NNARLEVLRI------KRC----DSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSC 902
            ++ + E+ R+      + C     ++ +        +  A  +  C+ L   L  R K  
Sbjct: 228  HSIQAELRRLLKSKPYENCLLVLLNVQN------AKAWNAFNLS-CKIL---LTTRFKQV 277

Query: 903  T----SSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFK 958
            T    +++ T  +++  S T    E        SL   +            R +D     
Sbjct: 278  TDFLSAATTTHISLDHHSMTLTPDEVK------SLLLKYLD---------CRPQD----- 317

Query: 959  VLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWI-SSCENLKSLPKGLSNLSH 1017
                   LP EV        S    IAE   D       W   +C+ L ++ +  S+L+ 
Sbjct: 318  -------LPREVLTTNPRRLS---IIAESIRDGLATWDNWKHVNCDKLTTIIE--SSLNV 365

Query: 1018 L--HEIRIVRC-HNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPG 1074
            L   E R  +    L   P  A                   IPT  LS +    +     
Sbjct: 366  LEPAEYR--KMFDRLSVFPPSAH------------------IPTILLSLIWFDVIKSDVM 405

Query: 1075 IVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVI 1134
            +VV   +    +L             + K       S+  +Y++      +   + + ++
Sbjct: 406  VVV--NKLHKYSL-------------VEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450

Query: 1135 ----LPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSL 1190
                +P +  S    D      L    + ++    HL   +  +        F    L  
Sbjct: 451  DHYNIPKTFDS---DDLIPP-YLDQYFYSHIG--HHLK--NIEHPERMTL--FRMVFLDF 500

Query: 1191 E-IQRCPLLEKCKMRK-GQEWPKIAHIPLTLINQERKHKVYF--DGPQEEE 1237
              +++       K+R     W     I L  + Q + +K Y   + P+ E 
Sbjct: 501  RFLEQ-------KIRHDSTAWNASGSI-LNTLQQLKFYKPYICDNDPKYER 543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 54.9 bits (131), Expect = 2e-07
 Identities = 108/718 (15%), Positives = 205/718 (28%), Gaps = 222/718 (30%)

Query: 226 SVLKLSYHHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWI-----AEGLVQQSEDNKQLE 280
              +  Y  + S  +  F        +++ K+ + +   I      + ++   +      
Sbjct: 12  GEHQYQYKDILSVFEDAFV------DNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT- 64

Query: 281 DLGSGYFHDLLSRSLFQKSSNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVF 340
                     L  +L  K      K+V   L  +  ++        L      +++    
Sbjct: 65  --------LRLFWTLLSKQEEMVQKFVEEVLRINY-KF--------LMSPIKTEQRQPSM 107

Query: 341 EKVRHFSYL-RSY-DCDGMDKFKV--LDKVVNLRTFL----PIFF----------KQWRI 382
               +     R Y D     K+ V  L   + LR  L    P             K W  
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-- 165

Query: 383 YPPNISPMVLSDLLPQCKK-LRV--LSLGSYCITEVPISIGCLKQLRYL---NFS----- 431
               ++  V      QCK   ++  L+L +    E  + +  L++L Y    N++     
Sbjct: 166 ----VALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEM--LQKLLYQIDPNWTSRSDH 219

Query: 432 ----RSEIQCLPDAICSLFNLE-----ILILRNCW-----------CLLKLPSRIGNLVN 471
               +  I  +   +  L   +     +L+L N             C + L +R   + +
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 472 LHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLE 531
                     +L    + +   +    L  ++      C  +DL           +S + 
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYL-----DCRPQDLPREVLTTNPRRLSII- 333

Query: 532 NVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHS 591
                       +R      D   +W+   + D +    E   L++L+P +  +++    
Sbjct: 334 ---------AESIRDGLATWD---NWK-HVNCDKLTTIIES-SLNVLEP-AEYRKM---- 374

Query: 592 YGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIY 651
                         F  ++V            P            I              
Sbjct: 375 --------------FDRLSV-----------FP--------PSAHI-------------- 387

Query: 652 GEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLS-IKKCPKLSGRLPNH 710
                 P   L  +       W  ++  + +   V    +L K S ++K PK    +   
Sbjct: 388 ------PTILLSLI-------W--FDVIKSDVMVVVN--KLHKYSLVEKQPK-ESTI--S 427

Query: 711 LPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMT--------- 761
           +PS+        + L V L +  AL    +D    +     S+   P  +          
Sbjct: 428 IPSIY-------LELKVKLENEYALHRSIVD-HYNIPKTFDSDDLIPPYLDQYFYSHIGH 479

Query: 762 -LCNISEFENWS--SEKF-------QKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKD 811
            L NI   E  +     F       QK+                    L  LQ+L   K 
Sbjct: 480 HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN-------ASGSILNTLQQLKFYKP 532

Query: 812 LLIGNCPTVVSLPKAC--FLPNLSEITI--QDCN----ALASLTDGMIYNNARLEVLR 861
            +  N P    L  A   FLP + E  I  +  +    AL +  +  I+  A  +V R
Sbjct: 533 YICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEA-IFEEAHKQVQR 589

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score =  101 bits (255), Expect = 2e-23
 Identities = 36/116 (31%), Positives = 46/116 (39%)

Query: 384 PPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAIC 443
           P  ++    S        L+ L L    I  +P SI  L+ L+ L    S +  L  AI 
Sbjct: 167 PEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIH 226

Query: 444 SLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L  LE L LR C  L   P   G    L  L ++  S L  LPL +  L  L  L
Sbjct: 227 HLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKL 282

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 88.5 bits (220), Expect = 6e-19
 Identities = 72/367 (19%), Positives = 113/367 (30%), Gaps = 75/367 (20%)

Query: 829  LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDC 888
                  +  Q   AL    D  +    R       R  S    +  + P     IE R  
Sbjct: 11   SSGRENLYFQGSTALRPYHDV-LSQWQRHYNADRNRWHSAWRQANSNNPQ----IETRTG 65

Query: 889  ETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSG-GRLPVTLK 947
              L+   D  E           +        L+L S+       L        RL   L+
Sbjct: 66   RALKATADLLE-----------DATQPGRVALELRSV------PLPQFPDQAFRL-SHLQ 107

Query: 948  RLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKS 1007
             + I+       L     LP  +++                     L ++ ++    L++
Sbjct: 108  HMTIDAAG----LME---LPDTMQQFA------------------GLETLTLARN-PLRA 141

Query: 1008 LPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLREL 1067
            LP  +++L+ L E+ I  C  L  LPE           +   D          L +L+ L
Sbjct: 142  LPASIASLNRLRELSIRACPELTELPEP----------LASTDASGEH---QGLVNLQSL 188

Query: 1068 ALSECPGIVVFPEE-GLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSF 1126
             L    GI   P       NL  L+I   +    L     H L  L +L + GC+   ++
Sbjct: 189  RLEWT-GIRSLPASIANLQNLKSLKIRN-SPLSALGP-AIHHLPKLEELDLRGCTALRNY 245

Query: 1127 PD-VGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPS 1185
            P   G        L  + + D   L  L       L  LE L +  C N +  P     +
Sbjct: 246  PPIFGG---R-APLKRLILKDCSNLLTLPL-DIHRLTQLEKLDLRGCVNLSRLPSL--IA 298

Query: 1186 SLLSLEI 1192
             L +  I
Sbjct: 299  QLPANCI 305

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 88.1 bits (219), Expect = 8e-19
 Identities = 58/293 (19%), Positives = 95/293 (32%), Gaps = 68/293 (23%)

Query: 392 LSDLLPQCK--KLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
            +DLL          L L S  + + P     L  L+++    + +  LPD +     LE
Sbjct: 71  TADLLEDATQPGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLE 130

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELP------LGMKELKCLRTLTNFI 503
            L L     L  LP+ I +L  L  L+I     L ELP          E + L  L +  
Sbjct: 131 TLTLARN-PLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLR 189

Query: 504 VGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDG 563
           +       +R L           I+ L+N                 L  LK+        
Sbjct: 190 L---EWTGIRSLPA--------SIANLQN-----------------LKSLKIR------- 214

Query: 564 DSVDEAREKNILDMLKPHS-----NIKRLEIHSYGG-TRFPSWVGDPSFSNVAVLILKNC 617
                    + L  L   +      ++ L++        +P   G    + +  LILK+C
Sbjct: 215 --------NSPLSAL-GPAIHHLPKLEELDLRGCTALRNYPPIFGG--RAPLKRLILKDC 263

Query: 618 RRSTSLP-SLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFED 669
               +LP  + +L  L+ L + G   L  + S I          +   +    
Sbjct: 264 SNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQ------LPANCIILVPP 310

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 86.2 bits (214), Expect = 3e-18
 Identities = 63/380 (16%), Positives = 123/380 (32%), Gaps = 98/380 (25%)

Query: 373 LPIFFKQWRI-YPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQ--LRYLN 429
                 QW+  Y  + +    +         ++ +     +      +    Q     L 
Sbjct: 28  YHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPGRVALE 87

Query: 430 FSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG 489
                +   PD    L +L+ + +     L++LP  +     L  L +   + LR LP  
Sbjct: 88  LRSVPLPQFPDQAFRLSHLQHMTIDAA-GLMELPDTMQQFAGLETLTLAR-NPLRALPAS 145

Query: 490 MKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEG 549
           +  L  LR L+                    +R    ++ L   + S +A+     +   
Sbjct: 146 IASLNRLRELS--------------------IRACPELTELPEPLASTDASGEHQGLV-N 184

Query: 550 LTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNV 609
           L  L+L+                         + I+ L          P+ +   +  N+
Sbjct: 185 LQSLRLE------------------------WTGIRSL----------PASIA--NLQNL 208

Query: 610 AVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFED 669
             L ++N   S   P++  L  L++L + G + L++      G         L+ L  +D
Sbjct: 209 KSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG------RAPLKRLILKD 262

Query: 670 LQEWEHWEPNRDNDEHVQAFP-------RLRKLSIKKCPKLSGRLPN---HLPSLEEIVI 719
                    +      +   P       +L KL ++ C  LS RLP+    LP+   I++
Sbjct: 263 C--------SN-----LLTLPLDIHRLTQLEKLDLRGCVNLS-RLPSLIAQLPANCIILV 308

Query: 720 AGCM------HLAVSLPSLP 733
              +      H  V+ P+ P
Sbjct: 309 PPHLQAQLDQHRPVARPAEP 328

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 75.4 bits (186), Expect = 1e-14
 Identities = 44/232 (18%), Positives = 77/232 (33%), Gaps = 29/232 (12%)

Query: 981  LESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSN 1040
            + S     H  +   +++      L+     LS     +     R H+          SN
Sbjct: 1    MGSSHHHHHHSSGRENLYFQGSTALRPYHDVLSQWQRHYNADRNRWHSAWRQAN----SN 56

Query: 1041 VVDVLIEDCDKLKAL---IPTGTLSSLRELALSECPGIVVFPEE-GLSTNLTDLEISGDN 1096
               +       LKA    +   T      L L   P +  FP++    ++L  + I    
Sbjct: 57   NPQIETRTGRALKATADLLEDATQPGRVALELRSVP-LPQFPDQAFRLSHLQHMTIDAAG 115

Query: 1097 MYK-PLVKWGFHKLTSLRKLYIDGCSDAVSFPD-VGKGVILPTSLTSITISDFPKLKRL- 1153
            + + P       +   L  L +       + P  +     L   L  ++I   P+L  L 
Sbjct: 116  LMELPD---TMQQFAGLETLTLARNP-LRALPASIAS---L-NRLRELSIRACPELTELP 167

Query: 1154 -------SSKGFQYLVSLEHLSVFSCPNFTSFPEA-GFPSSLLSLEIQRCPL 1197
                   +S   Q LV+L+ L +       S P +     +L SL+I+  PL
Sbjct: 168  EPLASTDASGEHQGLVNLQSLRL-EWTGIRSLPASIANLQNLKSLKIRNSPL 218

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 65.0 bits (159), Expect = 3e-11
 Identities = 61/332 (18%), Positives = 102/332 (30%), Gaps = 53/332 (15%)

Query: 710  HLPSLEEIVIAGCMHLAVSLPS----LPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNI 765
            H    E +   G   L                 + +          S +      T   +
Sbjct: 10   HSSGRENLYFQGSTAL-RPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRAL 68

Query: 766  SEF-ENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLP 824
                +            L +           L +      RL+ L+ + I     ++ LP
Sbjct: 69   KATADLLEDATQPGRVALELRSVP-------LPQFPDQAFRLSHLQHMTIDAAG-LMELP 120

Query: 825  KA-CFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAI 883
                    L  +T+     L +L    I +  RL  L I+ C  LT      LP  L   
Sbjct: 121  DTMQQFAGLETLTLARNP-LRALPAS-IASLNRLRELSIRACPELTE-----LPEPLA-- 171

Query: 884  EIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCL-WSGGRL 942
                            +   +                 L+SL +     +  L  S   L
Sbjct: 172  --------STDASGEHQGLVN-----------------LQSLRLEWT-GIRSLPASIANL 205

Query: 943  PVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSC 1002
               LK L+I +     +  +   L  ++EEL + GC+ L +    F   A L+ + +  C
Sbjct: 206  -QNLKSLKIRNSPLSALGPAIHHL-PKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDC 263

Query: 1003 ENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPE 1034
             NL +LP  +  L+ L ++ +  C NL  LP 
Sbjct: 264  SNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPS 295

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 45.3 bits (108), Expect = 7e-05
 Identities = 54/321 (16%), Positives = 90/321 (28%), Gaps = 86/321 (26%)

Query: 447 NLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGK 506
             E L  +    L      +      +  +     +              +  T      
Sbjct: 13  GRENLYFQGSTALRPYHDVLSQWQRHYNADRNRWHSAWRQA----NSNNPQIETR----- 63

Query: 507 DSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSV 566
            +G AL+                LE+                G   L+L           
Sbjct: 64  -TGRALKAT-----------ADLLEDATQ------------PGRVALELR---------- 89

Query: 567 DEAREKNILDMLKPHS-----NIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRST 621
                   L    P       +++ + I + G    P  +    F+ +  L L       
Sbjct: 90  -----SVPLPQF-PDQAFRLSHLQHMTIDAAGLMELPDTMQ--QFAGLETLTLARNPL-R 140

Query: 622 SLP-SLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNR 680
           +LP S+  L  L++L+I    EL  +   +     S   Q L  L    L          
Sbjct: 141 ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL---------E 191

Query: 681 DNDEHVQAFP-------RLRKLSIKKCPKLSGRLPN---HLPSLEEIVIAGCMHLAVSLP 730
                +++ P        L+ L I+    LS  L     HLP LEE+ + GC  L  + P
Sbjct: 192 WT--GIRSLPASIANLQNLKSLKIRNS-PLSA-LGPAIHHLPKLEELDLRGCTAL-RNYP 246

Query: 731 S----LPALCTMEIDGCKRLV 747
                   L  + +  C  L+
Sbjct: 247 PIFGGRAPLKRLILKDCSNLL 267

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 90.7 bits (225), Expect = 2e-18
 Identities = 69/394 (17%), Positives = 136/394 (34%), Gaps = 68/394 (17%)

Query: 14  RVIPLVGMGGIGKTTLAQEVYND--KLTEAFEPKA-WVCVSDDFDVLRISKAILDSIKRS 70
             + + GM G GK+ LA E   D   L   F     WV +    D   +   + +   R 
Sbjct: 148 GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQ-DKSGLLMKLQNLCMRL 206

Query: 71  SCKLEDLNSVQLELKETVFK---------KKFLIVLDDVWSERYDLWQALKSPFMAGAPG 121
             +      + L ++E   +          + L++LDDVW               A    
Sbjct: 207 DQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWV---------LKAFDNQ 257

Query: 122 SRIIVTTRSMDVALTMGSGKN--YELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQR 179
            +I++TTR   V  ++   K+       L  +                    +  +    
Sbjct: 258 CQILLTTRDKSVTDSVMGPKHVVPVESGLGREKG-----LEILSLFVNMKKEDLPAEAHS 312

Query: 180 VVEKCKGLPLAARALGGLLRSKQGVDEW--RAILDSKIWNLQDKTE-----IPSVLKLSY 232
           ++++CKG PL    +G LLR       +  R + + +   ++  +      +   + +S 
Sbjct: 313 IIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISV 372

Query: 233 HHLPSHLKRCFAYCAVLPKDYEFKEKELVLLWIAEGLVQQSEDNKQLEDLGSGYFHDLLS 292
             L   +K  +   ++L KD +   K L +LW          + +++ED+      + ++
Sbjct: 373 EMLREDIKDYYTDLSILQKDVKVPTKVLCVLW--------DLETEEVEDI----LQEFVN 420

Query: 293 RSLFQKSSNTES-KYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFS---- 347
           +SL   + N +S  Y +HDL  D           +   Q     +  V +  R++     
Sbjct: 421 KSLLFCNRNGKSFCYYLHDLQVDFLTE-------KNRSQLQDLHRKMVTQFQRYYQPHTL 473

Query: 348 --------YLRSYDCDGMDKFKVLDKVVNLRTFL 373
                   Y  ++    M    +  ++  L   L
Sbjct: 474 SPDQEDCMYWYNFLAYHMASANMHKELCALMFSL 507

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B* Length = 594

 Score = 68.8 bits (168), Expect = 7e-12
 Identities = 67/462 (14%), Positives = 127/462 (27%), Gaps = 96/462 (20%)

Query: 686  VQAFPRLRKLSIKKCPKLS----GRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEID 741
             ++F   + L +  C   S      +     +L+E+ +       VS   L        D
Sbjct: 126  AKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFP----D 181

Query: 742  GCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQ 801
                L                                   L I      V+   LE+ + 
Sbjct: 182  TYTSL---------------------------------VSLNISCLASEVSFSALERLVT 208

Query: 802  GLQRLTCLKDLLIGNCPTVVSLPK-ACFLPNLSEITIQDCNALASLTDGMIYNNARLEVL 860
                L  LK   +     +  L       P L E+      A          + A     
Sbjct: 209  RCPNLKSLK---LNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVYSGLSVALSGCK 265

Query: 861  RIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYL 920
             ++           +LP+         C  L  +      + + ++V   ++        
Sbjct: 266  ELRCLSGFWDAVPAYLPAVYSV-----CSRLTTL------NLSYATVQSYDLVKLLCQCP 314

Query: 921  DLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSN 980
             L+ L+V        L         L+ LR+     F +  +       +  +   GC  
Sbjct: 315  KLQRLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQGLVSV-SMGCPK 373

Query: 981  LESIAERFHD--DACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALP 1038
            LES+        +A L +I                N  ++   R+              P
Sbjct: 374  LESVLYFCRQMTNAALITI--------------ARNRPNMTRFRLCIIEPKAPDYLTLEP 419

Query: 1039 SNV-VDVLIEDCDKLKALIPTGTLS------------SLRELALSECPGIVVFPEEGLS- 1084
             ++    ++E C  L+ L  +G L+             +  L+++         + G+  
Sbjct: 420  LDIGFGAIVEHCKDLRRLSLSGLLTDKVFEYIGTYAKKMEMLSVAFAG----DSDLGMHH 475

Query: 1085 -----TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCS 1121
                  +L  LEI         +     KL ++R L++  CS
Sbjct: 476  VLSGCDSLRKLEIRDCPFGDKALLANASKLETMRSLWMSSCS 517

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B* Length = 594

 Score = 50.3 bits (120), Expect = 3e-06
 Identities = 63/409 (15%), Positives = 117/409 (28%), Gaps = 77/409 (18%)

Query: 386 NISPMVLSD-----LLPQCKKLRVLSLGSYC--ITEVPIS--IGCLKQLRYLNFSRSEI- 435
            +  MV++D     +    K  +VL L S C   +   ++      + L+ L+   S++ 
Sbjct: 111 RLKRMVVTDDCLELIAKSFKNFKVLVL-SSCEGFSTDGLAAIAATCRNLKELDLRESDVD 169

Query: 436 ----QCLPDAICSLFNLEILILRNC------WCLLKLPSRIGNLVNLHYLNIEGASALRE 485
                 L     +  +L  L +           L +L +R  NL +L          L  
Sbjct: 170 DVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLAT 229

Query: 486 LPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLR 545
           L     +L+ L     +                   +   C+SG  + +       A+  
Sbjct: 230 LLQRAPQLEELG-TGGYTAEVRPDVYSGLSVALSGCKELRCLSGFWDAVP--AYLPAVYS 286

Query: 546 VKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNI------------KRLEIHSYG 593
           V   LT L L +   +  D V    +   L  L     I            K L      
Sbjct: 287 VCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDYIEDAGLEVLASTCKDLRELRVF 346

Query: 594 GTRFPSWVGDPSFSNVAVL-ILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYG 652
            +       + + +   ++ +   C +  S+     L   + +T   +  +         
Sbjct: 347 PSEPFVMEPNVALTEQGLVSVSMGCPKLESV-----LYFCRQMTNAALITI--------A 393

Query: 653 EGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEH--------VQAFPRLRKLSIKKCPKLS 704
                    +       L   E   P+    E         V+    LR+LS+       
Sbjct: 394 RNRPN----MTRF---RLCIIEPKAPDYLTLEPLDIGFGAIVEHCKDLRRLSLSGLLTDK 446

Query: 705 G--RLPNHLPSLEEIVIAGC-------MHLAVSLPSLPALCTMEIDGCK 744
               +  +   +E + +A          H+     SL  L   EI  C 
Sbjct: 447 VFEYIGTYAKKMEMLSVAFAGDSDLGMHHVLSGCDSLRKL---EIRDCP 492

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B* Length = 594

 Score = 47.6 bits (113), Expect = 3e-05
 Identities = 48/371 (12%), Positives = 118/371 (31%), Gaps = 54/371 (14%)

Query: 856  RLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDD-REKSCTSSSVTEKNINS 914
            ++  + +K        +   +P           E +        E       VT+  +  
Sbjct: 67   KVRSVELKGKPHFADFNL--VPDGWGGYVYPWIEAMSSSYTWLEEIRLKRMVVTDDCLEL 124

Query: 915  SSSTYLDLESLFVYRCPSLTC--LWSGGRLPVTLKRLRIEDCSNFKV----LTSECQLPV 968
             + ++ + + L +  C   +   L +       LK L + +     V    L+       
Sbjct: 125  IAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDTYT 184

Query: 969  EVEELTIYGCSN------LESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIR 1022
             +  L I   ++      LE +  R  +   L+S+ ++    L+ L   L     L E+ 
Sbjct: 185  SLVSLNISCLASEVSFSALERLVTRCPN---LKSLKLNRAVPLEKLATLLQRAPQLEELG 241

Query: 1023 IVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEG 1082
                   V         + + V +  C +L+       LS   +   +  P +       
Sbjct: 242  TGGYTAEV----RPDVYSGLSVALSGCKELR------CLSGFWDAVPAYLPAVY-----S 286

Query: 1083 LSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSI 1142
            + + LT L +S   +    +     +   L++L++    +      +         L  +
Sbjct: 287  VCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDYIEDAGLEVLASTC---KDLREL 343

Query: 1143 TISDFPKLK-----RLSSKGFQYLVS----LEHLSVFSCPNFTSFPEAGFPSSLLSLEIQ 1193
             +             L+ +G   +      LE + ++ C   T+       ++L+++  +
Sbjct: 344  RVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESV-LYFCRQMTN-------AALITI-AR 394

Query: 1194 RCPLLEKCKMR 1204
              P + + ++ 
Sbjct: 395  NRPNMTRFRLC 405

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B* Length = 594

 Score = 42.6 bits (100), Expect = 8e-04
 Identities = 66/411 (16%), Positives = 126/411 (30%), Gaps = 75/411 (18%)

Query: 383 YPPNISPMVLSDLLPQCKKLRVLSL-GSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDA 441
               +S   L  L+ +C  L+ L L  +  + ++   +    QL  L       +  PD 
Sbjct: 194 LASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDV 253

Query: 442 ICSLFN-----LEILILRNCWCLLK--LPSRIGNLVNLHYLNIEGAS----ALRELPLGM 490
              L        E+  L   W  +   LP+       L  LN+  A+     L +L    
Sbjct: 254 YSGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQC 313

Query: 491 KELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEAN---EAMLRVK 547
            +L+ L  L    +       L      K LR  L +   E  +         + ++ V 
Sbjct: 314 PKLQRLWVLDY--IEDAGLEVL--ASTCKDLR-ELRVFPSEPFVMEPNVALTEQGLVSVS 368

Query: 548 EGLTDLK-LDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSF 606
            G   L+ + +  R+  ++        ++ + +   N+ R  +             +P  
Sbjct: 369 MGCPKLESVLYFCRQMTNAA-------LITIARNRPNMTRFRLCIIEPKAPDYLTLEPLD 421

Query: 607 SNVAVLILKNCRRSTSLPSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLY 666
                + +++C+    L     L  L  LT      +                + ++ L 
Sbjct: 422 IGFGAI-VEHCKDLRRL----SLSGL--LTDKVFEYI------------GTYAKKMEMLS 462

Query: 667 FEDLQEWEHWEPNRDNDEHVQAF----PRLRKLSIKKCPKLSGRLP---NHLPSLEEIVI 719
                         D+D  +         LRKL I+ CP     L    + L ++  + +
Sbjct: 463 VAF---------AGDSDLGMHHVLSGCDSLRKLEIRDCPFGDKALLANASKLETMRSLWM 513

Query: 720 AGC-------MHLAVSLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLC 763
           + C         L   +P L           +R   D   ES    ++ + 
Sbjct: 514 SSCSVSFGACKLLGQKMPKLNVEVI-----DERGAPDSRPESCPVERVFIY 559

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 68.6 bits (168), Expect = 7e-12
 Identities = 77/422 (18%), Positives = 139/422 (32%), Gaps = 55/422 (13%)

Query: 799  PLQGLQRLTCLKDL-LIGNCPTVVSLPKAC-FLPNLSEITIQDCNALASLTDGMIYNNAR 856
                   L+ LK L L+GN    + +      L NL  + I +    + +          
Sbjct: 90   SSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTS 149

Query: 857  LEVLRIKRCDSLTSISREHLPS--SLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINS 914
            L  L IK   SL +   + L S   +  + +   E    +L+      +       ++  
Sbjct: 150  LNELEIKAL-SLRNYQSQSLKSIRDIHHLTLHLSE-SAFLLEIFADILS-------SVRY 200

Query: 915  SSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELT 974
                  +L        P         +L    +   + D S F  L    +  +E+ E+ 
Sbjct: 201  LELRDTNLARFQFSPLPVDEVSSPMKKL--AFRGSVLTDES-FNELLKLLRYILELSEVE 257

Query: 975  IYGCSNL------ESIAERFHDDAC-----LRSIWISSCENLKSLPKGLSNLSHLHEIRI 1023
               C+         S ++   +        +R + I        L    S L  +  I +
Sbjct: 258  FDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITV 317

Query: 1024 VRCHNLVSLPEDA---LPS-NVVDV---LIEDCDKLKALIPTGTLSSLRELALSECPGIV 1076
                 +  +P      L S   +D+   L+ + + LK     G   SL+ L LS+   + 
Sbjct: 318  ENSK-VFLVPCSFSQHLKSLEFLDLSENLMVE-EYLKNSACKGAWPSLQTLVLSQN-HLR 374

Query: 1077 VFPEEGLS----TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKG 1132
               + G       NLT L+IS  N + P+          +R L +      V        
Sbjct: 375  SMQKTGEILLTLKNLTSLDISR-NTFHPMPD-SCQWPEKMRFLNLSSTGIRVVKTC---- 428

Query: 1133 VILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
              +P +L  + +S+   L   S     +L  L+ L +       + P+A     LL ++I
Sbjct: 429  --IPQTLEVLDVSNN-NLDSFSL----FLPRLQELYISRN-KLKTLPDASLFPVLLVMKI 480

Query: 1193 QR 1194
             R
Sbjct: 481  SR 482

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 51.6 bits (124), Expect = 1e-06
 Identities = 64/396 (16%), Positives = 130/396 (32%), Gaps = 87/396 (21%)

Query: 803  LQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARLEVL 860
               LT L+ L IGN  T   + +  F  L +L+E+ I+   +L +     + +   +  L
Sbjct: 119  FPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKA-LSLRNYQSQSLKSIRDIHHL 177

Query: 861  RIKRCDSLTSISREHLP--SSLQAIEIRDC-------------ETLQCVLDDREKSCTSS 905
             +        +        SS++ +E+RD              E    +     +    +
Sbjct: 178  TLHLS-ESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLT 236

Query: 906  SVTEKNINSSSSTYLDLESLFVYRCP----------SLTCLWSGGRLP-VTLKRLRIEDC 954
              +   +       L+L  +    C               +   G++  VT++RL I   
Sbjct: 237  DESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQF 296

Query: 955  SNFKVLTSECQLPVEVEELTIYG----------CSNLESIAE------RFHDDACLRSIW 998
              F  L++   L  +V+ +T+              +L+S+           ++    S  
Sbjct: 297  YLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSAC 356

Query: 999  ISSCENLKSLPKGLSNLSH--LHEIRIVR--CHNLVSLPEDALPSNVVDVLIEDCDKLKA 1054
              +  +L++L      LS   L  ++        L +L    +  N    + + C   + 
Sbjct: 357  KGAWPSLQTL-----VLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEK 411

Query: 1055 L------------IPTGTLSSLRELALSECP-------------------GIVVFPEEGL 1083
            +            + T    +L  L +S                       +   P+  L
Sbjct: 412  MRFLNLSSTGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASL 471

Query: 1084 STNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDG 1119
               L  ++IS  N  K +    F +LTSL+K+++  
Sbjct: 472  FPVLLVMKISR-NQLKSVPDGIFDRLTSLQKIWLHT 506

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 50.1 bits (120), Expect = 3e-06
 Identities = 84/502 (16%), Positives = 166/502 (33%), Gaps = 66/502 (13%)

Query: 402 LRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCLP-DAICSLFNLEILILRNCWCL 459
           ++ L L    IT +    +     L+ L    S I  +  DA  SL +LE L L +   L
Sbjct: 28  MKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDN-HL 86

Query: 460 LKLPSR-IGNLVNLHYLNIEGASALRELPLGM--KELKCLRTL----TNFIVGKDSGCAL 512
             L S   G L +L YLN+ G +  + L +      L  L+TL                 
Sbjct: 87  SSLSSSWFGPLSSLKYLNLMG-NPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRI-DF 144

Query: 513 RDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREK 572
             L +   L     I      + + ++    L+    +  L L          +      
Sbjct: 145 AGLTSLNELE----IKA--LSLRNYQSQS--LKSIRDIHHLTLHLSESAFLLEIFADILS 196

Query: 573 NILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQLCSL 632
           ++  +    +N+ R +          S +   +F    +           L  + +L  +
Sbjct: 197 SVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEV 256

Query: 633 K--DLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFP 690
           +  D T+ G+ +     S++  E       +++ L+      +       D         
Sbjct: 257 EFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFY------DLSTVYSLLE 310

Query: 691 RLRKLSIKKCP--KLSGRLPNHLPSLEEIVIAGCMHLAVSLPS------LPALCTMEIDG 742
           ++++++++      +      HL SLE + ++  + +   L +       P+L T+ +  
Sbjct: 311 KVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQ 370

Query: 743 CK--RLVCDGPSESKSPNKMTL----CNISEFENWSSEKFQKVEQLMIVGCEGFVNEI-- 794
                +   G       N  +L           +      Q  E++  +        I  
Sbjct: 371 NHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPD----SCQWPEKMRFLNLSS--TGIRV 424

Query: 795 ---CLEKPLQGL-----------QRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDC 840
              C+ + L+ L             L  L++L I     + +LP A   P L  + I   
Sbjct: 425 VKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNK-LKTLPDASLFPVLLVMKISR- 482

Query: 841 NALASLTDGMIYNNARLEVLRI 862
           N L S+ DG+      L+ + +
Sbjct: 483 NQLKSVPDGIFDRLTSLQKIWL 504

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 45.9 bits (109), Expect = 8e-05
 Identities = 30/163 (18%), Positives = 60/163 (36%), Gaps = 8/163 (4%)

Query: 345 HFSYLRSYDCDGMDKFKVLDKVVNLR--TFLPIFFKQWRIYPPNISPMVLSDLLPQCKKL 402
            F      D    +  K+L  ++ L    F          + P+ S +V      +   +
Sbjct: 229 AFRGSVLTDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTI 288

Query: 403 RVLSLGSYCITEVPISIGC-LKQLRYLNFSRSEIQCLPDAICS-LFNLEILILRNC---W 457
           R L +  + +     ++   L++++ +    S++  +P +    L +LE L L       
Sbjct: 289 RRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVE 348

Query: 458 CLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLT 500
             LK  +  G   +L  L +     LR +    + L  L+ LT
Sbjct: 349 EYLKNSACKGAWPSLQTLVLSQNH-LRSMQKTGEILLTLKNLT 390

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 18/100 (18%), Positives = 36/100 (36%), Gaps = 7/100 (7%)

Query: 398 QCKKLRVLSLGSYCITEVPISIG---CLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR 454
               L+ L L    +  +  +      LK L  L+ SR+    +PD+      +  L L 
Sbjct: 359 AWPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLS 418

Query: 455 NCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELK 494
           +   +  + +       L  L++   + L    L +  L+
Sbjct: 419 STG-IRVVKT--CIPQTLEVLDVSNNN-LDSFSLFLPRLQ 454

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 31/178 (17%), Positives = 65/178 (36%), Gaps = 18/178 (10%)

Query: 1023 IVRCH--NLVSLPEDALPSNVVDVLIEDCDKLKALIPT--GTLSSLRELALSECPGIVVF 1078
            +      +  S+P   L + +  + +    K+  +        ++L+ L L     I   
Sbjct: 9    VCDGRSRSFTSIPSG-LTAAMKSLDLSFN-KITYIGHGDLRACANLQVLILKSS-RINTI 65

Query: 1079 PEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILP 1136
              +      +L  L++S DN    L    F  L+SL+ L + G      +  +G   + P
Sbjct: 66   EGDAFYSLGSLEHLDLS-DNHLSSLSSSWFGPLSSLKYLNLMGNP----YQTLGVTSLFP 120

Query: 1137 --TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
              T+L ++ I +      +    F  L SL  L + +  +  ++       S+  +  
Sbjct: 121  NLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKAL-SLRNYQSQSL-KSIRDIHH 176

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 64.8 bits (158), Expect = 1e-10
 Identities = 94/526 (17%), Positives = 176/526 (33%), Gaps = 58/526 (11%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCITEV--PISIGCLKQLRYLNFSRSEIQCLP-DAICSLFN 447
           V +   P  ++L++L LGS          +   L  LR L+   S+I  L  DA   LF+
Sbjct: 39  VTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFH 98

Query: 448 LEILILRNC--WCLLKLPSRIGNLVNLHYLNIEGASALRELPL-----GMKELKCLRTLT 500
           L  L L  C     +       NL  L  L++   + +R L L      +  LK +   +
Sbjct: 99  LFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSK-NQIRSLYLHPSFGKLNSLKSIDFSS 157

Query: 501 NFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLD---W 557
           N I        L  L+        L  + L + +               L  L +    W
Sbjct: 158 NQIFLVCEH-ELEPLQGKTLSFFSLAANSLYSRVSVDWGKCMNPFRNMVLEILDVSGNGW 216

Query: 558 RPRRDGDSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNC 617
                G+  +   +     ++  H +I       +            +F+ +A   +++ 
Sbjct: 217 TVDITGNFSNAISKSQAFSLILAH-HIMGAGFGFHNIKDPDQ----NTFAGLARSSVRHL 271

Query: 618 RRSTSLPSLGQLCSLKDLTIVGMSELKSI---GSEIYG--EGCSKPFQSLQTLYFEDLQE 672
                L S G + SL       + +LK +    ++I    +       +LQ L       
Sbjct: 272 D----L-SHGFVFSLNSRVFETLKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSY--- 323

Query: 673 WEHWEPNRDNDEHVQAF---PRLRKLSIKKC--PKLSGRLPNHLPSLEEIVIAGCMHLAV 727
                 N   + +   F   P++  + ++K     +  +    L  L+ + +        
Sbjct: 324 ------NLLGELYSSNFYGLPKVAYIDLQKNHIAIIQDQTFKFLEKLQTLDLRDNAL--T 375

Query: 728 SLPSLPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGC 787
           ++  +P++  + + G K +    P  + + N + L               +V  L I+  
Sbjct: 376 TIHFIPSIPDIFLSGNKLVTL--PKINLTANLIHLSENRLENLDILYFLLRVPHLQILIL 433

Query: 788 EGFVNEICLEKPLQGLQRLTCLKDLLIGNC----PTVVSLPKACF--LPNLSEITIQDCN 841
               N        Q       L+ L +G           L    F  L +L  + +   N
Sbjct: 434 NQ--NRFSSCSGDQTPSENPSLEQLFLGENMLQLAWETELCWDVFEGLSHLQVLYLNH-N 490

Query: 842 ALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRD 887
            L SL  G+  +   L  L +     LT +S   LP++L+ ++I  
Sbjct: 491 YLNSLPPGVFSHLTALRGLSLNSN-RLTVLSHNDLPANLEILDISR 535

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 59.8 bits (145), Expect = 4e-09
 Identities = 66/440 (15%), Positives = 133/440 (30%), Gaps = 62/440 (14%)

Query: 797  EKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYN- 853
            +   + L+ LT L   L  N    + L  + F  L +L  I     N +  + +  +   
Sbjct: 116  DGYFRNLKALTRLD--LSKNQIRSLYLHPS-FGKLNSLKSIDFSS-NQIFLVCEHELEPL 171

Query: 854  -NARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNI 912
                L    +    SL S         +        E L   +     +   +      I
Sbjct: 172  QGKTLSFFSLAAN-SLYSRVSVDWGKCMNPFRNMVLEILD--VSGNGWTVDITGNFSNAI 228

Query: 913  NSSSSTYLDLESLFVYRCPSLTCLWS------GGRLPVTLKRLRIEDCSNFKVLTSECQL 966
            + S +  L L    +        +         G    +++ L +     F + +   + 
Sbjct: 229  SKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAGLARSSVRHLDLSHGFVFSLNSRVFET 288

Query: 967  PVEVEELTI-------------YGCSNLESI-----------AERFHDDACLRSIWISSC 1002
              +++ L +             YG  NL+ +           +  F+    +  I +   
Sbjct: 289  LKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYNLLGELYSSNFYGLPKVAYIDLQKN 348

Query: 1003 ENLKSLPKG-LSNLSHLHEI-----RIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALI 1056
             ++  +       L  L  +      +   H + S+P+  L  N           L  + 
Sbjct: 349  -HIAIIQDQTFKFLEKLQTLDLRDNALTTIHFIPSIPDIFLSGN-------KLVTLPKIN 400

Query: 1057 PTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLY 1116
             T  L  L E  L     +       +  +L  L ++ +            +  SL +L+
Sbjct: 401  LTANLIHLSENRLENLDILYFL--LRV-PHLQILILNQNRFSSCSGDQTPSENPSLEQLF 457

Query: 1117 IDGCS-DAVSFPDVGKGVILP-TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPN 1174
            +           ++   V    + L  + ++    L  L    F +L +L  LS+ S   
Sbjct: 458  LGENMLQLAWETELCWDVFEGLSHLQVLYLNH-NYLNSLPPGVFSHLTALRGLSLNSN-R 515

Query: 1175 FTSFPEAGFPSSLLSLEIQR 1194
             T       P++L  L+I R
Sbjct: 516  LTVLSHNDLPANLEILDISR 535

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 44.0 bits (104), Expect = 3e-04
 Identities = 33/212 (15%), Positives = 70/212 (33%), Gaps = 22/212 (10%)

Query: 992  ACLRSIWISSCE--NLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPS-NVVDVLIED 1048
            +C     I+     NL  +P+ L+    L     +  + + ++   + P    + +L   
Sbjct: 1    SCSFDGRIAFYRFCNLTQVPQVLNTTERLL----LSFNYIRTVTASSFPFLEQLQLLELG 56

Query: 1049 CDKLKALIPTGT---LSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVK 1103
                   I       L +LR L L     I     +      +L +L +    +   ++K
Sbjct: 57   SQYTPLTIDKEAFRNLPNLRILDLGSSK-IYFLHPDAFQGLFHLFELRLYFCGLSDAVLK 115

Query: 1104 WG-FHKLTSLRKLYIDGCS-DAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYL 1161
             G F  L +L +L +      ++        +    SL SI  S   ++  +     + L
Sbjct: 116  DGYFRNLKALTRLDLSKNQIRSLYLHPSFGKL---NSLKSIDFS-SNQIFLVCEHELEPL 171

Query: 1162 --VSLEHLSVFSCPNFTSFPEAGFPSSLLSLE 1191
               +L   S+ +  +  S     +   +    
Sbjct: 172  QGKTLSFFSL-AANSLYSRVSVDWGKCMNPFR 202

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B* Length = 592

 Score = 62.3 bits (151), Expect = 7e-10
 Identities = 70/566 (12%), Positives = 152/566 (26%), Gaps = 119/566 (21%)

Query: 686  VQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKR 745
             + FP LR L +K  P+ +        +    V      ++ +L  L ++          
Sbjct: 69   SRRFPNLRSLKLKGKPRAA-MFNLIPENWGGYVTPWVTEISNNLRQLKSVH---FRRMI- 123

Query: 746  LVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQR 805
             V D                 + +  +  +   +E L +  C GF  +  L      +  
Sbjct: 124  -VSD----------------LDLDRLAKARADDLETLKLDKCSGFTTDGLLSI----VTH 162

Query: 806  LTCLKDLLIGNC-------PTVVSLPKACFLPNLSEITIQDCNALASLTDGMIY---NNA 855
               +K LL+            +  L +     +L  +              +     N  
Sbjct: 163  CRKIKTLLMEESSFSEKDGKWLHELAQHN--TSLEVLNFYMTEFAKISPKDLETIARNCR 220

Query: 856  RLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSS 915
             L  +++   + L  +      ++L+            + +          +    ++  
Sbjct: 221  SLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYM 280

Query: 916  SSTYLD--------LESLFVYRCPSLT--CLWSGGRLPVTLKRLRIEDC---SNFKVLTS 962
                +         +  L +      T        + P  L+ L   +       +VL  
Sbjct: 281  GPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCP-NLEVLETRNVIGDRGLEVLAQ 339

Query: 963  ECQLPVEVEELTIYGCSNLESIAERFHD--DACLRSIWISSCENLKSL------------ 1008
             C+   +++ L I   ++ + + +         L ++    C+ L+ +            
Sbjct: 340  YCK---QLKRLRIERGADEQGMEDEEGLVSQRGLIAL-AQGCQELEYMAVYVSDITNESL 395

Query: 1009 ---PKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGT----- 1060
                  L NL     + + R   +  LP D      V  L+  C KL+            
Sbjct: 396  ESIGTYLKNLCDFRLVLLDREERITDLPLDNG----VRSLLIGCKKLRRFAFYLRQGGLT 451

Query: 1061 ----------LSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHK 1108
                        ++R + L           E      NL  LE+ G    +  +     K
Sbjct: 452  DLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRGCCFSERAIAAAVTK 511

Query: 1109 LTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLS 1168
            L SLR L++ G                       +++    ++       +   ++E + 
Sbjct: 512  LPSLRYLWVQGY--------------------RASMTGQDLMQMA-----RPYWNIELIP 546

Query: 1169 VFSCPNFTSFPEAGFPSSLLSLEIQR 1194
                P      E         +    
Sbjct: 547  SRRVPEVNQQGEIREMEHPAHILAYY 572

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B* Length = 592

 Score = 58.4 bits (141), Expect = 1e-08
 Identities = 56/460 (12%), Positives = 130/460 (28%), Gaps = 87/460 (18%)

Query: 803  LQRLTCLKDLLIGNCPTVVSLPK----------------ACFLPNLSEITIQDC----NA 842
             +R   L+ L +   P                       +  L  L  +  +        
Sbjct: 69   SRRFPNLRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLD 128

Query: 843  LASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSC 902
            L  L      +   LE L++ +C   T+         L +I +  C  ++  L   E S 
Sbjct: 129  LDRLAKARADD---LETLKLDKCSGFTT-------DGLLSI-VTHCRKIK-TLLMEESSF 176

Query: 903  TSSSVTEKNINSSSSTYLDLESLFVYRCPSLT--CLWSGGRLPVTLKRLRIEDCSNFKVL 960
            +       +  +  +T L++ + ++     ++   L +  R   +L  +++ D    + L
Sbjct: 177  SEKDGKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILE-L 235

Query: 961  TSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENL--KSLPKGLSNLSHL 1018
                +    +EE      +    + E++ +    R +       +    +P      + +
Sbjct: 236  VGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQI 295

Query: 1019 HEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLS------------SLRE 1066
             ++ ++              +     LI+ C  L+ L     +              L+ 
Sbjct: 296  RKLDLLYALLE---------TEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKR 346

Query: 1067 LALSECPGIVVFPEEGLS-------------TNLTDLEISGDNM----YKPLVKWGFHKL 1109
            L +          +E                  L  + +   ++     + +       L
Sbjct: 347  LRIERGADEQGMEDEEGLVSQRGLIALAQGCQELEYMAVYVSDITNESLESIGT-YLKNL 405

Query: 1110 TSLRKLYIDGCSDAVSFP-DVGKGVILP--TSLTSITISDFPKLKRLSSKGFQYLVS--- 1163
               R + +D        P D G   +L     L         +   L+  G  Y+     
Sbjct: 406  CDFRLVLLDREERITDLPLDNGVRSLLIGCKKLRRFAFYL--RQGGLTDLGLSYIGQYSP 463

Query: 1164 -LEHLSVFSCPNFTSFPEAGFPS--SLLSLEIQRCPLLEK 1200
             +  + +                  +L  LE++ C   E+
Sbjct: 464  NVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRGCCFSER 503

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B* Length = 592

 Score = 51.1 bits (122), Expect = 2e-06
 Identities = 55/405 (13%), Positives = 119/405 (29%), Gaps = 63/405 (15%)

Query: 385 PNISPMVLSDLLPQCKKLRVLSL-GSYCITEVPISIGCL----KQLRYLNFSRSEIQCLP 439
              +   L  ++  C+K++ L +  S    +    +  L      L  LNF  +E   + 
Sbjct: 149 SGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYMTEFAKIS 208

Query: 440 D-AICSLF----NLEILILRNCWC--LLKLPSRIGNLVNLHYLNIEGASALRELPLGMKE 492
              + ++     +L  + + +     L+       NL      ++     + E  + +  
Sbjct: 209 PKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVF 268

Query: 493 LKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTD 552
            + L  L    +G +    L        +R +L +       +    +  +++    L  
Sbjct: 269 PRKLCRLGLSYMGPNEMPIL--FPFAAQIR-KLDLLYALLETE---DHCTLIQKCPNLEV 322

Query: 553 LKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEI----HSYGGTRFPSWVGDPSFSN 608
           L+            +   ++ +  + +    +KRL I       G       V       
Sbjct: 323 LETR----------NVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIA 372

Query: 609 VAVL------ILKNCRRST--SLPSLGQLC-SLKDLTIVGMSELKSIGSEIYGEGCSKPF 659
           +A        +       T  SL S+G    +L D  +V +   + I       G     
Sbjct: 373 LAQGCQELEYMAVYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLL 432

Query: 660 QSLQTLYFEDLQEWEHWEPNRDNDEHVQAF----PRLRKLSIKKCPKLS---GRLPNHLP 712
              + L         +       D  +       P +R + +    +            P
Sbjct: 433 IGCKKLRRFAF----YLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCP 488

Query: 713 SLEEIVIAGC-------MHLAVSLPSLPAL----CTMEIDGCKRL 746
           +L+++ + GC             LPSL  L        + G   +
Sbjct: 489 NLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLM 533

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C* Length = 239

 Score = 59.2 bits (144), Expect = 1e-09
 Identities = 46/248 (18%), Positives = 79/248 (31%), Gaps = 37/248 (14%)

Query: 953  DCSNFKVLTSECQLPVEVEELTIYGCSNLESIAER-FHDDACLRSIWISSCENLKSLPKG 1011
              +    +     LP   + L +    +L +I    F +   +  I++S    L+ L   
Sbjct: 17   RVTCKD-IQRIPSLPPSTQTLKLIET-HLRTIPSHAFSNLPNISRIYVSIDVTLQQLESH 74

Query: 1012 L-SNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALS 1070
               NLS +  I I    NL  +  DAL                       L  L+ L + 
Sbjct: 75   SFYNLSKVTHIEIRNTRNLTYIDPDALKE---------------------LPLLKFLGIF 113

Query: 1071 ECPGIVVFPEE---GLSTNLTDLEISGDNMYKPLVKWGFHKLTS-LRKLYIDGCSDAVSF 1126
               G+ +FP+      +     LEI+ +     +    F  L +    L +        F
Sbjct: 114  NT-GLKMFPDLTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNN----GF 168

Query: 1127 PDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVS-LEHLSVFSCPNFTSFPEAGFPS 1185
              V       T L ++ ++    L  +    F  + S    L V    + T+ P  G   
Sbjct: 169  TSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDVSQT-SVTALPSKGL-E 226

Query: 1186 SLLSLEIQ 1193
             L  L  +
Sbjct: 227  HLKELIAR 234

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 61.8 bits (150), Expect = 1e-09
 Identities = 20/138 (14%), Positives = 46/138 (33%), Gaps = 15/138 (10%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           +S  + +  KL+++   +   T   I++                     +  +L +L  +
Sbjct: 440 ISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENE---ELSWSNLKDLTDV 496

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNI---------EGASALRELPLGMKELKCLRTLT-- 500
            L NC  + +LP  + +L  L  LNI         +  +    L         ++     
Sbjct: 497 ELYNCPNMTQLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMG 556

Query: 501 -NFIVGKDSGCALRDLKN 517
            N +    +  +L+ +  
Sbjct: 557 YNNLEEFPASASLQKMVK 574

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 59.9 bits (145), Expect = 4e-09
 Identities = 21/123 (17%), Positives = 41/123 (33%), Gaps = 17/123 (13%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVP--------ISIGCLKQLRYLNFSRSEIQCLPDAI-- 442
           ++L      +  + L +  +T +P         +      L  ++   +++  L D    
Sbjct: 690 TELFATGSPISTIILSNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRA 749

Query: 443 CSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE------GASALRELPLGMKELKCL 496
            +L  L  + +    C    P++  N   L    I       G   LR+ P G+     L
Sbjct: 750 TTLPYLSNMDVSYN-CFSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSL 808

Query: 497 RTL 499
             L
Sbjct: 809 IQL 811

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 56.8 bits (137), Expect = 4e-08
 Identities = 17/101 (16%), Positives = 29/101 (28%), Gaps = 8/101 (7%)

Query: 385 PNISPMVLSDLLPQCKKLRVLSLGSYCITEVP--ISIGCLKQLRYLNFSRSEIQCLPDAI 442
           P  S             L  + L    +T +        L  L  ++ S +     P   
Sbjct: 713 PENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYNCFSSFPTQP 772

Query: 443 CSLFNLEILILR------NCWCLLKLPSRIGNLVNLHYLNI 477
            +   L+   +R          L + P+ I    +L  L I
Sbjct: 773 LNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQI 813

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 53.7 bits (129), Expect = 3e-07
 Identities = 52/408 (12%), Positives = 119/408 (29%), Gaps = 65/408 (15%)

Query: 838  QDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISRE--HLPSSLQ-----------AIE 884
            ++ +         + NN R+  L +    +   +      L + L+           +  
Sbjct: 306  KELDMWGDQPGVDLDNNGRVTGLSLAGFGAKGRVPDAIGQL-TELKVLSFGTHSETVSGR 364

Query: 885  IRDCETLQCVLDDREKSCTSSSVTEKNINSSSS-TYLDLESLFVYRCPSLTCLWSGGRLP 943
            +   E L   + +  K        +  ++        DL    + R P +  +    R+ 
Sbjct: 365  LFGDEELTPDMSEERKHRIRMHYKKMFLDYDQRLNLSDLLQDAINRNPEMKPIKKDSRI- 423

Query: 944  VTLKRLRIEDCSN--------FKVLT-------SECQL-----PVEVEELTIYGCSNLES 983
             +LK  +I + +N         + LT       +          V+ E+         E+
Sbjct: 424  -SLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYEN 482

Query: 984  IAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHN-LVSLPEDALPSNVV 1042
                + +   L  + + +C N+  LP  L +L  L  + I    N  +S  +       +
Sbjct: 483  EELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLNI--ACNRGISAAQLKADWTRL 540

Query: 1043 DVLIEDCDKLKAL---------IPT----GTLSSLRELALSECPGIVVFPEEGLSTNLTD 1089
                +   K++            P       +  L  L       +      G +  LTD
Sbjct: 541  ADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHNK-VRHLEAFGTNVKLTD 599

Query: 1090 LEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISD--- 1146
            L++   N  + + +        +  L           P++     +   + S+  S    
Sbjct: 600  LKLD-YNQIEEIPEDFCAFTDQVEGLGFSHNK-LKYIPNIFNAKSV-YVMGSVDFSYNKI 656

Query: 1147 --FPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
                +     S      ++   +++        FP   F ++   +  
Sbjct: 657  GSEGR-NISCSMDDYKGINASTVTLSYN-EIQKFPTELF-ATGSPIST 701

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 53.7 bits (129), Expect = 4e-07
 Identities = 19/111 (17%), Positives = 43/111 (38%), Gaps = 8/111 (7%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLF-NLEIL 451
           S  L +  KL +L      +  +  + G   +L  L    ++I+ +P+  C+    +E L
Sbjct: 566 SASLQKMVKLGLLDCVHNKVRHLE-AFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGL 624

Query: 452 ILRNCWCLLKLPSR--IGNLVNLHYLNIEG---ASALRELPLGMKELKCLR 497
              +   L  +P+     ++  +  ++       S  R +   M + K + 
Sbjct: 625 GFSHNK-LKYIPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMDDYKGIN 674

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 43.7 bits (103), Expect = 4e-04
 Identities = 44/279 (15%), Positives = 84/279 (30%), Gaps = 49/279 (17%)

Query: 396 LPQCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR 454
           L    ++  LSL  +     VP +IG L +L+ L+F                 L   +  
Sbjct: 319 LDNNGRVTGLSLAGFGAKGRVPDAIGQLTELKVLSFGTHSETVSGRLF-GDEELTPDMSE 377

Query: 455 NCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRD 514
                +++  +   L     LN+        L   +     ++ +       DS  +L+D
Sbjct: 378 ERKHRIRMHYKKMFLDYDQRLNL-----SDLLQDAINRNPEMKPIKK-----DSRISLKD 427

Query: 515 LKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNI 574
            +          I  L N I         L     L  +        +     +    + 
Sbjct: 428 TQ----------IGNLTNRITFISKAIQRLT---KLQIIYF-----ANSPFTYDNIAVDW 469

Query: 575 LDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLP-SLGQLCSLK 633
            D    ++     E  S+               ++  + L NC   T LP  L  L  L+
Sbjct: 470 EDANSDYAKQYENEELSWSN-----------LKDLTDVELYNCPNMTQLPDFLYDLPELQ 518

Query: 634 DLT-----IVGMSELKSIGSEIYGEGCSKPFQSLQTLYF 667
            L       +  ++LK+  + +  +  +     +Q  Y 
Sbjct: 519 SLNIACNRGISAAQLKADWTRLADDEDT--GPKIQIFYM 555

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 42.9 bits (101), Expect = 7e-04
 Identities = 78/585 (13%), Positives = 153/585 (26%), Gaps = 113/585 (19%)

Query: 607  SNVAVLILKNCRRSTSLP-SLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTL 665
              V  L L        +P ++GQL  LK L   G       G     E  +      +  
Sbjct: 323  GRVTGLSLAGFGAKGRVPDAIGQLTELKVL-SFGTHSETVSGRLFGDEELTPDMSEERKH 381

Query: 666  YFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHL 725
                     H++    + +       L + +I + P++     +   SL++  I    + 
Sbjct: 382  RIRM-----HYKKMFLDYDQRLNLSDLLQDAINRNPEMKPIKKDSRISLKDTQIGNLTNR 436

Query: 726  AVSLPS----LPALCTMEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQ 781
               +      L  L  +          D  +              E E  S    + +  
Sbjct: 437  ITFISKAIQRLTKLQIIYFANSP-FTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTD 495

Query: 782  LMIVGCEGFVNEIC-LEKPLQGLQRLTCLKDL-------LIGNCPTVVSLPKA-CFLPNL 832
            + +  C      +  L   L  L  L  L ++                 L       P +
Sbjct: 496  VELYNC----PNMTQLPDFLYDLPELQSL-NIACNRGISAAQLKADWTRLADDEDTGPKI 550

Query: 833  SEITIQDCNALASL-TDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETL 891
                +   N L        +    +L +L       +  +        L  +++   + +
Sbjct: 551  QIFYMGY-NNLEEFPASASLQKMVKLGLLDCVHN-KVRHLEAFGTNVKLTDLKLDYNQ-I 607

Query: 892  QCVLDDREKSCTSSSVTEKNINSSSSTYL-DLESLFVYRCPSLTCLWSGGRLPVTLKRLR 950
            +                   I      +   +E L       L  + +      ++  + 
Sbjct: 608  E------------------EIPEDFCAFTDQVEGLGFSHN-KLKYIPNIFNAK-SVYVMG 647

Query: 951  IEDCSNFKVLTSECQLPVEV-EELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLP 1009
              D S  K + S       +   +  Y   N  ++              +S    ++  P
Sbjct: 648  SVDFSYNK-IGS---EGRNISCSMDDYKGINASTV-------------TLSYN-EIQKFP 689

Query: 1010 KG-LSNLSHLHEIRIVRCHN-LVSLPEDALPSNVVDVLIEDCDKLKAL------------ 1055
                +  S +  I +   +N + S+PE++L     D   ++   L  +            
Sbjct: 690  TELFATGSPISTIIL--SNNLMTSIPENSL--KPKDGNYKNTYLLTTIDLRFNKLTSLSD 745

Query: 1056 -IPTGTLSSLRELALSECPGIVVFPEE-GLSTNLTDLEISG-----DNMYKPLVKWGFHK 1108
                 TL  L  + +S       FP +   S+ L    I        N        G   
Sbjct: 746  DFRATTLPYLSNMDVSYNC-FSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITT 804

Query: 1109 LTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRL 1153
              SL +L I                     +  +     P+L  L
Sbjct: 805  CPSLIQLQIGSN-----------------DIRKVDEKLTPQLYIL 832

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 59.6 bits (145), Expect = 4e-09
 Identities = 24/112 (21%), Positives = 47/112 (41%), Gaps = 7/112 (6%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L  L      L  ++ G+  + E+P  +  L  L  +    + ++ LPD      +LE +
Sbjct: 165 LKKLPDLPPSLEFIAAGNNQLEELP-ELQNLPFLTAIYADNNSLKKLPD---LPLSLESI 220

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
           +  N   +L+    + NL  L  +  +  + L+ LP     L+ L    N++
Sbjct: 221 VAGN--NILEELPELQNLPFLTTIYADN-NLLKTLPDLPPSLEALNVRDNYL 269

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 56.2 bits (136), Expect = 4e-08
 Identities = 29/112 (25%), Positives = 46/112 (41%), Gaps = 9/112 (8%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           LS L      L  L      +TE+P     LK L   N +   +  LP        LE L
Sbjct: 83  LSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPP------LLEYL 136

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
            + N   L KLP  + N   L  ++++  ++L++LP     L+ +    N +
Sbjct: 137 GVSNN-QLEKLPE-LQNSSFLKIIDVDN-NSLKKLPDLPPSLEFIAAGNNQL 185

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 56.2 bits (136), Expect = 5e-08
 Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 6/106 (5%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L  L      L  +  G+  + E+P  +  L  L  +    + ++ LPD   SL  L + 
Sbjct: 207 LKKLPDLPLSLESIVAGNNILEELP-ELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVR 265

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLR 497
                  L  LP    +L  L        S L ELP  +  L    
Sbjct: 266 DNY----LTDLPELPQSLTFLDVSENIF-SGLSELPPNLYYLNASS 306

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 51.5 bits (124), Expect = 1e-06
 Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 12/105 (11%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           +  L      L  L++ +  + E+P       +L  L  S + +  +P+      NL+ L
Sbjct: 309 IRSLCDLPPSLEELNVSNNKLIELPALPP---RLERLIASFNHLAEVPE---LPQNLKQL 362

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCL 496
            +     L + P    ++ +L   +      L E+P   + LK L
Sbjct: 363 HVEYN-PLREFPDIPESVEDLRMNSH-----LAEVPELPQNLKQL 401

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 25/112 (22%), Positives = 46/112 (41%), Gaps = 12/112 (10%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L +L     +L  L      + EVP        L+ L+   + ++  PD   S+ +L + 
Sbjct: 329 LIELPALPPRLERLIASFNHLAEVPELPQ---NLKQLHVEYNPLREFPDIPESVEDLRMN 385

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
                  L ++P       NL  L++E  + LRE P   + ++ LR  +  +
Sbjct: 386 SH-----LAEVPELPQ---NLKQLHVET-NPLREFPDIPESVEDLRMNSERV 428

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 98/506 (19%), Positives = 164/506 (32%), Gaps = 71/506 (14%)

Query: 624  PSLGQLCSLKDLTIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDND 683
            P       L++  +   S L  +  E          +S    Y     EWE   P  + +
Sbjct: 5    PRNVSNTFLQEP-LRHSSNLTEMPVEAEN------VKSKTEYYNAW-SEWERNAPPGNGE 56

Query: 684  EHVQAFPRLRKLSIKKCPKLS------GRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCT 737
            +   A  RLR    ++  +L         LP   P LE +V +       SL  LP    
Sbjct: 57   QREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASCN-----SLTELPE--- 108

Query: 738  MEIDGCKRLVCDGPSE---SKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEI 794
                  K L+ D  +    S  P  +    +S  +     + Q    L I+  +   N +
Sbjct: 109  -LPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDN--NSL 165

Query: 795  -CLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYN 853
              L      L+ +    + L         LP+   LP L+ I   + N+L  L D     
Sbjct: 166  KKLPDLPPSLEFIAAGNNQL-------EELPELQNLPFLTAIYADN-NSLKKLPDLP--- 214

Query: 854  NARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNIN 913
               LE +       L  +        L  I   +   L+  L D   S  + +V +  + 
Sbjct: 215  -LSLESIVAGNN-ILEELPELQNLPFLTTIYADNNL-LKT-LPDLPPSLEALNVRDNYLT 270

Query: 914  SSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEEL 973
                    L  L V      + L     LP  L  L          + S C LP  +EEL
Sbjct: 271  DLPELPQSLTFLDVSEN-IFSGL---SELPPNLYYLNASSNE----IRSLCDLPPSLEEL 322

Query: 974  TIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLP 1033
             +     L  +         L  +  S   +L  +P+   NL  LH    V  + L   P
Sbjct: 323  NVSNN-KLIELPALPPR---LERLIASFN-HLAEVPELPQNLKQLH----VEYNPLREFP 373

Query: 1034 EDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEIS 1093
            +  +P +V D+ +     L  +       +L++L +   P +  FP+     ++ DL ++
Sbjct: 374  D--IPESVEDLRM--NSHLAEVPE--LPQNLKQLHVETNP-LREFPDI--PESVEDLRMN 424

Query: 1094 GDNMYKPLVKWGFHKLTSLRKLYIDG 1119
                     ++       L     + 
Sbjct: 425  -SERVVDPYEFAHETTDKLEDDVFEH 449

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 50.4 bits (121), Expect = 3e-06
 Identities = 30/133 (22%), Positives = 46/133 (34%), Gaps = 27/133 (20%)

Query: 382 IYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQC-LPD 440
           I P N+S   L + L            S  +TE+P+    +K       + SE +   P 
Sbjct: 3   INPRNVSNTFLQEPL----------RHSSNLTEMPVEAENVKSKTEYYNAWSEWERNAPP 52

Query: 441 AICSLFNLEILILRNCWC------------LLKLPSRIGNLVNLHYLNIEGASALRELPL 488
                  + +  LR+C              L  LP    +L +L        ++L ELP 
Sbjct: 53  GNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASC----NSLTELPE 108

Query: 489 GMKELKCLRTLTN 501
             + LK L    N
Sbjct: 109 LPQSLKSLLVDNN 121

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 48.5 bits (116), Expect = 1e-05
 Identities = 36/199 (18%), Positives = 62/199 (31%), Gaps = 30/199 (15%)

Query: 999  ISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPT 1058
            +    NL  +P    N+    E          + P         +       +L+  +  
Sbjct: 17   LRHSSNLTEMPVEAENVKSKTEYYNAWSEWERNAPPGNG-----EQREMAVSRLRDCLDR 71

Query: 1059 GTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYID 1118
                   EL L+   G+   PE     +L  L  S  N    L +     L SL     +
Sbjct: 72   ----QAHELELNNL-GLSSLPEL--PPHLESLVASC-NSLTELPE-LPQSLKSLLVDNNN 122

Query: 1119 GCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSF 1178
                  +  D      LP  L  + +S+  +L++L     Q    L+ + V +  +    
Sbjct: 123  LK----ALSD------LPPLLEYLGVSN-NQLEKLPE--LQNSSFLKIIDVDNN-SLKKL 168

Query: 1179 PEAGFPSSLLSLEIQRCPL 1197
            P+   P SL  +      L
Sbjct: 169  PD--LPPSLEFIAAGNNQL 185

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 66/375 (17%), Positives = 117/375 (31%), Gaps = 71/375 (18%)

Query: 824  PKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLP-SSLQA 882
            P+      L E  ++  + L  +      N            +   +    +     +  
Sbjct: 5    PRNVSNTFLQEP-LRHSSNLTEMPVE-AENVKSKTEYYNAWSEWERNAPPGNGEQREMAV 62

Query: 883  IEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRL 942
              +RDC          ++      +    ++S       LESL      SLT L     L
Sbjct: 63   SRLRDC---------LDRQAHELELNNLGLSSLPELPPHLESLVASCN-SLTELPE---L 109

Query: 943  PVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSC 1002
            P +LK L +++ +    L +   LP  +E L +     LE + E   + + L+ I + + 
Sbjct: 110  PQSLKSLLVDNNN----LKALSDLPPLLEYLGVSNN-QLEKLPE-LQNSSFLKIIDVDNN 163

Query: 1003 ENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLS 1062
             +LK LP    +L  +                    +N          +L+ L     L 
Sbjct: 164  -SLKKLPDLPPSLEFIA-----------------AGNN----------QLEELPELQNLP 195

Query: 1063 SLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSD 1122
             L  +       +   P+     +L  +    + + +         L  L  +Y D    
Sbjct: 196  FLTAIYADNNS-LKKLPDLP--LSLESIVAGNNILEEL---PELQNLPFLTTIYADNNL- 248

Query: 1123 AVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAG 1182
              + PD      LP SL ++ + D   L  L         SL  L V     F+   E  
Sbjct: 249  LKTLPD------LPPSLEALNVRDN-YLTDLPEL----PQSLTFLDVSEN-IFSGLSE-- 294

Query: 1183 FPSSLLSLEIQRCPL 1197
             P +L  L      +
Sbjct: 295  LPPNLYYLNASSNEI 309

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 46.9 bits (112), Expect = 3e-05
 Identities = 31/112 (27%), Positives = 45/112 (40%), Gaps = 14/112 (12%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L +L      L V       ++E+P        L YLN S +EI+ L D      +LE L
Sbjct: 272 LPELPQSLTFLDVSENIFSGLSELP------PNLYYLNASSNEIRSLCD---LPPSLEEL 322

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
            + N   L++LP+    L  L          L E+P   + LK L    N +
Sbjct: 323 NVSNN-KLIELPALPPRLERLIASFNH----LAEVPELPQNLKQLHVEYNPL 369

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 59.7 bits (145), Expect = 4e-09
 Identities = 63/399 (15%), Positives = 129/399 (32%), Gaps = 80/399 (20%)

Query: 809  LKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSL 868
            L  L + N    +++ K C    L+ + +        L  G   N   LE       + L
Sbjct: 202  LHKLTLRNNFDSLNVMKTCIQ-GLAGLEVHR------LVLGEFRNEGNLEKFDKSALEGL 254

Query: 869  TSISREHLP-SSLQAIEIRDCETLQCVLDDREKSCTSSSVTE--KNINSSSSTYLDLESL 925
             +++ E    + L        +   C+ +    S  S ++        +    +L+L + 
Sbjct: 255  CNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNC 314

Query: 926  FVYRCPSLTCLWSGGRLPV-TLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGC--SNLE 982
               + P+L        L   T    +  +  +   L S       +E L +     S   
Sbjct: 315  KFGQFPTLKL----KSLKRLTFTSNKGGNAFSEVDLPS-------LEFLDLSRNGLSFKG 363

Query: 983  SIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVV 1042
              ++       L+ + +S    + ++      L  L  +      NL  + E ++  +  
Sbjct: 364  CCSQSDFGTTSLKYLDLSFN-GVITMSSNFLGLEQLEHLDFQHS-NLKQMSEFSVFLS-- 419

Query: 1043 DVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKP 1100
                              L +L  L +S      V      +  ++L  L+++G++  + 
Sbjct: 420  ------------------LRNLIYLDISHTH-TRVAFNGIFNGLSSLEVLKMAGNSFQEN 460

Query: 1101 LVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQY 1160
             +   F +L +L  L +  C                            +L++LS   F  
Sbjct: 461  FLPDIFTELRNLTFLDLSQC----------------------------QLEQLSPTAFNS 492

Query: 1161 LVSLEHLSVFSCPNFTSFPEAGFP--SSLLSLEIQRCPL 1197
            L SL+ L++ S     S P+  F   +SL  + +   P 
Sbjct: 493  LSSLQVLNMASN-QLKSVPDGIFDRLTSLQKIWLHTNPW 530

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD--AICSLFNLEI 450
           S        L+ L L    +  +  +   L+QL +L+F  S ++ + +     SL NL  
Sbjct: 366 SQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIY 425

Query: 451 LILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
           L + +    +        L +L  L + G
Sbjct: 426 LDISHTHTRVAFNGIFNGLSSLEVLKMAG 454

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 47.0 bits (112), Expect = 4e-05
 Identities = 24/107 (22%), Positives = 39/107 (36%), Gaps = 8/107 (7%)

Query: 399 CKKLRVLSLGSYCITEVPI---SIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
              L  L L    ++       S      L+YL+ S + +  +      L  LE L  ++
Sbjct: 346 LPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQH 405

Query: 456 CWCLLKLPSRI--GNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
              L ++       +L NL YL+I   +  R    G+   L  L  L
Sbjct: 406 SN-LKQMSEFSVFLSLRNLIYLDISH-THTRVAFNGIFNGLSSLEVL 450

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 32/127 (25%), Positives = 46/127 (36%), Gaps = 9/127 (7%)

Query: 402 LRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCLP-DAICSLFNLEILILRNCWCL 459
            + L L    +  +   S     +L+ L+ SR EIQ +   A  SL +L  LIL     +
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGN-PI 88

Query: 460 LKLPSRI-GNLVNLHYLNIEGASALRELPLGM-KELKCLRTL---TNFIVGKDSGCALRD 514
             L       L +L  L     + L  L       LK L+ L    N I          +
Sbjct: 89  QSLALGAFSGLSSLQKLVAVE-TNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSN 147

Query: 515 LKNWKFL 521
           L N + L
Sbjct: 148 LTNLEHL 154

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 42.8 bits (101), Expect = 8e-04
 Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 7/105 (6%)

Query: 400 KKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQC--LPDAICSLFNLEILILRNC 456
           + L  L +           I   L  L  L  + +  Q   LPD    L NL  L L  C
Sbjct: 421 RNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC 480

Query: 457 WCLLKLPSRI-GNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
             L +L      +L +L  LN+   + L+ +P G+   L  L+ +
Sbjct: 481 -QLEQLSPTAFNSLSSLQVLNMAS-NQLKSVPDGIFDRLTSLQKI 523

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 57.3 bits (139), Expect = 1e-08
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 2/94 (2%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSL 445
            I  +  ++L      L  L+L    I +V   +    +L+ L+ S +++  +     S 
Sbjct: 155 EIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQV-VFAKLKTLDLSSNKLAFMGPEFQSA 213

Query: 446 FNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
             +  + LRN   L+ +   +    NL + ++ G
Sbjct: 214 AGVTWISLRNNK-LVLIEKALRFSQNLEHFDLRG 246

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 57.3 bits (139), Expect = 1e-08
 Identities = 18/124 (14%), Positives = 39/124 (31%), Gaps = 4/124 (3%)

Query: 398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN-- 455
              KL+ L L S  +  +         + +++   +++  +  A+    NLE   LR   
Sbjct: 189 VFAKLKTLDLSSNKLAFMGPEFQSAAGVTWISLRNNKLVLIEKALRFSQNLEHFDLRGNG 248

Query: 456 --CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALR 513
             C  L    S+   +  +    ++  +   E    +  L          +       L 
Sbjct: 249 FHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLI 308

Query: 514 DLKN 517
            L +
Sbjct: 309 ALGH 312

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 51.9 bits (125), Expect = 5e-07
 Identities = 15/110 (13%), Positives = 43/110 (39%), Gaps = 9/110 (8%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIG-CLKQLRYLNFSRSEIQCLP-DAICSLFNLE 449
           + ++     + ++  +    + +   S+      ++ L+ S + +  +    +     LE
Sbjct: 2   IHEIKQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLE 61

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
           +L L +   +L     + +L  L  L++   + ++EL         + TL
Sbjct: 62  LLNLSS--NVLYETLDLESLSTLRTLDLNN-NYVQELL----VGPSIETL 104

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 50.8 bits (122), Expect = 1e-06
 Identities = 17/106 (16%), Positives = 38/106 (35%), Gaps = 6/106 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILIL- 453
           L     +  L   +  I+ V  S    +  + +  + ++I  L D        ++ L L 
Sbjct: 95  LLVGPSIETLHAANNNISRVSCSR--GQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLK 152

Query: 454 RNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            N    +       +   L +LN++    + ++   +     L+TL
Sbjct: 153 LNEIDTVNFAELAASSDTLEHLNLQYNF-IYDVKGQVV-FAKLKTL 196

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 16/110 (14%), Positives = 39/110 (35%), Gaps = 10/110 (9%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
            L+ L      ++ L L    ++++    +    +L  LN S + +    D + SL  L 
Sbjct: 25  ALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLR 83

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L L N      +   +    ++  L+    + +  +       +  + +
Sbjct: 84  TLDLNNN----YV-QELLVGPSIETLHAAN-NNISRVSCSR--GQGKKNI 125

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 42.7 bits (101), Expect = 5e-04
 Identities = 38/298 (12%), Positives = 86/298 (28%), Gaps = 56/298 (18%)

Query: 946  LKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESI-AERFHDDACLRSIWISSCEN 1004
             K  ++ D S  + L S  Q    V+EL + G   L  I A        L  + +SS   
Sbjct: 12   YKIEKVTDSSLKQALASLRQSAWNVKELDLSGN-PLSQISAADLAPFTKLELLNLSSN-V 69

Query: 1005 LKSLP--KGLSNLSHLH----EIR-IVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIP 1057
            L      + LS L  L      ++ ++   ++ +L      +N           +   + 
Sbjct: 70   LYETLDLESLSTLRTLDLNNNYVQELLVGPSIETL---HAANN----------NISR-VS 115

Query: 1058 TGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKL 1115
                   + + L+    I +  +      + +  L++  + +             +L  L
Sbjct: 116  CSRGQGKKNIYLANNK-ITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHL 174

Query: 1116 YIDGCSDAVSFPDVGKGVILPTSLTSITISDF-PKLKRLS---------SKGFQYLVSLE 1165
             +                     +  +       KLK L             FQ    + 
Sbjct: 175  NLQYN-----------------FIYDVKGQVVFAKLKTLDLSSNKLAFMGPEFQSAAGVT 217

Query: 1166 HLSVFSCPNFTSFPEA-GFPSSLLSLEIQRCPLLEKCKMRKGQEWPKIAHIPLTLINQ 1222
             +S+ +        +A  F  +L   +++              +  ++  +    + +
Sbjct: 218  WISLRNN-KLVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKK 274

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 57.9 bits (140), Expect = 1e-08
 Identities = 18/94 (19%), Positives = 39/94 (41%), Gaps = 2/94 (2%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSL 445
            I  +  ++L      L  L+L    I +V   +    +L+ L+ S +++  +     S 
Sbjct: 155 EIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQV-VFAKLKTLDLSSNKLAFMGPEFQSA 213

Query: 446 FNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
             +  + LRN   L+ +   +    NL + ++ G
Sbjct: 214 AGVTWISLRNN-KLVLIEKALRFSQNLEHFDLRG 246

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 51.8 bits (124), Expect = 1e-06
 Identities = 15/110 (13%), Positives = 43/110 (39%), Gaps = 9/110 (8%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIG-CLKQLRYLNFSRSEIQCL-PDAICSLFNLE 449
           + ++     + ++  +    + +   S+      ++ L+ S + +  +    +     LE
Sbjct: 2   IHEIKQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLE 61

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
           +L L +   L +    + +L  L  L++   + ++EL         + TL
Sbjct: 62  LLNLSSNV-LYETLD-LESLSTLRTLDLNN-NYVQELL----VGPSIETL 104

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 51.4 bits (123), Expect = 1e-06
 Identities = 14/92 (15%), Positives = 30/92 (32%), Gaps = 1/92 (1%)

Query: 398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR-NC 456
              KL+ L L S  +  +         + +++   +++  +  A+    NLE   LR N 
Sbjct: 189 VFAKLKTLDLSSNKLAFMGPEFQSAAGVTWISLRNNKLVLIEKALRFSQNLEHFDLRGNG 248

Query: 457 WCLLKLPSRIGNLVNLHYLNIEGASALRELPL 488
           +    L         +  +  +    L     
Sbjct: 249 FHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNE 280

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 17/106 (16%), Positives = 39/106 (36%), Gaps = 6/106 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILR 454
           L     +  L   +  I+ V  S    +  + +  + ++I  L D        ++ L L+
Sbjct: 95  LLVGPSIETLHAANNNISRVSCSR--GQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLK 152

Query: 455 -NCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            N    +       +   L +LN++    + ++   +     L+TL
Sbjct: 153 LNEIDTVNFAELAASSDTLEHLNLQYNF-IYDVKGQVV-FAKLKTL 196

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A* Length = 567

 Score = 58.2 bits (140), Expect = 1e-08
 Identities = 29/150 (19%), Positives = 59/150 (39%), Gaps = 19/150 (12%)

Query: 355 DGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITE 414
           + +  F  L  V  +R       +   +   ++  M       +   +RVL L    +T 
Sbjct: 403 ETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKM-------EYADVRVLHLAHKDLTV 455

Query: 415 VPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY 474
           +   +  L  + +L+ S + ++ LP A+ +L  LE+L   +   L  +   + NL  L  
Sbjct: 456 LC-HLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDN-ALENVDG-VANLPRLQE 512

Query: 475 LN-----IEGASALRELPLGMKELKCLRTL 499
           L      ++ ++A++ L         L  L
Sbjct: 513 LLLCNNRLQQSAAIQPL----VSCPRLVLL 538

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 58.0 bits (140), Expect = 1e-08
 Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 19/132 (14%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSL 445
            I    L+ L     +LR L +    +T +P+    L +L   +   + +  LP  +C L
Sbjct: 67  VIPDNNLTSLPALPPELRTLEVSGNQLTSLPVLPPGLLELSIFSNPLTHLPALPSGLCKL 126

Query: 446 F--------------NLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMK 491
           +               L+ L + +   L  LP+    L  L   N    + L  LP+   
Sbjct: 127 WIFGNQLTSLPVLPPGLQELSVSDN-QLASLPALPSELCKLWAYN----NQLTSLPMLPS 181

Query: 492 ELKCLRTLTNFI 503
            L+ L    N +
Sbjct: 182 GLQELSVSDNQL 193

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 57.6 bits (139), Expect = 2e-08
 Identities = 28/118 (23%), Positives = 45/118 (38%), Gaps = 11/118 (9%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSL 445
           ++S   L+ L     +L  L   +  +T +P+       L+ L+ S +++  LP     L
Sbjct: 147 SVSDNQLASLPALPSELCKLWAYNNQLTSLPMLPS---GLQELSVSDNQLASLPTLPSEL 203

Query: 446 FNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
           + L     R    L  LP+    L  L          L  LP+   ELK L    N +
Sbjct: 204 YKLWAYNNR----LTSLPALPSGLKELIVSGNR----LTSLPVLPSELKELMVSGNRL 253

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 56.4 bits (136), Expect = 4e-08
 Identities = 20/99 (20%), Positives = 33/99 (33%), Gaps = 7/99 (7%)

Query: 399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWC 458
                VL++G   +T +P  +     +  L    + +  LP        L  L +     
Sbjct: 39  NNGNAVLNVGESGLTTLPDCLP--AHITTLVIPDNNLTSLPALPP---ELRTLEVSGN-Q 92

Query: 459 LLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLR 497
           L  LP     L+ L   +      L  LP G+ +L    
Sbjct: 93  LTSLPVLPPGLLELSIFSNPLTH-LPALPSGLCKLWIFG 130

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 53.0 bits (127), Expect = 5e-07
 Identities = 25/110 (22%), Positives = 38/110 (34%), Gaps = 13/110 (11%)

Query: 396 LPQC--KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILIL 453
           LP C    +  L +    +T +P       +LR L  S +++  LP     L  L I   
Sbjct: 55  LPDCLPAHITTLVIPDNNLTSLPALPP---ELRTLEVSGNQLTSLPVLPPGLLELSIFSN 111

Query: 454 RNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
                   LP+    L  L     +    L  LP+    L+ L    N +
Sbjct: 112 PLT----HLPALPSGLCKLWIFGNQ----LTSLPVLPPGLQELSVSDNQL 153

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 52.2 bits (125), Expect = 9e-07
 Identities = 41/233 (17%), Positives = 67/233 (28%), Gaps = 25/233 (10%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L  L  +  KL   +     +T +P        L+ L  S + +  LP        L+ L
Sbjct: 196 LPTLPSELYKLWAYNNR---LTSLPALPS---GLKELIVSGNRLTSLPVLPS---ELKEL 246

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCA 511
           ++     L  LP     L++L        + L  LP  +  L    T+         G  
Sbjct: 247 MVSGN-RLTSLPMLPSGLLSLSVYR----NQLTRLPESLIHLSSETTVNL------EGNP 295

Query: 512 LRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDW-RPRRDGDSVDEAR 570
           L +                  +I    A  +  R    L     DW  P R+G+     R
Sbjct: 296 LSERTLQALREITSAPGYSGPIIRFDMAGASAPRETRALHLAAADWLVPAREGEPAPADR 355

Query: 571 EKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSL 623
                 M     N     +     +   +++ D  F       L       +L
Sbjct: 356 ----WHMFGQEDNADAFSLFLDRLSETENFIKDAGFKAQISSWLAQLAEDEAL 404

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 50.3 bits (120), Expect = 3e-06
 Identities = 69/301 (22%), Positives = 114/301 (37%), Gaps = 36/301 (11%)

Query: 819  TVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPS 878
             VV   +AC     + + +   + L +L D  +  +  +  L I    +LTS+     P 
Sbjct: 29   AVVQKMRACLNNGNAVLNV-GESGLTTLPDC-LPAH--ITTLVIPDN-NLTSLPAL--PP 81

Query: 879  SLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWS 938
             L+ +E+   + L   L          S+    +    +    L  L+++    LT    
Sbjct: 82   ELRTLEVSGNQ-LTS-LPVLPPGLLELSIFSNPLTHLPALPSGLCKLWIFGN-QLT---- 134

Query: 939  GGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIW 998
               LPV    L+    S+ + L S   LP E+ +L  Y    L S+         L+ + 
Sbjct: 135  --SLPVLPPGLQELSVSDNQ-LASLPALPSELCKLWAYNN-QLTSLPMLPS---GLQELS 187

Query: 999  ISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPT 1058
            +S    L SLP   S L  L        + L SLP   LPS +   LI   ++L +L   
Sbjct: 188  VSDN-QLASLPTLPSELYKLW----AYNNRLTSLPA--LPSGLK-ELIVSGNRLTSLPVL 239

Query: 1059 GTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYID 1118
               S L+EL +S    +   P     + L  L +   N    L +     L+S   + ++
Sbjct: 240  --PSELKELMVSGN-RLTSLPML--PSGLLSLSVY-RNQLTRLPE-SLIHLSSETTVNLE 292

Query: 1119 G 1119
            G
Sbjct: 293  G 293

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 47.2 bits (112), Expect = 3e-05
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 422 LKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGAS 481
                 LN   S +  LPD + +  ++  L++ +   L  LP+    L  L     +   
Sbjct: 39  NNGNAVLNVGESGLTTLPDCLPA--HITTLVIPDNN-LTSLPALPPELRTLEVSGNQ--- 92

Query: 482 ALRELPLGMKELKCLRTLTN 501
            L  LP+    L  L   +N
Sbjct: 93  -LTSLPVLPPGLLELSIFSN 111

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 57.3 bits (139), Expect = 2e-08
 Identities = 74/411 (18%), Positives = 139/411 (33%), Gaps = 57/411 (13%)

Query: 797  EKPLQGLQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNN 854
            E  L G + L  L    I     + S+          L  + +   N ++S+     +  
Sbjct: 98   ETALSGPKALKHLF--FIQT--GISSIDFIPLHNQKTLESLYLGS-NHISSIKLPKGFPT 152

Query: 855  ARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSC-TSSSVTEKNIN 913
             +L+VL  +   ++  +S+E + SSLQ             +   E     S+     N  
Sbjct: 153  EKLKVLDFQNN-AIHYLSKEDM-SSLQQATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFG 210

Query: 914  SSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEEL 973
             + +  +  + L      SL           T + +  ED S   V    C++ VE   L
Sbjct: 211  GTQNLLVIFKGLKNSTIQSLWLG--------TFEDMDDEDISP-AVFEGLCEMSVESINL 261

Query: 974  TIYGCSNLESIAER-FHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSL 1032
                     +I+   FH  + L+ + +++  +L  LP GL  LS L ++ +       +L
Sbjct: 262  ---QKHYFFNISSNTFHCFSGLQELDLTAT-HLSELPSGLVGLSTLKKLVLSAN-KFENL 316

Query: 1033 PEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDL 1090
             + +                          SL  L++      +      L    NL +L
Sbjct: 317  CQISA---------------------SNFPSLTHLSIKGNTKRLELGTGCLENLENLREL 355

Query: 1091 EISGDNMYK-PLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPK 1149
            ++S D++            L+ L+ L +          +  K       L  + ++ F +
Sbjct: 356  DLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKEC---PQLELLDLA-FTR 411

Query: 1150 LKRLSSKG-FQYLVSLEHLSVFSCPNFTSFPEAGFP--SSLLSLEIQRCPL 1197
            LK   ++  FQ L  L+ L++          E  F    +L  L +Q    
Sbjct: 412  LKVKDAQSPFQNLHLLKVLNLSHS-LLDISSEQLFDGLPALQHLNLQGNHF 461

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 49.2 bits (118), Expect = 7e-06
 Identities = 71/417 (17%), Positives = 133/417 (31%), Gaps = 80/417 (19%)

Query: 822  SLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHL--P 877
            ++    F  L NL+ + +     +  + +    +  RL+ L +     L  ++   L  P
Sbjct: 47   TIQNTTFSRLINLTFLDLTR-CQIYWIHEDTFQSQHRLDTLVLTAN-PLIFMAETALSGP 104

Query: 878  SSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLD----LESLFVYRCPSL 933
             +L+ +                            I+S     L     LESL++     +
Sbjct: 105  KALKHLFFIQT----------------------GISSIDFIPLHNQKTLESLYLGSN-HI 141

Query: 934  TCL--WSGGRLPVTLKRLRIEDCSNFKVLTSE--CQLPVEVEELTIYGCSN-LESIAERF 988
            + +    G      LK L  ++      L+ E    L  +   L++    N +  I    
Sbjct: 142  SSIKLPKGFPTE-KLKVLDFQNN-AIHYLSKEDMSSLQ-QATNLSLNLNGNDIAGIEPGA 198

Query: 989  HDDACLRSIWISSCENLKSLPKGLSN--LSHLHEIRIVRCHNLVSLPEDALP-------- 1038
             D A  +S+     +NL  + KGL N  +  L         +   +              
Sbjct: 199  FDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTF-EDMDDEDISPAVFEGLCEMSVE 257

Query: 1039 ---------SNVVDVLIEDCDKLKAL---------IPTGT--LSSLRELALSECPGIVVF 1078
                      N+          L+ L         +P+G   LS+L++L LS        
Sbjct: 258  SINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSAN-KFENL 316

Query: 1079 PEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILP 1136
             +   S   +LT L I G+     L       L +LR+L +      +   D     +  
Sbjct: 317  CQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDD--IETSDCCNLQLRN 374

Query: 1137 -TSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
             + L S+ +S   +   L ++ F+    LE L +                +L  L++
Sbjct: 375  LSHLQSLNLSYN-EPLSLKTEAFKECPQLELLDLAFT-RLKVKDAQSPFQNLHLLKV 429

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 47.3 bits (113), Expect = 3e-05
 Identities = 23/101 (22%), Positives = 44/101 (43%), Gaps = 4/101 (3%)

Query: 402 LRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLL 460
           +  ++L  +    +   +  C   L+ L+ + + +  LP  +  L  L+ L+L       
Sbjct: 256 VESINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANK-FE 314

Query: 461 KLPSR-IGNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
            L      N  +L +L+I+G +   EL  G  + L+ LR L
Sbjct: 315 NLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLREL 355

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 46.9 bits (112), Expect = 3e-05
 Identities = 67/408 (16%), Positives = 126/408 (30%), Gaps = 96/408 (23%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLE 449
           + S+       L+ L L +  ++E+P  +  L  L+ L  S ++ + L   +  +  +L 
Sbjct: 269 ISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLT 328

Query: 450 ILILRNCWCLLKLPSR-IGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDS 508
            L ++     L+L +  + NL NL  L++     +        +L+ L  L +  +   S
Sbjct: 329 HLSIKGNTKRLELGTGCLENLENLRELDLSH-DDIETSDCCNLQLRNLSHLQSLNL---S 384

Query: 509 GCALRDLKN--WKFLRG--RLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGD 564
                 LK   +K       L ++     +  ++A      +   L  L L         
Sbjct: 385 YNEPLSLKTEAFKECPQLELLDLAF--TRLKVKDAQSPFQNLH-LLKVLNLS-------- 433

Query: 565 SVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCR-RSTSL 623
                           HS +       + G              +  L L+       ++
Sbjct: 434 ----------------HSLLDISSEQLFDGL-----------PALQHLNLQGNHFPKGNI 466

Query: 624 PSLGQLCSLKDLTIVGMSE--LKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRD 681
                L +L  L I+ +S   L SI    +        + +  +             NR 
Sbjct: 467 QKTNSLQTLGRLEILVLSFCDLSSIDQHAF-----TSLKMMNHVDLSH---------NRL 512

Query: 682 NDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEID 741
               ++A   L+ + +     L+    NH+  +              LP L    T+ + 
Sbjct: 513 TSSSIEALSHLKGIYLN----LAS---NHISIILP----------SLLPILSQQRTINLR 555

Query: 742 GCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEG 789
               L C              C+   F  W  E  QK+E      CE 
Sbjct: 556 QN-PLDCT-------------CSNIYFLEWYKENMQKLEDTEDTLCEN 589

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 46.2 bits (110), Expect = 7e-05
 Identities = 29/120 (24%), Positives = 40/120 (33%), Gaps = 7/120 (5%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGC---LKQLRYLNFSRSEIQCL-PDA 441
                + +  L   + LR L L    I            L  L+ LN S +E   L  +A
Sbjct: 336 TKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEA 395

Query: 442 ICSLFNLEILIL-RNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
                 LE+L L      +    S   NL  L  LN+   S L      +   L  L+ L
Sbjct: 396 FKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLNLSH-SLLDISSEQLFDGLPALQHL 454

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 18/134 (13%), Positives = 42/134 (31%), Gaps = 10/134 (7%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNL 448
           + +    +   L  L L    I  +   +     +L  L  + + +  + + A+     L
Sbjct: 48  IQNTTFSRLINLTFLDLTRCQIYWIHEDTFQSQHRLDTLVLTANPLIFMAETALSGPKAL 107

Query: 449 EILILRNCWCLLKLPSR-IGNLVNLHYLNIEGASALRELPLGM-KELKCLRTLT---NFI 503
           + L       +  +    + N   L  L +   + +  + L      + L+ L    N I
Sbjct: 108 KHLFFIQT-GISSIDFIPLHNQKTLESLYLGS-NHISSIKLPKGFPTEKLKVLDFQNNAI 165

Query: 504 VGKDSGCALRDLKN 517
                   +  L+ 
Sbjct: 166 HYLSKE-DMSSLQQ 178

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 17/102 (16%), Positives = 34/102 (33%), Gaps = 6/102 (5%)

Query: 402 LRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCL-PDAICSLFNLEILILRNCWCL 459
              L      +  +   +   L  L +L+ +R +I  +  D   S   L+ L+L     L
Sbjct: 35  TECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQIYWIHEDTFQSQHRLDTLVLTAN-PL 93

Query: 460 LKLPSRI-GNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
           + +          L +L     + +  +        K L +L
Sbjct: 94  IFMAETALSGPKALKHLFFIQ-TGISSIDFIPLHNQKTLESL 134

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 57.0 bits (138), Expect = 3e-08
 Identities = 19/109 (17%), Positives = 45/109 (41%), Gaps = 7/109 (6%)

Query: 396 LPQCKKLRVLSLGSYCITEVPI--SIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILIL 453
            P  +K++++ +G   +   P+  S+  +K+L  L    ++++    A  S   L  L L
Sbjct: 301 APVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGSEIKLASLNL 360

Query: 454 RNCWCLLKLPSRI-GNLVNLHYLNIEGASALRELP--LGMKELKCLRTL 499
                + ++P+   G    +  L+      L+ +P     K +  +  +
Sbjct: 361 AYNQ-ITEIPANFCGFTEQVENLSFAHNK-LKYIPNIFDAKSVSVMSAI 407

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 55.8 bits (135), Expect = 7e-08
 Identities = 17/101 (16%), Positives = 31/101 (30%), Gaps = 8/101 (7%)

Query: 385 PNISPMVLSDLLPQCKKLRVLSLGSYCITEVP--ISIGCLKQLRYLNFSRSEIQCLPDAI 442
           P  S    ++       L  + L    +T++        L  L  ++ S +     P   
Sbjct: 473 PKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYNSFSKFPTQP 532

Query: 443 CSLFNLEILILRNCWCLL------KLPSRIGNLVNLHYLNI 477
            +   L+   +RN           + P  I    +L  L I
Sbjct: 533 LNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQI 573

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 54.3 bits (131), Expect = 2e-07
 Identities = 31/295 (10%), Positives = 76/295 (25%), Gaps = 55/295 (18%)

Query: 913  NSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEV-- 970
                  + DL    +   P    +    R+ +   ++      +   +T    +   V  
Sbjct: 152  YDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQI---GQLSNN-ITF---VSKAVMR 204

Query: 971  ----EELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSLPKGLSNLSHLHEIRIVRC 1026
                 +  +     +              +      +  K+      NL  L ++ +  C
Sbjct: 205  LTKLRQFYMGNSPFVAENICEA-----WENENSEYAQQYKTEDLKWDNLKDLTDVEVYNC 259

Query: 1027 HNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSEC---------PGIVV 1077
             NL  LP            +              L  ++ + ++                
Sbjct: 260  PNLTKLPTF----------L------------KALPEMQLINVACNRGISGEQLKDDWQA 297

Query: 1078 FPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPT 1137
              +  +   +  + I  +N+    V+    K+  L  L           P  G       
Sbjct: 298  LADAPVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGS---E-I 353

Query: 1138 SLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
             L S+ ++   ++  + +    +   +E+LS          P      S+  +  
Sbjct: 354  KLASLNLAY-NQITEIPANFCGFTEQVENLSFAHN-KLKYIPNIFDAKSVSVMSA 406

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 53.5 bits (129), Expect = 4e-07
 Identities = 16/135 (11%), Positives = 35/135 (25%), Gaps = 21/135 (15%)

Query: 386 NISPMVLSDLLP-QCKKLRVLSLGS-YCITEVPISIGCLKQLRYLNFSRSEIQCLPDAIC 443
           +     +          L    + S      +  S     +   +    + I  +  A+ 
Sbjct: 144 HYQKTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQIGQLSNNITFVSKAVM 203

Query: 444 SLFNLEILILRN-------------------CWCLLKLPSRIGNLVNLHYLNIEGASALR 484
            L  L    + N                            +  NL +L  + +     L 
Sbjct: 204 RLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLT 263

Query: 485 ELPLGMKELKCLRTL 499
           +LP  +K L  ++ +
Sbjct: 264 KLPTFLKALPEMQLI 278

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 51.6 bits (124), Expect = 2e-06
 Identities = 17/119 (14%), Positives = 40/119 (33%), Gaps = 13/119 (10%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVP-ISIGCLKQLRYLNFS--------RSEIQCLPDAI 442
           L     +   +  ++L +  I++ P         L  +N          ++ ++   +  
Sbjct: 425 LDPTPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLKDENENF 484

Query: 443 CSLFNLEILILRNCWCLLKLPS--RIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            + + L  + LR    L KL    R   L  L  +++   ++  + P        L+  
Sbjct: 485 KNTYLLTSIDLRFN-KLTKLSDDFRATTLPYLVGIDLSY-NSFSKFPTQPLNSSTLKGF 541

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 51.2 bits (123), Expect = 2e-06
 Identities = 17/125 (13%), Positives = 40/125 (32%), Gaps = 19/125 (15%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVP--ISIGCLKQLRYLNFSR--------SEIQCLPDAI 442
           ++     +++  LS     +  +P       +  +  ++FS              L    
Sbjct: 370 ANFCGFTEQVENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTP 429

Query: 443 CSLFNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEG-------ASALRELPLGMKELK 494
               N+  + L N   + K P  +      L  +N+ G        ++L++     K   
Sbjct: 430 FKGINVSSINLSNN-QISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLKDENENFKNTY 488

Query: 495 CLRTL 499
            L ++
Sbjct: 489 LLTSI 493

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 49.7 bits (119), Expect = 6e-06
 Identities = 18/109 (16%), Positives = 37/109 (33%), Gaps = 7/109 (6%)

Query: 396 LPQCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR 454
           + +  KLR   +G+     E        +   Y    ++          +L +L  + + 
Sbjct: 202 VMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKT----EDLKWDNLKDLTDVEVY 257

Query: 455 NCWCLLKLPSRIGNLVNLHYLNIEG--ASALRELPLGMKELKCLRTLTN 501
           NC  L KLP+ +  L  +  +N+      +  +L    + L        
Sbjct: 258 NCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEK 306

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.8 bits (109), Expect = 1e-04
 Identities = 14/122 (11%), Positives = 29/122 (23%), Gaps = 19/122 (15%)

Query: 396 LPQCKKLRVLSLGS--------YCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICS-LF 446
                 +  +                 +  +      +  +N S ++I   P  + S   
Sbjct: 398 AKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSINLSNNQISKFPKELFSTGS 457

Query: 447 NLEILILRNC-------WCLLKLPSRIGNLVNLHYLNIEGASALRELP--LGMKELKCLR 497
            L  + L            L        N   L  +++     L +L        L  L 
Sbjct: 458 PLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNK-LTKLSDDFRATTLPYLV 516

Query: 498 TL 499
            +
Sbjct: 517 GI 518

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 32/263 (12%), Positives = 67/263 (25%), Gaps = 37/263 (14%)

Query: 417 ISIGCLKQLRYLNFSRSEIQC-LPDAICSLFNLEILILRN----CWCLLKLPSRIGNLVN 471
           +S+    ++  L+         +PDAI  L  LE+L L +        L  P  I   ++
Sbjct: 75  VSLNSNGRVTGLSLEGFGASGRVPDAIGQLTELEVLALGSHGEKVNERLFGPKGISANMS 134

Query: 472 LHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGLE 531
                       +              + + I       +++             I  L 
Sbjct: 135 DEQKQKMRMHYQKTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSR--ITLKDTQIGQLS 192

Query: 532 NVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEI-H 590
           N I         L     L    +                 +           +     +
Sbjct: 193 NNITFVSKAVMRLT---KLRQFYMG---------------NSPFVAENICEAWENENSEY 234

Query: 591 SYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLP-SLGQLCSLKDL-----TIVGMSELK 644
           +             +  ++  + + NC   T LP  L  L  ++ +       +   +LK
Sbjct: 235 AQQYKTEDLKWD--NLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLK 292

Query: 645 SIGSEIYGEGCSKPFQSLQTLYF 667
                +      +    +Q +Y 
Sbjct: 293 DDWQALADAPVGE---KIQIIYI 312

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 42.7 bits (101), Expect = 7e-04
 Identities = 16/110 (14%), Positives = 30/110 (27%), Gaps = 8/110 (7%)

Query: 401 KLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSR-----SEIQCLPDAICSLFNLEILILR 454
           ++  LSL  +  +  VP +IG L +L  L         +E    P  I +  + E     
Sbjct: 82  RVTGLSLEGFGASGRVPDAIGQLTELEVLALGSHGEKVNERLFGPKGISANMSDEQKQKM 141

Query: 455 NCWCLLKLPSRIGNLV--NLHYLNIEGASALRELPLGMKELKCLRTLTNF 502
                             +L    I      + +    +       +   
Sbjct: 142 RMHYQKTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQIGQL 191

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 42.7 bits (101), Expect = 8e-04
 Identities = 25/221 (11%), Positives = 60/221 (27%), Gaps = 57/221 (25%)

Query: 994  LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHN-LVSLPEDALPSNVVDVLIEDCDKL 1052
            L  +       L+       +   L  + +   +N +  +P +              +++
Sbjct: 332  LGMLECLYN-QLEGKLPAFGSEIKLASLNL--AYNQITEIPAN---------FCGFTEQV 379

Query: 1053 KAL---------IPT----GTLSSLRELALS-------ECPGIVVFPEE-GLSTNLTDLE 1091
            + L         IP      ++S +  +  S       +               N++ + 
Sbjct: 380  ENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSIN 439

Query: 1092 ISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLK 1151
            +S  N      K  F   + L  + + G                   LT I  +      
Sbjct: 440  LSN-NQISKFPKELFSTGSPLSSINLMGN-----------------MLTEIPKNSL---- 477

Query: 1152 RLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
            +  ++ F+    L  + +      T   +    ++L  L  
Sbjct: 478  KDENENFKNTYLLTSIDLRFN-KLTKLSDDFRATTLPYLVG 517

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 56.9 bits (137), Expect = 3e-08
 Identities = 24/114 (21%), Positives = 45/114 (39%), Gaps = 12/114 (10%)

Query: 392 LSDLLPQC--KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
              LL +C   +   L L    ++ +P ++    Q+  L  +++ +  LP+      +LE
Sbjct: 49  AVSLLKECLINQFSELQLNRLNLSSLPDNLP--PQITVLEITQNALISLPELPA---SLE 103

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
            L   +   L  LP    +L +L   N    + L  LP     L+ +    N +
Sbjct: 104 YLDACDN-RLSTLPELPASLKHLDVDN----NQLTMLPELPALLEYINADNNQL 152

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 54.2 bits (130), Expect = 2e-07
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 8/92 (8%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE-- 449
           L+ L      L VLS+ +  +T +P      + L  L+ S + ++ LP       + E  
Sbjct: 152 LTMLPELPTSLEVLSVRNNQLTFLP---ELPESLEALDVSTNLLESLPAVPVRNHHSEET 208

Query: 450 --ILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
                 R    +  +P  I +L     + +E 
Sbjct: 209 EIFFRCRENR-ITHIPENILSLDPTCTIILED 239

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 25/151 (16%), Positives = 43/151 (28%), Gaps = 38/151 (25%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLK-----------------QLRYL 428
            I+   L  L      L  L      ++ +P     LK                  L Y+
Sbjct: 86  EITQNALISLPELPASLEYLDACDNRLSTLPELPASLKHLDVDNNQLTMLPELPALLEYI 145

Query: 429 NFSRSEIQCLPDAICSL-----------------FNLEILILRNCWCLLKLPSRIGNLVN 471
           N   +++  LP+   SL                  +LE L +     L  LP+      +
Sbjct: 146 NADNNQLTMLPELPTSLEVLSVRNNQLTFLPELPESLEALDVSTN-LLESLPAVPVRNHH 204

Query: 472 LHYLNIE---GASALRELPLGMKELKCLRTL 499
                I      + +  +P  +  L    T+
Sbjct: 205 SEETEIFFRCRENRITHIPENILSLDPTCTI 235

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 56.2 bits (136), Expect = 4e-08
 Identities = 66/394 (16%), Positives = 125/394 (31%), Gaps = 93/394 (23%)

Query: 831  NLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCET 890
                I+ +    L SL     +N++  ++  I++   LT +      +++  +++     
Sbjct: 32   ATDTISEEQLATLTSLD---CHNSSITDMTGIEKLTGLTKLICTS--NNITTLDLSQNTN 86

Query: 891  LQCVLDDREKSCTSSSVTEKNINSSSS-TYLD-----LESLFVYRCPSLTCLWSGG---- 940
            L   L      C S+ +T  ++   +  TYL+     L  L V + P LT L        
Sbjct: 87   LT-YLA-----CDSNKLTNLDVTPLTKLTYLNCDTNKLTKLDVSQNPLLTYLNCARNTLT 140

Query: 941  RLPVT-LKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDAC----LR 995
             + V+   +L   DC   K +T           L +   + L ++        C    + 
Sbjct: 141  EIDVSHNTQLTELDCHLNKKITK----------LDVTPQTQLTTLD-------CSFNKIT 183

Query: 996  SIWISSCENLKSLPKGLSNLSH--LHEIRIVRCHNLVSLPEDALPSN-VVDVLIEDCDKL 1052
             + +S  + L  L     N     + ++ + +   L  L      SN + ++ +    +L
Sbjct: 184  ELDVSQNKLLNRL-----NCDTNNITKLDLNQNIQLTFL---DCSSNKLTEIDVTPLTQL 235

Query: 1053 KAL---------IPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVK 1103
                        +   TLS L  L   +   ++        T L   +  G    K L  
Sbjct: 236  TYFDCSVNPLTELDVSTLSKLTTLHCIQTD-LLEIDLTHN-TQLIYFQAEGCRKIKEL-- 291

Query: 1104 WGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKG------ 1157
                  T L  L                       +T + +S  PKL  L          
Sbjct: 292  -DVTHNTQLYLLDCQAAG-----------------ITELDLSQNPKLVYLYLNNTELTEL 333

Query: 1158 -FQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSL 1190
               +   L+ LS  +  +   F   G   +L + 
Sbjct: 334  DVSHNTKLKSLSCVNA-HIQDFSSVGKIPALNNN 366

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 48.1 bits (115), Expect = 2e-05
 Identities = 33/223 (14%), Positives = 61/223 (27%), Gaps = 51/223 (22%)

Query: 994  LRSIWISSCENLKSLPKGLSNLSH--LHEIRIVRCHNLVSLPEDALPSNVVDVL-IEDCD 1050
            + ++ +S   NL  L           L  + +     L  L      +N +  L +    
Sbjct: 76   ITTLDLSQNTNLTYL-----ACDSNKLTNLDVTPLTKLTYL---NCDTNKLTKLDVSQNP 127

Query: 1051 KLKAL---------IPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPL 1101
             L  L         I     + L EL       I         T LT L+ S +     +
Sbjct: 128  LLTYLNCARNTLTEIDVSHNTQLTELDCHLNKKITKLDVTPQ-TQLTTLDCSFNK----I 182

Query: 1102 VKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLK-------RLS 1154
             +    +   L +L  D  +                 +T + ++   +L        +L+
Sbjct: 183  TELDVSQNKLLNRLNCDTNN-----------------ITKLDLNQNIQLTFLDCSSNKLT 225

Query: 1155 SKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPL 1197
                  L  L +         T    +     L +L   +  L
Sbjct: 226  EIDVTPLTQLTYFDCSVN-PLTELDVSTLS-KLTTLHCIQTDL 266

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 27/109 (24%), Positives = 45/109 (41%), Gaps = 10/109 (9%)

Query: 392 LSDL-LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEI 450
           ++ L L Q  +L  L   S  +TE+ ++   L QL Y + S + +  L  +  S   L  
Sbjct: 203 ITKLDLNQNIQLTFLDCSSNKLTEIDVT--PLTQLTYFDCSVNPLTELDVSTLS--KLTT 258

Query: 451 LILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
           L       LL++   + +   L Y   EG   ++EL +       L  L
Sbjct: 259 LHCIQTD-LLEID--LTHNTQLIYFQAEGCRKIKELDVT--HNTQLYLL 302

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 45.8 bits (109), Expect = 8e-05
 Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 10/109 (9%)

Query: 392 LSDL-LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEI 450
           L++L +    KL  L+  +  +T++ +S      L YLN +R+ +  +   +     L  
Sbjct: 97  LTNLDVTPLTKLTYLNCDTNKLTKLDVSQ--NPLLTYLNCARNTLTEID--VSHNTQLTE 152

Query: 451 LILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
           L       + KL   +     L  L+      + EL +   + K L  L
Sbjct: 153 LDCHLNKKITKLD--VTPQTQLTTLDCSFNK-ITELDVS--QNKLLNRL 196

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 28/135 (20%), Positives = 46/135 (34%), Gaps = 11/135 (8%)

Query: 386 NISPMVLSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAIC 443
           +     ++D+  + +   L  L   S  IT + +S      L YL    +++  L   + 
Sbjct: 48  DCHNSSITDMTGIEKLTGLTKLICTSNNITTLDLSQ--NTNLTYLACDSNKLTNLD--VT 103

Query: 444 SLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG-MKELKCLRTLTNF 502
            L  L  L       L KL   +     L YLN    + L E+ +    +L  L    N 
Sbjct: 104 PLTKLTYLNCDTN-KLTKLD--VSQNPLLTYLNCAR-NTLTEIDVSHNTQLTELDCHLNK 159

Query: 503 IVGKDSGCALRDLKN 517
            + K        L  
Sbjct: 160 KITKLDVTPQTQLTT 174

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 56.2 bits (136), Expect = 5e-08
 Identities = 69/462 (14%), Positives = 134/462 (29%), Gaps = 102/462 (22%)

Query: 800  LQGLQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARL 857
                  LT L   L+ N   +  +    F    NL  + +   N L+S   G       L
Sbjct: 93   FAFCTNLTEL--HLMSNS--IQKIKNNPFVKQKNLITLDLSH-NGLSSTKLGTQVQLENL 147

Query: 858  EVLRIKRCDSLTSISREHL----PSSLQAIE-------------IRDCETLQ-CVLDDRE 899
            + L +     + ++  E L     SSL+ +E                   L    L++ +
Sbjct: 148  QELLLSNN-KIQALKSEELDIFANSSLKKLELSSNQIKEFSPGCFHAIGRLFGLFLNNVQ 206

Query: 900  KSCTSSSVTEKNINSSSSTYLDL----------ESLFVYRCPSLTCLW-SGGRLPVTLKR 948
               + +      + ++S   L L           +    +  +LT L  S   L   +  
Sbjct: 207  LGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNNL-NVVGN 265

Query: 949  LRIEDCSNFKVLT-SECQLPVEVEELTIYGCSNLESIAERFHDDACLRSIWISSCENLKS 1007
                     +        +   +   +++G  N+  +  +           IS     K 
Sbjct: 266  DSFAWLPQLEYFFLEYNNI-QHLFSHSLHGLFNVRYLNLKRS----FTKQSISLASLPKI 320

Query: 1008 LPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKAL-----------I 1056
                   L  L  + +     +  +  +                LK L           +
Sbjct: 321  DDFSFQWLKCLEHLNMEDND-IPGIKSNMF---------TGLINLKYLSLSNSFTSLRTL 370

Query: 1057 PTGTL-----SSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKL 1109
               T      S L  L L++   I     +  S   +L  L++  + + + L    +  L
Sbjct: 371  TNETFVSLAHSPLHILNLTKN-KISKIESDAFSWLGHLEVLDLGLNEIGQELTGQEWRGL 429

Query: 1110 TSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRL------------SSKG 1157
             ++ ++Y+                     LT  + +  P L+RL            S   
Sbjct: 430  ENIFEIYLSYNK------------Y--LQLTRNSFALVPSLQRLMLRRVALKNVDSSPSP 475

Query: 1158 FQYLVSLEHLSVFSCPNFTSFPEAGFPS--SLLSLEIQRCPL 1197
            FQ L +L  L + +  N  +  +        L  L++Q   L
Sbjct: 476  FQPLRNLTILDLSNN-NIANINDDMLEGLEKLEILDLQHNNL 516

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 49.6 bits (119), Expect = 5e-06
 Identities = 47/264 (17%), Positives = 97/264 (36%), Gaps = 23/264 (8%)

Query: 942  LPVTLKRLRIEDCSNFKVLTSEC--QLPVEVEELTIYGCSNLESIAERFHDDACLRSIWI 999
            LP  +  L +      + L +    +   ++  L +   +  +   E       L+ + +
Sbjct: 23   LPTNITVLNLTHN-QLRRLPAANFTRYS-QLTSLDVGFNTISKLEPELCQKLPMLKVLNL 80

Query: 1000 SSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDAL--PSNVVDVLIEDCDKLKALI 1056
                 L  L     +  ++L E+ ++   ++  +  +      N++ + +     L +  
Sbjct: 81   QHN-ELSQLSDKTFAFCTNLTELHLMSN-SIQKIKNNPFVKQKNLITLDLSHN-GLSSTK 137

Query: 1057 PT--GTLSSLRELALSECPGIVVFPEEGLS----TNLTDLEISGDNMYKPLVKWGFHKLT 1110
                  L +L+EL LS    I     E L     ++L  LE+S  N  K      FH + 
Sbjct: 138  LGTQVQLENLQELLLSNN-KIQALKSEELDIFANSSLKKLELSS-NQIKEFSPGCFHAIG 195

Query: 1111 SLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYL--VSLEHLS 1168
             L  L+++      S  +     +  TS+ ++++S+  +L   S+  F  L   +L  L 
Sbjct: 196  RLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNS-QLSTTSNTTFLGLKWTNLTMLD 254

Query: 1169 VFSCPNFTSFPEAGFPSSLLSLEI 1192
            +    N        F + L  LE 
Sbjct: 255  LSYN-NLNVVGNDSF-AWLPQLEY 276

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 48.8 bits (117), Expect = 1e-05
 Identities = 78/535 (14%), Positives = 179/535 (33%), Gaps = 97/535 (18%)

Query: 402 LRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCL-PDAICSLFNLEILILRNCWCL 459
           + VL+L    +  +   +     QL  L+   + I  L P+    L  L++L L++   L
Sbjct: 27  ITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQHNE-L 85

Query: 460 LKLPSR-IGNLVNLHYLNIEGASALRELPLGMKELKCLRTLT------NFIVGKDSGCAL 512
            +L  +      NL  L++   ++++++          + L       N +     G   
Sbjct: 86  SQLSDKTFAFCTNLTELHLMS-NSIQKIKNN--PFVKQKNLITLDLSHNGLSSTKLG-TQ 141

Query: 513 RDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREK 572
             L+N + L     +S   N I + ++ E  +     L  L+L                 
Sbjct: 142 VQLENLQELL----LSN--NKIQALKSEELDIFANSSLKKLELSS--------------- 180

Query: 573 NILDMLKPHS-----NIKRLEIHSY--GGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPS 625
           N +    P        +  L +++   G +       + + +++  L L N + ST+  +
Sbjct: 181 NQIKEFSPGCFHAIGRLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNT 240

Query: 626 LGQLCSLKDLTIVGMS--ELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDND 683
                   +LT++ +S   L  +G++ +          L+  + E          N    
Sbjct: 241 TFLGLKWTNLTMLDLSYNNLNVVGNDSFA-----WLPQLEYFFLEY---------NNIQH 286

Query: 684 EHVQAFPRLRKL--------------SIKKCPKLSGRLPNHLPSLEEIVIAGCMHLAVSL 729
               +   L  +              S+   PK+       L  LE + +     +    
Sbjct: 287 LFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDN-DIPGIK 345

Query: 730 PS----LPALCTMEIDGCKRLVCDGPSESKSPNKMTL--------CNISEFENWSSEKFQ 777
            +    L  L  + +      +    +E+      +           IS+ E+ +     
Sbjct: 346 SNMFTGLINLKYLSLSNSFTSLRTLTNETFVSLAHSPLHILNLTKNKISKIESDAFSWLG 405

Query: 778 KVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKDLLIGNCPTVVSLPKA-CFLPNLSEIT 836
            +E L +       NEI  E   Q  + L  + ++ +     +     +   +P+L  + 
Sbjct: 406 HLEVLDLGL-----NEIGQELTGQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSLQRLM 460

Query: 837 IQDCNALASLTD--GMIYNNARLEVLRIKRCDSLTSISREHLPS--SLQAIEIRD 887
           ++   AL ++            L +L +    ++ +I+ + L     L+ ++++ 
Sbjct: 461 LRR-VALKNVDSSPSPFQPLRNLTILDLSNN-NIANINDDMLEGLEKLEILDLQH 513

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 47.3 bits (113), Expect = 3e-05
 Identities = 25/155 (16%), Positives = 43/155 (27%), Gaps = 24/155 (15%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSR---SEIQCLPDA 441
            I   +        + +  + L      ++   S   +  L+ L   R     +   P  
Sbjct: 416 EIGQELTGQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSLQRLMLRRVALKNVDSSPSP 475

Query: 442 ICSLFNLEILILRNCWCLLKL----PSRIGNLVNLHYLNIEG--------ASALRELPLG 489
              L NL IL L N      +       +  L  L  L+++          +        
Sbjct: 476 FQPLRNLTILDLSNN----NIANINDDMLEGLEKLEILDLQHNNLARLWKHANPGGPIYF 531

Query: 490 MKELKCLRTLT---NFIVGKDSGCALRDLKNWKFL 521
           +K L  L  L    N           +DL   K +
Sbjct: 532 LKGLSHLHILNLESNGFDEIPVE-VFKDLFELKII 565

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 46.5 bits (111), Expect = 5e-05
 Identities = 28/126 (22%), Positives = 44/126 (34%), Gaps = 15/126 (11%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCL-PDAIC 443
             S      L  +   L +L L    +  V   S   L QL Y     + IQ L   ++ 
Sbjct: 236 TTSNTTFLGL--KWTNLTMLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLH 293

Query: 444 SLFNLEILILRNCWCLLKL---------PSRIGNLVNLHYLNIEGASALRELPLGM-KEL 493
            LFN+  L L+  +    +               L  L +LN+E  + +  +   M   L
Sbjct: 294 GLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMED-NDIPGIKSNMFTGL 352

Query: 494 KCLRTL 499
             L+ L
Sbjct: 353 INLKYL 358

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 45.8 bits (109), Expect = 9e-05
 Identities = 24/140 (17%), Positives = 47/140 (33%), Gaps = 14/140 (10%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVPISIGC----LKQLRYLNFSRSEIQCLPDAI---CSL 445
                   +L  L L +  +        C       +R L+ S S++    +        
Sbjct: 188 PGCFHAIGRLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKW 247

Query: 446 FNLEILILRNCWCLLKLPSR-IGNLVNLHYLNIEGASALRELP----LGMKELKCLRTLT 500
            NL +L L     L  + +     L  L Y  +E  + ++ L      G+  ++ L    
Sbjct: 248 TNLTMLDLSYN-NLNVVGNDSFAWLPQLEYFFLEYNN-IQHLFSHSLHGLFNVRYLNLKR 305

Query: 501 NFIVGKDSGCALRDLKNWKF 520
           +F     S  +L  + ++ F
Sbjct: 306 SFTKQSISLASLPKIDDFSF 325

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 62/398 (15%), Positives = 126/398 (31%), Gaps = 73/398 (18%)

Query: 822  SLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISREHLPSS 879
             +    F  LP L    ++  N +  L    ++    +  L +KR  +  SIS   L   
Sbjct: 262  VVGNDSFAWLPQLEYFFLEY-NNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASL-PK 319

Query: 880  LQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLW-S 938
            +     +  + L+  L+               +  +    +           +L  L  S
Sbjct: 320  IDDFSFQWLKCLE-HLN---------------MEDNDIPGIKSNMFT--GLINLKYLSLS 361

Query: 939  GGRLPVTLKRLRIEDCSNF-----KVLT-SECQLPVEVEELTIYGCSNLESIAERFHDDA 992
                  +L+ L  E   +       +L  ++ ++  ++E        +LE +        
Sbjct: 362  NSFT--SLRTLTNETFVSLAHSPLHILNLTKNKI-SKIESDAFSWLGHLEVL-------- 410

Query: 993  CLRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDA---LPS----NVVDV 1044
                  +   E  + L       L ++ EI +      + L  ++   +PS     +  V
Sbjct: 411  -----DLGLNEIGQELTGQEWRGLENIFEIYLSYN-KYLQLTRNSFALVPSLQRLMLRRV 464

Query: 1045 LIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISG-------D 1095
             +++ D   +      L +L  L LS    I    ++ L     L  L++          
Sbjct: 465  ALKNVDSSPSPF--QPLRNLTILDLSNN-NIANINDDMLEGLEKLEILDLQHNNLARLWK 521

Query: 1096 NMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILP-TSLTSITISDFPKLKRLS 1154
            +       +    L+ L  L ++       F ++   V      L  I +     L  L 
Sbjct: 522  HANPGGPIYFLKGLSHLHILNLESN----GFDEIPVEVFKDLFELKIIDLGL-NNLNTLP 576

Query: 1155 SKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
            +  F   VSL+ L++      TS  +  F  +  +L  
Sbjct: 577  ASVFNNQVSLKSLNL-QKNLITSVEKKVFGPAFRNLTE 613

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 55.0 bits (133), Expect = 1e-07
 Identities = 63/430 (14%), Positives = 112/430 (26%), Gaps = 95/430 (22%)

Query: 809  LKDLLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSL 868
            L +L +       ++ K C   NL+ + +        L  G   +   LE+      + L
Sbjct: 206  LHELTLRGNFNSSNIMKTCLQ-NLAGLHVHR------LILGEFKDERNLEIFEPSIMEGL 258

Query: 869  TSISREHL------PSSLQAIEIRDCETLQCV-LDDREKSCTSSSVTEKNINSSSSTYLD 921
              ++ +          S   ++      +  + L                  S S     
Sbjct: 259  CDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQ 318

Query: 922  LESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNL 981
            L+       P L  L        TL   +         L S       +  L +   +  
Sbjct: 319  LKQFPTLDLPFLKSL--------TLTMNKGSISFKKVALPS-------LSYLDLSRNALS 363

Query: 982  ESIAERFHDDAC--LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPS 1039
             S    + D     LR + +S       +      L  L  +     H+           
Sbjct: 364  FSGCCSYSDLGTNSLRHLDLSFN-GAIIMSANFMGLEELQHLDFQ--HS----------- 409

Query: 1040 NVVDVLIEDCDKLKALIPTGT---LSSLRELALSECPGIVVFPEEGLS--TNLTDLEISG 1094
                        LK +        L  L  L +S      +  +      T+L  L+++G
Sbjct: 410  -----------TLKRVTEFSAFLSLEKLLYLDISYT-NTKIDFDGIFLGLTSLNTLKMAG 457

Query: 1095 DNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRL- 1153
            ++     +   F   T+L  L +  C                  L  I+   F  L RL 
Sbjct: 458  NSFKDNTLSNVFANTTNLTFLDLSKC-----------------QLEQISWGVFDTLHRLQ 500

Query: 1154 ------------SSKGFQYLVSLEHLSVFSCPNFTSFPEAGFP--SSLLSLEIQRCPLLE 1199
                         S  +  L SL  L         +          SL    +    +  
Sbjct: 501  LLNMSHNNLLFLDSSHYNQLYSLSTLDCSFN-RIETSKGILQHFPKSLAFFNLTNNSVAC 559

Query: 1200 KCKMRKGQEW 1209
             C+ +K  +W
Sbjct: 560  ICEHQKFLQW 569

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 48.9 bits (117), Expect = 9e-06
 Identities = 83/507 (16%), Positives = 147/507 (28%), Gaps = 69/507 (13%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCL-PDAICSLFNL 448
           + S       +L+ L L    I  +   +   L  L  L  + + IQ   P +   L +L
Sbjct: 47  LKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSL 106

Query: 449 EILILRNCWCLLKLPSR-IGNLVNLHYLNIEGASALRELPLG--MKELKCLRTLT---NF 502
           E L+      L  L S  IG L+ L  LN+     +    L      L  L  +    N+
Sbjct: 107 ENLVAVET-KLASLESFPIGQLITLKKLNVAHNF-IHSCKLPAYFSNLTNLVHVDLSYNY 164

Query: 503 IVGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRD 562
           I        L+ L+    +   L +S   N ID  +              +KL       
Sbjct: 165 IQTITVN-DLQFLRENPQVNLSLDMSL--NPIDFIQDQ--------AFQGIKLHE----- 208

Query: 563 GDSVDEAREKNILDMLKP-HSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRST 621
              +      N  +++K    N+  L +H      F        F    +  L +     
Sbjct: 209 ---LTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDE 265

Query: 622 SLPSLGQLCSLKDLTIVGMSELKSI---GSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEP 678
              +     S   +    ++ + ++   G  I            Q+L             
Sbjct: 266 FRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIR--------- 316

Query: 679 NRDNDEHVQAFPRLRKLSIKKCPKLSGRLPN-HLPSLEEIVIAGCMHLAVSLPSLPALCT 737
            +         P L+ L++    K S       LPSL  + ++          S   L T
Sbjct: 317 CQLKQFPTLDLPFLKSLTLTMN-KGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGT 375

Query: 738 MEIDGCKRLVCDGPSESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLE 797
             +   + L             ++              F  +E+L  +  +   + +   
Sbjct: 376 NSL---RHL------------DLSFNGAIIMSAN----FMGLEELQHLDFQH--STLKRV 414

Query: 798 KPLQGLQRLTCLKDLLIGNCPTVVSLPKACF-LPNLSEITIQDCNALASLTDGMIYNNAR 856
                   L  L  L I    T +        L +L+ + +   +   +    +  N   
Sbjct: 415 TEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTN 474

Query: 857 LEVLRIKRCDSLTSISREHLP--SSLQ 881
           L  L + +C  L  IS         LQ
Sbjct: 475 LTFLDLSKC-QLEQISWGVFDTLHRLQ 500

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 22/122 (18%), Positives = 37/122 (30%), Gaps = 6/122 (4%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI-----GCLKQLRYLNFSRSEIQCLPD 440
            I    L         L  + L    I  + ++         +    L+ S + I  + D
Sbjct: 139 FIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQD 198

Query: 441 AICSLFNLEILILR-NCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
                  L  L LR N      + + + NL  LH   +       E  L + E   +  L
Sbjct: 199 QAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGL 258

Query: 500 TN 501
            +
Sbjct: 259 CD 260

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 66/454 (14%), Positives = 134/454 (29%), Gaps = 92/454 (20%)

Query: 803  LQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARLEVL 860
                + L+ L +  C  + ++    +  L +LS + +   N + S + G       LE L
Sbjct: 52   FSNFSELQWLDLSRCE-IETIEDKAWHGLHHLSNLILTG-NPIQSFSPGSFSGLTSLENL 109

Query: 861  RIKRCDSLTSISREHLP--SSLQAIEIRDCETLQCVLDDREKSCTS-----------SSV 907
                   L S+    +    +L+ + +       C L     + T+            ++
Sbjct: 110  VAVET-KLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTI 168

Query: 908  TEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLP 967
            T  ++           SL +   P +  +       + L  L +                
Sbjct: 169  TVNDLQFLRENPQVNLSLDMSLNP-IDFIQDQAFQGIKLHELTL----------RGNFNS 217

Query: 968  VEVEELTIYGCSNLES---IAERFHDDACLRSIWISSCENLKSL---------------- 1008
              + +  +   + L     I   F D+  L     S  E L  +                
Sbjct: 218  SNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDD 277

Query: 1009 PKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELA 1068
                  L+++  + +    ++  L +         + I  C +LK   PT  L  L+ L 
Sbjct: 278  IVKFHCLANVSAMSLAGV-SIKYLEDVPKHFKWQSLSIIRC-QLKQ-FPTLDLPFLKSLT 334

Query: 1069 LSECPGIVVFPEEGLS-------------------------TNLTDLEISGDNMYKPLVK 1103
            L+   G + F +  L                           +L  L++S +     ++ 
Sbjct: 335  LTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAI--IMS 392

Query: 1104 WGFHKLTSLRKLY-----IDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGF 1158
              F  L  L+ L      +   ++  +F  +         L  + IS     K      F
Sbjct: 393  ANFMGLEELQHLDFQHSTLKRVTEFSAFLSL-------EKLLYLDISY-TNTKIDFDGIF 444

Query: 1159 QYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEI 1192
              L SL  L   +  +F     +   ++  +L  
Sbjct: 445  LGLTSLNTLK-MAGNSFKDNTLSNVFANTTNLTF 477

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 43.1 bits (102), Expect = 6e-04
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 6/98 (6%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYC-ITEVPISI-GCLKQLRYLNFSRSEIQCLP-DAI 442
           +     LS++      L  L L S C + ++   +   L +L+ LN S + +  L     
Sbjct: 459 SFKDNTLSNVFANTTNLTFLDL-SKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHY 517

Query: 443 CSLFNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEG 479
             L++L  L       +      +     +L + N+  
Sbjct: 518 NQLYSLSTLDCSFNR-IETSKGILQHFPKSLAFFNLTN 554

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 39/213 (18%), Positives = 66/213 (30%), Gaps = 62/213 (29%)

Query: 994  LRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKL 1052
             ++I +S    LK L     SN S L  + + RC  + ++ + A                
Sbjct: 34   TKNIDLSFN-PLKILKSYSFSNFSELQWLDLSRCE-IETIEDKAW--------------- 76

Query: 1053 KALIPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLT 1110
                    L  L  L L+  P I  F     S  T+L +L    +     L  +   +L 
Sbjct: 77   ------HGLHHLSNLILTGNP-IQSFSPGSFSGLTSLENLVAV-ETKLASLESFPIGQLI 128

Query: 1111 SLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVF 1170
            +L+KL +                     + S  +  +          F  L +L H+   
Sbjct: 129  TLKKLNVAHN-----------------FIHSCKLPAY----------FSNLTNLVHVD-L 160

Query: 1171 SCPNFTSFPEAGF------PSSLLSLEIQRCPL 1197
            S     +            P   LSL++   P+
Sbjct: 161  SYNYIQTITVNDLQFLRENPQVNLSLDMSLNPI 193

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A* Length = 285

 Score = 51.9 bits (125), Expect = 5e-07
 Identities = 46/280 (16%), Positives = 91/280 (32%), Gaps = 70/280 (25%)

Query: 953  DCSNFKVLTSECQ----------LPVEVEELTIYGCSNLESIAER-FHDDACLRSIWISS 1001
             C N   +T+ C           +P   + + ++G + +  +    F     L  +W+ S
Sbjct: 7    VCYNEPKVTTSCPQQGLQAVPVGIPAASQRIFLHG-NRISHVPAASFRACRNLTILWLHS 65

Query: 1002 CENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKAL----- 1055
               L  +     + L+ L ++ +     L S+                  +L  L     
Sbjct: 66   N-VLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATF---------HGLGRLHTLHLDRC 115

Query: 1056 ----IPTGT---LSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGF 1106
                +  G    L++L+ L L +   +   P++      NLT L + G N    + +  F
Sbjct: 116  GLQELGPGLFRGLAALQYLYLQDN-ALQALPDDTFRDLGNLTHLFLHG-NRISSVPERAF 173

Query: 1107 HKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEH 1166
              L SL +L +                               ++  +    F+ L  L  
Sbjct: 174  RGLHSLDRLLLHQN----------------------------RVAHVHPHAFRDLGRLMT 205

Query: 1167 LSVFSCPNFTSFPEAGFP--SSLLSLEIQRCPLLEKCKMR 1204
            L +F+  N ++ P        +L  L +   P +  C+ R
Sbjct: 206  LYLFAN-NLSALPTEALAPLRALQYLRLNDNPWVCDCRAR 244

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 52.4 bits (126), Expect = 6e-07
 Identities = 49/251 (19%), Positives = 84/251 (33%), Gaps = 60/251 (23%)

Query: 971  EELTIYGCSNLESIAER-FHDDACLRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHN 1028
            E L +    ++ +I    F+  A L ++ +     L ++P G    LS L E+ +     
Sbjct: 91   EILQLSRN-HIRTIEIGAFNGLANLNTLELFDN-RLTTIPNGAFVYLSKLKELWLRNNP- 147

Query: 1029 LVSLPEDALPSNVVDVLIEDCDKLKAL----------IPTGT---LSSLRELALSECPGI 1075
            + S+P  A               L+ L          I  G    LS+LR L L+ C  +
Sbjct: 148  IESIPSYAF---------NRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCN-L 197

Query: 1076 VVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVIL 1135
               P       L +L++SG N    +    F  L  L+KL++                  
Sbjct: 198  REIPNLTPLIKLDELDLSG-NHLSAIRPGSFQGLMHLQKLWMIQS--------------- 241

Query: 1136 PTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPS--SLLSLEIQ 1193
                         +++ +    F  L SL  +++    N T  P   F     L  + + 
Sbjct: 242  -------------QIQVIERNAFDNLQSLVEINLAHN-NLTLLPHDLFTPLHHLERIHLH 287

Query: 1194 RCPLLEKCKMR 1204
              P    C + 
Sbjct: 288  HNPWNCNCDIL 298

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 50.5 bits (121), Expect = 3e-06
 Identities = 37/189 (19%), Positives = 73/189 (38%), Gaps = 22/189 (11%)

Query: 1019 HEIRIVRCH--NLVSLPEDALPSNVVDVLIEDCDKLKALIPT--GTLSSLRELALSECPG 1074
            ++   V C   NL  +P+  + +N   + + +  +++ +       L  L  L LS    
Sbjct: 43   NQFSKVICVRKNLREVPDG-ISTNTRLLNLHEN-QIQIIKVNSFKHLRHLEILQLSRN-H 99

Query: 1075 IVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCS----DAVSFPD 1128
            I        +   NL  LE+  DN    +    F  L+ L++L++         + +F  
Sbjct: 100  IRTIEIGAFNGLANLNTLELF-DNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNR 158

Query: 1129 VGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLL 1188
            +        SL  + + +  +L  +S   F+ L +L +L++  C N    P       L 
Sbjct: 159  I-------PSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMC-NLREIPNLTPLIKLD 210

Query: 1189 SLEIQRCPL 1197
             L++    L
Sbjct: 211  ELDLSGNHL 219

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 50.3 bits (121), Expect = 6e-07
 Identities = 18/111 (16%), Positives = 47/111 (42%), Gaps = 5/111 (4%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNL 448
           ++DL  +     ++ L++ +   T     I  L  L  L     ++       +  L +L
Sbjct: 56  VTDLTGIEYAHNIKDLTINNIHATNYN-PISGLSNLERLRIMGKDVTSDKIPNLSGLTSL 114

Query: 449 EILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            +L + +      + ++I  L  ++ +++    A+ ++   +K L  L++L
Sbjct: 115 TLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSL 164

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 9/96 (9%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS-IGCLKQLRYLNFSRSEIQCL-PDAIC 443
           N +P  +S L      L  L +    +T   I  +  L  L  L+ S S         I 
Sbjct: 80  NYNP--ISGL----SNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKIN 133

Query: 444 SLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
           +L  +  + L      +     +  L  L  LNI+ 
Sbjct: 134 TLPKVNSIDLSYN-GAITDIMPLKTLPELKSLNIQF 168

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 41.5 bits (98), Expect = 5e-04
 Identities = 12/95 (12%), Positives = 35/95 (36%), Gaps = 4/95 (4%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPIS-IGCLKQLRYLNFSRSEIQCLPDAICS 444
           +++   + +L      L +L +      +  ++ I  L ++  ++ S +        + +
Sbjct: 99  DVTSDKIPNL-SGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIMPLKT 157

Query: 445 LFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
           L  L+ L ++     +     I +   L+ L    
Sbjct: 158 LPELKSLNIQFD--GVHDYRGIEDFPKLNQLYAFS 190

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 52.0 bits (125), Expect = 7e-07
 Identities = 12/87 (13%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILI 452
                + ++L  L + +  +  + +    +  L+ L+ S + +  +         LE L 
Sbjct: 265 YHPFVKMQRLERLYISNNRLVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQFDRLENLY 324

Query: 453 LRNCWCLLKLPSRIGNLVNLHYLNIEG 479
           L +   ++ L   +     L  L +  
Sbjct: 325 LDHNS-IVTLK--LSTHHTLKNLTLSH 348

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 49.3 bits (118), Expect = 5e-06
 Identities = 19/104 (18%), Positives = 39/104 (37%), Gaps = 4/104 (3%)

Query: 397 PQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLP-DAICSLFNLEILILRN 455
           P   +L +L L    +T+    +     L  ++ S +E++ +       +  LE L + N
Sbjct: 223 PVNVELTILKLQHNNLTDTA-WLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISN 281

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
              L+ L      +  L  L++   + L  +     +   L  L
Sbjct: 282 N-RLVALNLYGQPIPTLKVLDLSH-NHLLHVERNQPQFDRLENL 323

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 16/82 (19%), Positives = 27/82 (32%), Gaps = 6/82 (7%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           L+        L+VL L    +  V  +     +L  L    + I  L  +  +   L+ L
Sbjct: 287 LNLYGQPIPTLKVLDLSHNHLLHVERNQPQFDRLENLYLDHNSIVTLKLS--THHTLKNL 344

Query: 452 ILRN----CWCLLKLPSRIGNL 469
            L +    C  L  L   +   
Sbjct: 345 TLSHNDWDCNSLRALFRNVARP 366

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 32/228 (14%), Positives = 64/228 (28%), Gaps = 50/228 (21%)

Query: 1004 NLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPS----NVVDVLIEDCDKLKAL--- 1055
            NL+ +        + L  +++     L  +    +PS    NV   L+       A+   
Sbjct: 152  NLERIEDDTFQATTSLQNLQLSSN-RLTHVDLSLIPSLFHANVSYNLLSTLAIPIAVEEL 210

Query: 1056 ---------IPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGF 1106
                     +       L  L L     +           L ++++S  N  + ++   F
Sbjct: 211  DASHNSINVVRGPVNVELTILKLQHNN-LTDTAWLLNYPGLVEVDLS-YNELEKIMYHPF 268

Query: 1107 HKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSI--TISDFPKLKRLS---------S 1155
             K+  L +LYI                     L ++       P LK L           
Sbjct: 269  VKMQRLERLYISN-----------------NRLVALNLYGQPIPTLKVLDLSHNHLLHVE 311

Query: 1156 KGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPLLEKCKM 1203
            +       LE+L +    +  +   +    +L +L +           
Sbjct: 312  RNQPQFDRLENLYLDHN-SIVTLKLSTHH-TLKNLTLSHNDWDCNSLR 357

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 597

 Score = 52.2 bits (125), Expect = 9e-07
 Identities = 12/87 (13%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 393 SDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILI 452
                + ++L  L + +  +  + +    +  L+ L+ S + +  +         LE L 
Sbjct: 271 YHPFVKMQRLERLYISNNRLVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQFDRLENLY 330

Query: 453 LRNCWCLLKLPSRIGNLVNLHYLNIEG 479
           L +   ++ L   +     L  L +  
Sbjct: 331 LDHNS-IVTLK--LSTHHTLKNLTLSH 354

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 597

 Score = 48.8 bits (116), Expect = 9e-06
 Identities = 18/102 (17%), Positives = 38/102 (37%), Gaps = 4/102 (3%)

Query: 399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLP-DAICSLFNLEILILRNCW 457
             +L +L L    +T+    +     L  ++ S +E++ +       +  LE L + N  
Sbjct: 231 NVELTILKLQHNNLTDTA-WLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNN- 288

Query: 458 CLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L+ L      +  L  L++   + L  +     +   L  L
Sbjct: 289 RLVALNLYGQPIPTLKVLDLSH-NHLLHVERNQPQFDRLENL 329

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 51.4 bits (124), Expect = 9e-07
 Identities = 23/110 (20%), Positives = 49/110 (44%), Gaps = 7/110 (6%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           +SD+  L    K+  L+LG+         +  +  L YL  + S+++ +   I +L +L 
Sbjct: 122 ISDISPLANLTKMYSLNLGANHNLSDLSPLSNMTGLNYLTVTESKVKDVT-PIANLTDLY 180

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L L      ++  S + +L +LHY      + + ++   +  +  L +L
Sbjct: 181 SLSLNY--NQIEDISPLASLTSLHYFTA-YVNQITDIT-PVANMTRLNSL 226

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 49.5 bits (119), Expect = 4e-06
 Identities = 24/110 (21%), Positives = 50/110 (45%), Gaps = 6/110 (5%)

Query: 392 LSDLLP--QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           ++DL P     +L  L +G+  I+++  ++  L +L+ LN   ++I  +   + +L  L 
Sbjct: 233 ITDLSPLANLSQLTWLEIGTNQISDIN-AVKDLTKLKMLNVGSNQISDIS-VLNNLSQLN 290

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L L N     +    IG L NL  L +   + + ++   +  L  + + 
Sbjct: 291 SLFLNNNQLGNEDMEVIGGLTNLTTLFLSQ-NHITDIR-PLASLSKMDSA 338

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 48.7 bits (117), Expect = 6e-06
 Identities = 26/132 (19%), Positives = 48/132 (36%), Gaps = 20/132 (15%)

Query: 386 NISPMVLSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAIC 443
              P  ++ +       +     L    +T+  ++   L+ +  L  +  ++  +   I 
Sbjct: 6   ATLPAPINQIFPDADLAEGIRAVLQKASVTD-VVTQEELESITKLVVAGEKVASIQ-GIE 63

Query: 444 SLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN-----------IEGASALRELPLG--- 489
            L NLE L L      +   S + NLV L  L            ++  + LREL L    
Sbjct: 64  YLTNLEYLNLNG--NQITDISPLSNLVKLTNLYIGTNKITDISALQNLTNLRELYLNEDN 121

Query: 490 MKELKCLRTLTN 501
           + ++  L  LT 
Sbjct: 122 ISDISPLANLTK 133

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 46.4 bits (111), Expect = 3e-05
 Identities = 19/91 (20%), Positives = 41/91 (45%), Gaps = 6/91 (6%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCL-PDAICSLFNL 448
           +SD+  +    KL++L++GS  I+++   +  L QL  L  + +++     + I  L NL
Sbjct: 255 ISDINAVKDLTKLKMLNVGSNQISDIS-VLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNL 313

Query: 449 EILILRNCWCLLKLPSRIGNLVNLHYLNIEG 479
             L L     +  +   + +L  +   +   
Sbjct: 314 TTLFLSQN-HITDIRP-LASLSKMDSADFAN 342

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A Length = 452

 Score = 51.7 bits (124), Expect = 1e-06
 Identities = 46/238 (19%), Positives = 79/238 (33%), Gaps = 58/238 (24%)

Query: 971  EELTIYGCSNLESIAER-FHDDACLRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHN 1028
              L ++    L  I    F   + LR +W+ +   ++S+P    + +  L  + +     
Sbjct: 126  NTLELFDN-WLTVIPSGAFEYLSKLRELWLRNN-PIESIPSYAFNRVPSLMRLDLGELKK 183

Query: 1029 LVSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLT 1088
            L  + E A                        L +L+ L L  C  I   P       L 
Sbjct: 184  LEYISEGAFEG---------------------LFNLKYLNLGMCN-IKDMPNLTPLVGLE 221

Query: 1089 DLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFP 1148
            +LE+SG N +  +    FH L+SL+KL++                               
Sbjct: 222  ELEMSG-NHFPEIRPGSFHGLSSLKKLWVMNS---------------------------- 252

Query: 1149 KLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPS--SLLSLEIQRCPLLEKCKMR 1204
            ++  +    F  L SL  L++    N +S P   F     L+ L +   P    C + 
Sbjct: 253  QVSLIERNAFDGLASLVELNLAHN-NLSSLPHDLFTPLRYLVELHLHHNPWNCDCDIL 309

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A Length = 452

 Score = 50.5 bits (121), Expect = 3e-06
 Identities = 41/190 (21%), Positives = 74/190 (38%), Gaps = 24/190 (12%)

Query: 1019 HEIRIVRCH--NLVSLPEDALPSNVVDVLIEDCDKLKALIPTGT---LSSLRELALSECP 1073
            ++   V C    L  +P+  +PSN   + + + + ++  I   T   L  L  L L    
Sbjct: 54   NQFSKVVCTRRGLSEVPQG-IPSNTRYLNLME-NNIQM-IQADTFRHLHHLEVLQLGRN- 109

Query: 1074 GIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCS----DAVSFP 1127
             I        +   +L  LE+  DN    +    F  L+ LR+L++         + +F 
Sbjct: 110  SIRQIEVGAFNGLASLNTLELF-DNWLTVIPSGAFEYLSKLRELWLRNNPIESIPSYAFN 168

Query: 1128 DVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSL 1187
             V        SL  + + +  KL+ +S   F+ L +L++L++  C N    P       L
Sbjct: 169  RV-------PSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMC-NIKDMPNLTPLVGL 220

Query: 1188 LSLEIQRCPL 1197
              LE+     
Sbjct: 221  EELEMSGNHF 230

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri} Length = 306

 Score = 51.2 bits (123), Expect = 1e-06
 Identities = 27/120 (22%), Positives = 45/120 (37%), Gaps = 12/120 (10%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGC---LKQLRYLNFSRSEIQCLPDAI 442
           ++   V   L     +L  LSL S  ++              L+YL+ S + +  +    
Sbjct: 42  SLPHGVFDKL----TQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNF 97

Query: 443 CSLFNLEILILRNCWCLLKLPSR--IGNLVNLHYLNIEGASALRELPLGM-KELKCLRTL 499
             L  LE L  ++   L ++       +L NL YL+I   +  R    G+   L  L  L
Sbjct: 98  LGLEQLEHLDFQHSN-LKQMSEFSVFLSLRNLIYLDISH-THTRVAFNGIFNGLSSLEVL 155

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri} Length = 306

 Score = 48.5 bits (116), Expect = 6e-06
 Identities = 35/220 (15%), Positives = 77/220 (35%), Gaps = 41/220 (18%)

Query: 994  LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLK 1053
            L+ + +S    + ++      L  L  +      NL  + E ++  +             
Sbjct: 80   LKYLDLSFN-GVITMSSNFLGLEQLEHLDFQHS-NLKQMSEFSVFLS------------- 124

Query: 1054 ALIPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTS 1111
                   L +L  L +S      V      +  ++L  L+++G++  +  +   F +L +
Sbjct: 125  -------LRNLIYLDISHT-HTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRN 176

Query: 1112 LRKLYIDGCS----DAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHL 1167
            L  L +  C        +F  +       +SL  + +S       L +  ++ L SL+ L
Sbjct: 177  LTFLDLSQCQLEQLSPTAFNSL-------SSLQVLNMSH-NNFFSLDTFPYKCLNSLQVL 228

Query: 1168 SVFSCPNFTSFPEAGF---PSSLLSLEIQRCPLLEKCKMR 1204
                  +  +  +      PSSL  L + +      C+ +
Sbjct: 229  DYSLN-HIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQ 267

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 49.4 bits (118), Expect = 5e-06
 Identities = 55/266 (20%), Positives = 82/266 (30%), Gaps = 48/266 (18%)

Query: 930  CPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAER-F 988
            C    C  S               C   KV      LP    EL     + L  I +  F
Sbjct: 2    CHHRICHCSNRVF----------LCQESKVTEIPSDLPRNAIELRFVL-TKLRVIQKGAF 50

Query: 989  HDDACLRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIE 1047
                 L  I IS  + L+ +     SNL  LHEIRI + +NL+ +  +A          +
Sbjct: 51   SGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAF---------Q 101

Query: 1048 DCDKLKAL---------IPTGT---LSSLRELALSECPGIVVFPE---EGLSTNLTDLEI 1092
            +   L+ L         +P            L + +   I         GLS     L +
Sbjct: 102  NLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWL 161

Query: 1093 SGDNMYKPLVKWGFHKLTSLRKLYIDG----CSDAVSFPDVGKGVIL---PTSLTSITIS 1145
            +  N  + +    F+          D           F      VIL    T + S+   
Sbjct: 162  NK-NGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSY 220

Query: 1146 DF---PKLKRLSSKGFQYLVSLEHLS 1168
                  KL+  S+   + L +LE L 
Sbjct: 221  GLENLKKLRARSTYNLKKLPTLEKLV 246

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 49.1 bits (117), Expect = 5e-06
 Identities = 48/255 (18%), Positives = 89/255 (34%), Gaps = 50/255 (19%)

Query: 822  SLPKACF--LPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSISR---EHL 876
             + K  F    +L +I I   + L  +   +  N  +L  +RI++ ++L  I+    ++L
Sbjct: 44   VIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNL 103

Query: 877  PSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCL 936
            P +LQ + I +   ++ + D               I+S     LD++        ++  +
Sbjct: 104  P-NLQYLLISNTG-IKHLPDVH------------KIHSLQKVLLDIQDN-----INIHTI 144

Query: 937  WSGGRLPVTLKRLRIEDCSNFKVLTSECQLPVEVEELTIYGCSNLESIAERFHDDACLRS 996
                                     S   L  E   L +     ++ I     +   L  
Sbjct: 145  ERN----------------------SFVGLSFESVILWLNKN-GIQEIHNSAFNGTQLDE 181

Query: 997  IWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKAL 1055
            + +S   NL+ LP       S    + I R   + SLP   L  N+  +       LK L
Sbjct: 182  LNLSDNNNLEELPNDVFHGASGPVILDISRT-RIHSLPSYGL-ENLKKLRARSTYNLKKL 239

Query: 1056 IPTGTLSSLRELALS 1070
                 L +L E +L+
Sbjct: 240  PTLEKLVALMEASLT 254

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 48.7 bits (116), Expect = 7e-06
 Identities = 37/187 (19%), Positives = 64/187 (34%), Gaps = 14/187 (7%)

Query: 1022 RIVRCH--NLVSLPEDALPSNVVDVLIEDCDKLKALIPTGT---LSSLRELALSECPGIV 1076
            R+  C    +  +P D LP N +++      KL+  I  G       L ++ +S+   + 
Sbjct: 12   RVFLCQESKVTEIPSD-LPRNAIELRFVLT-KLRV-IQKGAFSGFGDLEKIEISQNDVLE 68

Query: 1077 VFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVI 1134
            V   +  S    L ++ I   N    +    F  L +L+ L I         PDV K  I
Sbjct: 69   VIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTG-IKHLPDVHK--I 125

Query: 1135 LPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF-PSSLLSLEIQ 1193
                   + I D   +  +    F  L     +   +         + F  + L  L + 
Sbjct: 126  HSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLS 185

Query: 1194 RCPLLEK 1200
                LE+
Sbjct: 186  DNNNLEE 192

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 49.9 bits (120), Expect = 5e-06
 Identities = 30/117 (25%), Positives = 53/117 (45%), Gaps = 16/117 (13%)

Query: 392 LSDLLPQCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLE 449
           +   L  C +L  L L    ++  +P S+G L +LR L    + ++  +P  +  +  LE
Sbjct: 410 IPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLE 469

Query: 450 ILILRNCWCLL--KLPSRIGNLVNLHYL-----NIEGASALRELPLGMKELKCLRTL 499
            LIL      L  ++PS + N  NL+++      + G     E+P  +  L+ L  L
Sbjct: 470 TLILDF--NDLTGEIPSGLSNCTNLNWISLSNNRLTG-----EIPKWIGRLENLAIL 519

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 47.2 bits (113), Expect = 4e-05
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 396 LPQCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILIL 453
           L   K L  L L    +T E+P  +     L +++ S + +   +P  I  L NL IL L
Sbjct: 462 LMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKL 521

Query: 454 RNCWCLL--KLPSRIGNLVNLHYLNI 477
            N        +P+ +G+  +L +L++
Sbjct: 522 SN--NSFSGNIPAELGDCRSLIWLDL 545

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 44.5 bits (106), Expect = 2e-04
 Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 5/85 (5%)

Query: 395 LLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR 454
           L   C +L+ L++ S       + +     L +L+ S +        +     L+ L + 
Sbjct: 173 LSDGCGELKHLAI-SGNKISGDVDVSRCVNLEFLDVSSNNFSTGIPFLGDCSALQHLDIS 231

Query: 455 NCWCLL--KLPSRIGNLVNLHYLNI 477
                L       I     L  LNI
Sbjct: 232 G--NKLSGDFSRAISTCTELKLLNI 254

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 43.4 bits (103), Expect = 5e-04
 Identities = 21/115 (18%), Positives = 36/115 (31%), Gaps = 4/115 (3%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQ-CLPDA--ICSLFNL 448
           +S  L     L  L L +  I        C   L  L+ SR+ +   +     + S   L
Sbjct: 69  VSSSLLSLTGLESLFLSNSHINGSVSGFKCSASLTSLDLSRNSLSGPVTTLTSLGSCSGL 128

Query: 449 EILILRNCWCLLKLP-SRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNF 502
           + L + +         S    L +L  L++   S      +G         L + 
Sbjct: 129 KFLNVSSNTLDFPGKVSGGLKLNSLEVLDLSANSISGANVVGWVLSDGCGELKHL 183

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 49.6 bits (119), Expect = 5e-06
 Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 4/83 (4%)

Query: 399 CKKLRVLSLGS---YCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
              L  L L             S      L+YL+ S + +  +      L  LE L  ++
Sbjct: 346 LPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQH 405

Query: 456 CWCLLKLPSRI-GNLVNLHYLNI 477
                     +  +L NL YL+I
Sbjct: 406 SNLKQMSEFSVFLSLRNLIYLDI 428

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 46.9 bits (112), Expect = 4e-05
 Identities = 60/423 (14%), Positives = 134/423 (31%), Gaps = 74/423 (17%)

Query: 800  LQGLQRLTCLKDLL-IGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLE 858
            L+ L ++  L   L +   P     P A     L ++T+++     ++    I   A LE
Sbjct: 169  LRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLE 228

Query: 859  VLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINSSSST 918
            V R+   +     + E    S                    +   + ++ E  +      
Sbjct: 229  VHRLVLGEFRNEGNLEKFDKSAL------------------EGLCNLTIEEFRLAYLDYY 270

Query: 919  YLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLT-------SECQLPVEVE 971
              D+  LF     +++          +L  + IE   +F             C+      
Sbjct: 271  LDDIIDLF-NCLTNVSSF--------SLVSVTIERVKDFSYNFGWQHLELVNCKF----G 317

Query: 972  ELTIYGCSNLESIAERFHDDACLRSIWISSCENLKSL-------------PKGLSNLSHL 1018
            +       +L+ +   F  +    +       +L+ L              +     + L
Sbjct: 318  QFPTLKLKSLKRL--TFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSL 375

Query: 1019 HEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIPTGT---LSSLRELALSECPGI 1075
              + +     ++++  + L    ++ L      LK +        L +L  L +S     
Sbjct: 376  KYLDLSFN-GVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHT-HT 433

Query: 1076 VVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCS----DAVSFPDV 1129
             V      +  ++L  L+++G++  +  +   F +L +L  L +  C        +F  +
Sbjct: 434  RVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSL 493

Query: 1130 GKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLS 1189
                   +SL  + +S       L +  ++ L SL+ L   S  +  +  +        S
Sbjct: 494  -------SSLQVLNMSH-NNFFSLDTFPYKCLNSLQVLDY-SLNHIMTSKKQELQHFPSS 544

Query: 1190 LEI 1192
            L  
Sbjct: 545  LAF 547

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 46.2 bits (110), Expect = 7e-05
 Identities = 25/125 (20%), Positives = 38/125 (30%), Gaps = 6/125 (4%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEV-PISIGCLKQLRY----LNFSRSEIQCLPD 440
            I    L +       L  L L S  I  +    +  L Q+      L+ S + +  +  
Sbjct: 135 LIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQP 194

Query: 441 AICSLFNLEILILRNCWCLLKLPSR-IGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
                  L  L LRN +  L +    I  L  L    +       E  L   +   L  L
Sbjct: 195 GAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGL 254

Query: 500 TNFIV 504
            N  +
Sbjct: 255 CNLTI 259

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 46.2 bits (110), Expect = 7e-05
 Identities = 29/122 (23%), Positives = 43/122 (35%), Gaps = 7/122 (5%)

Query: 402 LRVLSLGSYCITEV-PISIGCLKQLRYLNFSRSEIQCL-PDAICSLFNLEILILRNCWCL 459
            + L L    +  +   S     +L+ L+ SR EIQ +   A  SL +L  LIL     +
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGN-PI 88

Query: 460 LKLPSR-IGNLVNLHYLNIEGASALRELPLGMKELKCLRTL---TNFIVGKDSGCALRDL 515
             L       L +L  L     +        +  LK L+ L    N I          +L
Sbjct: 89  QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNL 148

Query: 516 KN 517
            N
Sbjct: 149 TN 150

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYC-ITEV-PISIGCLKQLRYLNFSRSEIQCL-PDAI 442
           +     L D+  + + L  L L S C + ++ P +   L  L+ LN S +    L     
Sbjct: 456 SFQENFLPDIFTELRNLTFLDL-SQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPY 514

Query: 443 CSLFNLEILILRN 455
             L +L++L    
Sbjct: 515 KCLNSLQVLDYSL 527

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 49.2 bits (118), Expect = 6e-06
 Identities = 25/110 (22%), Positives = 46/110 (41%), Gaps = 8/110 (7%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           +S++  L     L  L L    + ++   I  LK L YL    + I  +   + SL  L+
Sbjct: 277 ISNISPLAGLTALTNLELNENQLEDIS-PISNLKNLTYLTLYFNNISDIS-PVSSLTKLQ 334

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L   N    +   S + NL N+++L+    + + +L   +  L  +  L
Sbjct: 335 RLFFYN--NKVSDVSSLANLTNINWLSAGH-NQISDLT-PLANLTRITQL 380

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 48.8 bits (117), Expect = 8e-06
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 10/102 (9%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           L+D+  L    KL  + + +  I ++   +  L  L  L    ++I  +   + +L NL 
Sbjct: 80  LTDITPLKNLTKLVDILMNNNQIADIT-PLANLTNLTGLTLFNNQITDID-PLKNLTNLN 137

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYL----NIEGASALRELP 487
            L L +    +   S +  L +L  L     +     L  L 
Sbjct: 138 RLELSS--NTISDISALSGLTSLQQLSFGNQVTDLKPLANLT 177

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 48.8 bits (117), Expect = 8e-06
 Identities = 25/110 (22%), Positives = 43/110 (39%), Gaps = 8/110 (7%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           +SD+  L     L  LSL    + ++  ++  L  L  L+ + ++I  L   +  L  L 
Sbjct: 211 ISDITPLGILTNLDELSLNGNQLKDIG-TLASLTNLTDLDLANNQISNLAP-LSGLTKLT 268

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
            L L      +   S +  L  L  L +     L ++   +  LK L  L
Sbjct: 269 ELKLGA--NQISNISPLAGLTALTNLELNENQ-LEDIS-PISNLKNLTYL 314

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 45.7 bits (109), Expect = 8e-05
 Identities = 44/248 (17%), Positives = 87/248 (35%), Gaps = 57/248 (22%)

Query: 392 LSDLLPQ--CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           ++D + Q    ++  L      I  +   +  L  L  +NFS +++  +   + +L  L 
Sbjct: 36  VTDTVSQTDLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQLTDIT-PLKNLTKLV 93

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSG 509
            +++ N    +   + + NL NL  L +   + + ++      LK L  L    +   S 
Sbjct: 94  DILMNNN--QIADITPLANLTNLTGLTLFN-NQITDID----PLKNLTNLNRLEL---SS 143

Query: 510 CALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEA 569
             + D+           +SGL +                 L  L                
Sbjct: 144 NTISDISA---------LSGLTS-----------------LQQLSFG------------- 164

Query: 570 REKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQL 629
               + D LKP +N+  LE       +          +N+  LI  N +  + +  LG L
Sbjct: 165 --NQVTD-LKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQ-ISDITPLGIL 220

Query: 630 CSLKDLTI 637
            +L +L++
Sbjct: 221 TNLDELSL 228

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 45.3 bits (108), Expect = 1e-04
 Identities = 22/172 (12%), Positives = 58/172 (33%), Gaps = 16/172 (9%)

Query: 994  LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLK 1053
            L  + + +   + ++   L+ L+ L  + +     L  +   +   N+  + +     + 
Sbjct: 267  LTELKLGAN-QISNIS-PLAGLTALTNLELNEN-QLEDISPISNLKNLTYLTLYFN-NIS 322

Query: 1054 ALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLR 1113
             + P  +L+ L+ L       +         TN+  L    + +           LT + 
Sbjct: 323  DISPVSSLTKLQRLFFYNNK-VSDVSSLANLTNINWLSAGHNQISDL---TPLANLTRIT 378

Query: 1114 KLYIDGCSDAVSFPDVGKGVILPTSLTSI--------TISDFPKLKRLSSKG 1157
            +L ++  +   +  +    V +P ++ ++        TISD           
Sbjct: 379  QLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITW 430

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 4/88 (4%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           +SD+  L     +  LS G   I+++   +  L ++  L  +       P    +  ++ 
Sbjct: 343 VSDVSSLANLTNINWLSAGHNQISDLT-PLANLTRITQLGLNDQAWTNAPVNYKANVSIP 401

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNI 477
             +  N    L  P+ I +  +    +I
Sbjct: 402 NTVK-NVTGALIAPATISDGGSYTEPDI 428

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 36/213 (16%), Positives = 73/213 (34%), Gaps = 35/213 (16%)

Query: 994  LRSIWISSCENLKSLPKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLK 1053
            L S+  ++   +  +   L  L++L E+ +     L  +   A  +N+ D+ + +  ++ 
Sbjct: 201  LESLIATNN-QISDIT-PLGILTNLDELSLNGN-QLKDIGTLASLTNLTDLDLANN-QIS 256

Query: 1054 ALIPTGTLSSLRELALSECPGIVVFPEEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLR 1113
             L P   L+ L EL L     I         T LT+LE++ + +           L +L 
Sbjct: 257  NLAPLSGLTKLTELKLGANQ-ISNISPLAGLTALTNLELNENQLEDIS---PISNLKNLT 312

Query: 1114 KLYIDGCSDAVSFPDVGKGVILPTSLTSIT-ISDFPKLKRL--------SSKGFQYLVSL 1164
             L +                    +++ I+ +S   KL+RL               L ++
Sbjct: 313  YLTLYFN-----------------NISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNI 355

Query: 1165 EHLSVFSCPNFTSFPEAGFPSSLLSLEIQRCPL 1197
              LS       +        + +  L +     
Sbjct: 356  NWLSAGHN-QISDLTPLANLTRITQLGLNDQAW 387

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A* Length = 330

 Score = 48.8 bits (117), Expect = 6e-06
 Identities = 32/212 (15%), Positives = 71/212 (33%), Gaps = 40/212 (18%)

Query: 1004 NLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKAL------- 1055
             +  +  G   NL +LH + ++    +  +   A               L  L       
Sbjct: 63   KITEIKDGDFKNLKNLHTLILINNK-ISKISPGAF------------APLVKLERLYLSK 109

Query: 1056 -----IPTGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWG-FH 1107
                 +P     +L+EL + E   I    +   +    +  +E+  + +    ++ G F 
Sbjct: 110  NQLKELPEKMPKTLQELRVHENE-ITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQ 168

Query: 1108 KLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHL 1167
             +  L  + I       +   + +G  LP SLT + +    K+ ++ +   + L +L  L
Sbjct: 169  GMKKLSYIRIADT----NITTIPQG--LPPSLTELHLDGN-KITKVDAASLKGLNNLAKL 221

Query: 1168 SVFSCPNFTSFPEAGFP--SSLLSLEIQRCPL 1197
             +    + ++           L  L +    L
Sbjct: 222  GLSFN-SISAVDNGSLANTPHLRELHLNNNKL 252

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A* Length = 330

 Score = 48.5 bits (116), Expect = 7e-06
 Identities = 29/168 (17%), Positives = 58/168 (34%), Gaps = 37/168 (22%)

Query: 387 ISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGC---LKQLRYLNFSRSEIQCLPDAIC 443
           +   V + L     ++ V+ LG+  +    I  G    +K+L Y+  + + I  +P  + 
Sbjct: 136 VRKSVFNGL----NQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLP 191

Query: 444 S----------------------LFNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEGA 480
                                  L NL  L L     +  + +    N  +L  L++   
Sbjct: 192 PSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFN-SISAVDNGSLANTPHLRELHLNNN 250

Query: 481 SALRELPLGMKELKCLRTLT---NFI--VGKDSGCALRDLKNWKFLRG 523
             L ++P G+ + K ++ +    N I  +G +  C            G
Sbjct: 251 K-LVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSG 297

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 48.9 bits (117), Expect = 7e-06
 Identities = 28/167 (16%), Positives = 56/167 (33%), Gaps = 36/167 (21%)

Query: 387 ISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLK--QLRYLNFSRSEIQCLP----- 439
           +   V S L    + +  + +G   +       G     +L YL  S +++  +P     
Sbjct: 138 VPKGVFSGL----RNMNCIEMGGNPLENSGFEPGAFDGLKLNYLRISEAKLTGIPKDLPE 193

Query: 440 -----------------DAICSLFNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEGAS 481
                            + +     L  L L +   +  + +     L  L  L+++   
Sbjct: 194 TLNELHLDHNKIQAIELEDLLRYSKLYRLGLGH-NQIRMIENGSLSFLPTLRELHLDNNK 252

Query: 482 ALRELPLGMKELKCLRTLT---NFI--VGKDSGCALRDLKNWKFLRG 523
            L  +P G+ +LK L+ +    N I  VG +  C +       +  G
Sbjct: 253 -LSRVPAGLPDLKLLQVVYLHTNNITKVGVNDFCPVGFGVKRAYYNG 298

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A Length = 605

 Score = 48.9 bits (116), Expect = 1e-05
 Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           L   K L  L L    I ++  S+  LK+L+ L+   + I  + + +  L  LE L L N
Sbjct: 83  LTNLKNLGWLFLDENKIKDLS-SLKDLKKLKSLSLEHNGISDI-NGLVHLPQLESLYLGN 140

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
               +   + +  L  L  L++E  + + ++   +  L  L+ L
Sbjct: 141 --NKITDITVLSRLTKLDTLSLED-NQISDIV-PLAGLTKLQNL 180

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A Length = 605

 Score = 48.2 bits (114), Expect = 2e-05
 Identities = 32/135 (23%), Positives = 54/135 (40%), Gaps = 10/135 (7%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           + DL  L   KKL+ LSL    I+++   +  L QL  L    ++I  +   +  L  L+
Sbjct: 99  IKDLSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKITDI-TVLSRLTKLD 156

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEG--ASALRELPLGMKELKCLRTLTNFIVGKD 507
            L L +   +  +   +  L  L  L +     S LR L  G+K L  L   +   + K 
Sbjct: 157 TLSLEDN-QISDIVP-LAGLTKLQNLYLSKNHISDLRALA-GLKNLDVLELFSQECLNKP 213

Query: 508 SGCALRDLKNWKFLR 522
                 +L     ++
Sbjct: 214 I-NHQSNLVVPNTVK 227

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A Length = 605

 Score = 46.6 bits (110), Expect = 4e-05
 Identities = 22/104 (21%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
                +    +L    +T+  ++   L  +  +  + S+I+ +   I  L N+  L L  
Sbjct: 17  DDAFAETIKDNLKKKSVTDA-VTQNELNSIDQIIANNSDIKSV-QGIQYLPNVTKLFLNG 74

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
               L     + NL NL +L +   + +++L   +K+LK L++L
Sbjct: 75  --NKLTDIKPLTNLKNLGWLFL-DENKIKDLS-SLKDLKKLKSL 114

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens} Length = 520

 Score = 47.6 bits (113), Expect = 2e-05
 Identities = 76/504 (15%), Positives = 153/504 (30%), Gaps = 59/504 (11%)

Query: 402 LRVLSLGSYCITEVPIS-IGCLKQLRYLNFSRSEIQCLPDAIC-SLFNLEILILRNCWCL 459
             +L++    I+E+  S I  L +LR L  S + IQ L  ++      LE L L +   L
Sbjct: 23  TTILNISQNYISELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHNK-L 81

Query: 460 LKLPSRIGNLVNLHYLNIEGASALRELPLGM--KELKCLRTLTNFIVGKDSGCALRDLKN 517
           +K+       VNL +L++   +A   LP+      +  L+ L        S   L     
Sbjct: 82  VKISC--HPTVNLKHLDLSF-NAFDALPICKEFGNMSQLKFLGL------STTHLEKSSV 132

Query: 518 WKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDM 577
                  L IS +  V+      +      +      L      + +             
Sbjct: 133 LPIA--HLNISKVLLVLGETYGEKEDPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVA 190

Query: 578 LKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRS-TSLPSLGQLCSLKDLT 636
               SNIK +   +             +   ++ L L N   +  S   + QL     + 
Sbjct: 191 NLELSNIKCVLEDNKCSYFLSILAKLQTNPKLSNLTLNNIETTWNSFIRILQLVWHTTVW 250

Query: 637 IVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLS 696
              +S +K +  ++          SL+ L    +        +         +     ++
Sbjct: 251 YFSISNVK-LQGQLDFRDFDYSGTSLKALSIHQVVS------DVFGFPQSYIYEIFSNMN 303

Query: 697 IK-----KCPKLSGRLPNHLPSLEEIVIAGCMHLAVSLPSLPALCTMEIDGCKRLVCDGP 751
           IK         +    P+ +     +  +        L          +   + L+    
Sbjct: 304 IKNFTVSGTRMVHMLCPSKISPFLHLDFSNN-----LLTDTVFENCGHLTELETLILQM- 357

Query: 752 SESKSPNKMTLCNISEFENWSSEKFQKVEQLMIVGCEGFVNEICLEKPLQGLQRLTCLKD 811
                 N++    +S+     +E   +++ L  +      N +  ++          L  
Sbjct: 358 ------NQLK--ELSK----IAEMTTQMKSLQQLDISQ--NSVSYDEKKGDCSWTKSLLS 403

Query: 812 LLIGNCPTVVSLPKACFLPNLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSI 871
           L + +   +      C  P +  + +   N + S+    +     L+ L +     L S+
Sbjct: 404 LNMSSN-ILTDTIFRCLPPRIKVLDLHS-NKIKSIPKQ-VVKLEALQELNVASN-QLKSV 459

Query: 872 SREHLPS--SLQAIEIR----DCE 889
                    SLQ I +     DC 
Sbjct: 460 PDGIFDRLTSLQKIWLHTNPWDCS 483

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens} Length = 520

 Score = 42.5 bits (100), Expect = 8e-04
 Identities = 68/412 (16%), Positives = 127/412 (30%), Gaps = 41/412 (9%)

Query: 800  LQGL--QRLTCLKDL-LIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNN 854
            L  +       LK L L  N    + + K  F  +  L  + +     L   +   I + 
Sbjct: 81   LVKISCHPTVNLKHLDLSFNAFDALPICKE-FGNMSQLKFLGLST-THLEKSSVLPIAHL 138

Query: 855  ARLEVLRIKRCDSLTSISREHLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNINS 914
               +VL         +   +  P  LQ         +     +       S  T  N+  
Sbjct: 139  NISKVLL----VLGETYGEKEDPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVANLEL 194

Query: 915  SSSTYLDLESLFVYRCPSLTCLWSGGRLP-VTLKRLRIEDCSNFKVLTSECQLPVEVEEL 973
            S+   +  ++   Y    L  L +  +L  +TL  +     S  ++L         V   
Sbjct: 195  SNIKCVLEDNKCSYFLSILAKLQTNPKLSNLTLNNIETTWNSFIRILQ--LVWHTTVWYF 252

Query: 974  TIYGCSNLESIAERFHDDAC--LRSIWISSCEN--LKSLPKGLSNLSHLHEIRIVRCHNL 1029
            +I        +  R  D +   L+++ I    +         +  +     I+       
Sbjct: 253  SISNVKLQGQLDFRDFDYSGTSLKALSIHQVVSDVFGFPQSYIYEIFSNMNIKNFTVSGT 312

Query: 1030 VSLPEDALPSNVVDVLIEDCD--KLKALIPT--GTLSSLRELALSEC------PGIVVFP 1079
              +     PS +   L  D     L   +    G L+ L  L L             +  
Sbjct: 313  RMVHMLC-PSKISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMT- 370

Query: 1080 EEGLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSL 1139
               +  +L  L+IS +++     K       SL  L +       +         LP  +
Sbjct: 371  -TQM-KSLQQLDISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIFRC-----LPPRI 423

Query: 1140 TSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGFPSSLLSLE 1191
              + +    K+K +  +  + L +L+ L+V S     S P+  F   L SL+
Sbjct: 424  KVLDLHS-NKIKSIPKQVVK-LEALQELNVASN-QLKSVPDGIF-DRLTSLQ 471

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 47.4 bits (113), Expect = 3e-05
 Identities = 41/219 (18%), Positives = 80/219 (36%), Gaps = 41/219 (18%)

Query: 994  LRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNLVSLPEDALP--SNVVDVLIEDCD 1050
            L  + +  C NL S+P   LS+L  L  +R+   + + ++ + +      +  + I    
Sbjct: 154  LEQLTLEKC-NLTSIPTEALSHLHGLIVLRLRHLN-INAIRDYSFKRLYRLKVLEISHWP 211

Query: 1051 KLKALIPTG-TLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFH 1107
             L  + P      +L  L+++ C  +   P   +     L  L +S  N    +     H
Sbjct: 212  YLDTMTPNCLYGLNLTSLSITHCN-LTAVPYLAVRHLVYLRFLNLSY-NPISTIEGSMLH 269

Query: 1108 KLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHL 1167
            +L  L+++ + G                             +L  +    F+ L  L  L
Sbjct: 270  ELLRLQEIQLVGG----------------------------QLAVVEPYAFRGLNYLRVL 301

Query: 1168 SVFSCPNFTSFPEAGFPS--SLLSLEIQRCPLLEKCKMR 1204
            +V      T+  E+ F S  +L +L +   PL   C++ 
Sbjct: 302  NVSGN-QLTTLEESVFHSVGNLETLILDSNPLACDCRLL 339

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 56/284 (19%), Positives = 91/284 (32%), Gaps = 57/284 (20%)

Query: 799  PLQGLQRLTCLKDLLIGNCPTVVSLPKACF--LPNLSEITIQDCNALASLTDGMIYNNAR 856
            PL     L+ L  L I     +V L    F  L NL  + + D N L  ++         
Sbjct: 96   PLGVFTGLSNLTKLDISEN-KIVILLDYMFQDLYNLKSLEVGD-NDLVYISHRAFSGLNS 153

Query: 857  LEVLRIKRCDSLTSISRE---HLPSSLQAIEIRDCETLQCVLDDREKSCTSSSVTEKNIN 913
            LE L +++C +LTSI  E   HL   L  + +R    +  + D   K             
Sbjct: 154  LEQLTLEKC-NLTSIPTEALSHLH-GLIVLRLRHLN-INAIRDYSFKRLYR--------- 201

Query: 914  SSSSTYLDLESLFVYRCPSLTCLWSGGRLPVTLKRLRIEDCSNFKVLTSEC--QLPVEVE 971
                    L+ L +   P L  +       + L  L I  C N   +       L   + 
Sbjct: 202  --------LKVLEISHWPYLDTMTPNCLYGLNLTSLSITHC-NLTAVPYLAVRHLV-YLR 251

Query: 972  ELTIYGCSNLESIAER-FHDDACLRSIWISSCENLKSLPKG-LSNLSHLHEIRIVRCHNL 1029
             L +   + + +I     H+   L+ I +     L  +       L++L  + +     L
Sbjct: 252  FLNLSY-NPISTIEGSMLHELLRLQEIQLVGG-QLAVVEPYAFRGLNYLRVLNVSGN-QL 308

Query: 1030 VSLPEDALPSNVVDVLIEDCDKLKALIPTGTLSSLRELALSECP 1073
             +L E    S                     + +L  L L   P
Sbjct: 309  TTLEESVFHS---------------------VGNLETLILDSNP 331

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A Length = 291

 Score = 46.2 bits (110), Expect = 4e-05
 Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 4/106 (3%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           L    +L  L LG+  IT++   +  L +L  L+   ++I  +   +  L  L+ L L  
Sbjct: 130 LVHLPQLESLYLGNNKITDIT-VLSRLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYLSK 187

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTN 501
              +  L + +  L NL  L +     L +       L    T+ N
Sbjct: 188 N-HISDLRA-LAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKN 231

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A Length = 291

 Score = 45.0 bits (107), Expect = 9e-05
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           L   KKL+ LSL    I+++   +  L QL  L    ++I  +   +  L  L+ L L +
Sbjct: 108 LKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLED 165

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEG 479
              +  +   +  L  L  L +  
Sbjct: 166 N-QISDIVP-LAGLTKLQNLYLSK 187

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A Length = 291

 Score = 42.7 bits (101), Expect = 5e-04
 Identities = 22/104 (21%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
                +    +L    +T+  ++   L  +  +  + S+I+ +   I  L N+  L L  
Sbjct: 20  DDAFAETIKDNLKKKSVTDA-VTQNELNSIDQIIANNSDIKSV-QGIQYLPNVTKLFLNG 77

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
               L     + NL NL +L +   + +++L   +K+LK L++L
Sbjct: 78  --NKLTDIKPLANLKNLGWLFL-DENKVKDLS-SLKDLKKLKSL 117

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 Length = 308

 Score = 45.1 bits (107), Expect = 9e-05
 Identities = 27/126 (21%), Positives = 52/126 (41%), Gaps = 20/126 (15%)

Query: 392 LSDL--LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           ++DL  L    K+  L L    +  V  +I  L+ ++ L+ + ++I  +   +  L NL+
Sbjct: 75  ITDLAPLKNLTKITELELSGNPLKNVS-AIAGLQSIKTLDLTSTQITDVT-PLAGLSNLQ 132

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLN-----------IEGASALRELPL---GMKELKC 495
           +L L     +  +   +  L NL YL+           +   S L  L      + ++  
Sbjct: 133 VLYLDLNQ-ITNISP-LAGLTNLQYLSIGNAQVSDLTPLANLSKLTTLKADDNKISDISP 190

Query: 496 LRTLTN 501
           L +L N
Sbjct: 191 LASLPN 196

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 Length = 308

 Score = 42.8 bits (101), Expect = 5e-04
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           L     L+ LS+G+  ++++   +  L +L  L    ++I  +   + SL NL  + L+N
Sbjct: 147 LAGLTNLQYLSIGNAQVSDLT-PLANLSKLTTLKADDNKISDIS-PLASLPNLIEVHLKN 204

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEG 479
              +  +   + N  NL  + +  
Sbjct: 205 N-QISDVSP-LANTSNLFIVTLTN 226

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 44.8 bits (107), Expect = 1e-04
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 11/85 (12%)

Query: 399 CKKLRVLSLGSYC-IT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILILRN 455
              L  L +G    +   +P +I  L QL YL  + + +   +PD +  +  L  L    
Sbjct: 75  LPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSY 134

Query: 456 CWCLLKL----PSRIGNLVNLHYLN 476
                 L    P  I +L NL  + 
Sbjct: 135 N----ALSGTLPPSISSLPNLVGIT 155

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 43.3 bits (103), Expect = 3e-04
 Identities = 21/97 (21%), Positives = 34/97 (35%), Gaps = 15/97 (15%)

Query: 391 VLSDLLPQCKKLRVLSLGSYCIT---EVPISIGCLKQLRYLNFSRS-----EIQCLPDAI 442
           VL D   Q  ++  L L    +     +P S+  L  L +L           I   P AI
Sbjct: 41  VLCDTDTQTYRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPI---PPAI 97

Query: 443 CSLFNLEILILRNCWCLL--KLPSRIGNLVNLHYLNI 477
             L  L  L + +    +   +P  +  +  L  L+ 
Sbjct: 98  AKLTQLHYLYITH--TNVSGAIPDFLSQIKTLVTLDF 132

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 42.1 bits (100), Expect = 8e-04
 Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 398 QCKKLRVLSLGSYCIT-EVPISIGCLKQLRYLNFSRSEIQ-CLPDAICSLFNLEILIL-R 454
           +  +L  L +    ++  +P  +  +K L  L+FS + +   LP +I SL NL  +    
Sbjct: 99  KLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDG 158

Query: 455 NCWCLLKL----PSRIGNLVNLH-YLNI 477
           N     ++    P   G+   L   + I
Sbjct: 159 N-----RISGAIPDSYGSFSKLFTSMTI 181

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A Length = 198

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 23/116 (19%), Positives = 43/116 (37%), Gaps = 20/116 (17%)

Query: 392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEIL 451
           +   L   K  + L+L +  I ++  S+  ++ LR L+  R+ I+ + +       LE L
Sbjct: 40  MDATLSTLKACKHLALSTNNIEKI-SSLSGMENLRILSLGRNLIKKIENLDAVADTLEEL 98

Query: 452 ILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLG------MKELKCLRTLTN 501
            +           +I +L  +  L       LR L +         E+  L  L  
Sbjct: 99  WISYN--------QIASLSGIEKL-----VNLRVLYMSNNKITNWGEIDKLAALDK 141

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A Length = 198

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILR- 454
           L   + LR+LSLG   I ++         L  L  S ++I  L   I  L NL +L +  
Sbjct: 66  LSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASL-SGIEKLVNLRVLYMSN 124

Query: 455 NCWCLLKLPSRIGNLVNLHYLNIEG 479
           N         ++  L  L  L + G
Sbjct: 125 NKITNWGEIDKLAALDKLEDLLLAG 149

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 26/120 (21%), Positives = 42/120 (35%), Gaps = 10/120 (8%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQCLPDAIC- 443
            I     S L      L  L L    ++ +  S    L  L +LN   +  + L +    
Sbjct: 90  TIEEDSFSSL----GSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF 145

Query: 444 -SLFNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEGASALRELPLGM-KELKCLRTLT 500
             L  L+IL + N     K+  +    L  L  L I+  S L+       K ++ +  L 
Sbjct: 146 SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDA-SDLQSYEPKSLKSIQNVSHLI 204

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 36/204 (17%), Positives = 66/204 (32%), Gaps = 37/204 (18%)

Query: 1001 SCEN--LKSLPKGL-SNLSHLHEIRIVRCHNLVSLPEDALPSNVVDVLIEDCDKLKALIP 1057
               +  L S+P GL   +  L     +  + +  +    L                    
Sbjct: 37   KGSSGSLNSIPSGLTEAVKSLD----LSNNRITYISNSDLQR------------------ 74

Query: 1058 TGTLSSLRELALSECPGIVVFPEEGLS--TNLTDLEISGDNMYKPLVKWGFHKLTSLRKL 1115
                 +L+ L L+   GI    E+  S   +L  L++S  N    L    F  L+SL  L
Sbjct: 75   ---CVNLQALVLTSN-GINTIEEDSFSSLGSLEHLDLS-YNYLSNLSSSWFKPLSSLTFL 129

Query: 1116 YIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNF 1175
             + G     +  +      L   L  + + +     ++  K F  L  LE L + +  + 
Sbjct: 130  NLLGNP-YKTLGETSLFSHLT-KLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDAS-DL 186

Query: 1176 TSFPEAGFPS--SLLSLEIQRCPL 1197
             S+      S  ++  L +     
Sbjct: 187  QSYEPKSLKSIQNVSHLILHMKQH 210

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A Length = 401

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 53/405 (13%), Positives = 111/405 (27%), Gaps = 122/405 (30%)

Query: 831  NLSEITIQDCNALASLTDGMIYNNARLEVLRIKRCDSLTSIS-------REHLPSSLQAI 883
            +            ASL D  I       +  +     LT ++        +  P  + + 
Sbjct: 8    DSPSAANPVEPIGASLEDFSIEQLPAKTIYALGENIDLTGLNVTGKYDDGKQRPVKVTSE 67

Query: 884  EIRDCETLQCVLDDREKSCTSSSVTEKNINSSSSTYLDLESLFVYRCPSLTCLWSGGRLP 943
            +I    +   V  D+++   +    +K+ +   S       +          +     LP
Sbjct: 68   QISGFSS--SVPVDKQEVTITIEGKQKSFSVHISPVRVENGVLTEILKGYNEI----ILP 121

Query: 944  VTLKRLRI---EDCSNFKV-----LTS-------ECQLPVEVEELTI------------Y 976
             ++K +      +    KV     L S          +    +E+              Y
Sbjct: 122  NSVKSIPKDAFRNSQIAKVVLNEGLKSIGDMAFFNSTV----QEIVFPSTLEQLKEDIFY 177

Query: 977  GCSNLESI----------AERFHDDACLRSIWISS------------CENLKS--LPKGL 1012
             C NL+                   A +  + +                 LK+  +P+ +
Sbjct: 178  YCYNLKKADLSKTKITKLPASTFVYAGIEEVLLPVTLKEIGSQAFLKTSQLKTIEIPENV 237

Query: 1013 SNL-------SHLHEIRI------------VRCHNLVSLPEDALPSNVVDVLI------- 1046
            S +       S +  +++              C  L  +       +  +          
Sbjct: 238  STIGQEAFRESGITTVKLPNGVTNIASRAFYYCPELAEV---TTYGSTFNDDPEAMIHPY 294

Query: 1047 --EDCDKLKAL-IPTGTLSSLRELALSECPGI--VVFPEEGLSTNLTDLEISGDNMYKPL 1101
              E C KL    IP   +  L +  L     +  +  P      N+T +           
Sbjct: 295  CLEGCPKLARFEIPES-IRILGQGLLGGNRKVTQLTIPA-----NVTQIN---------- 338

Query: 1102 VKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISD 1146
                F+  T ++++ ++G +    F  V  G   P  +T I +  
Sbjct: 339  -FSAFNN-TGIKEVKVEGTTPPQVFEKVWYGF--PDDITVIRVPA 379

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4 Length = 176

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 26/108 (24%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILIL-R 454
                + R L L  Y I  +      L Q   ++FS +EI+ L      L  L+ L++  
Sbjct: 15  YTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDG-FPLLRRLKTLLVNN 73

Query: 455 NCWCLLKLPSRIGNLVNLHYLNIEG--ASALRELPLGMKELKCLRTLT 500
           N  C +        L +L  L +       L +L   +  LK L  L 
Sbjct: 74  NRICRIG-EGLDQALPDLTELILTNNSLVELGDL-DPLASLKSLTYLC 119

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7 Length = 347

 Score = 43.6 bits (102), Expect = 3e-04
 Identities = 25/128 (19%), Positives = 36/128 (28%), Gaps = 30/128 (23%)

Query: 1085 TNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITI 1144
             NLT+L I      + L       L  LR L I                           
Sbjct: 31   ENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKS------------------------ 66

Query: 1145 SDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF-PSSLLSLEIQRCPLLEKCKM 1203
                 L+ ++   F +   L  L++       S         SL  L +   PL   C +
Sbjct: 67   ----GLRFVAPDAFHFTPRLSRLNLSFN-ALESLSWKTVQGLSLQELVLSGNPLHCSCAL 121

Query: 1204 RKGQEWPK 1211
            R  Q W +
Sbjct: 122  RWLQRWEE 129

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A Length = 290

 Score = 43.2 bits (102), Expect = 3e-04
 Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 8/105 (7%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSL 445
             S   L        +L  L+L    +T++ +    L  L  L+ S +++Q LP    +L
Sbjct: 45  TFSLATLMPY----TRLTQLNLDRAELTKLQVDGT-LPVLGTLDLSHNQLQSLPLLGQTL 99

Query: 446 FNLEILILRNCWCLLKLPSRI-GNLVNLHYLNIEGASALRELPLG 489
             L +L +     L  LP      L  L  L ++G + L+ LP G
Sbjct: 100 PALTVLDVSFNR-LTSLPLGALRGLGELQELYLKG-NELKTLPPG 142

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus} Length = 562

 Score = 42.9 bits (101), Expect = 6e-04
 Identities = 56/353 (15%), Positives = 110/353 (31%), Gaps = 46/353 (13%)

Query: 387 ISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI-GCLKQLRYLNFSRSEIQCLPDAICSL 445
           +    +S L     +LRVL L    I  +   +    + L YL+ S + +Q +      +
Sbjct: 67  LRMPDISFL----SELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHNRLQNISCC--PM 120

Query: 446 FNLEILIL-RNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGM-KELKCLRTLTNFI 503
            +L  L L  N + +L +    GNL  L +L +  A+  R+L L     L     L + +
Sbjct: 121 ASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGL-SAAKFRQLDLLPVAHLHLSCILLDLV 179

Query: 504 VGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKE-GLTDLKLDWRPRRD 562
                G     L         L +    N + S + N ++  +    L+++KL+    + 
Sbjct: 180 SYHIKGGETESL--QIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDENCQR 237

Query: 563 GDSVDEAREKN--ILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRS 620
             +      +   +L++   H               +P  V   +  N+ +    +    
Sbjct: 238 LMTFLSELTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEF 297

Query: 621 TSLPSLGQLCSLKDLTIVGMSELKS----------------IGSEIYGEGCSKPFQSLQT 664
           T   +  +   ++ +        K                   +      C     S   
Sbjct: 298 TYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTF 357

Query: 665 LYFEDLQEWEHWEPNRDNDEHVQAFPRLRKLSIKKCPKLSGRLPNHLPSLEEI 717
           L F           N   D   Q    L++L      +      N L +  ++
Sbjct: 358 LNFTQ---------NVFTDSVFQGCSTLKRLQTLILQR------NGLKNFFKV 395

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A Length = 149

 Score = 40.0 bits (94), Expect = 8e-04
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 25/108 (23%)

Query: 394 DLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAIC-SLFNLEILI 452
            L  + ++L  LS  +  +T +   +  L +L+ L  S + +    + +     NL  L 
Sbjct: 36  GLTDEFEELEFLSTINVGLTSIAN-LPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLN 94

Query: 453 LRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLT 500
           L           +I +L  +  L               K+L+ L++L 
Sbjct: 95  LSGN--------KIKDLSTIEPL---------------KKLENLKSLD 119

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	1237
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	8e-47
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	2e-06
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	8e-05
d2astb2	284	c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p1	2e-04
d1dcea3	124	c.10.2.2 (A:444-567) Rab geranylgeranyltransferase	2e-04
d1a9na_	162	c.10.2.4 (A:) Splicesomal U2A' protein {Human (Hom	4e-04
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	5e-04
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	0.002
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	0.003

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  167 bits (423), Expect = 8e-47
 Identities = 38/254 (14%), Positives = 75/254 (29%), Gaps = 28/254 (11%)

Query: 6   DPSDAANFRVIPLVGMGGIGKTTLAQEVYND---KLTEAFEPKAWVCVSDDFDVLRISKA 62
           D     +   + L G  G GK+ +A +  +     +   ++   W+  S           
Sbjct: 37  DEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLF 96

Query: 63  ILDSIKRSSC----------KLEDLNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALK 112
               +   S            +  +   ++     + +   L V DDV  E    W    
Sbjct: 97  TDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRW---- 152

Query: 113 SPFMAGAPGSRIIVTTRSMDVALTMGSGKN-YELKLLSDDDCWSVFVAHAFEGRDAGTHG 171
               A     R +VTTR ++++          E+  L  D+C+    A+           
Sbjct: 153 ----AQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEE 208

Query: 172 NFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLS 231
           +      + +E   G P            K   ++   + +      +    +  +   S
Sbjct: 209 DV---LNKTIELSSGNPATLMMFFKSCEPKT-FEKMAQLNNK--LESRGLVGVECITPYS 262

Query: 232 YHHLPSHLKRCFAY 245
           Y  L   L+RC   
Sbjct: 263 YKSLAMALQRCVEV 276

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]} Length = 384

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

 Score = 49.2 bits (116), Expect = 2e-06
 Identities = 52/341 (15%), Positives = 113/341 (33%), Gaps = 23/341 (6%)

Query: 392 LSDLLPQ--CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLE 449
           ++D + Q    ++  L      I  +   +  L  L  +NFS +++  +   + +L  L 
Sbjct: 34  VTDTVSQTDLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQLTDIT-PLKNLTKLV 91

Query: 450 ILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSG 509
            +++ N       P      +              +    +  L  L   +N I    + 
Sbjct: 92  DILMNNNQIADITPLANLTNLTGLT-LFNNQITDIDPLKNLTNLNRLELSSNTISDISAL 150

Query: 510 CALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEA 569
             L  L+   F      +  L N+   +  + +  +V +     KL         +    
Sbjct: 151 SGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATN---- 206

Query: 570 REKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSLPSLGQL 629
              N +  + P   +  L+  S  G +        S +N+  L L N  + ++L  L  L
Sbjct: 207 ---NQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANN-QISNLAPLSGL 262

Query: 630 CSLKDL-----TIVGMSELKSIGSEIYGEGCSKPFQSLQTLYFEDLQEWEHWEPNRDND- 683
             L +L      I  +S L  + +    E      + +  +       +     N  +D 
Sbjct: 263 TKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDI 322

Query: 684 EHVQAFPRLRKLSIKKCPKLSGRLPN--HLPSLEEIVIAGC 722
             V +  +L++L      K+S  + +  +L ++  +     
Sbjct: 323 SPVSSLTKLQRLFFANN-KVSD-VSSLANLTNINWLSAGHN 361

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]} Length = 384

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

 Score = 43.8 bits (102), Expect = 8e-05
 Identities = 32/169 (18%), Positives = 54/169 (31%), Gaps = 28/169 (16%)

Query: 354 CDGMDKFKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLP--QCKKLRVLSLGSYC 411
              +     L    N    +        +   +++   +S+L P     KL  L LG+  
Sbjct: 215 LGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQ 274

Query: 412 ITEVPISIGC---------------------LKQLRYLNFSRSEIQCLPDAICSLFNLEI 450
           I+ +    G                      LK L YL    + I  +   + SL  L+ 
Sbjct: 275 ISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDIS-PVSSLTKLQR 333

Query: 451 LILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTL 499
           L   N    +   S + NL N+++L+          PL    L  +  L
Sbjct: 334 LFFANN--KVSDVSSLANLTNINWLSAGHNQISDLTPLA--NLTRITQL 378

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]} Length = 284

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (98), Expect = 2e-04
 Identities = 30/247 (12%), Positives = 66/247 (26%), Gaps = 11/247 (4%)

Query: 386 NISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEI--QCLPDAIC 443
           N+ P V   LL Q   +         + +         ++++++ S S I    L   + 
Sbjct: 11  NLHPDVTGRLLSQ--GVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILS 68

Query: 444 SLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRELPLGMKELKCLRTLTNFI 503
               L+ L L        + + +    NL  LN+ G S   E  L      C R     +
Sbjct: 69  QCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNL 128

Query: 504 VGKDSGCALRDLKNWKFLRGRLCISGLENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDG 563
                            +   +    L     + + ++    V+                
Sbjct: 129 SWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRR-------CPNLVHLD 181

Query: 564 DSVDEAREKNILDMLKPHSNIKRLEIHSYGGTRFPSWVGDPSFSNVAVLILKNCRRSTSL 623
            S     + +        + ++ L +         + +       +  L +       +L
Sbjct: 182 LSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIVPDGTL 241

Query: 624 PSLGQLC 630
             L +  
Sbjct: 242 QLLKEAL 248

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 124

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 16/84 (19%), Positives = 32/84 (38%)

Query: 396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRN 455
           L Q   +  L L    +  +P ++  L+ L  L  S + ++ +          E+L+  N
Sbjct: 16  LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNN 75

Query: 456 CWCLLKLPSRIGNLVNLHYLNIEG 479
                     + +   L  LN++G
Sbjct: 76  RLQQSAAIQPLVSCPRLVLLNLQG 99

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]} Length = 162

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (93), Expect = 4e-04
 Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 1/65 (1%)

Query: 399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWC 458
             + R L L  Y I  +      L Q   ++FS +EI+ L      L  L+ L++ N   
Sbjct: 17  AVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDG-FPLLRRLKTLLVNNNRI 75

Query: 459 LLKLP 463
                
Sbjct: 76  CRIGE 80

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]} Length = 305

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 41.2 bits (95), Expect = 5e-04
 Identities = 46/272 (16%), Positives = 84/272 (30%), Gaps = 14/272 (5%)

Query: 412 ITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPSRIGNLV 470
           + +VP  +        L+   ++I  + D    +L NL  LIL N       P     LV
Sbjct: 22  LEKVPKDLP--PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLV 79

Query: 471 NLHYLNIEGASALRELPLGMKELKCLRTLTNFIVGKDSGCALRDLKNWKFLRGRLCISGL 530
            L  L +     L+ELP  M +      +    + K        L     +         
Sbjct: 80  KLERLYLSKNQ-LKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKS 138

Query: 531 ENVIDSQEANEAMLRVKEGLTDLKLDWRPRRDGDSVDEAREKNILDMLKPHSNIKRLEIH 590
             + +        L     + D  +   P+    S+ E             +++K L   
Sbjct: 139 SGIENGAFQGMKKLSYIR-IADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNL 197

Query: 591 SYGGTRFPSWVGDPSFSNVAVLILK-----NCRRSTSLPSLGQLCSLKDLTIVGMSELKS 645
           +  G  F S     + S      L+     N +       L     ++ + +   + + +
Sbjct: 198 AKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHN-NNISA 256

Query: 646 IGSEIY-GEGCSKPFQSLQTLYFED--LQEWE 674
           IGS  +   G +    S   +      +Q WE
Sbjct: 257 IGSNDFCPPGYNTKKASYSGVSLFSNPVQYWE 288

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]} Length = 353

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

 Score = 39.4 bits (90), Expect = 0.002
 Identities = 20/151 (13%), Positives = 43/151 (28%), Gaps = 3/151 (1%)

Query: 300 SNTESKYVMHDLVHDLAQWASGETCFRLDDQFSVDRQSNVFEKVRHFSYLRSYDCDGMDK 359
               + Y  ++L+  L           + D +  D                 +       
Sbjct: 204 PFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELP 263

Query: 360 FKVLDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISI 419
             +     +      +      +   N+S   L +L     +L  L      + EVP   
Sbjct: 264 PNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPPRLERLIASFNHLAEVPELP 323

Query: 420 GCLKQLRYLNFSRSEIQCLPDAICSLFNLEI 450
                L+ L+   + ++  PD   S+ +L +
Sbjct: 324 Q---NLKQLHVEYNPLREFPDIPESVEDLRM 351

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]} Length = 353

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

 Score = 39.0 bits (89), Expect = 0.003
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWC 458
            ++   L L +  ++ +P        L  L  S + +  LP+   SL +L +        
Sbjct: 37  DRQAHELELNNLGLSSLPELPP---HLESLVASCNSLTELPELPQSLKSLLVDNNNLKAL 93

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	1237
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.93
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.92
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.87
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.87
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.86
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.86
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.86
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.85
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.83
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.83
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.81
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.75
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.71
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.69
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.68
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.68
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.66
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.66
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.63
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.58
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.56
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.53
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.47
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.45
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.42
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.37
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.33
d2ifga3	156	High affinity nerve growth factor receptor, N-term	99.32
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.3
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.29
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.24
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.21
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.15
d2ifga3	156	High affinity nerve growth factor receptor, N-term	99.09
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.04
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.92
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.92
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.91
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.91
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.82
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.81
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.78
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.72
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.72
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.7
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.58
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.57
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.55
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.48
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.48
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.41
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.37
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.28
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	98.21
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.18
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.04
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	98.04
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.98
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.95
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.78
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.74
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.73
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.72
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.66
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	97.64
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.56
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.54
d1okkd2	207	GTPase domain of the signal recognition particle r	97.53
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.48
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	97.4
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.38
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.36
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.36
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.36
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.25
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.23
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.22
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.21
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.2
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.16
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.12
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.12
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.11
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	97.09
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.08
d1xpua3	289	Transcription termination factor Rho, ATPase domai	97.06
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	97.06
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.05
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.03
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.02
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	97.02
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.0
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.99
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.99
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.95
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.94
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.94
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.9
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.9
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.88
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.87
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.84
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.82
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.81
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	96.81
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.81
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.8
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.79
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.79
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.78
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.76
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.76
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.74
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.69
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.68
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.64
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.63
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	96.62
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.62
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	96.61
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.61
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	96.61
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.56
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.56
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.56
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.53
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.52
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	96.46
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.45
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.44
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.42
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	96.4
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	96.4
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.35
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	96.34
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	96.32
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.29
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.24
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.23
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.17
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	96.11
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.1
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.08
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	96.05
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.04
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.03
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.03
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.97
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.97
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.96
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.96
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.95
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.94
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.92
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.89
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	95.85
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.8
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	95.77
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	95.72
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.66
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.66
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.64
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.63
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.62
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.53
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.48
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.47
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	95.34
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.05
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.02
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.98
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.71
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	94.66
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.57
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.57
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.52
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	94.52
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.5
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.49
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.49
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.44
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.44
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.44
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.39
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.39
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	94.36
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	94.3
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.28
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.28
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	94.24
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	94.18
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.16
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.15
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	94.14
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	94.13
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	94.11
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	94.09
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.06
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.05
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	94.02
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	93.97
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.97
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.9
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	93.88
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.87
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	93.86
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.85
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.83
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.82
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.81
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	93.74
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.74
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	93.72
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.7
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	93.69
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	93.66
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.63
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	93.63
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	93.61
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.61
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	93.55
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.44
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.43
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.4
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.4
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.4
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	93.39
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.34
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.15
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	93.07
d1nrjb_	209	Signal recognition particle receptor beta-subunit	93.04
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	93.02
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	93.02
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.0
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.98
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	92.92
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.92
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.91
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	92.91
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	92.87
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.8
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	92.79
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	92.77
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.74
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.72
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	92.67
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.5
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	92.43
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.32
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.17
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.15
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	92.09
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	92.0
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	92.0
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.0
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.83
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	91.75
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.58
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.45
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.4
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	91.23
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.0
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	90.92
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	90.91
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	90.53
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.63
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	89.3
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	88.34
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	88.28
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	88.2
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	87.67
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	87.57
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	87.26
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	86.44
d1tuea_	205	Replication protein E1 helicase domain {Human papi	86.43
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	86.3
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	85.62
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	85.62
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	85.57
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	84.16
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	83.25
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	83.14
d1wxqa1	319	GTP-binding protein PH0525 {Pyrococcus horikoshii	82.57
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	81.72
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.9

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=1.7e-42  Score=258.88  Aligned_cols=223  Identities=16%  Similarity=0.184  Sum_probs=172.1

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCC---CCCCCCCEEEEEECCCCCHHHHHHHHHHHHH---CCCC-------CCCC
Q ss_conf             9993999999279982999999998000---1137898299997597699999999999833---0589-------9569
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK---LTEAFEPKAWVCVSDDFDVLRISKAILDSIK---RSSC-------KLED   76 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~---~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~---~~~~-------~~~~   76 (1237)
                      +.+.++|+|+||||+||||||+++|++.   .+.+|++++|+++++..+...+...+...+.   ....       ....
T Consensus        41 ~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (277)
T d2a5yb3          41 DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTS  120 (277)
T ss_dssp             TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHCCHHHCCCCCCHHHHH
T ss_conf             87840899977997888999999998556554012764899993687777789999999998722022027863212336


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHHHHHHHCCC-CEEECCCCCHHHHHH
Q ss_conf             7899999999966972999996887777626998312256899995999990745678752688-707478999243399
Q 000887           77 LNSVQLELKETVFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGSG-KNYELKLLSDDDCWS  155 (1237)
Q Consensus        77 ~~~~~~~l~~~l~~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~~~~~~~~~-~~~~l~~l~~~ea~~  155 (1237)
                      .......+.+.+.++++|+|+||||+.  +.+..+.      ..+++||||||+..++..+... +.+++++|+.+||++
T Consensus       121 ~~~~~~~~~~~L~~kr~LlVLDDv~~~--~~~~~~~------~~~srilvTTR~~~v~~~~~~~~~~~~l~~L~~~ea~~  192 (277)
T d2a5yb3         121 VVLKRMICNALIDRPNTLFVFDDVVQE--ETIRWAQ------ELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYD  192 (277)
T ss_dssp             HHHHHHHHHHHTTSTTEEEEEEEECCH--HHHHHHH------HTTCEEEEEESBGGGGGGCCSCEEEEECCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCEEEECCHHHHH--HHHHHHC------CCCCEEEEEEEHHHHHHHCCCCCCEEECCCCCHHHHHH
T ss_conf             999999999984468816752506677--6655520------45755999964489998637887168778899799999


Q ss_pred             HHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf             99997617899999987599999999980299137999976750589978999998201224589997458999976039
Q 000887          156 VFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQGVDEWRAILDSKIWNLQDKTEIPSVLKLSYHHL  235 (1237)
Q Consensus       156 l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~i~~~l~~s~~~L  235 (1237)
                      ||..+++...   ..+..++.+++|+++|||+||||+++|+.++.+ ....|.+........  ...++..++.+||+.|
T Consensus       193 Lf~~~~~~~~---~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k-~~~~~~~~~~~L~~~--~~~~v~~il~~sY~~L  266 (277)
T d2a5yb3         193 FLEAYGMPMP---VGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK-TFEKMAQLNNKLESR--GLVGVECITPYSYKSL  266 (277)
T ss_dssp             HHHHTSCCCC-----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS-SHHHHHHHHHHHHHH--CSSTTCCCSSSSSSSH
T ss_pred             HHHHHHCCCC---CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC-CHHHHHHHHHHHHCC--CHHHHHHHHHHHHHCC
T ss_conf             9999847766---742567999999999589989999999986559-899999999997348--6788999999988512


Q ss_pred             HHHHHHHHHHH
Q ss_conf             17788898563
Q 000887          236 PSHLKRCFAYC  246 (1237)
Q Consensus       236 ~~~~~~~~~~l  246 (1237)
                      |.+.|.||.++
T Consensus       267 ~~~lk~c~~~l  277 (277)
T d2a5yb3         267 AMALQRCVEVL  277 (277)
T ss_dssp             HHHHHHHHHTS
T ss_pred             CHHHHHHHHHC
T ss_conf             69999999739

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.93  E-value=1.1e-23  Score=149.74  Aligned_cols=85  Identities=18%  Similarity=0.322  Sum_probs=64.4

Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEEC
Q ss_conf             99974199825633434453422778778698137875013111106677649973763268558831105455658821
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI  477 (1237)
Q Consensus       398 ~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l  477 (1237)
                      .+.+|++|+++++.|+.+. ++..+++|++|++++|.|+.+|. ++++++|++|++++| .+..+++ ++.+++|+.|++
T Consensus        42 ~l~~l~~L~l~~~~I~~l~-gl~~L~nL~~L~Ls~N~l~~l~~-l~~L~~L~~L~L~~n-~i~~i~~-l~~l~~L~~L~~  117 (384)
T d2omza2          42 DLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNN-QIADITP-LANLTNLTGLTL  117 (384)
T ss_dssp             HHTTCCEEECCSSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEEC
T ss_pred             HHCCCCEEECCCCCCCCCC-CCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCC
T ss_conf             9578789989998987762-42458999989681881798863-347711010301343-3322221-112334333443


Q ss_pred             CCCCCCCCCC
Q ss_conf             6987544584
Q 000887          478 EGASALRELP  487 (1237)
Q Consensus       478 ~~~~~l~~ip  487 (1237)
                      .++ ....++
T Consensus       118 ~~~-~~~~~~  126 (384)
T d2omza2         118 FNN-QITDID  126 (384)
T ss_dssp             CSS-CCCCCG
T ss_pred             CCC-CCCCCC
T ss_conf             322-222222

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.92  E-value=3e-22  Score=141.49  Aligned_cols=90  Identities=23%  Similarity=0.270  Sum_probs=68.2

Q ss_pred             ECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCCCCCCCC
Q ss_conf             82563343445342277877869813787501311110667764997376326855883110545565882169875445
Q 000887          406 SLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALRE  485 (1237)
Q Consensus       406 ~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~~  485 (1237)
                      .+..+.++.... ...+.+|+.|+++++.|+++ +.+..+++|++|++++| .+..+|+ ++.+++|++|++++| .+..
T Consensus        28 ~l~~~~~~~~~~-~~~l~~l~~L~l~~~~I~~l-~gl~~L~nL~~L~Ls~N-~l~~l~~-l~~L~~L~~L~L~~n-~i~~  102 (384)
T d2omza2          28 VLGKTNVTDTVS-QTDLDQVTTLQADRLGIKSI-DGVEYLNNLTQINFSNN-QLTDITP-LKNLTKLVDILMNNN-QIAD  102 (384)
T ss_dssp             HTTCSSTTSEEC-HHHHTTCCEEECCSSCCCCC-TTGGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCC
T ss_pred             HHCCCCCCCCCC-HHHHCCCCEEECCCCCCCCC-CCCCCCCCCCEEECCCC-CCCCCCC-CCCCCCCCCCCCCCC-CCCC
T ss_conf             867777788639-88957878998999898776-24245899998968188-1798863-347711010301343-3322


Q ss_pred             CCCCCCCCCCCCCCCE
Q ss_conf             8424324533233450
Q 000887          486 LPLGMKELKCLRTLTN  501 (1237)
Q Consensus       486 ip~~~~~L~~L~~L~~  501 (1237)
                      ++. ++.+++|+.|..
T Consensus       103 i~~-l~~l~~L~~L~~  117 (384)
T d2omza2         103 ITP-LANLTNLTGLTL  117 (384)
T ss_dssp             CGG-GTTCTTCCEEEC
T ss_pred             CCC-CCCCCCCCCCCC
T ss_conf             221-112334333443

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4e-21  Score=135.01  Aligned_cols=100  Identities=19%  Similarity=0.326  Sum_probs=40.7

Q ss_pred             CCCCCCCCEEEECCCCCCEECCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC-C
Q ss_conf             478787735998479993112688974336888570654378884334934678889987165168999655888898-8
Q 000887         1106 FHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF-P 1184 (1237)
Q Consensus      1106 ~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~-~ 1184 (1237)
                      +..+.+++.|.++++ .+..++.  ..+..+.+|+.+++.+ +.++.++...|..+++|++|+++++ .++++|...+ .
T Consensus       120 ~~~l~~l~~L~l~~n-~l~~l~~--~~~~~l~~l~~l~l~~-N~l~~~~~~~~~~l~~L~~L~Ls~N-~L~~lp~~~~~~  194 (266)
T d1p9ag_         120 LRGLGELQELYLKGN-ELKTLPP--GLLTPTPKLEKLSLAN-NNLTELPAGLLNGLENLDTLLLQEN-SLYTIPKGFFGS  194 (266)
T ss_dssp             TTTCTTCCEEECTTS-CCCCCCT--TTTTTCTTCCEEECTT-SCCSCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTT
T ss_pred             CCCCCCCCCCCCCCC-CCCEECC--CCCCCCCCCHHCCCCC-CCCCCCCCCCCCCCCCCCEEECCCC-CCCCCCHHHCCC
T ss_conf             222211112212434-2102212--3332211100000001-5652237200134212423430139-785568667778


Q ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             76657663389882102344795456
Q 000887         1185 SSLLSLEIQRCPLLEKCKMRKGQEWP 1210 (1237)
Q Consensus      1185 ~~L~~L~i~~~p~l~~~~~~~~~~~~ 1210 (1237)
                      ++|+.|+++++|..|.|...|+..|.
T Consensus       195 ~~L~~L~L~~Np~~CdC~~~~l~~wl  220 (266)
T d1p9ag_         195 HLLPFAFLHGNPWLCNCEILYFRRWL  220 (266)
T ss_dssp             CCCSEEECCSCCBCCSGGGHHHHHHH
T ss_pred             CCCCEEEECCCCCCCCCCHHHHHHHH
T ss_conf             88999983699987886437999999

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.87  E-value=1.2e-21  Score=137.94  Aligned_cols=104  Identities=23%  Similarity=0.304  Sum_probs=65.2

Q ss_pred             HHHCCCCCCCCEEECCC-CCCC-CCCCCCCCCCCCCEEECCCCCCCCC-CHHHCCCCCCCEEECCCCCCCCCCCHHHCCC
Q ss_conf             21058999741998256-3343-4453422778778698137875013-1111066776499737632685588311054
Q 000887          393 SDLLPQCKKLRVLSLGS-YCIT-EVPISIGCLKQLRYLNFSRSEIQCL-PDAICSLFNLEILILRNCWCLLKLPSRIGNL  469 (1237)
Q Consensus       393 ~~~~~~l~~Lr~L~L~~-~~i~-~lp~~~~~l~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L  469 (1237)
                      |..+..+++|++|+|++ |.+. .+|..|+++++|++|++++|.+..+ |..+..+.+|+++++++|.....+|..++.+
T Consensus        69 p~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l  148 (313)
T d1ogqa_          69 PSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSL  148 (313)
T ss_dssp             CGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGC
T ss_pred             CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHCCC
T ss_conf             84784675335202026543330024311454200110203564344332222201110011112245555685122067


Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             556588216987544584243245332
Q 000887          470 VNLHYLNIEGASALRELPLGMKELKCL  496 (1237)
Q Consensus       470 ~~L~~L~l~~~~~l~~ip~~~~~L~~L  496 (1237)
                      ++|+++++++|.....+|..+..+..+
T Consensus       149 ~~L~~l~l~~n~l~~~ip~~~~~l~~l  175 (313)
T d1ogqa_         149 PNLVGITFDGNRISGAIPDSYGSFSKL  175 (313)
T ss_dssp             TTCCEEECCSSCCEEECCGGGGCCCTT
T ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             400000023553356203121443112

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.2e-20  Score=132.29  Aligned_cols=217  Identities=19%  Similarity=0.339  Sum_probs=147.0

Q ss_pred             CCCCCEEEECCCCCCCCCC-CCCCCCCCCCEEEECCCCCCCCC-CCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCHHH
Q ss_conf             8851289891877742321-21377655547850356563444-423457777761542367785448988899741134
Q 000887          967 PVEVEELTIYGCSNLESIA-ERFHDDACLRSIWISSCENLKSL-PKGLSNLSHLHEIRIVRCHNLVSLPEDALPSNVVDV 1044 (1237)
Q Consensus       967 ~~~L~~L~l~~c~~l~~~~-~~~~~~~~L~~L~L~~~~~l~~l-~~~~~~l~~L~~L~l~~c~~l~~l~~~~~~~~l~~l 1044 (1237)
                      ++++++|++++|. ++.++ ..+.++++|++|+++++ .+..+ +..+..++.++.+.+..+..+..++....       
T Consensus        31 p~~~~~L~Ls~N~-i~~i~~~~f~~l~~L~~L~ls~n-~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~-------  101 (284)
T d1ozna_          31 PAASQRIFLHGNR-ISHVPAASFRACRNLTILWLHSN-VLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATF-------  101 (284)
T ss_dssp             CTTCSEEECTTSC-CCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTT-------
T ss_pred             CCCCCEEECCCCC-CCCCCHHHHHCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH-------
T ss_conf             9998889774881-79879778641421300001344-54332111212222222222221022354462010-------


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCC--CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCC
Q ss_conf             3201200002588888775458852589995202788--97787673573188786664222347878773599847999
Q 000887         1045 LIEDCDKLKALIPTGTLSSLRELALSECPGIVVFPEE--GLSTNLTDLEISGDNMYKPLVKWGFHKLTSLRKLYIDGCSD 1122 (1237)
Q Consensus      1045 ~l~~~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~~~~--~~~~~L~~L~l~~~~~l~~~~~~~~~~l~~L~~L~l~~c~~ 1122 (1237)
                                    ..+++|++|++++|. +..++..  ...++|+.++++++.. +.++...+..+++|++|++++| .
T Consensus       102 --------------~~l~~L~~L~l~~n~-~~~~~~~~~~~~~~L~~l~l~~N~l-~~i~~~~f~~~~~L~~L~l~~N-~  164 (284)
T d1ozna_         102 --------------HGLGRLHTLHLDRCG-LQELGPGLFRGLAALQYLYLQDNAL-QALPDDTFRDLGNLTHLFLHGN-R  164 (284)
T ss_dssp             --------------TTCTTCCEEECTTSC-CCCCCTTTTTTCTTCCEEECCSSCC-CCCCTTTTTTCTTCCEEECCSS-C
T ss_pred             --------------CCCCCCCEEECCCCC-CCCCCCCCCCHHCCCCHHHHCCCCC-CCCCHHHHCCCCCHHHCCCCCC-C
T ss_conf             --------------101027787568854-4320135332000121102001431-4458057404340502231417-6


Q ss_pred             CEECCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC--CCCCCEEEECCCCCCCC
Q ss_conf             3112688974336888570654378884334934678889987165168999655888898--87665766338988210
Q 000887         1123 AVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF--PSSLLSLEIQRCPLLEK 1200 (1237)
Q Consensus      1123 l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~--~~~L~~L~i~~~p~l~~ 1200 (1237)
                      +..++.  .++..+++|+.+.+.+ +.+..+.+..|.++++|++|+++++ .+..++...+  .++|+.++++++|..|.
T Consensus       165 l~~l~~--~~f~~l~~L~~l~l~~-N~l~~i~~~~f~~l~~L~~L~l~~N-~i~~~~~~~~~~~~~L~~L~l~~N~l~C~  240 (284)
T d1ozna_         165 ISSVPE--RAFRGLHSLDRLLLHQ-NRVAHVHPHAFRDLGRLMTLYLFAN-NLSALPTEALAPLRALQYLRLNDNPWVCD  240 (284)
T ss_dssp             CCEECT--TTTTTCTTCCEEECCS-SCCCEECTTTTTTCTTCCEEECCSS-CCSCCCHHHHTTCTTCCEEECCSSCEECS
T ss_pred             CCCCCH--HHHCCCCCCCHHHHHH-CCCCCCCHHHHHHHHHCCCCCCCCC-CCCCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf             566256--6654656341314211-4346628167665320002333335-22100000235546568898119988787


Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             2344795456433
Q 000887         1201 CKMRKGQEWPKIA 1213 (1237)
Q Consensus      1201 ~~~~~~~~~~~~~ 1213 (1237)
                      |...|+..|.+-.
T Consensus       241 C~~~~l~~~l~~~  253 (284)
T d1ozna_         241 CRARPLWAWLQKF  253 (284)
T ss_dssp             GGGHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHC
T ss_conf             5646999999867

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=99.86  E-value=4.1e-18  Score=117.53  Aligned_cols=89  Identities=22%  Similarity=0.313  Sum_probs=56.2

Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCCC
Q ss_conf             74199825633434453422778778698137875013111106677649973763268558831105455658821698
Q 000887          401 KLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGA  480 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~  480 (1237)
                      ++++|||+++.++.+|+.   +++|++|++++|.|+++|..   +.+|+.|++++| .+..++. +  ..+|++|++++|
T Consensus        39 ~l~~LdLs~~~L~~lp~~---~~~L~~L~Ls~N~l~~lp~~---~~~L~~L~l~~n-~l~~l~~-l--p~~L~~L~L~~n  108 (353)
T d1jl5a_          39 QAHELELNNLGLSSLPEL---PPHLESLVASCNSLTELPEL---PQSLKSLLVDNN-NLKALSD-L--PPLLEYLGVSNN  108 (353)
T ss_dssp             TCSEEECTTSCCSCCCSC---CTTCSEEECCSSCCSSCCCC---CTTCCEEECCSS-CCSCCCS-C--CTTCCEEECCSS
T ss_pred             CCCEEEECCCCCCCCCCC---CCCCCEEECCCCCCCCCCCC---HHHHHHHHHHHC-CCCHHHH-H--CCCCCCCCCCCC
T ss_conf             998999379998878898---78988898999979633620---332033266551-4320321-0--221111133455


Q ss_pred             CCCCCCCCCCCCCCCCCCCCE
Q ss_conf             754458424324533233450
Q 000887          481 SALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       481 ~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                       .+..+|. ++.+++|++|.+
T Consensus       109 -~l~~lp~-~~~l~~L~~L~l  127 (353)
T d1jl5a_         109 -QLEKLPE-LQNSSFLKIIDV  127 (353)
T ss_dssp             -CCSSCCC-CTTCTTCCEEEC
T ss_pred             -CCCCCCC-HHHHCCCEEECC
T ss_conf             -4322210-011013123113

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.86  E-value=5.8e-20  Score=128.26  Aligned_cols=85  Identities=29%  Similarity=0.421  Sum_probs=55.2

Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCCCCCCCC-CHHHCCCCCCCEEECC
Q ss_conf             7419982563343445342277877869813787501311-1106677649973763268558-8311054556588216
Q 000887          401 KLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKL-PSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~l~  478 (1237)
                      ..+.++.++..++++|..+.  +++++|++++|.|+.+|+ +|.++++|++|++++| .+..+ |..|..+++|++|+++
T Consensus        11 ~~~~~~C~~~~L~~lP~~l~--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n-~~~~i~~~~f~~l~~L~~L~l~   87 (305)
T d1xkua_          11 HLRVVQCSDLGLEKVPKDLP--PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINN-KISKISPGAFAPLVKLERLYLS   87 (305)
T ss_dssp             ETTEEECTTSCCCSCCCSCC--TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECC
T ss_pred             CCCEEEECCCCCCCCCCCCC--CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCC-CCCCCCHHHHHCCCCCCEECCC
T ss_conf             59999855999885198889--99798978499189869657604656523112344-3445235665279855783156


Q ss_pred             CCCCCCCCCCC
Q ss_conf             98754458424
Q 000887          479 GASALRELPLG  489 (1237)
Q Consensus       479 ~~~~l~~ip~~  489 (1237)
                      +| .++.+|..
T Consensus        88 ~n-~l~~l~~~   97 (305)
T d1xkua_          88 KN-QLKELPEK   97 (305)
T ss_dssp             SS-CCSBCCSS
T ss_pred             CC-CCCCCCCC
T ss_conf             87-56767640

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.85  E-value=3.3e-19  Score=123.89  Aligned_cols=93  Identities=27%  Similarity=0.327  Sum_probs=70.2

Q ss_pred             CHHHHHCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCEEECCCCCCCCC-CHHHCCCCCCCEEECCCCCCCCCCCHHHC
Q ss_conf             0132105899974199825633434453-422778778698137875013-11110667764997376326855883110
Q 000887          390 MVLSDLLPQCKKLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCL-PDAICSLFNLEILILRNCWCLLKLPSRIG  467 (1237)
Q Consensus       390 ~~~~~~~~~l~~Lr~L~L~~~~i~~lp~-~~~~l~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~L~~~~~l~~lp~~i~  467 (1237)
                      ++|+.+.   +.+++|+|++|.|+.+|+ .|.++++|++|++++|.+..+ |..|.++++|++|++++| .+..+|..+ 
T Consensus        24 ~lP~~l~---~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n-~l~~l~~~~-   98 (305)
T d1xkua_          24 KVPKDLP---PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKN-QLKELPEKM-   98 (305)
T ss_dssp             SCCCSCC---TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSS-CCSBCCSSC-
T ss_pred             CCCCCCC---CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCEECCCCC-CCCCCCCCH-
T ss_conf             5198889---99798978499189869657604656523112344344523566527985578315687-567676400-


Q ss_pred             CCCCCCEEECCCCCCCCCCCCC
Q ss_conf             5455658821698754458424
Q 000887          468 NLVNLHYLNIEGASALRELPLG  489 (1237)
Q Consensus       468 ~L~~L~~L~l~~~~~l~~ip~~  489 (1237)
                       ...|+.|++.++ .+..++..
T Consensus        99 -~~~l~~L~~~~n-~l~~l~~~  118 (305)
T d1xkua_          99 -PKTLQELRVHEN-EITKVRKS  118 (305)
T ss_dssp             -CTTCCEEECCSS-CCCBBCHH
T ss_pred             -HHHHHHHHCCCC-CHHHHHHH
T ss_conf             -111323210246-10234444

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.83  E-value=3.8e-20  Score=129.31  Aligned_cols=102  Identities=21%  Similarity=0.284  Sum_probs=86.2

Q ss_pred             CCCCEEECCCCCCC---CCCCCCCCCCCCCEEECCC-CCCC-CCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCE
Q ss_conf             97419982563343---4453422778778698137-8750-13111106677649973763268558831105455658
Q 000887          400 KKLRVLSLGSYCIT---EVPISIGCLKQLRYLNFSR-SEIQ-CLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHY  474 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~---~lp~~~~~l~~L~~L~L~~-~~i~-~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~  474 (1237)
                      .+++.|+|+++.+.   .+|.+++++++|++|+|++ |.+. .+|.+|++|++|++|++++|......|..+..+.+|++
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~  129 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             EEEEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHHCC
T ss_conf             79889989899888888798478467533520202654333002431145420011020356434433222220111001


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             821698754458424324533233450
Q 000887          475 LNIEGASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       475 L~l~~~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      +++..|.....+|..++.+++++.+.+
T Consensus       130 l~l~~N~~~~~~p~~l~~l~~L~~l~l  156 (313)
T d1ogqa_         130 LDFSYNALSGTLPPSISSLPNLVGITF  156 (313)
T ss_dssp             EECCSSEEESCCCGGGGGCTTCCEEEC
T ss_pred             CCCCCCCCCCCCCHHHCCCCCCCEEEC
T ss_conf             111224555568512206740000002

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=3.1e-19  Score=124.03  Aligned_cols=97  Identities=23%  Similarity=0.222  Sum_probs=49.0

Q ss_pred             CCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECC
Q ss_conf             97419982563343445342277877869813787501311-11066776499737632685588311054556588216
Q 000887          400 KKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      ..+...+.++++++.+|..+.  +++++|+|++|.|..+|. .|.++++|++|++++| .+..+|. ++.+++|++|+++
T Consensus        10 ~~~~~v~C~~~~L~~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N-~l~~l~~-~~~l~~L~~L~Ls   85 (266)
T d1p9ag_          10 ASHLEVNCDKRNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRA-ELTKLQV-DGTLPVLGTLDLS   85 (266)
T ss_dssp             TTCCEEECTTSCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTS-CCCEEEC-CSCCTTCCEEECC
T ss_pred             CCCEEEECCCCCCCEECCCCC--CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCCC
T ss_conf             898699806999886196757--68898988499289859778634565522135665-4444311-1112232111112


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             98754458424324533233450
Q 000887          479 GASALRELPLGMKELKCLRTLTN  501 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L~~L~~  501 (1237)
                      +| .+..+|..+..+++|+.|.+
T Consensus        86 ~N-~l~~~~~~~~~l~~L~~L~l  107 (266)
T d1p9ag_          86 HN-QLQSLPLLGQTLPALTVLDV  107 (266)
T ss_dssp             SS-CCSSCCCCTTTCTTCCEEEC
T ss_pred             CC-CCCCCCCCCCCCCCCCCCCC
T ss_conf             22-22111112122222222222

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=99.81  E-value=7.9e-17  Score=110.09  Aligned_cols=89  Identities=26%  Similarity=0.303  Sum_probs=66.6

Q ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECC
Q ss_conf             99741998256334344534227787786981378750131111066776499737632685588311054556588216
Q 000887          399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       399 l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      .++|++|+|++|.|+++|..+   .+|+.|++++|.+..++.-   ...|++|++++| .+..+|. ++.+++|++|++.
T Consensus        57 ~~~L~~L~Ls~N~l~~lp~~~---~~L~~L~l~~n~l~~l~~l---p~~L~~L~L~~n-~l~~lp~-~~~l~~L~~L~l~  128 (353)
T d1jl5a_          57 PPHLESLVASCNSLTELPELP---QSLKSLLVDNNNLKALSDL---PPLLEYLGVSNN-QLEKLPE-LQNSSFLKIIDVD  128 (353)
T ss_dssp             CTTCSEEECCSSCCSSCCCCC---TTCCEEECCSSCCSCCCSC---CTTCCEEECCSS-CCSSCCC-CTTCTTCCEEECC
T ss_pred             CCCCCEEECCCCCCCCCCCCH---HHHHHHHHHHCCCCHHHHH---CCCCCCCCCCCC-CCCCCCC-HHHHCCCEEECCC
T ss_conf             789888989999796336203---3203326655143203210---221111133455-4322210-0110131231135


Q ss_pred             CCCCCCCCCCCCCCCCCC
Q ss_conf             987544584243245332
Q 000887          479 GASALRELPLGMKELKCL  496 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L  496 (1237)
                      ++ .+...|.....+..+
T Consensus       129 ~~-~~~~~~~~~~~l~~l  145 (353)
T d1jl5a_         129 NN-SLKKLPDLPPSLEFI  145 (353)
T ss_dssp             SS-CCSCCCCCCTTCCEE
T ss_pred             CC-CCCCCCCCCCCCCCH
T ss_conf             65-100132233332100

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.3e-16  Score=107.42  Aligned_cols=99  Identities=26%  Similarity=0.312  Sum_probs=55.3

Q ss_pred             CCCCEEECCCCCCCCCCC-CCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCCCCCCCC-CHHHCCCCCCCEEE
Q ss_conf             974199825633434453-42277877869813787501311-1106677649973763268558-83110545565882
Q 000887          400 KKLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKL-PSRIGNLVNLHYLN  476 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~lp~-~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~~~l~~l-p~~i~~L~~L~~L~  476 (1237)
                      +.+++|+|++|.|+.+|. .|..+++|++|+++++.+..++. .+..+..++.++...+..+..+ |..+..+++|++|+
T Consensus        32 ~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L~  111 (284)
T d1ozna_          32 AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLH  111 (284)
T ss_dssp             TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEE
T ss_pred             CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEE
T ss_conf             99888977488179879778641421300001344543321112122222222222210223544620101010277875


Q ss_pred             CCCCCCCCCCCCC-CCCCCCCCCC
Q ss_conf             1698754458424-3245332334
Q 000887          477 IEGASALRELPLG-MKELKCLRTL  499 (1237)
Q Consensus       477 l~~~~~l~~ip~~-~~~L~~L~~L  499 (1237)
                      +++| .+..++.. +....+|+.+
T Consensus       112 l~~n-~~~~~~~~~~~~~~~L~~l  134 (284)
T d1ozna_         112 LDRC-GLQELGPGLFRGLAALQYL  134 (284)
T ss_dssp             CTTS-CCCCCCTTTTTTCTTCCEE
T ss_pred             CCCC-CCCCCCCCCCCHHCCCCHH
T ss_conf             6885-4432013533200012110

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=8.9e-16  Score=104.00  Aligned_cols=24  Identities=17%  Similarity=0.122  Sum_probs=8.6

Q ss_pred             CCCCCCCCCCCCCCCCCCEEEECC
Q ss_conf             884334934678889987165168
Q 000887         1148 PKLKRLSSKGFQYLVSLEHLSVFS 1171 (1237)
Q Consensus      1148 ~~l~~l~~~~~~~l~~L~~L~l~~ 1171 (1237)
                      +.++.++...|+++++|++|++++
T Consensus       187 n~l~~l~~~~f~~l~~L~~L~Ls~  210 (242)
T d1xwdc1         187 NNLEELPNDVFHGASGPVILDISR  210 (242)
T ss_dssp             TTCCCCCTTTTTTSCCCSEEECTT
T ss_pred             CCCCCCCHHHHCCCCCCCEEECCC
T ss_conf             324642478866899999898979

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.69  E-value=5.7e-16  Score=105.12  Aligned_cols=80  Identities=19%  Similarity=0.230  Sum_probs=54.6

Q ss_pred             CCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEE
Q ss_conf             89997419982563343445342277877869813787501311110667764997376326855883110545565882
Q 000887          397 PQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLN  476 (1237)
Q Consensus       397 ~~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~  476 (1237)
                      ..+..|+.|++.+|+|+.++ .+..+++|++|++++|.+..+++ +.++++|+++++++| .+..++. +.++++|+.++
T Consensus        38 ~~l~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~ls~n~i~~~~~-l~~l~~l~~l~~~~n-~~~~i~~-l~~l~~L~~l~  113 (227)
T d1h6ua2          38 ADLDGITTLSAFGTGVTTIE-GVQYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGN-PLKNVSA-IAGLQSIKTLD  113 (227)
T ss_dssp             HHHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSC-CCSCCGG-GTTCTTCCEEE
T ss_pred             HHCCCCCEEECCCCCCCCCH-HHHCCCCCCEEECCCCEEECCCC-CCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCC
T ss_conf             78488689977799997664-57448888376357853202543-112334320121112-2222222-22222221221


Q ss_pred             CCCC
Q ss_conf             1698
Q 000887          477 IEGA  480 (1237)
Q Consensus       477 l~~~  480 (1237)
                      ++++
T Consensus       114 l~~~  117 (227)
T d1h6ua2         114 LTST  117 (227)
T ss_dssp             CTTS
T ss_pred             CCCC
T ss_conf             2224

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.4e-18  Score=120.28  Aligned_cols=12  Identities=33%  Similarity=0.683  Sum_probs=4.0

Q ss_pred             CCCCCEEEECCC
Q ss_conf             787735998479
Q 000887         1109 LTSLRKLYIDGC 1120 (1237)
Q Consensus      1109 l~~L~~L~l~~c 1120 (1237)
                      +++|++|++++|
T Consensus       199 ~~~L~~L~L~~C  210 (284)
T d2astb2         199 LNYLQHLSLSRC  210 (284)
T ss_dssp             CTTCCEEECTTC
T ss_pred             CCCCCEEECCCC
T ss_conf             576877989999

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.68  E-value=5.6e-16  Score=105.17  Aligned_cols=97  Identities=21%  Similarity=0.274  Sum_probs=69.9

Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEEC
Q ss_conf             99974199825633434453422778778698137875013111106677649973763268558831105455658821
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI  477 (1237)
Q Consensus       398 ~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l  477 (1237)
                      .+..|+.|+++++.++.++. +..+++|+.|++++|.++.++. ++.+++|++|++++| .+..+|. +..+++|+.|++
T Consensus        44 ~L~~L~~L~l~~~~i~~l~~-l~~l~~L~~L~L~~n~i~~l~~-~~~l~~L~~L~l~~n-~i~~l~~-l~~l~~L~~L~l  119 (210)
T d1h6ta2          44 ELNSIDQIIANNSDIKSVQG-IQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDEN-KVKDLSS-LKDLKKLKSLSL  119 (210)
T ss_dssp             HHHTCCEEECTTSCCCCCTT-GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCGGG-GTTCTTCCEEEC
T ss_pred             HHCCCCEEECCCCCCCCCHH-HHHCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCC
T ss_conf             95484589782798887444-7648998987698960258601-135862120143333-3212221-212221112234


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             69875445842432453323345
Q 000887          478 EGASALRELPLGMKELKCLRTLT  500 (1237)
Q Consensus       478 ~~~~~l~~ip~~~~~L~~L~~L~  500 (1237)
                      .+| ....++ .+..+++++.+.
T Consensus       120 ~~~-~~~~~~-~l~~l~~l~~l~  140 (210)
T d1h6ta2         120 EHN-GISDIN-GLVHLPQLESLY  140 (210)
T ss_dssp             TTS-CCCCCG-GGGGCTTCCEEE
T ss_pred             CCC-CCCCCC-CCCCCCCCCCCC
T ss_conf             565-322112-201111122211

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.66  E-value=1.1e-15  Score=103.57  Aligned_cols=97  Identities=20%  Similarity=0.319  Sum_probs=64.5

Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEEC
Q ss_conf             99974199825633434453422778778698137875013111106677649973763268558831105455658821
Q 000887          398 QCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNI  477 (1237)
Q Consensus       398 ~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l  477 (1237)
                      .+..+++|+++++.++.++. +..+++|++|++++|.++.++. ++++++|++|++++| .+..+|. ++.+.+|++|++
T Consensus        38 ~l~~l~~L~l~~~~i~~l~~-l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n-~~~~~~~-l~~l~~L~~L~l  113 (199)
T d2omxa2          38 DLDQVTTLQADRLGIKSIDG-VEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNN-QIADITP-LANLTNLTGLTL  113 (199)
T ss_dssp             HHTTCCEEECTTSCCCCCTT-GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCCGG-GTTCTTCSEEEC
T ss_pred             HHCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCC
T ss_conf             94687899899999977520-2137886757545655667640-167752231111222-2222211-111223222111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             69875445842432453323345
Q 000887          478 EGASALRELPLGMKELKCLRTLT  500 (1237)
Q Consensus       478 ~~~~~l~~ip~~~~~L~~L~~L~  500 (1237)
                      +++ ....++ .+..+++|+.|.
T Consensus       114 ~~~-~~~~~~-~~~~l~~L~~L~  134 (199)
T d2omxa2         114 FNN-QITDID-PLKNLTNLNRLE  134 (199)
T ss_dssp             CSS-CCCCCG-GGTTCTTCSEEE
T ss_pred             CCC-CCCCCC-CCCHHHHHHHHH
T ss_conf             222-222321-000122367764

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=3.3e-15  Score=100.73  Aligned_cols=85  Identities=18%  Similarity=0.240  Sum_probs=41.5

Q ss_pred             CCCEEECCCCCCCCCCC-CCCCCCCCCEEECCCCCCCC-CCH-HHCCCCCCCEEECCCCCCCCCCC-HHHCCCCCCCEEE
Q ss_conf             74199825633434453-42277877869813787501-311-11066776499737632685588-3110545565882
Q 000887          401 KLRVLSLGSYCITEVPI-SIGCLKQLRYLNFSRSEIQC-LPD-AICSLFNLEILILRNCWCLLKLP-SRIGNLVNLHYLN  476 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~lp~-~~~~l~~L~~L~L~~~~i~~-lp~-~~~~L~~L~~L~L~~~~~l~~lp-~~i~~L~~L~~L~  476 (1237)
                      ++++|++++|.|+.+|. .|.++++|++|++++|.+.. ++. .|.++++++.+.+..+..+..++ ..+.++.+|++++
T Consensus        30 ~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~~l~  109 (242)
T d1xwdc1          30 NAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLL  109 (242)
T ss_dssp             CCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEECCTTCCEEE
T ss_pred             CCCEEECCCCCCCCCCHHHHHCCCHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             88999876991896496686146432321102211242010011222222222111112343222222122222222223


Q ss_pred             CCCCCCCCCC
Q ss_conf             1698754458
Q 000887          477 IEGASALREL  486 (1237)
Q Consensus       477 l~~~~~l~~i  486 (1237)
                      +.++ .+...
T Consensus       110 l~~~-~l~~~  118 (242)
T d1xwdc1         110 ISNT-GIKHL  118 (242)
T ss_dssp             EESC-CCCSC
T ss_pred             CCHH-HHCCC
T ss_conf             4211-11255

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.63  E-value=4.9e-15  Score=99.71  Aligned_cols=89  Identities=20%  Similarity=0.320  Sum_probs=47.8

Q ss_pred             EECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCCCCCCC
Q ss_conf             98256334344534227787786981378750131111066776499737632685588311054556588216987544
Q 000887          405 LSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALR  484 (1237)
Q Consensus       405 L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~  484 (1237)
                      ++++.+.++.+. .+..+.+|+.|++.+|.|++++ .+..+++|++|++++| .+..+++ +.++.+|+++++.+| .++
T Consensus        24 ~~l~~~~~~d~~-~~~~l~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~ls~n-~i~~~~~-l~~l~~l~~l~~~~n-~~~   98 (227)
T d1h6ua2          24 IAAGKSNVTDTV-TQADLDGITTLSAFGTGVTTIE-GVQYLNNLIGLELKDN-QITDLAP-LKNLTKITELELSGN-PLK   98 (227)
T ss_dssp             HHTTCSSTTSEE-CHHHHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSS-CCCCCGG-GTTCCSCCEEECCSC-CCS
T ss_pred             HHHCCCCCCCCC-CHHHCCCCCEEECCCCCCCCCH-HHHCCCCCCEEECCCC-EEECCCC-CCCCCCCCCCCCCCC-CCC
T ss_conf             984888767757-9878488689977799997664-5744888837635785-3202543-112334320121112-222


Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             584243245332334
Q 000887          485 ELPLGMKELKCLRTL  499 (1237)
Q Consensus       485 ~ip~~~~~L~~L~~L  499 (1237)
                      .++ .+..+++|+.+
T Consensus        99 ~i~-~l~~l~~L~~l  112 (227)
T d1h6ua2          99 NVS-AIAGLQSIKTL  112 (227)
T ss_dssp             CCG-GGTTCTTCCEE
T ss_pred             CCC-CCCCCCCCCCC
T ss_conf             222-22222222122

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.58  E-value=1.6e-14  Score=96.66  Aligned_cols=88  Identities=23%  Similarity=0.273  Sum_probs=47.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf             25633434453422778778698137875013111106677649973763268558831105455658821698754458
Q 000887          407 LGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASALREL  486 (1237)
Q Consensus       407 L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~l~~i  486 (1237)
                      ++.+.++..+. ...+.++++|+++++.+.+++ .+..+++|++|++++| .+..+++ ++.+++|++|++++| .+..+
T Consensus        25 l~~~~~~~~~~-~~~l~~l~~L~l~~~~i~~l~-~l~~l~nL~~L~Ls~N-~l~~~~~-l~~l~~L~~L~l~~n-~~~~~   99 (199)
T d2omxa2          25 LGKTNVTDTVS-QTDLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNN-QLTDITP-LKNLTKLVDILMNNN-QIADI   99 (199)
T ss_dssp             TTCSSTTSEEC-HHHHTTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSS-CCCCC
T ss_pred             HCCCCCCCCCC-HHHHCCCCEEECCCCCCCCCC-CCCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCCCCC-CCCCC
T ss_conf             67787788559-879468789989999997752-0213788675754565-5667640-167752231111222-22222


Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             42432453323345
Q 000887          487 PLGMKELKCLRTLT  500 (1237)
Q Consensus       487 p~~~~~L~~L~~L~  500 (1237)
                      + .++.+++|+.|.
T Consensus       100 ~-~l~~l~~L~~L~  112 (199)
T d2omxa2         100 T-PLANLTNLTGLT  112 (199)
T ss_dssp             G-GGTTCTTCSEEE
T ss_pred             C-CCCCCCCCCCCC
T ss_conf             1-111122322211

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.56  E-value=4.4e-14  Score=94.20  Aligned_cols=78  Identities=19%  Similarity=0.264  Sum_probs=29.0

Q ss_pred             CCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECC
Q ss_conf             99741998256334344534227787786981378750131111066776499737632685588311054556588216
Q 000887          399 CKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       399 l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      +++|++|++++|.++.++. ++.+++|++|++++|.++.+| .+..+++|+.|++++| ....++. +..+.+|+.+++.
T Consensus        67 l~~L~~L~L~~n~i~~l~~-~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~~~-~~~~~~~-l~~l~~l~~l~~~  142 (210)
T d1h6ta2          67 LPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVKDLS-SLKDLKKLKSLSLEHN-GISDING-LVHLPQLESLYLG  142 (210)
T ss_dssp             CTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCGG-GGTTCTTCCEEECTTS-CCCCCGG-GGGCTTCCEEECC
T ss_pred             CCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCC-CCCCCCC-CCCCCCCCCCCCC
T ss_conf             8998987698960258601-135862120143333321222-1212221112234565-3221122-0111112221122


Q ss_pred             CC
Q ss_conf             98
Q 000887          479 GA  480 (1237)
Q Consensus       479 ~~  480 (1237)
                      ++
T Consensus       143 ~n  144 (210)
T d1h6ta2         143 NN  144 (210)
T ss_dssp             SS
T ss_pred             CC
T ss_conf             23

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.53  E-value=3.7e-14  Score=94.64  Aligned_cols=101  Identities=18%  Similarity=0.164  Sum_probs=67.9

Q ss_pred             CCCCEEECCCCCCCC-C-CCCCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCCCCCCCCCH-HHCCCCCCCEE
Q ss_conf             974199825633434-4-5342277877869813787501311-110667764997376326855883-11054556588
Q 000887          400 KKLRVLSLGSYCITE-V-PISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPS-RIGNLVNLHYL  475 (1237)
Q Consensus       400 ~~Lr~L~L~~~~i~~-l-p~~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L  475 (1237)
                      .++++|+|++|.|+. + +..|..+++|+.|++++|.+..++. .+..+++|++|++++| .+..+|+ .|.++.+|++|
T Consensus        29 ~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~N-~l~~l~~~~F~~l~~L~~L  107 (192)
T d1w8aa_          29 LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGEN-KIKEISNKMFLGLHQLKTL  107 (192)
T ss_dssp             TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSC-CCCEECSSSSTTCTTCCEE
T ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEECCC-CCCCCCHHHHHCCCCCCCC
T ss_conf             787889848987755302002578762721301363221212122211222210100355-3443497998079746552


Q ss_pred             ECCCCCCCCCCCCC-CCCCCCCCCCCEE
Q ss_conf             21698754458424-3245332334505
Q 000887          476 NIEGASALRELPLG-MKELKCLRTLTNF  502 (1237)
Q Consensus       476 ~l~~~~~l~~ip~~-~~~L~~L~~L~~~  502 (1237)
                      +|++| .+..+|.+ +..+++|++|.+.
T Consensus       108 ~L~~N-~l~~i~~~~f~~l~~L~~l~L~  134 (192)
T d1w8aa_         108 NLYDN-QISCVMPGSFEHLNSLTSLNLA  134 (192)
T ss_dssp             ECCSS-CCCEECTTSSTTCTTCCEEECT
T ss_pred             CCCCC-CCCCCCHHHHCCCCCCCCCCCC
T ss_conf             45774-5353597785687533420003

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=4.6e-14  Score=94.10  Aligned_cols=104  Identities=25%  Similarity=0.272  Sum_probs=78.4

Q ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHH-CCCCCCCE
Q ss_conf             58999741998256334344534227787786981378750131111066776499737632685588311-05455658
Q 000887          396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRI-GNLVNLHY  474 (1237)
Q Consensus       396 ~~~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i-~~L~~L~~  474 (1237)
                      |.....+|.|+|++|.|+.++..+..+.+|++|++++|.|.+++ .+..+++|++|++++| .+..+|..+ ..+++|++
T Consensus        14 ~~n~~~lr~L~L~~n~I~~i~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N-~i~~l~~~~~~~l~~L~~   91 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNN-RICRIGEGLDQALPDLTE   91 (162)
T ss_dssp             EECTTSCEEEECTTSCCCSCCCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSS-CCCEECSCHHHHCTTCCE
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCC-CCCCCCCHHHHHCCCC-CCCCCCCCCCCCCCCCCC
T ss_conf             16857484897889978865762004145998989799787647-7445761306431021-345777632233453443


Q ss_pred             EECCCCCCCCCCCC--CCCCCCCCCCCCEE
Q ss_conf             82169875445842--43245332334505
Q 000887          475 LNIEGASALRELPL--GMKELKCLRTLTNF  502 (1237)
Q Consensus       475 L~l~~~~~l~~ip~--~~~~L~~L~~L~~~  502 (1237)
                      |++++| .+..++.  .+..+++|++|.+.
T Consensus        92 L~L~~N-~i~~~~~l~~l~~l~~L~~L~l~  120 (162)
T d1a9na_          92 LILTNN-SLVELGDLDPLASLKSLTYLCIL  120 (162)
T ss_dssp             EECCSC-CCCCGGGGGGGGGCTTCCEEECC
T ss_pred             CEECCC-CCCCCCCCCCCCCCCCCCHHHCC
T ss_conf             420300-01665421100136532066407

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.45  E-value=1.8e-13  Score=90.59  Aligned_cols=95  Identities=24%  Similarity=0.262  Sum_probs=71.3

Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCCCCC
Q ss_conf             19982563343445342277877869813787501311110667764997376326855883110545565882169875
Q 000887          403 RVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEGASA  482 (1237)
Q Consensus       403 r~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~~~~  482 (1237)
                      |+|+|++|+++.++. +..+.+|++|++++|.++.+|+.++.+++|++|++++| .+..+|. ++.+++|++|++++| .
T Consensus         1 R~L~Ls~n~l~~l~~-l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N-~i~~l~~-~~~l~~L~~L~l~~N-~   76 (124)
T d1dcea3           1 RVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDN-ALENVDG-VANLPRLQELLLCNN-R   76 (124)
T ss_dssp             SEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSS-CCCCCGG-GTTCSSCCEEECCSS-C
T ss_pred             CEEECCCCCCCCCCC-CCCCCCCCEEECCCCCCCCCHHHHHHHHCCCCCCCCCC-CCCCCCC-CCCCCCCCEEECCCC-C
T ss_conf             989868998988710-10589889897978716865215655431354532432-1123574-123355576888898-6


Q ss_pred             CCCCCC--CCCCCCCCCCCCE
Q ss_conf             445842--4324533233450
Q 000887          483 LRELPL--GMKELKCLRTLTN  501 (1237)
Q Consensus       483 l~~ip~--~~~~L~~L~~L~~  501 (1237)
                      +..+|.  .+..+++|+.|++
T Consensus        77 i~~~~~~~~l~~~~~L~~L~l   97 (124)
T d1dcea3          77 LQQSAAIQPLVSCPRLVLLNL   97 (124)
T ss_dssp             CCSSSTTGGGGGCTTCCEEEC
T ss_pred             CCCCCCCHHHCCCCCCCEEEC
T ss_conf             588888256537999999989

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=3.1e-13  Score=89.24  Aligned_cols=127  Identities=20%  Similarity=0.222  Sum_probs=92.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCH-H
Q ss_conf             332445441111112354458999992013210589997419982563343445342277877869813787501311-1
Q 000887          363 LDKVVNLRTFLPIFFKQWRIYPPNISPMVLSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPD-A  441 (1237)
Q Consensus       363 ~~~~~~lr~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~-~  441 (1237)
                      +....++|.+.+.+.+         ...+ +..+..+++|++|+|++|.|..++ .|..+++|++|++++|.+..+|. .
T Consensus        14 ~~n~~~lr~L~L~~n~---------I~~i-~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~~~   82 (162)
T d1a9na_          14 YTNAVRDRELDLRGYK---------IPVI-ENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNRICRIGEGL   82 (162)
T ss_dssp             EECTTSCEEEECTTSC---------CCSC-CCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSCCCEECSCH
T ss_pred             CCCCCCCCEEECCCCC---------CCCC-CCCCCCCCCCCEEECCCCCCCCCC-CCCCCCCHHHHHCCCCCCCCCCCCC
T ss_conf             1685748489788997---------8865-762004145998989799787647-7445761306431021345777632


Q ss_pred             HCCCCCCCEEECCCCCCCCCCCH--HHCCCCCCCEEECCCCCCCCCCCC----CCCCCCCCCCCCEE
Q ss_conf             10667764997376326855883--110545565882169875445842----43245332334505
Q 000887          442 ICSLFNLEILILRNCWCLLKLPS--RIGNLVNLHYLNIEGASALRELPL----GMKELKCLRTLTNF  502 (1237)
Q Consensus       442 ~~~L~~L~~L~L~~~~~l~~lp~--~i~~L~~L~~L~l~~~~~l~~ip~----~~~~L~~L~~L~~~  502 (1237)
                      +..+++|+.|++++| .+..++.  .+..+++|++|++.+| .+...|.    .+..+++|+.|+..
T Consensus        83 ~~~l~~L~~L~L~~N-~i~~~~~l~~l~~l~~L~~L~l~~N-~i~~~~~~r~~~i~~lp~L~~LD~~  147 (162)
T d1a9na_          83 DQALPDLTELILTNN-SLVELGDLDPLASLKSLTYLCILRN-PVTNKKHYRLYVIYKVPQVRVLDFQ  147 (162)
T ss_dssp             HHHCTTCCEEECCSC-CCCCGGGGGGGGGCTTCCEEECCSS-GGGGSTTHHHHHHHHCTTCSEETTE
T ss_pred             CCCCCCCCCCEECCC-CCCCCCCCCCCCCCCCCCHHHCCCC-CCCCCCCHHHHHHHHCCCCCEECCC
T ss_conf             233453443420300-0166542110013653206640799-6345610699999878995833797

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.37  E-value=8.8e-13  Score=86.63  Aligned_cols=97  Identities=16%  Similarity=0.122  Sum_probs=66.3

Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCC-CC-HHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECCC
Q ss_conf             419982563343445342277877869813787501-31-1110667764997376326855883110545565882169
Q 000887          402 LRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQC-LP-DAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIEG  479 (1237)
Q Consensus       402 Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~-lp-~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~~  479 (1237)
                      .++++.++++++.+|..+.  .++++|+|++|.|.. ++ ..|.++++|+.|++++|......+..+..+.+|++|++++
T Consensus        10 ~~~v~Cs~~~L~~iP~~lp--~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~   87 (192)
T d1w8aa_          10 GTTVDCTGRGLKEIPRDIP--LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGE   87 (192)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS
T ss_pred             CCEEEEECCCCCCCCCCCC--CCCCEEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEECC
T ss_conf             9999970899670298989--78788984898775530200257876272130136322121212221122221010035


Q ss_pred             CCCCCCCCCC-CCCCCCCCCCCE
Q ss_conf             8754458424-324533233450
Q 000887          480 ASALRELPLG-MKELKCLRTLTN  501 (1237)
Q Consensus       480 ~~~l~~ip~~-~~~L~~L~~L~~  501 (1237)
                      | .+..+|.+ |+.+++|++|++
T Consensus        88 N-~l~~l~~~~F~~l~~L~~L~L  109 (192)
T d1w8aa_          88 N-KIKEISNKMFLGLHQLKTLNL  109 (192)
T ss_dssp             C-CCCEECSSSSTTCTTCCEEEC
T ss_pred             C-CCCCCCHHHHHCCCCCCCCCC
T ss_conf             5-344349799807974655245

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.33  E-value=2.8e-12  Score=83.77  Aligned_cols=89  Identities=22%  Similarity=0.276  Sum_probs=76.5

Q ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCC--HHHCCCCCCC
Q ss_conf             58999741998256334344534227787786981378750131111066776499737632685588--3110545565
Q 000887          396 LPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLP--SRIGNLVNLH  473 (1237)
Q Consensus       396 ~~~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp--~~i~~L~~L~  473 (1237)
                      +..++.|++|++++|.++.+|+.++.+++|++|++++|.++.+|. +..+++|+.|++++| .+..+|  ..++.+++|+
T Consensus        16 l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N~i~~l~~-~~~l~~L~~L~l~~N-~i~~~~~~~~l~~~~~L~   93 (124)
T d1dcea3          16 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDG-VANLPRLQELLLCNN-RLQQSAAIQPLVSCPRLV   93 (124)
T ss_dssp             GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSS-CCCSSSTTGGGGGCTTCC
T ss_pred             CCCCCCCCEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCEEECCCC-CCCCCCCCHHHCCCCCCC
T ss_conf             105898898979787168652156554313545324321123574-123355576888898-658888825653799999


Q ss_pred             EEECCCCCCCCCCC
Q ss_conf             88216987544584
Q 000887          474 YLNIEGASALRELP  487 (1237)
Q Consensus       474 ~L~l~~~~~l~~ip  487 (1237)
                      +|++++| .+...+
T Consensus        94 ~L~l~~N-~i~~~~  106 (124)
T d1dcea3          94 LLNLQGN-SLCQEE  106 (124)
T ss_dssp             EEECTTS-GGGGSS
T ss_pred             EEECCCC-CCCCCC
T ss_conf             9989799-688682

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.8e-12  Score=81.51  Aligned_cols=84  Identities=21%  Similarity=0.218  Sum_probs=39.9

Q ss_pred             CCCCCCCCEEECCCCC-CCCCC-CCCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCCCCCCCCCHHHCCCCCC
Q ss_conf             5899974199825633-43445-342277877869813787501311-11066776499737632685588311054556
Q 000887          396 LPQCKKLRVLSLGSYC-ITEVP-ISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNCWCLLKLPSRIGNLVNL  472 (1237)
Q Consensus       396 ~~~l~~Lr~L~L~~~~-i~~lp-~~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L  472 (1237)
                      +..+++|+.|++.+++ ++.++ ..|..+++|+.|++++|.|..+++ .|..+++|++|+|++| .+..+|..+....+|
T Consensus        27 l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N-~l~~l~~~~~~~~~l  105 (156)
T d2ifga3          27 LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFN-ALESLSWKTVQGLSL  105 (156)
T ss_dssp             SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSS-CCSCCCSTTTCSCCC
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEECCCC-CCCCCCHHHHCCCCC
T ss_conf             2576565743168986644369212256666672162021247742011124554333322678-785157456335321


Q ss_pred             CEEECCCC
Q ss_conf             58821698
Q 000887          473 HYLNIEGA  480 (1237)
Q Consensus       473 ~~L~l~~~  480 (1237)
                      ++|++++|
T Consensus       106 ~~L~L~~N  113 (156)
T d2ifga3         106 QELVLSGN  113 (156)
T ss_dssp             CEEECCSS
T ss_pred             CCCCCCCC
T ss_conf             24335798

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=1e-14  Score=97.87  Aligned_cols=99  Identities=14%  Similarity=0.162  Sum_probs=53.5

Q ss_pred             CCCEEECCCCCCCCC--CCCCCCCCCCCEEECCCCCCC-----CCCHHHCCCCCCCEEECCCCCCCCC-----CCHHHC-
Q ss_conf             741998256334344--534227787786981378750-----1311110667764997376326855-----883110-
Q 000887          401 KLRVLSLGSYCITEV--PISIGCLKQLRYLNFSRSEIQ-----CLPDAICSLFNLEILILRNCWCLLK-----LPSRIG-  467 (1237)
Q Consensus       401 ~Lr~L~L~~~~i~~l--p~~~~~l~~L~~L~L~~~~i~-----~lp~~~~~L~~L~~L~L~~~~~l~~-----lp~~i~-  467 (1237)
                      +|++||+++++++..  ..-+..++++|+|+|++|.++     .++..+...++|+.|+|++| .+..     +...+. 
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N-~i~~~~~~~l~~~l~~   81 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSN-ELGDVGVHCVLQGLQT   81 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTC-CCHHHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCC-CCCHHHHHHHHHHHHC
T ss_conf             877798208958868999999767799999828999988999999999853999888979598-5972899999999843


Q ss_pred             CCCCCCEEECCCCCCCCCC-----CCCCCCCCCCCCCCE
Q ss_conf             5455658821698754458-----424324533233450
Q 000887          468 NLVNLHYLNIEGASALREL-----PLGMKELKCLRTLTN  501 (1237)
Q Consensus       468 ~L~~L~~L~l~~~~~l~~i-----p~~~~~L~~L~~L~~  501 (1237)
                      ...+|++|++++| .+...     +..+..+++|++|.+
T Consensus        82 ~~~~L~~L~L~~n-~it~~~~~~l~~~l~~~~~L~~L~L  119 (460)
T d1z7xw1          82 PSCKIQKLSLQNC-CLTGAGCGVLSSTLRTLPTLQELHL  119 (460)
T ss_dssp             TTCCCCEEECTTS-CCBGGGHHHHHHHTTSCTTCCEEEC
T ss_pred             CCCCCCEEECCCC-CCCCCCCCCCCCHHHCCCCCCCCCC
T ss_conf             7887788778887-7543221012110000343200244

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.29  E-value=1.8e-11  Score=79.12  Aligned_cols=179  Identities=15%  Similarity=0.147  Sum_probs=99.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC-----CCHHHHHHHHHHHHHCC-----------------
Q ss_conf             39999992799829999999980001137898299997597-----69999999999983305-----------------
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD-----FDVLRISKAILDSIKRS-----------------   70 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~-----~~~~~~~~~i~~~l~~~-----------------   70 (1237)
                      .+++.|+|++|+|||+|+++++... ..   ...|+.+...     .....+...+.......                 
T Consensus        29 ~~~i~i~G~~G~GKTsLl~~~~~~~-~~---~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSIIKIGINEL-NL---PYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGI  104 (283)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHH-TC---CEEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHC-CC---CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9879998699982999999999977-99---8699972145333324399999999997544555557777777753033


Q ss_pred             ------------CCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCC----HHHHHHHHCCCCCCCCCCEEEEEECCHHHH
Q ss_conf             ------------8995697899999999966972999996887777----626998312256899995999990745678
Q 000887           71 ------------SCKLEDLNSVQLELKETVFKKKFLIVLDDVWSER----YDLWQALKSPFMAGAPGSRIIVTTRSMDVA  134 (1237)
Q Consensus        71 ------------~~~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~~----~~~~~~l~~~~~~~~~~~~ilvTtR~~~~~  134 (1237)
                                  ........+....+. ....++.++++|++....    ..-...+.... ........+++.+.....
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~i~id~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~i~~~~~~~~~  182 (283)
T d2fnaa2         105 VIMGNEIKFNWNRKDRLSFANLLESFE-QASKDNVIIVLDEAQELVKLRGVNLLPALAYAY-DNLKRIKFIMSGSEMGLL  182 (283)
T ss_dssp             EECSSSEEEC-----CCCHHHHHHHHH-HTCSSCEEEEEETGGGGGGCTTCCCHHHHHHHH-HHCTTEEEEEEESSHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHH-HHCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHH-HHHHHHHHHHCCCCCHHH
T ss_conf             434432223410013458999999987-631555545664055413332699999999998-753113442035650678


Q ss_pred             HHHC------------CCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf             7526------------8870747899924339999997617899999987599999999980299137999976750589
Q 000887          135 LTMG------------SGKNYELKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALGGLLRSKQ  202 (1237)
Q Consensus       135 ~~~~------------~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~~~l~~~~  202 (1237)
                      ....            ....+.+++++.+|+.+++.......+. .. +    .+.++++.+||+|..+..++..+....
T Consensus       183 ~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~-~~-~----~~~~i~~~~~G~P~~L~~~~~~~~~~~  256 (283)
T d2fnaa2         183 YDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI-DF-K----DYEVVYEKIGGIPGWLTYFGFIYLDNK  256 (283)
T ss_dssp             HHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTC-CC-C----CHHHHHHHHCSCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCC-CH-H----HHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             99997542100010341058862887889999999966545699-99-9----999999996997999999999998056


Q ss_pred             C
Q ss_conf             9
Q 000887          203 G  203 (1237)
Q Consensus       203 ~  203 (1237)
                      .
T Consensus       257 ~  257 (283)
T d2fnaa2         257 N  257 (283)
T ss_dssp             C
T ss_pred             C
T ss_conf             5

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=99.24  E-value=6.2e-14  Score=93.32  Aligned_cols=106  Identities=23%  Similarity=0.271  Sum_probs=78.1

Q ss_pred             HHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCC
Q ss_conf             32105899974199825633434453422778778698137875013111106677649973763268558831105455
Q 000887          392 LSDLLPQCKKLRVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVN  471 (1237)
Q Consensus       392 ~~~~~~~l~~Lr~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~  471 (1237)
                      .+..+..+++|+.|+|++|.|+.++ .+..+++|++|++++|.|+.+|..+..+++|+.|++++| .+..++. +..+++
T Consensus        40 l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N-~i~~l~~-~~~l~~  116 (198)
T d1m9la_          40 MDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYN-QIASLSG-IEKLVN  116 (198)
T ss_dssp             CHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEE-ECCCHHH-HHHHHH
T ss_pred             HHHHHHCCCCCCEEECCCCCCCCCC-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCC-CCCCCC
T ss_conf             2467762604615199446899864-424782535734135343210000332212333333332-2222222-222223


Q ss_pred             CCEEECCCCCCCCCCCC--CCCCCCCCCCCCE
Q ss_conf             65882169875445842--4324533233450
Q 000887          472 LHYLNIEGASALRELPL--GMKELKCLRTLTN  501 (1237)
Q Consensus       472 L~~L~l~~~~~l~~ip~--~~~~L~~L~~L~~  501 (1237)
                      |++|++++| .+..++.  .++.+++|+.|.+
T Consensus       117 L~~L~L~~N-~i~~~~~~~~l~~l~~L~~L~L  147 (198)
T d1m9la_         117 LRVLYMSNN-KITNWGEIDKLAALDKLEDLLL  147 (198)
T ss_dssp             SSEEEESEE-ECCCHHHHHHHTTTTTCSEEEE
T ss_pred             CCCCCCCCC-HHCCCCCCCCCCCCCCCCEEEC
T ss_conf             411123410-2125542212367776302342

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=99.21  E-value=2e-13  Score=90.31  Aligned_cols=98  Identities=22%  Similarity=0.244  Sum_probs=67.7

Q ss_pred             CCCEEECCCC--CCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHCCCCCCCEEECCCCCCCCCCCHHHCCCCCCCEEECC
Q ss_conf             7419982563--34344534227787786981378750131111066776499737632685588311054556588216
Q 000887          401 KLRVLSLGSY--CITEVPISIGCLKQLRYLNFSRSEIQCLPDAICSLFNLEILILRNCWCLLKLPSRIGNLVNLHYLNIE  478 (1237)
Q Consensus       401 ~Lr~L~L~~~--~i~~lp~~~~~l~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~L~~~~~l~~lp~~i~~L~~L~~L~l~  478 (1237)
                      .++.+++.+.  .+..++.++..+++|++|++++|.|+.++ .+..+++|++|++++| .+..+|..+..+.+|++|+++
T Consensus        24 ~~~~~~l~~~~~~i~~l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N-~i~~i~~~~~~~~~L~~L~l~  101 (198)
T d1m9la_          24 EAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRN-LIKKIENLDAVADTLEELWIS  101 (198)
T ss_dssp             TCSCEECCBCCTTCCCCHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEE-EECSCSSHHHHHHHCCEEECS
T ss_pred             CCCEEEEECCCCCHHHHHHHHHCCCCCCEEECCCCCCCCCC-CCCCCCCCCCHHHCCC-CCCCCCCCCCCCCCCCCCCCC
T ss_conf             33100255556852002467762604615199446899864-4247825357341353-432100003322123333333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             987544584243245332334505
Q 000887          479 GASALRELPLGMKELKCLRTLTNF  502 (1237)
Q Consensus       479 ~~~~l~~ip~~~~~L~~L~~L~~~  502 (1237)
                      +| .+..++ .+..+++|++|++.
T Consensus       102 ~N-~i~~l~-~~~~l~~L~~L~L~  123 (198)
T d1m9la_         102 YN-QIASLS-GIEKLVNLRVLYMS  123 (198)
T ss_dssp             EE-ECCCHH-HHHHHHHSSEEEES
T ss_pred             CC-CCCCCC-CCCCCCCCCCCCCC
T ss_conf             32-222222-22222234111234

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=9.7e-13  Score=86.39  Aligned_cols=90  Identities=23%  Similarity=0.390  Sum_probs=55.5

Q ss_pred             CHHHHHCCCCCCCCEEECCCCCCC-----CCCCCCCCCCCCCEEECCCCCCCCC-----CHHHC-CCCCCCEEECCCCCC
Q ss_conf             013210589997419982563343-----4453422778778698137875013-----11110-667764997376326
Q 000887          390 MVLSDLLPQCKKLRVLSLGSYCIT-----EVPISIGCLKQLRYLNFSRSEIQCL-----PDAIC-SLFNLEILILRNCWC  458 (1237)
Q Consensus       390 ~~~~~~~~~l~~Lr~L~L~~~~i~-----~lp~~~~~l~~L~~L~L~~~~i~~l-----p~~~~-~L~~L~~L~L~~~~~  458 (1237)
                      ......++.++++++|+|++|.++     .+...+...++|+.|+|++|.|...     ...+. ...+|++|++++| .
T Consensus        17 ~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~~~~L~~L~L~~n-~   95 (460)
T d1z7xw1          17 ARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNC-C   95 (460)
T ss_dssp             HHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTS-C
T ss_pred             HHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCC-C
T ss_conf             899999976779999982899998899999999985399988897959859728999999998437887788778887-7


Q ss_pred             CCC-----CCHHHCCCCCCCEEECCCC
Q ss_conf             855-----8831105455658821698
Q 000887          459 LLK-----LPSRIGNLVNLHYLNIEGA  480 (1237)
Q Consensus       459 l~~-----lp~~i~~L~~L~~L~l~~~  480 (1237)
                      +..     ++..+..+++|++|++++|
T Consensus        96 it~~~~~~l~~~l~~~~~L~~L~L~~N  122 (460)
T d1z7xw1          96 LTGAGCGVLSSTLRTLPTLQELHLSDN  122 (460)
T ss_dssp             CBGGGHHHHHHHTTSCTTCCEEECCSS
T ss_pred             CCCCCCCCCCCHHHCCCCCCCCCCCCC
T ss_conf             543221012110000343200244433

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=2.5e-10  Score=72.39  Aligned_cols=102  Identities=21%  Similarity=0.282  Sum_probs=56.3

Q ss_pred             CCCCCCCCEEEECCCCCCEECCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC-C
Q ss_conf             478787735998479993112688974336888570654378884334934678889987165168999655888898-8
Q 000887         1106 FHKLTSLRKLYIDGCSDAVSFPDVGKGVILPTSLTSITISDFPKLKRLSSKGFQYLVSLEHLSVFSCPNFTSFPEAGF-P 1184 (1237)
Q Consensus      1106 ~~~l~~L~~L~l~~c~~l~~l~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~~l~~L~~L~l~~c~~l~~l~~~~~-~ 1184 (1237)
                      +..+++|++|++++++.++.++.  .+|..+++|+.|++++ +.|+.++...|..+++|++|++++ +.++.+|...+ .
T Consensus        27 l~~l~~l~~L~l~~n~~l~~i~~--~~f~~l~~L~~L~Ls~-N~l~~i~~~~f~~l~~L~~L~Ls~-N~l~~l~~~~~~~  102 (156)
T d2ifga3          27 LPGAENLTELYIENQQHLQHLEL--RDLRGLGELRNLTIVK-SGLRFVAPDAFHFTPRLSRLNLSF-NALESLSWKTVQG  102 (156)
T ss_dssp             SCSCSCCSEEECCSCSSCCEECG--GGSCSCCCCSEEECCS-SCCCEECTTGGGSCSCCCEEECCS-SCCSCCCSTTTCS
T ss_pred             CCCCCCCCEEECCCCCCCCCCCC--HHHCCCCCCCCCEEEC-CCCCCCCCCCCCCCCCCCCEECCC-CCCCCCCHHHHCC
T ss_conf             25765657431689866443692--1225666667216202-124774201112455433332267-8785157456335


Q ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             766576633898821023447954564
Q 000887         1185 SSLLSLEIQRCPLLEKCKMRKGQEWPK 1211 (1237)
Q Consensus      1185 ~~L~~L~i~~~p~l~~~~~~~~~~~~~ 1211 (1237)
                      .+|+.|+++++|..|.|...|+..|..
T Consensus       103 ~~l~~L~L~~Np~~C~C~~~~l~~~~~  129 (156)
T d2ifga3         103 LSLQELVLSGNPLHCSCALRWLQRWEE  129 (156)
T ss_dssp             CCCCEEECCSSCCCCCGGGHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             321243357986338811799999998

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.04  E-value=1e-07  Score=57.36  Aligned_cols=152  Identities=14%  Similarity=0.106  Sum_probs=93.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHHHC
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589-95697899999999966
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-KLEDLNSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~l~~~l~   89 (1237)
                      ..++.+.|+|++|+|||++|+.++...........+|+..............+....+.... ...........+.+...
T Consensus        41 ~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (276)
T d1fnna2          41 HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLR  120 (276)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             88881688898999899999999999754468857873230011246665456776433455532543578999999875


Q ss_pred             --CCCEEEEEECCCCCCHHHHHHH---HCCCC-CCCCCCEEEEEECCHHHHHHH-------CCCCEEECCCCCHHHHHHH
Q ss_conf             --9729999968877776269983---12256-899995999990745678752-------6887074789992433999
Q 000887           90 --KKKFLIVLDDVWSERYDLWQAL---KSPFM-AGAPGSRIIVTTRSMDVALTM-------GSGKNYELKLLSDDDCWSV  156 (1237)
Q Consensus        90 --~~~~LlvlDdv~~~~~~~~~~l---~~~~~-~~~~~~~ilvTtR~~~~~~~~-------~~~~~~~l~~l~~~ea~~l  156 (1237)
                        ......++|+++..........   ..... .......++.++.........       .....+.+.+.+.+|.+++
T Consensus       121 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~i  200 (276)
T d1fnna2         121 ERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDI  200 (276)
T ss_dssp             HTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHH
T ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHHHHHHCCHHHHHHHCCHHCCCCCHHHHHHHHH
T ss_conf             20654332036888753543106888874044335652488625876454431130366551101103441238889999


Q ss_pred             HHHHHC
Q ss_conf             999761
Q 000887          157 FVAHAF  162 (1237)
Q Consensus       157 ~~~~~~  162 (1237)
                      +..++.
T Consensus       201 l~~r~~  206 (276)
T d1fnna2         201 LLDRAK  206 (276)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
T ss_conf             999999

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.92  E-value=1.8e-08  Score=61.68  Aligned_cols=173  Identities=12%  Similarity=0.097  Sum_probs=98.7

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCC--CCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHC
Q ss_conf             939999992799829999999980001--137898299997597699999999999833058995697899999999966
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKL--TEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~--~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ....+.++|++|+|||++|+.+++...  .........+..+...........+-...... .......    .+.....
T Consensus        32 ~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~----~~~~~~~  106 (237)
T d1sxjd2          32 NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLT-VSKPSKH----DLENYPC  106 (237)
T ss_dssp             TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSC-CCCCCTT----HHHHSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCHHHEECCCCCCCHHHHHHHHHHHHHH-HHHHHHH----HHHHCCC
T ss_conf             9885999899999849999999999709763343212200211356067899998876544-4324678----7761356


Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHH-HHHHH-CCCCEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             9729999968877776269983122568999959999907456-78752-688707478999243399999976178999
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      .+.-++|+|+++.........+..........+++++|+.... ..... .....+.+.+++.++..+++...+...+..
T Consensus       107 ~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~  186 (237)
T d1sxjd2         107 PPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVK  186 (237)
T ss_dssp             CSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf             67369999551336777788876301222233332122466422233111000110233333321100101145552675


Q ss_pred             CCCCCHHHHHHHHHHHCCCCCH-HHHH
Q ss_conf             9998759999999998029913-7999
Q 000887          168 GTHGNFESTRQRVVEKCKGLPL-AARA  193 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~Pl-al~~  193 (1237)
                      ..    .+....|++.++|-.. ||..
T Consensus       187 i~----~~~l~~ia~~s~gd~R~ai~~  209 (237)
T d1sxjd2         187 CD----DGVLERILDISAGDLRRGITL  209 (237)
T ss_dssp             CC----HHHHHHHHHHTSSCHHHHHHH
T ss_pred             CC----HHHHHHHHHHCCCCHHHHHHH
T ss_conf             78----999999999859989999999

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.92  E-value=1.2e-08  Score=62.72  Aligned_cols=161  Identities=17%  Similarity=0.128  Sum_probs=96.2

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCC-CEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             93999999279982999999998000113789-82999975976999999999998330589956978999999999669
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ....+.++|++|+||||+|+.+++......+. .++-++.+.......+...+...........              ..
T Consensus        35 ~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~--------------~~  100 (224)
T d1sxjb2          35 NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLP--------------PG  100 (224)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCC--------------TT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHCCCC--------------CC
T ss_conf             9874999889998705469999999725664322111113455785211667887887622477--------------76


Q ss_pred             CCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCH-HHHHHH-CCCCEEECCCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             72999996887777626998312256899995999990745-678752-6887074789992433999999761789999
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDAG  168 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~  168 (1237)
                      +.-++|+|+++.........+..........+++++++... .+.... .....+.+.+++.++-.+.+...+...+...
T Consensus       101 ~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i  180 (224)
T d1sxjb2         101 KHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKY  180 (224)
T ss_dssp             CCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             35999982443232157787752011233333665314743021067887777765313322456788877777404678


Q ss_pred             CCCCHHHHHHHHHHHCCCCCHH
Q ss_conf             9987599999999980299137
Q 000887          169 THGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       169 ~~~~~~~~~~~i~~~~~g~Pla  190 (1237)
                      +    .+....|++.++|-+..
T Consensus       181 ~----~~~l~~I~~~s~Gd~R~  198 (224)
T d1sxjb2         181 T----NDGLEAIIFTAEGDMRQ  198 (224)
T ss_dssp             C----HHHHHHHHHHHTTCHHH
T ss_pred             C----HHHHHHHHHHCCCCHHH
T ss_conf             9----99999999986996999

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.91  E-value=2.1e-07  Score=55.46  Aligned_cols=171  Identities=14%  Similarity=0.103  Sum_probs=91.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCC-CCCCEEEEEECCCCCHHHHHHHHHHHHH-----CCCCCCCCHHHHHHHHHH
Q ss_conf             3999999279982999999998000113-7898299997597699999999999833-----058995697899999999
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE-AFEPKAWVCVSDDFDVLRISKAILDSIK-----RSSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~-~f~~~~w~~~~~~~~~~~~~~~i~~~l~-----~~~~~~~~~~~~~~~l~~   86 (1237)
                      +..+-++|++|+|||++|+.+++..... ....       ...........+...-.     .........++....+..
T Consensus        34 ~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~-------~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~  106 (239)
T d1njfa_          34 HHAYLFSGTRGVGKTSIARLLAKGLNCETGITA-------TPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDN  106 (239)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCS-------SCCSCSHHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCC-------CCCCCCHHHHHHHCCCCCEEEEECCHHCCCHHHHHHHHHH
T ss_conf             705988889987589999999998468556666-------7555424799997479870799611200789999999999


Q ss_pred             H----HCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHH-HHHHH-CCCCEEECCCCCHHHHHHHHHHH
Q ss_conf             9----669729999968877776269983122568999959999907456-78752-68870747899924339999997
Q 000887           87 T----VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVAH  160 (1237)
Q Consensus        87 ~----l~~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~~  160 (1237)
                      .    ..++..++|+|+++......-..+...+.....++.+|.+|.+.. +.... .....+.+.+++.++-.+.+...
T Consensus       107 ~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i  186 (239)
T d1njfa_         107 VQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHI  186 (239)
T ss_dssp             CCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHH
T ss_pred             HHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf             97465259987999978110899999999999856898869999738856367657612102222467678766688787


Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHCCCCCH-HHHHH
Q ss_conf             61789999998759999999998029913-79999
Q 000887          161 AFEGRDAGTHGNFESTRQRVVEKCKGLPL-AARAL  194 (1237)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl-al~~~  194 (1237)
                      +.......    ..+.+..+++.++|.+. |+.++
T Consensus       187 ~~~e~~~~----~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         187 LNEEHIAH----EPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             HHHHTCCB----CHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHCCCC----CHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             76431478----99999999997699799999999

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.91  E-value=1.4e-08  Score=62.29  Aligned_cols=157  Identities=14%  Similarity=0.108  Sum_probs=92.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCC-EEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCC
Q ss_conf             39999992799829999999980001137898-29999759769999999999983305899569789999999996697
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKK   91 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~   91 (1237)
                      ...+-++|++|+|||++|+.+++......+.. ++-...+...+................               ....+
T Consensus        35 ~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~   99 (227)
T d1sxjc2          35 LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQ---------------IFSKG   99 (227)
T ss_dssp             CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHHHBCC---------------SSSCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCEEEEECCHHHCCCCCC---------------CCCCC
T ss_conf             985999889987755899999998516777641577315556875432100010111000---------------25777


Q ss_pred             CEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHHH-HHH-HCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCC
Q ss_conf             299999688777762699831225689999599999074567-875-268870747899924339999997617899999
Q 000887           92 KFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMDV-ALT-MGSGKNYELKLLSDDDCWSVFVAHAFEGRDAGT  169 (1237)
Q Consensus        92 ~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~~-~~~-~~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~~  169 (1237)
                      ...+|+|+++.........+...+......+++++++....- ... ......+++.+++.++-.+.+...+...+...+
T Consensus       100 ~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~  179 (227)
T d1sxjc2         100 FKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLS  179 (227)
T ss_dssp             CEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBC
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             18999966320002378999988631120023201267087759999988754012356520001102122111124589


Q ss_pred             CCCHHHHHHHHHHHCCCCC
Q ss_conf             9875999999999802991
Q 000887          170 HGNFESTRQRVVEKCKGLP  188 (1237)
Q Consensus       170 ~~~~~~~~~~i~~~~~g~P  188 (1237)
                          .+....|++.++|-.
T Consensus       180 ----~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         180 ----PNAEKALIELSNGDM  194 (227)
T ss_dssp             ----HHHHHHHHHHHTTCH
T ss_pred             ----HHHHHHHHHHCCCCH
T ss_conf             ----899999999849969

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.82  E-value=1.2e-07  Score=56.86  Aligned_cols=150  Identities=18%  Similarity=0.153  Sum_probs=86.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCE
Q ss_conf             99999927998299999999800011378982999975976999999999998330589956978999999999669729
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      ..+.|+|++|+|||.|+.++++...+. ...+++++      ..+....+...+...     ...+.    .+.+. .--
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~-~~~~~~~~------~~~~~~~~~~~~~~~-----~~~~~----~~~~~-~~d   99 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR-GYRVIYSS------ADDFAQAMVEHLKKG-----TINEF----RNMYK-SVD   99 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT-TCCEEEEE------HHHHHHHHHHHHHHT-----CHHHH----HHHHH-TCS
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHCCC-CCCEEEEC------HHHHHHHHHHHHHCC-----CHHHH----HHHHH-HCC
T ss_conf             857998889983999999999874467-65048844------378799999998716-----62667----89876-213


Q ss_pred             EEEEECCCCCC-HHHHHH-HHCCCCC-CCCCCEEEEEECCHH---------HHHHHCCCCEEECCCCCHHHHHHHHHHHH
Q ss_conf             99996887777-626998-3122568-999959999907456---------78752688707478999243399999976
Q 000887           94 LIVLDDVWSER-YDLWQA-LKSPFMA-GAPGSRIIVTTRSMD---------VALTMGSGKNYELKLLSDDDCWSVFVAHA  161 (1237)
Q Consensus        94 LlvlDdv~~~~-~~~~~~-l~~~~~~-~~~~~~ilvTtR~~~---------~~~~~~~~~~~~l~~l~~~ea~~l~~~~~  161 (1237)
                      ++++||++... ...|+. +...+.. ...|.++|+|++...         +..++.....++++ .++++..+++++++
T Consensus       100 ll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a  178 (213)
T d1l8qa2         100 LLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKL  178 (213)
T ss_dssp             EEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHCCCCCHHHHHHHHCCEEEEEC-CCCHHHHHHHHHHH
T ss_conf             01011265505865778899999998763166389954875100134326788886185689978-88279999999999


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf             178999999875999999999802
Q 000887          162 FEGRDAGTHGNFESTRQRVVEKCK  185 (1237)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~i~~~~~  185 (1237)
                      ...+...+    .+.+.-++++..
T Consensus       179 ~~rgl~l~----~~v~~yl~~~~~  198 (213)
T d1l8qa2         179 KEFNLELR----KEVIDYLLENTK  198 (213)
T ss_dssp             HHTTCCCC----HHHHHHHHHHCS
T ss_pred             HHCCCCCC----HHHHHHHHHHCC
T ss_conf             98299999----999999998568

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.81  E-value=1.6e-08  Score=62.01  Aligned_cols=159  Identities=17%  Similarity=0.105  Sum_probs=90.9

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCC-EEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             939999992799829999999980001137898-2999975976999999999998330589956978999999999669
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEP-KAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~-~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..+.+.++|++|+|||++|+.++.......+.. .+-++++.......+...+.......               .....
T Consensus        44 ~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~~~~~~~~~~~~~~~~~~---------------~~~~~  108 (231)
T d1iqpa2          44 SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTK---------------PIGGA  108 (231)
T ss_dssp             CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSC---------------CGGGC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHH---------------HCCCC
T ss_conf             997699978999748799999999987314677715875676666348888888887510---------------01578


Q ss_pred             CCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCH-HHHHHH-CCCCEEECCCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             72999996887777626998312256899995999990745-678752-6887074789992433999999761789999
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTM-GSGKNYELKLLSDDDCWSVFVAHAFEGRDAG  168 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~-~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~~  168 (1237)
                      ++.++++|+++.........+...+........++.|+... .+.... .....+.+.+.+.++..+.++..+.......
T Consensus       109 ~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~i  188 (231)
T d1iqpa2         109 SFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLEL  188 (231)
T ss_dssp             SCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCEE
T ss_pred             CCEEEEEHHHHHCCHHHHHHHHHHCCCCCCCEEEEECCCCHHHCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             72288614344312147898764112477644788614876656576847312101233430467789988899839998


Q ss_pred             CCCCHHHHHHHHHHHCCCCCH
Q ss_conf             998759999999998029913
Q 000887          169 THGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       169 ~~~~~~~~~~~i~~~~~g~Pl  189 (1237)
                          ..+....|++.++|-..
T Consensus       189 ----~~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         189 ----TEEGLQAILYIAEGDMR  205 (231)
T ss_dssp             ----CHHHHHHHHHHHTTCHH
T ss_pred             ----CHHHHHHHHHHCCCCHH
T ss_conf             ----99999999998399799

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=98.78  E-value=6.9e-11  Score=75.68  Aligned_cols=83  Identities=17%  Similarity=0.129  Sum_probs=34.4

Q ss_pred             CCCCCCCEEECCCCCCCC-----CCCCCCCCCCCCEEECCCCCCCC-----------CCHHHCCCCCCCEEECCCCCCCC
Q ss_conf             899974199825633434-----45342277877869813787501-----------31111066776499737632685
Q 000887          397 PQCKKLRVLSLGSYCITE-----VPISIGCLKQLRYLNFSRSEIQC-----------LPDAICSLFNLEILILRNCWCLL  460 (1237)
Q Consensus       397 ~~l~~Lr~L~L~~~~i~~-----lp~~~~~l~~L~~L~L~~~~i~~-----------lp~~~~~L~~L~~L~L~~~~~l~  460 (1237)
                      .....++.|+|++|.+..     +...+...++|+.|+++++....           +...+...++|+.|++++| .+.
T Consensus        28 ~~~~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n-~i~  106 (344)
T d2ca6a1          28 LEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDN-AFG  106 (344)
T ss_dssp             HHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSC-CCC
T ss_pred             HHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCC-CCC
T ss_conf             6389978897849837789999999999858998888887775433454210678799988754777563300001-345


Q ss_pred             C-----CCHHHCCCCCCCEEECCCC
Q ss_conf             5-----8831105455658821698
Q 000887          461 K-----LPSRIGNLVNLHYLNIEGA  480 (1237)
Q Consensus       461 ~-----lp~~i~~L~~L~~L~l~~~  480 (1237)
                      .     +...+...++|++|++++|
T Consensus       107 ~~~~~~l~~~l~~~~~L~~L~l~~n  131 (344)
T d2ca6a1         107 PTAQEPLIDFLSKHTPLEHLYLHNN  131 (344)
T ss_dssp             TTTHHHHHHHHHHCTTCCEEECCSS
T ss_pred             CCCCCCHHHHHCCCCCCHHEECCCC
T ss_conf             5433310111002343210000024

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.72  E-value=7.4e-08  Score=58.10  Aligned_cols=98  Identities=13%  Similarity=0.092  Sum_probs=59.6

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHH-HHHH-HCCCCEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             9729999968877776269983122568999959999907456-7875-2688707478999243399999976178999
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALT-MGSGKNYELKLLSDDDCWSVFVAHAFEGRDA  167 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~-~~~~-~~~~~~~~l~~l~~~ea~~l~~~~~~~~~~~  167 (1237)
                      .+.-++|+|+++.........+...+.....++++|.||.+.. +... ......+.+.+++.++..+.+...+...+..
T Consensus       130 ~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~  209 (252)
T d1sxje2         130 HRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ  209 (252)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE
T ss_pred             CCCEEEEECCCCCCCCCCCHHHHCCCCCCCCCCCCEEEECCCCCHHHHHHCCHHEEEECCCCHHHHHHHHHHHHHHCCCC
T ss_conf             87249994243334543111221002213566430001021110025442100024303533046899999999983999


Q ss_pred             CCCCCHHHHHHHHHHHCCCCCHH
Q ss_conf             99987599999999980299137
Q 000887          168 GTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       168 ~~~~~~~~~~~~i~~~~~g~Pla  190 (1237)
                      .. +  .+....|++.+.|-+..
T Consensus       210 ~~-~--~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         210 LE-T--KDILKRIAQASNGNLRV  229 (252)
T ss_dssp             EC-C--SHHHHHHHHHHTTCHHH
T ss_pred             CC-C--HHHHHHHHHHCCCCHHH
T ss_conf             89-6--99999999986994999

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.72  E-value=8e-07  Score=52.12  Aligned_cols=169  Identities=10%  Similarity=0.048  Sum_probs=95.1

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHC----CCCCCCCHHHHHHHHHH
Q ss_conf             99399999927998299999999800011378982999975976999999999998330----58995697899999999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKR----SSCKLEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~----~~~~~~~~~~~~~~l~~   86 (1237)
                      .-+..+-++|+.|+|||++|+.++...........  -......+...+.......+..    ........+++.. +.+
T Consensus        22 ~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~--~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~-l~~   98 (207)
T d1a5ta2          22 RGHHALLIQALPGMGDDALIYALSRYLLCQQPQGH--KSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVRE-VTE   98 (207)
T ss_dssp             CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTT--BCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHH-HHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCC--CCCCCCCHHHHHHHCCCCCCCHHHHHHCCCCCCCCHHHH-HHH
T ss_conf             96737988899987599999999982101012321--223342015565430343110123431345333211467-765


Q ss_pred             HH-----CCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCHH-HHHHH-CCCCEEECCCCCHHHHHHHHHH
Q ss_conf             96-----69729999968877776269983122568999959999907456-78752-6887074789992433999999
Q 000887           87 TV-----FKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSMD-VALTM-GSGKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        87 ~l-----~~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~~-~~~~~-~~~~~~~l~~l~~~ea~~l~~~  159 (1237)
                      .+     .+++-++|+|+++....+....+...+-....+..+|.||++.. +...+ .....+.+.+++.++..+.+..
T Consensus        99 ~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~  178 (207)
T d1a5ta2          99 KLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSR  178 (207)
T ss_dssp             HTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHH
T ss_pred             HHHHCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHH
T ss_conf             32110035764047731344200001499999998501111045530686551032002157882689999999999997


Q ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHH
Q ss_conf             76178999999875999999999802991379
Q 000887          160 HAFEGRDAGTHGNFESTRQRVVEKCKGLPLAA  191 (1237)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal  191 (1237)
                      ..    . .+    .+.+..+++.++|.|...
T Consensus       179 ~~----~-~~----~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         179 EV----T-MS----QDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             HC----C-CC----HHHHHHHHHHTTTCHHHH
T ss_pred             CC----C-CC----HHHHHHHHHHCCCCHHHH
T ss_conf             48----9-99----999999999769999999

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.70  E-value=1.8e-07  Score=55.88  Aligned_cols=172  Identities=16%  Similarity=0.101  Sum_probs=88.4

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHC
Q ss_conf             99939999992799829999999980001137898299997597699999999999833058995697899999999966
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVF   89 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~   89 (1237)
                      ....+.+.++|++|+|||++|+.+++...    ..+++++.+...+...+...+-...... ........  ........
T Consensus        49 ~~~~~~lll~GPpG~GKTt~a~~la~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~  121 (253)
T d1sxja2          49 SGVFRAAMLYGPPGIGKTTAAHLVAQELG----YDILEQNASDVRSKTLLNAGVKNALDNM-SVVGYFKH--NEEAQNLN  121 (253)
T ss_dssp             TTSCSEEEEECSTTSSHHHHHHHHHHHTT----CEEEEECTTSCCCHHHHHHTGGGGTTBC-CSTTTTTC------CCSS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHH----HHHHCCCCCCCHHHHHHHHHHHHHHHCC-HHHHHHHH--HHHCCCCC
T ss_conf             88874499987999988899999999987----5120134432211688999998876312-12101334--32014556


Q ss_pred             CCCEEEEEECCCCCCH---HHHHHHHCCCCCCCCCCEEEEEECC--HHHHHHH-CCCCEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9729999968877776---2699831225689999599999074--5678752-68870747899924339999997617
Q 000887           90 KKKFLIVLDDVWSERY---DLWQALKSPFMAGAPGSRIIVTTRS--MDVALTM-GSGKNYELKLLSDDDCWSVFVAHAFE  163 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~---~~~~~l~~~~~~~~~~~~ilvTtR~--~~~~~~~-~~~~~~~l~~l~~~ea~~l~~~~~~~  163 (1237)
                      .+..++++|++.....   ..+..+.......  ...+++|+..  ....... .....+++.+.+.++-.+.+...+..
T Consensus       122 ~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~--~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~  199 (253)
T d1sxja2         122 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIR  199 (253)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             65137776301111100013467776540123--4222111355552113532440365311453146788999999998


Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCC-HHHHHH
Q ss_conf             8999999875999999999802991-379999
Q 000887          164 GRDAGTHGNFESTRQRVVEKCKGLP-LAARAL  194 (1237)
Q Consensus       164 ~~~~~~~~~~~~~~~~i~~~~~g~P-lal~~~  194 (1237)
                      .+....    .+...+|++.++|-. -||..+
T Consensus       200 e~i~i~----~~~l~~i~~~s~GDiR~ai~~L  227 (253)
T d1sxja2         200 EKFKLD----PNVIDRLIQTTRGDIRQVINLL  227 (253)
T ss_dssp             HTCCCC----TTHHHHHHHHTTTCHHHHHHHH
T ss_pred             HCCCCC----HHHHHHHHHHCCCCHHHHHHHH
T ss_conf             099999----9999999996797099999999

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.58  E-value=9e-06  Score=46.02  Aligned_cols=170  Identities=15%  Similarity=0.121  Sum_probs=90.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCC----CCC-CCEEEEEECCCCCHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHH
Q ss_conf             399999927998299999999800011----378-982999975976999999999998330589-95697899999999
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLT----EAF-EPKAWVCVSDDFDVLRISKAILDSIKRSSC-KLEDLNSVQLELKE   86 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~----~~f-~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~l~~   86 (1237)
                      ..++.++|++|+|||++++.++.....    ... ....++..................++.... ...........+.+
T Consensus        46 ~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  125 (287)
T d1w5sa2          46 NMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVD  125 (287)
T ss_dssp             EEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH
T ss_conf             34899678999899999999999987541555678416630333346504678887653043233345127889999999


Q ss_pred             HH--CCCCEEEEEECCCC------CCHHHHHHH---HCCCCCC--CCCCE-EEEEECCHHHHH------HH--CCCCEEE
Q ss_conf             96--69729999968877------776269983---1225689--99959-999907456787------52--6887074
Q 000887           87 TV--FKKKFLIVLDDVWS------ERYDLWQAL---KSPFMAG--APGSR-IIVTTRSMDVAL------TM--GSGKNYE  144 (1237)
Q Consensus        87 ~l--~~~~~LlvlDdv~~------~~~~~~~~l---~~~~~~~--~~~~~-ilvTtR~~~~~~------~~--~~~~~~~  144 (1237)
                      ..  .+...++++|.++.      ...+....+   ...+...  ..... |++++.......      ..  .....+.
T Consensus       126 ~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~  205 (287)
T d1w5sa2         126 NLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLH  205 (287)
T ss_dssp             HHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEE
T ss_pred             HHHHCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCHHHCCCCEEEEEECCCHHHHHHHHHHCCCHHCCCCEEEE
T ss_conf             99854676654125788851566554267898899987432010456514776243089999998625201123220652


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             7899924339999997617899999987599999999980
Q 000887          145 LKLLSDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKC  184 (1237)
Q Consensus       145 l~~l~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~  184 (1237)
                      .++++.+|..+++..++........  -.++..+.|++..
T Consensus       206 f~~y~~~el~~Il~~r~~~~~~~~~--~~~~al~~ia~~~  243 (287)
T d1w5sa2         206 LPAYKSRELYTILEQRAELGLRDTV--WEPRHLELISDVY  243 (287)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHBCTTS--CCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH
T ss_conf             2577599999987666777524687--7999999999997

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.57  E-value=2.6e-06  Score=49.11  Aligned_cols=134  Identities=13%  Similarity=0.105  Sum_probs=83.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCC-----CCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             999999279982999999998000113-----789829999759769999999999983305899569789999999996
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE-----AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~-----~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .-+.++|.+|+|||+++..++.+....     .....+|......             +-.......+.++....+...+
T Consensus        40 ~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~-------------liag~~~~g~~e~r~~~i~~~~  106 (268)
T d1r6bx2          40 NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS-------------LLAGTKYRGDFEKRFKALLKQL  106 (268)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC----------------CCCCCSSCHHHHHHHHHHHH
T ss_pred             CCCEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECH-------------HHCCCCCCHHHHHHHHHHHHHH
T ss_conf             896798889886779999999999817845000354127864056-------------7506763005899999999986


Q ss_pred             CC-CCEEEEEECCCCC--------CHHHHHHHHCCCCCCCCCCEEEEEECCHHHHHHHCC-------CCEEECCCCCHHH
Q ss_conf             69-7299999688777--------762699831225689999599999074567875268-------8707478999243
Q 000887           89 FK-KKFLIVLDDVWSE--------RYDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMGS-------GKNYELKLLSDDD  152 (1237)
Q Consensus        89 ~~-~~~LlvlDdv~~~--------~~~~~~~l~~~~~~~~~~~~ilvTtR~~~~~~~~~~-------~~~~~l~~l~~~e  152 (1237)
                      .. ++.++++|++...        ...+...+..++... ..-++|.||...+.......       ...+.+++.+.++
T Consensus       107 ~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~r-g~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~e~  185 (268)
T d1r6bx2         107 EQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS-GKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEE  185 (268)
T ss_dssp             SSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS-CCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHH
T ss_pred             HCCCCCEEEECCHHHHHCCCCCCCCCCCHHHHHHHHHHC-CCCEEEEECCHHHHHHHHHHCHHHHHHHCCCCCCCCCHHH
T ss_conf             126784688433698862777788641179876488747-9875999579999999986167888652100368989999


Q ss_pred             HHHHHHHHH
Q ss_conf             399999976
Q 000887          153 CWSVFVAHA  161 (1237)
Q Consensus       153 a~~l~~~~~  161 (1237)
                      +.+++....
T Consensus       186 t~~IL~~~~  194 (268)
T d1r6bx2         186 TVQIINGLK  194 (268)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
T ss_conf             999999866

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.55  E-value=9.7e-06  Score=45.84  Aligned_cols=156  Identities=17%  Similarity=0.115  Sum_probs=84.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589956978999999999669
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..++-+.++|++|+|||++|+.++.....    ..+.++.+.-.+              . ........+...+...-..
T Consensus        43 ~~~~~iLL~GppGtGKT~la~~iA~~~~~----~~~~i~~~~l~~--------------~-~~g~~~~~l~~~f~~A~~~  103 (256)
T d1lv7a_          43 KIPKGVLMVGPPGTGKTLLAKAIAGEAKV----PFFTISGSDFVE--------------M-FVGVGASRVRDMFEQAKKA  103 (256)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHHHTC----CEEEECSCSSTT--------------S-CCCCCHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHCCC----CEEEEEHHHHHH--------------C-CHHHHHHHHHHHHHHHHHC
T ss_conf             98886786689988822899999998299----879988699426--------------0-0107899999999999975


Q ss_pred             CCEEEEEECCCCC----------CHHH----HHHHHCCCC--CCCCCCEEEEEECCHHHH-HHH---C-CCCEEECCCCC
Q ss_conf             7299999688777----------7626----998312256--899995999990745678-752---6-88707478999
Q 000887           91 KKFLIVLDDVWSE----------RYDL----WQALKSPFM--AGAPGSRIIVTTRSMDVA-LTM---G-SGKNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~----------~~~~----~~~l~~~~~--~~~~~~~ilvTtR~~~~~-~~~---~-~~~~~~l~~l~  149 (1237)
                      .+++|++||++..          ....    ...+...+.  ....+.-+|-||..+... ..+   + -++.+.++..+
T Consensus       104 ~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~  183 (256)
T d1lv7a_         104 APCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPD  183 (256)
T ss_dssp             CSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCC
T ss_pred             CCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCHHHCCCCCCCEEEECCCCC
T ss_conf             99899997756657567898888748999999999999538777799899980799310798576898787798779959


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHH
Q ss_conf             24339999997617899999987599999999980299137
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA  190 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pla  190 (1237)
                      .++..++++.+..+... ....+    ...+++.+.|..-|
T Consensus       184 ~~~R~~il~~~l~~~~~-~~~~~----~~~la~~t~G~s~a  219 (256)
T d1lv7a_         184 VRGREQILKVHMRRVPL-APDID----AAIIARGTPGFSGA  219 (256)
T ss_dssp             HHHHHHHHHHHHTTSCB-CTTCC----HHHHHHTCTTCCHH
T ss_pred             HHHHHHHHHHHCCCCCC-CCCCC----HHHHHHHCCCCCHH
T ss_conf             99999999984259986-86569----99999868998999

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.48  E-value=5.5e-06  Score=47.27  Aligned_cols=152  Identities=15%  Similarity=0.074  Sum_probs=78.6

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589956978999999999669
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..++-+-++|++|+|||++|+.++....    ....+.+.+..........                     .+.+.. +
T Consensus        33 ~~~~~~Ll~GPpG~GKTtla~~la~~~~----~~~~~~~~~~~~~~~~~~~---------------------~~~~~~-~   86 (239)
T d1ixsb2          33 EPLEHLLLFGPPGLGKTTLAHVIAHELG----VNLRVTSGPAIEKPGDLAA---------------------ILANSL-E   86 (239)
T ss_dssp             SCCCCEEEECCTTSCHHHHHHHHHHHHT----CCEEEEETTTCCSHHHHHH---------------------HHHTTC-C
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHC----CCEEECCCCCCCCCHHHHH---------------------HHHHHC-C
T ss_conf             8887389889799878889999999849----8747546875343214689---------------------988510-3


Q ss_pred             CCEEEEEECCCCCCHHHHHHHHCCC------------------CCCCCCCEEEEEE-CCHHHH--HHHCCCCEEECCCCC
Q ss_conf             7299999688777762699831225------------------6899995999990-745678--752688707478999
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPF------------------MAGAPGSRIIVTT-RSMDVA--LTMGSGKNYELKLLS  149 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~l~~~~------------------~~~~~~~~ilvTt-R~~~~~--~~~~~~~~~~l~~l~  149 (1237)
                      .+..+++|.++......-+.+....                  ....+...++.++ +.....  ........+.+...+
T Consensus        87 ~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~  166 (239)
T d1ixsb2          87 EGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYT  166 (239)
T ss_dssp             TTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSCGGGGGCSEEEECCCCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCEEEEEECCCCCCCCCHHHCCCCEEEEEECCC
T ss_conf             88734431100110447875001243332121104655654334689977999630683334410101221456752057


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHH
Q ss_conf             2433999999761789999998759999999998029913799
Q 000887          150 DDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       150 ~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~  192 (1237)
                      .++..+.+...+.......    ..+....+++.++|-+....
T Consensus       167 ~~~~~~i~~~~~~~~~i~~----~~~~l~~ia~~s~gd~R~a~  205 (239)
T d1ixsb2         167 PEELAQGVMRDARLLGVRI----TEEAALEIGRRSRGTMRVAK  205 (239)
T ss_dssp             HHHHHHHHHHHHGGGCCCB----CHHHHHHHHHHTTSSHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCC----CHHHHHHHHHHCCCCHHHHH
T ss_conf             4555578899999848765----26789999997699999999

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.48  E-value=5.6e-06  Score=47.24  Aligned_cols=149  Identities=15%  Similarity=0.116  Sum_probs=77.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             39999992799829999999980001137898299997597699999999999833058995697899999999966972
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKK   92 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~   92 (1237)
                      .+-+.++|++|+|||++|+.++....   ++ .+.++........++.. ++..                      ..++
T Consensus        35 ~~~~L~~GPpGtGKT~lA~~la~~~~---~~-~~~~~~~~~~~~~~~~~-~~~~----------------------~~~~   87 (238)
T d1in4a2          35 LDHVLLAGPPGLGKTTLAHIIASELQ---TN-IHVTSGPVLVKQGDMAA-ILTS----------------------LERG   87 (238)
T ss_dssp             CCCEEEESSTTSSHHHHHHHHHHHHT---CC-EEEEETTTCCSHHHHHH-HHHH----------------------CCTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCCC---CC-CCCCCCCCCCCHHHHHH-HHHH----------------------HCCC
T ss_conf             77489879999738899999985038---88-53325744224888999-9875----------------------4358


Q ss_pred             EEEEEECCCCCCHHHHHHHHCCC------------------CCCCCCCEEEEEECCH-HHHHHH--CCCCEEECCCCCHH
Q ss_conf             99999688777762699831225------------------6899995999990745-678752--68870747899924
Q 000887           93 FLIVLDDVWSERYDLWQALKSPF------------------MAGAPGSRIIVTTRSM-DVALTM--GSGKNYELKLLSDD  151 (1237)
Q Consensus        93 ~LlvlDdv~~~~~~~~~~l~~~~------------------~~~~~~~~ilvTtR~~-~~~~~~--~~~~~~~l~~l~~~  151 (1237)
                      ..+++|.+.......-+.+....                  ........+|.+|... ......  .....+.++..+.+
T Consensus        88 ~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~  167 (238)
T d1in4a2          88 DVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVK  167 (238)
T ss_dssp             CEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHH
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEEEEECCCCHH
T ss_conf             82477789884067776421402441454454376002444457887699995478755554311330079984478778


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHH
Q ss_conf             33999999761789999998759999999998029913799
Q 000887          152 DCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAAR  192 (1237)
Q Consensus       152 ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~  192 (1237)
                      +...++...+.......    ..+....+++.++|-+..+.
T Consensus       168 ~~~~~l~~~~~~~~~~~----~~~~l~~i~~~s~gd~R~ai  204 (238)
T d1in4a2         168 ELKEIIKRAASLMDVEI----EDAAAEMIAKRSRGTPRIAI  204 (238)
T ss_dssp             HHHHHHHHHHHHTTCCB----CHHHHHHHHHTSTTCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHH----HHHHHHHHHHHCCCCHHHHH
T ss_conf             77777777653011002----57999999996799899999

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.41  E-value=6e-06  Score=47.03  Aligned_cols=154  Identities=16%  Similarity=0.108  Sum_probs=81.1

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH-HC
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589956978999999999-66
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET-VF   89 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~-l~   89 (1237)
                      ..++-+.++|++|+|||++|+++++...   . ..+.++.+      .+    ..    .  ...+.+.....+.+. -.
T Consensus        40 ~~~~giLl~GppGtGKT~la~aia~~~~---~-~~~~i~~~------~l----~~----~--~~g~~~~~l~~~f~~a~~   99 (247)
T d1ixza_          40 RIPKGVLLVGPPGVGKTHLARAVAGEAR---V-PFITASGS------DF----VE----M--FVGVGAARVRDLFETAKR   99 (247)
T ss_dssp             CCCSEEEEECCTTSSHHHHHHHHHHHTT---C-CEEEEEHH------HH----HH----S--CTTHHHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCC---C-CEEEEEHH------HH----HH----C--CCCHHHHHHHHHHHHHHH
T ss_conf             9886488766898883599999998739---9-77997869------96----46----2--453899999999999997


Q ss_pred             CCCEEEEEECCCCC-------C---HH----HHHHHHCCCC--CCCCCCEEEEEECCHHHH-HHH---C-CCCEEECCCC
Q ss_conf             97299999688777-------7---62----6998312256--899995999990745678-752---6-8870747899
Q 000887           90 KKKFLIVLDDVWSE-------R---YD----LWQALKSPFM--AGAPGSRIIVTTRSMDVA-LTM---G-SGKNYELKLL  148 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~-------~---~~----~~~~l~~~~~--~~~~~~~ilvTtR~~~~~-~~~---~-~~~~~~l~~l  148 (1237)
                      ..+++|++||++..       .   ..    ....+...+.  ....+.-+|-||..+... ..+   + -...+.++..
T Consensus       100 ~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P  179 (247)
T d1ixza_         100 HAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAP  179 (247)
T ss_dssp             SSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSC
T ss_pred             CCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCHHHCCCCCCCEEEEECCC
T ss_conf             69979999773664746789988875899999999999963877789989998079940069967589878579997996


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCH
Q ss_conf             92433999999761789999998759999999998029913
Q 000887          149 SDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPL  189 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pl  189 (1237)
                      +.++..++++.+...... .....    ...+++.+.|..-
T Consensus       180 ~~~eR~~il~~~l~~~~~-~~~~~----~~~la~~t~g~s~  215 (247)
T d1ixza_         180 DVKGREQILRIHARGKPL-AEDVD----LALLAKRTPGFVG  215 (247)
T ss_dssp             CHHHHHHHHHHHHTTSCB-CTTCC----HHHHHHTCTTCCH
T ss_pred             CHHHHHHHHHHHHCCCCC-CCCCC----HHHHHHHCCCCCH
T ss_conf             999999999987506577-65468----9999977889889

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.37  E-value=5e-06  Score=47.49  Aligned_cols=161  Identities=15%  Similarity=0.108  Sum_probs=85.5

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589956978999999999669
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..++-+-++|++|+|||++|++++......    .+.+..+.              +.... ...............-..
T Consensus        36 ~~~~giLL~GppGtGKT~l~~ala~~~~~~----~~~i~~~~--------------l~~~~-~g~~~~~l~~~f~~A~~~   96 (258)
T d1e32a2          36 KPPRGILLYGPPGTGKTLIARAVANETGAF----FFLINGPE--------------IMSKL-AGESESNLRKAFEEAEKN   96 (258)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHHTTCE----EEEECHHH--------------HTTSC-TTHHHHHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCCE----EEEEECHH--------------HCCCC-CCCHHHHHHHHHHHHHHC
T ss_conf             988646876699888308999999874883----79997304--------------30254-561788889999999864


Q ss_pred             CCEEEEEECCCCCCH-------HH----HHHHHCCC--CCCCCCCEEEEEECCHHHHHH-HC----CCCEEECCCCCHHH
Q ss_conf             729999968877776-------26----99831225--689999599999074567875-26----88707478999243
Q 000887           91 KKFLIVLDDVWSERY-------DL----WQALKSPF--MAGAPGSRIIVTTRSMDVALT-MG----SGKNYELKLLSDDD  152 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~-------~~----~~~l~~~~--~~~~~~~~ilvTtR~~~~~~~-~~----~~~~~~l~~l~~~e  152 (1237)
                      ++++|++||++..-.       +.    ...+....  .....+.-||.||..+..... +.    -...+.++..+.++
T Consensus        97 ~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~  176 (258)
T d1e32a2          97 APAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG  176 (258)
T ss_dssp             CSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHH
T ss_pred             CCEEEEEHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCHHHHHCCCCCCEEECCCCCHHH
T ss_conf             99499852111322578877770689998775001101234688117975799310252454246302323789999889


Q ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHH-HHHHH
Q ss_conf             39999997617899999987599999999980299137-99997
Q 000887          153 CWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA-ARALG  195 (1237)
Q Consensus       153 a~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pla-l~~~~  195 (1237)
                      ..++|..+..+. ......+    ...+++.+.|+--| |..+.
T Consensus       177 R~~il~~~l~~~-~~~~~~~----~~~la~~t~G~s~adl~~lv  215 (258)
T d1e32a2         177 RLEILQIHTKNM-KLADDVD----LEQVANETHGHVGADLAALC  215 (258)
T ss_dssp             HHHHHHHTTTTS-CBCTTCC----HHHHHHHCTTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCC-CCCCCCC----HHHHHHCCCCCCHHHHHHHH
T ss_conf             998732204576-3345530----34444206677899999999

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.28  E-value=4.1e-06  Score=48.02  Aligned_cols=159  Identities=12%  Similarity=0.104  Sum_probs=84.7

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHHC
Q ss_conf             9939999992799829999999980001137898299997597699999999999833058995697-899999999966
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDL-NSVQLELKETVF   89 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~-~~~~~~l~~~l~   89 (1237)
                      ..++-|-++|++|+|||++|++++.....     - ++.+.    ...+.        ..  ..... ......+...-.
T Consensus        39 ~~~~giLL~Gp~GtGKT~l~~ala~~~~~-----~-~~~~~----~~~l~--------~~--~~~~~~~~l~~~f~~A~~   98 (265)
T d1r7ra3          39 TPSKGVLFYGPPGCGKTLLAKAIANECQA-----N-FISIK----GPELL--------TM--WFGESEANVREIFDKARQ   98 (265)
T ss_dssp             CCCCEEEEBCCTTSSHHHHHHHHHHHTTC-----E-EEEEC----HHHHH--------TS--CTTTHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHCC-----C-EEEEE----HHHHH--------HC--CCCCHHHHHHHHHHHHHH
T ss_conf             98875788789987630477887877189-----4-79988----79952--------53--165158999999999986


Q ss_pred             CCCEEEEEECCCCCCH----------H----HHHHHHCCCCC--CCCCCEEEEEECCHHHH-HHHC----CCCEEECCCC
Q ss_conf             9729999968877776----------2----69983122568--99995999990745678-7526----8870747899
Q 000887           90 KKKFLIVLDDVWSERY----------D----LWQALKSPFMA--GAPGSRIIVTTRSMDVA-LTMG----SGKNYELKLL  148 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~----------~----~~~~l~~~~~~--~~~~~~ilvTtR~~~~~-~~~~----~~~~~~l~~l  148 (1237)
                      ..++++++||++..-.          .    ....+...+..  ...+.-+|.||..+... ..+.    -...++++..
T Consensus        99 ~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p  178 (265)
T d1r7ra3          99 AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLP  178 (265)
T ss_dssp             TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCC
T ss_pred             CCCCCEEHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHCCHHHHCCCCCCEEEEECCH
T ss_conf             39843568754632455787678873799999999999962867779989999179922279978078776479995660


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHH-HHHH
Q ss_conf             924339999997617899999987599999999980299137-9999
Q 000887          149 SDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLA-ARAL  194 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Pla-l~~~  194 (1237)
                      +.++..++|+...... ......+    ..++++.+.|...+ |..+
T Consensus       179 ~~~~R~~il~~~l~~~-~~~~~~~----l~~la~~t~g~s~~di~~l  220 (265)
T d1r7ra3         179 DEKSRVAILKANLRKS-PVAKDVD----LEFLAKMTNGFSGADLTEI  220 (265)
T ss_dssp             CCHHHHHHHHHHTTCC-----CCC----CHHHHHHHCSSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCC-CCHHHHH----HHHHHHCCCCCCHHHHHHH
T ss_conf             7888999999996057-7102436----8999825899999999999

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.21  E-value=1.2e-07  Score=56.97  Aligned_cols=63  Identities=19%  Similarity=0.159  Sum_probs=30.8

Q ss_pred             HHCCCCCCCCEEECCCCCCCCCC---CCCCCCCCCCEEECCCCCCCCCCH-HHCCCCCCCEEECCCC
Q ss_conf             10589997419982563343445---342277877869813787501311-1106677649973763
Q 000887          394 DLLPQCKKLRVLSLGSYCITEVP---ISIGCLKQLRYLNFSRSEIQCLPD-AICSLFNLEILILRNC  456 (1237)
Q Consensus       394 ~~~~~l~~Lr~L~L~~~~i~~lp---~~~~~l~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~L~~~  456 (1237)
                      .++..++.|++|+|++|.|+.++   ..+..+++|++|++++|.|++++. .+.+..+|+.|++++|
T Consensus        59 ~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~N  125 (162)
T d1koha1          59 IIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGN  125 (162)
T ss_dssp             HHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTS
T ss_pred             HHHHHCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCC
T ss_conf             8897487878863777666677315889865885610004357213423442220331042664899

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.18  E-value=9e-05  Score=40.22  Aligned_cols=131  Identities=11%  Similarity=0.074  Sum_probs=74.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHCCCCC-----CCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-C
Q ss_conf             9999279982999999998000113-----789829999759769999999999983305899569789999999996-6
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDKLTE-----AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV-F   89 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~~~~-----~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-~   89 (1237)
                      +.++|.+|||||+++..++.+....     ..+..+|..-...         +.    .......+.++....+...+ .
T Consensus        46 ~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~---------l~----ag~~~~g~~e~r~~~i~~~~~~  112 (387)
T d1qvra2          46 PVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS---------LL----AGAKYRGEFEERLKAVIQEVVQ  112 (387)
T ss_dssp             CEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------------------CHHHHHHHHHHHHHT
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHCCCCHHHCCCEEEEEEHHH---------HH----CCCCCCHHHHHHHHHHHHHHCC
T ss_conf             7687999988999999999999808999788696689955766---------65----2667413689999999998505


Q ss_pred             C-CCEEEEEECCCCCC-------HHHHHHHHCCCCCCCCCCEEEEEECCHHHHHHHC-------CCCEEECCCCCHHHHH
Q ss_conf             9-72999996887777-------6269983122568999959999907456787526-------8870747899924339
Q 000887           90 K-KKFLIVLDDVWSER-------YDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMG-------SGKNYELKLLSDDDCW  154 (1237)
Q Consensus        90 ~-~~~LlvlDdv~~~~-------~~~~~~l~~~~~~~~~~~~ilvTtR~~~~~~~~~-------~~~~~~l~~l~~~ea~  154 (1237)
                      . .+.++++|++...-       ..+...+..|.... ..-++|-+|....... +.       ..+.+.+++.+.+++.
T Consensus       113 ~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~r-g~~~~I~~tT~~ey~~-~e~d~al~rrF~~v~v~ep~~~~~~  190 (387)
T d1qvra2         113 SQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR-GELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTVEETI  190 (387)
T ss_dssp             TCSSEEEEECCC-------------------HHHHHT-TCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCHHHHH
T ss_pred             CCCCEEEEECCHHHHHCCCCCCCCCCHHHHHHHHHHC-CCCCEEEECCHHHHHH-HCCCHHHHHHCCCCCCCCCCHHHHH
T ss_conf             8996698724088884277787741389999999737-8851666368999987-6336799982461127998678899


Q ss_pred             HHHHHHH
Q ss_conf             9999976
Q 000887          155 SVFVAHA  161 (1237)
Q Consensus       155 ~l~~~~~  161 (1237)
                      ++++...
T Consensus       191 ~il~~~~  197 (387)
T d1qvra2         191 SILRGLK  197 (387)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
T ss_conf             9999999

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.04  E-value=0.00011  Score=39.63  Aligned_cols=69  Identities=19%  Similarity=0.237  Sum_probs=39.0

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC---CHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             9399999927998299999999800011378982999975976---9999999999983305899569789999999996
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF---DVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~---~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .++-|-++|++|+|||++|++++.....    ..+.+..+...   ......                 ..+...+....
T Consensus        39 p~~~vLL~GppGtGKT~la~alA~~~~~----~~~~i~~~~~~~g~~~~~~~-----------------~~i~~if~~A~   97 (246)
T d1d2na_          39 PLVSVLLEGPPHSGKTALAAKIAEESNF----PFIKICSPDKMIGFSETAKC-----------------QAMKKIFDDAY   97 (246)
T ss_dssp             SEEEEEEECSTTSSHHHHHHHHHHHHTC----SEEEEECGGGCTTCCHHHHH-----------------HHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCC----CCCCCCCCCCCCCCCCCCHH-----------------HHHHHHHHHHH
T ss_conf             9807998896999889999998620100----23334565223565421122-----------------44444565555


Q ss_pred             CCCCEEEEEECCC
Q ss_conf             6972999996887
Q 000887           89 FKKKFLIVLDDVW  101 (1237)
Q Consensus        89 ~~~~~LlvlDdv~  101 (1237)
                      +..+.++++|+++
T Consensus        98 ~~~p~il~iDEid  110 (246)
T d1d2na_          98 KSQLSCVVVDDIE  110 (246)
T ss_dssp             TSSEEEEEECCHH
T ss_pred             HCCCCEEEHHHHH
T ss_conf             3242223310256

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.04  E-value=1.4e-07  Score=56.51  Aligned_cols=77  Identities=23%  Similarity=0.146  Sum_probs=46.0

Q ss_pred             CEEECCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCC---HHHCCCCCCCEEECCCCCCCCCCCH-HHCCCCCCCEEECC
Q ss_conf             1998256334344534227787786981378750131---1110667764997376326855883-11054556588216
Q 000887          403 RVLSLGSYCITEVPISIGCLKQLRYLNFSRSEIQCLP---DAICSLFNLEILILRNCWCLLKLPS-RIGNLVNLHYLNIE  478 (1237)
Q Consensus       403 r~L~L~~~~i~~lp~~~~~l~~L~~L~L~~~~i~~lp---~~~~~L~~L~~L~L~~~~~l~~lp~-~i~~L~~L~~L~l~  478 (1237)
                      ..+....+....++..+..+++|++|+|++|.|+.++   ..+..+++|+.|++++| .+..+++ ...+..+|+.|++.
T Consensus        45 ~~l~~~~~~~~~l~~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N-~i~~l~~l~~l~~~~L~~L~L~  123 (162)
T d1koha1          45 VVLNRRSSMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGN-ELKSERELDKIKGLKLEELWLD  123 (162)
T ss_dssp             CCTTSHHHHHHHHHHHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTS-CCCCGGGHHHHTTCCCSSCCCT
T ss_pred             HHCCHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCC-CCCCCHHHHHHHCCCCCEEECC
T ss_conf             112255567666078897487878863777666677315889865885610004357-2134234422203310426648


Q ss_pred             CC
Q ss_conf             98
Q 000887          479 GA  480 (1237)
Q Consensus       479 ~~  480 (1237)
                      +|
T Consensus       124 ~N  125 (162)
T d1koha1         124 GN  125 (162)
T ss_dssp             TS
T ss_pred             CC
T ss_conf             99

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.98  E-value=5.3e-06  Score=47.34  Aligned_cols=130  Identities=10%  Similarity=0.066  Sum_probs=71.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCC-----CCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             999999279982999999998000113-----789829999759769999999999983305899569789999999996
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE-----AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~-----~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .-+.++|.+|+|||+++..++.+....     .-+..+|..     +...    +   +... ....+.++....+.+.+
T Consensus        44 ~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-----d~~~----L---iAg~-~~rG~~E~rl~~il~e~  110 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-----DMGA----L---VAGA-KYRGEFEERLKGVLNDL  110 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-----CHHH----H---HTTT-CSHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHCCCCHHHCCCEEEEE-----EHHH----H---HCCC-CCCHHHHHHHHHHHHHH
T ss_conf             87399835875447999999999980899978818569996-----6999----8---6458-74077999999999987


Q ss_pred             -C-CCCEEEEEECCCCCC-------HHHHHHHHCCCCCCCCCCEEEEEECCHHHHHHHC-------CCCEEECCCCCHHH
Q ss_conf             -6-972999996887777-------6269983122568999959999907456787526-------88707478999243
Q 000887           89 -F-KKKFLIVLDDVWSER-------YDLWQALKSPFMAGAPGSRIIVTTRSMDVALTMG-------SGKNYELKLLSDDD  152 (1237)
Q Consensus        89 -~-~~~~LlvlDdv~~~~-------~~~~~~l~~~~~~~~~~~~ilvTtR~~~~~~~~~-------~~~~~~l~~l~~~e  152 (1237)
                       . ..+.++++|++...-       ..+...+..+.... ..-++|.||...+......       ....+.+++.+.++
T Consensus       111 ~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r-g~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~  189 (195)
T d1jbka_         111 AKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR-GELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVED  189 (195)
T ss_dssp             HHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT-TSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCCHHH
T ss_pred             HCCCCCEEEECCHHHHHHCCCCCCCCCCHHHHHHHHHHC-CCCEEEECCCHHHHHHHHHCCHHHHHCCCEEECCCCCHHH
T ss_conf             317980899726089984378777752389999999857-9954985189999999987388999639875458989899


Q ss_pred             HHHHH
Q ss_conf             39999
Q 000887          153 CWSVF  157 (1237)
Q Consensus       153 a~~l~  157 (1237)
                      +.+++
T Consensus       190 t~~IL  194 (195)
T d1jbka_         190 TIAIL  194 (195)
T ss_dssp             HHTTC
T ss_pred             HHHHH
T ss_conf             99985

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.95  E-value=8.8e-05  Score=40.29  Aligned_cols=130  Identities=11%  Similarity=-0.013  Sum_probs=72.8

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCC--CCCCCCEEEEEECC-CCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf             9939999992799829999999980001--13789829999759-76999999999998330589956978999999999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKL--TEAFEPKAWVCVSD-DFDVLRISKAILDSIKRSSCKLEDLNSVQLELKET   87 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~--~~~f~~~~w~~~~~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~   87 (1237)
                      +....+-++|.+|+|||++|..+++...  ...++.++++.... ...+.++. .+...+.....               
T Consensus        13 ~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR-~i~~~~~~~~~---------------   76 (198)
T d2gnoa2          13 SEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIR-TIKDFLNYSPE---------------   76 (198)
T ss_dssp             CSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHH-HHHHHHTSCCS---------------
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHH-HHHHHHHHCCC---------------
T ss_conf             99855998898998889999999999843456799889980776789989999-99999961754---------------


Q ss_pred             HCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCCEEEEEECCH-HHHHHHCC-CCEEECCCCCHHHHHHHHHH
Q ss_conf             66972999996887777626998312256899995999990745-67875268-87074789992433999999
Q 000887           88 VFKKKFLIVLDDVWSERYDLWQALKSPFMAGAPGSRIIVTTRSM-DVALTMGS-GKNYELKLLSDDDCWSVFVA  159 (1237)
Q Consensus        88 l~~~~~LlvlDdv~~~~~~~~~~l~~~~~~~~~~~~ilvTtR~~-~~~~~~~~-~~~~~l~~l~~~ea~~l~~~  159 (1237)
                       .+++-++|+|+++.-......++...+-.-..++..+.+|.+. .+...... ...+.+...  .+...+...
T Consensus        77 -~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p--~~~~~~~~~  147 (198)
T d2gnoa2          77 -LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVP--KEFRDLVKE  147 (198)
T ss_dssp             -SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEECCCC--HHHHHHHHH
T ss_pred             -CCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCHHHCHHHHHCCEEEEECCCC--HHHHHHHHH
T ss_conf             -58987999947310366666478887737898852222069956687887352277767993--688999999

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.78  E-value=0.00023  Score=37.88  Aligned_cols=92  Identities=16%  Similarity=0.096  Sum_probs=52.1

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCC-HHHHHHHHHHHHHCCCC---CCCCHHHHHHHH
Q ss_conf             99993999999279982999999998000113789829999759769-99999999998330589---956978999999
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD-VLRISKAILDSIKRSSC---KLEDLNSVQLEL   84 (1237)
Q Consensus         9 ~~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~-~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l   84 (1237)
                      ...+.+|+.+.|+.|+||||.+.+++.+..++ ...+..++...... ..+-++..++.++.+..   ...+........
T Consensus         6 ~~~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~-g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~   84 (207)
T d1ls1a2           6 VLKDRNLWFLVGLQGSGKTTTAAKLALYYKGK-GRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRV   84 (207)
T ss_dssp             CCCSSEEEEEECCTTTTHHHHHHHHHHHHHHT-TCCEEEEECCSSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf             78998689998999998899999999999977-99279995443464088889999986288631112442036788889


Q ss_pred             H--HHHCCCCEEEEEECCCC
Q ss_conf             9--99669729999968877
Q 000887           85 K--ETVFKKKFLIVLDDVWS  102 (1237)
Q Consensus        85 ~--~~l~~~~~LlvlDdv~~  102 (1237)
                      .  ....+.. ++++|=+..
T Consensus        85 ~~~~~~~~~d-~vlIDTaGr  103 (207)
T d1ls1a2          85 EEKARLEARD-LILVDTAGR  103 (207)
T ss_dssp             HHHHHHHTCC-EEEEECCCC
T ss_pred             HHHHHHCCCC-CEEECCCCC
T ss_conf             8887633676-403345442

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.74  E-value=0.0001  Score=39.86  Aligned_cols=83  Identities=17%  Similarity=0.126  Sum_probs=56.6

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHHH
Q ss_conf             9399999927998299999999800011378982999975976999999999998330589-----95697899999999
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKE   86 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~   86 (1237)
                      .-+++-|+|.+|.|||++|.+++....+. -..++|++.....+..     ++..++....     ...+.++....+..
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~-g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~  129 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKA-GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  129 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT-TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCEEEEEECCCCCCHH-----HHHHHCCCCHHEEEECCCCHHHHHHHHHH
T ss_conf             75478980587652279999999999707-9989999887658999-----99982898123799748999999999999


Q ss_pred             HHCC-CCEEEEEECC
Q ss_conf             9669-7299999688
Q 000887           87 TVFK-KKFLIVLDDV  100 (1237)
Q Consensus        87 ~l~~-~~~LlvlDdv  100 (1237)
                      .... ..-|+|+|.+
T Consensus       130 l~~~~~~~liIiDSi  144 (268)
T d1xp8a1         130 LVRSGAIDVVVVDSV  144 (268)
T ss_dssp             HHTTTCCSEEEEECT
T ss_pred             HHHCCCCCEEEEECC
T ss_conf             986589719999454

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.73  E-value=0.00027  Score=37.51  Aligned_cols=91  Identities=16%  Similarity=0.131  Sum_probs=53.8

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCH-HHHHHHHHHHHHCCCC---CCCCHHHHHHHHH
Q ss_conf             99939999992799829999999980001137898299997597699-9999999998330589---9569789999999
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDV-LRISKAILDSIKRSSC---KLEDLNSVQLELK   85 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~-~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~   85 (1237)
                      ...+.+|.++|+.|+||||.+.+++++...+ -..+..+........ .+-++..++.++.+..   ...+.........
T Consensus         8 ~~~p~vi~lvGptGvGKTTTiAKLAa~~~~~-~~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~   86 (213)
T d1vmaa2           8 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVDE-GKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV   86 (213)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHHT-TCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             9999899998999998899999999999977-990699960133420467888776432764103677776899878878


Q ss_pred             H-HHCCCCEEEEEECCC
Q ss_conf             9-966972999996887
Q 000887           86 E-TVFKKKFLIVLDDVW  101 (1237)
Q Consensus        86 ~-~l~~~~~LlvlDdv~  101 (1237)
                      . ...+..=++++|=+-
T Consensus        87 ~~~~~~~~d~ilIDTaG  103 (213)
T d1vmaa2          87 AHALARNKDVVIIDTAG  103 (213)
T ss_dssp             HHHHHTTCSEEEEEECC
T ss_pred             HHHHHCCCCEEEEECCC
T ss_conf             99987699989982455

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.72  E-value=0.00012  Score=39.53  Aligned_cols=84  Identities=18%  Similarity=0.106  Sum_probs=56.4

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHH
Q ss_conf             99399999927998299999999800011378982999975976999999999998330589-----9569789999999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELK   85 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~   85 (1237)
                      ..-+++-++|.+|+|||++|.+++.... ..-..++|++.....+...     +.+++....     .....++....+.
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q-~~g~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~  131 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQ-AAGGVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIAD  131 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHH-HTTCEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHH-CCCCEEEEEECCCCCCHHH-----HHHHCCCHHHEEEECCCCHHHHHHHHH
T ss_conf             6633699964887488999999999875-4898899998976679999-----998099889958966998999999999


Q ss_pred             HHHCC-CCEEEEEECC
Q ss_conf             99669-7299999688
Q 000887           86 ETVFK-KKFLIVLDDV  100 (1237)
Q Consensus        86 ~~l~~-~~~LlvlDdv  100 (1237)
                      ..... +.-|+|+|.+
T Consensus       132 ~l~~~~~~~liIiDSi  147 (269)
T d1mo6a1         132 MLIRSGALDIVVIDSV  147 (269)
T ss_dssp             HHHHTTCEEEEEEECS
T ss_pred             HHHHCCCCCEEEEECC
T ss_conf             9985599878999330

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=97.66  E-value=0.0001  Score=39.94  Aligned_cols=81  Identities=17%  Similarity=0.129  Sum_probs=51.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHHHHH
Q ss_conf             99999927998299999999800011378982999975976999999999998330589-----9569789999999996
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC-----KLEDLNSVQLELKETV   88 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~~~l   88 (1237)
                      +++-|+|.+|+|||++|.+++....+ .-..++|++.....+...     +..++....     .....++....+....
T Consensus        55 ~itei~G~~gsGKTtl~l~~~~~~q~-~g~~~vyidtE~~~~~~~-----a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~  128 (263)
T d1u94a1          55 RIVEIYGPESSGKTTLTLQVIAAAQR-EGKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICDALA  128 (263)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHH-TTCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHC-CCCEEEEECCCCCCCHHH-----HHHHCCCHHHEEEECCCCHHHHHHHHHHHH
T ss_conf             58998057774789999999999870-898799986544548999-----998399879979962898999999999998


Q ss_pred             C-CCCEEEEEECC
Q ss_conf             6-97299999688
Q 000887           89 F-KKKFLIVLDDV  100 (1237)
Q Consensus        89 ~-~~~~LlvlDdv  100 (1237)
                      + +..-|+|+|.+
T Consensus       129 ~~~~~~liViDSi  141 (263)
T d1u94a1         129 RSGAVDVIVVDSV  141 (263)
T ss_dssp             HHTCCSEEEEECG
T ss_pred             HCCCCCEEEEECC
T ss_conf             5499989999886

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.64  E-value=0.00028  Score=37.33  Aligned_cols=86  Identities=20%  Similarity=0.203  Sum_probs=54.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC-CHHHHHHHHHHHHHC--CC----------CCCCCHH---
Q ss_conf             9999927998299999999800011378982999975976-999999999998330--58----------9956978---
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKR--SS----------CKLEDLN---   78 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~--~~----------~~~~~~~---   78 (1237)
                      -++|.|.+|+|||+|+.+++.+..+.+-+.++++-+++.. ++.++.+.+...-..  ..          .......   
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~~~~~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~~~r~  149 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARA  149 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHTTTCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCHHHHH
T ss_conf             77766799989899999999988761799699999555759999999998861765456664238999978999999999


Q ss_pred             ---HHHHHHHHHHC---CCCEEEEEECC
Q ss_conf             ---99999999966---97299999688
Q 000887           79 ---SVQLELKETVF---KKKFLIVLDDV  100 (1237)
Q Consensus        79 ---~~~~~l~~~l~---~~~~LlvlDdv  100 (1237)
                         ...-.+.++++   ++.+|+++||.
T Consensus       150 ~~~~~a~~iAEyf~~~~G~~VLv~~Dsl  177 (276)
T d2jdid3         150 RVALTGLTVAEYFRDQEGQDVLLFIDNI  177 (276)
T ss_dssp             HHHHHHHHHHHHHHHTTCSCEEEEEECT
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECCH
T ss_conf             9999999999998863798489997060

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.56  E-value=0.00025  Score=37.64  Aligned_cols=91  Identities=18%  Similarity=0.049  Sum_probs=52.6

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHH-HHHHHHHHHHHCCCCCC---CCHHHHHH-HH
Q ss_conf             999399999927998299999999800011378982999975976999-99999999833058995---69789999-99
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVL-RISKAILDSIKRSSCKL---EDLNSVQL-EL   84 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~-~~~~~i~~~l~~~~~~~---~~~~~~~~-~l   84 (1237)
                      +..+.||.++|+.|+||||.+.+++++...+ -..+..++........ +-++..+..++.+....   .+...... .+
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~~~-g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~a~   87 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYKKK-GFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGV   87 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHHHT-TCCEEEEECCCSSHHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEEEECCCCCHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHH
T ss_conf             9999899998999999899999999999977-993699972023551567898740146842230244102447899999


Q ss_pred             HHHHCCCCEEEEEECCC
Q ss_conf             99966972999996887
Q 000887           85 KETVFKKKFLIVLDDVW  101 (1237)
Q Consensus        85 ~~~l~~~~~LlvlDdv~  101 (1237)
                      ........=++++|=+-
T Consensus        88 ~~~~~~~~d~IlIDTaG  104 (211)
T d1j8yf2          88 EKFLSEKMEIIIVDTAG  104 (211)
T ss_dssp             HHHHHTTCSEEEEECCC
T ss_pred             HHHHCCCCCEEEEECCC
T ss_conf             87402677369985377

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.54  E-value=4.1e-05  Score=42.20  Aligned_cols=38  Identities=16%  Similarity=0.044  Sum_probs=29.6

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             93999999279982999999998000113789829999
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      +-.+|.+.|++|+||||+|++++......+++.+.++.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~~~~~~~~~~   42 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLL   42 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             97699988999999999999999998650798403211

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.53  E-value=0.00014  Score=39.18  Aligned_cols=89  Identities=13%  Similarity=0.037  Sum_probs=52.4

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC-CHHHHHHHHHHHHHCCCC---CCCCHHHHHHHHHH
Q ss_conf             99399999927998299999999800011378982999975976-999999999998330589---95697899999999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRSSC---KLEDLNSVQLELKE   86 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~   86 (1237)
                      ++.+++.++|+.|+||||.+.+++++..+. -..+..++..... ...+-++..++.++.+..   ...+..........
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~~~~   82 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNL-GKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQ   82 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTT-TCCEEEECCCCSSTTHHHHHHHHHHHHTCCEECCCTTCCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEEECCCCCCCHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHH
T ss_conf             997799998999998899999999999977-9907999813666540266764054568238961677427889999899


Q ss_pred             HHC-CCCEEEEEECC
Q ss_conf             966-97299999688
Q 000887           87 TVF-KKKFLIVLDDV  100 (1237)
Q Consensus        87 ~l~-~~~~LlvlDdv  100 (1237)
                      ..+ ...=++++|=.
T Consensus        83 ~~~~~~~d~ilIDTa   97 (207)
T d1okkd2          83 AMKARGYDLLFVDTA   97 (207)
T ss_dssp             HHHHHTCSEEEECCC
T ss_pred             HHHHCCCCEEECCCC
T ss_conf             999879999971752

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.48  E-value=0.00024  Score=37.71  Aligned_cols=90  Identities=17%  Similarity=0.130  Sum_probs=51.6

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCH--HHHHHHHHHHHHCCCCCC---CCHHHHHHHH
Q ss_conf             99939999992799829999999980001137898299997597699--999999999833058995---6978999999
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDV--LRISKAILDSIKRSSCKL---EDLNSVQLEL   84 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~--~~~~~~i~~~l~~~~~~~---~~~~~~~~~l   84 (1237)
                      ...+.||.++|+.|+||||.+.+++++..++ -..+..+. .+.+..  .+-++..++.++.+....   .+........
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~-g~kV~lit-~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~   83 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ-GKSVMLAA-GDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDA   83 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT-TCCEEEEC-CCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCEEEEE-CCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHH
T ss_conf             9999799998999999899999999999977-99479982-321366612045554343388621135687799999999


Q ss_pred             HHHHC-CCCEEEEEECCC
Q ss_conf             99966-972999996887
Q 000887           85 KETVF-KKKFLIVLDDVW  101 (1237)
Q Consensus        85 ~~~l~-~~~~LlvlDdv~  101 (1237)
                      .+..+ +..=++++|=.-
T Consensus        84 ~~~a~~~~~d~ilIDTaG  101 (211)
T d2qy9a2          84 IQAAKARNIDVLIADTAG  101 (211)
T ss_dssp             HHHHHHTTCSEEEECCCC
T ss_pred             HHHHHHCCCCEEEECCCC
T ss_conf             999987699889965688

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=97.40  E-value=0.00037  Score=36.65  Aligned_cols=88  Identities=11%  Similarity=0.041  Sum_probs=50.8

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCC--CCEEEEEECCCCCHHHHHHHHHHHHH--CCCCCCCCHHHHHHHHH
Q ss_conf             999399999927998299999999800011378--98299997597699999999999833--05899569789999999
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAF--EPKAWVCVSDDFDVLRISKAILDSIK--RSSCKLEDLNSVQLELK   85 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f--~~~~w~~~~~~~~~~~~~~~i~~~l~--~~~~~~~~~~~~~~~l~   85 (1237)
                      ...+-+|||.|..|+||||+|+.+... ..+.+  ..+.-++...-.-.......  +.+.  .....+-+.+.....+.
T Consensus        77 ~k~P~iIGIaG~sgSGKSTla~~L~~l-L~~~~~~~~v~~Is~D~F~~~~~~l~~--~~~~~~~g~Pes~D~~~L~~~L~  153 (308)
T d1sq5a_          77 QRIPYIISIAGSVAVGKSTTARVLQAL-LSRWPEHRRVELITTDGFLHPNQVLKE--RGLMKKKGFPESYDMHRLVKFVS  153 (308)
T ss_dssp             CCCCEEEEEEECTTSSHHHHHHHHHHH-HTTSTTCCCEEEEEGGGGBCCHHHHHH--HTCTTCTTSGGGBCHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHH-HHHHCCCCCEEEEEEEEEECCCHHHHH--HCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             899889999689999876899999999-730468996599952156898458888--36876688167631999999999


Q ss_pred             HHHCCCC-E-EEEEECC
Q ss_conf             9966972-9-9999688
Q 000887           86 ETVFKKK-F-LIVLDDV  100 (1237)
Q Consensus        86 ~~l~~~~-~-LlvlDdv  100 (1237)
                      ....+++ + .=++|-.
T Consensus       154 ~lk~g~~~v~~P~yd~~  170 (308)
T d1sq5a_         154 DLKSGVPNVTAPVYSHL  170 (308)
T ss_dssp             HHTTTCSCEEECCEETT
T ss_pred             HHHCCCCCCEEECCCHH
T ss_conf             99759986421053001

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.38  E-value=0.00013  Score=39.21  Aligned_cols=110  Identities=17%  Similarity=0.233  Sum_probs=54.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCC--CCCCHHHHHHHHHHHHCC
Q ss_conf             399999927998299999999800011378982999975976999999999998330589--956978999999999669
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSC--KLEDLNSVQLELKETVFK   90 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~--~~~~~~~~~~~l~~~l~~   90 (1237)
                      ..++.++|+.|+|||.+|+.++...... ....+-++.+...+......-+    +.+..  .......+...++   +.
T Consensus        53 ~~~~lf~Gp~G~GKt~lak~la~~l~~~-~~~~~~~~~~~~~~~~~~~~L~----g~~~gyvG~~~~~~l~~~~~---~~  124 (315)
T d1qvra3          53 IGSFLFLGPTGVGKTELAKTLAATLFDT-EEAMIRIDMTEYMEKHAVSRLI----GAPPGYVGYEEGGQLTEAVR---RR  124 (315)
T ss_dssp             SEEEEEBSCSSSSHHHHHHHHHHHHHSS-GGGEEEECTTTCCSSGGGGGC------------------CHHHHHH---HC
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHCCC-CCCEEEEECCCCCCCHHHHHHC----CCCCCCCCCCCCCHHHHHHH---HC
T ss_conf             6699997888624899999999983588-7534887315545421566514----89998767466784899998---49


Q ss_pred             CCEEEEEECCCCCCHHHHHHHHCCCCCC-----------CCCCEEEEEECC
Q ss_conf             7299999688777762699831225689-----------999599999074
Q 000887           91 KKFLIVLDDVWSERYDLWQALKSPFMAG-----------APGSRIIVTTRS  130 (1237)
Q Consensus        91 ~~~LlvlDdv~~~~~~~~~~l~~~~~~~-----------~~~~~ilvTtR~  130 (1237)
                      ...+++||+++....+.+..+...+..+           ..++-+|+||..
T Consensus       125 p~~Vvl~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsnl  175 (315)
T d1qvra3         125 PYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNL  175 (315)
T ss_dssp             SSEEEEESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECCT
T ss_pred             CCCEEEEEHHHHCCHHHHHHHHHHHCCCCEECCCCCEECCCCEEEEEECCC
T ss_conf             983799714754078999899998613834279996853754289874245

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.36  E-value=0.00016  Score=38.84  Aligned_cols=110  Identities=15%  Similarity=0.112  Sum_probs=55.6

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-C
Q ss_conf             993999999279982999999998000113789829999759769999999999983305899569789999999996-6
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETV-F   89 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l-~   89 (1237)
                      ....++.+.|+.|+|||.||+.++...    +...+-++.+.-.+...    ....++.+. ... .......+...+ .
T Consensus        50 ~p~~~~lf~Gp~GvGKT~lak~la~~l----~~~~i~~d~s~~~~~~~----~~~l~g~~~-gy~-g~~~~~~l~~~~~~  119 (315)
T d1r6bx3          50 KPVGSFLFAGPTGVGKTEVTVQLSKAL----GIELLRFDMSEYMERHT----VSRLIGAPP-GYV-GFDQGGLLTDAVIK  119 (315)
T ss_dssp             SCSEEEEEECSTTSSHHHHHHHHHHHH----TCEEEEEEGGGCSSSSC----CSSSCCCCS-CSH-HHHHTTHHHHHHHH
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHC----CCCEEEECCCCCCCHHH----HHHHCCCCC-CCC-CCCCCCHHHHHHHH
T ss_conf             876589997787500699999998633----67706741544455446----665214678-750-11468703377773


Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHCCCCCC-----------CCCCEEEEEECC
Q ss_conf             97299999688777762699831225689-----------999599999074
Q 000887           90 KKKFLIVLDDVWSERYDLWQALKSPFMAG-----------APGSRIIVTTRS  130 (1237)
Q Consensus        90 ~~~~LlvlDdv~~~~~~~~~~l~~~~~~~-----------~~~~~ilvTtR~  130 (1237)
                      ....++.||+++....+.+..+...+..+           ..++-+|.||..
T Consensus       120 ~~~~vvl~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsni  171 (315)
T d1r6bx3         120 HPHAVLLLDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTNA  171 (315)
T ss_dssp             CSSEEEEEETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEECS
T ss_pred             CCCCHHHHCCCCCCCCHHHHHHHHHHCCCEECCCCCCCCCCCCEEEEECCCH
T ss_conf             8543022122230163376656776214602588997268632588841440

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.36  E-value=5.9e-05  Score=41.29  Aligned_cols=25  Identities=16%  Similarity=0.267  Sum_probs=22.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9399999927998299999999800
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -++.|+|.|++|+||||||++++..
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             6328999899999899999999998

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.36  E-value=0.00042  Score=36.37  Aligned_cols=28  Identities=36%  Similarity=0.414  Sum_probs=23.7

Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999399999927998299999999800
Q 000887            9 DAANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus         9 ~~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ....+.+|.++|++|+||||+|++.+..
T Consensus        10 ~~~~p~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          10 LSPNPEVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             SCSSCCEEEEECCTTSSHHHHHHHHTGG
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             7999989999899999899999999976

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.25  E-value=0.00019  Score=38.31  Aligned_cols=23  Identities=22%  Similarity=0.486  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++|.|.|++|+||||+|++++..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             08999899999989999999998

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.23  E-value=0.00018  Score=38.43  Aligned_cols=39  Identities=23%  Similarity=0.144  Sum_probs=27.9

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             9993999999279982999999998000113789829999
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      ..++-+|+|.|.+|.||||+|+++...... ....+...+
T Consensus        19 ~~~~~iIgI~G~~GSGKSTla~~L~~~l~~-~~~~~~~~~   57 (198)
T d1rz3a_          19 TAGRLVLGIDGLSRSGKTTLANQLSQTLRE-QGISVCVFH   57 (198)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHHHHH-TTCCEEEEE
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHCC-CCCCCEECC
T ss_conf             799889997898878999999999998363-466520012

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.00011  Score=39.64  Aligned_cols=27  Identities=33%  Similarity=0.401  Sum_probs=22.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCC
Q ss_conf             999999279982999999998000113
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE   40 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~   40 (1237)
                      |.|.|.|++|+|||||+++++......
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             699998899971999999999999977

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.21  E-value=7.2e-05  Score=40.79  Aligned_cols=39  Identities=23%  Similarity=0.152  Sum_probs=29.1

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             993999999279982999999998000113789829999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      .+..+|.+.|++|.||||+|+++...........+++++
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   60 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             998699998999999899999999887774275089975

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=97.20  E-value=0.00012  Score=39.58  Aligned_cols=30  Identities=23%  Similarity=0.383  Sum_probs=25.3

Q ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999993999999279982999999998000
Q 000887            8 SDAANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus         8 ~~~~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+.+.++.|.++|++|+|||++|+.++...
T Consensus        27 ~~~~~P~~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          27 KAVESPTAFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             CCCSSCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             278999799988979988999999999986

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.16  E-value=0.00018  Score=38.42  Aligned_cols=27  Identities=26%  Similarity=0.352  Sum_probs=24.1

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             999399999927998299999999800
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...+.+|.|.|++|+||||+|+.++..
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             889948999899999889999999999

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.12  E-value=0.00066  Score=35.21  Aligned_cols=12  Identities=17%  Similarity=0.207  Sum_probs=4.7

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             410346799997
Q 000887          305 KYVMHDLVHDLA  316 (1237)
Q Consensus       305 ~~~~H~lv~~~~  316 (1237)
                      ++.+-.++..+.
T Consensus       177 Tt~i~~~l~~l~  188 (359)
T d1w36d1         177 TTTVAKLLAALI  188 (359)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             EEHHHHHHHHHH
T ss_conf             216999999999

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.12  E-value=0.00015  Score=39.02  Aligned_cols=31  Identities=19%  Similarity=0.351  Sum_probs=24.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf             3999999279982999999998000113789
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE   43 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~   43 (1237)
                      .+|++|.|..|+|||||+.++......+.+.
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~g~~   32 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCARGIR   32 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             7889999189998999999999999977976

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=97.11  E-value=9.9e-05  Score=40.00  Aligned_cols=23  Identities=39%  Similarity=0.553  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.|.+.|++|+||||+|+.++..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             74999899999999999999999

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.09  E-value=0.0024  Score=32.00  Aligned_cols=83  Identities=13%  Similarity=0.048  Sum_probs=41.6

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCC----CEEEEEECCCC---CHHHHHHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf             93999999279982999999998000113789----82999975976---999999999998330589956978999999
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE----PKAWVCVSDDF---DVLRISKAILDSIKRSSCKLEDLNSVQLEL   84 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~----~~~w~~~~~~~---~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l   84 (1237)
                      ++-+|+|.|..|.||||+|+++........++    .+.-+.....+   ..............-......+.+.....+
T Consensus         1 ~P~iIgI~G~~gSGKSTla~~L~~~l~~~~~~~~~~~~~vi~~D~yy~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~   80 (213)
T d1uj2a_           1 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTL   80 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGGGGBCCCCHHHHHHHHTTCSCTTSGGGBCHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHCHHCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             99899998999787999999999996410134578843999346532244022203555145555782788877777666


Q ss_pred             HHHHCCCCEE
Q ss_conf             9996697299
Q 000887           85 KETVFKKKFL   94 (1237)
Q Consensus        85 ~~~l~~~~~L   94 (1237)
                      .....++...
T Consensus        81 ~~~~~~~~~~   90 (213)
T d1uj2a_          81 KEITEGKTVQ   90 (213)
T ss_dssp             HHHHTTCCEE
T ss_pred             HHHHCCCCCC
T ss_conf             6653288631

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.08  E-value=0.00018  Score=38.43  Aligned_cols=23  Identities=35%  Similarity=0.557  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++|.|.|++|+||||+|+++...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             79999899999999999999995

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=97.06  E-value=0.00044  Score=36.26  Aligned_cols=84  Identities=19%  Similarity=0.192  Sum_probs=45.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE-ECCCCCHHHHHHHHHHHHHC---CCCCCCCHH------HHHHH
Q ss_conf             999999279982999999998000113789829999-75976999999999998330---589956978------99999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC-VSDDFDVLRISKAILDSIKR---SSCKLEDLN------SVQLE   83 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~-~~~~~~~~~~~~~i~~~l~~---~~~~~~~~~------~~~~~   83 (1237)
                      .-++|.|.+|+|||+|+.+++.....++-..++.+. +++...  .+ ..+......   .........      .....
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~~~~~~~~v~~~~~iger~~--ev-~~~~~~~~~~vv~~t~d~~~~~r~~~~~~a~~  120 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPE--EV-TEMQRLVKGEVVASTFDEPASRHVQVAEMVIE  120 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHHHHCTTSEEEEEEEEECHH--HH-HHHHHHCSSEEEEEETTSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECEEHH--HH-HHHHHHCCEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             7556867999887899999999775158976999876110087--88-76775405079960588835678999999999


Q ss_pred             HHHHHC--CCCEEEEEECC
Q ss_conf             999966--97299999688
Q 000887           84 LKETVF--KKKFLIVLDDV  100 (1237)
Q Consensus        84 l~~~l~--~~~~LlvlDdv  100 (1237)
                      +.++++  ++.+|+++||+
T Consensus       121 iAEyfrd~G~dVLli~Dsl  139 (289)
T d1xpua3         121 KAKRLVEHKKDVIILLDSI  139 (289)
T ss_dssp             HHHHHHTTTCEEEEEESCH
T ss_pred             HHHHHHHHCCCCEEECCCH
T ss_conf             9999998265751551768

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.06  E-value=0.0023  Score=32.05  Aligned_cols=91  Identities=16%  Similarity=0.142  Sum_probs=53.3

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCC-C-CCEEEEEECCCCCHHHHHHHHHHHHH-------CCCCCCCCHHHH
Q ss_conf             99939999992799829999999980001137-8-98299997597699999999999833-------058995697899
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEA-F-EPKAWVCVSDDFDVLRISKAILDSIK-------RSSCKLEDLNSV   80 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~-f-~~~~w~~~~~~~~~~~~~~~i~~~l~-------~~~~~~~~~~~~   80 (1237)
                      ...+-+|||.|..|+||||+|..+.......+ . ..++-++..+-+-...-...+.....       .......+.+-.
T Consensus        24 ~~~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll  103 (286)
T d1odfa_          24 NKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLL  103 (286)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCEECCCCCCHHHHHH
T ss_conf             99988998379987889999999999999872778606763567777888999998521355531100478740348899


Q ss_pred             HHHHHHHHCCC------CE-EEEEECC
Q ss_conf             99999996697------29-9999688
Q 000887           81 QLELKETVFKK------KF-LIVLDDV  100 (1237)
Q Consensus        81 ~~~l~~~l~~~------~~-LlvlDdv  100 (1237)
                      ...+.....+.      .+ +=++|-.
T Consensus       104 ~~~l~~l~~~~~~~~~~~v~iP~fDk~  130 (286)
T d1odfa_         104 QEVLNTIFNNNEHPDQDTVVLPKYDKS  130 (286)
T ss_dssp             HHHHHHHTC------CCEEEECCEETT
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCHHHH
T ss_conf             999999974023124566668846777

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.05  E-value=0.00049  Score=35.99  Aligned_cols=40  Identities=20%  Similarity=0.216  Sum_probs=30.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             39999992799829999999980001137898299997597
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      -.++.|+|.+|+|||++|.+++.+.. +....++|++....
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~-~~~~~~~~is~e~~   65 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENAC-ANKERAILFAYEES   65 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHH-TTTCCEEEEESSSC
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHH-HHCCCCCEEECCCC
T ss_conf             84999991899999999999999998-72324411212679

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.03  E-value=0.00034  Score=36.86  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=24.4

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             999399999927998299999999800
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+..++|.|.|++|+||||+|+.++..
T Consensus         5 ~~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           5 PDQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             999728999899999989999999998

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.02  E-value=0.0003  Score=37.24  Aligned_cols=26  Identities=23%  Similarity=0.276  Sum_probs=22.6

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCC
Q ss_conf             39999992799829999999980001
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL   38 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~   38 (1237)
                      +.+|.++|.+|+||||+|++++....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             98999989999999999999999997

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=97.02  E-value=0.0018  Score=32.67  Aligned_cols=70  Identities=19%  Similarity=0.208  Sum_probs=38.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCE
Q ss_conf             99999927998299999999800011378982999975976999999999998330589956978999999999669729
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNSVQLELKETVFKKKF   93 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~   93 (1237)
                      +++.++|++|+|||.+|++++.... ..+. -+-+..+.-.+                .-..+.++....+.+..+ ++.
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~-~~~~-~~~~~~~~~~~----------------~~~G~~e~~~~~~f~~a~-~~~  184 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALG-GKDK-YATVRFGEPLS----------------GYNTDFNVFVDDIARAML-QHR  184 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHH-TTSC-CEEEEBSCSST----------------TCBCCHHHHHHHHHHHHH-HCS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC-CCCC-EEEEEHHHHHH----------------CCCCHHHHHHHHHHHHHH-HCC
T ss_conf             6388877998508899999999863-7998-08978268544----------------244457899999999986-265


Q ss_pred             EEEEECCCC
Q ss_conf             999968877
Q 000887           94 LIVLDDVWS  102 (1237)
Q Consensus        94 LlvlDdv~~  102 (1237)
                      +|.+|.++.
T Consensus       185 ilf~DEid~  193 (321)
T d1w44a_         185 VIVIDSLKN  193 (321)
T ss_dssp             EEEEECCTT
T ss_pred             EEEEEHHHH
T ss_conf             897410122

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.00  E-value=0.00027  Score=37.48  Aligned_cols=30  Identities=27%  Similarity=0.460  Sum_probs=24.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf             999999279982999999998000113789
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFE   43 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~   43 (1237)
                      ++|+|.|++|+||||+++.++.........
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~~~~   31 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVN   31 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             889998999989899999999999876998

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=96.99  E-value=0.00052  Score=35.79  Aligned_cols=39  Identities=26%  Similarity=0.314  Sum_probs=30.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             9999992799829999999980001137898299997597
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      |.|+|+|-||+||||+|..++....+..+ .+.-+++..+
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~G~-rVllID~D~q   40 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGK-TIMVVGCDPK   40 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTC-CEEEEEECTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEECCCC
T ss_conf             79999899857799999999999996899-5899963799

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.99  E-value=0.00045  Score=36.19  Aligned_cols=88  Identities=11%  Similarity=0.116  Sum_probs=50.7

Q ss_pred             HHHHCCCCCCCCEEECCCC-CCCC-----CCCCCCCCCCCCEEECCCCCCCC-----CCHHHCCCCCCCEEECCCCCCCC
Q ss_conf             3210589997419982563-3434-----45342277877869813787501-----31111066776499737632685
Q 000887          392 LSDLLPQCKKLRVLSLGSY-CITE-----VPISIGCLKQLRYLNFSRSEIQC-----LPDAICSLFNLEILILRNCWCLL  460 (1237)
Q Consensus       392 ~~~~~~~l~~Lr~L~L~~~-~i~~-----lp~~~~~l~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~L~~~~~l~  460 (1237)
                      +..+....+.|+.|+|+++ .+..     +-..+...+.|+.|++++|.+..     +...+...+.|+.|++++| .+.
T Consensus         7 l~~l~~n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n-~i~   85 (167)
T d1pgva_           7 INRLREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESN-FLT   85 (167)
T ss_dssp             HHHHHTTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSS-BCC
T ss_pred             HHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEHH-HCC
T ss_conf             9999828999819782799998989999999997637764540120156215679887531000234330033010-214


Q ss_pred             C-----CCHHHCCCCCCCEEECCCC
Q ss_conf             5-----8831105455658821698
Q 000887          461 K-----LPSRIGNLVNLHYLNIEGA  480 (1237)
Q Consensus       461 ~-----lp~~i~~L~~L~~L~l~~~  480 (1237)
                      .     +-..+..-+.|++|++.++
T Consensus        86 ~~g~~~l~~aL~~n~sL~~L~l~~n  110 (167)
T d1pgva_          86 PELLARLLRSTLVTQSIVEFKADNQ  110 (167)
T ss_dssp             HHHHHHHHHHTTTTCCCSEEECCCC
T ss_pred             HHHHHHHHHHHHHCCCCCEEECCCC
T ss_conf             5999999999984893898778877

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.95  E-value=0.00041  Score=36.39  Aligned_cols=27  Identities=30%  Similarity=0.527  Sum_probs=23.7

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             993999999279982999999998000
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ...+++.|.|++|+||||+|+.++...
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             987189998999989899999999986

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.94  E-value=0.00061  Score=35.43  Aligned_cols=44  Identities=16%  Similarity=0.165  Sum_probs=29.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             993999999279982999999998000113789829999759769
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD   55 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~   55 (1237)
                      ..++++.+.|-||+||||+|..++...-+.. ..+..++.....+
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G-~rVLlvD~Dp~~~   49 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQG-KRVLLVSTDPASN   49 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTT-CCEEEEECCTTCC
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCCCC
T ss_conf             8985999979986749999999999999789-9789995799988

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00021  Score=38.05  Aligned_cols=35  Identities=23%  Similarity=0.110  Sum_probs=25.3

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             399999927998299999999800011378982999
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWV   48 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~   48 (1237)
                      -.+|.+.|++|+||||+|++++... ...+....++
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l-~~~~~~~~~~   53 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYL-VCHGIPCYTL   53 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHH-HHTTCCEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH-HHCCCCCCCH
T ss_conf             9699988999999999999999999-7447973100

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.93  E-value=0.0026  Score=31.76  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|+|||||.+.++.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCCCHHHHHCCC
T ss_conf             7999988999982165575068

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.90  E-value=0.00029  Score=37.25  Aligned_cols=24  Identities=25%  Similarity=0.281  Sum_probs=21.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             399999927998299999999800
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .++|.|.|++|+||||+|+.++..
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             859999899999989999999997

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.90  E-value=0.00027  Score=37.43  Aligned_cols=23  Identities=43%  Similarity=0.611  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..|.|.|++|+||||+|+.++..
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             97989899999989999999999

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.88  E-value=0.003  Score=31.37  Aligned_cols=23  Identities=39%  Similarity=0.534  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..++|.|..|.|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHC
T ss_conf             99999999999899999999735

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.87  E-value=0.00044  Score=36.26  Aligned_cols=35  Identities=17%  Similarity=0.286  Sum_probs=26.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             999999279982999999998000113789829999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      ++|.|.|++|+||||+|+.++.......+. +..+.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~~~~-~~~~~   36 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQGIN-NKIIN   36 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTTTCC-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEE
T ss_conf             199998989989899999999999876998-89997

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.84  E-value=0.00018  Score=38.42  Aligned_cols=24  Identities=29%  Similarity=0.544  Sum_probs=19.3

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +++| +.|++|+||||+|+.++...
T Consensus         2 p~Iv-liG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           2 PKAV-LVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             CSEE-EECSTTSSHHHHHHHHHHHH
T ss_pred             CCEE-EECCCCCCHHHHHHHHHHHH
T ss_conf             9489-98899998899999999984

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.82  E-value=0.00089  Score=34.47  Aligned_cols=43  Identities=26%  Similarity=0.329  Sum_probs=31.5

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf             99399999927998299999999800011378982999975976
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF   54 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~   54 (1237)
                      .+.++|.+.|-||+||||+|..++....+..+ .+.-++.....
T Consensus        18 ~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G~-rVllvD~Dp~~   60 (279)
T d1ihua2          18 NEHGLIMLMGKGGVGKTTMAAAIAVRLADMGF-DVHLTTSDPAA   60 (279)
T ss_dssp             TSCEEEEEECSTTSSHHHHHHHHHHHHHHTTC-CEEEEESCCC-
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEECCCCC
T ss_conf             79789999799988789999999999997899-38999379998

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.81  E-value=0.0024  Score=31.96  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||.+.++.
T Consensus        27 ei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999998999829999999965

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=96.81  E-value=0.0011  Score=33.97  Aligned_cols=41  Identities=27%  Similarity=0.281  Sum_probs=30.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCC
Q ss_conf             999999279982999999998000113789829999759769
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFD   55 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~   55 (1237)
                      |.|+|.|=||+||||+|..++....+..+ .+.-+++..+.+
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA~~G~-rVLlID~DpQ~~   43 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALAEMGK-KVMIVGCDPKAD   43 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTC-CEEEEEECSSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEECCCCCC
T ss_conf             28999899987799999999999997899-789995189997

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.81  E-value=0.0023  Score=32.09  Aligned_cols=22  Identities=32%  Similarity=0.447  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||++.++.
T Consensus        30 e~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999809999999964

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.80  E-value=0.00046  Score=36.12  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=21.4

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             399999927998299999999800
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -++|.|.|++|+||||+|+.++..
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             859999889999889999999999

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.79  E-value=0.00043  Score=36.32  Aligned_cols=32  Identities=28%  Similarity=0.336  Sum_probs=25.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCE
Q ss_conf             99999927998299999999800011378982
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPK   45 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~   45 (1237)
                      ++++|.|..|+|||||+.++......+.+...
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~g~~v~   33 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVG   33 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             09999809999899999999999986798379

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.79  E-value=0.0005  Score=35.93  Aligned_cols=26  Identities=27%  Similarity=0.363  Sum_probs=22.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +..-.|.|.|++|+||||+|+.++..
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHH
T ss_conf             99888999828999889999999998

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.78  E-value=0.003  Score=31.39  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||.+.+..
T Consensus        33 e~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999829999999975

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.00054  Score=35.74  Aligned_cols=35  Identities=17%  Similarity=0.246  Sum_probs=26.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             999999279982999999998000113789829999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      +.|+|-|+.|+||||+++.+++......+. ++++.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~-v~~~~   38 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAAGHR-AELLR   38 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCC-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEE
T ss_conf             599998998889999999999999877996-89996

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=96.76  E-value=0.0004  Score=36.46  Aligned_cols=46  Identities=22%  Similarity=0.205  Sum_probs=32.2

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000113789829999759769999999999983305
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRS   70 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~   70 (1237)
                      ++||+|.|++|+||||+|+.++.+.     . ..++      +.-+++++++......
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~-----g-l~~i------StGdLlR~~a~~~~~~   48 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL-----Q-WHLL------DSGAIYRVLALAALHH   48 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH-----T-CEEE------EHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH-----C-CCEE------CHHHHHHHHHHHHHHC
T ss_conf             9889977999889899999999996-----9-9089------8889999999999872

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.74  E-value=0.00039  Score=36.55  Aligned_cols=76  Identities=17%  Similarity=0.220  Sum_probs=39.9

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC---CHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             9399999927998299999999800011378982999975976---9999999999983305899569789999999996
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF---DVLRISKAILDSIKRSSCKLEDLNSVQLELKETV   88 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~---~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~l   88 (1237)
                      .++.+.++|++|+|||.||++++...    +...+-++.+.-.   ..........+.+.......  ...         
T Consensus        48 ~~~~iLl~GPpG~GKT~lAkalA~~~----~~~~~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~--~~~---------  112 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARRLAKLA----NAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGA--IDA---------  112 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH----TCCEEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTC--HHH---------
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHCC----CCCHHCCCCCCCCCCEEEEEECCCCCCCCCHHHHCC--CCC---------
T ss_conf             98669998999988889999986213----221000344330101157641133333321233123--200---------


Q ss_pred             CCCCEEEEEECCCC
Q ss_conf             69729999968877
Q 000887           89 FKKKFLIVLDDVWS  102 (1237)
Q Consensus        89 ~~~~~LlvlDdv~~  102 (1237)
                      ..++.+|.||.++.
T Consensus       113 ~~~~~IIf~DEIdk  126 (309)
T d1ofha_         113 VEQNGIVFIDEIDK  126 (309)
T ss_dssp             HHHHCEEEEECGGG
T ss_pred             CCCCCEEEEHHHHH
T ss_conf             35785688424645

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.69  E-value=0.00049  Score=35.95  Aligned_cols=22  Identities=41%  Similarity=0.629  Sum_probs=19.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.+.||+|+||||+|+.++...
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
T ss_conf             9998999998899999999983

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.68  E-value=0.001  Score=34.14  Aligned_cols=60  Identities=18%  Similarity=0.117  Sum_probs=22.4

Q ss_pred             CCCCCCCEEECCCCCCCC-----CCCCCCCCCCCCEEECCCCCCCC-----CCHHHCCCCCCCEEECCCC
Q ss_conf             899974199825633434-----45342277877869813787501-----3111106677649973763
Q 000887          397 PQCKKLRVLSLGSYCITE-----VPISIGCLKQLRYLNFSRSEIQC-----LPDAICSLFNLEILILRNC  456 (1237)
Q Consensus       397 ~~l~~Lr~L~L~~~~i~~-----lp~~~~~l~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~L~~~  456 (1237)
                      ...+.|+.|+|++|.+..     +...+...+.|+.|++++|.+..     +-..+..-+.|+.|++++|
T Consensus        41 ~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~~aL~~n~sL~~L~l~~n  110 (167)
T d1pgva_          41 CNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQ  110 (167)
T ss_dssp             TTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCC
T ss_pred             HHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEHHHCCHHHHHHHHHHHHHCCCCCEEECCCC
T ss_conf             6377645401201562156798875310002343300330102145999999999984893898778877

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.64  E-value=0.003  Score=31.38  Aligned_cols=22  Identities=36%  Similarity=0.629  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||++.+..
T Consensus        42 e~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             9999999999859999999862

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.63  E-value=0.002  Score=32.39  Aligned_cols=23  Identities=22%  Similarity=0.276  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||.+.++.-
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl   47 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCCHHHHHHHHHHCC
T ss_conf             79999979998099999999739

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=96.62  E-value=0.0033  Score=31.18  Aligned_cols=22  Identities=32%  Similarity=0.513  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||++.++-
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHCC
T ss_conf             7999989998988899998758

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.62  E-value=0.0094  Score=28.53  Aligned_cols=23  Identities=26%  Similarity=0.520  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||++.++.-
T Consensus        63 e~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCHHHHHHHHHHCC
T ss_conf             99999989998299999999579

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=96.61  E-value=0.0031  Score=31.36  Aligned_cols=86  Identities=15%  Similarity=0.106  Sum_probs=48.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC-CHHHHHHHHHHHHHCC--------CCCC----CCHHHHH
Q ss_conf             9999927998299999999800011378982999975976-9999999999983305--------8995----6978999
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF-DVLRISKAILDSIKRS--------SCKL----EDLNSVQ   81 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~-~~~~~~~~i~~~l~~~--------~~~~----~~~~~~~   81 (1237)
                      -++|.|.+|+|||+|+.+..... ....+.++++-++... ......+.+...-...        ..+.    .-.....
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~~-~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~a  147 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILNQ-QGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTG  147 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTC-CTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHH
T ss_pred             EEEECCCCCCCHHHHHHHHHHHH-CCCCCEEEEEEECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             67600677888579999977654-04675355555221267788999851157750331001234676599999999999


Q ss_pred             HHHHHHH--CCCCEEEEEECCC
Q ss_conf             9999996--6972999996887
Q 000887           82 LELKETV--FKKKFLIVLDDVW  101 (1237)
Q Consensus        82 ~~l~~~l--~~~~~LlvlDdv~  101 (1237)
                      -.+.+++  +++++|+++||+.
T Consensus       148 ~tiAEyfrd~G~~Vlll~Dslt  169 (276)
T d1fx0a3         148 AALAEYFMYRERHTLIIYDDLS  169 (276)
T ss_dssp             HHHHHHHHHTTCEEEEEEECHH
T ss_pred             HHHHHHHHHCCCCEEEEEECCH
T ss_conf             9888899975996457750538

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.61  E-value=0.00076  Score=34.86  Aligned_cols=24  Identities=25%  Similarity=0.297  Sum_probs=21.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             399999927998299999999800
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.+|.|.|++|.||||+|+.++..
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             939999799999989999999998

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.0076  Score=29.08  Aligned_cols=36  Identities=22%  Similarity=0.258  Sum_probs=27.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             999999279982999999998000113789829999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      +.|+|-|+.|+||||+++.+........+..+.+..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~g~~~~~~~~   38 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTR   38 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             789998998887999999999999967997399832

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.56  E-value=0.00067  Score=35.18  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .|.+.|++|+||||+|+.++...
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
T ss_conf             88998899998899999999994

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.56  E-value=0.0036  Score=30.92  Aligned_cols=47  Identities=23%  Similarity=0.244  Sum_probs=32.6

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCCCC-----CCCCEEEEEECCCCCHHHH
Q ss_conf             3999999279982999999998000113-----7898299997597699999
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKLTE-----AFEPKAWVCVSDDFDVLRI   59 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~~~-----~f~~~~w~~~~~~~~~~~~   59 (1237)
                      =+++.|.|.+|+|||++|.+++.+....     ....++|+......+....
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECCCHHHHHHH
T ss_conf             8799998589898899999999986344876388962899831012589999

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.56  E-value=0.00098  Score=34.22  Aligned_cols=45  Identities=16%  Similarity=0.099  Sum_probs=31.4

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCC-CEEEEEECCCC
Q ss_conf             9993999999279982999999998000113789-82999975976
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDF   54 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~   54 (1237)
                      .++..+|+|.|++|+|||||..++..+.....+. +++-++-+...
T Consensus        48 ~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          48 TGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGS
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHH
T ss_conf             6981598611799888999999999987636875134434655478

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.53  E-value=0.00082  Score=34.68  Aligned_cols=53  Identities=19%  Similarity=0.238  Sum_probs=34.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             99999279982999999998000113789829999759769999999999983305899569789
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNS   79 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~   79 (1237)
                      +|+|-|++|+||||+|+.++...     . ..++      +.-++++.++...............
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l-----g-~~~i------stGdl~R~~a~~~~~~~~~~~~~~~   57 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF-----G-FTYL------DTGAMYRAATYMALKNQLGVEEVEA   57 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH-----C-CEEE------EHHHHHHHHHHHHHHTTCCTTCHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-----C-CCEE------CHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             99978999879899999999996-----9-9478------7799999999999870898037778

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.52  E-value=0.0011  Score=33.89  Aligned_cols=52  Identities=19%  Similarity=0.087  Sum_probs=32.5

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCC-CEEEEEECCCCCHHHHHH
Q ss_conf             9993999999279982999999998000113789-829999759769999999
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFE-PKAWVCVSDDFDVLRISK   61 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~-~~~w~~~~~~~~~~~~~~   61 (1237)
                      .++..+|+|.|.+|+|||||..++.......... +++-++-+...+...++.
T Consensus        51 ~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailg  103 (327)
T d2p67a1          51 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILG  103 (327)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC----------
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCEEEECCCCCC
T ss_conf             69832897438999989999999999997569833220377761000651554

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=96.46  E-value=0.00052  Score=35.82  Aligned_cols=81  Identities=11%  Similarity=0.082  Sum_probs=44.1

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCC--CHHHHHHHHHH---HH----HCCCCCCCCHHHHH
Q ss_conf             99399999927998299999999800011378982999975976--99999999999---83----30589956978999
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDF--DVLRISKAILD---SI----KRSSCKLEDLNSVQ   81 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~--~~~~~~~~i~~---~l----~~~~~~~~~~~~~~   81 (1237)
                      .+..+|+|.|.+|.||||+|+++.+...+.... ++.+....-.  +....-..+..   .-    ......+.+.+...
T Consensus         2 ~k~pIIgIaG~SGSGKTTva~~l~~i~~~~~v~-~~iI~~Dsfyr~~R~~~~~~~~~~~~~~~~~~~~~~P~A~d~dlL~   80 (288)
T d1a7ja_           2 KKHPIISVTGSSGAGTSTVKHTFDQIFRREGVK-AVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELE   80 (288)
T ss_dssp             TTSCEEEEESCC---CCTHHHHHHHHHHHHTCC-EEEEEGGGGBSCCHHHHHHHHHHHHHHTCTTCSTTSGGGBCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH
T ss_conf             988899998999780999999999997156997-6999477787565022011133333540467798984426599999


Q ss_pred             HHHHHHHCCCC
Q ss_conf             99999966972
Q 000887           82 LELKETVFKKK   92 (1237)
Q Consensus        82 ~~l~~~l~~~~   92 (1237)
                      ..++....++.
T Consensus        81 ~~l~~L~~g~~   91 (288)
T d1a7ja_          81 RVFREYGETGQ   91 (288)
T ss_dssp             HHHHHHHHHSC
T ss_pred             HHHHHHHCCCC
T ss_conf             99999987996

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.45  E-value=0.00066  Score=35.23  Aligned_cols=88  Identities=13%  Similarity=0.111  Sum_probs=45.3

Q ss_pred             HHHHHCCCCCCCCEEECCCC-CCC-----CCCCCCCCCCCCCEEECCCCCCCC-----CCHHHCCCCCCCEEECCCCCCC
Q ss_conf             13210589997419982563-343-----445342277877869813787501-----3111106677649973763268
Q 000887          391 VLSDLLPQCKKLRVLSLGSY-CIT-----EVPISIGCLKQLRYLNFSRSEIQC-----LPDAICSLFNLEILILRNCWCL  459 (1237)
Q Consensus       391 ~~~~~~~~l~~Lr~L~L~~~-~i~-----~lp~~~~~l~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~L~~~~~l  459 (1237)
                      +........+.|+.|+++++ .++     .+-..+...++|+.|++++|.+..     +-..+.....++.+++++| .+
T Consensus         8 ~l~~~~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~-~~   86 (166)
T d1io0a_           8 TLKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESN-FI   86 (166)
T ss_dssp             HHHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSS-CC
T ss_pred             HHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCHHHHHCCC-CC
T ss_conf             99999955999868876899998989999999888419825743015896117789999987752122101210254-32


Q ss_pred             C-----CCCHHHCCCCCCCEEECCC
Q ss_conf             5-----5883110545565882169
Q 000887          460 L-----KLPSRIGNLVNLHYLNIEG  479 (1237)
Q Consensus       460 ~-----~lp~~i~~L~~L~~L~l~~  479 (1237)
                      .     .+-..+...++|+.+++..
T Consensus        87 ~~~g~~~l~~~l~~~~~L~~l~L~l  111 (166)
T d1io0a_          87 SGSGILALVEALQSNTSLIELRIDN  111 (166)
T ss_dssp             CHHHHHHHHHGGGGCSSCCEEECCC
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEECC
T ss_conf             2014788999998486524773216

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.44  E-value=0.0032  Score=31.22  Aligned_cols=22  Identities=36%  Similarity=0.573  Sum_probs=19.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      ..++|.|..|.|||||++.+..
T Consensus        45 e~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             8999988999809999999971

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=96.42  E-value=0.013  Score=27.76  Aligned_cols=52  Identities=15%  Similarity=0.146  Sum_probs=33.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             999999279982999999998000113789829999759769999999999983
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSI   67 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l   67 (1237)
                      .++.|.|.+|+|||++|.+++.+.....-..+.+++...  +...+...++...
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E~--~~~~~~~r~~~~~   87 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEE--SVEETAEDLIGLH   87 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESSS--CHHHHHHHHHHHH
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEECC--CHHHHHHHHHHHH
T ss_conf             089999479997999999999726553366345764011--1135776999986

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=96.40  E-value=0.006  Score=29.68  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||.+.++.-
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999999999999999669

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.40  E-value=0.0029  Score=31.53  Aligned_cols=123  Identities=16%  Similarity=0.242  Sum_probs=58.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCC----CCC-----------------CEEEEEECC-------------------C
Q ss_conf             999999279982999999998000113----789-----------------829999759-------------------7
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTE----AFE-----------------PKAWVCVSD-------------------D   53 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~----~f~-----------------~~~w~~~~~-------------------~   53 (1237)
                      .+++|.|+.|.||||+.+.+..-....    .|+                 .+-++.-..                   .
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~~p~~G~I~~~g~~i~~~~~~~~~~~rr~ig~vfQ~~~L~p~ltv~eni~~~l~~~~  111 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMK  111 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSSCCSEEEEEETTEEEEETTEESSCGGGSCEEEEETTSCCCTTSCHHHHHHGGGTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCCCCCEEEECCEEEECCCHHHCCHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             89999989998099999999758688874599999995137311153120451477304334666657777665567613


Q ss_pred             CC---HHHHHHHHHHHHHCCCC------CCCCHHHHHHHHHHHHCCCCEEEEEECCCCC-C---HHHHHHHHCCCCCCCC
Q ss_conf             69---99999999998330589------9569789999999996697299999688777-7---6269983122568999
Q 000887           54 FD---VLRISKAILDSIKRSSC------KLEDLNSVQLELKETVFKKKFLIVLDDVWSE-R---YDLWQALKSPFMAGAP  120 (1237)
Q Consensus        54 ~~---~~~~~~~i~~~l~~~~~------~~~~~~~~~~~l~~~l~~~~~LlvlDdv~~~-~---~~~~~~l~~~~~~~~~  120 (1237)
                      .+   ..+-...++..++....      ..+...+..-.+.+.+..++-+|++|.-... +   ......+...+.. ..
T Consensus       112 ~~~~~~~~~v~~~l~~~gL~~~~~~~p~~LSGGqkQRvaiARaL~~~P~llllDEPt~~LD~~~~~~i~~~i~~l~~-~~  190 (242)
T d1oxxk2         112 MSKEEIRKRVEEVAKILDIHHVLNHFPRELSGAQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQS-RL  190 (242)
T ss_dssp             CCHHHHHHHHHHHHHHTTCGGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCGGGHHHHHHHHHHHHH-HH
T ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHCCHHHCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHH-CC
T ss_conf             79999999999998665917666489545999998589987577604661454478667998998899899999986-35


Q ss_pred             CCEEEEEECCHHHHHHH
Q ss_conf             95999990745678752
Q 000887          121 GSRIIVTTRSMDVALTM  137 (1237)
Q Consensus       121 ~~~ilvTtR~~~~~~~~  137 (1237)
                      |..+|++|-+...+..+
T Consensus       191 g~tvi~vTHd~~~~~~~  207 (242)
T d1oxxk2         191 GVTLLVVSHDPADIFAI  207 (242)
T ss_dssp             CCEEEEEESCHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHH
T ss_conf             98799997999999996

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=96.35  E-value=0.0011  Score=33.85  Aligned_cols=25  Identities=28%  Similarity=0.424  Sum_probs=22.4

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9399999927998299999999800
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.++|.|.|++|.||||+|+.++..
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             7828999899999879999999998

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.34  E-value=0.0011  Score=33.83  Aligned_cols=22  Identities=36%  Similarity=0.591  Sum_probs=19.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |+|.|+.|+|||||++.++...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l   24 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHCC
T ss_conf             9999899938999999998148

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.32  E-value=0.0013  Score=33.43  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=23.4

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             93999999279982999999998000
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +++.|+|-|+-|+||||+++.+....
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98199998998885999999999987

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.29  E-value=0.015  Score=27.34  Aligned_cols=22  Identities=23%  Similarity=0.407  Sum_probs=18.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|.|.|..|+|||.+|+.+.+.
T Consensus        25 pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2          25 PVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
T ss_conf             7899899981799999999996

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=96.24  E-value=0.0011  Score=33.82  Aligned_cols=25  Identities=16%  Similarity=0.092  Sum_probs=20.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +-.|.|.|++|+||||+|+.++...
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             7299998899999899999999987

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=96.23  E-value=0.0017  Score=32.85  Aligned_cols=25  Identities=32%  Similarity=0.505  Sum_probs=20.8

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .++++| |.|++|+||||+|+.++..
T Consensus         2 ~~~rii-l~G~pGSGKsT~a~~La~~   26 (190)
T d1ak2a1           2 KGVRAV-LLGPPGAGKGTQAPKLAKN   26 (190)
T ss_dssp             CCCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEE-EECCCCCCHHHHHHHHHHH
T ss_conf             963899-9899999889999999998

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=96.17  E-value=0.0018  Score=32.64  Aligned_cols=27  Identities=22%  Similarity=0.142  Sum_probs=23.2

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             999399999927998299999999800
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..++-+|+|-|..|+||||+|+.+...
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             998619998899998889999999987

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.11  E-value=0.0042  Score=30.58  Aligned_cols=39  Identities=26%  Similarity=0.231  Sum_probs=29.5

Q ss_pred             EEEEEE-CCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             999999-2799829999999980001137898299997597
Q 000887           14 RVIPLV-GMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        14 ~vv~i~-G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      |+|+|. |-||+||||+|..++....+ .-..+..+++...
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~-~g~~VlliD~D~~   41 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQ-LGHDVTIVDADIT   41 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHH-TTCCEEEEECCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEECCCC
T ss_conf             799997999998099999999999996-8998999959899

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.10  E-value=0.019  Score=26.74  Aligned_cols=22  Identities=45%  Similarity=0.594  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||++.+..
T Consensus        41 e~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999999999849999999861

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.08  E-value=0.012  Score=28.01  Aligned_cols=45  Identities=13%  Similarity=0.070  Sum_probs=31.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCCC-----CCCCCCEEEEEECCCCCHH
Q ss_conf             39999992799829999999980001-----1378982999975976999
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDKL-----TEAFEPKAWVCVSDDFDVL   57 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~~-----~~~f~~~~w~~~~~~~~~~   57 (1237)
                      =+++.|.|.+|+|||++|.+++....     ...+..+.|+.........
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHH
T ss_conf             97999988998878899999999997444316666248874017777899

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=96.05  E-value=0.0025  Score=31.86  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=11.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      +.+.++|++|+|||++|..++.
T Consensus       155 ~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             7699989999888999999999

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=96.04  E-value=0.002  Score=32.37  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=20.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .-.+++ |.|++|+||||+|+.++..
T Consensus         5 r~mrIi-liG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           5 RLLRAA-IMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CCCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEE-EECCCCCCHHHHHHHHHHH
T ss_conf             621699-9889999879999999999

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.03  E-value=0.0015  Score=33.16  Aligned_cols=22  Identities=32%  Similarity=0.644  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|+|.|++|+|||||+++++..
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             1999999999999999999974

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.03  E-value=0.002  Score=32.45  Aligned_cols=21  Identities=33%  Similarity=0.580  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHC
Q ss_conf             999927998299999999800
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |.|.|++|+||||+|+.++..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             999889999989999999998

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.97  E-value=0.0031  Score=31.34  Aligned_cols=31  Identities=23%  Similarity=0.330  Sum_probs=23.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCCCCCCE
Q ss_conf             9999927998299999999800011378982
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTEAFEPK   45 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~   45 (1237)
                      .|+|-|+.|+||||+++.+........+..+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~g~~v~   32 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAAGRSVA   32 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEE
T ss_conf             8999899878999999999999987899789

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.97  E-value=0.0023  Score=32.11  Aligned_cols=23  Identities=30%  Similarity=0.343  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .|.|.|++|+||||+|+.++...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
T ss_conf             89998899999799999999998

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.96  E-value=0.0022  Score=32.24  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++|.|.|++|+|||||++.+...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             49999899999999999999845

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.96  E-value=0.009  Score=28.64  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .++.|.|.+|+|||++|.+++.+.
T Consensus        35 ~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          35 SVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             599999179999899999999999

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.95  E-value=0.0039  Score=30.74  Aligned_cols=44  Identities=14%  Similarity=0.135  Sum_probs=30.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC-CCC----CCCCEEEEEECCCCCHH
Q ss_conf             999999279982999999998000-113----78982999975976999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTE----AFEPKAWVCVSDDFDVL   57 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~-~~~----~f~~~~w~~~~~~~~~~   57 (1237)
                      +++-|.|.+|+|||++|.+++... ...    ....++|++.....+..
T Consensus        35 ~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          35 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCHHHHH
T ss_conf             6999983899988999999999863124312689639999402307899

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.94  E-value=0.0029  Score=31.47  Aligned_cols=23  Identities=30%  Similarity=0.335  Sum_probs=19.9

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Q ss_conf             93999999279982999999998
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVY   34 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~   34 (1237)
                      .+-+|||.|+.|.||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
T ss_conf             99899998988778999999999

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.92  E-value=0.0031  Score=31.32  Aligned_cols=24  Identities=33%  Similarity=0.559  Sum_probs=19.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9399999927998299999999800
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..++| |.|++|+||||+|+.++..
T Consensus         2 ~mrIv-l~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           2 SIRMV-LIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHH
T ss_pred             CEEEE-EECCCCCCHHHHHHHHHHH
T ss_conf             56999-9899999989999999999

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.89  E-value=0.0018  Score=32.67  Aligned_cols=23  Identities=35%  Similarity=0.668  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |-|+|.|++|+|||||+++++..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             76999899999989999999974

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.85  E-value=0.0031  Score=31.35  Aligned_cols=23  Identities=39%  Similarity=0.502  Sum_probs=20.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ||+|.|+.|.|||||..++.++.
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
T ss_conf             89999189983999999999988

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=95.80  E-value=0.0029  Score=31.51  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .|.|.|++|.||||+|+.++...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
T ss_conf             89998899998799999999987

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.77  E-value=0.027  Score=25.88  Aligned_cols=86  Identities=17%  Similarity=0.157  Sum_probs=46.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCCCC------CCC-CEEEEEECCCC-CHHHHHHHHHHHHHCC------CCCCCCHHH-
Q ss_conf             99999279982999999998000113------789-82999975976-9999999999983305------899569789-
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKLTE------AFE-PKAWVCVSDDF-DVLRISKAILDSIKRS------SCKLEDLNS-   79 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~~~------~f~-~~~w~~~~~~~-~~~~~~~~i~~~l~~~------~~~~~~~~~-   79 (1237)
                      -++|.|.+|+|||+++.++.....+.      .-. .+++.-++... .+..+.+.+...-...      ......... 
T Consensus        70 r~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tvvv~~ts~~~~~~r  149 (285)
T d2jdia3          70 RELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQ  149 (285)
T ss_dssp             BCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHH
T ss_conf             78765688888589999999757764156544563289996307638789999998614561200499997899999999


Q ss_pred             -----HHHHHHHHH--CCCCEEEEEECC
Q ss_conf             -----999999996--697299999688
Q 000887           80 -----VQLELKETV--FKKKFLIVLDDV  100 (1237)
Q Consensus        80 -----~~~~l~~~l--~~~~~LlvlDdv  100 (1237)
                           ..-.+.+++  +++++|+++||+
T Consensus       150 ~~~~~~a~tiAEyfrd~G~~VLll~Dsl  177 (285)
T d2jdia3         150 YLAPYSGCSMGEYFRDNGKHALIIYDDL  177 (285)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEEETH
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECCH
T ss_conf             9999999999999997699679997172

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=95.72  E-value=0.0059  Score=29.72  Aligned_cols=15  Identities=7%  Similarity=-0.059  Sum_probs=5.6

Q ss_pred             CCCCCCEEECCCCCC
Q ss_conf             999741998256334
Q 000887          398 QCKKLRVLSLGSYCI  412 (1237)
Q Consensus       398 ~l~~Lr~L~L~~~~i  412 (1237)
                      ..++|+.|++++|.+
T Consensus        44 ~n~~L~~L~Ls~n~l   58 (166)
T d1io0a_          44 TNTYVKKFSIVGTRS   58 (166)
T ss_dssp             TCCSCCEEECTTSCC
T ss_pred             CCCCCCEEECCCCCC
T ss_conf             198257430158961

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.66  E-value=0.0055  Score=29.90  Aligned_cols=37  Identities=30%  Similarity=0.331  Sum_probs=28.5

Q ss_pred             EEEEEE-CCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEC
Q ss_conf             999999-27998299999999800011378982999975
Q 000887           14 RVIPLV-GMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVS   51 (1237)
Q Consensus        14 ~vv~i~-G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~   51 (1237)
                      |+|+|+ +-||+||||+|..++....+.. ..+..++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g-~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRG-RKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTT-CCEEEEECC
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCC-CCEEEEECC
T ss_conf             29999899998819999999999999689-989999498

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.66  E-value=0.014  Score=27.47  Aligned_cols=163  Identities=12%  Similarity=0.059  Sum_probs=76.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC-CCC-------------CCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             993999999279982999999998000-113-------------789829999759769999999999983305899569
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK-LTE-------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLED   76 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~-~~~-------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~   76 (1237)
                      .+-+++.|.|+-+.|||++.+.++... ..+             -|+ .++...+...++..-.......+         
T Consensus        39 ~~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d-~I~~~~~~~d~~~~~~S~F~~E~---------  108 (234)
T d1wb9a2          39 PQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPID-RIFTRVGAADDLASGRSTFMVEM---------  108 (234)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCC-EEEEEEC-----------CHHHH---------
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCEEECCCEECCCCH-HHEEEECCCCCCCCCHHHHHHHH---------
T ss_conf             99539999546731368999987999999872976741766613442-02348746753436531899999---------


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCC-HHHH----HHHHCCCCCCCCCCEEEEEECCHHHHHHHC---CCCEEECCCC
Q ss_conf             7899999999966972999996887777-6269----983122568999959999907456787526---8870747899
Q 000887           77 LNSVQLELKETVFKKKFLIVLDDVWSER-YDLW----QALKSPFMAGAPGSRIIVTTRSMDVALTMG---SGKNYELKLL  148 (1237)
Q Consensus        77 ~~~~~~~l~~~l~~~~~LlvlDdv~~~~-~~~~----~~l~~~~~~~~~~~~ilvTtR~~~~~~~~~---~~~~~~l~~l  148 (1237)
                       .+....+. . ..++.|+++|..-... ..+-    .++...+. ...++.+++||-.........   ....+.++..
T Consensus       109 -~~~~~il~-~-~~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~-~~~~~~~i~tTH~~~l~~~~~~~~~v~~~~~~~~  184 (234)
T d1wb9a2         109 -TETANILH-N-ATEYSLVLMDEIGRGTSTYDGLSLAWACAENLA-NKIKALTLFATHYFELTQLPEKMEGVANVHLDAL  184 (234)
T ss_dssp             -HHHHHHHH-H-CCTTEEEEEESCCCCSSSSHHHHHHHHHHHHHH-HTTCCEEEEECSCGGGGGHHHHSTTEEEEEEEEE
T ss_pred             -HHHHHHHH-H-CCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHH-CCCCCEEEEECCHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             -99999997-4-546608853222358774566678987645432-0454428985246877643312455478998876


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             92433999999761789999998759999999998029913799997
Q 000887          149 SDDDCWSVFVAHAFEGRDAGTHGNFESTRQRVVEKCKGLPLAARALG  195 (1237)
Q Consensus       149 ~~~ea~~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~g~Plal~~~~  195 (1237)
                      ..++...+..+...+  ...     ...+-++++.+| +|-.+.--|
T Consensus       185 ~~~~~i~f~YkL~~G--~~~-----~s~ai~iA~~~G-lp~~ii~~A  223 (234)
T d1wb9a2         185 EHGDTIAFMHSVQDG--AAS-----KSYGLAVAALAG-VPKEVIKRA  223 (234)
T ss_dssp             EETTEEEEEEEEEES--CCS-----SCCHHHHHHHTT-CCHHHHHHH
T ss_pred             ECCCCCEEEEEECCC--CCC-----CCHHHHHHHHHC-CCHHHHHHH
T ss_conf             036840178774679--999-----729999999919-699999999

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.64  E-value=0.0034  Score=31.06  Aligned_cols=23  Identities=17%  Similarity=0.546  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.|.|.|++|+|||||++++...
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
T ss_conf             71999998999999999999970

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.63  E-value=0.0056  Score=29.84  Aligned_cols=40  Identities=25%  Similarity=0.388  Sum_probs=28.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             9999992799829999999980001137898299997597
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDD   53 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~   53 (1237)
                      .++.|+|.+|+|||++|.+++.......-..+.|++....
T Consensus        27 ~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e~~   66 (242)
T d1tf7a1          27 RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEET   66 (242)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSC
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             3999994799999999999999999856887420126679

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=95.62  E-value=0.031  Score=25.55  Aligned_cols=24  Identities=38%  Similarity=0.447  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .++.|+|.+|+|||++|.+++...
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             589999289998999999999999

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.53  E-value=0.0028  Score=31.62  Aligned_cols=25  Identities=20%  Similarity=0.194  Sum_probs=22.0

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -+.|+|-|+.|+||||+|+.++...
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9889998788877999999999997

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.48  E-value=0.0042  Score=30.53  Aligned_cols=23  Identities=22%  Similarity=0.359  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +++.|.|++|+|||||.+.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             09999999999999999999863

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.47  E-value=0.0044  Score=30.43  Aligned_cols=21  Identities=38%  Similarity=0.359  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHC
Q ss_conf             999927998299999999800
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |.|.|++|.||||+|+.++..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             999879999989999999998

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=95.34  E-value=0.0083  Score=28.86  Aligned_cols=35  Identities=14%  Similarity=0.165  Sum_probs=26.7

Q ss_pred             EEEEEECCC-CCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             999999279-982999999998000113789829999
Q 000887           14 RVIPLVGMG-GIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        14 ~vv~i~G~~-G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      +.+.|.|-| ||||||++..++....+..+. +..++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~r-Vl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYR-TAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCC-EEEEC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCE-EEEEC
T ss_conf             5199998999942999999999999977993-99988

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.05  E-value=0.0078  Score=29.00  Aligned_cols=24  Identities=17%  Similarity=0.194  Sum_probs=21.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +++.|.|.+|+|||++|.+++.+.
T Consensus        24 ~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          24 SITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             799999589999999999999999

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.02  E-value=0.0074  Score=29.13  Aligned_cols=22  Identities=32%  Similarity=0.539  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||++.++-
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             7999998999829999999974

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=94.98  E-value=0.0083  Score=28.85  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=18.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             999999279982999999998
Q 000887           14 RVIPLVGMGGIGKTTLAQEVY   34 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~   34 (1237)
                      -+|||.|+.|.||||+|+.+.
T Consensus         4 ~iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           4 YIVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
T ss_conf             799978988688999999999

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=94.71  E-value=0.011  Score=28.16  Aligned_cols=21  Identities=38%  Similarity=0.419  Sum_probs=18.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHH
Q ss_conf             999999279982999999998
Q 000887           14 RVIPLVGMGGIGKTTLAQEVY   34 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~   34 (1237)
                      -+|||.|..|.||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
T ss_conf             899988888788999999999

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=94.66  E-value=0.013  Score=27.62  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++|||.|..|.||||+|..+...
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~   24 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSN   24 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             89999799998899999999986

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=94.57  E-value=0.016  Score=27.19  Aligned_cols=26  Identities=27%  Similarity=0.429  Sum_probs=21.8

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -..+-|-+.|+.|+|||-||+.++..
T Consensus        47 i~ksNILliGPTGvGKTlLAr~LAk~   72 (443)
T d1g41a_          47 VTPKNILMIGPTGVGKTEIARRLAKL   72 (443)
T ss_dssp             CCCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             56564799899998899999999987

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.57  E-value=0.0087  Score=28.72  Aligned_cols=23  Identities=39%  Similarity=0.566  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|+|||||.+.++..
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCHHHHHHHHHHCC
T ss_conf             89999999997199999999662

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.52  E-value=0.013  Score=27.64  Aligned_cols=23  Identities=22%  Similarity=0.442  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|+.++....
T Consensus         5 KivvvG~~~vGKTsli~r~~~~~   27 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDKR   27 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999939999999996299

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.52  E-value=0.016  Score=27.20  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=20.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999929899999997399

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=94.50  E-value=0.014  Score=27.52  Aligned_cols=27  Identities=22%  Similarity=0.455  Sum_probs=22.6

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             999399999927998299999999800
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++..+.|+|.|.+|+|||||...+...
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHCCC
T ss_conf             889989999899998799999985298

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=94.49  E-value=0.013  Score=27.63  Aligned_cols=22  Identities=27%  Similarity=0.412  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      ..++|.|+.|.|||||++.+..
T Consensus        29 e~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          29 SIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999999999979999999999

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.49  E-value=0.016  Score=27.16  Aligned_cols=25  Identities=28%  Similarity=0.430  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCC
Q ss_conf             9999992799829999999980001
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKL   38 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~   38 (1237)
                      |-|.|.|.+|+|||+|..++.....
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~~   25 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQY   25 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             9899999999898999999980998

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.44  E-value=0.017  Score=27.04  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|+.++....
T Consensus         6 KivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999949899999997299

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.44  E-value=0.018  Score=26.84  Aligned_cols=23  Identities=26%  Similarity=0.598  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~~~   26 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVKGT   26 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             89999989979899999997099

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.44  E-value=0.017  Score=27.06  Aligned_cols=22  Identities=27%  Similarity=0.495  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.+.|.+|+|||+|+.++....
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHHCC
T ss_conf             9999989909899999998499

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=94.39  E-value=0.018  Score=26.91  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=19.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.|.|.+|+|||+|..++....
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHCCC
T ss_conf             9999999989899999996598

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.39  E-value=0.015  Score=27.39  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=21.7

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -+.|+|-|+.|+||||+++.++...
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             6899998998886999999999999

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.36  E-value=0.018  Score=26.85  Aligned_cols=23  Identities=35%  Similarity=0.567  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~~   27 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCENK   27 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999939899999998299

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.30  E-value=0.019  Score=26.78  Aligned_cols=22  Identities=23%  Similarity=0.604  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.+.|.+|+|||+|..++....
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHHCC
T ss_conf             9999989978999999997398

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=94.28  E-value=0.012  Score=28.01  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.||||+.+.++--
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl   49 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGF   49 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             89999989998299999999647

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.28  E-value=0.021  Score=26.52  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=19.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |.+.|.+|+|||+|+.++....
T Consensus         5 v~liG~~~vGKSsLi~rl~~~~   26 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKGI   26 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHHCC
T ss_conf             9999989959899999998298

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.24  E-value=0.02  Score=26.69  Aligned_cols=24  Identities=29%  Similarity=0.547  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      --|.|.|.+|+|||+|+..+....
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             799999979969899999997399

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.18  E-value=0.021  Score=26.56  Aligned_cols=23  Identities=26%  Similarity=0.488  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|..++....
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             89999989949999999997398

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.16  E-value=0.021  Score=26.49  Aligned_cols=23  Identities=22%  Similarity=0.447  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999949899999998598

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=94.15  E-value=0.0072  Score=29.22  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      +-|-+.|.+|+|||++|+.++.
T Consensus        29 h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_          29 GGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             7089988998529999999987

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.14  E-value=0.022  Score=26.39  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=22.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...+.|+|.|.+|+|||+|..++...
T Consensus         3 ~~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           3 TYSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             54769999999999999999999688

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.13  E-value=0.025  Score=26.04  Aligned_cols=26  Identities=23%  Similarity=0.482  Sum_probs=21.3

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             93999999279982999999998000
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +..-|.|.|.+|+|||+|..++....
T Consensus         3 k~~Kv~liG~~~vGKTsLl~~~~~~~   28 (167)
T d1xtqa1           3 KSRKIAILGYRSVGKSSLTIQFVEGQ   28 (167)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             63389999989929899999997198

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.11  E-value=0.022  Score=26.36  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~~   29 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADDS   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999919899999997398

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.09  E-value=0.027  Score=25.83  Aligned_cols=24  Identities=33%  Similarity=0.439  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +-|.|.|.+|+|||+|..++....
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             799999989938899999997199

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.06  E-value=0.029  Score=25.66  Aligned_cols=27  Identities=26%  Similarity=0.284  Sum_probs=21.7

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             993999999279982999999998000
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+.--|.|.|.+|+|||+|..++....
T Consensus         3 p~~iKivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           3 PQAIKCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             606999999999979999999997498

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.05  E-value=0.023  Score=26.29  Aligned_cols=23  Identities=30%  Similarity=0.492  Sum_probs=20.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|+|.|.+|+|||||..++....
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999989999999996798

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.02  E-value=0.03  Score=25.65  Aligned_cols=23  Identities=26%  Similarity=0.563  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         5 KivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999989989999999997098

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.97  E-value=0.018  Score=26.88  Aligned_cols=23  Identities=30%  Similarity=0.413  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||++.+.--
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999998499999999779

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.97  E-value=0.024  Score=26.22  Aligned_cols=23  Identities=35%  Similarity=0.536  Sum_probs=19.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999919899999997299

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.90  E-value=0.021  Score=26.48  Aligned_cols=23  Identities=26%  Similarity=0.596  Sum_probs=19.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999989939999999997199

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=93.88  E-value=0.019  Score=26.72  Aligned_cols=23  Identities=30%  Similarity=0.534  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+++|.|+.|.|||||.+.+.--
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999998599999999678

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.87  E-value=0.024  Score=26.18  Aligned_cols=23  Identities=39%  Similarity=0.657  Sum_probs=19.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|++.|.+|+|||+|..++....
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~~   26 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVNDK   26 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999969899999997098

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.86  E-value=0.032  Score=25.44  Aligned_cols=24  Identities=33%  Similarity=0.351  Sum_probs=20.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCC
Q ss_conf             999992799829999999980001
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL   38 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~   38 (1237)
                      -|.+.|..|+|||+|+..+.....
T Consensus         4 KivliG~~~vGKTsli~r~~~~~f   27 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKDCF   27 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCCC
T ss_conf             999999999598999999972999

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.85  E-value=0.026  Score=26.00  Aligned_cols=23  Identities=39%  Similarity=0.479  Sum_probs=19.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|..++....
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999989999999996499

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.83  E-value=0.027  Score=25.91  Aligned_cols=23  Identities=17%  Similarity=0.449  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|..|+|||+|..++....
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999919899999997299

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.82  E-value=0.026  Score=25.94  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             89999999979999999997399

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.81  E-value=0.033  Score=25.34  Aligned_cols=23  Identities=30%  Similarity=0.690  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999979989999999998098

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.74  E-value=0.027  Score=25.83  Aligned_cols=23  Identities=26%  Similarity=0.484  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~~   29 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEKK   29 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999909999999997098

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.74  E-value=0.022  Score=26.45  Aligned_cols=23  Identities=30%  Similarity=0.465  Sum_probs=19.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|+.++....
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~~   29 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDNK   29 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999919899999996199

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=93.72  E-value=0.029  Score=25.72  Aligned_cols=26  Identities=31%  Similarity=0.341  Sum_probs=22.0

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             93999999279982999999998000
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+-.|.|-|.-|+||||+++.+++..
T Consensus         5 ~~~rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           5 TIVRIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHSGG
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             65899998886678999999999986

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=93.70  E-value=0.061  Score=23.84  Aligned_cols=51  Identities=8%  Similarity=0.064  Sum_probs=26.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCC-CCCC--CCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             999992799829999999980001-1378--982999975976999999999998
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL-TEAF--EPKAWVCVSDDFDVLRISKAILDS   66 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~-~~~f--~~~~w~~~~~~~~~~~~~~~i~~~   66 (1237)
                      .+.|.|.+|.||||.+.+-+.+.. ....  ..+..+..+.. ....+...+...
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~-aa~~~~~~~~~~   79 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNK-AAREMRERVQSL   79 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHH-HHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCCCCHHHEEEEECCHH-HHHHHHHHHHHH
T ss_conf             989995298668999999999999808998789375766498-999899999862

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.69  E-value=0.029  Score=25.74  Aligned_cols=23  Identities=30%  Similarity=0.551  Sum_probs=19.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|+..+....
T Consensus         8 KivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999909899999996198

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.66  E-value=0.03  Score=25.65  Aligned_cols=23  Identities=35%  Similarity=0.439  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|++.|.+|+|||+|+.++....
T Consensus         5 KvvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999969999999997199

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.63  E-value=0.038  Score=24.99  Aligned_cols=23  Identities=35%  Similarity=0.658  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~~   30 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTNK   30 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999979999999998497

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.63  E-value=0.024  Score=26.16  Aligned_cols=23  Identities=30%  Similarity=0.447  Sum_probs=19.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+..+....
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~~   25 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGVE   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99998989939999999981885

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.61  E-value=0.023  Score=26.29  Aligned_cols=26  Identities=38%  Similarity=0.544  Sum_probs=22.5

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.+.|..|.|.-|.||||+.+++...
T Consensus         1 ~~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           1 NPIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CCEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHC
T ss_conf             99788998648889999999999856

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.61  E-value=0.022  Score=26.39  Aligned_cols=25  Identities=36%  Similarity=0.421  Sum_probs=20.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9399999927998299999999800
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ..+.+-..|+.|||||.+|++++..
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             8753244189986378999999864

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=93.55  E-value=0.032  Score=25.44  Aligned_cols=24  Identities=33%  Similarity=0.668  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      --|.+.|.+|+|||+|+.++....
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             699999989958899999997299

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.44  E-value=0.033  Score=25.38  Aligned_cols=23  Identities=35%  Similarity=0.608  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+..+....
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~~   26 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNKK   26 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999919899999997198

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=93.43  E-value=0.029  Score=25.70  Aligned_cols=22  Identities=27%  Similarity=0.504  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|+|.|.+|+|||||..++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999999899999999677

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=93.40  E-value=0.033  Score=25.38  Aligned_cols=26  Identities=27%  Similarity=0.461  Sum_probs=20.5

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             93999999279982999999998000
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      +..-|++.|.+|+|||||..++....
T Consensus        12 k~~kI~lvG~~~vGKTsLl~~l~~~~   37 (186)
T d1f6ba_          12 KTGKLVFLGLDNAGKTTLLHMLKDDR   37 (186)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSCC-
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             77789999999989899999996788

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.40  E-value=0.029  Score=25.69  Aligned_cols=23  Identities=39%  Similarity=0.596  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999967899999998688

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=93.40  E-value=0.043  Score=24.69  Aligned_cols=27  Identities=30%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             993999999279982999999998000
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ++.--|.+.|.+|+|||+|..++....
T Consensus        14 ~~~~kI~vvG~~~vGKSsLi~~l~~~~   40 (176)
T d1fzqa_          14 DQEVRILLLGLDNAGKTTLLKQLASED   40 (176)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCSC
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             987799999999989999999996487

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.39  E-value=0.025  Score=26.03  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=18.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|.+.|.+|+|||+|..++...
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999998889999988408

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=93.34  E-value=0.033  Score=25.36  Aligned_cols=23  Identities=22%  Similarity=0.488  Sum_probs=19.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|...+....
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~   26 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGED   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHCCCC
T ss_conf             99999999989999999980899

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.15  E-value=0.029  Score=25.68  Aligned_cols=19  Identities=37%  Similarity=0.616  Sum_probs=17.1

Q ss_pred             EEEEECCCCCCHHHHHHHH
Q ss_conf             9999927998299999999
Q 000887           15 VIPLVGMGGIGKTTLAQEV   33 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~   33 (1237)
                      -|.+.|.+|+|||+|..++
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
T ss_conf             9999989999989999988

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.07  E-value=0.042  Score=24.75  Aligned_cols=25  Identities=28%  Similarity=0.478  Sum_probs=21.7

Q ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9399999927998299999999800
Q 000887           12 NFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        12 ~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -.+.|+|.|.+|+|||||..++...
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             3619999979999899999999589

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.04  E-value=0.032  Score=25.43  Aligned_cols=24  Identities=29%  Similarity=0.324  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ..|.|.|.+|+|||||..++....
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             899999999988999999996799

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.02  E-value=0.034  Score=25.31  Aligned_cols=23  Identities=35%  Similarity=0.486  Sum_probs=19.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.|.|.+|+|||+|+.++....
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~~   30 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDGA   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999929999999997199

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.02  E-value=0.043  Score=24.73  Aligned_cols=23  Identities=30%  Similarity=0.652  Sum_probs=19.3

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|+.++....
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999989959899999997098

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=93.00  E-value=0.038  Score=25.01  Aligned_cols=24  Identities=33%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -+|.+.|.=|+||||+++.++...
T Consensus        34 ~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             299996687765889999987642

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.98  E-value=0.035  Score=25.26  Aligned_cols=23  Identities=26%  Similarity=0.544  Sum_probs=19.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|..|+|||+|+.++....
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~~   28 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRNE   28 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999909899999998299

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.92  E-value=0.047  Score=24.50  Aligned_cols=24  Identities=17%  Similarity=0.284  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      --|++.|.+|+|||+|..++....
T Consensus         6 ~ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           6 LRLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             799999989978999999997197

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.92  E-value=0.048  Score=24.42  Aligned_cols=23  Identities=30%  Similarity=0.583  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             89999989908899999997199

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=92.91  E-value=0.047  Score=24.51  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCC
Q ss_conf             999992799829999999980001
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL   38 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~   38 (1237)
                      -|.+.|.+|+|||+|..++.....
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~~~   27 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASGQF   27 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             999999999898999999971978

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=92.91  E-value=0.036  Score=25.17  Aligned_cols=22  Identities=27%  Similarity=0.481  Sum_probs=18.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .-|.+.|.+|+|||+|..++..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             7799998999988999998950

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.87  E-value=0.036  Score=25.17  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=18.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|.+.|.+|+|||+|..++...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999999889999999679

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.80  E-value=0.037  Score=25.10  Aligned_cols=22  Identities=36%  Similarity=0.505  Sum_probs=18.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|.+.|.+|+|||+|+..+...
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999998992999999999728

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=92.79  E-value=0.026  Score=25.98  Aligned_cols=22  Identities=36%  Similarity=0.600  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .+++|.|+.|.|||||.+.++.
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999998999809999999948

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.77  E-value=0.041  Score=24.84  Aligned_cols=28  Identities=21%  Similarity=0.212  Sum_probs=23.9

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9993999999279982999999998000
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -.+.|-|+|.|-+|.|||||+.++....
T Consensus         3 ~~~iRni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           3 LKRLRNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             GGGEEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHCEEEEEEECCCCCHHHHHHHHHHHC
T ss_conf             3020299999589899899999999964

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=92.74  E-value=0.049  Score=24.37  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +-|.|.|.+|+|||++|.++..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHC
T ss_conf             99999808999989999999985

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=92.72  E-value=0.06  Score=23.88  Aligned_cols=24  Identities=25%  Similarity=0.425  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      --|.|.|.+|+|||||..++....
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~~   39 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMNE   39 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             799999999989899999996688

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=92.67  E-value=0.05  Score=24.34  Aligned_cols=23  Identities=35%  Similarity=0.494  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +-|.|.|.+|+|||++|.++..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             99999818999989999999985

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.50  E-value=0.056  Score=24.03  Aligned_cols=23  Identities=30%  Similarity=0.465  Sum_probs=20.0

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|++.|.+|+|||||..++....
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~~   24 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGKK   24 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             89999999988999999996898

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=92.43  E-value=0.033  Score=25.39  Aligned_cols=24  Identities=29%  Similarity=0.279  Sum_probs=20.5

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             399999927998299999999800
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ...|+|-|.-|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             429999898677899999999998

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.17  E-value=0.032  Score=25.43  Aligned_cols=21  Identities=29%  Similarity=0.452  Sum_probs=18.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHC
Q ss_conf             999927998299999999800
Q 000887           16 IPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~   36 (1237)
                      |+|.|.+|+|||||..++...
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
T ss_conf             999899999899999999689

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.15  E-value=0.049  Score=24.36  Aligned_cols=23  Identities=35%  Similarity=0.572  Sum_probs=19.8

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|++.|.+|+|||+|...+....
T Consensus         2 KI~liG~~nvGKSSLln~l~~~~   24 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKNDR   24 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             89999999999999999995899

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=92.09  E-value=0.091  Score=22.83  Aligned_cols=37  Identities=16%  Similarity=0.138  Sum_probs=21.4

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCCC-CCCC--CCEEEEEEC
Q ss_conf             999992799829999999980001-1378--982999975
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDKL-TEAF--EPKAWVCVS   51 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~~-~~~f--~~~~w~~~~   51 (1237)
                      .+.|.|.+|.|||+.+.+-+.+.. ....  ..+..++.+
T Consensus        16 ~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~t   55 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFT   55 (306)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESS
T ss_pred             CEEEEEECCCCHHHHHHHHHHHHHHHCCCCHHHEEEEECC
T ss_conf             9899962884389999999999999569995578999686

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=92.00  E-value=0.043  Score=24.73  Aligned_cols=24  Identities=46%  Similarity=0.418  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -.|+|-|.-|+||||+++.+.+..
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~~l   29 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLHHF   29 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             699998887788999999999987

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.00  E-value=0.037  Score=25.08  Aligned_cols=22  Identities=36%  Similarity=0.502  Sum_probs=19.1

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|+|.|.+++|||||..++...
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             6999899998799999999689

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=92.00  E-value=0.11  Score=22.43  Aligned_cols=36  Identities=19%  Similarity=0.188  Sum_probs=24.7

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             999999279982999999998000113789829999
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVC   49 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~   49 (1237)
                      +-|.|.|.+|+|||++|.+...+-.+---|..+++.
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~g~~li~DD~~~~~   51 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKRGHRLVADDNVEIR   51 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHTTCEEEESSEEEEE
T ss_pred             EEEEEEECCCCCHHHHHHHHHHCCCEEEECCEEEEE
T ss_conf             999998089999999999999849938817868999

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.83  E-value=0.028  Score=25.78  Aligned_cols=23  Identities=39%  Similarity=0.602  Sum_probs=18.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~~   27 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTGE   27 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC---
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999908899999998498

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=91.75  E-value=0.035  Score=25.24  Aligned_cols=26  Identities=27%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             993999999279982999999998000
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+.+ |.+.|.+|+|||+|..++....
T Consensus        11 k~~k-IvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          11 KEMR-ILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             CCEE-EEEEEETTSSHHHHHHHTTCCC
T ss_pred             CEEE-EEEECCCCCCHHHHHHHHHCCC
T ss_conf             7479-9999999987899999984488

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=91.58  E-value=0.041  Score=24.85  Aligned_cols=26  Identities=31%  Similarity=0.546  Sum_probs=20.1

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             993999999279982999999998000
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      ...+ |.+.|.+|+|||||..++....
T Consensus        16 k~~K-I~lvG~~~vGKTsLi~~l~~~~   41 (182)
T d1moza_          16 KELR-ILILGLDGAGKTTILYRLQIGE   41 (182)
T ss_dssp             SCEE-EEEEEETTSSHHHHHHHTCCSE
T ss_pred             CEEE-EEEECCCCCCHHHHHHHHHCCC
T ss_conf             6689-9999999998899998873387

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=91.45  E-value=0.047  Score=24.50  Aligned_cols=26  Identities=15%  Similarity=0.216  Sum_probs=21.6

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++..-|+|.|.+++|||+|..++...
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             66978999889999899999998589

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.40  E-value=0.056  Score=24.06  Aligned_cols=10  Identities=20%  Similarity=-0.061  Sum_probs=3.3

Q ss_pred             HHHHHHHHCC
Q ss_conf             8999999929
Q 000887          259 ELVLLWIAEG  268 (1237)
Q Consensus       259 ~l~~~w~~~g  268 (1237)
                      ..|...+..|
T Consensus       195 CaVk~av~~g  204 (225)
T d1u0la2         195 CGVKEAVENG  204 (225)
T ss_dssp             CHHHHHHHHT
T ss_pred             CHHHHHHHCC
T ss_conf             7899999869

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=91.23  E-value=0.075  Score=23.32  Aligned_cols=22  Identities=18%  Similarity=0.326  Sum_probs=18.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHC
Q ss_conf             9999927998299999999800
Q 000887           15 VIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      -|++.|.+|+|||||..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999899999899999999688

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.00  E-value=0.16  Score=21.36  Aligned_cols=25  Identities=28%  Similarity=0.575  Sum_probs=20.4

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +.++ |+|.|..|+|||||..++...
T Consensus         7 ~~~k-V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           7 DAIK-VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             SCEE-EEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCE-EEEECCCCCCHHHHHHHHHCC
T ss_conf             8888-999999999999999999778

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=90.92  E-value=0.1  Score=22.59  Aligned_cols=24  Identities=42%  Similarity=0.682  Sum_probs=20.9

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             399999927998299999999800
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .|-|+|.|-.|.|||||+.++...
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             509999948898099999999997

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=90.91  E-value=0.19  Score=21.01  Aligned_cols=105  Identities=13%  Similarity=0.133  Sum_probs=54.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC-CCC-------------CCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             999999279982999999998000-113-------------789829999759769999999999983305899569789
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK-LTE-------------AFEPKAWVCVSDDFDVLRISKAILDSIKRSSCKLEDLNS   79 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~-~~~-------------~f~~~~w~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~   79 (1237)
                      +++.|.|+-..|||++.+.++-.. ..+             .|+ .++...+...++..-......              
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d-~I~~~~~~~d~~~~~~StF~~--------------  100 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFD-GIYTRIGASDDLAGGKSTFMV--------------  100 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCS-EEEEECCC------CCSHHHH--------------
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEECCCEEEEECC-EEEEEECCCCCCCCCCCHHHH--------------
T ss_conf             67999788734532345565899999852504613751994011-699998777602378307898--------------


Q ss_pred             HHHHHHHHH--CCCCEEEEEECCCCCC-HHHH----HHHHCCCCCCCCCCEEEEEECCHHHHH
Q ss_conf             999999996--6972999996887777-6269----983122568999959999907456787
Q 000887           80 VQLELKETV--FKKKFLIVLDDVWSER-YDLW----QALKSPFMAGAPGSRIIVTTRSMDVAL  135 (1237)
Q Consensus        80 ~~~~l~~~l--~~~~~LlvlDdv~~~~-~~~~----~~l~~~~~~~~~~~~ilvTtR~~~~~~  135 (1237)
                      -..++...+  .+++.|+++|..-... ..+-    .++...+.  ..++++++||-..++..
T Consensus       101 el~~~~~il~~~~~~sLvliDE~~~gT~~~eg~ala~aile~L~--~~~~~~i~tTH~~eL~~  161 (224)
T d1ewqa2         101 EMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALH--ERRAYTLFATHYFELTA  161 (224)
T ss_dssp             HHHHHHHHHHHCCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEECCCHHHHT
T ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHCCHHHHHHHHHH--HCCCCEEEEEECHHHHH
T ss_conf             67889877502897727855454568623320025888888886--23761378652023332

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.53  E-value=0.046  Score=24.53  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=18.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|.+.|.+|+|||+|..++....
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSEDA   30 (173)
T ss_dssp             EEEEECCCCC-------------
T ss_pred             EEEEECCCCCCHHHHHHHHHHCC
T ss_conf             99999999949999999997098

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=89.30  E-value=0.14  Score=21.81  Aligned_cols=25  Identities=24%  Similarity=0.565  Sum_probs=20.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             3999999279982999999998000
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .--|.+.|..|+||||+...+....
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             7489998999986999999985898

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=88.34  E-value=0.35  Score=19.43  Aligned_cols=53  Identities=21%  Similarity=0.160  Sum_probs=33.0

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             9939999992799829999999980001137898299997597699999999999833
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCVSDDFDVLRISKAILDSIK   68 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~~~~~~~~~~~~~i~~~l~   68 (1237)
                      .+.++..|.++-|.|||+++..++..     ....+.+.+....-..+..+.+...+.
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~~-----~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYAA-----QGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHT-----TTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHH-----CCCCEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             67888999968877999999999998-----699399976769999999999999852

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=88.28  E-value=0.12  Score=22.16  Aligned_cols=22  Identities=27%  Similarity=0.282  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHHH
Q ss_conf             9999992799829999999980
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      --|+|.|-.++|||||..++..
T Consensus         6 inIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           6 INLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHH
T ss_conf             7999990778709999999997

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=88.20  E-value=0.051  Score=24.26  Aligned_cols=16  Identities=19%  Similarity=0.183  Sum_probs=8.5

Q ss_pred             CHHHHHHHHHHCCCCC
Q ss_conf             8588999999929975
Q 000887          256 KEKELVLLWIAEGLVQ  271 (1237)
Q Consensus       256 ~~~~l~~~w~~~g~~~  271 (1237)
                      +.+..|.-.+.+|-+.
T Consensus       195 EpgCaV~~av~~g~i~  210 (231)
T d1t9ha2         195 EPKCAVKQAVEDGELK  210 (231)
T ss_dssp             CSSCHHHHHHHHTSSC
T ss_pred             CCCCHHHHHHHCCCCC
T ss_conf             9986499999869987

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=87.67  E-value=0.23  Score=20.47  Aligned_cols=23  Identities=26%  Similarity=0.416  Sum_probs=19.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|||.|.+-+|||||-.++-...
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~~   26 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKAG   26 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             48888999998899999997799

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.57  E-value=0.23  Score=20.54  Aligned_cols=27  Identities=22%  Similarity=0.384  Sum_probs=23.9

Q ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             999399999927998299999999800
Q 000887           10 AANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        10 ~~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      +..+.||+|.|+-+.|||+|+..++..
T Consensus        29 ~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          29 TQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             CSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             CCCEEEEEEECCCCCCHHHHHHHHCCC
T ss_conf             998799998899999799999998099

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.26  E-value=0.21  Score=20.70  Aligned_cols=23  Identities=17%  Similarity=0.352  Sum_probs=19.8

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             39999992799829999999980
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      +--|+|.|.+|+|||+|..++..
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHC
T ss_conf             71799989999978999999958

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=86.44  E-value=0.24  Score=20.35  Aligned_cols=39  Identities=26%  Similarity=0.198  Sum_probs=25.3

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             9939999992799829999999980001137898299997
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYNDKLTEAFEPKAWVCV   50 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~~~~~~f~~~~w~~~   50 (1237)
                      ...+-+.|.|..|.|||+++..+......... .++-++.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l~~li~~~~~~g~-~~iiiD~   86 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLLRELAYTGLLRGD-RMVIVDP   86 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHHHHHHHHHHHTTC-EEEEEEE
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCC-CEEEEEC
T ss_conf             35265899907999689999999999984799-8899968

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=86.43  E-value=0.2  Score=20.84  Aligned_cols=26  Identities=12%  Similarity=0.166  Sum_probs=22.5

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      .+-..+.++|+++.|||.+|..+.+-
T Consensus        51 PKkn~i~~~GP~~TGKS~f~~sl~~~   76 (205)
T d1tuea_          51 PKKNCLVFCGPANTGKSYFGMSFIHF   76 (205)
T ss_dssp             TTCSEEEEESCGGGCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             87318999889985689999999998

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.62  E-value=0.062  Score=23.79  Aligned_cols=23  Identities=30%  Similarity=0.559  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             99999279982999999998000
Q 000887           15 VIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        15 vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      -|++.|.+|+|||+|..++....
T Consensus         2 kI~liG~~n~GKSSLin~l~g~~   24 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNED   24 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             89999999999999999995899

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=85.57  E-value=0.32  Score=19.64  Aligned_cols=24  Identities=25%  Similarity=0.416  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHCC
Q ss_conf             999999279982999999998000
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      .+|+|.|-.+.|||||+.++....
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHC
T ss_conf             879999699854999999998236

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=84.16  E-value=0.34  Score=19.53  Aligned_cols=23  Identities=26%  Similarity=0.442  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99999927998299999999800
Q 000887           14 RVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      =-|||.|.+.+|||||-.++-..
T Consensus        11 ~kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1          11 LKTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             37999789999899999999778

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.25  E-value=0.31  Score=19.71  Aligned_cols=26  Identities=23%  Similarity=0.376  Sum_probs=22.8

Q ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHC
Q ss_conf             99399999927998299999999800
Q 000887           11 ANFRVIPLVGMGGIGKTTLAQEVYND   36 (1237)
Q Consensus        11 ~~~~vv~i~G~~G~GKT~La~~~~~~   36 (1237)
                      ++.|-|+|.|-.|.|||||+..+...
T Consensus        15 ~~IRNI~iiGhvd~GKTTL~d~Ll~~   40 (341)
T d1n0ua2          15 TNVRNMSVIAHVDHGKSTLTDSLVQR   40 (341)
T ss_dssp             GGEEEEEEECCGGGTHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHH
T ss_conf             16748999968888699999999997

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=83.14  E-value=0.17  Score=21.31  Aligned_cols=19  Identities=42%  Similarity=0.719  Sum_probs=16.4

Q ss_pred             EEEEEECCCCCCHHHHHHH
Q ss_conf             9999992799829999999
Q 000887           14 RVIPLVGMGGIGKTTLAQE   32 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~   32 (1237)
                      .+-...|.+|.|||||...
T Consensus        15 ~valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          15 DVAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             CEEEEEECTTSCHHHHTCB
T ss_pred             CEEEEECCCCCCCCCCCCC
T ss_conf             8899973687981422107

>d1wxqa1 c.37.1.8 (A:1-319) GTP-binding protein PH0525 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein PH0525
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=82.57  E-value=0.46  Score=18.73  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=19.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHCC
Q ss_conf             9999279982999999998000
Q 000887           16 IPLVGMGGIGKTTLAQEVYNDK   37 (1237)
Q Consensus        16 v~i~G~~G~GKT~La~~~~~~~   37 (1237)
                      |+|.|.+-+|||||-.++-...
T Consensus         3 v~lvG~pn~GKStlfn~lt~~~   24 (319)
T d1wxqa1           3 IGVVGKPNVGKSTFFSAATLVD   24 (319)
T ss_dssp             EEEEECTTSSHHHHHHHHHC--
T ss_pred             EEEECCCCCCHHHHHHHHHCCC
T ss_conf             7688999998999999997889

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.72  E-value=0.54  Score=18.33  Aligned_cols=23  Identities=17%  Similarity=0.372  Sum_probs=19.6

Q ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             39999992799829999999980
Q 000887           13 FRVIPLVGMGGIGKTTLAQEVYN   35 (1237)
Q Consensus        13 ~~vv~i~G~~G~GKT~La~~~~~   35 (1237)
                      .++-+|+|.-|.|||++..++.-
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~   47 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISF   47 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
T ss_conf             99899999999988999999999

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=80.90  E-value=0.23  Score=20.53  Aligned_cols=19  Identities=42%  Similarity=0.719  Sum_probs=15.8

Q ss_pred             EEEEEECCCCCCHHHHHHH
Q ss_conf             9999992799829999999
Q 000887           14 RVIPLVGMGGIGKTTLAQE   32 (1237)
Q Consensus        14 ~vv~i~G~~G~GKT~La~~   32 (1237)
                      .+-...|.+|.|||||...
T Consensus        15 ~~alfFGLSGTGKTTLs~d   33 (313)
T d2olra1          15 DVAVFFGLSGTGKTTLSTD   33 (313)
T ss_dssp             CEEEEECSTTSSHHHHHCC
T ss_pred             CEEEEECCCCCCCCCCEEC
T ss_conf             8899970477985602327