Citrus Sinensis ID: 003090

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------85
Protein Sequence
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQAMESGISSETTSSYTEN
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEEEEccccccHHHHHHHHHHHHHHcccccEEEEEEEccccccHHHHHHccccccccccccccccccccccccccHHHHHHccccccccccHHHHcccccccEEEcccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHHcccccEEEEcccccccccHHccccccccEEEEEccccccccccHHHcccccccEEEcccccccccccccccccccccccHHHHcccccccEEEEEcccccccccccHHccccccEEcccccccccccccHHHHHHHHHcccccccccccccccccHHHHHHHHHcccccHHcccccccccccccccccccccccEEEEEcccccEEEccccccccccccccccccccccccccEEcccccccccccccccEEEEcccccccccccHHHHcccccccEEEEccccccEEEEEcccccccHHcccccccccEEEccccccccccccccccccccccccEEEEEcccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccEEEEEcccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccEEEEEcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccEEcccccccccccccccccccccHHHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHHHHHHccccHEEEEEEcccccHHHcHHHHHHHccccEEEEccccHHHccccccccccEEEEEcccccccccHHHHHcccccEEEEcccccccccccccccccccccccccccccHHHHHHHcccEEEccccccccccccHHcccccEEEEcccccHHHccHHHHHHHcccEEEcccccccccccHHHHHHHHHccEEEEcccccEEEEcccccccccccccHHHHHccccccEEEEEccccccccccccHHHHcEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcEEcHcccccccHccccccccccccccEEEEccccccEEcccccccccHcccccccEEEEcccHcHHHHccccccccccccccEEEEcccccccEcccHHHHHccccccEEEEcccHHHHHHHcccccccccccccHcccccEEEEcccHcHHHHcccccccccccccEEEEEcccHHHHHccHHHHHHHHcccEEEEEccccEEEEEcccccccccccccccccEEEEcccccHHHcccHHHHHHcHcccEEEEcccHHHHHHHcccccHcccccccccEEEcccccEEEEcccccccHccccccccccccccEEEEEEccccEEEEcccccccEEcc
Coil and Loop (DISEMBL)
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVgnfgkgvsrpapppaiisssegvyaFKSRESTMKDIMEAMKDENVSItgicgmggvgkTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDltgislmfndihevpdelecpklqalflqensplaipdrFFQGMKDlqvldlggirrfsfsvrfpflfpplpssplfllpssLSFLINLRTLRLHDRRIQGDLSligelsgleildlsesdvseipvsfgrlshlrlldltgcyilelipRGVLSRLRKLEELYMShsfrhwqfeseseedsssnakFIELGALSRLTSlhihipegkimpsdmsfqnltSFSIaigdleerplsdFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEIchgqlpagclsnvkrsdvvdcGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEkltlwdlprmtdiwkgdTQFVSLHNLKKVRVEECDELRQvfpanfgkkAAAEEMVLYRKRRDQihihattstssptpslgnlvsITIRGCGKLRNLFTTSMVKSLVRleslevrscptlqeiimddegevglqgastkkitfpslfgiklcdldslacfcstahhFNFVFHLGQKIREkqamesgissettssyten
Flexible Loop (DISEMBL)
matetvasvtqpiteriVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAeidaatrnrevikDEVKSWIAEVNDIIPKAEKFLEDEVKvnkkclgglcvdlksrYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPpaiisssegvyAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQfeseseedssSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRqvfpanfgkkaaAEEMVLYRKRRDQIHIhattstssptpslgNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQamesgissettssyten
Low Complexity Region (SEG)
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVGNFGKGVsrpapppaiisssEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIrrfsfsvrfpflfpplpssplfllpsslsflINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFeseseedsssNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAttstssptpsLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQAMESGISSETTSSYTEN
Disordered region (IsUnstruct)
*********TQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKL*********EIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKL************************************************************NVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF*************FIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHA**********LGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKI*********************
Disordered Region (DISOPRED)
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVG*****************************STMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSV*****************SLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANF*********VLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIM***************ITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQ*****************
Disordered Region (DISEMBL)
*********TQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW************NAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREK******************
Disordered Region (DISPRO)
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEG*V*LQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQAMESGISSETTS*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNFVFHLGQKIREKQAMESGISSETTSSYTEN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	848	2.2.26 [Sep-21-2011]
Q42484	909	Disease resistance protei	yes	no	0.392	0.366	0.252	8e-17
Q9FLB4	874	Putative disease resistan	no	no	0.227	0.220	0.303	7e-14
Q9T048	985	Disease resistance protei	no	no	0.242	0.209	0.318	1e-13
P60838	894	Probable disease resistan	no	no	0.259	0.246	0.258	2e-13
O22727	967	Probable disease resistan	no	no	0.239	0.209	0.306	9e-13
O81825	919	Probable disease resistan	no	no	0.489	0.451	0.261	1e-12
O64789	925	Probable disease resistan	no	no	0.259	0.237	0.285	7e-12
Q940K0	889	Probable disease resistan	no	no	0.255	0.244	0.285	2e-11
Q9LMP6	851	Probable disease resistan	no	no	0.233	0.232	0.292	1e-09
Q8RXS5	888	Probable disease resistan	no	no	0.234	0.224	0.275	2e-09

>sp|Q42484|RPS2_ARATH Disease resistance protein RPS2 OS=Arabidopsis thaliana GN=RPS2 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 110/436 (25%), Positives = 172/436 (39%), Gaps = 103/436 (23%)

Query: 231 GWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDLGGI 289
            W     ISL+ N I  +P++L CPKL  L LQ+NS L  IP  FF  M  L+VLDL   
Sbjct: 509 NWRQALVISLLDNRIQTLPEKLICPKLTTLMLQQNSSLKKIPTGFFMHMPVLRVLDLS-- 566

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEIL 349
                       F  +   PL     S+ +L+ L                         L
Sbjct: 567 ------------FTSITEIPL-----SIKYLVELYH-----------------------L 586

Query: 350 DLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFE 409
            +S + +S +P   G L  L+ LDL     L+ IPR  +  L KLE L + +S+  W+ +
Sbjct: 587 SMSGTKISVLPQELGNLRKLKHLDLQRTQFLQTIPRDAICWLSKLEVLNLYYSYAGWELQ 646

Query: 410 SESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSF-QNLTSFSIAIGDLEERPL 468
           S  E+++       ELG                   +D+ + +NLT+  I +  LE    
Sbjct: 647 SFGEDEAE------ELGF------------------ADLEYLENLTTLGITVLSLE---- 678

Query: 469 SDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLA 528
                               L       ALH  I++L     +    E+ YF   +  L 
Sbjct: 679 -------------------TLKTLFEFGALHKHIQHL----HVEECNELLYFN--LPSLT 713

Query: 529 NDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCL 588
           N G N L  L I  C++++YL+   +      L  LE L +    N   +    +   CL
Sbjct: 714 NHGRN-LRRLSIKSCHDLEYLVTPADFE-NDWLPSLEVLTLHSLHNLTRVWGNSVSQDCL 771

Query: 589 SNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFS 648
            N++  ++  C  +  +     VQ    L+ + ++ C  +  +   E  + + E+  LF 
Sbjct: 772 RNIRCINISHCNKLKNV---SWVQKLPKLEVIELFDCREIEELIS-EHESPSVEDPTLFP 827

Query: 649 SLEKLTLWDLPRMTDI 664
           SL+ L   DLP +  I
Sbjct: 828 SLKTLRTRDLPELNSI 843

Disease resistance (R) protein that specifically recognizes the AvrRpt2 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 degraded by AvrRpt2.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLB4|DRL31_ARATH Putative disease resistance protein At5g05400 OS=Arabidopsis thaliana GN=At5g05400 PE=2 SV=1

 Score = 80.1 bits (196), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 100/204 (49%), Gaps = 11/204 (5%)

Query: 38  YIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFL-EDEV 96
           ++ AL+   ++L  RR+DL   I         + DEV+ W++EV   + +A   L + + 
Sbjct: 35  HVAALKKTVRQLEARRDDLLKRIKVQEDRGLNLLDEVQQWLSEVESRVCEAHDILSQSDE 94

Query: 97  KVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAI---ISS 152
           +++  C G  C    K  Y  S+    K   +  L++ G F + V++  P P +   +  
Sbjct: 95  EIDNLCCGQYCSKRCKYSYDYSKSVINKLQDVENLLSKGVFDE-VAQKGPIPKVEERLFH 153

Query: 153 SEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKM-FDDV 211
            E V      EST   +ME      V + GI GMGGVGKTTL+ +I  + + +   FD  
Sbjct: 154 QEIVGQEAIVESTWNSMMEV----GVGLLGIYGMGGVGKTTLLSQINNKFRTVSNDFDIA 209

Query: 212 AMAVVSQTPSITKIQYEIAGWLDL 235
              VVS+ P++ +IQ +I   LDL
Sbjct: 210 IWVVVSKNPTVKRIQEDIGKRLDL 233

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T048|DRL27_ARATH Disease resistance protein At4g27190 OS=Arabidopsis thaliana GN=At4g27190 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 103/232 (44%), Gaps = 26/232 (11%)

Query: 235 LTGISLMFNDIHEVPDELE--CPKLQALFLQENSPLA-IPDRFFQGMKDLQVLDLGGIRR 291
           L  +SLM N +  +PD +E  C K   L LQ N  L  +P  F Q    L++L+L G R 
Sbjct: 503 LRRVSLMNNKLESLPDLVEEFCVKTSVLLLQGNFLLKEVPIGFLQAFPTLRILNLSGTRI 562

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDL 351
            SF           PS        SL  L +L +L L D      L  +  L+ LE+LDL
Sbjct: 563 KSF-----------PSC-------SLLRLFSLHSLFLRDCFKLVKLPSLETLAKLELLDL 604

Query: 352 SESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESE 411
             + + E P     L   R LDL+    LE IP  V+SRL  LE L M+ S   W  + E
Sbjct: 605 CGTHILEFPRGLEELKRFRHLDLSRTLHLESIPARVVSRLSSLETLDMTSSHYRWSVQGE 664

Query: 412 SEEDSSSNAKFIELGALSRLTSLHIHIPEGKIM--PSDMSFQNLTSFSIAIG 461
           +++     A   E+G L RL  L I +     +    +   + L  F + +G
Sbjct: 665 TQK---GQATVEEIGCLQRLQVLSIRLHSSPFLLNKRNTWIKRLKKFQLVVG 713

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60838|DRL1_ARATH Probable disease resistance protein At1g12280 OS=Arabidopsis thaliana GN=At1g12280 PE=3 SV=1

 Score = 78.6 bits (192), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 112/228 (49%), Gaps = 8/228 (3%)

Query: 15  ERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAA--TRNREVIKD 72
           + +V+ +        GY+C+    + A++ + + L  +R+D++  +D    TR RE +  
Sbjct: 12  DEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERL-S 70

Query: 73  EVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSAL 130
           +V+ W+  V+ +  K  + L  ++ ++ + CL G C  ++K  Y   +        + +L
Sbjct: 71  QVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESL 130

Query: 131 MAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVG 190
            + G+F       A P A I           +E+ ++ +   + ++   I G+ GMGGVG
Sbjct: 131 SSQGDFD--TVTLATPIARIEEMPIQPTIVGQETMLERVWTRLTEDGDEIVGLYGMGGVG 188

Query: 191 KTTLVKEIQKQ-AKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTG 237
           KTTL+  I  + +++   F  V   VVS++P I +IQ +I   LDL G
Sbjct: 189 KTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGG 236

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O22727|DRL16_ARATH Probable disease resistance protein At1g61190 OS=Arabidopsis thaliana GN=At1g61190 PE=3 SV=1

 Score = 76.3 bits (186), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 102/209 (48%), Gaps = 6/209 (2%)

Query: 30  GYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAE 89
           GY+   +  + AL+ E + L   ++++Q ++       +   + V+ W+  VN I  + +
Sbjct: 26  GYIRNLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIECK 85

Query: 90  KFLE-DEVKVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPP 147
             L    V++ K CL GLC   + S YK  +        ++ L + GNF + VS+P  PP
Sbjct: 86  DLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNFDE-VSQP--PP 142

Query: 148 AIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQ-KQAKEMK 206
                         +E  +K     + ++ V I G+ GMGGVGKTTL K+I  K A+   
Sbjct: 143 RSEVEERPTQPTIGQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAETGG 202

Query: 207 MFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
            FD V   VVSQ   ++K+Q +IA  L L
Sbjct: 203 TFDIVIWIVVSQGAKLSKLQEDIAEKLHL 231

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O81825|DRL28_ARATH Probable disease resistance protein At4g27220 OS=Arabidopsis thaliana GN=At4g27220 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 124/474 (26%), Positives = 200/474 (42%), Gaps = 59/474 (12%)

Query: 238 ISLMFNDIHEVPDE-LECPKLQALFLQENSPLA-IPDRFFQGMKDLQVLDLGGIRRFSFS 295
           +SLM N +  +P+  +E  +   L LQ NS +  +P+ F Q   +L++LDL G+R     
Sbjct: 475 VSLMANKLERLPNNVIEGVETLVLLLQGNSHVKEVPNGFLQAFPNLRILDLSGVR----- 529

Query: 296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD 355
                         +  LP S S L +LR+L L + +   +L  +  L  L+ LDL ES 
Sbjct: 530 --------------IRTLPDSFSNLHSLRSLVLRNCKKLRNLPSLESLVKLQFLDLHESA 575

Query: 356 VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED 415
           + E+P     LS LR + ++  Y L+ IP G + +L  LE L M+ S   W  + E  E 
Sbjct: 576 IRELPRGLEALSSLRYICVSNTYQLQSIPAGTILQLSSLEVLDMAGSAYSWGIKGEERE- 634

Query: 416 SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLF 475
               A   E+  L  L  L I +             ++ SFS     L +R L+ F  LF
Sbjct: 635 --GQATLDEVTCLPHLQFLAIKL------------LDVLSFSYEFDSLTKR-LTKFQFLF 679

Query: 476 LQKFKKRCSRAMGLS----QDMRIS-ALHSWIKNLLLRSEILALAEVN-YFENIVSDLAN 529
               +       G       D+ +S A   W+   +   ++     +N  FEN+V+  + 
Sbjct: 680 -SPIRSVSPPGTGEGCLAISDVNVSNASIGWLLQHVTSLDLNYCEGLNGMFENLVTK-SK 737

Query: 530 DGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGC-- 587
             F  +  L I     +  L +  E  L +    LE L + +N N   I  G+L      
Sbjct: 738 SSFVAMKALSIHYFPSLS-LASGCESQLDL-FPNLEELSL-DNVNLESI--GELNGFLGM 792

Query: 588 -LSNVKRSDVVDCGSILKILLSHLVQ-SFQNLQRLRVYSCGLLVSVFEIERVNIAKEETE 645
            L  +K   V  C  + ++    ++  +  NLQ ++V SC  L  +F    V +      
Sbjct: 793 RLQKLKLLQVSGCRQLKRLFSDQILAGTLPNLQEIKVVSCLRLEELFNFSSVPVDFCAES 852

Query: 646 LFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQV--FPANFG 697
           L   L  + L  LP++  +       V L +L+ + VE C+ L+ +   P N G
Sbjct: 853 LLPKLTVIKLKYLPQLRSLCNDR---VVLESLEHLEVESCESLKNLPFVPGNTG 903

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O64789|DRL18_ARATH Probable disease resistance protein At1g61310 OS=Arabidopsis thaliana GN=At1g61310 PE=2 SV=1

 Score = 73.6 bits (179), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 108/231 (46%), Gaps = 11/231 (4%)

Query: 8   SVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNR 67
           +V      RI D L   +     Y+   +  + AL+ E + L   ++++Q ++       
Sbjct: 10  AVGDQTMNRIFDCLIGKS-----YIRTLEKNLRALQREMEDLRATQHEVQNKVAREESRH 64

Query: 68  EVIKDEVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCVD-LKSRYKLSREAEEKTL 125
           +   + V+ W+  VN I  + +  L    V++ K CL GLC   + S YK  ++      
Sbjct: 65  QQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFLLLE 124

Query: 126 AMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICG 185
            +  L + GNF + VS+P  PP              +E  ++     + ++ V I G+ G
Sbjct: 125 EVKILKSEGNFDE-VSQP--PPRSEVEERPTQPTIGQEEMLEKAWNRLMEDGVGIMGLHG 181

Query: 186 MGGVGKTTLVKEIQKQAKEM-KMFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
           MGGVGKTTL K+I  +  E+   FD V   VVSQ   ++K+Q +IA  L L
Sbjct: 182 MGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHL 232

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q940K0|DRL15_ARATH Probable disease resistance protein At1g61180 OS=Arabidopsis thaliana GN=At1g61180 PE=2 SV=2

 Score = 71.6 bits (174), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 115/228 (50%), Gaps = 11/228 (4%)

Query: 13  ITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEI--DAATRNREVI 70
           ++++ ++ +FN  + +  Y+   +  + AL+ E + L   ++++Q ++  D A   R + 
Sbjct: 9   VSDQTLNRIFNCLIGK-SYIRTLEKNLRALQREMEDLRAIQHEVQNKVARDEARHQRRL- 66

Query: 71  KDEVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMS 128
            + V+ W+  VN +  + +  L    V++ K CL GLC   + S YK  ++       + 
Sbjct: 67  -EAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLLLEEVK 125

Query: 129 ALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGG 188
            L + GNF + VS+P  PP              +E  ++     + ++ V I G+ GMGG
Sbjct: 126 KLNSEGNFDE-VSQP--PPRSEVEERPTQPTIGQEDMLEKAWNRLMEDGVGIMGLHGMGG 182

Query: 189 VGKTTLVKEIQKQAKEM-KMFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
           VGKTTL K+I  +  E+   FD V   VVS+   I+K+Q +IA  L L
Sbjct: 183 VGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHL 230

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LMP6|DRL3_ARATH Probable disease resistance protein At1g15890 OS=Arabidopsis thaliana GN=At1g15890 PE=3 SV=2

 Score = 65.9 bits (159), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 99/212 (46%), Gaps = 14/212 (6%)

Query: 31  YLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEK 90
           Y+ K +  +EAL+   ++L +RR+DL   +            +V+ W++ V D+  +   
Sbjct: 28  YILKMEANLEALQNTMQELEERRDDLLRRVVIEEDKGLQRLAQVQGWLSRVKDVCSQVND 87

Query: 91  FLEDE-VKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPA 148
            L+ + ++  + CL G C  +  S         +K   +  L+A G F + V+   P P 
Sbjct: 88  LLKAKSIQTERLCLCGYCSKNFISGRNYGINVLKKLKHVEGLLAKGVF-EVVAEKIPAPK 146

Query: 149 I----ISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKE 204
           +    I ++ G+ A   R          MKDE  ++ G+ GMGGVGKTTL+  I  +  E
Sbjct: 147 VEKKHIQTTVGLDAMVGRAWN-----SLMKDERRTL-GLYGMGGVGKTTLLASINNKFLE 200

Query: 205 -MKMFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
            M  FD V   VVS+      IQ +I G L L
Sbjct: 201 GMNGFDLVIWVVVSKDLQNEGIQEQILGRLGL 232

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RXS5|DRL40_ARATH Probable disease resistance protein At5g63020 OS=Arabidopsis thaliana GN=At5g63020 PE=2 SV=2

 Score = 65.5 bits (158), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 94/207 (45%), Gaps = 8/207 (3%)

Query: 27  RQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIP 86
           R   Y+   +  + AL+   +++  RR DL  +I +  R        V+ W+++V  I+P
Sbjct: 24  RNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSEERRGLQRLSVVQGWVSKVEAIVP 83

Query: 87  KAEKFLE-DEVKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSRPA 144
           +  + +    V+V + CL G C  +L S Y+  +   +    +  L   G+F     R  
Sbjct: 84  RVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVMKMIEEVEVLRYQGDFAVVAERVD 143

Query: 145 PPPAIISSSEGVYAFKSR-ESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQ-A 202
                   +  + A     ES    +ME    + + I G+ GMGGVGKTTL+  I  + +
Sbjct: 144 AARVEERPTRPMVAMDPMLESAWNRLME----DEIGILGLHGMGGVGKTTLLSHINNRFS 199

Query: 203 KEMKMFDDVAMAVVSQTPSITKIQYEI 229
           +    FD V   VVS+   I +IQ EI
Sbjct: 200 RVGGEFDIVIWIVVSKELQIQRIQDEI 226

Probable 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	848
224111296	1315	cc-nbs-lrr resistance protein [Populus t	0.669	0.431	0.320	1e-63
359494129	1144	PREDICTED: disease resistance protein At	0.714	0.529	0.308	2e-61
359488103	1530	PREDICTED: disease resistance protein At	0.604	0.335	0.306	4e-57
224143316	1337	cc-nbs-lrr resistance protein [Populus t	0.630	0.400	0.337	4e-57
224111284	1340	cc-nbs-lrr resistance protein [Populus t	0.669	0.423	0.324	7e-57
255542484	2460	phosphoprotein phosphatase, putative [Ri	0.627	0.216	0.320	9e-56
359488095	1347	PREDICTED: probable disease resistance p	0.602	0.379	0.304	1e-55
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.586	0.293	0.305	2e-54
359488025	1781	PREDICTED: uncharacterized protein LOC10	0.608	0.289	0.297	8e-54
297735461	1063	unnamed protein product [Vitis vinifera]	0.623	0.497	0.315	1e-53

>gi|224111296|ref|XP_002332952.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222834264|gb|EEE72741.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  251 bits (641), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 203/634 (32%), Positives = 309/634 (48%), Gaps = 66/634 (10%)

Query: 205  MKMFDDV---AMAVVSQTPSITKIQYEIAGW------LDLTGISLMFNDIHEVPDELECP 255
            +KM D V   A++V  +   +  +  E   W         T ISL F  I ++P  LECP
Sbjct: 458  VKMHDVVHSFAISVALRDHHVLTVADEFKEWPANDVLQQYTAISLPFRKIPDLPAILECP 517

Query: 256  KLQALFLQENSP-LAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP 314
             L +  L    P L IPD FF+ MK+L++LDL  +                  SPL   P
Sbjct: 518  NLNSFLLLNKDPSLQIPDSFFREMKELKILDLTEVNL----------------SPL---P 558

Query: 315  SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDL 374
            SSL FL NL+TL L D  +  D+S+IGEL+ L++L L  S++  +P   G+++ L+LLDL
Sbjct: 559  SSLQFLENLQTLCL-DHCVLEDISIIGELNKLKVLSLMSSNIVRLPREIGKVTRLQLLDL 617

Query: 375  TGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL 434
            + C  LE+I    LS L +LE+LYM +SF  W+ E  S +   +NA   EL  LS L++L
Sbjct: 618  SNCERLEVISPNALSSLTRLEDLYMGNSFVKWETEGSSSQ--RNNACLSELKHLSNLSTL 675

Query: 435  HIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQD 492
            H+ I +   MP D+  SFQNL  F I IGD  +  + D             SR + L  +
Sbjct: 676  HMQITDADNMPKDLFSSFQNLERFRIFIGDGWDWSVKD-----------ATSRTLKLKLN 724

Query: 493  MRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNS 552
              I  L   +  LL  +E L L E+N  ++I++DL  +GF +L  L +  C  ++Y++NS
Sbjct: 725  TVIQ-LEEGVNTLLKITEELHLQELNGVKSILNDLDGEGFPQLRHLHVQNCPGVQYIINS 783

Query: 553  LERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQ 612
            +    R     L+ LF+    N  +ICHGQL A  L N++   V  C  +  +    + +
Sbjct: 784  IRMGPRTAFLNLDSLFLENLDNLEKICHGQLMAESLGNLRILKVESCHRLKNLFSVSMAR 843

Query: 613  SFQNLQRLRVYSCGLLVSVFEIERVNIAKEETEL--FSSLEKLTLWDLPRMTDIWKGDTQ 670
                L+ + +  C ++  V   E  N A +   +  F+ L +LTL  LP+ T       +
Sbjct: 844  RLVRLEEITIIDCKIMEEVVAEESENDAADGEPIIEFTQLRRLTLQCLPQFTSFHSNVEE 903

Query: 671  FVSLHNLKKVRVEECDELRQVFPANFGKKAA----------AEEMVLYRKRRDQIHIHAT 720
                   +K+   E      V     G   +           E++ L   + ++I  H  
Sbjct: 904  SSDSQRRQKLLASEARSKEIVAGNELGTSMSLFNTKILFPNLEDLKLSSIKVEKIW-HDQ 962

Query: 721  TSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIM-DDEG 779
             S  SP   + NL SI +  C  L  L T+SMV+SL +L+ LE+ +C +++EI++ +D G
Sbjct: 963  PSVQSPC--VKNLASIAVENCRNLNYLLTSSMVESLAQLKKLEICNCKSMEEIVVPEDIG 1020

Query: 780  EVGLQGASTKKITFPSLFGIKLCDLDSLACFCST 813
            E    G    K+ FP L  + L  L  L  FC++
Sbjct: 1021 E----GKMMSKMLFPKLLILSLIRLPKLTRFCTS 1050

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494129|ref|XP_002278428.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  244 bits (623), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 203/657 (30%), Positives = 313/657 (47%), Gaps = 51/657 (7%)

Query: 188  GVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTG---------- 237
            G+  + L+ +  K    +KM D V +  +S T S  K  + +   + L            
Sbjct: 448  GLKASCLLMDGDKSKGSLKMHDLVRVFAISIT-STEKYAFMVKAGVGLKNWPKKGTFEHY 506

Query: 238  --ISLMFNDIHEVPDELECPKLQALFLQENSPLAI-PDRFFQGMKDLQVLDLGGIRRFSF 294
              ISLM N+I  +P  LECPKL  L L  N  L I PD FF GMK L+VLDL  I +  +
Sbjct: 507  ALISLMANNISSLPVGLECPKLHTLLLGGNRGLKIFPDAFFVGMKTLKVLDLTAISKKLY 566

Query: 295  SVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSES 354
              R+     PLP+S        L  L +LR L LH R++ GD+S++G+L  LEIL    S
Sbjct: 567  --RYSLHITPLPAS--------LQLLTDLRMLHLHHRKL-GDISILGKLKKLEILSFFAS 615

Query: 355  DVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE 414
             +SE+P   G L +L+LLDLT C  L+ IP  ++S L  LEELYM  SF+ W     + E
Sbjct: 616  HISELPKEMGELKNLKLLDLTYCRSLKKIPPNLISGLSALEELYMRGSFQQWDVGGTTIE 675

Query: 415  DSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGL 474
             SS++   +   +L  LT+LH+ I   K +P+   F N   F I IG      LS     
Sbjct: 676  RSSASLSELN--SLLNLTTLHVEIINAKCIPNSFLFPNQLRFQIYIGS----KLS--FAT 727

Query: 475  FLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEV-NYFENIVSDLANDGFN 533
            F +K K     +  L      S +   +K L  R+E L+L  +     NI+ +L + GFN
Sbjct: 728  FTRKLKYDYPTSKALELKGIDSPIPIGVKMLFERTEDLSLISLLEGSRNILPNLGSRGFN 787

Query: 534  ELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKR 593
             L  L +  C E + ++++ +    V    +E + +        +  G LP G    ++ 
Sbjct: 788  GLTSLSVRNCVEFECIIDTTQGVHPVAFPNIETIHLTHLCGMKVLSSGTLPMGSFRKLRV 847

Query: 594  SDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKL 653
              V  CG +  +  + L+Q  QNL+ +++  C  +  VF+IE + + +E     SSL +L
Sbjct: 848  LTVEQCGGLSTLFPADLLQLLQNLEIVQITCCQEMQDVFQIEGILVGEEHVLPLSSLREL 907

Query: 654  TLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRD 713
             L  LP++  +WKG    +SLHNL+ + +E C+ LR +F  +  +     E   Y K  D
Sbjct: 908  KLDTLPQLEHLWKGFGAHLSLHNLEVIEIERCNRLRNLFQPSIAQSLFKLE---YLKIVD 964

Query: 714  QIHIHATTSTSSPTPSLGN-----------LVSITIRGCGKLRNLFTTSMVKSLVRLESL 762
             + +    +       + N           L  + +  C KL++LF+ S  +S ++L+ L
Sbjct: 965  CMELQQIIAEDGLEQEVSNVEDKKSLNLPKLKVLEVEDCKKLKSLFSVSSAQSFLQLKQL 1024

Query: 763  EVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHFNF 819
            +V     L+ II  + GE+    A+  K   P L  ++L  L  L  FC     F +
Sbjct: 1025 KVSGSNELKAIISCECGEI---SAAVDKFVLPQLSNLELKALPVLESFCKGNFPFEW 1078

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488103|ref|XP_002263579.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  229 bits (585), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 193/629 (30%), Positives = 292/629 (46%), Gaps = 116/629 (18%)

Query: 233  LDLTGISLMFNDIHEVPDELECPKLQAL--FLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
            L +T + L   DIHE+P+ L CPKL+    FL+ N  + IP+ FF+GMK L+VLDL G++
Sbjct: 501  LQVTWVKLHHCDIHELPEGLVCPKLEFFECFLKTNLAVKIPNTFFEGMKQLKVLDLTGMQ 560

Query: 291  RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILD 350
                          LPS PL     SL  L NLRTL L   ++ GD+ +I EL  LEIL 
Sbjct: 561  --------------LPSLPL-----SLQSLANLRTLCLDGCKL-GDIVIIAELKKLEILS 600

Query: 351  LSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFES 410
            L +SD+ ++P    +L+HLRL DL   + L++IP  V+S L +LE+L M +SF  W+ E 
Sbjct: 601  LMDSDIEQLPREIAQLTHLRLFDLKSSFKLKVIPSDVISSLFRLEDLCMENSFTQWEGEG 660

Query: 411  ESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSD 470
            +      SNA   EL  LS LT+L I IP+ K++P DM F NL  + I +GD        
Sbjct: 661  K------SNACLAELKHLSHLTALDIQIPDAKLLPKDMVFDNLMRYRIFVGD-------- 706

Query: 471  FIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLAND 530
             I ++ + +K   +R + L++      L   I  LL R+E L L E+    N++S L  +
Sbjct: 707  -IWIWEKNYKT--NRILKLNKFDTSLHLVDGISKLLKRTEDLHLRELCGGTNVLSKLNRE 763

Query: 531  GFNELMFLVIFRCNEMKYLLNSLERT-LRVTLHKLEWLFIRENQNFVEICHGQLPAGCLS 589
            GF +L  L +    E++Y++NS++ T        +E L + +  N  E+CHGQ PAG   
Sbjct: 764  GFLKLKHLNVESSPEIQYIVNSMDLTSSHAAFPVMETLSLNQLINLQEVCHGQFPAGSFG 823

Query: 590  NVKRSDVVDCGSILKILLS-HLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETE--L 646
             +++ +V DC   LK L S  + +    L+  +V  C  +V +    R  I ++     L
Sbjct: 824  CLRKVEVEDCDG-LKFLFSLSVARGLSRLEETKVTRCKSMVEMVSQGRKEIKEDAVNVPL 882

Query: 647  FSSLEKLTLWDLPRMTD----------------------------IWKGDTQFVSLHNLK 678
            F  L  LTL DLP++++                            I  G        NL+
Sbjct: 883  FPELRSLTLKDLPKLSNFCFEENPVLSKPASTIVGPSTPPLNQPEIRDGQLLLSLGGNLR 942

Query: 679  KVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITI 738
             ++++ C  L ++FP +                                  L NL  +T+
Sbjct: 943  SLKLKNCMSLLKLFPPSL---------------------------------LQNLQELTL 969

Query: 739  RGCGKLRNLF-------TTSMVKSLVRLESLEVRSCPTLQEII----MDDEGEVGLQGAS 787
            + C KL  +F           V+ L +L+ L +   P L+ I       +     +  A 
Sbjct: 970  KDCDKLEQVFDLEELNVDDGHVELLPKLKELRLIGLPKLRHICNCGSSRNHFPSSMASAP 1029

Query: 788  TKKITFPSLFGIKLCDLDSLACFCSTAHH 816
               I FP L  I L  L +L  F S  +H
Sbjct: 1030 VGNIIFPKLSDITLESLPNLTSFVSPGYH 1058

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143316|ref|XP_002336027.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222838884|gb|EEE77235.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  229 bits (584), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 198/587 (33%), Positives = 295/587 (50%), Gaps = 52/587 (8%)

Query: 236  TGISLMFNDIHEVPDELECPKLQALFLQENSP-LAIPDRFFQGMKDLQVLDLGGIRRFSF 294
            T ISL F  I ++P  LECP L +  L    P L IP+ FF+ MK+L+VLDL G+     
Sbjct: 498  TAISLPFRKIPDLPAILECPNLNSFLLLSTDPSLQIPENFFREMKELKVLDLTGVNL--- 554

Query: 295  SVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSES 354
                         SPL   PSSL FL NL+TL L D  +  D+S++GEL  L++L L  S
Sbjct: 555  -------------SPL---PSSLQFLENLQTLCL-DFCVLEDISIVGELKKLKVLSLMGS 597

Query: 355  DVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE 414
            D+  +P   G+L+ L LLDL+ C  LE+I   VLS L +LEELYM +SF  W+ E  S E
Sbjct: 598  DIVCLPREIGKLTRLLLLDLSNCERLEVISPNVLSSLTRLEELYMGNSFLKWEAEGPSSE 657

Query: 415  DSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD--MSFQNLTSFSIAIGDLEERPLSDFI 472
             +S  A   EL  L+ L +L + I +   MP D  + FQ L  F I IGD  +       
Sbjct: 658  RNS--ACLSELKLLANLITLDMQITDADHMPKDLFLCFQKLERFRIFIGDGWD------- 708

Query: 473  GLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGF 532
                   K   SR + L  +  I  L   +  LL  +E L L E+N  ++I++DL  +GF
Sbjct: 709  ----WSVKYATSRTLKLKLNTVIQ-LEERVNTLLKITEELHLQELNGVKSILNDLDEEGF 763

Query: 533  NELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVK 592
             +L  L +  C  ++Y++NS+    R     L+ LF+    N  +ICHGQL A  L N++
Sbjct: 764  CQLKDLHVQNCPGVQYIINSMRMGPRTAFLNLDSLFLENLDNLEKICHGQLMAESLGNLR 823

Query: 593  RSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVN-IAKEETELFSSLE 651
               V  C  +  +    + +    L+ + +  C ++  V   E  N  A  E   F+ L 
Sbjct: 824  ILKVESCHRLKNLFSVSIARRVVRLEEITIIDCKIMEEVVAEESENDTADGEPIEFTQLR 883

Query: 652  KLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKK---AAAEEMVLY 708
            +LTL  LP+ T       Q +   +++   +   +EL     + F  K      E+++L 
Sbjct: 884  RLTLQCLPQFTSFHSNRRQKLLASDVRSKEIVAGNELGTSM-SLFNTKILFPKLEDLMLS 942

Query: 709  RKRRDQI--HIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRS 766
              + ++I    HA        P + NL SI +  C  L  L T+SMV+SL +L+SLE+ +
Sbjct: 943  SIKVEKIWHDQHAVQP-----PCVKNLASIVVESCSNLNYLLTSSMVESLAQLKSLEICN 997

Query: 767  CPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCST 813
            C +++EI++  EG +G +G    K+ FP L  + L  L  L  FC++
Sbjct: 998  CKSMEEIVV-PEG-IG-EGKMMSKMLFPKLHILSLIRLPKLTRFCTS 1041

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111284|ref|XP_002332949.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222834261|gb|EEE72738.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  228 bits (582), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 203/625 (32%), Positives = 304/625 (48%), Gaps = 57/625 (9%)

Query: 205  MKMFDDV---AMAVVSQTPSITKIQYEIAGW------LDLTGISLMFNDIHEVPDELECP 255
            +KM D V   A +V S+   +  +  E   W         T ISL +  I ++P  LECP
Sbjct: 458  VKMHDVVQSFAFSVASRDHHVLIVADEFKEWPTSDVLQQYTAISLPYRKIPDLPAILECP 517

Query: 256  KLQALFLQENSP-LAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP 314
             L +  L    P L IPD FF+ MK+L+VLDL  +                  SPL   P
Sbjct: 518  NLNSFILLNKDPSLQIPDNFFREMKELKVLDLTRVNL----------------SPL---P 558

Query: 315  SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDL 374
            SSL FL NL+TL L D  +  D+S++GEL  L++L L  SD+  +P   G+L+ L LLDL
Sbjct: 559  SSLQFLENLQTLCL-DGCVLEDISIVGELKKLKVLSLISSDIVCLPREIGKLTRLLLLDL 617

Query: 375  TGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL 434
            + C  LE+I   VLS L +LEELYM +SF  W+ E  S +   +NA   EL  LS L +L
Sbjct: 618  SNCERLEVISPNVLSSLTRLEELYMGNSFVKWETEGSSSQ--RNNACLSELKRLSNLITL 675

Query: 435  HIHIPEGKIMPSDMS--FQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQD 492
            H+ I +   M  D+S  FQ L  F I IGD  +              K   SR + L  +
Sbjct: 676  HMQITDADNMLKDLSFLFQKLERFRIFIGDGWD-----------WSVKYATSRTLKLKLN 724

Query: 493  MRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNS 552
              I  L  W+  LL  +E L L E+   ++I++DL  + F  L  L +  C  ++Y++NS
Sbjct: 725  TVIQ-LEEWVNTLLKSTEELHLQELKGVKSILNDLDGEDFPRLKHLHVQNCPGVQYIINS 783

Query: 553  LERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQ 612
            +    R     L+ LF+    N  +ICHGQL A  L  ++   V  C  +  +    + +
Sbjct: 784  IRMGPRTAFLNLDSLFLENLDNLEKICHGQLMAESLGKLRILKVESCHRLKNLFSVSMAR 843

Query: 613  SFQNLQRLRVYSCGLLVSVFEIERVN-IAKEETELFSSLEKLTLWDLPRMTDIWKGDTQF 671
                L+ + +  C ++  V   E  N  A  E   F+ L +LTL  LP+ T       Q 
Sbjct: 844  RLVRLEEITIIDCKIMEEVVAEESENDTADGEPIEFAQLRRLTLQCLPQFTSFHSNRRQK 903

Query: 672  VSLHNLKKVRVEECDELRQVFPANFGKK---AAAEEMVLYRKRRDQIHIHATTSTSSPTP 728
            +   +++   +   +EL       F  K      E++ L   + ++I  H   +   P  
Sbjct: 904  LLASDVRSKEIVAGNELGTSMSL-FNTKILFPNLEDLKLSSIKVEKIW-HDQPAVQPPC- 960

Query: 729  SLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGAST 788
             + NL S+ +  C  L  L T+SMV+SL +LE LE+ +C +++EI++  EG +G +G   
Sbjct: 961  -VKNLASMVVESCSNLNYLLTSSMVESLAQLERLEICNCESMEEIVV-PEG-IG-EGKMM 1016

Query: 789  KKITFPSLFGIKLCDLDSLACFCST 813
             K+ FP L  ++L  L  L  FC++
Sbjct: 1017 SKMLFPKLHLLELSGLPKLTRFCTS 1041

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255542484|ref|XP_002512305.1| phosphoprotein phosphatase, putative [Ricinus communis] gi|223548266|gb|EEF49757.1| phosphoprotein phosphatase, putative [Ricinus communis]

 Score =  225 bits (573), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 186/581 (32%), Positives = 289/581 (49%), Gaps = 49/581 (8%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFL-QENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
            T ISL    I ++P+  ECP LQ+  L  ++S L IPD FF  MK L+++DL  +    
Sbjct: 454 FTAISLPDCKIPKLPEVFECPDLQSFLLYNKDSSLKIPDNFFSRMKKLKLMDLSNVHL-- 511

Query: 294 FSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSE 353
                         SP+   P SL  L NL+TL L DR    D++ IGEL  L++L    
Sbjct: 512 --------------SPM---PLSLQCLENLQTLCL-DRCTLEDIAAIGELKKLQVLSFIG 553

Query: 354 SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE 413
           S + ++P   G+L+ L+LLDL+ C  LE+IP+GVLS L KLEELYM +SF  W  ESE  
Sbjct: 554 STMVQLPREVGKLTRLQLLDLSRCQKLEVIPKGVLSCLTKLEELYMGNSFVQW--ESEEH 611

Query: 414 EDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIG 473
           +   +NA   EL  L  L +L +HI   +I+P D+  + L  + + IG  EE        
Sbjct: 612 DGDRNNASLDELKLLPNLVTLELHIINAEILPRDVFSEKLDLYKVFIG--EEWS------ 663

Query: 474 LFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFN 533
            +  K++   +  + L+  + I      +K LL+ +E L L E+    N++ +L   GF 
Sbjct: 664 -WFGKYEASRTLKLKLNSSIEIEK----VKVLLMTTEDLYLDELEGVRNVLYELDGQGFP 718

Query: 534 ELMFLVIFRCNEMKYLLNSLER-TLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVK 592
           +L  L I   +E++Y+++ L      +   +LE L +    N  +IC+GQL +G  S ++
Sbjct: 719 QLKHLHIQNSSEIQYIVDCLSMGNHYIAFPRLESLLVDNLNNLGQICYGQLMSGSFSKLR 778

Query: 593 RSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIA-KEETELFSSLE 651
           +  V  C ++  +    + +    L+ + V SC ++  +   E  + + ++E      L 
Sbjct: 779 KLKVEHCNALKNLFYFSMFRGLVQLEEIDVSSCNIMEEIVVEEIEDDSGRDEIIKPIRLR 838

Query: 652 KLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMV-LYRK 710
            LTL  LPR T       Q   L  L     +   E   V    FG+K     ++ L   
Sbjct: 839 TLTLEYLPRFTSFCSQRMQ--KLAGLDAGCAQIISETPSVL---FGQKIEFSNLLNLKLS 893

Query: 711 RRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTL 770
             + +          P  S+ NL S+ + GCGKL  LFT+SMV++L +LE LE+  C  +
Sbjct: 894 SINNMEKIWRNQVKEPPSSVQNLTSLIVEGCGKLSYLFTSSMVENLSQLEYLEISDCSFM 953

Query: 771 QEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFC 811
           +EII+ +    GL   ++ K+ FP L  +KL  L +L  FC
Sbjct: 954 EEIIVAE----GLTKHNS-KLHFPILHTLKLKSLPNLIRFC 989

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488095|ref|XP_002270726.2| PREDICTED: probable disease resistance protein At4g27220-like [Vitis vinifera]

 Score =  224 bits (572), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 192/631 (30%), Positives = 290/631 (45%), Gaps = 120/631 (19%)

Query: 233  LDLTGISLMFNDIHEVPDELECPKLQAL--FLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
            L +T + L   DIHE+P+ L CPKL+    FL+ +S + IP+ FF+GMK L+VLD   ++
Sbjct: 501  LQVTWVKLHDCDIHELPEGLVCPKLEFFECFLKTHSAVKIPNTFFEGMKQLKVLDFSRMQ 560

Query: 291  RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILD 350
                          LPS PL     S+  L NLRTL L   ++ GD+ +I EL  LEIL 
Sbjct: 561  --------------LPSLPL-----SIQCLANLRTLCLDGCKL-GDIVIIAELKKLEILS 600

Query: 351  LSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFES 410
            L  SD+ ++P    +L+HLRLLDL+    +++IP GV+S L +LE+L M +SF  W+ E 
Sbjct: 601  LMSSDMEQLPREIAQLTHLRLLDLSDSSTIKVIPSGVISSLFRLEDLCMENSFTQWEGEG 660

Query: 411  ESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL--EERPL 468
            +      SNA   EL  LS LT L I IP+ K++P D+ F+NL  + I +GD+   E   
Sbjct: 661  K------SNACLAELKHLSHLTFLDIQIPDAKLLPKDIVFENLVRYRILVGDVWSWEEIF 714

Query: 469  SDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLA 528
                 L L KF        G+S+             LL R+E L L E+    N++S L 
Sbjct: 715  EANSTLKLNKFDTSLHLVDGISK-------------LLKRTEDLHLRELCGGTNVLSKLN 761

Query: 529  NDGFNELMFLVIFRCNEMKYLLNSLERT-LRVTLHKLEWLFIRENQNFVEICHGQLPAGC 587
             +GF +L  L +    E++Y++NS++ T        +E L + +  N  E+CHGQ PAG 
Sbjct: 762  REGFLKLKHLNVESSPEIQYIVNSMDLTSSHGAFPVMETLSLNQLINLQEVCHGQFPAGS 821

Query: 588  LSNVKRSDVVDCGSILKILLS-HLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETE- 645
            L  +++ +V DC   LK L S  + +    L+  +V  C  +V +    R  I ++    
Sbjct: 822  LGCLRKVEVEDCDG-LKFLFSLSVARGLSRLEETKVTRCKSMVEMVSQGRKEIKEDAVNV 880

Query: 646  -LFSSLEKLTLWDLPRMTD----------------------------IWKGDTQFVSLHN 676
             LF  L  LTL DLP++++                            I  G        N
Sbjct: 881  PLFPELRYLTLEDLPKLSNFCFEENPVLSKPASTIVGPSTPPLNQPEIRDGQLLLSLGGN 940

Query: 677  LKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSI 736
            L+ ++++ C  L ++FP +                                  L NL  +
Sbjct: 941  LRSLKLKNCMSLLKLFPPSL---------------------------------LQNLEEL 967

Query: 737  TIRGCGKLRNLF-------TTSMVKSLVRLESLEVRSCPTLQEII----MDDEGEVGLQG 785
             +  CG+L ++F           V+ L +L+ L +   P L+ I       +     +  
Sbjct: 968  IVENCGQLEHVFDLEELNVDDGHVELLPKLKELRLSGLPKLRHICNCGSSRNHFPSSMAS 1027

Query: 786  ASTKKITFPSLFGIKLCDLDSLACFCSTAHH 816
            A    I FP L  IKL  L +L  F S  +H
Sbjct: 1028 APVGNIIFPKLSDIKLESLPNLTSFVSPGYH 1058

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865073|emb|CAN83232.1| hypothetical protein VITISV_021876 [Vitis vinifera]

 Score =  221 bits (562), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 192/628 (30%), Positives = 287/628 (45%), Gaps = 131/628 (20%)

Query: 244  DIHEVPDELECPKLQALF--LQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFL 301
            DIHE+P+ L CPKL+     L+ NS + IP+ FF+GMK LQVLD   +            
Sbjct: 513  DIHELPEGLVCPKLKLFICCLKTNSAVKIPNTFFEGMKQLQVLDFTQMH----------- 561

Query: 302  FPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV 361
               LPS     LPSSL  L NL+TL L+  ++ GD+ +I EL  LEIL L +SD+ ++P 
Sbjct: 562  ---LPS-----LPSSLQCLANLQTLLLYGCKL-GDIGIITELKKLEILSLIDSDIEQLPR 612

Query: 362  SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAK 421
               +L+HLRLLDL+    +++IP GV+S L +LE+L M +SF  W+ E +      SNA 
Sbjct: 613  EIAQLTHLRLLDLSDSSTIKVIPSGVISSLSQLEDLCMENSFTQWEGEGK------SNAC 666

Query: 422  FIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGD--LEERPLSDFIGLFLQKF 479
              EL  LS LTSL I IP+ K++P D+ F+NL  + I +GD  + E        L L+KF
Sbjct: 667  LAELKHLSHLTSLDIQIPDAKLLPKDVVFENLVRYRIFVGDVWIWEENYKTNRTLKLKKF 726

Query: 480  KKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLV 539
                    G+S+ ++I             +E L L E+    N++S L  +GF +L  L 
Sbjct: 727  DTSLHLVDGISKLLKI-------------TEDLHLRELCGGTNVLSKLDGEGFFKLKHLN 773

Query: 540  IFRCNEMKYLLNSLERT-LRVTLHKLEWLFIRENQNFVEICHGQLPA--------GCLSN 590
            +    E++Y++NSL+ T        +E L + +  N  E+CHGQ P         GCL  
Sbjct: 774  VESSPEIQYIVNSLDLTSPHGAFPVMETLSLNQLINLQEVCHGQFPVESSRKQSFGCLRK 833

Query: 591  VKRSDVVDCGSILKILLS-HLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAK--EETELF 647
            V   +V DC   LK L S  + +    L+ ++V  C  +V +   ER  I +  +   LF
Sbjct: 834  V---EVEDCDG-LKFLFSLSVARGLSQLEEIKVTRCKSMVEMVSQERKEIREDADNVPLF 889

Query: 648  SSLEKLTLWDLPRMTD----------------------------IWKGDTQFVSLHNLKK 679
              L  LTL DLP++++                            I  G        NL+ 
Sbjct: 890  PELRHLTLEDLPKLSNFCFEENPVLPKPASTIVGPSTPPLNQPEIRDGQLLLSFGGNLRS 949

Query: 680  VRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIR 739
            ++++ C  L ++FP +                                  L NL  + + 
Sbjct: 950  LKLKNCMSLLKLFPPSL---------------------------------LQNLEELIVE 976

Query: 740  GCGKLRNLF-------TTSMVKSLVRLESLEVRSCPTLQEII----MDDEGEVGLQGAST 788
             CG+L ++F           V+ L +L+ L +   P L+ I       +     +  A  
Sbjct: 977  NCGQLEHVFDLEELNVDDGHVELLPKLKELRLIGLPKLRHICNCGSSRNHFPSSMASAPV 1036

Query: 789  KKITFPSLFGIKLCDLDSLACFCSTAHH 816
              I FP L  I L  L +L  F S  +H
Sbjct: 1037 GNIIFPKLSDITLESLPNLTSFVSPGYH 1064

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488025|ref|XP_003633688.1| PREDICTED: uncharacterized protein LOC100852821 [Vitis vinifera]

 Score =  218 bits (556), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 191/641 (29%), Positives = 298/641 (46%), Gaps = 125/641 (19%)

Query: 229  IAGW--LD----LTGISLMFNDIHEVPDELECPKLQALF----LQENSPLAIPDRFFQGM 278
            + GW  +D    +T +SL   DIHE+P+ L CPKL+ LF    +  NS + IP++FF+ M
Sbjct: 492  VEGWPRIDELQKVTWVSLHDCDIHELPEGLVCPKLE-LFGCYDVNTNSAVQIPNKFFEEM 550

Query: 279  KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
            K L+VLDL  ++              LPS PL     SL  L NLRTL L   ++ GD+ 
Sbjct: 551  KQLKVLDLSRMQ--------------LPSLPL-----SLHCLTNLRTLCLDGCKV-GDIV 590

Query: 339  LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
            +I +L  LEIL L +SD+ ++P    +L+HLRLLDL+G   L++IP  V+S L +LE L 
Sbjct: 591  IIAKLKKLEILSLKDSDMEQLPREIAQLTHLRLLDLSGSSKLKVIPSDVISSLSQLENLC 650

Query: 399  MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSI 458
            M++SF  W+ E++      SNA   EL  LS LTSL I I + K++P D+ F NL  + I
Sbjct: 651  MANSFTQWEGEAK------SNACLAELKHLSHLTSLDIQIRDAKLLPKDIVFDNLVRYRI 704

Query: 459  AIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQ-DMRISALHSWIKNLLLRSEILALAEV 517
             +GD         +  + + F+   ++ + L++ D  +  +H  IK LL R+E L L E+
Sbjct: 705  FVGD---------VWRWRENFET--NKTLKLNKFDTSLHLVHGIIK-LLKRTEDLHLREL 752

Query: 518  NYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTL-RVTLHKLEWLFIRENQNFV 576
                N++S L  +GF +L  L +    E++Y++NS++ T        +E L + +  N  
Sbjct: 753  CGGTNVLSKLDGEGFLKLKHLNVESSPEIQYIVNSMDLTPSHGAFPVMETLSLNQLINLQ 812

Query: 577  EICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIER 636
            E+C GQ PAG    +++ +V DC  +  +    + +    L+ ++V  C  +V +    R
Sbjct: 813  EVCRGQFPAGSFGYLRKVEVKDCNGLKCLFSLSVARGLSRLEEIKVTRCESMVEMVSQGR 872

Query: 637  VNI--AKEETELFSSLEKLTLWDLPRMTD----------------------------IWK 666
              I  A     LF  L  LTL DLP++++                            I  
Sbjct: 873  KEIKEAAVNVPLFPELRSLTLEDLPKLSNFCFEENPVLSKPPSTIVGPSTPPLNQPEIRD 932

Query: 667  GDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSP 726
            G        NL+ + ++ C  L ++FP +                               
Sbjct: 933  GQLLLSLGGNLRSLELKNCMSLLKLFPPSL------------------------------ 962

Query: 727  TPSLGNLVSITIRGCGKLRNLF-------TTSMVKSLVRLESLEVRSCPTLQEIIMDDEG 779
               L NL  + +  CG+L ++F           V+ L +L+ L +   P L+ I   D  
Sbjct: 963  ---LQNLEELRVENCGQLEHVFDLEELNVDDGHVELLPKLKELMLSGLPKLRHICNCDSS 1019

Query: 780  E----VGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHH 816
                   +  A    I FP L  I L  L +L  F S  +H
Sbjct: 1020 RNHFPSSMASAPVGNIIFPKLSDITLESLPNLTSFVSPGYH 1060

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735461|emb|CBI17901.3| unnamed protein product [Vitis vinifera]

 Score =  218 bits (555), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 178/565 (31%), Positives = 273/565 (48%), Gaps = 36/565 (6%)

Query: 214  AVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLA-IPD 272
            A + Q+ S  K+      +   T ISLM N+I E+PD L CPKLQ L LQ N+ +  IPD
Sbjct: 490  AFMVQSGSALKVWPTKDSYEAYTAISLMSNEIEELPDGLVCPKLQTLLLQNNNDIQEIPD 549

Query: 273  RFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR 332
             FF     L+VLDL G                +PS     LP SL  L +LRTL L   +
Sbjct: 550  DFFGSFHSLRVLDLNG--------------ADIPS-----LPPSLGLLRSLRTLCLDCCQ 590

Query: 333  IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR 392
               D+S++G+L  LEIL L ES + ++P    +L++LR+LD T    ++ IP  V+S L 
Sbjct: 591  SITDISILGKLEKLEILSLRESYIEDLPEELAQLANLRMLDFTMSNNIKSIPPKVISSLS 650

Query: 393  KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQ- 451
            +LEE+YM  SF  W    E    S +NA F EL  L RL  L + I + + MP  + F  
Sbjct: 651  RLEEMYMQGSFADWGLLLEGTS-SGANAGFDELTCLHRLNILKVDISDAECMPKTVRFDP 709

Query: 452  NLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLL-RSE 510
            N  +F I I     +  + F+ + L +     SRA+ L  D+ I+ L  W   +   R+E
Sbjct: 710  NWVNFDICIS---RKLFTRFMNVHLSRVTAARSRALIL--DVTINTLPDWFNKVATERTE 764

Query: 511  ILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTL-RVTLHKLEWLFI 569
             L   E    +NI+ +      N L  L++  C+++ +L++++     R     LE L +
Sbjct: 765  KLYYIECRGLDNILMEYDQGSLNGLKILLVQSCHQIVHLMDAVTYVPNRPLFPSLEELRV 824

Query: 570  RENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILL-SHLVQSFQNLQRLRVYSCGLL 628
                   EIC GQLP G L N+K   V  C  ++  LL ++L++  ++L+ L V S   L
Sbjct: 825  HNLDYLKEICIGQLPPGSLGNMKFLQVEQCNELVNGLLPANLLRRLESLEVLDV-SGSYL 883

Query: 629  VSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDEL 688
              +F  E +   +E   +   L +L L +LP + +IW G TQ    HNLK + V +C +L
Sbjct: 884  EDIFRTEGL---REGEVVVGKLRELKLDNLPELKNIWNGPTQLAIFHNLKILTVIKCKKL 940

Query: 689  RQVFPANFGK--KAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRN 746
            R +F  +  +  +   E  + Y    + +                NL +++++    LR+
Sbjct: 941  RNLFTYSVAQSLRYLEELWIEYCNGLEGVIGMHEGGDVVERIIFQNLKNLSLQNLPVLRS 1000

Query: 747  LFTTSMVKSLVRLESLEVRSCPTLQ 771
             +          LE L V+ CPT +
Sbjct: 1001 FYEGDARIECPSLEQLHVQGCPTFR 1025

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	848
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.259	0.246	0.245	7.4e-25
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.268	0.256	0.246	7.6e-22
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.239	0.209	0.282	1.5e-20
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.255	0.241	0.263	9.3e-20
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.253	0.218	0.228	1.3e-19
TAIR|locus:2153474	874	AT5G05400 [Arabidopsis thalian	0.226	0.219	0.297	2e-19
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.234	0.224	0.280	4.1e-17
TAIR|locus:2034765	884	AT1G12290 [Arabidopsis thalian	0.253	0.243	0.226	1.2e-16
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.246	0.236	0.253	1.2e-15
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.412	0.380	0.262	1.5e-13

TAIR|locus:2034770 SUMM2 "AT1G12280" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 7.4e-25, Sum P(4) = 7.4e-25
 Identities = 56/228 (24%), Positives = 109/228 (47%)

Query:    15 ERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAA--TRNREVIKD 72
             + +V+ +        GY+C+    + A++ + + L  +R+D++  +D    TR RE +  
Sbjct:    12 DEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLS- 70

Query:    73 EVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSAL 130
             +V+ W+  V+ +  K  + L  ++ ++ + CL G C  ++K  Y   +        + +L
Sbjct:    71 QVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESL 130

Query:   131 MAVGNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVG 190
              + G+F                 +       +E+ ++ +   + ++   I G+ GMGGVG
Sbjct:   131 SSQGDFDTVTLATPIARIEEMPIQPTIV--GQETMLERVWTRLTEDGDEIVGLYGMGGVG 188

Query:   191 KTTLVKEIQ-KQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTG 237
             KTTL+  I  K +++   F  V   VVS++P I +IQ +I   LDL G
Sbjct:   189 KTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGG 236

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 154 (59.3 bits), Expect = 7.6e-22, Sum P(4) = 7.6e-22
 Identities = 58/235 (24%), Positives = 103/235 (43%)

Query:     8 SVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAAT-RN 66
             SV+ P  +++V         +  Y+      + +L+   + L  R+ D+   ++      
Sbjct:     6 SVSLPC-DQVVSQFSQLLCVRGSYIHNLSKNLASLQKAMRMLKARQYDVIRRLETEEFTG 64

Query:    67 REVIKDEVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCV-DLKSRYKLSREAEEKT 124
             R+    +V+ W+  V  I  +    L  +EV++ + CL G C  DLK  Y+  +      
Sbjct:    65 RQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRVIMML 124

Query:   125 LAMSALMAVGNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGIC 184
               + +L + G F   V                     +E  ++     + ++   I G+ 
Sbjct:   125 KEVESLSSQGFFD--VVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMEDGSGILGLY 182

Query:   185 GMGGVGKTTLVKEIQ-KQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGI 238
             GMGGVGKTTL+ +I  K +K    FD V   VVS++ ++ KIQ +IA  + L G+
Sbjct:   183 GMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGM 237

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

TAIR|locus:2008510 AT1G61190 "AT1G61190" [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 1.5e-20, Sum P(4) = 1.5e-20
 Identities = 59/209 (28%), Positives = 97/209 (46%)

Query:    30 GYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAE 89
             GY+   +  + AL+ E + L   ++++Q ++       +   + V+ W+  VN I  + +
Sbjct:    26 GYIRNLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIECK 85

Query:    90 KFLE-DEVKVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMSALMAVGNFGKGVXXXXXXX 147
               L    V++ K CL GLC   + S YK  +        ++ L + GNF +         
Sbjct:    86 DLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNFDEVSQPPPRSE 145

Query:   148 XXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQ-KQAKEMK 206
                   +       +E  +K     + ++ V I G+ GMGGVGKTTL K+I  K A+   
Sbjct:   146 VEERPTQPTIG---QEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAETGG 202

Query:   207 MFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
              FD V   VVSQ   ++K+Q +IA  L L
Sbjct:   203 TFDIVIWIVVSQGAKLSKLQEDIAEKLHL 231

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2008440 AT1G61180 [Arabidopsis thaliana (taxid:3702)]

 Score = 177 (67.4 bits), Expect = 9.3e-20, Sum P(4) = 9.3e-20
 Identities = 60/228 (26%), Positives = 110/228 (48%)

Query:    13 ITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEI--DAATRNREVI 70
             ++++ ++ +FN  + +  Y+   +  + AL+ E + L   ++++Q ++  D A   R + 
Sbjct:     9 VSDQTLNRIFNCLIGK-SYIRTLEKNLRALQREMEDLRAIQHEVQNKVARDEARHQRRL- 66

Query:    71 KDEVKSWIAEVNDIIPKAEKFLE-DEVKVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMS 128
              + V+ W+  VN +  + +  L    V++ K CL GLC   + S YK  ++       + 
Sbjct:    67 -EAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLLLEEVK 125

Query:   129 ALMAVGNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGG 188
              L + GNF +               +       +E  ++     + ++ V I G+ GMGG
Sbjct:   126 KLNSEGNFDEVSQPPPRSEVEERPTQPTIG---QEDMLEKAWNRLMEDGVGIMGLHGMGG 182

Query:   189 VGKTTLVKEIQKQAKEMK-MFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
             VGKTTL K+I  +  E+   FD V   VVS+   I+K+Q +IA  L L
Sbjct:   183 VGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHL 230

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2136447 AT4G27190 [Arabidopsis thaliana (taxid:3702)]

 Score = 146 (56.5 bits), Expect = 1.3e-19, Sum P(3) = 1.3e-19
 Identities = 52/228 (22%), Positives = 100/228 (43%)

Query:    12 PITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIK 71
             P+   I+ +++ +T  +     K+K  ++AL    ++LT+ + ++  + +      + ++
Sbjct:     6 PVIGEILRLMYESTFSRVANAIKFKSNVKALNESLERLTELKGNMSEDHETLLTKDKPLR 65

Query:    72 DEVKSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEE-KTLAMSAL 130
              ++  W  E  ++I KA   LE+ V     C  G+ +  +   KL +  +E K L    +
Sbjct:    66 LKLMRWQREAEEVISKARLKLEERVS----C--GMSLRPRMSRKLVKILDEVKMLEKDGI 119

Query:   131 MAVGNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVG 190
               V      V               V+   +     K I + +  E     G+ GMGGVG
Sbjct:   120 EFVDMLS--VESTPERVEHVPGVSVVHQTMASNMLAK-IRDGLTSEKAQKIGVWGMGGVG 176

Query:   191 KTTLVKEIQKQAKE---MKMFDDVAMAVVSQTPSITKIQYEIAGWLDL 235
             KTTLV+ +  + +E    + F  V   +VS+     ++Q +IA  LD+
Sbjct:   177 KTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQKQIAERLDI 224

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2153474 AT5G05400 [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 2.0e-19, Sum P(4) = 2.0e-19
 Identities = 61/205 (29%), Positives = 96/205 (46%)

Query:    38 YIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFL-EDEV 96
             ++ AL+   ++L  RR+DL   I         + DEV+ W++EV   + +A   L + + 
Sbjct:    35 HVAALKKTVRQLEARRDDLLKRIKVQEDRGLNLLDEVQQWLSEVESRVCEAHDILSQSDE 94

Query:    97 KVNKKCLGGLCVD-LKSRYKLSREAEEKTLAMSALMAVGNFG----KGVXXXXXXXXXXX 151
             +++  C G  C    K  Y  S+    K   +  L++ G F     KG            
Sbjct:    95 EIDNLCCGQYCSKRCKYSYDYSKSVINKLQDVENLLSKGVFDEVAQKGPIPKVEERLFHQ 154

Query:   152 XXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDV 211
                G  A    EST   +ME      V + GI GMGGVGKTTL+ +I  + + +    D+
Sbjct:   155 EIVGQEAIV--ESTWNSMMEV----GVGLLGIYGMGGVGKTTLLSQINNKFRTVSNDFDI 208

Query:   212 AM-AVVSQTPSITKIQYEIAGWLDL 235
             A+  VVS+ P++ +IQ +I   LDL
Sbjct:   209 AIWVVVSKNPTVKRIQEDIGKRLDL 233

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0006826 "iron ion transport" evidence=RCA

GO:0010106 "cellular response to iron ion starvation" evidence=RCA

GO:0010167 "response to nitrate" evidence=RCA

GO:0015706 "nitrate transport" evidence=RCA

TAIR|locus:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 4.1e-17, Sum P(4) = 4.1e-17
 Identities = 58/207 (28%), Positives = 92/207 (44%)

Query:    27 RQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIP 86
             R   Y+   +  + AL+   +++  RR DL  +I +  R        V+ W+++V  I+P
Sbjct:    24 RNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSEERRGLQRLSVVQGWVSKVEAIVP 83

Query:    87 KAEKFLE-DEVKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSALMAVGNFGKGVXXXX 144
             +  + +    V+V + CL G C  +L S Y+  +   +    +  L   G+F        
Sbjct:    84 RVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVMKMIEEVEVLRYQGDFAVVAERVD 143

Query:   145 XXXXXXXXXEGVYAFKSR-ESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK 203
                        + A     ES    +ME   DE + I G+ GMGGVGKTTL+  I  +  
Sbjct:   144 AARVEERPTRPMVAMDPMLESAWNRLME---DE-IGILGLHGMGGVGKTTLLSHINNRFS 199

Query:   204 EMK-MFDDVAMAVVSQTPSITKIQYEI 229
              +   FD V   VVS+   I +IQ EI
Sbjct:   200 RVGGEFDIVIWIVVSKELQIQRIQDEI 226

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2034765 AT1G12290 [Arabidopsis thaliana (taxid:3702)]

 Score = 119 (46.9 bits), Expect = 1.2e-16, Sum P(4) = 1.2e-16
 Identities = 52/230 (22%), Positives = 93/230 (40%)

Query:    19 DVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKD------ 72
             D L N   R F   C+  +YI+ ++     L +   DL+A  D   R  +  ++      
Sbjct:    12 DQLLNHLGRCF---CRKLYYIQNIKENLTSLEEAMEDLKALRDDLLRKVQTAEEGGLQRL 68

Query:    73 -EVKSWIAEVNDIIPKAEKFLEDE-VKVNKKCLGGL-CVDLKSRYKLSREAEEKTLAMSA 129
              ++K W+  V  I  +         V++ + C  G+   +L+  Y   R        +  
Sbjct:    69 HQIKVWLKRVKTIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRVFLMLNIVED 128

Query:   130 LMAVGNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGV 189
             L + G F +               +       +E+ ++   + + D+   I G+ GMGGV
Sbjct:   129 LKSKGIFEEVAHPATRAVGEERPLQPTIV--GQETILEKAWDHLMDDGTKIMGLYGMGGV 186

Query:   190 GKTTLVKEIQKQAKEMKMFDDVAM-AVVSQTPSITKIQYEIAGWLDLTGI 238
             GKTTL+ +I  +  +     ++ +  VVS    I KIQ EI   +   G+
Sbjct:   187 GKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFIGV 236

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2201986 RFL1 "AT1G12210" [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 1.2e-15, Sum P(4) = 1.2e-15
 Identities = 57/225 (25%), Positives = 96/225 (42%)

Query:    26 VRQFG-YLCKYKHYIEALR---TEAKK----LTDRRNDLQAEIDAA--TRNREVIKDEVK 75
             V QF  +LC    YI+ L       +K    L  +R+D+Q  I+    T +R  +  +V+
Sbjct:    15 VNQFSQWLCVSGSYIQNLSENLASLQKAMGVLNAKRDDVQGRINREEFTGHRRRLA-QVQ 73

Query:    76 SWIAEVNDIIPKAEKFLED-EVKVNKKCLGGLCV-DLKSRYKLSREAEEKTLAMSALMAV 133
              W+  +  I  +    L     ++ + CL G C  ++K  Y   +        +  L + 
Sbjct:    74 VWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRVIVLLREVEGLSSQ 133

Query:   134 GNFGKGVXXXXXXXXXXXXXEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTT 193
             G F                 +       ++S +  +   + ++ V I G+ GMGGVGKTT
Sbjct:   134 GVFDIVTEAAPIAEVEELPIQSTIV--GQDSMLDKVWNCLMEDKVWIVGLYGMGGVGKTT 191

Query:   194 LVKEIQKQAKEMKM-FDDVAMAVVSQTPSITKIQYEIAGWLDLTG 237
             L+ +I  +  ++   FD V   VVS+  ++ KIQ  I   L L G
Sbjct:   192 LLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVG 236

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009617 "response to bacterium" evidence=ISS

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

TAIR|locus:2131689 AT4G27220 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 1.5e-13, Sum P(2) = 1.5e-13
 Identities = 102/388 (26%), Positives = 165/388 (42%)

Query:   322 NLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE 381
             +LR+L L + +   +L  +  L  L+ LDL ES + E+P     LS LR + ++  Y L+
Sbjct:   542 SLRSLVLRNCKKLRNLPSLESLVKLQFLDLHESAIRELPRGLEALSSLRYICVSNTYQLQ 601

Query:   382 LIPRGVLSRLRKLEELYMSHSFRHWQFXXXXXXXXXXNAKFIELGALSRLTSLHIHIPEG 441
              IP G + +L  LE L M+ S   W             A   E+  L  L  L I     
Sbjct:   602 SIPAGTILQLSSLEVLDMAGSAYSWGIKGEEREG---QATLDEVTCLPHLQFLAI----- 653

Query:   442 KIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMG---LS-QDMRIS- 496
             K++       ++ SFS     L +R L+ F  LF    +       G   L+  D+ +S 
Sbjct:   654 KLL-------DVLSFSYEFDSLTKR-LTKFQFLF-SPIRSVSPPGTGEGCLAISDVNVSN 704

Query:   497 ALHSWIKNLLLRSEILALAEVN-YFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLER 555
             A   W+   +   ++     +N  FEN+V+  +   F  +  L I     +  L +  E 
Sbjct:   705 ASIGWLLQHVTSLDLNYCEGLNGMFENLVTK-SKSSFVAMKALSIHYFPSLS-LASGCES 762

Query:   556 TLRVTLHKLEWLFIRENQNFVEICHGQLPA--GC-LSNVKRSDVVDCGSILKILLSHLVQ 612
              L +    LE L + +N N   I  G+L    G  L  +K   V  C  + ++    ++ 
Sbjct:   763 QLDL-FPNLEELSL-DNVNLESI--GELNGFLGMRLQKLKLLQVSGCRQLKRLFSDQILA 818

Query:   613 -SFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQF 671
              +  NLQ ++V SC  L  +F    V +      L   L  + L  LP++  +   D   
Sbjct:   819 GTLPNLQEIKVVSCLRLEELFNFSSVPVDFCAESLLPKLTVIKLKYLPQLRSLCN-DR-- 875

Query:   672 VSLHNLKKVRVEECDELRQV-F-PANFG 697
             V L +L+ + VE C+ L+ + F P N G
Sbjct:   876 VVLESLEHLEVESCESLKNLPFVPGNTG 903

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00027341001 SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (963 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	848
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	3e-08
PLN03150	623	PLN03150, PLN03150, hypothetical protein; Provisio	5e-07
pfam13855	60	pfam13855, LRR_8, Leucine rich repeat	9e-07
COG4886	394	COG4886, COG4886, Leucine-rich repeat (LRR) protei	4e-06
PLN00113	968	PLN00113, PLN00113, leucine-rich repeat receptor-l	4e-04
PLN00113	968	PLN00113, PLN00113, leucine-rich repeat receptor-l	9e-04
pfam13855	60	pfam13855, LRR_8, Leucine rich repeat	0.003

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

 Score = 55.8 bits (135), Expect = 3e-08
 Identities = 31/92 (33%), Positives = 50/92 (54%), Gaps = 6/92 (6%)

Query: 167 KDIMEAMKD------ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTP 220
           +D++EA+ +      +N+ + GI GMGGVGKTTL K+I         FD VA  VVS+T 
Sbjct: 2   EDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTY 61

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL 252
           +  ++Q +I   L L     +  +  E+  ++
Sbjct: 62  TEFRLQKDILQELGLDDSDWVEKNESELAVKI 93

Length = 285

>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional

 Score = 53.3 bits (128), Expect = 5e-07
 Identities = 27/81 (33%), Positives = 50/81 (61%), Gaps = 2/81 (2%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSL-IGELSGLEILDLSESDVS-EIPVSFGRLSHLR 370
           +P+ +S L +L+++ L    I+G++   +G ++ LE+LDLS +  +  IP S G+L+ LR
Sbjct: 434 IPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLR 493

Query: 371 LLDLTGCYILELIPRGVLSRL 391
           +L+L G  +   +P  +  RL
Sbjct: 494 ILNLNGNSLSGRVPAALGGRL 514

Length = 623

>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat

 Score = 46.4 bits (111), Expect = 9e-07
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 345 GLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            L+ LDLS + ++ IP  +F  L +L++LDL+G  +   I     S L  L  L +S 
Sbjct: 1   NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNL-TSISPEAFSGLPSLRSLDLSG 57

Length = 60

>gnl|CDD|227223 COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function unknown]

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 57/230 (24%), Positives = 92/230 (40%), Gaps = 20/230 (8%)

Query: 235 LTGISLMFNDIHEVPDELE--CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           LT + L  N+I ++P  +      L+ L L +N   ++P    + + +L+ LDL     F
Sbjct: 118 LTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPL-RNLPNLKNLDLS----F 172

Query: 293 SFSVRFPFLFPPLPS--------SPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELS 344
           +     P L   L +        + +  LP  +  L  L  L L +  I   LS +  L 
Sbjct: 173 NDLSDLPKLLSNLSNLNNLDLSGNKISDLPPEIELLSALEELDLSNNSIIELLSSLSNLK 232

Query: 345 GLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL-----EELYM 399
            L  L+LS + + ++P S G LS+L  LDL+   I  +   G L+ LR+L          
Sbjct: 233 NLSGLELSNNKLEDLPESIGNLSNLETLDLSNNQISSISSLGSLTNLRELDLSGNSLSNA 292

Query: 400 SHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMS 449
                      E   +     K +EL   S L + +I        P  +S
Sbjct: 293 LPLIALLLLLLELLLNLLLTLKALELKLNSILLNNNILSNGETSSPEALS 342

Length = 394

>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein kinase; Provisional

 Score = 44.1 bits (104), Expect = 4e-04
 Identities = 56/191 (29%), Positives = 84/191 (43%), Gaps = 41/191 (21%)

Query: 304 PLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS-EIPVS 362
           P+P   +F   SSL      R L L +    G +   G +  LE LDLS + +S EIP  
Sbjct: 108 PIPDD-IFTTSSSL------RYLNLSNNNFTGSIPR-GSIPNLETLDLSNNMLSGEIPND 159

Query: 363 FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESE--SEEDSSSNA 420
            G  S L++LDL G  ++  IP   L+ L  LE L ++ +    Q   +   E     + 
Sbjct: 160 IGSFSSLKVLDLGGNVLVGKIP-NSLTNLTSLEFLTLASN----QLVGQIPRELGQMKSL 214

Query: 421 KFIELG----------ALSRLTSLHIHIPEGKIMPSDMSFQNLT-SFSIAIGDLEERPLS 469
           K+I LG           +  LTSL+ H+        D+ + NLT     ++G+     L 
Sbjct: 215 KWIYLGYNNLSGEIPYEIGGLTSLN-HL--------DLVYNNLTGPIPSSLGN-----LK 260

Query: 470 DFIGLFLQKFK 480
           +   LFL + K
Sbjct: 261 NLQYLFLYQNK 271

Length = 968

>gnl|CDD|215061 PLN00113, PLN00113, leucine-rich repeat receptor-like protein kinase; Provisional

 Score = 42.5 bits (100), Expect = 9e-04
 Identities = 49/158 (31%), Positives = 72/158 (45%), Gaps = 28/158 (17%)

Query: 253 ECPKLQALFLQENSPLA-IPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF 311
           + P LQ L L  N     +PD F  G K L+ LDL    +FS +V               
Sbjct: 450 DMPSLQMLSLARNKFFGGLPDSF--GSKRLENLDLSR-NQFSGAV--------------- 491

Query: 312 LLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSG---LEILDLSESDVS-EIPVSFGRLS 367
             P  L  L  L  L+L + ++ G++    ELS    L  LDLS + +S +IP SF  + 
Sbjct: 492 --PRKLGSLSELMQLKLSENKLSGEIP--DELSSCKKLVSLDLSHNQLSGQIPASFSEMP 547

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRH 405
            L  LDL+   +   IP+  L  +  L ++ +SH+  H
Sbjct: 548 VLSQLDLSQNQLSGEIPKN-LGNVESLVQVNISHNHLH 584

Length = 968

>gnl|CDD|206026 pfam13855, LRR_8, Leucine rich repeat

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 322 NLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYI 379
           NL++L L + R+          L  L++LDLS ++++ I P +F  L  LR LDL+G  +
Sbjct: 1   NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNNL 60

Length = 60

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	848
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	100.0
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.97
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.9
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.87
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.86
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.86
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.86
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.86
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.83
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.82
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.74
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.61
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.57
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.44
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.43
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.4
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.37
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.29
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.22
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.18
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	99.16
KOG4341	483	consensus F-box protein containing LRR [General fu	99.14
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	99.07
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	99.05
KOG4341	483	consensus F-box protein containing LRR [General fu	99.02
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.96
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.9
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.86
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.81
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	98.74
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.7
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.7
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.66
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.65
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.64
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.47
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.45
PLN03150	623	hypothetical protein; Provisional	98.36
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	98.32
PRK15386	426	type III secretion protein GogB; Provisional	98.27
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.23
PLN03150	623	hypothetical protein; Provisional	98.23
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.13
PRK15386	426	type III secretion protein GogB; Provisional	98.11
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.02
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.95
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.88
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.87
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.8
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.76
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.74
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.72
KOG1947	482	consensus Leucine rich repeat proteins, some prote	97.68
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.67
PRK09376	416	rho transcription termination factor Rho; Provisio	97.52
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.52
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.52
KOG1947	482	consensus Leucine rich repeat proteins, some prote	97.47
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	97.46
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	97.4
cd01128	249	rho_factor Transcription termination factor rho is	97.39
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	97.32
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.22
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	97.16
PTZ00202	550	tuzin; Provisional	97.0
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.98
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.93
KOG2982	418	consensus Uncharacterized conserved protein [Funct	96.91
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	96.85
PRK08118	167	topology modulation protein; Reviewed	96.67
TIGR00767	415	rho transcription termination factor Rho. Members	96.52
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	96.52
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.4
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	96.2
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.1
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	95.9
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	95.87
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	95.31
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.29
KOG3864	221	consensus Uncharacterized conserved protein [Funct	95.24
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	95.14
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	95.09
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	95.07
KOG2123	388	consensus Uncharacterized conserved protein [Funct	94.98
PRK07261	171	topology modulation protein; Provisional	94.65
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.64
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	94.6
KOG3864	221	consensus Uncharacterized conserved protein [Funct	94.57
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	94.51
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	94.43
PRK06696	223	uridine kinase; Validated	94.03
KOG2028	554	consensus ATPase related to the helicase subunit o	94.02
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	93.89
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	93.62
PRK04195	482	replication factor C large subunit; Provisional	93.61
PRK13342	413	recombination factor protein RarA; Reviewed	93.43
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.43
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	93.33
PRK15455	644	PrkA family serine protein kinase; Provisional	93.32
PRK07667	193	uridine kinase; Provisional	93.16
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.07
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	92.96
PLN03025	319	replication factor C subunit; Provisional	92.94
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	92.93
CHL00095	821	clpC Clp protease ATP binding subunit	92.85
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.84
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	92.8
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	92.66
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	92.55
PRK12402	337	replication factor C small subunit 2; Reviewed	92.54
PRK06547	172	hypothetical protein; Provisional	92.27
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	92.19
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	92.11
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	92.07
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	91.96
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.87
PTZ00301	210	uridine kinase; Provisional	91.85
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.75
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	91.75
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	91.71
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	91.69
PRK05480	209	uridine/cytidine kinase; Provisional	91.66
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	91.58
PHA02544	316	44 clamp loader, small subunit; Provisional	91.57
CHL00181	287	cbbX CbbX; Provisional	91.46
PF13173	128	AAA_14: AAA domain	91.45
PF05729	166	NACHT: NACHT domain	91.36
TIGR00235	207	udk uridine kinase. Model contains a number of lon	91.36
PRK10865	857	protein disaggregation chaperone; Provisional	91.31
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	91.21
PHA00729	226	NTP-binding motif containing protein	91.18
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	91.07
PTZ00112	1164	origin recognition complex 1 protein; Provisional	90.98
) 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	90.88
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	90.87
PRK13341	725	recombination factor protein RarA/unknown domain f	90.83
COG2256	436	MGS1 ATPase related to the helicase subunit of the	90.81
PRK08233	182	hypothetical protein; Provisional	90.8
KOG0473	326	consensus Leucine-rich repeat protein [Function un	90.48
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	90.38
PRK06762	166	hypothetical protein; Provisional	90.35
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	90.27
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	90.19
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	89.99
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	89.79
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	89.71
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	89.69
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	89.65
PRK10865	857	protein disaggregation chaperone; Provisional	89.63
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	89.51
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	89.31
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	89.23
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	89.22
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	89.2
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	89.14
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	88.99
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	88.95
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	88.87
PRK03992	389	proteasome-activating nucleotidase; Provisional	88.86
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	88.85
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	88.75
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	88.71
KOG0473	326	consensus Leucine-rich repeat protein [Function un	88.57
PRK03839	180	putative kinase; Provisional	88.54
COG1084	346	Predicted GTPase [General function prediction only	88.53
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	88.52
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	88.49
PRK05541	176	adenylylsulfate kinase; Provisional	88.43
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	88.4
PRK00771	437	signal recognition particle protein Srp54; Provisi	88.34
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	88.2
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	88.19
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	88.08
PRK08903	227	DnaA regulatory inactivator Hda; Validated	88.03
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	88.0
PRK05564	313	DNA polymerase III subunit delta'; Validated	87.94
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	87.89
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	87.79
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	87.75
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	87.7
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	87.66
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	87.56
PRK04040	188	adenylate kinase; Provisional	87.54
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	87.49
KOG1969	877	consensus DNA replication checkpoint protein CHL12	87.47
PRK00889	175	adenylylsulfate kinase; Provisional	87.45
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	87.44
PRK10536	262	hypothetical protein; Provisional	87.4
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	87.39
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	87.37
smart00369	26	LRR_TYP Leucine-rich repeats, typical (most popula	87.34
smart00370	26	LRR Leucine-rich repeats, outliers.	87.34
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	87.29
PRK00625	173	shikimate kinase; Provisional	87.13
PRK08084	235	DNA replication initiation factor; Provisional	87.09
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	87.02
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	86.83
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	86.37
PRK10867	433	signal recognition particle protein; Provisional	86.21
PRK03846	198	adenylylsulfate kinase; Provisional	86.18
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	86.18
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	86.17
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	86.14
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	86.04
PRK06217	183	hypothetical protein; Validated	86.0
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	85.96
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	85.85
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	85.67
PRK00131	175	aroK shikimate kinase; Reviewed	85.63
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	85.62
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.61
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	85.51
PRK13531	498	regulatory ATPase RavA; Provisional	85.47
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	85.35
PRK13949	169	shikimate kinase; Provisional	85.32
PRK08727	233	hypothetical protein; Validated	84.93
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	84.83
smart00382	148	AAA ATPases associated with a variety of cellular	84.77
PRK09087	226	hypothetical protein; Validated	84.75
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	84.71
PRK06893	229	DNA replication initiation factor; Validated	84.69
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	84.65
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	84.65
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	84.64
PRK00300	205	gmk guanylate kinase; Provisional	84.63
PRK13695	174	putative NTPase; Provisional	84.56
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	84.53
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	84.5
PF00005	137	ABC_tran: ABC transporter This structure is on hol	84.44
PRK05057	172	aroK shikimate kinase I; Reviewed	84.44
PRK13975	196	thymidylate kinase; Provisional	84.43
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	84.37
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	84.34
PRK06620	214	hypothetical protein; Validated	84.31
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	84.25
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	84.17
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	84.07
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	84.06
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	84.04
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	84.03
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	84.01
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	84.0
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	83.95
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	83.92
PF00004	132	AAA: ATPase family associated with various cellula	83.92
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	83.81
cd03116	159	MobB Molybdenum is an essential trace element in t	83.79
TIGR02237	209	recomb_radB DNA repair and recombination protein R	83.74
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	83.69
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	83.5
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	83.43
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	83.25
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	83.22
PRK13947	171	shikimate kinase; Provisional	83.15
CHL00095	821	clpC Clp protease ATP binding subunit	83.1
TIGR01287	275	nifH nitrogenase iron protein. This model describe	82.96
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	82.95
smart00367	26	LRR_CC Leucine-rich repeat - CC (cysteine-containi	82.95
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	82.94
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	82.88
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	82.85
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	82.81
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	82.8
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	82.8
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	82.77
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	82.57
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	82.54
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	82.48
PRK09825	176	idnK D-gluconate kinase; Provisional	82.38
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	82.36
PLN02796	347	D-glycerate 3-kinase	82.28
PRK09112	351	DNA polymerase III subunit delta'; Validated	82.13
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	82.12
PRK13946	184	shikimate kinase; Provisional	81.96
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	81.91
PRK14490	369	putative bifunctional molybdopterin-guanine dinucl	81.89
smart00370	26	LRR Leucine-rich repeats, outliers.	81.77
smart00369	26	LRR_TYP Leucine-rich repeats, typical (most popula	81.77
PRK13236	296	nitrogenase reductase; Reviewed	81.75
TIGR00959	428	ffh signal recognition particle protein. This mode	81.72
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	81.69
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	81.64
KOG0781	587	consensus Signal recognition particle receptor, al	81.63
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	81.59
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	81.57
PRK13232	273	nifH nitrogenase reductase; Reviewed	81.57
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	81.52
PRK12339	197	2-phosphoglycerate kinase; Provisional	81.49
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	81.48
PRK04182	180	cytidylate kinase; Provisional	81.41
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	81.39
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	81.39
PRK14530	215	adenylate kinase; Provisional	81.38
PRK13230	279	nitrogenase reductase-like protein; Reviewed	81.38
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	81.35
PLN02348	395	phosphoribulokinase	81.32
cd02117	212	NifH_like This family contains the NifH (iron prot	81.31
PLN02318	656	phosphoribulokinase/uridine kinase	81.29
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	81.26
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	81.21
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	81.21
COG1100	219	GTPase SAR1 and related small G proteins [General	81.0
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	80.91
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	80.9
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	80.89
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	80.89
PRK15453	290	phosphoribulokinase; Provisional	80.87
PRK05439	311	pantothenate kinase; Provisional	80.87
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	80.73
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	80.72
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	80.65
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	80.6
PRK13948	182	shikimate kinase; Provisional	80.56
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	80.5
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	80.46
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	80.46
PRK07471	365	DNA polymerase III subunit delta'; Validated	80.44
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	80.41
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	80.41
PRK06761	282	hypothetical protein; Provisional	80.32
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	80.26
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	80.23
PRK05642	234	DNA replication initiation factor; Validated	80.18
cd02040	270	NifH NifH gene encodes component II (iron protein)	80.09
PRK08939	306	primosomal protein DnaI; Reviewed	80.03

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=2.7e-39  Score=372.60  Aligned_cols=365  Identities=26%  Similarity=0.333  Sum_probs=271.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------hhccc
Q 003090           40 EALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKFLEDEVK-----------------VNKKC  102 (848)
Q Consensus        40 ~~~~~~l~~L~~~l~~i~~~l~~a~~~~~~~~~~v~~wl~~lk~~~~d~eD~lde~~~-----------------~~~~~  102 (848)
                      .+.++.+..|++.+..++.++++|+++ +.....+..|.+.+++++|++||+++.+..                 .+.-|
T Consensus        24 ~~~~~~i~~Lk~~L~~l~~~l~d~~a~-~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c  102 (889)
T KOG4658|consen   24 DGKDNYILELKENLKALQSALEDLDAK-RDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLC  102 (889)
T ss_pred             hchHHHHHHHHHHHHHHHHHHHHHHhh-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHh
Confidence            377889999999999999999999998 788999999999999999999999998821                 12233


Q ss_pred             cCCccc-chhhHhHHhHHHHHHHHHHHHHHHcCCCCCcccc-CCCCCCcccCCc-ccccccchhHHHHHHHHHHhcCCcc
Q 003090          103 LGGLCV-DLKSRYKLSREAEEKTLAMSALMAVGNFGKGVSR-PAPPPAIISSSE-GVYAFKSRESTMKDIMEAMKDENVS  179 (848)
Q Consensus       103 ~~~~~~-~~~~~~~~~~~i~~~~~~v~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~vG~~~~~~~i~~~L~~~~~~  179 (848)
                      +.+++. .....+.+++++.++.+.++.+..++.|+. +.. ..++......+. .+.. ||.++.++++++.|.+++..
T Consensus       103 ~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~-~~~~~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~~  180 (889)
T KOG4658|consen  103 LCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEV-VGESLDPREKVETRPIQSESD-VGLETMLEKLWNRLMEDDVG  180 (889)
T ss_pred             hhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceec-ccccccchhhcccCCCCcccc-ccHHHHHHHHHHHhccCCCC
Confidence            334442 345566778888888888888877776766 332 223333333333 2223 99999999999999988889


Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh-hccccCcEEEEEeccCCchhHHHHHHHhccCCCc---------------------
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK-EMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTG---------------------  237 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~l~~~i~~~~~l~~---------------------  237 (848)
                      +++|+||||+||||||+.|||+.. ++.+||.++||+||++|+...++++|++.+....                     
T Consensus       181 iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~  260 (889)
T KOG4658|consen  181 IVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEG  260 (889)
T ss_pred             EEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhcc
Confidence            999999999999999999999998 9999999999999999999999999999665411                     


Q ss_pred             --------------------------------------------------------------------------------
Q 003090          238 --------------------------------------------------------------------------------  237 (848)
Q Consensus       238 --------------------------------------------------------------------------------  237 (848)
                                                                                                      
T Consensus       261 krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~  340 (889)
T KOG4658|consen  261 KRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPD  340 (889)
T ss_pred             CceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhcccccccccc
Confidence                                                                                            


Q ss_pred             ------------------------------------------------------------eeeecC--------------
Q 003090          238 ------------------------------------------------------------ISLMFN--------------  243 (848)
Q Consensus       238 ------------------------------------------------------------l~l~~n--------------  243 (848)
                                                                                  +.+|+.              
T Consensus       341 i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CFLyca  420 (889)
T KOG4658|consen  341 IEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCFLYCA  420 (889)
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHHHhhc
Confidence                                                                        000000              


Q ss_pred             --------------------------------------------------------------------------------
Q 003090          244 --------------------------------------------------------------------------------  243 (848)
Q Consensus       244 --------------------------------------------------------------------------------  243 (848)
                                                                                                      
T Consensus       421 lFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~~~~~~~kmHDvvRe~al~ias~~~~  500 (889)
T KOG4658|consen  421 LFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDEGRKETVKMHDVVREMALWIASDFGK  500 (889)
T ss_pred             cCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccccceeEEEeeHHHHHHHHHHhccccc
Confidence                                                                                            


Q ss_pred             -----------CCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCC--CCCCCC
Q 003090          244 -----------DIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPP--LPSSPL  310 (848)
Q Consensus       244 -----------~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~--l~~~~~  310 (848)
                                 ...+.|+.......|...+-+|.+..++.+  ...+.|++|-+.+              +.  +...  
T Consensus       501 ~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~~~~~~~--~~~~~L~tLll~~--------------n~~~l~~i--  562 (889)
T KOG4658|consen  501 QEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKIEHIAGS--SENPKLRTLLLQR--------------NSDWLLEI--  562 (889)
T ss_pred             cccceEEECCcCccccccccchhheeEEEEeccchhhccCC--CCCCccceEEEee--------------cchhhhhc--
Confidence                       111122222334445555555555555554  3566788888888              43  4441  


Q ss_pred             CCCCchhhhcccCcEEEccCcccc-CCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhh
Q 003090          311 FLLPSSLSFLINLRTLRLHDRRIQ-GDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~~~-~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                        -+..|..+++|++|||++|.-. ..|..|++|.+||+|+++++.++.+|.++++|.+|.+|++..+.....+|.. ..
T Consensus       563 --s~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i-~~  639 (889)
T KOG4658|consen  563 --SGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGI-LL  639 (889)
T ss_pred             --CHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccch-hh
Confidence              2234778999999999987554 4568999999999999999999999999999999999999987776666553 67


Q ss_pred             ccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeecc
Q 003090          390 RLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIP  439 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~  439 (848)
                      .|.+|++|.+......           .......++.++.+|+.+.+...
T Consensus       640 ~L~~Lr~L~l~~s~~~-----------~~~~~l~el~~Le~L~~ls~~~~  678 (889)
T KOG4658|consen  640 ELQSLRVLRLPRSALS-----------NDKLLLKELENLEHLENLSITIS  678 (889)
T ss_pred             hcccccEEEeeccccc-----------cchhhHHhhhcccchhhheeecc
Confidence            7999999998766421           22335666777777777766443

>PLN03210 Resistant to P

Probab=100.00  E-value=1.1e-31  Score=327.94  Aligned_cols=390  Identities=20%  Similarity=0.238  Sum_probs=229.9

Q ss_pred             cChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcc-cCcEEEccCccccCCchhhccccCCCE
Q 003090          270 IPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLI-NLRTLRLHDRRIQGDLSLIGELSGLEI  348 (848)
Q Consensus       270 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~-~L~~L~L~~~~~~~~~~~i~~l~~L~~  348 (848)
                      +....|.+|++|+.|.+..++...        .+.+...    +|..+..++ +||+|++.++.....|..+ ...+|++
T Consensus       549 i~~~aF~~m~~L~~L~~~~~~~~~--------~~~~~~~----lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f-~~~~L~~  615 (1153)
T PLN03210        549 IHENAFKGMRNLLFLKFYTKKWDQ--------KKEVRWH----LPEGFDYLPPKLRLLRWDKYPLRCMPSNF-RPENLVK  615 (1153)
T ss_pred             ecHHHHhcCccccEEEEecccccc--------cccceee----cCcchhhcCcccEEEEecCCCCCCCCCcC-CccCCcE
Confidence            344557788888888876521000        0112222    566666664 5888888888666666555 5688888


Q ss_pred             EEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhccc
Q 003090          349 LDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGAL  428 (848)
Q Consensus       349 L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l  428 (848)
                      |++.++.+..+|.++..+++|+.|++++|..++.+|.  ++.+++|++|++.+|.....             .+..++++
T Consensus       616 L~L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~ip~--ls~l~~Le~L~L~~c~~L~~-------------lp~si~~L  680 (1153)
T PLN03210        616 LQMQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEIPD--LSMATNLETLKLSDCSSLVE-------------LPSSIQYL  680 (1153)
T ss_pred             EECcCccccccccccccCCCCCEEECCCCCCcCcCCc--cccCCcccEEEecCCCCccc-------------cchhhhcc
Confidence            8888888888888888888888888888777777775  68888888888888764433             55677888


Q ss_pred             CCCcEEEeeccC-CCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHh
Q 003090          429 SRLTSLHIHIPE-GKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLL  507 (848)
Q Consensus       429 ~~L~~L~l~~~~-~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~  507 (848)
                      ++|+.|++++|. +..+|..+.+++|+.|.+.+                                               
T Consensus       681 ~~L~~L~L~~c~~L~~Lp~~i~l~sL~~L~Lsg-----------------------------------------------  713 (1153)
T PLN03210        681 NKLEDLDMSRCENLEILPTGINLKSLYRLNLSG-----------------------------------------------  713 (1153)
T ss_pred             CCCCEEeCCCCCCcCccCCcCCCCCCCEEeCCC-----------------------------------------------
Confidence            888888888753 55666555555566555542                                               


Q ss_pred             hcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccccccccccccc-----c
Q 003090          508 RSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHG-----Q  582 (848)
Q Consensus       508 ~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~-----~  582 (848)
                               |..++.++.     ..++|++|.+.++. ++.+      +....+++|++|.+.++.... ++..     .
T Consensus       714 ---------c~~L~~~p~-----~~~nL~~L~L~~n~-i~~l------P~~~~l~~L~~L~l~~~~~~~-l~~~~~~l~~  771 (1153)
T PLN03210        714 ---------CSRLKSFPD-----ISTNISWLDLDETA-IEEF------PSNLRLENLDELILCEMKSEK-LWERVQPLTP  771 (1153)
T ss_pred             ---------CCCcccccc-----ccCCcCeeecCCCc-cccc------cccccccccccccccccchhh-ccccccccch
Confidence                     222211111     11344444444332 2211      111124444444444432111 0000     0


Q ss_pred             cccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcccc
Q 003090          583 LPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMT  662 (848)
Q Consensus       583 ~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~  662 (848)
                      .....+++|+.|++++|+.+ ..+|..+ +.+++|+.|+|++|..++.+|.         .. .+++|++|++++|..+.
T Consensus       772 ~~~~~~~sL~~L~Ls~n~~l-~~lP~si-~~L~~L~~L~Ls~C~~L~~LP~---------~~-~L~sL~~L~Ls~c~~L~  839 (1153)
T PLN03210        772 LMTMLSPSLTRLFLSDIPSL-VELPSSI-QNLHKLEHLEIENCINLETLPT---------GI-NLESLESLDLSGCSRLR  839 (1153)
T ss_pred             hhhhccccchheeCCCCCCc-cccChhh-hCCCCCCEEECCCCCCcCeeCC---------CC-CccccCEEECCCCCccc
Confidence            00112456777777777666 6666653 6677777777777777776652         11 56677777777777766


Q ss_pred             ccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCC
Q 003090          663 DIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCG  742 (848)
Q Consensus       663 ~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~  742 (848)
                      .++..      .++|+.|++++. .++.                                .|..+..+++|+.|++.+|+
T Consensus       840 ~~p~~------~~nL~~L~Ls~n-~i~~--------------------------------iP~si~~l~~L~~L~L~~C~  880 (1153)
T PLN03210        840 TFPDI------STNISDLNLSRT-GIEE--------------------------------VPWWIEKFSNLSFLDMNGCN  880 (1153)
T ss_pred             ccccc------ccccCEeECCCC-CCcc--------------------------------ChHHHhcCCCCCEEECCCCC
Confidence            65432      356666666553 2222                                24445677888888888888


Q ss_pred             CCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccccccccccccc
Q 003090          743 KLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLAC  809 (848)
Q Consensus       743 ~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~  809 (848)
                      +|+.+|.  ....+++|+.|++.+|++|..+...................+|+...+.+.+|.+|.+
T Consensus       881 ~L~~l~~--~~~~L~~L~~L~l~~C~~L~~~~l~~~~~~~~~~~~n~~~~~p~~~~l~f~nC~~L~~  945 (1153)
T PLN03210        881 NLQRVSL--NISKLKHLETVDFSDCGALTEASWNGSPSEVAMATDNIHSKLPSTVCINFINCFNLDQ  945 (1153)
T ss_pred             CcCccCc--ccccccCCCeeecCCCcccccccCCCCchhhhhhcccccccCCchhccccccccCCCc
Confidence            8888764  3567788888888888888765322110000000000011244555566777777653

syringae 6; Provisional

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

Probab=100.00  E-value=8.3e-32  Score=330.36  Aligned_cols=482  Identities=19%  Similarity=0.199  Sum_probs=260.0

Q ss_pred             HHHHHhccCCCceeeecCCCc-ccCCcc--cccccceeecccCcCc-ccChHHHccCCceeEEEccCcccccccccCCCC
Q 003090          226 QYEIAGWLDLTGISLMFNDIH-EVPDEL--ECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFL  301 (848)
Q Consensus       226 ~~~i~~~~~l~~l~l~~n~l~-~lp~~~--~~~~L~~L~l~~~~~~-~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~  301 (848)
                      ...+.....++.|++++|.+. .+|..+  .+++|++|++++|.+. .+|.   ..+++|++|++++             
T Consensus        86 ~~~~~~l~~L~~L~Ls~n~~~~~ip~~~~~~l~~L~~L~Ls~n~l~~~~p~---~~l~~L~~L~Ls~-------------  149 (968)
T PLN00113         86 SSAIFRLPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLSNNNFTGSIPR---GSIPNLETLDLSN-------------  149 (968)
T ss_pred             ChHHhCCCCCCEEECCCCccCCcCChHHhccCCCCCEEECcCCccccccCc---cccCCCCEEECcC-------------
Confidence            344445556677777777765 566554  6677777777777543 3443   3566777777777             


Q ss_pred             CCCCCCCCCCCCCchhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCcc
Q 003090          302 FPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       302 ~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~  379 (848)
                       +.+.+.    +|..++.+++|++|++++|.+.+. +..++++++|++|++++|.+. .+|..++++++|++|++++|..
T Consensus       150 -n~~~~~----~p~~~~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l  224 (968)
T PLN00113        150 -NMLSGE----IPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNL  224 (968)
T ss_pred             -Cccccc----CChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCcc
Confidence             556544    666777777777777777765543 356677777777777777665 5677777777777777777766


Q ss_pred             ccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC-CCCCCC-ccCCCCeEE
Q 003090          380 LELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK-IMPSDM-SFQNLTSFS  457 (848)
Q Consensus       380 ~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~-~~~~~~-~~~~L~~L~  457 (848)
                      .+.+|.. ++++++|++|++++|.+...             .+..++++++|+.|++++|.+. .+|..+ .+++|+.|+
T Consensus       225 ~~~~p~~-l~~l~~L~~L~L~~n~l~~~-------------~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~  290 (968)
T PLN00113        225 SGEIPYE-IGGLTSLNHLDLVYNNLTGP-------------IPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLD  290 (968)
T ss_pred             CCcCChh-HhcCCCCCEEECcCceeccc-------------cChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEE
Confidence            6666666 67777777777777766544             4456666777777777766654 344444 566677776


Q ss_pred             EEeCCC------CCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccC
Q 003090          458 IAIGDL------EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDG  531 (848)
Q Consensus       458 l~~~~~------~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~  531 (848)
                      +..+..      +....+.++.+.+.+..             -...+|.++.. +++|+.|.+.++......+..+  ..
T Consensus       291 Ls~n~l~~~~p~~~~~l~~L~~L~l~~n~-------------~~~~~~~~~~~-l~~L~~L~L~~n~l~~~~p~~l--~~  354 (968)
T PLN00113        291 LSDNSLSGEIPELVIQLQNLEILHLFSNN-------------FTGKIPVALTS-LPRLQVLQLWSNKFSGEIPKNL--GK  354 (968)
T ss_pred             CcCCeeccCCChhHcCCCCCcEEECCCCc-------------cCCcCChhHhc-CCCCCEEECcCCCCcCcCChHH--hC
Confidence            664433      12222333333332211             00122222222 3566666666665544444333  34


Q ss_pred             CCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHH
Q 003090          532 FNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLV  611 (848)
Q Consensus       532 l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~  611 (848)
                      +++|+.|+++++.....++     .....+++|+.|++.++. +....  ....+.+++|+.|++.+|.-. ..+|..+ 
T Consensus       355 ~~~L~~L~Ls~n~l~~~~p-----~~~~~~~~L~~L~l~~n~-l~~~~--p~~~~~~~~L~~L~L~~n~l~-~~~p~~~-  424 (968)
T PLN00113        355 HNNLTVLDLSTNNLTGEIP-----EGLCSSGNLFKLILFSNS-LEGEI--PKSLGACRSLRRVRLQDNSFS-GELPSEF-  424 (968)
T ss_pred             CCCCcEEECCCCeeEeeCC-----hhHhCcCCCCEEECcCCE-ecccC--CHHHhCCCCCCEEECcCCEee-eECChhH-
Confidence            5666666666654322211     112234556666666553 21110  001124566666666665433 3444432 


Q ss_pred             HhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccccc
Q 003090          612 QSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQV  691 (848)
Q Consensus       612 ~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~  691 (848)
                      ..+++|+.|++++|.-...++         ..+..+++|+.|++++|.-...+|..    ...++|+.|++++|. +...
T Consensus       425 ~~l~~L~~L~Ls~N~l~~~~~---------~~~~~l~~L~~L~L~~n~~~~~~p~~----~~~~~L~~L~ls~n~-l~~~  490 (968)
T PLN00113        425 TKLPLVYFLDISNNNLQGRIN---------SRKWDMPSLQMLSLARNKFFGGLPDS----FGSKRLENLDLSRNQ-FSGA  490 (968)
T ss_pred             hcCCCCCEEECcCCcccCccC---------hhhccCCCCcEEECcCceeeeecCcc----cccccceEEECcCCc-cCCc
Confidence            556666666666554332222         22345566666666666544443332    123566666666653 2222


Q ss_pred             ccCccccccccceeeeccccccceeeeec---CCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEeccc
Q 003090          692 FPANFGKKAAAEEMVLYRKRRDQIHIHAT---TSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCP  768 (848)
Q Consensus       692 ~p~~~~~~~~~~~l~l~~l~~~~l~i~~c---~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~  768 (848)
                      .|..+..        +.++  ..+++.+|   ...|..+..+++|+.|++++|.-...+|  ..+.++++|++|++++|.
T Consensus       491 ~~~~~~~--------l~~L--~~L~Ls~N~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p--~~~~~l~~L~~L~Ls~N~  558 (968)
T PLN00113        491 VPRKLGS--------LSEL--MQLKLSENKLSGEIPDELSSCKKLVSLDLSHNQLSGQIP--ASFSEMPVLSQLDLSQNQ  558 (968)
T ss_pred             cChhhhh--------hhcc--CEEECcCCcceeeCChHHcCccCCCEEECCCCcccccCC--hhHhCcccCCEEECCCCc
Confidence            3333221        2223  33444443   1234455566666666666654322332  245566666666666665


Q ss_pred             ccceeecCCcccccccCCCccceeccccccccccccccc
Q 003090          769 TLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSL  807 (848)
Q Consensus       769 ~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L  807 (848)
                      -...++.      .+.       .+++|+.|++++|+-.
T Consensus       559 l~~~~p~------~l~-------~l~~L~~l~ls~N~l~  584 (968)
T PLN00113        559 LSGEIPK------NLG-------NVESLVQVNISHNHLH  584 (968)
T ss_pred             ccccCCh------hHh-------cCcccCEEeccCCcce
Confidence            4333311      111       1456666666666633

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

Probab=99.97  E-value=7.1e-31  Score=322.13  Aligned_cols=482  Identities=19%  Similarity=0.175  Sum_probs=355.2

Q ss_pred             cCcEEEEEeccCCchhHHHHHHH-hccCCCceeeecCCCcccCCcccccccceeecccCcCc-ccChHHHccCCceeEEE
Q 003090          208 FDDVAMAVVSQTPSITKIQYEIA-GWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLD  285 (848)
Q Consensus       208 F~~~~wv~vs~~~~~~~l~~~i~-~~~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~-~~~~~~~~~~~~Lr~L~  285 (848)
                      +...-...++.+.-...++..+. ....++.|++++|.+....+...+++|++|++++|.+. .+|.. ++++++|++|+
T Consensus        92 l~~L~~L~Ls~n~~~~~ip~~~~~~l~~L~~L~Ls~n~l~~~~p~~~l~~L~~L~Ls~n~~~~~~p~~-~~~l~~L~~L~  170 (968)
T PLN00113         92 LPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLSNNNFTGSIPRGSIPNLETLDLSNNMLSGEIPND-IGSFSSLKVLD  170 (968)
T ss_pred             CCCCCEEECCCCccCCcCChHHhccCCCCCEEECcCCccccccCccccCCCCEEECcCCcccccCChH-HhcCCCCCEEE
Confidence            33444455665433346677776 56679999999999985433456899999999999775 56655 68999999999


Q ss_pred             ccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCc-ccChhh
Q 003090          286 LGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVS-EIPVSF  363 (848)
Q Consensus       286 l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~-~lp~~i  363 (848)
                      +++              +.+.+.    +|..++++++|++|++++|.+.+. +..++++++|++|++++|.+. .+|..+
T Consensus       171 L~~--------------n~l~~~----~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l  232 (968)
T PLN00113        171 LGG--------------NVLVGK----IPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEI  232 (968)
T ss_pred             Ccc--------------Cccccc----CChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCccCCcCChhH
Confidence            999              777765    899999999999999999988765 488999999999999999888 889999


Q ss_pred             ccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC-
Q 003090          364 GRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK-  442 (848)
Q Consensus       364 ~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~-  442 (848)
                      +++++|++|++++|...+.+|.. ++++++|++|++++|.+.+.             .+..+.++++|+.|++++|.+. 
T Consensus       233 ~~l~~L~~L~L~~n~l~~~~p~~-l~~l~~L~~L~L~~n~l~~~-------------~p~~l~~l~~L~~L~Ls~n~l~~  298 (968)
T PLN00113        233 GGLTSLNHLDLVYNNLTGPIPSS-LGNLKNLQYLFLYQNKLSGP-------------IPPSIFSLQKLISLDLSDNSLSG  298 (968)
T ss_pred             hcCCCCCEEECcCceeccccChh-HhCCCCCCEEECcCCeeecc-------------CchhHhhccCcCEEECcCCeecc
Confidence            99999999999999888888888 89999999999999987765             5667888999999999999876 


Q ss_pred             CCCCCC-ccCCCCeEEEEeCCC------CCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeec
Q 003090          443 IMPSDM-SFQNLTSFSIAIGDL------EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALA  515 (848)
Q Consensus       443 ~~~~~~-~~~~L~~L~l~~~~~------~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~  515 (848)
                      .+|..+ .+++|+.|++..+..      +....+.++.+.+....             -...+|.++.. +++|+.|+++
T Consensus       299 ~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~-------------l~~~~p~~l~~-~~~L~~L~Ls  364 (968)
T PLN00113        299 EIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQLWSNK-------------FSGEIPKNLGK-HNNLTVLDLS  364 (968)
T ss_pred             CCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEECcCCC-------------CcCcCChHHhC-CCCCcEEECC
Confidence            455555 788999999876654      23344556666665431             00234444443 4789999999


Q ss_pred             cccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEE
Q 003090          516 EVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSD  595 (848)
Q Consensus       516 ~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~  595 (848)
                      ++......+..+  ..+++|+.|.+.++.....+     ......+++|+.|++.+|. +....  ......+++|+.|+
T Consensus       365 ~n~l~~~~p~~~--~~~~~L~~L~l~~n~l~~~~-----p~~~~~~~~L~~L~L~~n~-l~~~~--p~~~~~l~~L~~L~  434 (968)
T PLN00113        365 TNNLTGEIPEGL--CSSGNLFKLILFSNSLEGEI-----PKSLGACRSLRRVRLQDNS-FSGEL--PSEFTKLPLVYFLD  434 (968)
T ss_pred             CCeeEeeCChhH--hCcCCCCEEECcCCEecccC-----CHHHhCCCCCCEEECcCCE-eeeEC--ChhHhcCCCCCEEE
Confidence            887665555544  35688999999888643332     1234568999999999885 32211  11123688999999


Q ss_pred             EecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCcccccc
Q 003090          596 VVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLH  675 (848)
Q Consensus       596 l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~  675 (848)
                      +++|.-. ..+|.. ...+++|+.|++++|.....+|.          ....++|+.|++++|.-...++..   +..++
T Consensus       435 Ls~N~l~-~~~~~~-~~~l~~L~~L~L~~n~~~~~~p~----------~~~~~~L~~L~ls~n~l~~~~~~~---~~~l~  499 (968)
T PLN00113        435 ISNNNLQ-GRINSR-KWDMPSLQMLSLARNKFFGGLPD----------SFGSKRLENLDLSRNQFSGAVPRK---LGSLS  499 (968)
T ss_pred             CcCCccc-CccChh-hccCCCCcEEECcCceeeeecCc----------ccccccceEEECcCCccCCccChh---hhhhh
Confidence            9987643 444443 36789999999999977666542          224578999999988654444432   56788


Q ss_pred             CccEEEeecCccccccccCccccccccceeeeccccccceeeeec---CCCCCCCCCCCCccEEEEecCCCCceecccch
Q 003090          676 NLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT---TSTSSPTPSLGNLVSITIRGCGKLRNLFTTSM  752 (848)
Q Consensus       676 ~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c---~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~  752 (848)
                      +|+.|++++|. +....|..+..        +.+|  +.+++.+|   ...|..+..+++|++|++++|.-...+|  ..
T Consensus       500 ~L~~L~Ls~N~-l~~~~p~~~~~--------l~~L--~~L~Ls~N~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p--~~  566 (968)
T PLN00113        500 ELMQLKLSENK-LSGEIPDELSS--------CKKL--VSLDLSHNQLSGQIPASFSEMPVLSQLDLSQNQLSGEIP--KN  566 (968)
T ss_pred             ccCEEECcCCc-ceeeCChHHcC--------ccCC--CEEECCCCcccccCChhHhCcccCCEEECCCCcccccCC--hh
Confidence            99999999874 44445654432        3444  55666665   2345667889999999999977555665  46


Q ss_pred             hhccccccEEEEecccccceee
Q 003090          753 VKSLVRLESLEVRSCPTLQEII  774 (848)
Q Consensus       753 ~~~l~~L~~L~i~~C~~L~~l~  774 (848)
                      +.++++|+.|++++|+-...++
T Consensus       567 l~~l~~L~~l~ls~N~l~~~~p  588 (968)
T PLN00113        567 LGNVESLVQVNISHNHLHGSLP  588 (968)
T ss_pred             HhcCcccCEEeccCCcceeeCC
Confidence            7889999999999998766664

>PLN03210 Resistant to P

Probab=99.90  E-value=7.2e-23  Score=250.84  Aligned_cols=353  Identities=22%  Similarity=0.312  Sum_probs=263.1

Q ss_pred             ccCCcc-cc-cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCc
Q 003090          247 EVPDEL-EC-PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLR  324 (848)
Q Consensus       247 ~lp~~~-~~-~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~  324 (848)
                      .+|..+ .+ .+|+.|.+.++....+|..+  ...+|+.|++.+              +.+..     +|..+..+++|+
T Consensus       579 ~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f--~~~~L~~L~L~~--------------s~l~~-----L~~~~~~l~~Lk  637 (1153)
T PLN03210        579 HLPEGFDYLPPKLRLLRWDKYPLRCMPSNF--RPENLVKLQMQG--------------SKLEK-----LWDGVHSLTGLR  637 (1153)
T ss_pred             ecCcchhhcCcccEEEEecCCCCCCCCCcC--CccCCcEEECcC--------------ccccc-----cccccccCCCCC
Confidence            345544 22 46888888888888888764  567888888888              77777     888888899999


Q ss_pred             EEEccCccccCCchhhccccCCCEEEccCC-CCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccc
Q 003090          325 TLRLHDRRIQGDLSLIGELSGLEILDLSES-DVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       325 ~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~-~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~  403 (848)
                      +|+++++.....++.++.+++|++|++++| .+..+|..++++++|++|++++|..++.+|.. + ++++|+.|++++|.
T Consensus       638 ~L~Ls~~~~l~~ip~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~-i-~l~sL~~L~Lsgc~  715 (1153)
T PLN03210        638 NIDLRGSKNLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTG-I-NLKSLYRLNLSGCS  715 (1153)
T ss_pred             EEECCCCCCcCcCCccccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCc-C-CCCCCCEEeCCCCC
Confidence            999998876666677888999999999887 56688999999999999999998888888886 3 78899999998886


Q ss_pred             cccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccc
Q 003090          404 RHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRC  483 (848)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c  483 (848)
                      ....++             .   ...+|+.|+++++.+..+|..+.+++|..|.+..+...          .+..     
T Consensus       716 ~L~~~p-------------~---~~~nL~~L~L~~n~i~~lP~~~~l~~L~~L~l~~~~~~----------~l~~-----  764 (1153)
T PLN03210        716 RLKSFP-------------D---ISTNISWLDLDETAIEEFPSNLRLENLDELILCEMKSE----------KLWE-----  764 (1153)
T ss_pred             Cccccc-------------c---ccCCcCeeecCCCccccccccccccccccccccccchh----------hccc-----
Confidence            443321             1   24578899999998888888777788888777532210          0000     


Q ss_pred             cccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCC
Q 003090          484 SRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHK  563 (848)
Q Consensus       484 ~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~  563 (848)
                                .+..++......+++|+.|.+++|.....++..+  +.+++|+.|++.+|..++.++.      ...+++
T Consensus       765 ----------~~~~l~~~~~~~~~sL~~L~Ls~n~~l~~lP~si--~~L~~L~~L~Ls~C~~L~~LP~------~~~L~s  826 (1153)
T PLN03210        765 ----------RVQPLTPLMTMLSPSLTRLFLSDIPSLVELPSSI--QNLHKLEHLEIENCINLETLPT------GINLES  826 (1153)
T ss_pred             ----------cccccchhhhhccccchheeCCCCCCccccChhh--hCCCCCCEEECCCCCCcCeeCC------CCCccc
Confidence                      0011111122235789999999998887777765  5789999999999998887642      225899


Q ss_pred             ccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecccccccccc
Q 003090          564 LEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEE  643 (848)
Q Consensus       564 L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~  643 (848)
                      |++|++++|.++..+     +. ..++|+.|++.++ .+ +.+|..+ ..+++|+.|++.+|++++.++         ..
T Consensus       827 L~~L~Ls~c~~L~~~-----p~-~~~nL~~L~Ls~n-~i-~~iP~si-~~l~~L~~L~L~~C~~L~~l~---------~~  888 (1153)
T PLN03210        827 LESLDLSGCSRLRTF-----PD-ISTNISDLNLSRT-GI-EEVPWWI-EKFSNLSFLDMNGCNNLQRVS---------LN  888 (1153)
T ss_pred             cCEEECCCCCccccc-----cc-cccccCEeECCCC-CC-ccChHHH-hcCCCCCEEECCCCCCcCccC---------cc
Confidence            999999999887654     21 3578999999884 67 7888764 789999999999999999986         45


Q ss_pred             ccccCCcCEEecCCCccccccccCCCc----------cccccCccEEEeecCcccc
Q 003090          644 TELFSSLEKLTLWDLPRMTDIWKGDTQ----------FVSLHNLKKVRVEECDELR  689 (848)
Q Consensus       644 ~~~l~~L~~L~l~~c~~L~~l~~~~~~----------l~~l~~L~~L~i~~C~~L~  689 (848)
                      ...+++|+.|++++|++|+.++....+          ...+|+...+.+.+|.++.
T Consensus       889 ~~~L~~L~~L~l~~C~~L~~~~l~~~~~~~~~~~~n~~~~~p~~~~l~f~nC~~L~  944 (1153)
T PLN03210        889 ISKLKHLETVDFSDCGALTEASWNGSPSEVAMATDNIHSKLPSTVCINFINCFNLD  944 (1153)
T ss_pred             cccccCCCeeecCCCcccccccCCCCchhhhhhcccccccCCchhccccccccCCC
Confidence            668899999999999999865432211          1234455666777887775

syringae 6; Provisional

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

Probab=99.87  E-value=6.6e-26  Score=223.99  Aligned_cols=453  Identities=17%  Similarity=0.195  Sum_probs=271.1

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      .....++.+|.+...+..+++++|.+..+|+.+ ...+++.|+.+.|....+++++ +.+..|..++..+          
T Consensus        78 n~l~~lp~aig~l~~l~~l~vs~n~ls~lp~~i~s~~~l~~l~~s~n~~~el~~~i-~~~~~l~dl~~~~----------  146 (565)
T KOG0472|consen   78 NKLSQLPAAIGELEALKSLNVSHNKLSELPEQIGSLISLVKLDCSSNELKELPDSI-GRLLDLEDLDATN----------  146 (565)
T ss_pred             chhhhCCHHHHHHHHHHHhhcccchHhhccHHHhhhhhhhhhhccccceeecCchH-HHHhhhhhhhccc----------
Confidence            556667777777777777777888777777776 7777778888877777777775 4666777777777          


Q ss_pred             CCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCc
Q 003090          299 PFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCY  378 (848)
Q Consensus       299 ~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~  378 (848)
                          |++..     +|.++..+.+|..|++.+|.....++..-+++.|++||...|.++.+|+.++.+.+|..|+++.|.
T Consensus       147 ----N~i~s-----lp~~~~~~~~l~~l~~~~n~l~~l~~~~i~m~~L~~ld~~~N~L~tlP~~lg~l~~L~~LyL~~Nk  217 (565)
T KOG0472|consen  147 ----NQISS-----LPEDMVNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCNSNLLETLPPELGGLESLELLYLRRNK  217 (565)
T ss_pred             ----ccccc-----CchHHHHHHHHHHhhccccchhhCCHHHHHHHHHHhcccchhhhhcCChhhcchhhhHHHHhhhcc
Confidence                77777     888888888888888888877777766555888888888888888888888888888888888864


Q ss_pred             cccccChhhhhccccccEEeccccccccccccccccccCcccchhh-hcccCCCcEEEeeccCCCCCCCCC-ccCCCCeE
Q 003090          379 ILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIE-LGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSF  456 (848)
Q Consensus       379 ~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~-L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L  456 (848)
                       ...+|+  |..+..|.+|+++.|++.-              .+++ ++++.+|..||+..|+++++|..+ .+++|+.|
T Consensus       218 -i~~lPe--f~gcs~L~Elh~g~N~i~~--------------lpae~~~~L~~l~vLDLRdNklke~Pde~clLrsL~rL  280 (565)
T KOG0472|consen  218 -IRFLPE--FPGCSLLKELHVGENQIEM--------------LPAEHLKHLNSLLVLDLRDNKLKEVPDEICLLRSLERL  280 (565)
T ss_pred             -cccCCC--CCccHHHHHHHhcccHHHh--------------hHHHHhcccccceeeeccccccccCchHHHHhhhhhhh
Confidence             456774  7888888888888777653              3444 458899999999999999999988 78889999


Q ss_pred             EEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHH--Hhhcceeee-ccccccccccccccccCCC
Q 003090          457 SIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNL--LLRSEILAL-AEVNYFENIVSDLANDGFN  533 (848)
Q Consensus       457 ~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~--~~~L~~L~l-~~~~~~~~~~~~l~~~~l~  533 (848)
                      +++++.. ..-+..+..+.+....     +.+    ..+..+...+-..  ..-|++|+= ..+.+.            .
T Consensus       281 DlSNN~i-s~Lp~sLgnlhL~~L~-----leG----NPlrTiRr~ii~~gT~~vLKyLrs~~~~dgl------------S  338 (565)
T KOG0472|consen  281 DLSNNDI-SSLPYSLGNLHLKFLA-----LEG----NPLRTIRREIISKGTQEVLKYLRSKIKDDGL------------S  338 (565)
T ss_pred             cccCCcc-ccCCcccccceeeehh-----hcC----CchHHHHHHHHcccHHHHHHHHHHhhccCCC------------C
Confidence            9886554 1112222222221110     000    0012222111100  001111110 000000            0


Q ss_pred             CCcEEEEecCCCcee-ecccccc--cccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHH
Q 003090          534 ELMFLVIFRCNEMKY-LLNSLER--TLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHL  610 (848)
Q Consensus       534 ~L~~L~l~~~~~l~~-l~~~~~~--~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~  610 (848)
                      +        -..-+. -++.+.+  +.....-+.+.|.+++- +++.+....+..+.-.-....++++ .++ ..+|..+
T Consensus       339 ~--------se~~~e~~~t~~~~~~~~~~~~i~tkiL~~s~~-qlt~VPdEVfea~~~~~Vt~Vnfsk-NqL-~elPk~L  407 (565)
T KOG0472|consen  339 Q--------SEGGTETAMTLPSESFPDIYAIITTKILDVSDK-QLTLVPDEVFEAAKSEIVTSVNFSK-NQL-CELPKRL  407 (565)
T ss_pred             C--------CcccccccCCCCCCcccchhhhhhhhhhccccc-ccccCCHHHHHHhhhcceEEEeccc-chH-hhhhhhh
Confidence            0        000000 0000001  11222345566666554 3443322222222222245566666 355 6666654


Q ss_pred             HHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccc
Q 003090          611 VQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQ  690 (848)
Q Consensus       611 ~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~  690 (848)
                       ..+..+.+.-+.+...+..++         ..+..+++|..|++++.+ |.++|...   +.+..|++|+|+.- ....
T Consensus       408 -~~lkelvT~l~lsnn~isfv~---------~~l~~l~kLt~L~L~NN~-Ln~LP~e~---~~lv~Lq~LnlS~N-rFr~  472 (565)
T KOG0472|consen  408 -VELKELVTDLVLSNNKISFVP---------LELSQLQKLTFLDLSNNL-LNDLPEEM---GSLVRLQTLNLSFN-RFRM  472 (565)
T ss_pred             -HHHHHHHHHHHhhcCccccch---------HHHHhhhcceeeecccch-hhhcchhh---hhhhhhheeccccc-cccc
Confidence             445555554455555555554         457788888888888743 66777653   45667888888753 2222


Q ss_pred             cccCccccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEeccc
Q 003090          691 VFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCP  768 (848)
Q Consensus       691 ~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~  768 (848)
                       .|.........|.+-.+..     +|..  -.+.++..+.+|.+|++.+ +.++.+||  .++++++|++|++.+.|
T Consensus       473 -lP~~~y~lq~lEtllas~n-----qi~~--vd~~~l~nm~nL~tLDL~n-Ndlq~IPp--~LgnmtnL~hLeL~gNp  539 (565)
T KOG0472|consen  473 -LPECLYELQTLETLLASNN-----QIGS--VDPSGLKNMRNLTTLDLQN-NDLQQIPP--ILGNMTNLRHLELDGNP  539 (565)
T ss_pred             -chHHHhhHHHHHHHHhccc-----cccc--cChHHhhhhhhcceeccCC-CchhhCCh--hhccccceeEEEecCCc
Confidence             2322211000011100100     0000  1134578888999999988 78999986  68899999999999887

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

Probab=99.86  E-value=6.9e-23  Score=211.81  Aligned_cols=355  Identities=19%  Similarity=0.178  Sum_probs=216.9

Q ss_pred             ceeeecCCCcccCCc--ccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          237 GISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~--~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      .|++++|.+..+...  .++++|+.+++..|.+..+|.. .....+|..|+|.+              |.+...    -.
T Consensus        82 ~LdlsnNkl~~id~~~f~nl~nLq~v~l~~N~Lt~IP~f-~~~sghl~~L~L~~--------------N~I~sv----~s  142 (873)
T KOG4194|consen   82 TLDLSNNKLSHIDFEFFYNLPNLQEVNLNKNELTRIPRF-GHESGHLEKLDLRH--------------NLISSV----TS  142 (873)
T ss_pred             eeeccccccccCcHHHHhcCCcceeeeeccchhhhcccc-cccccceeEEeeec--------------cccccc----cH
Confidence            366666666644333  2666666666666666666652 13344566666666              555543    23


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      +++..++.||.|||+.|.+...+ +.+..=.++++|+|++|.|+.+-. .+..+.+|-+|.++.|.. ..+|...|.+|+
T Consensus       143 e~L~~l~alrslDLSrN~is~i~~~sfp~~~ni~~L~La~N~It~l~~~~F~~lnsL~tlkLsrNri-ttLp~r~Fk~L~  221 (873)
T KOG4194|consen  143 EELSALPALRSLDLSRNLISEIPKPSFPAKVNIKKLNLASNRITTLETGHFDSLNSLLTLKLSRNRI-TTLPQRSFKRLP  221 (873)
T ss_pred             HHHHhHhhhhhhhhhhchhhcccCCCCCCCCCceEEeeccccccccccccccccchheeeecccCcc-cccCHHHhhhcc
Confidence            44566666666666666555555 556666666666666666665432 355666666666666543 446655566666


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCC------C
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDL------E  464 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~------~  464 (848)
                      +|+.|++..|.+...             .-..+++|++|+.|.+..|++..+....  .+.+++.|++..+..      |
T Consensus       222 ~L~~LdLnrN~iriv-------------e~ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~  288 (873)
T KOG4194|consen  222 KLESLDLNRNRIRIV-------------EGLTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLETNRLQAVNEGW  288 (873)
T ss_pred             hhhhhhccccceeee-------------hhhhhcCchhhhhhhhhhcCcccccCcceeeecccceeecccchhhhhhccc
Confidence            677666666665432             2234566666666666666666655554  666666666655443      5


Q ss_pred             CCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCC
Q 003090          465 ERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCN  544 (848)
Q Consensus       465 ~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~  544 (848)
                      ......++.|.+...              .+.+++..-....++|+.|+|+.+...+--...+  ..+..|++|.+.++.
T Consensus       289 lfgLt~L~~L~lS~N--------------aI~rih~d~WsftqkL~~LdLs~N~i~~l~~~sf--~~L~~Le~LnLs~Ns  352 (873)
T KOG4194|consen  289 LFGLTSLEQLDLSYN--------------AIQRIHIDSWSFTQKLKELDLSSNRITRLDEGSF--RVLSQLEELNLSHNS  352 (873)
T ss_pred             ccccchhhhhccchh--------------hhheeecchhhhcccceeEeccccccccCChhHH--HHHHHhhhhcccccc
Confidence            555555555554432              1233332223345789999998776443222222  346788888888774


Q ss_pred             CceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEec
Q 003090          545 EMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYS  624 (848)
Q Consensus       545 ~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~  624 (848)
                       +..+    .-..+..+.+|++|+|+++.--.-+-.+..+...+++|++|.+.+ +++ +.+|...+..+++|++|++.+
T Consensus       353 -i~~l----~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~g-Nql-k~I~krAfsgl~~LE~LdL~~  425 (873)
T KOG4194|consen  353 -IDHL----AEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTG-NQL-KSIPKRAFSGLEALEHLDLGD  425 (873)
T ss_pred             -hHHH----HhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecC-cee-eecchhhhccCcccceecCCC
Confidence             3222    112455679999999998742111112223344699999999998 578 999998888999999999998


Q ss_pred             cCCceeeeeccccccccccccccCCcCEEecCC
Q 003090          625 CGLLVSVFEIERVNIAKEETELFSSLEKLTLWD  657 (848)
Q Consensus       625 c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~  657 (848)
                      +.-.+-.+         ..+..+ .|++|.+..
T Consensus       426 NaiaSIq~---------nAFe~m-~Lk~Lv~nS  448 (873)
T KOG4194|consen  426 NAIASIQP---------NAFEPM-ELKELVMNS  448 (873)
T ss_pred             Ccceeecc---------cccccc-hhhhhhhcc
Confidence            76444333         345455 788887764

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

Probab=99.86  E-value=2.5e-22  Score=207.75  Aligned_cols=368  Identities=21%  Similarity=0.198  Sum_probs=267.3

Q ss_pred             ceeeecCCCcccCCcc----cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          237 GISLMFNDIHEVPDEL----ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~~----~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      -++.+++.+..+...-    -.+.-++|++++|.+..+...+|.++++|+.+++.+              |.+..     
T Consensus        56 lldcs~~~lea~~~~~l~g~lp~~t~~LdlsnNkl~~id~~~f~nl~nLq~v~l~~--------------N~Lt~-----  116 (873)
T KOG4194|consen   56 LLDCSDRELEAIDKSRLKGFLPSQTQTLDLSNNKLSHIDFEFFYNLPNLQEVNLNK--------------NELTR-----  116 (873)
T ss_pred             eeecCccccccccccccCCcCccceeeeeccccccccCcHHHHhcCCcceeeeecc--------------chhhh-----
Confidence            3677777776542211    124567799999999999888899999999999999              88888     


Q ss_pred             CCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      +|...+...||+.|+|.+|.+...- +.+.-++.|+.|||+.|.|+++|. ++..-.++++|++++|.+ +.+..+.|..
T Consensus       117 IP~f~~~sghl~~L~L~~N~I~sv~se~L~~l~alrslDLSrN~is~i~~~sfp~~~ni~~L~La~N~I-t~l~~~~F~~  195 (873)
T KOG4194|consen  117 IPRFGHESGHLEKLDLRHNLISSVTSEELSALPALRSLDLSRNLISEIPKPSFPAKVNIKKLNLASNRI-TTLETGHFDS  195 (873)
T ss_pred             cccccccccceeEEeeeccccccccHHHHHhHhhhhhhhhhhchhhcccCCCCCCCCCceEEeeccccc-cccccccccc
Confidence            8988888889999999999666655 788999999999999999998875 466667899999999765 4466555889


Q ss_pred             cccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC-C-ccCCCCeEEEEeCCCCCCCC
Q 003090          391 LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD-M-SFQNLTSFSIAIGDLEERPL  468 (848)
Q Consensus       391 l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~-~-~~~~L~~L~l~~~~~~~~~~  468 (848)
                      +.+|-+|.++.|+++..             -+..+++|++|+.|++..|.+..+... + .+++|+.|.+..+..     
T Consensus       196 lnsL~tlkLsrNrittL-------------p~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~nlklqrN~I-----  257 (873)
T KOG4194|consen  196 LNSLLTLKLSRNRITTL-------------PQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQNLKLQRNDI-----  257 (873)
T ss_pred             cchheeeecccCccccc-------------CHHHhhhcchhhhhhccccceeeehhhhhcCchhhhhhhhhhcCc-----
Confidence            99999999999998765             456788899999999999987654322 2 666677666654432     


Q ss_pred             CcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCcee
Q 003090          469 SDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKY  548 (848)
Q Consensus       469 ~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~  548 (848)
                                                 ..+....+-.+.+++.|+|+.+....--..|+  -++..|+.|+++.+..-+ 
T Consensus       258 ---------------------------~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~l--fgLt~L~~L~lS~NaI~r-  307 (873)
T KOG4194|consen  258 ---------------------------SKLDDGAFYGLEKMEHLNLETNRLQAVNEGWL--FGLTSLEQLDLSYNAIQR-  307 (873)
T ss_pred             ---------------------------ccccCcceeeecccceeecccchhhhhhcccc--cccchhhhhccchhhhhe-
Confidence                                       22222222225678888887555433222333  367889999998874322 


Q ss_pred             ecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCc
Q 003090          549 LLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLL  628 (848)
Q Consensus       549 l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l  628 (848)
                      +    ......-.++|++|+|+.+ +++++..+.+  ..+..|++|.+++ +.+ ..+-...+..+.+|++|+++++.--
T Consensus       308 i----h~d~WsftqkL~~LdLs~N-~i~~l~~~sf--~~L~~Le~LnLs~-Nsi-~~l~e~af~~lssL~~LdLr~N~ls  378 (873)
T KOG4194|consen  308 I----HIDSWSFTQKLKELDLSSN-RITRLDEGSF--RVLSQLEELNLSH-NSI-DHLAEGAFVGLSSLHKLDLRSNELS  378 (873)
T ss_pred             e----ecchhhhcccceeEecccc-ccccCChhHH--HHHHHhhhhcccc-cch-HHHHhhHHHHhhhhhhhcCcCCeEE
Confidence            2    1122234689999999988 5666533322  2577889999988 467 7888877788999999999986533


Q ss_pred             eeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccccc
Q 003090          629 VSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQV  691 (848)
Q Consensus       629 ~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~  691 (848)
                      -.+-+      ....+..+++|+.|++.+ .++++++...  +..+++|++|++.+-+ +.++
T Consensus       379 ~~IED------aa~~f~gl~~LrkL~l~g-Nqlk~I~krA--fsgl~~LE~LdL~~Na-iaSI  431 (873)
T KOG4194|consen  379 WCIED------AAVAFNGLPSLRKLRLTG-NQLKSIPKRA--FSGLEALEHLDLGDNA-IASI  431 (873)
T ss_pred             EEEec------chhhhccchhhhheeecC-ceeeecchhh--hccCcccceecCCCCc-ceee
Confidence            33311      124566789999999998 5788888764  7789999999998743 4444

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

Probab=99.86  E-value=1.8e-23  Score=217.22  Aligned_cols=343  Identities=21%  Similarity=0.261  Sum_probs=247.6

Q ss_pred             CcEEEEEeccCCchhHHHHHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcC--cccChHHHccCCceeEEE
Q 003090          209 DDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSP--LAIPDRFFQGMKDLQVLD  285 (848)
Q Consensus       209 ~~~~wv~vs~~~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~--~~~~~~~~~~~~~Lr~L~  285 (848)
                      ....|..+.. ..+..++.++.....++.|++++|++..+-..+ .++.||.+.+..|.+  ..+|+++| +++.|.+||
T Consensus        32 t~~~WLkLnr-t~L~~vPeEL~~lqkLEHLs~~HN~L~~vhGELs~Lp~LRsv~~R~N~LKnsGiP~diF-~l~dLt~lD  109 (1255)
T KOG0444|consen   32 TQMTWLKLNR-TKLEQVPEELSRLQKLEHLSMAHNQLISVHGELSDLPRLRSVIVRDNNLKNSGIPTDIF-RLKDLTILD  109 (1255)
T ss_pred             hheeEEEech-hhhhhChHHHHHHhhhhhhhhhhhhhHhhhhhhccchhhHHHhhhccccccCCCCchhc-ccccceeee
Confidence            3467888765 677889999999999999999999998777666 889999999988854  46899987 899999999


Q ss_pred             ccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChhhc
Q 003090          286 LGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVSFG  364 (848)
Q Consensus       286 l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~  364 (848)
                      |++              |.+..     .|..+..-+++-+|+|++|++...| +.+-+|..|-+|||++|++..+|+.+.
T Consensus       110 LSh--------------NqL~E-----vP~~LE~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~R  170 (1255)
T KOG0444|consen  110 LSH--------------NQLRE-----VPTNLEYAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIR  170 (1255)
T ss_pred             cch--------------hhhhh-----cchhhhhhcCcEEEEcccCccccCCchHHHhhHhHhhhccccchhhhcCHHHH
Confidence            999              89998     9999999999999999999988888 677899999999999999999999999


Q ss_pred             cCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCC
Q 003090          365 RLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIM  444 (848)
Q Consensus       365 ~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~  444 (848)
                      +|.+|++|++++|.....--.. +..+++|+.|.+++.+.+..            ..|..+..+.||+.++++.|++..+
T Consensus       171 RL~~LqtL~Ls~NPL~hfQLrQ-LPsmtsL~vLhms~TqRTl~------------N~Ptsld~l~NL~dvDlS~N~Lp~v  237 (1255)
T KOG0444|consen  171 RLSMLQTLKLSNNPLNHFQLRQ-LPSMTSLSVLHMSNTQRTLD------------NIPTSLDDLHNLRDVDLSENNLPIV  237 (1255)
T ss_pred             HHhhhhhhhcCCChhhHHHHhc-Cccchhhhhhhcccccchhh------------cCCCchhhhhhhhhccccccCCCcc
Confidence            9999999999998654322223 56677888888888765432            2677888999999999999999999


Q ss_pred             CCCC-ccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccc
Q 003090          445 PSDM-SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENI  523 (848)
Q Consensus       445 ~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~  523 (848)
                      |..+ .+.+|+.|+++.+..        ..|.                    -....|     .+|+.|+++.+... .+
T Consensus       238 Pecly~l~~LrrLNLS~N~i--------teL~--------------------~~~~~W-----~~lEtLNlSrNQLt-~L  283 (1255)
T KOG0444|consen  238 PECLYKLRNLRRLNLSGNKI--------TELN--------------------MTEGEW-----ENLETLNLSRNQLT-VL  283 (1255)
T ss_pred             hHHHhhhhhhheeccCcCce--------eeee--------------------ccHHHH-----hhhhhhccccchhc-cc
Confidence            9888 889999988874432        0110                    011122     55666666655432 22


Q ss_pred             cccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhh
Q 003090          524 VSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSIL  603 (848)
Q Consensus       524 ~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~  603 (848)
                      +..+  -.++.|+.|.+.++. +..   ..--+..+.+.+|+++...++ +|+-+..   ....++.|++|.+. |+.+ 
T Consensus       284 P~av--cKL~kL~kLy~n~Nk-L~F---eGiPSGIGKL~~Levf~aanN-~LElVPE---glcRC~kL~kL~L~-~NrL-  351 (1255)
T KOG0444|consen  284 PDAV--CKLTKLTKLYANNNK-LTF---EGIPSGIGKLIQLEVFHAANN-KLELVPE---GLCRCVKLQKLKLD-HNRL-  351 (1255)
T ss_pred             hHHH--hhhHHHHHHHhccCc-ccc---cCCccchhhhhhhHHHHhhcc-ccccCch---hhhhhHHHHHhccc-ccce-
Confidence            3333  245666666665542 221   011123455666676666665 3443311   12256677777775 3555 


Q ss_pred             HhhhHHHHHhhccCcEEEEeccCCceeee
Q 003090          604 KILLSHLVQSFQNLQRLRVYSCGLLVSVF  632 (848)
Q Consensus       604 ~~l~~~~~~~l~~L~~L~l~~c~~l~~~~  632 (848)
                      -.+|..+ ..++.|+.|++..++++.--|
T Consensus       352 iTLPeaI-HlL~~l~vLDlreNpnLVMPP  379 (1255)
T KOG0444|consen  352 ITLPEAI-HLLPDLKVLDLRENPNLVMPP  379 (1255)
T ss_pred             eechhhh-hhcCCcceeeccCCcCccCCC
Confidence            5677654 666777777777777766544

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

Probab=99.86  E-value=1.3e-23  Score=218.34  Aligned_cols=369  Identities=21%  Similarity=0.296  Sum_probs=279.6

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      |.-...+.++-+...++-|.|....+..+|+.+ .+.+|++|.++.|.+.++... +..++.||.+++..          
T Consensus        19 Fsg~~FP~~v~qMt~~~WLkLnrt~L~~vPeEL~~lqkLEHLs~~HN~L~~vhGE-Ls~Lp~LRsv~~R~----------   87 (1255)
T KOG0444|consen   19 FSGDRFPHDVEQMTQMTWLKLNRTKLEQVPEELSRLQKLEHLSMAHNQLISVHGE-LSDLPRLRSVIVRD----------   87 (1255)
T ss_pred             CCCCcCchhHHHhhheeEEEechhhhhhChHHHHHHhhhhhhhhhhhhhHhhhhh-hccchhhHHHhhhc----------
Confidence            444556666666666777777777777777777 777788888887777766665 36777788887777          


Q ss_pred             CCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCC
Q 003090          299 PFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGC  377 (848)
Q Consensus       299 ~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~  377 (848)
                          |+++...   +|..+-++..|..|+|++|.+...|..+..-+++-+|+|++|+|.++|.. +-+|+.|-.|++++|
T Consensus        88 ----N~LKnsG---iP~diF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS~N  160 (1255)
T KOG0444|consen   88 ----NNLKNSG---IPTDIFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLSNN  160 (1255)
T ss_pred             ----cccccCC---CCchhcccccceeeecchhhhhhcchhhhhhcCcEEEEcccCccccCCchHHHhhHhHhhhccccc
Confidence                7776554   89999999999999999999999999999999999999999999999976 568999999999996


Q ss_pred             ccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccC--CCCCCCCC-ccCCCC
Q 003090          378 YILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE--GKIMPSDM-SFQNLT  454 (848)
Q Consensus       378 ~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~--~~~~~~~~-~~~~L~  454 (848)
                       .+..+|+. +..|.+|++|.+++|.+...             ....|..+++|+.|.+++++  ...+|..+ .+.||.
T Consensus       161 -rLe~LPPQ-~RRL~~LqtL~Ls~NPL~hf-------------QLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~  225 (1255)
T KOG0444|consen  161 -RLEMLPPQ-IRRLSMLQTLKLSNNPLNHF-------------QLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLR  225 (1255)
T ss_pred             -hhhhcCHH-HHHHhhhhhhhcCCChhhHH-------------HHhcCccchhhhhhhcccccchhhcCCCchhhhhhhh
Confidence             56789999 89999999999999987654             45667777888899999887  45888888 899999


Q ss_pred             eEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCC
Q 003090          455 SFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNE  534 (848)
Q Consensus       455 ~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~  534 (848)
                      .++++.++.                                ..+|..+.. +++|..|+|+++...+--   +..+...+
T Consensus       226 dvDlS~N~L--------------------------------p~vPecly~-l~~LrrLNLS~N~iteL~---~~~~~W~~  269 (1255)
T KOG0444|consen  226 DVDLSENNL--------------------------------PIVPECLYK-LRNLRRLNLSGNKITELN---MTEGEWEN  269 (1255)
T ss_pred             hccccccCC--------------------------------CcchHHHhh-hhhhheeccCcCceeeee---ccHHHHhh
Confidence            988874433                                555655555 488999999988754321   12245588


Q ss_pred             CcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccc--cccCCCcceEEEecCchhhHhhhHHHHH
Q 003090          535 LMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLP--AGCLSNVKRSDVVDCGSILKILLSHLVQ  612 (848)
Q Consensus       535 L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~--~~~l~~L~~L~l~~c~~l~~~l~~~~~~  612 (848)
                      |++|+++.+. ++.++     .....+++|++|.+.++. |.   ...+|  .|.+..|+.+...+ +.+ +-+|..+ .
T Consensus       270 lEtLNlSrNQ-Lt~LP-----~avcKL~kL~kLy~n~Nk-L~---FeGiPSGIGKL~~Levf~aan-N~L-ElVPEgl-c  336 (1255)
T KOG0444|consen  270 LETLNLSRNQ-LTVLP-----DAVCKLTKLTKLYANNNK-LT---FEGIPSGIGKLIQLEVFHAAN-NKL-ELVPEGL-C  336 (1255)
T ss_pred             hhhhccccch-hccch-----HHHhhhHHHHHHHhccCc-cc---ccCCccchhhhhhhHHHHhhc-ccc-ccCchhh-h
Confidence            9999998874 44432     234567899999888763 32   11233  34777888888877 567 8888876 8


Q ss_pred             hhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEee
Q 003090          613 SFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVE  683 (848)
Q Consensus       613 ~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~  683 (848)
                      .++.|+.|.+.. +.+..+|         ..+..+|.|+.|+++..|+|.--|.-.   ..-++|+.-+|.
T Consensus       337 RC~kL~kL~L~~-NrLiTLP---------eaIHlL~~l~vLDlreNpnLVMPPKP~---da~~~lefYNID  394 (1255)
T KOG0444|consen  337 RCVKLQKLKLDH-NRLITLP---------EAIHLLPDLKVLDLRENPNLVMPPKPN---DARKKLEFYNID  394 (1255)
T ss_pred             hhHHHHHhcccc-cceeech---------hhhhhcCCcceeeccCCcCccCCCCcc---hhhhcceeeecc
Confidence            899999999985 5566666         578889999999999999997643321   122456555554

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

Probab=99.83  E-value=1.1e-23  Score=208.29  Aligned_cols=463  Identities=18%  Similarity=0.234  Sum_probs=223.5

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCC
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFP  299 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~  299 (848)
                      ++..+..++-....++.+.+++|.+.++|+.+ .+..++.++.+.|.+..+|+.+ .....|+.|++++           
T Consensus        56 ~l~~l~~dl~nL~~l~vl~~~~n~l~~lp~aig~l~~l~~l~vs~n~ls~lp~~i-~s~~~l~~l~~s~-----------  123 (565)
T KOG0472|consen   56 DLEVLREDLKNLACLTVLNVHDNKLSQLPAAIGELEALKSLNVSHNKLSELPEQI-GSLISLVKLDCSS-----------  123 (565)
T ss_pred             chhhccHhhhcccceeEEEeccchhhhCCHHHHHHHHHHHhhcccchHhhccHHH-hhhhhhhhhhccc-----------
Confidence            33444444444444455555555555555544 4455555555555555555543 3444555555555           


Q ss_pred             CCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcc
Q 003090          300 FLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       300 ~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~  379 (848)
                         +.+..     +|++++.+..|..|+..+|.+...|+.++.+..|..|++.+|++..+|+..-+++.|++|+...| .
T Consensus       124 ---n~~~e-----l~~~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l~~l~~~~n~l~~l~~~~i~m~~L~~ld~~~N-~  194 (565)
T KOG0472|consen  124 ---NELKE-----LPDSIGRLLDLEDLDATNNQISSLPEDMVNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCNSN-L  194 (565)
T ss_pred             ---cceee-----cCchHHHHhhhhhhhccccccccCchHHHHHHHHHHhhccccchhhCCHHHHHHHHHHhcccchh-h
Confidence               44444     55555555555555555555555555555555555555555555555544444555555555442 3


Q ss_pred             ccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEE
Q 003090          380 LELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFS  457 (848)
Q Consensus       380 ~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~  457 (848)
                      ++.+|++ ++.+.+|..|++..|.+..               ..++..+..|.+|++..|.+..+|...  .+.++..|+
T Consensus       195 L~tlP~~-lg~l~~L~~LyL~~Nki~~---------------lPef~gcs~L~Elh~g~N~i~~lpae~~~~L~~l~vLD  258 (565)
T KOG0472|consen  195 LETLPPE-LGGLESLELLYLRRNKIRF---------------LPEFPGCSLLKELHVGENQIEMLPAEHLKHLNSLLVLD  258 (565)
T ss_pred             hhcCChh-hcchhhhHHHHhhhccccc---------------CCCCCccHHHHHHHhcccHHHhhHHHHhcccccceeee
Confidence            3445555 4555555555555554432               124455555555555555555554443  344444444


Q ss_pred             EEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcE
Q 003090          458 IAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMF  537 (848)
Q Consensus       458 l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~  537 (848)
                      +..+                                +++.+|..+.- +.+|++|+++++... ..+..+  +++ +|+.
T Consensus       259 LRdN--------------------------------klke~Pde~cl-LrsL~rLDlSNN~is-~Lp~sL--gnl-hL~~  301 (565)
T KOG0472|consen  259 LRDN--------------------------------KLKEVPDEICL-LRSLERLDLSNNDIS-SLPYSL--GNL-HLKF  301 (565)
T ss_pred             cccc--------------------------------ccccCchHHHH-hhhhhhhcccCCccc-cCCccc--ccc-eeee
Confidence            4322                                23555555443 467777777766533 233333  455 7777


Q ss_pred             EEEecCCCcee---ecccccccccccCCCccEEeccccccccccccc-----ccc------cccCCCcceEEEecCchhh
Q 003090          538 LVIFRCNEMKY---LLNSLERTLRVTLHKLEWLFIRENQNFVEICHG-----QLP------AGCLSNVKRSDVVDCGSIL  603 (848)
Q Consensus       538 L~l~~~~~l~~---l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~-----~~~------~~~l~~L~~L~l~~c~~l~  603 (848)
                      |.+.++|--+.   +...   +....+..|+.=  ..+..+..--.+     ..+      .....+.+.|.+++ .++ 
T Consensus       302 L~leGNPlrTiRr~ii~~---gT~~vLKyLrs~--~~~dglS~se~~~e~~~t~~~~~~~~~~~~i~tkiL~~s~-~ql-  374 (565)
T KOG0472|consen  302 LALEGNPLRTIRREIISK---GTQEVLKYLRSK--IKDDGLSQSEGGTETAMTLPSESFPDIYAIITTKILDVSD-KQL-  374 (565)
T ss_pred             hhhcCCchHHHHHHHHcc---cHHHHHHHHHHh--hccCCCCCCcccccccCCCCCCcccchhhhhhhhhhcccc-ccc-
Confidence            77777763221   0000   000111111110  001111000000     001      11344567777776 456 


Q ss_pred             HhhhHHHHHhhc--cCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEE
Q 003090          604 KILLSHLVQSFQ--NLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVR  681 (848)
Q Consensus       604 ~~l~~~~~~~l~--~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~  681 (848)
                      +.+|..++..-.  -....+++.+ ++.++|         ..+..+..+.+.-+..-..+ +++..  .+..+++|..|+
T Consensus       375 t~VPdEVfea~~~~~Vt~VnfskN-qL~elP---------k~L~~lkelvT~l~lsnn~i-sfv~~--~l~~l~kLt~L~  441 (565)
T KOG0472|consen  375 TLVPDEVFEAAKSEIVTSVNFSKN-QLCELP---------KRLVELKELVTDLVLSNNKI-SFVPL--ELSQLQKLTFLD  441 (565)
T ss_pred             ccCCHHHHHHhhhcceEEEecccc-hHhhhh---------hhhHHHHHHHHHHHhhcCcc-ccchH--HHHhhhcceeee
Confidence            677776544322  1334444442 344444         22223333333333332222 22222  256788899999


Q ss_pred             eecCccccccccCccccccccceeeeccccccceeeeec--CCCCCCCCCCCCccEEEEecCCCCceecccchhhccccc
Q 003090          682 VEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT--TSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRL  759 (848)
Q Consensus       682 i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c--~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L  759 (848)
                      +++-+ +.+ +|...+...        .+  +.++++..  ...|..+..+..|+.+-.++ ..+..+++ ++++++..|
T Consensus       442 L~NN~-Ln~-LP~e~~~lv--------~L--q~LnlS~NrFr~lP~~~y~lq~lEtllas~-nqi~~vd~-~~l~nm~nL  507 (565)
T KOG0472|consen  442 LSNNL-LND-LPEEMGSLV--------RL--QTLNLSFNRFRMLPECLYELQTLETLLASN-NQIGSVDP-SGLKNMRNL  507 (565)
T ss_pred             cccch-hhh-cchhhhhhh--------hh--heecccccccccchHHHhhHHHHHHHHhcc-ccccccCh-HHhhhhhhc
Confidence            88732 333 454443321        12  22333221  12233333334444444443 56777755 477888889


Q ss_pred             cEEEEecccccceeecCCcccccccCCCccceeccccccccccccc
Q 003090          760 ESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLD  805 (848)
Q Consensus       760 ~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp  805 (848)
                      ..|++.+.. +++++.             ..-.+++|++|.++|-|
T Consensus       508 ~tLDL~nNd-lq~IPp-------------~LgnmtnL~hLeL~gNp  539 (565)
T KOG0472|consen  508 TTLDLQNND-LQQIPP-------------ILGNMTNLRHLELDGNP  539 (565)
T ss_pred             ceeccCCCc-hhhCCh-------------hhccccceeEEEecCCc
Confidence            999988764 455532             22227889999988887

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

Probab=99.82  E-value=1.4e-22  Score=221.12  Aligned_cols=443  Identities=20%  Similarity=0.203  Sum_probs=211.0

Q ss_pred             HHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCC
Q 003090          228 EIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLP  306 (848)
Q Consensus       228 ~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~  306 (848)
                      .+-+.+.+..|++++|.+..+|..+ .+.+|+.|+++.|.+..+|.+ ..++++|++|.|.+              +.+.
T Consensus        40 ~~~~~v~L~~l~lsnn~~~~fp~~it~l~~L~~ln~s~n~i~~vp~s-~~~~~~l~~lnL~~--------------n~l~  104 (1081)
T KOG0618|consen   40 FVEKRVKLKSLDLSNNQISSFPIQITLLSHLRQLNLSRNYIRSVPSS-CSNMRNLQYLNLKN--------------NRLQ  104 (1081)
T ss_pred             HhhheeeeEEeeccccccccCCchhhhHHHHhhcccchhhHhhCchh-hhhhhcchhheecc--------------chhh
Confidence            3333555666777777777777666 666677777777766666654 35667777777766              5565


Q ss_pred             CCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCC-CCcccChhhccCCcccEEeccCCccccccCh
Q 003090          307 SSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSES-DVSEIPVSFGRLSHLRLLDLTGCYILELIPR  385 (848)
Q Consensus       307 ~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~-~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~  385 (848)
                      .     +|.++..+++|++|++++|.+...|..+..+..+..+..++| .+..++...     ++++++..+...+.++.
T Consensus       105 ~-----lP~~~~~lknl~~LdlS~N~f~~~Pl~i~~lt~~~~~~~s~N~~~~~lg~~~-----ik~~~l~~n~l~~~~~~  174 (1081)
T KOG0618|consen  105 S-----LPASISELKNLQYLDLSFNHFGPIPLVIEVLTAEEELAASNNEKIQRLGQTS-----IKKLDLRLNVLGGSFLI  174 (1081)
T ss_pred             c-----CchhHHhhhcccccccchhccCCCchhHHhhhHHHHHhhhcchhhhhhcccc-----chhhhhhhhhcccchhc
Confidence            5     677777777777777777766666666666666666666666 232333211     55556655555555555


Q ss_pred             hhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCC-
Q 003090          386 GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLE-  464 (848)
Q Consensus       386 ~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~-  464 (848)
                      + +..++.  .|++.+|.+.                ...+..+.+|+.|....|.+..+.-  .-++|+.|....+... 
T Consensus       175 ~-i~~l~~--~ldLr~N~~~----------------~~dls~~~~l~~l~c~rn~ls~l~~--~g~~l~~L~a~~n~l~~  233 (1081)
T KOG0618|consen  175 D-IYNLTH--QLDLRYNEME----------------VLDLSNLANLEVLHCERNQLSELEI--SGPSLTALYADHNPLTT  233 (1081)
T ss_pred             c-hhhhhe--eeecccchhh----------------hhhhhhccchhhhhhhhcccceEEe--cCcchheeeeccCccee
Confidence            5 455555  5667666554                1234444555555544444332211  2233444444433321 


Q ss_pred             CC---CCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEe
Q 003090          465 ER---PLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIF  541 (848)
Q Consensus       465 ~~---~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~  541 (848)
                      ..   .+..++.+.+.              ..++..+|.|+... .+|+.+....+..+ ..+...  ....+|+.|.+.
T Consensus       234 ~~~~p~p~nl~~~dis--------------~n~l~~lp~wi~~~-~nle~l~~n~N~l~-~lp~ri--~~~~~L~~l~~~  295 (1081)
T KOG0618|consen  234 LDVHPVPLNLQYLDIS--------------HNNLSNLPEWIGAC-ANLEALNANHNRLV-ALPLRI--SRITSLVSLSAA  295 (1081)
T ss_pred             eccccccccceeeecc--------------hhhhhcchHHHHhc-ccceEecccchhHH-hhHHHH--hhhhhHHHHHhh
Confidence            00   11111111111              12345566665553 56666655444432 222222  123455555555


Q ss_pred             cCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEE
Q 003090          542 RCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLR  621 (848)
Q Consensus       542 ~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~  621 (848)
                      .|. ++.++     ...+++.+|++|++..+ +|.++....+.. .-.+|..|+.+ |.++ ..+|..-...++.|+.|.
T Consensus       296 ~ne-l~yip-----~~le~~~sL~tLdL~~N-~L~~lp~~~l~v-~~~~l~~ln~s-~n~l-~~lp~~~e~~~~~Lq~Ly  365 (1081)
T KOG0618|consen  296 YNE-LEYIP-----PFLEGLKSLRTLDLQSN-NLPSLPDNFLAV-LNASLNTLNVS-SNKL-STLPSYEENNHAALQELY  365 (1081)
T ss_pred             hhh-hhhCC-----Ccccccceeeeeeehhc-cccccchHHHhh-hhHHHHHHhhh-hccc-cccccccchhhHHHHHHH
Confidence            542 33321     13334566666666555 232221100000 00112222222 1233 333333223344455555


Q ss_pred             EeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccc
Q 003090          622 VYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAA  701 (848)
Q Consensus       622 l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~  701 (848)
                      +.++.--...+         ..+..+++||.|+++. ..|.++|...  +..+..|+.|.+++ .+|+.+ |...+..-.
T Consensus       366 lanN~Ltd~c~---------p~l~~~~hLKVLhLsy-NrL~~fpas~--~~kle~LeeL~LSG-NkL~~L-p~tva~~~~  431 (1081)
T KOG0618|consen  366 LANNHLTDSCF---------PVLVNFKHLKVLHLSY-NRLNSFPASK--LRKLEELEELNLSG-NKLTTL-PDTVANLGR  431 (1081)
T ss_pred             HhcCcccccch---------hhhccccceeeeeecc-cccccCCHHH--HhchHHhHHHhccc-chhhhh-hHHHHhhhh
Confidence            55443322222         2344566666666664 3455555543  45556666666665 344442 222211100


Q ss_pred             cceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccc
Q 003090          702 AEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPT  769 (848)
Q Consensus       702 ~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~  769 (848)
                      .+.|...+.  ..      ..+| .+..+++|+.++++ |++|+.+........ +.|++|++++.+.
T Consensus       432 L~tL~ahsN--~l------~~fP-e~~~l~qL~~lDlS-~N~L~~~~l~~~~p~-p~LkyLdlSGN~~  488 (1081)
T KOG0618|consen  432 LHTLRAHSN--QL------LSFP-ELAQLPQLKVLDLS-CNNLSEVTLPEALPS-PNLKYLDLSGNTR  488 (1081)
T ss_pred             hHHHhhcCC--ce------eech-hhhhcCcceEEecc-cchhhhhhhhhhCCC-cccceeeccCCcc
Confidence            011111100  00      1122 34456667777776 366655421111111 5677777776654

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

Probab=99.74  E-value=2.4e-19  Score=196.03  Aligned_cols=413  Identities=21%  Similarity=0.247  Sum_probs=248.8

Q ss_pred             eeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCch
Q 003090          238 ISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSS  316 (848)
Q Consensus       238 l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~  316 (848)
                      ++.++..++-+|..+ ....+..|++..|.....|-.+..+.-+|+.|++++              +.+..     +|..
T Consensus         3 vd~s~~~l~~ip~~i~~~~~~~~ln~~~N~~l~~pl~~~~~~v~L~~l~lsn--------------n~~~~-----fp~~   63 (1081)
T KOG0618|consen    3 VDASDEQLELIPEQILNNEALQILNLRRNSLLSRPLEFVEKRVKLKSLDLSN--------------NQISS-----FPIQ   63 (1081)
T ss_pred             cccccccCcccchhhccHHHHHhhhccccccccCchHHhhheeeeEEeeccc--------------ccccc-----CCch
Confidence            566777888888776 445588888888887777777777777799999998              77777     8888


Q ss_pred             hhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccE
Q 003090          317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE  396 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~  396 (848)
                      +..+.+|+.|+++.|.+...+..++++.+|++|+|.+|.+..+|.++..+.+|+.|+++.|.+ ..+|.- +..++.+..
T Consensus        64 it~l~~L~~ln~s~n~i~~vp~s~~~~~~l~~lnL~~n~l~~lP~~~~~lknl~~LdlS~N~f-~~~Pl~-i~~lt~~~~  141 (1081)
T KOG0618|consen   64 ITLLSHLRQLNLSRNYIRSVPSSCSNMRNLQYLNLKNNRLQSLPASISELKNLQYLDLSFNHF-GPIPLV-IEVLTAEEE  141 (1081)
T ss_pred             hhhHHHHhhcccchhhHhhCchhhhhhhcchhheeccchhhcCchhHHhhhcccccccchhcc-CCCchh-HHhhhHHHH
Confidence            999999999999999888888888999999999999999999999999999999999998755 557776 788888888


Q ss_pred             EeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC-CCCCCC-ccCCCCeEEEEeCCCCCCCCCcccce
Q 003090          397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK-IMPSDM-SFQNLTSFSIAIGDLEERPLSDFIGL  474 (848)
Q Consensus       397 L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~-~~~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l  474 (848)
                      +..++|...                 ..++... .+++++..+.+. .++.++ .++.  .|++..+..           
T Consensus       142 ~~~s~N~~~-----------------~~lg~~~-ik~~~l~~n~l~~~~~~~i~~l~~--~ldLr~N~~-----------  190 (1081)
T KOG0618|consen  142 LAASNNEKI-----------------QRLGQTS-IKKLDLRLNVLGGSFLIDIYNLTH--QLDLRYNEM-----------  190 (1081)
T ss_pred             Hhhhcchhh-----------------hhhcccc-chhhhhhhhhcccchhcchhhhhe--eeecccchh-----------
Confidence            888877211                 2233332 555566555432 233322 2222  233321111           


Q ss_pred             EEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeeccccc
Q 003090          475 FLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLE  554 (848)
Q Consensus       475 ~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~  554 (848)
                                           ..   .....+++|+.|....+....     +. ..-++|+.|+...|+..+..     
T Consensus       191 ---------------------~~---~dls~~~~l~~l~c~rn~ls~-----l~-~~g~~l~~L~a~~n~l~~~~-----  235 (1081)
T KOG0618|consen  191 ---------------------EV---LDLSNLANLEVLHCERNQLSE-----LE-ISGPSLTALYADHNPLTTLD-----  235 (1081)
T ss_pred             ---------------------hh---hhhhhccchhhhhhhhcccce-----EE-ecCcchheeeeccCcceeec-----
Confidence                                 00   000002233333322211110     00 12366777777777654321     


Q ss_pred             ccccccCCCccEEeccccc--ccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeee
Q 003090          555 RTLRVTLHKLEWLFIRENQ--NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVF  632 (848)
Q Consensus       555 ~~~~~~~p~L~~L~l~~~~--~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~  632 (848)
                        ....-.+|++++++...  ++.+|      .+.+++|+.|.+.+ ..+ ..+|..+ ....+|+.|.+.+| .++.++
T Consensus       236 --~~p~p~nl~~~dis~n~l~~lp~w------i~~~~nle~l~~n~-N~l-~~lp~ri-~~~~~L~~l~~~~n-el~yip  303 (1081)
T KOG0618|consen  236 --VHPVPLNLQYLDISHNNLSNLPEW------IGACANLEALNANH-NRL-VALPLRI-SRITSLVSLSAAYN-ELEYIP  303 (1081)
T ss_pred             --cccccccceeeecchhhhhcchHH------HHhcccceEecccc-hhH-HhhHHHH-hhhhhHHHHHhhhh-hhhhCC
Confidence              11122466777776542  22222      23567777777766 345 5666554 55667777776665 344444


Q ss_pred             eccccccccccccccCCcCEEecCCCccccccccCCCcccccc-CccEEEeecCccccccccCcccccccc-ceeeeccc
Q 003090          633 EIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLH-NLKKVRVEECDELRQVFPANFGKKAAA-EEMVLYRK  710 (848)
Q Consensus       633 ~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~-~L~~L~i~~C~~L~~~~p~~~~~~~~~-~~l~l~~l  710 (848)
                               .....+.+|++|++.. .+|.++|...  +.-.. +|..|+++. .++.. .|..-...... +.|.+.+.
T Consensus       304 ---------~~le~~~sL~tLdL~~-N~L~~lp~~~--l~v~~~~l~~ln~s~-n~l~~-lp~~~e~~~~~Lq~LylanN  369 (1081)
T KOG0618|consen  304 ---------PFLEGLKSLRTLDLQS-NNLPSLPDNF--LAVLNASLNTLNVSS-NKLST-LPSYEENNHAALQELYLANN  369 (1081)
T ss_pred             ---------Ccccccceeeeeeehh-ccccccchHH--HhhhhHHHHHHhhhh-ccccc-cccccchhhHHHHHHHHhcC
Confidence                     3345677788888775 3566655532  22222 255555542 33333 23222111111 22222222


Q ss_pred             cccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEeccccccee
Q 003090          711 RRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEI  773 (848)
Q Consensus       711 ~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l  773 (848)
                        .   +.  ++....+.++..|+.|++++ +.|..+| .+.+.++..|++|++++.. |+.+
T Consensus       370 --~---Lt--d~c~p~l~~~~hLKVLhLsy-NrL~~fp-as~~~kle~LeeL~LSGNk-L~~L  422 (1081)
T KOG0618|consen  370 --H---LT--DSCFPVLVNFKHLKVLHLSY-NRLNSFP-ASKLRKLEELEELNLSGNK-LTTL  422 (1081)
T ss_pred             --c---cc--ccchhhhccccceeeeeecc-cccccCC-HHHHhchHHhHHHhcccch-hhhh
Confidence              0   00  12233567888999999998 7788885 4678899999999998853 4444

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

Probab=99.61  E-value=1.6e-17  Score=145.66  Aligned_cols=165  Identities=28%  Similarity=0.421  Sum_probs=88.8

Q ss_pred             ccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEE
Q 003090          247 EVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTL  326 (848)
Q Consensus       247 ~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L  326 (848)
                      ++|..+.+.++..|-++.|.+..+|+.+ ..+++|++|++.+              ++++.     +|.+++.+++||.|
T Consensus        25 ~~~gLf~~s~ITrLtLSHNKl~~vppni-a~l~nlevln~~n--------------nqie~-----lp~~issl~klr~l   84 (264)
T KOG0617|consen   25 ELPGLFNMSNITRLTLSHNKLTVVPPNI-AELKNLEVLNLSN--------------NQIEE-----LPTSISSLPKLRIL   84 (264)
T ss_pred             hcccccchhhhhhhhcccCceeecCCcH-HHhhhhhhhhccc--------------chhhh-----cChhhhhchhhhhe
Confidence            3444444455555555555555555543 4555555555555              55555     55555555555555


Q ss_pred             EccCccccCCchhhccccCCCEEEccCCCCc--ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccc
Q 003090          327 RLHDRRIQGDLSLIGELSGLEILDLSESDVS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFR  404 (848)
Q Consensus       327 ~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~  404 (848)
                      ++..|+....|..++.++.|++||+.+|++.  .+|..+-.+..|+.|++++|.+ ..+|++ ++++++||.|.+..|.+
T Consensus        85 nvgmnrl~~lprgfgs~p~levldltynnl~e~~lpgnff~m~tlralyl~dndf-e~lp~d-vg~lt~lqil~lrdndl  162 (264)
T KOG0617|consen   85 NVGMNRLNILPRGFGSFPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDNDF-EILPPD-VGKLTNLQILSLRDNDL  162 (264)
T ss_pred             ecchhhhhcCccccCCCchhhhhhccccccccccCCcchhHHHHHHHHHhcCCCc-ccCChh-hhhhcceeEEeeccCch
Confidence            5555555555555555555555555555554  5555555555555555555433 445555 45555555555555544


Q ss_pred             ccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC
Q 003090          405 HWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD  447 (848)
Q Consensus       405 ~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~  447 (848)
                      ..              .+.+++.++.|++|++.+|.++-+|..
T Consensus       163 l~--------------lpkeig~lt~lrelhiqgnrl~vlppe  191 (264)
T KOG0617|consen  163 LS--------------LPKEIGDLTRLRELHIQGNRLTVLPPE  191 (264)
T ss_pred             hh--------------CcHHHHHHHHHHHHhcccceeeecChh
Confidence            32              455555555566666665555555543

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

Probab=99.57  E-value=8.9e-17  Score=141.10  Aligned_cols=150  Identities=24%  Similarity=0.391  Sum_probs=136.5

Q ss_pred             CCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .+.|.+++|.++.+|+.+ .+.+|+.|++++|.+..+|.++ +.+++||.|+++-              +.+..     +
T Consensus        35 ITrLtLSHNKl~~vppnia~l~nlevln~~nnqie~lp~~i-ssl~klr~lnvgm--------------nrl~~-----l   94 (264)
T KOG0617|consen   35 ITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQIEELPTSI-SSLPKLRILNVGM--------------NRLNI-----L   94 (264)
T ss_pred             hhhhhcccCceeecCCcHHHhhhhhhhhcccchhhhcChhh-hhchhhhheecch--------------hhhhc-----C
Confidence            356889999999999999 9999999999999999999985 7999999999998              77777     9


Q ss_pred             CchhhhcccCcEEEccCccccCC--chhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGD--LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~--~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                      |..|+.++.|++|+|.+|+....  |..+..+..|+.|.++.|.++-+|..+++|++|+.|.+++|..+ .+|++ ++.+
T Consensus        95 prgfgs~p~levldltynnl~e~~lpgnff~m~tlralyl~dndfe~lp~dvg~lt~lqil~lrdndll-~lpke-ig~l  172 (264)
T KOG0617|consen   95 PRGFGSFPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGDNDFEILPPDVGKLTNLQILSLRDNDLL-SLPKE-IGDL  172 (264)
T ss_pred             ccccCCCchhhhhhccccccccccCCcchhHHHHHHHHHhcCCCcccCChhhhhhcceeEEeeccCchh-hCcHH-HHHH
Confidence            99999999999999999977654  47888899999999999999999999999999999999997665 59999 8999


Q ss_pred             ccccEEecccccccc
Q 003090          392 RKLEELYMSHSFRHW  406 (848)
Q Consensus       392 ~~L~~L~l~~~~~~~  406 (848)
                      +.|++|.+.+|+++.
T Consensus       173 t~lrelhiqgnrl~v  187 (264)
T KOG0617|consen  173 TRLRELHIQGNRLTV  187 (264)
T ss_pred             HHHHHHhcccceeee
Confidence            999999999998865

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.44  E-value=1.3e-13  Score=158.08  Aligned_cols=176  Identities=19%  Similarity=0.271  Sum_probs=128.2

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ...++++++.++.+|..+. +.++.|++++|.+..+|..++   .+|+.|++++              |.++.     +|
T Consensus       180 ~~~L~L~~~~LtsLP~~Ip-~~L~~L~Ls~N~LtsLP~~l~---~nL~~L~Ls~--------------N~Lts-----LP  236 (754)
T PRK15370        180 KTELRLKILGLTTIPACIP-EQITTLILDNNELKSLPENLQ---GNIKTLYANS--------------NQLTS-----IP  236 (754)
T ss_pred             ceEEEeCCCCcCcCCcccc-cCCcEEEecCCCCCcCChhhc---cCCCEEECCC--------------Ccccc-----CC
Confidence            4678888889998887663 578999999998888988654   5889999998              77776     77


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..+.  .+|+.|++++|.+...+..+.  .+|++|++++|+++.+|..+.  .+|++|++++|.+ ..+|.. +.  ++|
T Consensus       237 ~~l~--~~L~~L~Ls~N~L~~LP~~l~--s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~L-t~LP~~-lp--~sL  306 (754)
T PRK15370        237 ATLP--DTIQEMELSINRITELPERLP--SALQSLDLFHNKISCLPENLP--EELRYLSVYDNSI-RTLPAH-LP--SGI  306 (754)
T ss_pred             hhhh--ccccEEECcCCccCcCChhHh--CCCCEEECcCCccCccccccC--CCCcEEECCCCcc-ccCccc-ch--hhH
Confidence            6554  478999999998776665554  478999999888888887654  4789999988755 456664 22  467


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEe
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAI  460 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~  460 (848)
                      +.|++++|.+...              +..+  .++|+.|++++|.++.+|..+ .++|+.|++..
T Consensus       307 ~~L~Ls~N~Lt~L--------------P~~l--~~sL~~L~Ls~N~Lt~LP~~l-~~sL~~L~Ls~  355 (754)
T PRK15370        307 THLNVQSNSLTAL--------------PETL--PPGLKTLEAGENALTSLPASL-PPELQVLDVSK  355 (754)
T ss_pred             HHHHhcCCccccC--------------Cccc--cccceeccccCCccccCChhh-cCcccEEECCC
Confidence            8888888876532              1112  257888888888777766543 24566666553

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.43  E-value=1.1e-12  Score=149.33  Aligned_cols=168  Identities=20%  Similarity=0.202  Sum_probs=126.8

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      -..|+++.+.++.+|..+. ++|+.|++.+|.+..+|.    ..++|++|++++              |.++.     +|
T Consensus       203 ~~~LdLs~~~LtsLP~~l~-~~L~~L~L~~N~Lt~LP~----lp~~Lk~LdLs~--------------N~Lts-----LP  258 (788)
T PRK15387        203 NAVLNVGESGLTTLPDCLP-AHITTLVIPDNNLTSLPA----LPPELRTLEVSG--------------NQLTS-----LP  258 (788)
T ss_pred             CcEEEcCCCCCCcCCcchh-cCCCEEEccCCcCCCCCC----CCCCCcEEEecC--------------CccCc-----cc
Confidence            4569999999999998774 479999999999999885    368999999999              88887     77


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..   .++|+.|++++|.+...+..   ..+|+.|++++|+++.+|..   +++|++|++++|.+. .+|.. .   .+|
T Consensus       259 ~l---p~sL~~L~Ls~N~L~~Lp~l---p~~L~~L~Ls~N~Lt~LP~~---p~~L~~LdLS~N~L~-~Lp~l-p---~~L  324 (788)
T PRK15387        259 VL---PPGLLELSIFSNPLTHLPAL---PSGLCKLWIFGNQLTSLPVL---PPGLQELSVSDNQLA-SLPAL-P---SEL  324 (788)
T ss_pred             Cc---ccccceeeccCCchhhhhhc---hhhcCEEECcCCcccccccc---ccccceeECCCCccc-cCCCC-c---ccc
Confidence            53   36889999999977655542   35788999999999998863   578999999998654 46652 2   357


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      +.|++++|.+...              +. +  ..+|+.|++++|.++.+|..  ..+|+.|.+.
T Consensus       325 ~~L~Ls~N~L~~L--------------P~-l--p~~Lq~LdLS~N~Ls~LP~l--p~~L~~L~Ls  370 (788)
T PRK15387        325 CKLWAYNNQLTSL--------------PT-L--PSGLQELSVSDNQLASLPTL--PSELYKLWAY  370 (788)
T ss_pred             cccccccCccccc--------------cc-c--ccccceEecCCCccCCCCCC--Ccccceehhh
Confidence            7888888877532              11 1  14789999999988877753  2455555544

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.40  E-value=1e-12  Score=150.70  Aligned_cols=191  Identities=18%  Similarity=0.290  Sum_probs=149.9

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCC
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFP  299 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~  299 (848)
                      .++..++..|..  .++.|++++|.+..+|..+. .+|++|++++|.+..+|..+.   .+|+.|++++           
T Consensus       188 ~~LtsLP~~Ip~--~L~~L~Ls~N~LtsLP~~l~-~nL~~L~Ls~N~LtsLP~~l~---~~L~~L~Ls~-----------  250 (754)
T PRK15370        188 LGLTTIPACIPE--QITTLILDNNELKSLPENLQ-GNIKTLYANSNQLTSIPATLP---DTIQEMELSI-----------  250 (754)
T ss_pred             CCcCcCCccccc--CCcEEEecCCCCCcCChhhc-cCCCEEECCCCccccCChhhh---ccccEEECcC-----------
Confidence            566667766654  57889999999999998764 689999999999999987653   4799999999           


Q ss_pred             CCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcc
Q 003090          300 FLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       300 ~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~  379 (848)
                         |.+..     +|..+.  .+|++|++++|.+...+..+.  .+|++|++++|+++.+|..+.  .+|++|++++|..
T Consensus       251 ---N~L~~-----LP~~l~--s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~Lt~LP~~lp--~sL~~L~Ls~N~L  316 (754)
T PRK15370        251 ---NRITE-----LPERLP--SALQSLDLFHNKISCLPENLP--EELRYLSVYDNSIRTLPAHLP--SGITHLNVQSNSL  316 (754)
T ss_pred             ---CccCc-----CChhHh--CCCCEEECcCCccCccccccC--CCCcEEECCCCccccCcccch--hhHHHHHhcCCcc
Confidence               77876     887764  589999999998877665554  589999999999999987654  4799999999765


Q ss_pred             ccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          380 LELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       380 ~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      . .+|.. +  .++|+.|++++|.+...              +..+.  ++|+.|++++|.+..+|..+ .++|+.|++.
T Consensus       317 t-~LP~~-l--~~sL~~L~Ls~N~Lt~L--------------P~~l~--~sL~~L~Ls~N~L~~LP~~l-p~~L~~LdLs  375 (754)
T PRK15370        317 T-ALPET-L--PPGLKTLEAGENALTSL--------------PASLP--PELQVLDVSKNQITVLPETL-PPTITTLDVS  375 (754)
T ss_pred             c-cCCcc-c--cccceeccccCCccccC--------------Chhhc--CcccEEECCCCCCCcCChhh-cCCcCEEECC
Confidence            4 57765 2  36899999999987642              22332  68999999999998887654 3678888887


Q ss_pred             eCC
Q 003090          460 IGD  462 (848)
Q Consensus       460 ~~~  462 (848)
                      .+.
T Consensus       376 ~N~  378 (754)
T PRK15370        376 RNA  378 (754)
T ss_pred             CCc
Confidence            543

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.37  E-value=1.9e-12  Score=147.58  Aligned_cols=188  Identities=20%  Similarity=0.187  Sum_probs=140.2

Q ss_pred             EEEEEeccCCchhHHHHHHHhccCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcc
Q 003090          211 VAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIR  290 (848)
Q Consensus       211 ~~wv~vs~~~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~  290 (848)
                      ..++.++.. .+..++..+..  .++.|++++|.++.+|..  .++|++|++++|.+..+|.    ..++|+.|++++  
T Consensus       203 ~~~LdLs~~-~LtsLP~~l~~--~L~~L~L~~N~Lt~LP~l--p~~Lk~LdLs~N~LtsLP~----lp~sL~~L~Ls~--  271 (788)
T PRK15387        203 NAVLNVGES-GLTTLPDCLPA--HITTLVIPDNNLTSLPAL--PPELRTLEVSGNQLTSLPV----LPPGLLELSIFS--  271 (788)
T ss_pred             CcEEEcCCC-CCCcCCcchhc--CCCEEEccCCcCCCCCCC--CCCCcEEEecCCccCcccC----cccccceeeccC--
Confidence            345666663 66677776664  578999999999999864  5889999999999998885    246899999999  


Q ss_pred             cccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCccc
Q 003090          291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLR  370 (848)
Q Consensus       291 ~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~  370 (848)
                                  |.+..     +|...   .+|+.|++++|++...+.   .+++|++|++++|.++.+|...   .+|+
T Consensus       272 ------------N~L~~-----Lp~lp---~~L~~L~Ls~N~Lt~LP~---~p~~L~~LdLS~N~L~~Lp~lp---~~L~  325 (788)
T PRK15387        272 ------------NPLTH-----LPALP---SGLCKLWIFGNQLTSLPV---LPPGLQELSVSDNQLASLPALP---SELC  325 (788)
T ss_pred             ------------Cchhh-----hhhch---hhcCEEECcCCccccccc---cccccceeECCCCccccCCCCc---cccc
Confidence                        77776     66533   568899999998776654   2478999999999999888633   3577


Q ss_pred             EEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCcc
Q 003090          371 LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSF  450 (848)
Q Consensus       371 ~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~  450 (848)
                      .|++++|.. ..+|..    ..+|+.|++++|.+...              +. +  ..+|+.|++++|.+..+|..  .
T Consensus       326 ~L~Ls~N~L-~~LP~l----p~~Lq~LdLS~N~Ls~L--------------P~-l--p~~L~~L~Ls~N~L~~LP~l--~  381 (788)
T PRK15387        326 KLWAYNNQL-TSLPTL----PSGLQELSVSDNQLASL--------------PT-L--PSELYKLWAYNNRLTSLPAL--P  381 (788)
T ss_pred             ccccccCcc-cccccc----ccccceEecCCCccCCC--------------CC-C--CcccceehhhccccccCccc--c
Confidence            888988755 456652    25799999999988642              11 1  24678889999988877653  2


Q ss_pred             CCCCeEEEE
Q 003090          451 QNLTSFSIA  459 (848)
Q Consensus       451 ~~L~~L~l~  459 (848)
                      .+|+.|++.
T Consensus       382 ~~L~~LdLs  390 (788)
T PRK15387        382 SGLKELIVS  390 (788)
T ss_pred             cccceEEec
Confidence            456666665

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

Probab=99.29  E-value=5.6e-13  Score=133.06  Aligned_cols=141  Identities=26%  Similarity=0.339  Sum_probs=74.2

Q ss_pred             ecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhc
Q 003090          241 MFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFL  320 (848)
Q Consensus       241 ~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l  320 (848)
                      ++-.++++|..+. +.-..+.|..|.+..+|+..|+.+++||.|||++              |.|+..    -|++|..+
T Consensus        54 r~~GL~eVP~~LP-~~tveirLdqN~I~~iP~~aF~~l~~LRrLdLS~--------------N~Is~I----~p~AF~GL  114 (498)
T KOG4237|consen   54 RGKGLTEVPANLP-PETVEIRLDQNQISSIPPGAFKTLHRLRRLDLSK--------------NNISFI----APDAFKGL  114 (498)
T ss_pred             cCCCcccCcccCC-CcceEEEeccCCcccCChhhccchhhhceecccc--------------cchhhc----ChHhhhhh
Confidence            3334445554442 2344555556666666666666666666666666              555554    55556666


Q ss_pred             ccCcEEEccC-ccccCCc-hhhccccCCCEEEccCCCCcccC-hhhccCCcccEEeccCCccccccChhhhhccccccEE
Q 003090          321 INLRTLRLHD-RRIQGDL-SLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEEL  397 (848)
Q Consensus       321 ~~L~~L~L~~-~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L  397 (848)
                      ..|-.|.+-+ |++...+ ..|++|..|+-|.+.-|++.-++ ..+..|++|..|.+.+|. ...++.+.+..+..++++
T Consensus       115 ~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLllNan~i~Cir~~al~dL~~l~lLslyDn~-~q~i~~~tf~~l~~i~tl  193 (498)
T KOG4237|consen  115 ASLLSLVLYGNNKITDLPKGAFGGLSSLQRLLLNANHINCIRQDALRDLPSLSLLSLYDNK-IQSICKGTFQGLAAIKTL  193 (498)
T ss_pred             HhhhHHHhhcCCchhhhhhhHhhhHHHHHHHhcChhhhcchhHHHHHHhhhcchhcccchh-hhhhccccccchhccchH
Confidence            5555555444 4444444 45555555666555555555333 235555555555555532 233444334555555555


Q ss_pred             eccc
Q 003090          398 YMSH  401 (848)
Q Consensus       398 ~l~~  401 (848)
                      .+..
T Consensus       194 hlA~  197 (498)
T KOG4237|consen  194 HLAQ  197 (498)
T ss_pred             hhhc
Confidence            4443

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.22  E-value=1.1e-11  Score=144.60  Aligned_cols=325  Identities=26%  Similarity=0.296  Sum_probs=210.4

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCc--CcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENS--PLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~--~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      .+++++.+|.+..++....+++|++|-+..|.  +..++..+|..++.||+|||++|             ..+..     
T Consensus       525 ~rr~s~~~~~~~~~~~~~~~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~-------------~~l~~-----  586 (889)
T KOG4658|consen  525 VRRMSLMNNKIEHIAGSSENPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGN-------------SSLSK-----  586 (889)
T ss_pred             eeEEEEeccchhhccCCCCCCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCC-------------CccCc-----
Confidence            35688899999999998888999999999995  78899999999999999999985             56666     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCC-CcccChhhccCCcccEEeccCCccccccChhhhhcc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD-VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~-l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                      +|..++.|.|||||+++++.+...|..+++|+.|.+||+..+. +..+|..+..|.+||+|.+......  .....++.+
T Consensus       587 LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~--~~~~~l~el  664 (889)
T KOG4658|consen  587 LPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSALS--NDKLLLKEL  664 (889)
T ss_pred             CChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccchhhhcccccEEEeeccccc--cchhhHHhh
Confidence            9999999999999999999999999999999999999999984 4466666777999999999874311  111114444


Q ss_pred             ccccEEeccccccccccccccccccCcccchhhhcccCCCc----EEEeeccCCCCCCCCC-ccCCCCeEEEEeCCCCCC
Q 003090          392 RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLT----SLHIHIPEGKIMPSDM-SFQNLTSFSIAIGDLEER  466 (848)
Q Consensus       392 ~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~----~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~~~~~  466 (848)
                      .+|++|..-.+.....            .....+..+..|+    .+.+.++.....+... .+.+|+.|.|..+..+..
T Consensus       665 ~~Le~L~~ls~~~~s~------------~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~~~l~~L~~L~i~~~~~~e~  732 (889)
T KOG4658|consen  665 ENLEHLENLSITISSV------------LLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSLGSLGNLEELSILDCGISEI  732 (889)
T ss_pred             hcccchhhheeecchh------------HhHhhhhhhHHHHHHhHhhhhcccccceeecccccccCcceEEEEcCCCchh
Confidence            4444443322221110            1233344444444    3333333333333334 788888888886554211


Q ss_pred             CCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCc
Q 003090          467 PLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEM  546 (848)
Q Consensus       467 ~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l  546 (848)
                      .........                     . .    ..++++..+.+.+|.........   ...|+|+.|.+..|..+
T Consensus       733 ~~~~~~~~~---------------------~-~----~~f~~l~~~~~~~~~~~r~l~~~---~f~~~L~~l~l~~~~~~  783 (889)
T KOG4658|consen  733 VIEWEESLI---------------------V-L----LCFPNLSKVSILNCHMLRDLTWL---LFAPHLTSLSLVSCRLL  783 (889)
T ss_pred             hcccccccc---------------------h-h----hhHHHHHHHHhhccccccccchh---hccCcccEEEEeccccc
Confidence            110000000                     0 0    01455555556666555443222   23488999999998887


Q ss_pred             eeeccccccc-----ccccCCCccEE-ecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEE
Q 003090          547 KYLLNSLERT-----LRVTLHKLEWL-FIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRL  620 (848)
Q Consensus       547 ~~l~~~~~~~-----~~~~~p~L~~L-~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L  620 (848)
                      +.+.......     ....|++++.+ .+.+.+.+.++....++   +++|..+.+..||++         ..+|.+..+
T Consensus       784 e~~i~~~k~~~~l~~~i~~f~~~~~l~~~~~l~~l~~i~~~~l~---~~~l~~~~ve~~p~l---------~~~P~~~~~  851 (889)
T KOG4658|consen  784 EDIIPKLKALLELKELILPFNKLEGLRMLCSLGGLPQLYWLPLS---FLKLEELIVEECPKL---------GKLPLLSTL  851 (889)
T ss_pred             ccCCCHHHHhhhcccEEecccccccceeeecCCCCceeEecccC---ccchhheehhcCccc---------ccCcccccc
Confidence            7653221111     12345666666 46666655555443333   555778888888777         555667777


Q ss_pred             EEecc-CCceeee
Q 003090          621 RVYSC-GLLVSVF  632 (848)
Q Consensus       621 ~l~~c-~~l~~~~  632 (848)
                      .+.+| ..+...|
T Consensus       852 ~i~~~~~~~~~~~  864 (889)
T KOG4658|consen  852 TIVGCEEKLKEYP  864 (889)
T ss_pred             ceeccccceeecC
Confidence            77776 5555544

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

Probab=99.18  E-value=1.3e-12  Score=130.54  Aligned_cols=137  Identities=24%  Similarity=0.318  Sum_probs=96.0

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      .+.+|+.++....  ..+.|..|.|+.+|+..  .+++||.|+|+.|.+..|.+..|++++.|-.|-+.++         
T Consensus        57 GL~eVP~~LP~~t--veirLdqN~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~---------  125 (498)
T KOG4237|consen   57 GLTEVPANLPPET--VEIRLDQNQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGN---------  125 (498)
T ss_pred             CcccCcccCCCcc--eEEEeccCCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcC---------
Confidence            3444444444333  45778888888888876  7888888888888888888888888888777766653         


Q ss_pred             CCCCCCCCCCCCCCCCc-hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEecc
Q 003090          299 PFLFPPLPSSPLFLLPS-SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLT  375 (848)
Q Consensus       299 ~~~~~~l~~~~~~~lp~-~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~  375 (848)
                          |.|+.     +|. .|+.|..|+.|.+.-|.+.-.. ..+..+++|..|.+..|.+..++. .+..+..++++.+.
T Consensus       126 ----NkI~~-----l~k~~F~gL~slqrLllNan~i~Cir~~al~dL~~l~lLslyDn~~q~i~~~tf~~l~~i~tlhlA  196 (498)
T KOG4237|consen  126 ----NKITD-----LPKGAFGGLSSLQRLLLNANHINCIRQDALRDLPSLSLLSLYDNKIQSICKGTFQGLAAIKTLHLA  196 (498)
T ss_pred             ----Cchhh-----hhhhHhhhHHHHHHHhcChhhhcchhHHHHHHhhhcchhcccchhhhhhccccccchhccchHhhh
Confidence                66666     553 4677777777777777666555 667777777777777777776665 56666666666655


Q ss_pred             CC
Q 003090          376 GC  377 (848)
Q Consensus       376 ~~  377 (848)
                      .|
T Consensus       197 ~n  198 (498)
T KOG4237|consen  197 QN  198 (498)
T ss_pred             cC
Confidence            43

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

Probab=99.16  E-value=6.1e-11  Score=126.67  Aligned_cols=89  Identities=21%  Similarity=0.227  Sum_probs=39.2

Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccC---CCEEEccCCCCc-----ccChhhccC-CcccEEeccCCccccc---
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSG---LEILDLSESDVS-----EIPVSFGRL-SHLRLLDLTGCYILEL---  382 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~---L~~L~l~~~~l~-----~lp~~i~~L-~~L~~L~l~~~~~~~~---  382 (848)
                      .+..+++|++|++++|.+.... ..+..+.+   |++|++++|.+.     .+...+..+ ++|+.|++++|.....   
T Consensus        76 ~l~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~  155 (319)
T cd00116          76 GLTKGCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCE  155 (319)
T ss_pred             HHHhcCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHH
Confidence            3444445555555555443222 22322222   555555555444     122233444 5555555555544311   


Q ss_pred             -cChhhhhccccccEEeccccccc
Q 003090          383 -IPRGVLSRLRKLEELYMSHSFRH  405 (848)
Q Consensus       383 -~p~~~l~~l~~L~~L~l~~~~~~  405 (848)
                       ++.. +..+++|++|++++|.+.
T Consensus       156 ~~~~~-~~~~~~L~~L~l~~n~l~  178 (319)
T cd00116         156 ALAKA-LRANRDLKELNLANNGIG  178 (319)
T ss_pred             HHHHH-HHhCCCcCEEECcCCCCc
Confidence             1222 344445555555555443

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).

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

Probab=99.14  E-value=1.2e-12  Score=131.93  Aligned_cols=268  Identities=16%  Similarity=0.150  Sum_probs=172.0

Q ss_pred             HHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccccccccccccc
Q 003090          502 IKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHG  581 (848)
Q Consensus       502 ~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~  581 (848)
                      +....++|++|.+..|..+++..-......+++|++|++++|+.++.-  + --....+...|+++.+.+|..++.=...
T Consensus       185 la~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~kL~~lNlSwc~qi~~~--g-v~~~~rG~~~l~~~~~kGC~e~~le~l~  261 (483)
T KOG4341|consen  185 LARYCRKLRHLNLHSCSSITDVSLKYLAEGCRKLKYLNLSWCPQISGN--G-VQALQRGCKELEKLSLKGCLELELEALL  261 (483)
T ss_pred             HHHhcchhhhhhhcccchhHHHHHHHHHHhhhhHHHhhhccCchhhcC--c-chHHhccchhhhhhhhcccccccHHHHH
Confidence            344467788888888877776544433457888888888888877641  0 0113345566777777777655421111


Q ss_pred             ccccccCCCcceEEEecCchhhHhhh-HHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcc
Q 003090          582 QLPAGCLSNVKRSDVVDCGSILKILL-SHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPR  660 (848)
Q Consensus       582 ~~~~~~l~~L~~L~l~~c~~l~~~l~-~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~  660 (848)
                       .-.+..+-+.++++..|..+ ++.. ..+...+..|+.|..++|.++...+-.       .-..+.++|+.|.+.+|..
T Consensus       262 -~~~~~~~~i~~lnl~~c~~l-TD~~~~~i~~~c~~lq~l~~s~~t~~~d~~l~-------aLg~~~~~L~~l~l~~c~~  332 (483)
T KOG4341|consen  262 -KAAAYCLEILKLNLQHCNQL-TDEDLWLIACGCHALQVLCYSSCTDITDEVLW-------ALGQHCHNLQVLELSGCQQ  332 (483)
T ss_pred             -HHhccChHhhccchhhhccc-cchHHHHHhhhhhHhhhhcccCCCCCchHHHH-------HHhcCCCceEEEeccccch
Confidence             11224666777777788777 4433 223456788888888888876654321       1123558888888888887


Q ss_pred             ccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEec
Q 003090          661 MTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRG  740 (848)
Q Consensus       661 L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~  740 (848)
                      +........ -.+++.|+.+++.+|...++.                              .+...-.+++.|+.|.+++
T Consensus       333 fsd~~ft~l-~rn~~~Le~l~~e~~~~~~d~------------------------------tL~sls~~C~~lr~lslsh  381 (483)
T KOG4341|consen  333 FSDRGFTML-GRNCPHLERLDLEECGLITDG------------------------------TLASLSRNCPRLRVLSLSH  381 (483)
T ss_pred             hhhhhhhhh-hcCChhhhhhcccccceehhh------------------------------hHhhhccCCchhccCChhh
Confidence            766533321 156788888888888665542                              0112235789999999999


Q ss_pred             CCCCceecc---cchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccccccccccccccc--CCCc
Q 003090          741 CGKLRNLFT---TSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFC--STAH  815 (848)
Q Consensus       741 C~~L~~l~~---~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~~~--~~~~  815 (848)
                      |..+++...   .+...++..|+.|++.+||.+.+-        .+.++    ...++|+++++.+|...++-.  .-..
T Consensus       382 ce~itD~gi~~l~~~~c~~~~l~~lEL~n~p~i~d~--------~Le~l----~~c~~Leri~l~~~q~vtk~~i~~~~~  449 (483)
T KOG4341|consen  382 CELITDEGIRHLSSSSCSLEGLEVLELDNCPLITDA--------TLEHL----SICRNLERIELIDCQDVTKEAISRFAT  449 (483)
T ss_pred             hhhhhhhhhhhhhhccccccccceeeecCCCCchHH--------HHHHH----hhCcccceeeeechhhhhhhhhHHHHh
Confidence            998877521   123455677999999999988553        22221    126899999999999887732  3345


Q ss_pred             ccccccccc
Q 003090          816 HFNFVFHLG  824 (848)
Q Consensus       816 ~~~~~~i~~  824 (848)
                      |.|.+++..
T Consensus       450 ~lp~i~v~a  458 (483)
T KOG4341|consen  450 HLPNIKVHA  458 (483)
T ss_pred             hCccceehh
Confidence            666666554

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

Probab=99.07  E-value=1.2e-11  Score=129.41  Aligned_cols=175  Identities=26%  Similarity=0.365  Sum_probs=138.9

Q ss_pred             CceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ...+++.|++..+|... .+..|..+.+..|.+..+|..+ .++..|.+++|+.              |+++.     +|
T Consensus        78 ~~aDlsrNR~~elp~~~~~f~~Le~liLy~n~~r~ip~~i-~~L~~lt~l~ls~--------------NqlS~-----lp  137 (722)
T KOG0532|consen   78 VFADLSRNRFSELPEEACAFVSLESLILYHNCIRTIPEAI-CNLEALTFLDLSS--------------NQLSH-----LP  137 (722)
T ss_pred             hhhhccccccccCchHHHHHHHHHHHHHHhccceecchhh-hhhhHHHHhhhcc--------------chhhc-----CC
Confidence            34678888888888877 7777888888888888888775 5788888888888              77777     88


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..++.|+ |+.|-+++|++...+..|+.+..|..||.+.|.+..+|..++.+.+|+.|+++.|.. ..+|++ +..| .|
T Consensus       138 ~~lC~lp-Lkvli~sNNkl~~lp~~ig~~~tl~~ld~s~nei~slpsql~~l~slr~l~vrRn~l-~~lp~E-l~~L-pL  213 (722)
T KOG0532|consen  138 DGLCDLP-LKVLIVSNNKLTSLPEEIGLLPTLAHLDVSKNEIQSLPSQLGYLTSLRDLNVRRNHL-EDLPEE-LCSL-PL  213 (722)
T ss_pred             hhhhcCc-ceeEEEecCccccCCcccccchhHHHhhhhhhhhhhchHHhhhHHHHHHHHHhhhhh-hhCCHH-HhCC-ce
Confidence            8887777 888888888888788888888888888888888888888888888888888888644 557777 5644 47


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM  448 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~  448 (848)
                      ..||++.|++..              +|..+.+|++|++|-|.+|.+..-|..+
T Consensus       214 i~lDfScNkis~--------------iPv~fr~m~~Lq~l~LenNPLqSPPAqI  253 (722)
T KOG0532|consen  214 IRLDFSCNKISY--------------LPVDFRKMRHLQVLQLENNPLQSPPAQI  253 (722)
T ss_pred             eeeecccCceee--------------cchhhhhhhhheeeeeccCCCCCChHHH
Confidence            788888887764              5777888888888888888888777766

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

Probab=99.05  E-value=1.4e-11  Score=128.87  Aligned_cols=160  Identities=24%  Similarity=0.362  Sum_probs=103.7

Q ss_pred             hHHHHHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCC
Q 003090          223 TKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFL  301 (848)
Q Consensus       223 ~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~  301 (848)
                      ..++.++-....+..+.+..|.+..+|..+ .+..|.+|+++.|.+..+|..++  .--|++|-+++             
T Consensus        88 ~elp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC--~lpLkvli~sN-------------  152 (722)
T KOG0532|consen   88 SELPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGLC--DLPLKVLIVSN-------------  152 (722)
T ss_pred             ccCchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhhh--cCcceeEEEec-------------
Confidence            344455555555566666667666666666 66667777777776666666653  22366676666             


Q ss_pred             CCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcccc
Q 003090          302 FPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE  381 (848)
Q Consensus       302 ~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~  381 (848)
                       |++..     +|..++.+.+|..|+.+.|.+...++.++.+..|+.|++..|++..+|..+..| .|..||++.|+ +.
T Consensus       153 -Nkl~~-----lp~~ig~~~tl~~ld~s~nei~slpsql~~l~slr~l~vrRn~l~~lp~El~~L-pLi~lDfScNk-is  224 (722)
T KOG0532|consen  153 -NKLTS-----LPEEIGLLPTLAHLDVSKNEIQSLPSQLGYLTSLRDLNVRRNHLEDLPEELCSL-PLIRLDFSCNK-IS  224 (722)
T ss_pred             -Ccccc-----CCcccccchhHHHhhhhhhhhhhchHHhhhHHHHHHHHHhhhhhhhCCHHHhCC-ceeeeecccCc-ee
Confidence             66666     666677666677777777766666666777777777777777777777666643 36667776643 34


Q ss_pred             ccChhhhhccccccEEecccccccc
Q 003090          382 LIPRGVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       382 ~~p~~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      .+|.. |.+|+.|++|-|.+|.+..
T Consensus       225 ~iPv~-fr~m~~Lq~l~LenNPLqS  248 (722)
T KOG0532|consen  225 YLPVD-FRKMRHLQVLQLENNPLQS  248 (722)
T ss_pred             ecchh-hhhhhhheeeeeccCCCCC
Confidence            56666 6777777777776666654

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

Probab=99.02  E-value=4.1e-12  Score=128.17  Aligned_cols=251  Identities=15%  Similarity=0.157  Sum_probs=133.2

Q ss_pred             hcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccccccccccccccccccc
Q 003090          508 RSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGC  587 (848)
Q Consensus       508 ~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~  587 (848)
                      .|+.|.+.+|..+..-........+|+++.|.+.+|.++++   .........+++|+.|.+..|.++++.....+.. .
T Consensus       139 ~lk~LSlrG~r~v~~sslrt~~~~CpnIehL~l~gc~~iTd---~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~-g  214 (483)
T KOG4341|consen  139 FLKELSLRGCRAVGDSSLRTFASNCPNIEHLALYGCKKITD---SSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAE-G  214 (483)
T ss_pred             ccccccccccccCCcchhhHHhhhCCchhhhhhhcceeccH---HHHHHHHHhcchhhhhhhcccchhHHHHHHHHHH-h
Confidence            35555555555544433333334456666666666654432   1112233345666666666665555432111111 3


Q ss_pred             CCCcceEEEecCchhhHh-hhHHHHHhhccCcEEEEeccCCc--------------------------eeeeeccccccc
Q 003090          588 LSNVKRSDVVDCGSILKI-LLSHLVQSFQNLQRLRVYSCGLL--------------------------VSVFEIERVNIA  640 (848)
Q Consensus       588 l~~L~~L~l~~c~~l~~~-l~~~~~~~l~~L~~L~l~~c~~l--------------------------~~~~~~~~~~~~  640 (848)
                      +|+|++|++++|+.+ .. --......+..++.+...+|..+                          ++....      
T Consensus       215 C~kL~~lNlSwc~qi-~~~gv~~~~rG~~~l~~~~~kGC~e~~le~l~~~~~~~~~i~~lnl~~c~~lTD~~~~------  287 (483)
T KOG4341|consen  215 CRKLKYLNLSWCPQI-SGNGVQALQRGCKELEKLSLKGCLELELEALLKAAAYCLEILKLNLQHCNQLTDEDLW------  287 (483)
T ss_pred             hhhHHHhhhccCchh-hcCcchHHhccchhhhhhhhcccccccHHHHHHHhccChHhhccchhhhccccchHHH------
Confidence            566666666666555 22 11111233444555544455433                          322100      


Q ss_pred             cccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeec
Q 003090          641 KEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT  720 (848)
Q Consensus       641 ~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c  720 (848)
                       ..-..+..|+.|..++|..+....-... ..++++|+.|.+.+|..+++.                             
T Consensus       288 -~i~~~c~~lq~l~~s~~t~~~d~~l~aL-g~~~~~L~~l~l~~c~~fsd~-----------------------------  336 (483)
T KOG4341|consen  288 -LIACGCHALQVLCYSSCTDITDEVLWAL-GQHCHNLQVLELSGCQQFSDR-----------------------------  336 (483)
T ss_pred             -HHhhhhhHhhhhcccCCCCCchHHHHHH-hcCCCceEEEeccccchhhhh-----------------------------
Confidence             0111234555555555555443221111 134556666666666555442                             


Q ss_pred             CCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceecccccccc
Q 003090          721 TSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIK  800 (848)
Q Consensus       721 ~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~  800 (848)
                       .+.....+.+.|+.+++.+|..+.+-.-.....+++.|++|.++.|..+.+-        ++.++.........|+.+.
T Consensus       337 -~ft~l~rn~~~Le~l~~e~~~~~~d~tL~sls~~C~~lr~lslshce~itD~--------gi~~l~~~~c~~~~l~~lE  407 (483)
T KOG4341|consen  337 -GFTMLGRNCPHLERLDLEECGLITDGTLASLSRNCPRLRVLSLSHCELITDE--------GIRHLSSSSCSLEGLEVLE  407 (483)
T ss_pred             -hhhhhhcCChhhhhhcccccceehhhhHhhhccCCchhccCChhhhhhhhhh--------hhhhhhhccccccccceee
Confidence             1112235778899999999987765533345678899999999999877543        4444444444467899999


Q ss_pred             ccccccccc
Q 003090          801 LCDLDSLAC  809 (848)
Q Consensus       801 i~~cp~L~~  809 (848)
                      +.+||.+++
T Consensus       408 L~n~p~i~d  416 (483)
T KOG4341|consen  408 LDNCPLITD  416 (483)
T ss_pred             ecCCCCchH
Confidence            999998887

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

Probab=98.96  E-value=4.4e-10  Score=120.04  Aligned_cols=15  Identities=27%  Similarity=0.441  Sum_probs=6.7

Q ss_pred             hccCCcccEEeccCC
Q 003090          363 FGRLSHLRLLDLTGC  377 (848)
Q Consensus       363 i~~L~~L~~L~l~~~  377 (848)
                      +..+++|++|++++|
T Consensus       217 ~~~~~~L~~L~ls~n  231 (319)
T cd00116         217 LASLKSLEVLNLGDN  231 (319)
T ss_pred             hcccCCCCEEecCCC
Confidence            333444444444444

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).

>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=98.90  E-value=2.9e-09  Score=111.56  Aligned_cols=75  Identities=29%  Similarity=0.524  Sum_probs=67.6

Q ss_pred             hhHHHHHHHHHHhc--CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHhccCCC
Q 003090          162 RESTMKDIMEAMKD--ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLT  236 (848)
Q Consensus       162 ~~~~~~~i~~~L~~--~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~~~l~  236 (848)
                      ||.++++|.++|.+  .+..+|+|+||||+||||||+.++++..++.+|+.++|+.++...+...+...|...+...
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~   77 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEP   77 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccccccccccccccccccccccccccccccccccccc
Confidence            68899999999997  8899999999999999999999999888899999999999999999999999998877654

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.

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

Probab=98.86  E-value=3.3e-09  Score=99.04  Aligned_cols=137  Identities=28%  Similarity=0.319  Sum_probs=33.3

Q ss_pred             ecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhc
Q 003090          241 MFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFL  320 (848)
Q Consensus       241 ~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l  320 (848)
                      ..+.+...|...+..++++|+|.+|.+..+.. +-..+.+|++|++++              |.++.     ++ .+..+
T Consensus         5 t~~~i~~~~~~~n~~~~~~L~L~~n~I~~Ie~-L~~~l~~L~~L~Ls~--------------N~I~~-----l~-~l~~L   63 (175)
T PF14580_consen    5 TANMIEQIAQYNNPVKLRELNLRGNQISTIEN-LGATLDKLEVLDLSN--------------NQITK-----LE-GLPGL   63 (175)
T ss_dssp             -------------------------------S---TT-TT--EEE-TT--------------S--S-------T-T----
T ss_pred             cccccccccccccccccccccccccccccccc-hhhhhcCCCEEECCC--------------CCCcc-----cc-CccCh
Confidence            34445555555555566666666666655543 112455666666666              55555     32 35556


Q ss_pred             ccCcEEEccCccccCCchhh-ccccCCCEEEccCCCCcccC--hhhccCCcccEEeccCCccccc--cChhhhhcccccc
Q 003090          321 INLRTLRLHDRRIQGDLSLI-GELSGLEILDLSESDVSEIP--VSFGRLSHLRLLDLTGCYILEL--IPRGVLSRLRKLE  395 (848)
Q Consensus       321 ~~L~~L~L~~~~~~~~~~~i-~~l~~L~~L~l~~~~l~~lp--~~i~~L~~L~~L~l~~~~~~~~--~p~~~l~~l~~L~  395 (848)
                      ++|++|++++|++....+.+ ..+++|++|++++|+|..+.  ..+..+++|++|++.+|.....  .-..++..+++|+
T Consensus        64 ~~L~~L~L~~N~I~~i~~~l~~~lp~L~~L~L~~N~I~~l~~l~~L~~l~~L~~L~L~~NPv~~~~~YR~~vi~~lP~Lk  143 (175)
T PF14580_consen   64 PRLKTLDLSNNRISSISEGLDKNLPNLQELYLSNNKISDLNELEPLSSLPKLRVLSLEGNPVCEKKNYRLFVIYKLPSLK  143 (175)
T ss_dssp             TT--EEE--SS---S-CHHHHHH-TT--EEE-TTS---SCCCCGGGGG-TT--EEE-TT-GGGGSTTHHHHHHHH-TT-S
T ss_pred             hhhhhcccCCCCCCccccchHHhCCcCCEEECcCCcCCChHHhHHHHcCCCcceeeccCCcccchhhHHHHHHHHcChhh
Confidence            66666666666555443333 24566666666666555332  2344555555555555543321  1112244555555


Q ss_pred             EEe
Q 003090          396 ELY  398 (848)
Q Consensus       396 ~L~  398 (848)
                      .||
T Consensus       144 ~LD  146 (175)
T PF14580_consen  144 VLD  146 (175)
T ss_dssp             EET
T ss_pred             eeC
Confidence            554

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

Probab=98.81  E-value=6.2e-09  Score=97.17  Aligned_cols=123  Identities=27%  Similarity=0.347  Sum_probs=58.0

Q ss_pred             cCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      ..++.|+|++|.|+.+...- .+.+|+.|++++|.+..++.  +..+++|+.|++++              |.++.    
T Consensus        19 ~~~~~L~L~~n~I~~Ie~L~~~l~~L~~L~Ls~N~I~~l~~--l~~L~~L~~L~L~~--------------N~I~~----   78 (175)
T PF14580_consen   19 VKLRELNLRGNQISTIENLGATLDKLEVLDLSNNQITKLEG--LPGLPRLKTLDLSN--------------NRISS----   78 (175)
T ss_dssp             -----------------S--TT-TT--EEE-TTS--S--TT------TT--EEE--S--------------S---S----
T ss_pred             cccccccccccccccccchhhhhcCCCEEECCCCCCccccC--ccChhhhhhcccCC--------------CCCCc----
Confidence            34688999999999886544 57899999999999999875  67899999999999              88988    


Q ss_pred             CCCchh-hhcccCcEEEccCccccCC--chhhccccCCCEEEccCCCCcccCh----hhccCCcccEEeccC
Q 003090          312 LLPSSL-SFLINLRTLRLHDRRIQGD--LSLIGELSGLEILDLSESDVSEIPV----SFGRLSHLRLLDLTG  376 (848)
Q Consensus       312 ~lp~~~-~~l~~L~~L~L~~~~~~~~--~~~i~~l~~L~~L~l~~~~l~~lp~----~i~~L~~L~~L~l~~  376 (848)
                       ++..+ ..+++|+.|++++|++...  ...+..+++|++|++.+|.+...+.    .+..+++|+.||-..
T Consensus        79 -i~~~l~~~lp~L~~L~L~~N~I~~l~~l~~L~~l~~L~~L~L~~NPv~~~~~YR~~vi~~lP~Lk~LD~~~  149 (175)
T PF14580_consen   79 -ISEGLDKNLPNLQELYLSNNKISDLNELEPLSSLPKLRVLSLEGNPVCEKKNYRLFVIYKLPSLKVLDGQD  149 (175)
T ss_dssp             --CHHHHHH-TT--EEE-TTS---SCCCCGGGGG-TT--EEE-TT-GGGGSTTHHHHHHHH-TT-SEETTEE
T ss_pred             -cccchHHhCCcCCEEECcCCcCCChHHhHHHHcCCCcceeeccCCcccchhhHHHHHHHHcChhheeCCEE
Confidence             76655 4699999999999987654  3788899999999999999886553    478899999998654

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

Probab=98.74  E-value=1.3e-08  Score=101.15  Aligned_cols=257  Identities=19%  Similarity=0.196  Sum_probs=170.1

Q ss_pred             hhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHH-------HHHHhccC
Q 003090          162 RESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQ-------YEIAGWLD  234 (848)
Q Consensus       162 ~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~-------~~i~~~~~  234 (848)
                      -+++.+.+.+.+...+ ++..|.=-|..==|.-|+.+.+...-.+.+..+-|...--.-....++       +.+..+-.
T Consensus        15 t~ed~~~v~~~~~~~~-s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~   93 (382)
T KOG1909|consen   15 TEEDEKDVEEELEPMD-SLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPK   93 (382)
T ss_pred             hHhhhhhHHHHhcccC-ceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCc
Confidence            3455566666665444 334443333222255677777766655666666665433322333333       34444446


Q ss_pred             CCceeeecCCCc--cc---CCcc-cccccceeecccCcCcccChHH-------------HccCCceeEEEccCccccccc
Q 003090          235 LTGISLMFNDIH--EV---PDEL-ECPKLQALFLQENSPLAIPDRF-------------FQGMKDLQVLDLGGIRRFSFS  295 (848)
Q Consensus       235 l~~l~l~~n~l~--~l---p~~~-~~~~L~~L~l~~~~~~~~~~~~-------------~~~~~~Lr~L~l~~~~~~~~~  295 (848)
                      ++.++||+|-|.  .+   ...+ ++..|++|.|++|-++......             ...-+.||++...+       
T Consensus        94 L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~N~Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~r-------  166 (382)
T KOG1909|consen   94 LQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLNNCGLGPEAGGRLGRALFELAVNKKAASKPKLRVFICGR-------  166 (382)
T ss_pred             eeEeeccccccCccchHHHHHHHHhccCHHHHhhhcCCCChhHHHHHHHHHHHHHHHhccCCCcceEEEEeec-------
Confidence            889999999887  22   2223 7899999999999776543322             23456799999999       


Q ss_pred             ccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-----hhhccccCCCEEEccCCCCc-----ccChhhcc
Q 003090          296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-----SLIGELSGLEILDLSESDVS-----EIPVSFGR  365 (848)
Q Consensus       296 ~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~  365 (848)
                             |.+.......+...+...+.|+.+.+..|.+...-     ..+..+++|++||+..|.++     .+...+..
T Consensus       167 -------Nrlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~LakaL~s  239 (382)
T KOG1909|consen  167 -------NRLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALAKALSS  239 (382)
T ss_pred             -------cccccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHHHHhcc
Confidence                   66655322224456778889999999999765431     67889999999999999776     44556777


Q ss_pred             CCcccEEeccCCccccc----cChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCC
Q 003090          366 LSHLRLLDLTGCYILEL----IPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       366 L~~L~~L~l~~~~~~~~----~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~  441 (848)
                      +++|+.|++++|.....    +-..+-...++|+.|.+.+|.++..         ...+....+...+.|+.|++++|.+
T Consensus       240 ~~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNeIt~d---------a~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  240 WPHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNEITRD---------AALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             cchheeecccccccccccHHHHHHHHhccCCCCceeccCcchhHHH---------HHHHHHHHHhcchhhHHhcCCcccc
Confidence            88999999999865432    2222234578999999999988653         2233455666789999999999987


Q ss_pred             C
Q 003090          442 K  442 (848)
Q Consensus       442 ~  442 (848)
                      .
T Consensus       311 ~  311 (382)
T KOG1909|consen  311 G  311 (382)
T ss_pred             c
Confidence            4

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

Probab=98.70  E-value=2.5e-09  Score=103.31  Aligned_cols=134  Identities=25%  Similarity=0.281  Sum_probs=101.6

Q ss_pred             CCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCc
Q 003090          278 MKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS  357 (848)
Q Consensus       278 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~  357 (848)
                      -+.|..+||++              |.++.     +..++.-++.+|.|++++|++.. ...+..+++|+.||+++|.++
T Consensus       283 Wq~LtelDLS~--------------N~I~~-----iDESvKL~Pkir~L~lS~N~i~~-v~nLa~L~~L~~LDLS~N~Ls  342 (490)
T KOG1259|consen  283 WQELTELDLSG--------------NLITQ-----IDESVKLAPKLRRLILSQNRIRT-VQNLAELPQLQLLDLSGNLLA  342 (490)
T ss_pred             Hhhhhhccccc--------------cchhh-----hhhhhhhccceeEEeccccceee-ehhhhhcccceEeecccchhH
Confidence            45677888888              77777     77778888888888888885543 344888888888888888888


Q ss_pred             ccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEee
Q 003090          358 EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH  437 (848)
Q Consensus       358 ~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~  437 (848)
                      ++-..-.+|-+.++|.+++|. ...+..  +++|.+|..|++++|++...            .....+++++.|++|.+.
T Consensus       343 ~~~Gwh~KLGNIKtL~La~N~-iE~LSG--L~KLYSLvnLDl~~N~Ie~l------------deV~~IG~LPCLE~l~L~  407 (490)
T KOG1259|consen  343 ECVGWHLKLGNIKTLKLAQNK-IETLSG--LRKLYSLVNLDLSSNQIEEL------------DEVNHIGNLPCLETLRLT  407 (490)
T ss_pred             hhhhhHhhhcCEeeeehhhhh-Hhhhhh--hHhhhhheeccccccchhhH------------HHhcccccccHHHHHhhc
Confidence            776666678888888888864 344543  78888888888888887654            234668888888888888


Q ss_pred             ccCCCCCCC
Q 003090          438 IPEGKIMPS  446 (848)
Q Consensus       438 ~~~~~~~~~  446 (848)
                      +|.+..++.
T Consensus       408 ~NPl~~~vd  416 (490)
T KOG1259|consen  408 GNPLAGSVD  416 (490)
T ss_pred             CCCccccch
Confidence            887765553

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

Probab=98.70  E-value=7.9e-09  Score=105.41  Aligned_cols=207  Identities=18%  Similarity=0.137  Sum_probs=137.7

Q ss_pred             cCCCceeeecCCCcccCC--cc-cccccceeecccCcCcccC--hHHHccCCceeEEEccCcccccccccCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPD--EL-ECPKLQALFLQENSPLAIP--DRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPS  307 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~--~~-~~~~L~~L~l~~~~~~~~~--~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~  307 (848)
                      ..|+.+.|.+......+.  .. .|++++.|+|+.|.+..+.  ..+...+++|+.|+++.|              .+..
T Consensus       121 kkL~~IsLdn~~V~~~~~~~~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~N--------------rl~~  186 (505)
T KOG3207|consen  121 KKLREISLDNYRVEDAGIEEYSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSN--------------RLSN  186 (505)
T ss_pred             HhhhheeecCccccccchhhhhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccc--------------cccC
Confidence            345677777777776663  23 7899999999999654432  345678999999999994              3332


Q ss_pred             CCCCCCCchhhhcccCcEEEccCccccCCc--hhhccccCCCEEEccCCC-CcccChhhccCCcccEEeccCCccccccC
Q 003090          308 SPLFLLPSSLSFLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESD-VSEIPVSFGRLSHLRLLDLTGCYILELIP  384 (848)
Q Consensus       308 ~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~~-l~~lp~~i~~L~~L~~L~l~~~~~~~~~p  384 (848)
                      ..   -...-..+.+|+.|.+++|.+...-  ...-.+++|+.|++.+|. +..-......+..|+.|+|++|.+...-.
T Consensus       187 ~~---~s~~~~~l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li~~~~  263 (505)
T KOG3207|consen  187 FI---SSNTTLLLSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNNLIDFDQ  263 (505)
T ss_pred             Cc---cccchhhhhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCccccccc
Confidence            10   0011236778999999999777432  455678999999999984 33222334557789999999987654321


Q ss_pred             hhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC--C-ccCCCCeEEEEeC
Q 003090          385 RGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD--M-SFQNLTSFSIAIG  461 (848)
Q Consensus       385 ~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~--~-~~~~L~~L~l~~~  461 (848)
                      -...+.++.|..|+++.+.+...-       .-..........+++|+.|++..|++..++.-  + .+++|+.|.+..+
T Consensus       264 ~~~~~~l~~L~~Lnls~tgi~si~-------~~d~~s~~kt~~f~kL~~L~i~~N~I~~w~sl~~l~~l~nlk~l~~~~n  336 (505)
T KOG3207|consen  264 GYKVGTLPGLNQLNLSSTGIASIA-------EPDVESLDKTHTFPKLEYLNISENNIRDWRSLNHLRTLENLKHLRITLN  336 (505)
T ss_pred             ccccccccchhhhhccccCcchhc-------CCCccchhhhcccccceeeecccCccccccccchhhccchhhhhhcccc
Confidence            112688899999998888765430       01111233356778999999999988655543  2 6677777776654


Q ss_pred             CC
Q 003090          462 DL  463 (848)
Q Consensus       462 ~~  463 (848)
                      +.
T Consensus       337 ~l  338 (505)
T KOG3207|consen  337 YL  338 (505)
T ss_pred             cc
Confidence            44

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

Probab=98.66  E-value=3.9e-09  Score=101.94  Aligned_cols=130  Identities=22%  Similarity=0.202  Sum_probs=66.0

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      ..|.++++++|.+..+.++. .-.+.+|+|++++              |.+..     + .++..+++|..|+|++|...
T Consensus       284 q~LtelDLS~N~I~~iDESv-KL~Pkir~L~lS~--------------N~i~~-----v-~nLa~L~~L~~LDLS~N~Ls  342 (490)
T KOG1259|consen  284 QELTELDLSGNLITQIDESV-KLAPKLRRLILSQ--------------NRIRT-----V-QNLAELPQLQLLDLSGNLLA  342 (490)
T ss_pred             hhhhhccccccchhhhhhhh-hhccceeEEeccc--------------cceee-----e-hhhhhcccceEeecccchhH
Confidence            34555555555555555442 4455555555555              44443     2 23555555555555555444


Q ss_pred             CCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccc
Q 003090          335 GDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       335 ~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      ....+-.++-|.++|.+++|.++.+. ++++|.+|..||+++|++-.--...-|++|+.|+++.+.+|.+..
T Consensus       343 ~~~Gwh~KLGNIKtL~La~N~iE~LS-GL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~NPl~~  413 (490)
T KOG1259|consen  343 ECVGWHLKLGNIKTLKLAQNKIETLS-GLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTGNPLAG  413 (490)
T ss_pred             hhhhhHhhhcCEeeeehhhhhHhhhh-hhHhhhhheeccccccchhhHHHhcccccccHHHHHhhcCCCccc
Confidence            33344445555555555555555543 455555566666555433211111115566666666665555543

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

Probab=98.65  E-value=2.3e-08  Score=109.88  Aligned_cols=150  Identities=32%  Similarity=0.417  Sum_probs=76.7

Q ss_pred             CCCceeeecCCCcccCCccccc--ccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECP--KLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~--~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.+++.+|.+.++|......  +|+.|+++.|.+..+|.. ...+++|+.|++++              +++..    
T Consensus       117 ~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~-~~~l~~L~~L~l~~--------------N~l~~----  177 (394)
T COG4886         117 NLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSP-LRNLPNLKNLDLSF--------------NDLSD----  177 (394)
T ss_pred             ceeEEecCCcccccCccccccchhhcccccccccchhhhhhh-hhccccccccccCC--------------chhhh----
Confidence            3455555555555555555322  555555555555555432 24555555555555              55555    


Q ss_pred             CCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcc
Q 003090          312 LLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       312 ~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                       +|...+.+..|+.|++++|.+...+..++...+|++|.+++|.+...+..+.++.++..+.+.++.. ..++.. ++.+
T Consensus       178 -l~~~~~~~~~L~~L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~n~~-~~~~~~-~~~l  254 (394)
T COG4886         178 -LPKLLSNLSNLNNLDLSGNKISDLPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNKL-EDLPES-IGNL  254 (394)
T ss_pred             -hhhhhhhhhhhhheeccCCccccCchhhhhhhhhhhhhhcCCcceecchhhhhcccccccccCCcee-eeccch-hccc
Confidence             4544445555555555555554444444455555555555554444444555555555555444322 222333 4555


Q ss_pred             ccccEEeccccccc
Q 003090          392 RKLEELYMSHSFRH  405 (848)
Q Consensus       392 ~~L~~L~l~~~~~~  405 (848)
                      ++++.|++++|.+.
T Consensus       255 ~~l~~L~~s~n~i~  268 (394)
T COG4886         255 SNLETLDLSNNQIS  268 (394)
T ss_pred             cccceecccccccc
Confidence            55555555555544

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

Probab=98.64  E-value=3e-08  Score=109.05  Aligned_cols=191  Identities=31%  Similarity=0.376  Sum_probs=158.0

Q ss_pred             ceeeecCCC-cccCCcccccccceeecccCcCcccChHHHccCC-ceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          237 GISLMFNDI-HEVPDELECPKLQALFLQENSPLAIPDRFFQGMK-DLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       237 ~l~l~~n~l-~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~-~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      .+.+..+.+ ..+......+.+..|.+.+|.+..+++.. ..++ +|+.|++++              +.+..     +|
T Consensus        97 ~l~~~~~~~~~~~~~~~~~~~l~~L~l~~n~i~~i~~~~-~~~~~nL~~L~l~~--------------N~i~~-----l~  156 (394)
T COG4886          97 SLDLNLNRLRSNISELLELTNLTSLDLDNNNITDIPPLI-GLLKSNLKELDLSD--------------NKIES-----LP  156 (394)
T ss_pred             eeeccccccccCchhhhcccceeEEecCCcccccCcccc-ccchhhcccccccc--------------cchhh-----hh
Confidence            466777776 34443346688999999999999999864 4553 999999999              88888     88


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..++.+++|+.|++++|.+...+...+.+.+|+.|++++|.+..+|..+..+..|++|.+++|.... .+.. +.++.++
T Consensus       157 ~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~~~~-~~~~-~~~~~~l  234 (394)
T COG4886         157 SPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNNLDLSGNKISDLPPEIELLSALEELDLSNNSIIE-LLSS-LSNLKNL  234 (394)
T ss_pred             hhhhccccccccccCCchhhhhhhhhhhhhhhhheeccCCccccCchhhhhhhhhhhhhhcCCccee-cchh-hhhcccc
Confidence            8899999999999999988888887779999999999999999999988888889999999975444 4444 7899999


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCC
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL  463 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~  463 (848)
                      ..|.+.++.+..              .+..++.+.+|+.|++++|.+..++....+.+++.|++..+..
T Consensus       235 ~~l~l~~n~~~~--------------~~~~~~~l~~l~~L~~s~n~i~~i~~~~~~~~l~~L~~s~n~~  289 (394)
T COG4886         235 SGLELSNNKLED--------------LPESIGNLSNLETLDLSNNQISSISSLGSLTNLRELDLSGNSL  289 (394)
T ss_pred             cccccCCceeee--------------ccchhccccccceeccccccccccccccccCccCEEeccCccc
Confidence            999888777653              2567888899999999999999888844889999999875554

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

Probab=98.47  E-value=4.1e-08  Score=100.32  Aligned_cols=152  Identities=22%  Similarity=0.214  Sum_probs=101.0

Q ss_pred             ccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC--chhhhcccCcEEEccCccccCCc---hhhccccCCCEEE
Q 003090          276 QGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP--SSLSFLINLRTLRLHDRRIQGDL---SLIGELSGLEILD  350 (848)
Q Consensus       276 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp--~~~~~l~~L~~L~L~~~~~~~~~---~~i~~l~~L~~L~  350 (848)
                      +++++||...|.+              ..+..     .+  .....|++++.|+|++|-+....   .....|++|+.|+
T Consensus       118 sn~kkL~~IsLdn--------------~~V~~-----~~~~~~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LN  178 (505)
T KOG3207|consen  118 SNLKKLREISLDN--------------YRVED-----AGIEEYSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLN  178 (505)
T ss_pred             hhHHhhhheeecC--------------ccccc-----cchhhhhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcc
Confidence            5678888888888              44444     33  35678889999999988443322   4567889999999


Q ss_pred             ccCCCCcccChh--hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhccc
Q 003090          351 LSESDVSEIPVS--FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGAL  428 (848)
Q Consensus       351 l~~~~l~~lp~~--i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l  428 (848)
                      ++.|++...-.+  -..+.+|+.|.++.|.+...--......+++|+.|++.+|.....             ....-.-+
T Consensus       179 ls~Nrl~~~~~s~~~~~l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~-------------~~~~~~i~  245 (505)
T KOG3207|consen  179 LSSNRLSNFISSNTTLLLSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILI-------------KATSTKIL  245 (505)
T ss_pred             cccccccCCccccchhhhhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccce-------------ecchhhhh
Confidence            999877633222  235778888889888766433333356788888888888842211             12233445


Q ss_pred             CCCcEEEeeccCCCCCCCCC---ccCCCCeEEEE
Q 003090          429 SRLTSLHIHIPEGKIMPSDM---SFQNLTSFSIA  459 (848)
Q Consensus       429 ~~L~~L~l~~~~~~~~~~~~---~~~~L~~L~l~  459 (848)
                      ..|+.|+|++|.+-.++...   .+++|..|.+.
T Consensus       246 ~~L~~LdLs~N~li~~~~~~~~~~l~~L~~Lnls  279 (505)
T KOG3207|consen  246 QTLQELDLSNNNLIDFDQGYKVGTLPGLNQLNLS  279 (505)
T ss_pred             hHHhhccccCCcccccccccccccccchhhhhcc
Confidence            67888888888876555322   66666666665

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

Probab=98.45  E-value=2e-08  Score=97.17  Aligned_cols=186  Identities=19%  Similarity=0.118  Sum_probs=101.1

Q ss_pred             CCCEEEccCCCCc--ccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccch
Q 003090          345 GLEILDLSESDVS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKF  422 (848)
Q Consensus       345 ~L~~L~l~~~~l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~  422 (848)
                      .||+||++...|+  .+-.-+..+.+|+.|.+.++.....+-.. +.+=.+|+.|+++.+.--.           ..+.-
T Consensus       186 Rlq~lDLS~s~it~stl~~iLs~C~kLk~lSlEg~~LdD~I~~~-iAkN~~L~~lnlsm~sG~t-----------~n~~~  253 (419)
T KOG2120|consen  186 RLQHLDLSNSVITVSTLHGILSQCSKLKNLSLEGLRLDDPIVNT-IAKNSNLVRLNLSMCSGFT-----------ENALQ  253 (419)
T ss_pred             hhHHhhcchhheeHHHHHHHHHHHHhhhhccccccccCcHHHHH-Hhccccceeeccccccccc-----------hhHHH
Confidence            3677777776665  44444555666666666665554444444 5555666666666553111           11223


Q ss_pred             hhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHH
Q 003090          423 IELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWI  502 (848)
Q Consensus       423 ~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~  502 (848)
                      --+..++.|..|+++|+....-                                                    .+...+
T Consensus       254 ll~~scs~L~~LNlsWc~l~~~----------------------------------------------------~Vtv~V  281 (419)
T KOG2120|consen  254 LLLSSCSRLDELNLSWCFLFTE----------------------------------------------------KVTVAV  281 (419)
T ss_pred             HHHHhhhhHhhcCchHhhccch----------------------------------------------------hhhHHH
Confidence            3345555566666665543210                                                    011112


Q ss_pred             HHHHhhcceeeecccccccc--ccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccc
Q 003090          503 KNLLLRSEILALAEVNYFEN--IVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICH  580 (848)
Q Consensus       503 ~~~~~~L~~L~l~~~~~~~~--~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~  580 (848)
                      ....++|+.|+++||...-.  ....+ ...+|+|..|++++|..++.    .-......|+.|++|.++.|..+.-  .
T Consensus       282 ~hise~l~~LNlsG~rrnl~~sh~~tL-~~rcp~l~~LDLSD~v~l~~----~~~~~~~kf~~L~~lSlsRCY~i~p--~  354 (419)
T KOG2120|consen  282 AHISETLTQLNLSGYRRNLQKSHLSTL-VRRCPNLVHLDLSDSVMLKN----DCFQEFFKFNYLQHLSLSRCYDIIP--E  354 (419)
T ss_pred             hhhchhhhhhhhhhhHhhhhhhHHHHH-HHhCCceeeeccccccccCc----hHHHHHHhcchheeeehhhhcCCCh--H
Confidence            22235566666666543211  01111 13678888888888877664    1223455688888888888875421  1


Q ss_pred             cccccccCCCcceEEEecCch
Q 003090          581 GQLPAGCLSNVKRSDVVDCGS  601 (848)
Q Consensus       581 ~~~~~~~l~~L~~L~l~~c~~  601 (848)
                      ..+.....|+|.+|++.+|-.
T Consensus       355 ~~~~l~s~psl~yLdv~g~vs  375 (419)
T KOG2120|consen  355 TLLELNSKPSLVYLDVFGCVS  375 (419)
T ss_pred             HeeeeccCcceEEEEeccccC
Confidence            123345788888888888743

>PLN03150 hypothetical protein; Provisional

Probab=98.36  E-value=1.1e-06  Score=101.21  Aligned_cols=106  Identities=25%  Similarity=0.328  Sum_probs=85.3

Q ss_pred             cCcEEEccCccccCCc-hhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCccccccChhhhhccccccEEec
Q 003090          322 NLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM  399 (848)
Q Consensus       322 ~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l  399 (848)
                      .++.|+|++|.+.+.+ ..++++++|+.|++++|.+. .+|..++.+++|+.|++++|.+.+.+|.. ++++++|+.|++
T Consensus       419 ~v~~L~L~~n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~-l~~L~~L~~L~L  497 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPES-LGQLTSLRILNL  497 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchH-HhcCCCCCEEEC
Confidence            4778888888777654 77888999999999998887 88888889999999999998888888887 788999999999


Q ss_pred             cccccccccccccccccCcccchhhhccc-CCCcEEEeeccCC
Q 003090          400 SHSFRHWQFESESEEDSSSNAKFIELGAL-SRLTSLHIHIPEG  441 (848)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~l-~~L~~L~l~~~~~  441 (848)
                      ++|.+.+.             .+..++.+ .++..+++.+|..
T Consensus       498 s~N~l~g~-------------iP~~l~~~~~~~~~l~~~~N~~  527 (623)
T PLN03150        498 NGNSLSGR-------------VPAALGGRLLHRASFNFTDNAG  527 (623)
T ss_pred             cCCccccc-------------CChHHhhccccCceEEecCCcc
Confidence            98888766             44455543 4677888888764

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

Probab=98.32  E-value=2e-07  Score=92.79  Aligned_cols=114  Identities=18%  Similarity=0.063  Sum_probs=59.9

Q ss_pred             hcccCcEEEccCccccCCc-----hhhccccCCCEEEccCCCCcccC--------------hhhccCCcccEEeccCCcc
Q 003090          319 FLINLRTLRLHDRRIQGDL-----SLIGELSGLEILDLSESDVSEIP--------------VSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L~l~~~~l~~lp--------------~~i~~L~~L~~L~l~~~~~  379 (848)
                      .+++|++|+|+.|-+-..-     .-|..++.|++|.|.+|.+....              .-+..-++||++...+|..
T Consensus        90 ~~~~L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~N~Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~rNrl  169 (382)
T KOG1909|consen   90 GCPKLQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLNNCGLGPEAGGRLGRALFELAVNKKAASKPKLRVFICGRNRL  169 (382)
T ss_pred             cCCceeEeeccccccCccchHHHHHHHHhccCHHHHhhhcCCCChhHHHHHHHHHHHHHHHhccCCCcceEEEEeecccc
Confidence            3445555555555332211     23444555666666555544111              1123345677777666533


Q ss_pred             ccccCh----hhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          380 LELIPR----GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       380 ~~~~p~----~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                       ..-+.    ..+...+.|+++.+..|.+...         ...+....+..+++|+.|+|..|-++
T Consensus       170 -en~ga~~~A~~~~~~~~leevr~~qN~I~~e---------G~~al~eal~~~~~LevLdl~DNtft  226 (382)
T KOG1909|consen  170 -ENGGATALAEAFQSHPTLEEVRLSQNGIRPE---------GVTALAEALEHCPHLEVLDLRDNTFT  226 (382)
T ss_pred             -ccccHHHHHHHHHhccccceEEEecccccCc---------hhHHHHHHHHhCCcceeeecccchhh
Confidence             22221    1145566777777777665432         22345566777778888887777544

>PRK15386 type III secretion protein GogB; Provisional

Probab=98.27  E-value=2.5e-06  Score=89.64  Aligned_cols=166  Identities=16%  Similarity=0.217  Sum_probs=92.1

Q ss_pred             cCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecccccc
Q 003090          560 TLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNI  639 (848)
Q Consensus       560 ~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~  639 (848)
                      .++++++|++++| .++.+     | ...++|++|.+.+|..+ ..+|..+   .++|++|.+++|..+..+|       
T Consensus        50 ~~~~l~~L~Is~c-~L~sL-----P-~LP~sLtsL~Lsnc~nL-tsLP~~L---P~nLe~L~Ls~Cs~L~sLP-------  111 (426)
T PRK15386         50 EARASGRLYIKDC-DIESL-----P-VLPNELTEITIENCNNL-TTLPGSI---PEGLEKLTVCHCPEISGLP-------  111 (426)
T ss_pred             HhcCCCEEEeCCC-CCccc-----C-CCCCCCcEEEccCCCCc-ccCCchh---hhhhhheEccCcccccccc-------
Confidence            3577788888877 56554     2 12235888888888877 7777533   2577777777777666554       


Q ss_pred             ccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeee
Q 003090          640 AKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHA  719 (848)
Q Consensus       640 ~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~  719 (848)
                              ++|+.|++. +..+..+..-      .++|+.|.+.++......                            
T Consensus       112 --------~sLe~L~L~-~n~~~~L~~L------PssLk~L~I~~~n~~~~~----------------------------  148 (426)
T PRK15386        112 --------ESVRSLEIK-GSATDSIKNV------PNGLTSLSINSYNPENQA----------------------------  148 (426)
T ss_pred             --------cccceEEeC-CCCCcccccC------cchHhheecccccccccc----------------------------
Confidence                    246666654 2222222110      135666665432111000                            


Q ss_pred             cCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccc
Q 003090          720 TTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGI  799 (848)
Q Consensus       720 c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L  799 (848)
                        ..+  ...+++|+.|+|.+|..+. +|+ .   -..+|+.|++..+... ++.....   .+         ++++ .|
T Consensus       149 --~lp--~~LPsSLk~L~Is~c~~i~-LP~-~---LP~SLk~L~ls~n~~~-sLeI~~~---sL---------P~nl-~L  205 (426)
T PRK15386        149 --RID--NLISPSLKTLSLTGCSNII-LPE-K---LPESLQSITLHIEQKT-TWNISFE---GF---------PDGL-DI  205 (426)
T ss_pred             --ccc--cccCCcccEEEecCCCccc-Ccc-c---ccccCcEEEecccccc-cccCccc---cc---------cccc-Ee
Confidence              001  1234789999999998764 322 1   1258999998775311 1100111   12         5667 88


Q ss_pred             cccccccccc
Q 003090          800 KLCDLDSLAC  809 (848)
Q Consensus       800 ~i~~cp~L~~  809 (848)
                      .+.+|-++..
T Consensus       206 ~f~n~lkL~~  215 (426)
T PRK15386        206 DLQNSVLLSP  215 (426)
T ss_pred             chhhhcccCH
Confidence            8888865544

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

Probab=98.23  E-value=7.3e-08  Score=93.42  Aligned_cols=16  Identities=19%  Similarity=0.092  Sum_probs=8.9

Q ss_pred             cCCCCCcEEEEecCCC
Q 003090          530 DGFNELMFLVIFRCNE  545 (848)
Q Consensus       530 ~~l~~L~~L~l~~~~~  545 (848)
                      .++..|.+|+|++|..
T Consensus       257 ~scs~L~~LNlsWc~l  272 (419)
T KOG2120|consen  257 SSCSRLDELNLSWCFL  272 (419)
T ss_pred             HhhhhHhhcCchHhhc
Confidence            3455566666666643

>PLN03150 hypothetical protein; Provisional

Probab=98.23  E-value=2.9e-06  Score=97.77  Aligned_cols=104  Identities=24%  Similarity=0.287  Sum_probs=88.9

Q ss_pred             CCCEEEccCCCCc-ccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchh
Q 003090          345 GLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI  423 (848)
Q Consensus       345 ~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~  423 (848)
                      .++.|+|++|.+. .+|..++++++|++|++++|.+.+.+|.. ++.+++|+.|++++|.+.+.             .+.
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~  484 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPS-LGSITSLEVLDLSYNSFNGS-------------IPE  484 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChH-HhCCCCCCEEECCCCCCCCC-------------Cch
Confidence            4789999999998 89999999999999999999998899988 89999999999999998876             677


Q ss_pred             hhcccCCCcEEEeeccCCC-CCCCCC--ccCCCCeEEEEeCC
Q 003090          424 ELGALSRLTSLHIHIPEGK-IMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       424 ~L~~l~~L~~L~l~~~~~~-~~~~~~--~~~~L~~L~l~~~~  462 (848)
                      .++++++|+.|++++|.+. .+|..+  ...++..+.+..+.
T Consensus       485 ~l~~L~~L~~L~Ls~N~l~g~iP~~l~~~~~~~~~l~~~~N~  526 (623)
T PLN03150        485 SLGQLTSLRILNLNGNSLSGRVPAALGGRLLHRASFNFTDNA  526 (623)
T ss_pred             HHhcCCCCCEEECcCCcccccCChHHhhccccCceEEecCCc
Confidence            8999999999999999876 666655  23456666666443

>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=98.13  E-value=1.2e-06  Score=66.92  Aligned_cols=60  Identities=37%  Similarity=0.512  Sum_probs=39.8

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      ++|++|++++|.+..+|+..|.++++|++|++++              +.+...    -|..|..+++|++|++++|+
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~--------------N~l~~i----~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSN--------------NNLTSI----PPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETS--------------SSESEE----ETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccC--------------CccCcc----CHHHHcCCCCCCEEeCcCCc
Confidence            4566777777777777766677777777777776              666552    33456666677777766664

...

>PRK15386 type III secretion protein GogB; Provisional

Probab=98.11  E-value=7e-06  Score=86.32  Aligned_cols=58  Identities=19%  Similarity=0.168  Sum_probs=34.7

Q ss_pred             CCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceecccccccccccc
Q 003090          729 SLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDL  804 (848)
Q Consensus       729 ~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~c  804 (848)
                      .+++|++|.+.++......+..  ..-.++|++|.|.+|..+. +  ++    ++         +.+|+.|.+..+
T Consensus       130 LPssLk~L~I~~~n~~~~~~lp--~~LPsSLk~L~Is~c~~i~-L--P~----~L---------P~SLk~L~ls~n  187 (426)
T PRK15386        130 VPNGLTSLSINSYNPENQARID--NLISPSLKTLSLTGCSNII-L--PE----KL---------PESLQSITLHIE  187 (426)
T ss_pred             CcchHhheeccccccccccccc--cccCCcccEEEecCCCccc-C--cc----cc---------cccCcEEEeccc
Confidence            3456888888654322111100  0112689999999998663 1  21    22         678999998664

>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=98.02  E-value=5.4e-06  Score=63.27  Aligned_cols=58  Identities=40%  Similarity=0.558  Sum_probs=32.8

Q ss_pred             CCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEeccccc
Q 003090          345 GLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       345 ~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~  403 (848)
                      +|++|++++|+++.+|. .+..+++|++|++++|.. ..++++.+.++++|++|++++|.
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l-~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNL-TSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETSSSE-SEEETTTTTTSTTESEEEETSSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCcc-CccCHHHHcCCCCCCEEeCcCCc
Confidence            45566666666665553 345566666666665444 33444445666666666666554

...

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

Probab=97.95  E-value=7e-07  Score=96.92  Aligned_cols=119  Identities=24%  Similarity=0.224  Sum_probs=92.1

Q ss_pred             CCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccc
Q 003090          303 PPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILEL  382 (848)
Q Consensus       303 ~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~  382 (848)
                      |.+..     +..++.-+++|+.|+|++|++... ..+..|++|++|||++|.+..+|.--..-.+|+.|++++|.. ..
T Consensus       174 N~L~~-----mD~SLqll~ale~LnLshNk~~~v-~~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc~L~~L~lrnN~l-~t  246 (1096)
T KOG1859|consen  174 NRLVL-----MDESLQLLPALESLNLSHNKFTKV-DNLRRLPKLKHLDLSYNCLRHVPQLSMVGCKLQLLNLRNNAL-TT  246 (1096)
T ss_pred             hhHHh-----HHHHHHHHHHhhhhccchhhhhhh-HHHHhcccccccccccchhccccccchhhhhheeeeecccHH-Hh
Confidence            55555     667788899999999999966554 488999999999999999998885322223499999999754 44


Q ss_pred             cChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          383 IPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       383 ~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      +- + +.+|.+|+.|++++|.+...            ....-|..|..|+.|.|.+|.+-
T Consensus       247 L~-g-ie~LksL~~LDlsyNll~~h------------seL~pLwsLs~L~~L~LeGNPl~  292 (1096)
T KOG1859|consen  247 LR-G-IENLKSLYGLDLSYNLLSEH------------SELEPLWSLSSLIVLWLEGNPLC  292 (1096)
T ss_pred             hh-h-HHhhhhhhccchhHhhhhcc------------hhhhHHHHHHHHHHHhhcCCccc
Confidence            44 3 78999999999999987653            24556777888999999998765

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.88  E-value=1.4e-06  Score=84.74  Aligned_cols=110  Identities=24%  Similarity=0.283  Sum_probs=76.4

Q ss_pred             cccCcEEEccCccccCC--chhh-ccccCCCEEEccCCCCc---ccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          320 LINLRTLRLHDRRIQGD--LSLI-GELSGLEILDLSESDVS---EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       320 l~~L~~L~L~~~~~~~~--~~~i-~~l~~L~~L~l~~~~l~---~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      +..+..|.+.++.+-..  ...| ...++++.||+.+|.|+   ++...+.+|+.|++|+++.|.....+... -.-+.+
T Consensus        44 ~ra~ellvln~~~id~~gd~~~~~~~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~l-p~p~~n  122 (418)
T KOG2982|consen   44 LRALELLVLNGSIIDNEGDVMLFGSSVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSL-PLPLKN  122 (418)
T ss_pred             ccchhhheecCCCCCcchhHHHHHHHhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCccccC-cccccc
Confidence            33455666777644433  2334 46788999999999887   55566778999999999988665444331 124568


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      |+.|.+.+..+.|.            ..-..+..++.++.|+++.|+..
T Consensus       123 l~~lVLNgT~L~w~------------~~~s~l~~lP~vtelHmS~N~~r  159 (418)
T KOG2982|consen  123 LRVLVLNGTGLSWT------------QSTSSLDDLPKVTELHMSDNSLR  159 (418)
T ss_pred             eEEEEEcCCCCChh------------hhhhhhhcchhhhhhhhccchhh
Confidence            99999999888875            23456778888888888877443

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

Probab=97.87  E-value=2.1e-06  Score=94.48  Aligned_cols=182  Identities=29%  Similarity=0.318  Sum_probs=99.6

Q ss_pred             eeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCch
Q 003090          238 ISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSS  316 (848)
Q Consensus       238 l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~  316 (848)
                      +++..|.+..+-..+ .+.+|..|++..|.+..+... +..+++|++|++++              |.|..     + ..
T Consensus        77 l~l~~n~i~~~~~~l~~~~~l~~l~l~~n~i~~i~~~-l~~~~~L~~L~ls~--------------N~I~~-----i-~~  135 (414)
T KOG0531|consen   77 LNLRQNLIAKILNHLSKLKSLEALDLYDNKIEKIENL-LSSLVNLQVLDLSF--------------NKITK-----L-EG  135 (414)
T ss_pred             hccchhhhhhhhcccccccceeeeeccccchhhcccc-hhhhhcchheeccc--------------ccccc-----c-cc
Confidence            334555555433323 556666666666666655542 24566777777776              56655     2 33


Q ss_pred             hhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhcccccc
Q 003090          317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE  395 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~  395 (848)
                      +..+..|+.|++.+|. ...+..+..+++|+.+++++|.+..+... ...+.+|+.+.+.+|.... +..  +..+..+.
T Consensus       136 l~~l~~L~~L~l~~N~-i~~~~~~~~l~~L~~l~l~~n~i~~ie~~~~~~~~~l~~l~l~~n~i~~-i~~--~~~~~~l~  211 (414)
T KOG0531|consen  136 LSTLTLLKELNLSGNL-ISDISGLESLKSLKLLDLSYNRIVDIENDELSELISLEELDLGGNSIRE-IEG--LDLLKKLV  211 (414)
T ss_pred             hhhccchhhheeccCc-chhccCCccchhhhcccCCcchhhhhhhhhhhhccchHHHhccCCchhc-ccc--hHHHHHHH
Confidence            5566667777777763 33344444567777777777777666543 4666777777777654322 211  23344444


Q ss_pred             EEeccccccccccccccccccCcccchhhhcccCC--CcEEEeeccCCCCCCCCC-ccCCCCeEEEE
Q 003090          396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR--LTSLHIHIPEGKIMPSDM-SFQNLTSFSIA  459 (848)
Q Consensus       396 ~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~--L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~  459 (848)
                      .+++..|.+...               ..+..+..  |+.+++.++.+...+..+ .+.++..|++.
T Consensus       212 ~~~l~~n~i~~~---------------~~l~~~~~~~L~~l~l~~n~i~~~~~~~~~~~~l~~l~~~  263 (414)
T KOG0531|consen  212 LLSLLDNKISKL---------------EGLNELVMLHLRELYLSGNRISRSPEGLENLKNLPVLDLS  263 (414)
T ss_pred             Hhhcccccceec---------------cCcccchhHHHHHHhcccCccccccccccccccccccchh
Confidence            445555544321               22233332  677777777766553333 55555555544

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

Probab=97.80  E-value=2.9e-06  Score=72.95  Aligned_cols=107  Identities=22%  Similarity=0.332  Sum_probs=63.8

Q ss_pred             ceeeecCCCcccCCcc----cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          237 GISLMFNDIHEVPDEL----ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~~----~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      .++|+.+.+-.+++..    ....|...++++|.+.++|+.+-.+++.+..|++.+              |.+..     
T Consensus        31 ~ldLssc~lm~i~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~--------------neisd-----   91 (177)
T KOG4579|consen   31 FLDLSSCQLMYIADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLAN--------------NEISD-----   91 (177)
T ss_pred             hcccccchhhHHHHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcch--------------hhhhh-----
Confidence            3555555544443332    334455556666666666666555566666666666              66666     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChh
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS  362 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~  362 (848)
                      +|..+..++.||.|+++.|.+...+..|..|.+|-+|+..+|.+..+|-.
T Consensus        92 vPeE~Aam~aLr~lNl~~N~l~~~p~vi~~L~~l~~Lds~~na~~eid~d  141 (177)
T KOG4579|consen   92 VPEELAAMPALRSLNLRFNPLNAEPRVIAPLIKLDMLDSPENARAEIDVD  141 (177)
T ss_pred             chHHHhhhHHhhhcccccCccccchHHHHHHHhHHHhcCCCCccccCcHH
Confidence            66666666666666666666666665565566666666666666655543

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

Probab=97.76  E-value=1.2e-06  Score=95.16  Aligned_cols=50  Identities=24%  Similarity=0.308  Sum_probs=25.1

Q ss_pred             ceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccC
Q 003090          237 GISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG  288 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~  288 (848)
                      ..+.++|.+..+...+ -++.++.|+|+.|...++.  .+..+++|+.|||++
T Consensus       168 ~a~fsyN~L~~mD~SLqll~ale~LnLshNk~~~v~--~Lr~l~~LkhLDlsy  218 (1096)
T KOG1859|consen  168 TASFSYNRLVLMDESLQLLPALESLNLSHNKFTKVD--NLRRLPKLKHLDLSY  218 (1096)
T ss_pred             hhhcchhhHHhHHHHHHHHHHhhhhccchhhhhhhH--HHHhccccccccccc
Confidence            3445555555444444 3455555555555544443  234555555555555

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

Probab=97.74  E-value=1.7e-05  Score=91.11  Aligned_cols=155  Identities=22%  Similarity=0.270  Sum_probs=104.3

Q ss_pred             CCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhh-hcccCcEEEccCccccCCc--hhhccccCCCEEEccCC
Q 003090          278 MKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS-FLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSES  354 (848)
Q Consensus       278 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~-~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~  354 (848)
                      -.+|+.|++++.             ..+...    .|..++ .|++|+.|.+.+-.+...-  .-..+++||..||++++
T Consensus       121 r~nL~~LdI~G~-------------~~~s~~----W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~T  183 (699)
T KOG3665|consen  121 RQNLQHLDISGS-------------ELFSNG----WPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGT  183 (699)
T ss_pred             HHhhhhcCcccc-------------chhhcc----HHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCC
Confidence            457888998882             222222    445554 6789999999997665442  45578999999999999


Q ss_pred             CCcccChhhccCCcccEEeccCCcccccc-ChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcE
Q 003090          355 DVSEIPVSFGRLSHLRLLDLTGCYILELI-PRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTS  433 (848)
Q Consensus       355 ~l~~lp~~i~~L~~L~~L~l~~~~~~~~~-p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~  433 (848)
                      +++.+ .++++|++|+.|.+.+-.+...- -.+ +.+|++|+.||++........       .-.....+.-..|++||.
T Consensus       184 nI~nl-~GIS~LknLq~L~mrnLe~e~~~~l~~-LF~L~~L~vLDIS~~~~~~~~-------~ii~qYlec~~~LpeLrf  254 (699)
T KOG3665|consen  184 NISNL-SGISRLKNLQVLSMRNLEFESYQDLID-LFNLKKLRVLDISRDKNNDDT-------KIIEQYLECGMVLPELRF  254 (699)
T ss_pred             CccCc-HHHhccccHHHHhccCCCCCchhhHHH-HhcccCCCeeeccccccccch-------HHHHHHHHhcccCccccE
Confidence            99988 78999999999999874443211 123 789999999999986543320       001112334456889999


Q ss_pred             EEeeccCCCC-CCCCC--ccCCCCeEEE
Q 003090          434 LHIHIPEGKI-MPSDM--SFQNLTSFSI  458 (848)
Q Consensus       434 L~l~~~~~~~-~~~~~--~~~~L~~L~l  458 (848)
                      ||.+++.+.. +...+  ..++|+....
T Consensus       255 LDcSgTdi~~~~le~ll~sH~~L~~i~~  282 (699)
T KOG3665|consen  255 LDCSGTDINEEILEELLNSHPNLQQIAA  282 (699)
T ss_pred             EecCCcchhHHHHHHHHHhCccHhhhhh
Confidence            9999887652 11111  4555655443

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

Probab=97.72  E-value=3.5e-05  Score=88.52  Aligned_cols=144  Identities=22%  Similarity=0.273  Sum_probs=86.2

Q ss_pred             CCchhHHHHHHHhcc---CCCceeeecCCCc--ccCCcc--cccccceeecccCcCcc-cChHHHccCCceeEEEccCcc
Q 003090          219 TPSITKIQYEIAGWL---DLTGISLMFNDIH--EVPDEL--ECPKLQALFLQENSPLA-IPDRFFQGMKDLQVLDLGGIR  290 (848)
Q Consensus       219 ~~~~~~l~~~i~~~~---~l~~l~l~~n~l~--~lp~~~--~~~~L~~L~l~~~~~~~-~~~~~~~~~~~Lr~L~l~~~~  290 (848)
                      .-|+..+.+.++...   .++.|++++...-  .-|..+  .+|.|++|.+++-.... --..++.++++|+.||+++  
T Consensus       105 ~idi~~lL~~~Ln~~sr~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~--  182 (699)
T KOG3665|consen  105 TIDIISLLKDLLNEESRQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISG--  182 (699)
T ss_pred             hccHHHHHHHHHhHHHHHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCC--
Confidence            356677777776544   3667777664322  112222  56788888777653211 1123456788888888888  


Q ss_pred             cccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC--chhhccccCCCEEEccCCCCcccChh------
Q 003090          291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD--LSLIGELSGLEILDLSESDVSEIPVS------  362 (848)
Q Consensus       291 ~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~--~~~i~~l~~L~~L~l~~~~l~~lp~~------  362 (848)
                                  ++++.     + ..+++|++|+.|.+.+-.+...  +..+.+|++|++||+|......-+..      
T Consensus       183 ------------TnI~n-----l-~GIS~LknLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~~~ii~qYle  244 (699)
T KOG3665|consen  183 ------------TNISN-----L-SGISRLKNLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDDTKIIEQYLE  244 (699)
T ss_pred             ------------CCccC-----c-HHHhccccHHHHhccCCCCCchhhHHHHhcccCCCeeeccccccccchHHHHHHHH
Confidence                        66666     4 5677888888887777655542  36677788888888877644433311      


Q ss_pred             -hccCCcccEEeccCCccccc
Q 003090          363 -FGRLSHLRLLDLTGCYILEL  382 (848)
Q Consensus       363 -i~~L~~L~~L~l~~~~~~~~  382 (848)
                       -..|++||.||.++......
T Consensus       245 c~~~LpeLrfLDcSgTdi~~~  265 (699)
T KOG3665|consen  245 CGMVLPELRFLDCSGTDINEE  265 (699)
T ss_pred             hcccCccccEEecCCcchhHH
Confidence             12356666666665443333

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=97.68  E-value=4.5e-06  Score=94.88  Aligned_cols=174  Identities=18%  Similarity=0.173  Sum_probs=96.6

Q ss_pred             HhhcceeeeccccccccccccccccCCCCCcEEEEecC-CCceeecccccccccccCCCccEEecccccccccccccccc
Q 003090          506 LLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRC-NEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLP  584 (848)
Q Consensus       506 ~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~-~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~  584 (848)
                      .+.|+.|.+.++..+.+.........+++|+.|++.+| ...... ..........+++|+.|+++.+..+++.....+.
T Consensus       187 ~~~L~~l~l~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~-~~~~~~~~~~~~~L~~l~l~~~~~isd~~l~~l~  265 (482)
T KOG1947|consen  187 CPLLKRLSLSGCSKITDDSLDALALKCPNLEELDLSGCCLLITLS-PLLLLLLLSICRKLKSLDLSGCGLVTDIGLSALA  265 (482)
T ss_pred             CchhhHhhhcccccCChhhHHHHHhhCchhheecccCcccccccc-hhHhhhhhhhcCCcCccchhhhhccCchhHHHHH
Confidence            57788888888877665221111246688888888874 222211 1011123445688888888888765544221111


Q ss_pred             cccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCC---ccc
Q 003090          585 AGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDL---PRM  661 (848)
Q Consensus       585 ~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c---~~L  661 (848)
                      . .+++|+.|.+.+|..++..--..+...+++|++|++++|..+++-.-.       .....+++|+.|.+..+   +.+
T Consensus       266 ~-~c~~L~~L~l~~c~~lt~~gl~~i~~~~~~L~~L~l~~c~~~~d~~l~-------~~~~~c~~l~~l~~~~~~~c~~l  337 (482)
T KOG1947|consen  266 S-RCPNLETLSLSNCSNLTDEGLVSIAERCPSLRELDLSGCHGLTDSGLE-------ALLKNCPNLRELKLLSLNGCPSL  337 (482)
T ss_pred             h-hCCCcceEccCCCCccchhHHHHHHHhcCcccEEeeecCccchHHHHH-------HHHHhCcchhhhhhhhcCCCccH
Confidence            1 378888888888886523333445577888888888888877332100       11334565555554443   334


Q ss_pred             cccccCCCccccc--cCccEEEeecCccccc
Q 003090          662 TDIWKGDTQFVSL--HNLKKVRVEECDELRQ  690 (848)
Q Consensus       662 ~~l~~~~~~l~~l--~~L~~L~i~~C~~L~~  690 (848)
                      +...-..  ....  ..+..+.+.+|+++++
T Consensus       338 ~~~~l~~--~~~~~~d~~~~~~~~~~~~l~~  366 (482)
T KOG1947|consen  338 TDLSLSG--LLTLTSDDLAELILRSCPKLTD  366 (482)
T ss_pred             HHHHHHH--hhccCchhHhHHHHhcCCCcch
Confidence            4432111  1111  1456666666666655

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

Probab=97.67  E-value=6.3e-06  Score=90.72  Aligned_cols=170  Identities=26%  Similarity=0.268  Sum_probs=114.6

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+..+..+++..|.+..+... +..+++|..|++.+              +.+..     +...+..+.+|++|++++| 
T Consensus        70 ~l~~l~~l~l~~n~i~~~~~~-l~~~~~l~~l~l~~--------------n~i~~-----i~~~l~~~~~L~~L~ls~N-  128 (414)
T KOG0531|consen   70 SLTSLKELNLRQNLIAKILNH-LSKLKSLEALDLYD--------------NKIEK-----IENLLSSLVNLQVLDLSFN-  128 (414)
T ss_pred             HhHhHHhhccchhhhhhhhcc-cccccceeeeeccc--------------cchhh-----cccchhhhhcchheecccc-
Confidence            455666677777777663332 46788899999998              88877     5444778889999999998 


Q ss_pred             ccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccCh-hhhhccccccEEeccccccccccccc
Q 003090          333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHWQFESE  411 (848)
Q Consensus       333 ~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~~~~~~  411 (848)
                      ....+..+..+..|+.|++++|.++.++ .+..+.+|+.+++++|.... +.. . ...+.+++.+++.+|.+..     
T Consensus       129 ~I~~i~~l~~l~~L~~L~l~~N~i~~~~-~~~~l~~L~~l~l~~n~i~~-ie~~~-~~~~~~l~~l~l~~n~i~~-----  200 (414)
T KOG0531|consen  129 KITKLEGLSTLTLLKELNLSGNLISDIS-GLESLKSLKLLDLSYNRIVD-IENDE-LSELISLEELDLGGNSIRE-----  200 (414)
T ss_pred             ccccccchhhccchhhheeccCcchhcc-CCccchhhhcccCCcchhhh-hhhhh-hhhccchHHHhccCCchhc-----
Confidence            4555666777778999999999888775 45668888999998876543 333 2 3678888888888887653     


Q ss_pred             cccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCC--CCeEEEEeC
Q 003090          412 SEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQN--LTSFSIAIG  461 (848)
Q Consensus       412 ~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~--L~~L~l~~~  461 (848)
                                +..+..+..+..+++..|.+..+........  |+.+++..+
T Consensus       201 ----------i~~~~~~~~l~~~~l~~n~i~~~~~l~~~~~~~L~~l~l~~n  242 (414)
T KOG0531|consen  201 ----------IEGLDLLKKLVLLSLLDNKISKLEGLNELVMLHLRELYLSGN  242 (414)
T ss_pred             ----------ccchHHHHHHHHhhcccccceeccCcccchhHHHHHHhcccC
Confidence                      2334444455555666666554332222222  555555533

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.52  E-value=0.00013  Score=76.04  Aligned_cols=51  Identities=16%  Similarity=0.149  Sum_probs=45.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCC--chhHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTP--SITKIQYEIA  230 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~  230 (848)
                      ....|+|.+|+||||||+.||++.... +|+.++|+++++.+  ++..+++.+.
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIl  222 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVK  222 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhc
Confidence            458899999999999999999998766 89999999999988  7788888775

>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=97.52  E-value=9.5e-05  Score=51.45  Aligned_cols=36  Identities=33%  Similarity=0.572  Sum_probs=23.6

Q ss_pred             cCCCEEEccCCCCcccChhhccCCcccEEeccCCcc
Q 003090          344 SGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       344 ~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~  379 (848)
                      ++|++|++++|+|+.+|..+++|++|++|++++|.+
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i   36 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPI   36 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCC
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCC
Confidence            356777777777777776677777777777777644

...

>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=97.52  E-value=0.00011  Score=51.20  Aligned_cols=40  Identities=33%  Similarity=0.457  Sum_probs=28.6

Q ss_pred             ccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccC
Q 003090          321 INLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIP  360 (848)
Q Consensus       321 ~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp  360 (848)
                      ++|++|++++|.+...++.+++|++|++|++++|+++.+|
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCc
Confidence            3678888888877655556888888888888888777665

...

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=97.47  E-value=5.9e-06  Score=93.92  Aligned_cols=145  Identities=21%  Similarity=0.142  Sum_probs=91.2

Q ss_pred             CCCCCcEEEEecCCCceeecccccccccccCCCccEEecccc-ccccccccc-ccccccCCCcceEEEecCchhhHhhhH
Q 003090          531 GFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIREN-QNFVEICHG-QLPAGCLSNVKRSDVVDCGSILKILLS  608 (848)
Q Consensus       531 ~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~-~~L~~~~~~-~~~~~~l~~L~~L~l~~c~~l~~~l~~  608 (848)
                      .+++|+.|.+.+|..+...   .........+.|++|++.++ ......... ..-...+++|+.|++..|..++...-.
T Consensus       186 ~~~~L~~l~l~~~~~~~~~---~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~L~~l~l~~~~~isd~~l~  262 (482)
T KOG1947|consen  186 SCPLLKRLSLSGCSKITDD---SLDALALKCPNLEELDLSGCCLLITLSPLLLLLLLSICRKLKSLDLSGCGLVTDIGLS  262 (482)
T ss_pred             hCchhhHhhhcccccCChh---hHHHHHhhCchhheecccCcccccccchhHhhhhhhhcCCcCccchhhhhccCchhHH
Confidence            4799999999999887642   11234556799999999873 222111000 011225689999999999866334444


Q ss_pred             HHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCc
Q 003090          609 HLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECD  686 (848)
Q Consensus       609 ~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~  686 (848)
                      .++..+++|++|.+.+|..++.-.-       ......++.|++|+|++|..+..-.-... ..++++|+.|.+..++
T Consensus       263 ~l~~~c~~L~~L~l~~c~~lt~~gl-------~~i~~~~~~L~~L~l~~c~~~~d~~l~~~-~~~c~~l~~l~~~~~~  332 (482)
T KOG1947|consen  263 ALASRCPNLETLSLSNCSNLTDEGL-------VSIAERCPSLRELDLSGCHGLTDSGLEAL-LKNCPNLRELKLLSLN  332 (482)
T ss_pred             HHHhhCCCcceEccCCCCccchhHH-------HHHHHhcCcccEEeeecCccchHHHHHHH-HHhCcchhhhhhhhcC
Confidence            4555689999999999987543311       02345678899999999988743211111 2446666665555444

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=97.46  E-value=0.0016  Score=58.83  Aligned_cols=113  Identities=12%  Similarity=0.167  Sum_probs=83.8

Q ss_pred             hhHHHHHHHHHHHHHHHHhhhhHHHHhhhhhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHH
Q 003090            2 ATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEV   81 (848)
Q Consensus         2 a~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~L~~~l~~i~~~l~~a~~~~~~~~~~v~~wl~~l   81 (848)
                      |+.++++|++++++.+..    .+.+..       +.....+.-+++|..+++.|...+++.+..+..-+..-+.=++++
T Consensus         3 ~eL~~gaalG~~~~eLlk----~v~~~~-------~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L   71 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLK----AVIDAS-------KKSLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERL   71 (147)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHH-------HHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHH
Confidence            455677778888877777    333332       223466778888999999999999988876444444447778899


Q ss_pred             HHHHHHHHHHHHHHHHhhccccCCcccchhhHhHHhHHHHHHHHHHHHHHH
Q 003090           82 NDIIPKAEKFLEDEVKVNKKCLGGLCVDLKSRYKLSREAEEKTLAMSALMA  132 (848)
Q Consensus        82 k~~~~d~eD~lde~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~v~~~~~  132 (848)
                      ++...++++++.++.+..       .+++...++.+++|+++.+.+....+
T Consensus        72 ~~~L~~g~~LV~k~sk~~-------r~n~~kk~~y~~Ki~~le~~l~~f~~  115 (147)
T PF05659_consen   72 KELLEKGKELVEKCSKVR-------RWNLYKKPRYARKIEELEESLRRFIQ  115 (147)
T ss_pred             HHHHHHHHHHHHHhcccc-------HHHHHhhHhHHHHHHHHHHHHHHHhc
Confidence            999999999988874432       35677888999999999999887664

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=97.40  E-value=0.00015  Score=67.07  Aligned_cols=101  Identities=27%  Similarity=0.308  Sum_probs=53.4

Q ss_pred             ccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccC
Q 003090          256 KLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG  335 (848)
Q Consensus       256 ~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~  335 (848)
                      ....+++++|.+..++.  |..++.|..|.+.+              |.+...    -|.--..+++|..|.|.+|++..
T Consensus        43 ~~d~iDLtdNdl~~l~~--lp~l~rL~tLll~n--------------NrIt~I----~p~L~~~~p~l~~L~LtnNsi~~  102 (233)
T KOG1644|consen   43 QFDAIDLTDNDLRKLDN--LPHLPRLHTLLLNN--------------NRITRI----DPDLDTFLPNLKTLILTNNSIQE  102 (233)
T ss_pred             ccceecccccchhhccc--CCCccccceEEecC--------------Ccceee----ccchhhhccccceEEecCcchhh
Confidence            34445555555544443  44555555555555              444442    22222234445555555554443


Q ss_pred             C--chhhccccCCCEEEccCCCCcccCh----hhccCCcccEEeccC
Q 003090          336 D--LSLIGELSGLEILDLSESDVSEIPV----SFGRLSHLRLLDLTG  376 (848)
Q Consensus       336 ~--~~~i~~l~~L~~L~l~~~~l~~lp~----~i~~L~~L~~L~l~~  376 (848)
                      .  +..+..++.|++|.+-+|.++..+.    -+.++++|++||+.+
T Consensus       103 l~dl~pLa~~p~L~~Ltll~Npv~~k~~YR~yvl~klp~l~~LDF~k  149 (233)
T KOG1644|consen  103 LGDLDPLASCPKLEYLTLLGNPVEHKKNYRLYVLYKLPSLRTLDFQK  149 (233)
T ss_pred             hhhcchhccCCccceeeecCCchhcccCceeEEEEecCcceEeehhh
Confidence            2  3455556666666666666553332    366777777777765

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

Probab=97.39  E-value=0.00024  Score=71.09  Aligned_cols=50  Identities=18%  Similarity=0.181  Sum_probs=45.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccC--CchhHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQT--PSITKIQYEI  229 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~l~~~i  229 (848)
                      ..+.|+|.+|+||||+++.+|++.... +|+..+|++++.+  +++.++++.+
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I   68 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSV   68 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHh
Confidence            579999999999999999999987655 8999999998887  7888998888

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.

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=97.32  E-value=0.00043  Score=64.19  Aligned_cols=51  Identities=25%  Similarity=0.318  Sum_probs=23.8

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccC
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG  288 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~  288 (848)
                      +++++|++..++..-++++|.+|.+++|.+..+.+.+-.-+++|..|.|.+
T Consensus        47 iDLtdNdl~~l~~lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~Ltn   97 (233)
T KOG1644|consen   47 IDLTDNDLRKLDNLPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTN   97 (233)
T ss_pred             ecccccchhhcccCCCccccceEEecCCcceeeccchhhhccccceEEecC
Confidence            444444444444333444455555555544444444433344444555444

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

Probab=97.22  E-value=9.2e-05  Score=63.91  Aligned_cols=95  Identities=25%  Similarity=0.325  Sum_probs=82.3

Q ss_pred             hHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCC
Q 003090          223 TKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPF  300 (848)
Q Consensus       223 ~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~  300 (848)
                      .+....+.+...++..++++|.+..+|+.+  ..+.++.|++++|.+..+|.+ +..++.||.|+++.            
T Consensus        43 ~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE-~Aam~aLr~lNl~~------------  109 (177)
T KOG4579|consen   43 ADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEE-LAAMPALRSLNLRF------------  109 (177)
T ss_pred             HHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHH-HhhhHHhhhccccc------------
Confidence            344455566666788999999999999887  667999999999999999999 68999999999999            


Q ss_pred             CCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          301 LFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       301 ~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                        |.+..     .|..+..|.+|-+|+..++.....+
T Consensus       110 --N~l~~-----~p~vi~~L~~l~~Lds~~na~~eid  139 (177)
T KOG4579|consen  110 --NPLNA-----EPRVIAPLIKLDMLDSPENARAEID  139 (177)
T ss_pred             --Ccccc-----chHHHHHHHhHHHhcCCCCccccCc
Confidence              89988     8999999999999999999766655

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

Probab=97.16  E-value=0.00056  Score=66.22  Aligned_cols=48  Identities=15%  Similarity=0.173  Sum_probs=28.0

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCc-----ccCCcc-cccccceeecccCcC
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIH-----EVPDEL-ECPKLQALFLQENSP  267 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~-----~lp~~~-~~~~L~~L~l~~~~~  267 (848)
                      -|++.+...+...-.+..++||+|.|.     .+...+ +-.+|+..+++.-+.
T Consensus        17 eDvk~v~eel~~~d~~~evdLSGNtigtEA~e~l~~~ia~~~~L~vvnfsd~ft   70 (388)
T COG5238          17 EDVKGVVEELEMMDELVEVDLSGNTIGTEAMEELCNVIANVRNLRVVNFSDAFT   70 (388)
T ss_pred             chhhHHHHHHHhhcceeEEeccCCcccHHHHHHHHHHHhhhcceeEeehhhhhh
Confidence            466667777766666777778877776     222222 345555555554433

>PTZ00202 tuzin; Provisional

Probab=97.00  E-value=0.014  Score=61.72  Aligned_cols=77  Identities=17%  Similarity=0.214  Sum_probs=56.6

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcC--C-ccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDE--N-VSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQY  227 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~--~-~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  227 (848)
                      ..|.+...++||+++...+...|..-  . ..++.|.|..|+||||+++.+.....      ..+.  +.+......+..
T Consensus       256 ~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~------~~qL--~vNprg~eElLr  327 (550)
T PTZ00202        256 SAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG------MPAV--FVDVRGTEDTLR  327 (550)
T ss_pred             CCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC------ceEE--EECCCCHHHHHH
Confidence            34556789999999999999998632  2 24889999999999999999885432      1222  233336688888


Q ss_pred             HHHhccCC
Q 003090          228 EIAGWLDL  235 (848)
Q Consensus       228 ~i~~~~~l  235 (848)
                      .++..++.
T Consensus       328 ~LL~ALGV  335 (550)
T PTZ00202        328 SVVKALGV  335 (550)
T ss_pred             HHHHHcCC
Confidence            88887765

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.98  E-value=7.5e-05  Score=72.32  Aligned_cols=107  Identities=24%  Similarity=0.247  Sum_probs=74.9

Q ss_pred             hcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEe
Q 003090          319 FLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY  398 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~  398 (848)
                      .+.+.+.|++.+| ...++....+++.|++|.|+-|+|+++. .+..+++|+.|+|+.|.+..--.-..+.++++|+.|+
T Consensus        17 dl~~vkKLNcwg~-~L~DIsic~kMp~lEVLsLSvNkIssL~-pl~rCtrLkElYLRkN~I~sldEL~YLknlpsLr~LW   94 (388)
T KOG2123|consen   17 DLENVKKLNCWGC-GLDDISICEKMPLLEVLSLSVNKISSLA-PLQRCTRLKELYLRKNCIESLDELEYLKNLPSLRTLW   94 (388)
T ss_pred             HHHHhhhhcccCC-CccHHHHHHhcccceeEEeeccccccch-hHHHHHHHHHHHHHhcccccHHHHHHHhcCchhhhHh
Confidence            3556777888888 4556677778889999999999888875 5788888999988887553322223367888888888


Q ss_pred             ccccccccccccccccccCcccchhhhcccCCCcEEE
Q 003090          399 MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLH  435 (848)
Q Consensus       399 l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~  435 (848)
                      +..|.-.+.        ...+.....|.-|++|++||
T Consensus        95 L~ENPCc~~--------ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   95 LDENPCCGE--------AGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             hccCCcccc--------cchhHHHHHHHHcccchhcc
Confidence            887754433        22233445677777777776

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.93  E-value=0.0042  Score=66.64  Aligned_cols=70  Identities=20%  Similarity=0.177  Sum_probs=58.4

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQY  227 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  227 (848)
                      ..++++.++..+.++..|....  .+-++|+.|+|||++|+.+.+.......|+.+.||++++.++...+..
T Consensus       174 l~d~~i~e~~le~l~~~L~~~~--~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~  243 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIKK--NIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQ  243 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcCC--CEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhc
Confidence            3568899999999999987544  577899999999999999998876667788999999998887766553

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.91  E-value=0.00033  Score=68.65  Aligned_cols=21  Identities=14%  Similarity=0.140  Sum_probs=12.1

Q ss_pred             chhhhcccCCCcEEEeeccCC
Q 003090          421 KFIELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       421 ~~~~L~~l~~L~~L~l~~~~~  441 (848)
                      ...+|..++.|+.|.++.+.+
T Consensus       241 svD~Ln~f~~l~dlRv~~~Pl  261 (418)
T KOG2982|consen  241 SVDALNGFPQLVDLRVSENPL  261 (418)
T ss_pred             HHHHHcCCchhheeeccCCcc
Confidence            455566666666666655543

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

Probab=96.85  E-value=0.0051  Score=59.82  Aligned_cols=143  Identities=22%  Similarity=0.243  Sum_probs=77.7

Q ss_pred             hHHHHHHHhccCCCceeeecCCCc-ccCCc----c-cccccceeecccCcCcccChH-----HH--------ccCCceeE
Q 003090          223 TKIQYEIAGWLDLTGISLMFNDIH-EVPDE----L-ECPKLQALFLQENSPLAIPDR-----FF--------QGMKDLQV  283 (848)
Q Consensus       223 ~~l~~~i~~~~~l~~l~l~~n~l~-~lp~~----~-~~~~L~~L~l~~~~~~~~~~~-----~~--------~~~~~Lr~  283 (848)
                      .-+.+.++.+-.++.++||+|-|. ..|+.    + +...|.+|.+++|..+.+...     +|        .+-+.|++
T Consensus        82 ~~Ll~aLlkcp~l~~v~LSDNAfg~~~~e~L~d~is~~t~l~HL~l~NnGlGp~aG~rigkal~~la~nKKaa~kp~Le~  161 (388)
T COG5238          82 VMLLKALLKCPRLQKVDLSDNAFGSEFPEELGDLISSSTDLVHLKLNNNGLGPIAGGRIGKALFHLAYNKKAADKPKLEV  161 (388)
T ss_pred             HHHHHHHhcCCcceeeeccccccCcccchHHHHHHhcCCCceeEEeecCCCCccchhHHHHHHHHHHHHhhhccCCCceE
Confidence            345566667777888888888776 33432    2 567888888888866654321     11        23456777


Q ss_pred             EEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc------hhhccccCCCEEEccCCCCc
Q 003090          284 LDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL------SLIGELSGLEILDLSESDVS  357 (848)
Q Consensus       284 L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~------~~i~~l~~L~~L~l~~~~l~  357 (848)
                      .....              |.+......-....+....+|+.+.+..|.+...-      ..+..+++|++||+..|.++
T Consensus       162 vicgr--------------NRlengs~~~~a~~l~sh~~lk~vki~qNgIrpegv~~L~~~gl~y~~~LevLDlqDNtft  227 (388)
T COG5238         162 VICGR--------------NRLENGSKELSAALLESHENLKEVKIQQNGIRPEGVTMLAFLGLFYSHSLEVLDLQDNTFT  227 (388)
T ss_pred             EEecc--------------chhccCcHHHHHHHHHhhcCceeEEeeecCcCcchhHHHHHHHHHHhCcceeeeccccchh
Confidence            77776              44443100001111223345666666666544321      33455666666666666555


Q ss_pred             cc-----ChhhccCCcccEEeccCCcc
Q 003090          358 EI-----PVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       358 ~l-----p~~i~~L~~L~~L~l~~~~~  379 (848)
                      ..     ...+...+.|+.|.+.+|-.
T Consensus       228 ~~gS~~La~al~~W~~lrEL~lnDCll  254 (388)
T COG5238         228 LEGSRYLADALCEWNLLRELRLNDCLL  254 (388)
T ss_pred             hhhHHHHHHHhcccchhhhccccchhh
Confidence            22     22233344456666665543

>PRK08118 topology modulation protein; Reviewed

Probab=96.67  E-value=0.0013  Score=62.00  Aligned_cols=50  Identities=22%  Similarity=0.321  Sum_probs=36.1

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHhhc-cccCcEE----EEEeccCCchhHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAKEM-KMFDDVA----MAVVSQTPSITKIQYEIA  230 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~~~-~~F~~~~----wv~vs~~~~~~~l~~~i~  230 (848)
                      .|.|+|.+|+||||+|+.+++..... -+||...    |..+++. ....++++++
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~-~~~~~~~~~~   57 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKE-EQITVQNELV   57 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHH-HHHHHHHHHh
Confidence            58899999999999999999987655 5577777    5555542 3444444444

>TIGR00767 rho transcription termination factor Rho

Probab=96.52  E-value=0.0045  Score=65.29  Aligned_cols=52  Identities=17%  Similarity=0.199  Sum_probs=45.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccC--CchhHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQT--PSITKIQYEIAG  231 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~l~~~i~~  231 (848)
                      ..+.|+|.+|.||||+++.+++..... +|+..+|+.+++.  .++..+++.+..
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg  222 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKG  222 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhc
Confidence            568999999999999999999987644 8999999999977  788888888853

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

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

Probab=96.52  E-value=0.005  Score=59.43  Aligned_cols=48  Identities=21%  Similarity=0.363  Sum_probs=34.0

Q ss_pred             cccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHHhhc
Q 003090          158 AFKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQAKEM  205 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~  205 (848)
                      .+|||+++.+++...+.   ....+.+-|+|..|+|||++.+.++......
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            37999999999999993   4556889999999999999999999877655

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.40  E-value=0.012  Score=64.64  Aligned_cols=79  Identities=23%  Similarity=0.161  Sum_probs=54.4

Q ss_pred             cccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHh
Q 003090          156 VYAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAG  231 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  231 (848)
                      ...++||+++++++...+.    ......+-|+|..|+|||++++.++++.......-..+++......+...+...+..
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~  108 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIAR  108 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHH
Confidence            3679999999999999985    233355779999999999999999987654331122334433344455566666666


Q ss_pred             ccC
Q 003090          232 WLD  234 (848)
Q Consensus       232 ~~~  234 (848)
                      .+.
T Consensus       109 ~l~  111 (394)
T PRK00411        109 QLF  111 (394)
T ss_pred             Hhc
Confidence            553

>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=96.20  E-value=0.006  Score=61.44  Aligned_cols=44  Identities=27%  Similarity=0.406  Sum_probs=36.9

Q ss_pred             ccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          159 FKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       159 ~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++||+++.+.+.+++.......+.|+|..|+|||+|++.+.+..
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~   44 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINEL   44 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHh
Confidence            58999999999999987767899999999999999999998765

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

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.10  E-value=0.018  Score=62.45  Aligned_cols=77  Identities=21%  Similarity=0.253  Sum_probs=53.3

Q ss_pred             ccccchhHHHHHHHHHHhc----CCccEEEEEeCCCCchhHHHHHHHHHHhhc-cccC---cEEEEEeccCCchhHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD----ENVSITGICGMGGVGKTTLVKEIQKQAKEM-KMFD---DVAMAVVSQTPSITKIQYE  228 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~----~~~~vi~i~G~gG~GKTtla~~v~~~~~~~-~~F~---~~~wv~vs~~~~~~~l~~~  228 (848)
                      +.++||+++++.+..++..    .....+-|+|..|+|||++++.+++..... ...+   ..+|+......+...+...
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~   94 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVE   94 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHH
Confidence            5799999999999999872    333578899999999999999999865321 1111   2344443443445566666


Q ss_pred             HHhcc
Q 003090          229 IAGWL  233 (848)
Q Consensus       229 i~~~~  233 (848)
                      |.+.+
T Consensus        95 i~~~l   99 (365)
T TIGR02928        95 LANQL   99 (365)
T ss_pred             HHHHH
Confidence            76655

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.

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=95.90  E-value=0.006  Score=59.47  Aligned_cols=83  Identities=24%  Similarity=0.342  Sum_probs=47.5

Q ss_pred             cccCcEEEccCccccCCchhhccccCCCEEEccCC--CCc-ccChhhccCCcccEEeccCCccc--cccChhhhhccccc
Q 003090          320 LINLRTLRLHDRRIQGDLSLIGELSGLEILDLSES--DVS-EIPVSFGRLSHLRLLDLTGCYIL--ELIPRGVLSRLRKL  394 (848)
Q Consensus       320 l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~--~l~-~lp~~i~~L~~L~~L~l~~~~~~--~~~p~~~l~~l~~L  394 (848)
                      +..|+.|++.++.. .....+-.|++|++|.++.|  ++. .++....++++|++|++++|.+.  ..+++  +..+.+|
T Consensus        42 ~~~le~ls~~n~gl-tt~~~~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~p--l~~l~nL  118 (260)
T KOG2739|consen   42 FVELELLSVINVGL-TTLTNFPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRP--LKELENL  118 (260)
T ss_pred             ccchhhhhhhccce-eecccCCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccch--hhhhcch
Confidence            34455555554422 22344455667777777777  444 55555555677777777776443  33444  4666666


Q ss_pred             cEEeccccccc
Q 003090          395 EELYMSHSFRH  405 (848)
Q Consensus       395 ~~L~l~~~~~~  405 (848)
                      ..|++..|..+
T Consensus       119 ~~Ldl~n~~~~  129 (260)
T KOG2739|consen  119 KSLDLFNCSVT  129 (260)
T ss_pred             hhhhcccCCcc
Confidence            67776666544

>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=95.87  E-value=0.03  Score=51.43  Aligned_cols=57  Identities=21%  Similarity=0.170  Sum_probs=43.4

Q ss_pred             cchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc
Q 003090          160 KSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ  218 (848)
Q Consensus       160 vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~  218 (848)
                      +|++..++.+...+.......+-|+|..|+||||+++.+++.....  -...+++...+
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~   57 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASD   57 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhh
Confidence            4788888999988887667789999999999999999999876411  12345554444

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.

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=95.31  E-value=0.011  Score=57.79  Aligned_cols=80  Identities=29%  Similarity=0.414  Sum_probs=38.2

Q ss_pred             hcccCcEEEccCc--cccCCc-hhhccccCCCEEEccCCCCc---ccChhhccCCcccEEeccCCcccc--ccChhhhhc
Q 003090          319 FLINLRTLRLHDR--RIQGDL-SLIGELSGLEILDLSESDVS---EIPVSFGRLSHLRLLDLTGCYILE--LIPRGVLSR  390 (848)
Q Consensus       319 ~l~~L~~L~L~~~--~~~~~~-~~i~~l~~L~~L~l~~~~l~---~lp~~i~~L~~L~~L~l~~~~~~~--~~p~~~l~~  390 (848)
                      .|++|++|.++.|  +..... ....++++|++|++++|++.   +++ .+..+.+|..|++.+|....  .--..++.-
T Consensus        63 ~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~-pl~~l~nL~~Ldl~n~~~~~l~dyre~vf~l  141 (260)
T KOG2739|consen   63 KLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLR-PLKELENLKSLDLFNCSVTNLDDYREKVFLL  141 (260)
T ss_pred             CcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccc-hhhhhcchhhhhcccCCccccccHHHHHHHH
Confidence            3445555555555  333222 22334455555555555544   222 24455555666665554332  111233556


Q ss_pred             cccccEEec
Q 003090          391 LRKLEELYM  399 (848)
Q Consensus       391 l~~L~~L~l  399 (848)
                      +++|..|+-
T Consensus       142 l~~L~~LD~  150 (260)
T KOG2739|consen  142 LPSLKYLDG  150 (260)
T ss_pred             hhhhccccc
Confidence            666766653

>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=95.29  E-value=0.0067  Score=34.93  Aligned_cols=21  Identities=48%  Similarity=0.770  Sum_probs=12.9

Q ss_pred             CCCEEEccCCCCcccChhhcc
Q 003090          345 GLEILDLSESDVSEIPVSFGR  365 (848)
Q Consensus       345 ~L~~L~l~~~~l~~lp~~i~~  365 (848)
                      +|++||+++|+++.+|.++++
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSN   21 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT
T ss_pred             CccEEECCCCcCEeCChhhcC
Confidence            356666666666666665543

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 ....

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.24  E-value=0.0038  Score=58.21  Aligned_cols=71  Identities=18%  Similarity=0.252  Sum_probs=47.1

Q ss_pred             ccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCce
Q 003090          557 LRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLV  629 (848)
Q Consensus       557 ~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~  629 (848)
                      ....+++++.|.+.+|..+.+|+.+.+.. ..|+|+.|+|++|+.+ ++---..+..+++|+.|.+++.+.+.
T Consensus       120 ~L~~l~~i~~l~l~~ck~~dD~~L~~l~~-~~~~L~~L~lsgC~rI-T~~GL~~L~~lknLr~L~l~~l~~v~  190 (221)
T KOG3864|consen  120 HLRDLRSIKSLSLANCKYFDDWCLERLGG-LAPSLQDLDLSGCPRI-TDGGLACLLKLKNLRRLHLYDLPYVA  190 (221)
T ss_pred             HHhccchhhhheeccccchhhHHHHHhcc-cccchheeeccCCCee-chhHHHHHHHhhhhHHHHhcCchhhh
Confidence            44556777777888888877777665554 5778888888888777 44333334566777777776655443

>smart00763 AAA_PrkA PrkA AAA domain

Probab=95.14  E-value=0.036  Score=57.99  Aligned_cols=47  Identities=26%  Similarity=0.364  Sum_probs=40.9

Q ss_pred             cccchhHHHHHHHHHHhc------CCccEEEEEeCCCCchhHHHHHHHHHHhh
Q 003090          158 AFKSRESTMKDIMEAMKD------ENVSITGICGMGGVGKTTLVKEIQKQAKE  204 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~~------~~~~vi~i~G~gG~GKTtla~~v~~~~~~  204 (848)
                      .++|.++.++++++++..      ....++.++|..|.||||+|+.+.+....
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            799999999999999973      23578999999999999999999887643

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=95.09  E-value=0.41  Score=55.28  Aligned_cols=62  Identities=23%  Similarity=0.268  Sum_probs=48.2

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccC---cEEEEEec
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFD---DVAMAVVS  217 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~---~~~wv~vs  217 (848)
                      -++++|.+..+..+...+.......+.++|..|+||||+|+.+++.......+.   ...|+.+.
T Consensus       153 ~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~  217 (615)
T TIGR02903       153 FSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVD  217 (615)
T ss_pred             HHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEe
Confidence            357899999999888887666667899999999999999999998775444432   34566554

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=95.07  E-value=0.23  Score=55.71  Aligned_cols=47  Identities=30%  Similarity=0.283  Sum_probs=39.8

Q ss_pred             cccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.+-+|.++-++.|++.|-      .-.-.++..||..|+|||.|++.|.+..
T Consensus       322 d~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al  374 (782)
T COG0466         322 DKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKAL  374 (782)
T ss_pred             cccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHh
Confidence            3567899999999999986      2333699999999999999999998765

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.98  E-value=0.0026  Score=61.99  Aligned_cols=101  Identities=22%  Similarity=0.177  Sum_probs=76.4

Q ss_pred             cCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCC
Q 003090          277 GMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDV  356 (848)
Q Consensus       277 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l  356 (848)
                      .+.+.+.|++-+              +.+.+.      ....+++.|++|.|+-|++ ..+..+..|++|+.|.|..|.|
T Consensus        17 dl~~vkKLNcwg--------------~~L~DI------sic~kMp~lEVLsLSvNkI-ssL~pl~rCtrLkElYLRkN~I   75 (388)
T KOG2123|consen   17 DLENVKKLNCWG--------------CGLDDI------SICEKMPLLEVLSLSVNKI-SSLAPLQRCTRLKELYLRKNCI   75 (388)
T ss_pred             HHHHhhhhcccC--------------CCccHH------HHHHhcccceeEEeecccc-ccchhHHHHHHHHHHHHHhccc
Confidence            355667777777              566652      3456888999999999844 4556788899999999999988


Q ss_pred             cccCh--hhccCCcccEEeccCCccccccCh----hhhhccccccEEe
Q 003090          357 SEIPV--SFGRLSHLRLLDLTGCYILELIPR----GVLSRLRKLEELY  398 (848)
Q Consensus       357 ~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~----~~l~~l~~L~~L~  398 (848)
                      ..+-+  .+.++++|+.|.+..|.-.+.-+.    .++.-|++|+.|+
T Consensus        76 ~sldEL~YLknlpsLr~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   76 ESLDELEYLKNLPSLRTLWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             ccHHHHHHHhcCchhhhHhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            86653  578899999999988766655543    3477888998886

>PRK07261 topology modulation protein; Provisional

Probab=94.65  E-value=0.068  Score=50.59  Aligned_cols=35  Identities=23%  Similarity=0.377  Sum_probs=25.7

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHhhc-cccCcEEEE
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAKEM-KMFDDVAMA  214 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~~~-~~F~~~~wv  214 (848)
                      .|.|+|++|+||||+|+.+.....+. -+.|...|-
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~   37 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQ   37 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEec
Confidence            48899999999999999987654322 235555564

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.64  E-value=0.043  Score=57.82  Aligned_cols=47  Identities=23%  Similarity=0.304  Sum_probs=38.9

Q ss_pred             ccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          157 YAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+++|+++.++.+..++.     ......+-++|..|+|||++|+.+.+...
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~   55 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMG   55 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            578999999999888886     23345677999999999999999987653

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.

>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=94.60  E-value=0.034  Score=49.24  Aligned_cols=23  Identities=39%  Similarity=0.567  Sum_probs=20.8

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|.|+|..|+||||+|+.+.+..
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998754

...

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.57  E-value=0.0062  Score=56.87  Aligned_cols=70  Identities=20%  Similarity=0.341  Sum_probs=46.5

Q ss_pred             CCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccccccccccc
Q 003090          728 PSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSL  807 (848)
Q Consensus       728 ~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L  807 (848)
                      ..+++++.|.+.+|..+.+......-+-.++|+.|+|++|+.+++-     +.+.|-.       +++|+.|.|.+.|..
T Consensus       122 ~~l~~i~~l~l~~ck~~dD~~L~~l~~~~~~L~~L~lsgC~rIT~~-----GL~~L~~-------lknLr~L~l~~l~~v  189 (221)
T KOG3864|consen  122 RDLRSIKSLSLANCKYFDDWCLERLGGLAPSLQDLDLSGCPRITDG-----GLACLLK-------LKNLRRLHLYDLPYV  189 (221)
T ss_pred             hccchhhhheeccccchhhHHHHHhcccccchheeeccCCCeechh-----HHHHHHH-------hhhhHHHHhcCchhh
Confidence            4567778888888887765532222234577888888888887543     3333333       688888888888766


Q ss_pred             cc
Q 003090          808 AC  809 (848)
Q Consensus       808 ~~  809 (848)
                      ..
T Consensus       190 ~~  191 (221)
T KOG3864|consen  190 AN  191 (221)
T ss_pred             hc
Confidence            55

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=94.51  E-value=0.079  Score=47.45  Aligned_cols=117  Identities=16%  Similarity=0.304  Sum_probs=42.2

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+.+|+.+.+.. .+..++...|.++.+|+.+.+..              + +...    -...+..+..|+.+.+..+ 
T Consensus        10 ~~~~l~~i~~~~-~~~~I~~~~F~~~~~l~~i~~~~--------------~-~~~i----~~~~F~~~~~l~~i~~~~~-   68 (129)
T PF13306_consen   10 NCSNLESITFPN-TIKKIGENAFSNCTSLKSINFPN--------------N-LTSI----GDNAFSNCKSLESITFPNN-   68 (129)
T ss_dssp             T-TT--EEEETS-T--EE-TTTTTT-TT-SEEEESS--------------T-TSCE-----TTTTTT-TT-EEEEETST-
T ss_pred             CCCCCCEEEECC-CeeEeChhhcccccccccccccc--------------c-cccc----ceeeeeccccccccccccc-
Confidence            455666666553 34455555566666666666654              2 2221    1123455555666666442 


Q ss_pred             ccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          333 IQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       333 ~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..... ..+..+.+|+.+++..+ +..++. .+.+. +|+.+.+..  ....++...+.++++|
T Consensus        69 ~~~i~~~~F~~~~~l~~i~~~~~-~~~i~~~~f~~~-~l~~i~~~~--~~~~i~~~~F~~~~~l  128 (129)
T PF13306_consen   69 LKSIGDNAFSNCTNLKNIDIPSN-ITEIGSSSFSNC-NLKEINIPS--NITKIEENAFKNCTKL  128 (129)
T ss_dssp             T-EE-TTTTTT-TTECEEEETTT--BEEHTTTTTT--T--EEE-TT--B-SS----GGG-----
T ss_pred             ccccccccccccccccccccCcc-ccEEchhhhcCC-CceEEEECC--CccEECCccccccccC
Confidence            22222 34455566666666443 433332 23333 555555543  2233444434444443

>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=94.43  E-value=0.092  Score=50.78  Aligned_cols=49  Identities=22%  Similarity=0.298  Sum_probs=34.3

Q ss_pred             ccccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .-.+++|-++-++...-++.     .+.+..+=.||..|+||||||+-|-+...
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~   75 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELG   75 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccC
Confidence            45789999888876544443     34567788999999999999999988764

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.

>PRK06696 uridine kinase; Validated

Probab=94.03  E-value=0.09  Score=52.36  Aligned_cols=43  Identities=28%  Similarity=0.376  Sum_probs=34.3

Q ss_pred             chhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          161 SRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       161 G~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .|++-+++|.+.+.   .....+|+|.|.+|.||||+|+.+.....
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~   47 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIK   47 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35666777777775   45667999999999999999999987653

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

Probab=94.02  E-value=0.079  Score=54.03  Aligned_cols=56  Identities=21%  Similarity=0.294  Sum_probs=38.3

Q ss_pred             HHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc----CCchhHHHHH
Q 003090          169 IMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ----TPSITKIQYE  228 (848)
Q Consensus       169 i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~----~~~~~~l~~~  228 (848)
                      +.+++..+.+..+-.||..|+||||||+.+.+..+-...    -+|..|-    ..|+..+.++
T Consensus       153 lrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~Sy----rfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  153 LRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHSY----RFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             HHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCce----EEEEEeccccchHHHHHHHHH
Confidence            444555778888999999999999999999987654443    3444443    3444444443

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=93.89  E-value=0.08  Score=56.29  Aligned_cols=51  Identities=22%  Similarity=0.312  Sum_probs=40.9

Q ss_pred             CcccccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          153 SEGVYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      |..-.+++|+++.++.+..++.     ......+-++|..|+||||+|+.+.+...
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~   76 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMG   76 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhC
Confidence            3345789999999998887775     23345678999999999999999988763

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

Probab=93.62  E-value=0.087  Score=47.30  Aligned_cols=58  Identities=29%  Similarity=0.302  Sum_probs=41.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHhhcc---ccCcEEEEEeccCCchhHHHHHHHhccCC
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAKEMK---MFDDVAMAVVSQTPSITKIQYEIAGWLDL  235 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~~~~---~F~~~~wv~vs~~~~~~~l~~~i~~~~~l  235 (848)
                      -+++-|+|..|+|||++++.+.+......   .-...+|+......+...+...+.+.+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~   64 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGL   64 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCc
Confidence            46789999999999999999997653210   12446788888877888999999887754

>PRK04195 replication factor C large subunit; Provisional

Probab=93.61  E-value=0.073  Score=59.81  Aligned_cols=52  Identities=17%  Similarity=0.178  Sum_probs=43.6

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCC----ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDEN----VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~----~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|..-.+++|.++.++.+.+|+..+.    ...+-++|..|+||||+|+.+.+..
T Consensus         8 yrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el   63 (482)
T PRK04195          8 YRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY   63 (482)
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            344455779999999999999998543    5788899999999999999998865

>PRK13342 recombination factor protein RarA; Reviewed

Probab=93.43  E-value=0.085  Score=58.02  Aligned_cols=47  Identities=21%  Similarity=0.258  Sum_probs=38.6

Q ss_pred             cccccchhHHHHH---HHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKD---IMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~---i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.++||.+..+..   +.+++.......+-++|..|+||||+|+.+.+..
T Consensus        11 l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~   60 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT   60 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4568888877655   7777777777788899999999999999998765

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

Probab=93.43  E-value=0.25  Score=50.98  Aligned_cols=65  Identities=22%  Similarity=0.256  Sum_probs=40.8

Q ss_pred             HHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHhccC
Q 003090          167 KDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLD  234 (848)
Q Consensus       167 ~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~~~  234 (848)
                      +.++..+.   .....++.++|..|+||||+++.+++...... . ...|+. ....+...+...+....+
T Consensus        29 ~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~-~-~~~~~~-~~~~~~~~~l~~i~~~lG   96 (269)
T TIGR03015        29 KRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQER-V-VAAKLV-NTRVDAEDLLRMVAADFG   96 (269)
T ss_pred             HHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCC-e-EEeeee-CCCCCHHHHHHHHHHHcC
Confidence            34444443   34456899999999999999999998754221 1 122332 233566667777765553

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.

>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=93.33  E-value=0.052  Score=28.88  Aligned_cols=16  Identities=38%  Similarity=0.719  Sum_probs=7.5

Q ss_pred             CCCEEEccCCCCcccC
Q 003090          345 GLEILDLSESDVSEIP  360 (848)
Q Consensus       345 ~L~~L~l~~~~l~~lp  360 (848)
                      +|+.|++++|+++++|
T Consensus         2 ~L~~L~l~~n~L~~lP   17 (17)
T PF13504_consen    2 NLRTLDLSNNRLTSLP   17 (17)
T ss_dssp             T-SEEEETSS--SSE-
T ss_pred             ccCEEECCCCCCCCCc
Confidence            5666666666666554

...

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=93.32  E-value=0.12  Score=57.25  Aligned_cols=45  Identities=22%  Similarity=0.378  Sum_probs=39.9

Q ss_pred             cccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          158 AFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +++|.++.++.|++.|.      +..-.++-++|..|+||||||+.+.+-.
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHH
Confidence            58999999999999994      4556799999999999999999998754

>PRK07667 uridine kinase; Provisional

Probab=93.16  E-value=0.12  Score=50.16  Aligned_cols=38  Identities=37%  Similarity=0.581  Sum_probs=29.5

Q ss_pred             HHHHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          166 MKDIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       166 ~~~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+.|.+.+.  .....+|+|.|..|.||||+|+.+.....
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~   42 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMK   42 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            455666665  34446999999999999999999987653

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.07  E-value=0.32  Score=51.64  Aligned_cols=51  Identities=18%  Similarity=0.260  Sum_probs=43.1

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|+++.++.+..++.......+-++|..|+||||+|+.+.+..
T Consensus        12 rP~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l   62 (319)
T PRK00440         12 RPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALAREL   62 (319)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            344456789999999999999987777778999999999999999998765

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=92.96  E-value=0.15  Score=50.94  Aligned_cols=28  Identities=32%  Similarity=0.523  Sum_probs=24.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ....+++|.|..|.||||+++.+.....
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~   58 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQ   58 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            5567999999999999999999987654

>PLN03025 replication factor C subunit; Provisional

Probab=92.94  E-value=0.31  Score=51.52  Aligned_cols=52  Identities=17%  Similarity=0.217  Sum_probs=42.3

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|..-.+++|.++-++.+.+++...+...+=++|..|+||||+|+.+.+..
T Consensus         7 yrP~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l   58 (319)
T PLN03025          7 YRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHEL   58 (319)
T ss_pred             cCCCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3444557789999988888888777776677799999999999999988764

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=92.93  E-value=0.63  Score=52.23  Aligned_cols=47  Identities=26%  Similarity=0.285  Sum_probs=40.5

Q ss_pred             cccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +++-+|+++-++.|++.+-      +-+-.++..+|..|||||.+|+.|....
T Consensus       410 deDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~AL  462 (906)
T KOG2004|consen  410 DEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARAL  462 (906)
T ss_pred             cccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHh
Confidence            4567899999999999986      3445799999999999999999998765

>CHL00095 clpC Clp protease ATP binding subunit

Probab=92.85  E-value=0.13  Score=61.87  Aligned_cols=46  Identities=17%  Similarity=0.321  Sum_probs=39.6

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++||+++++.++++|......-+-++|..|+|||++|+.+....
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i  224 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRI  224 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999986555566799999999999999887654

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=92.84  E-value=3  Score=48.52  Aligned_cols=46  Identities=20%  Similarity=0.338  Sum_probs=38.3

Q ss_pred             ccccchhHHHHHHHHHHh---------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|+|-|+.++.+.+.+.         +..+.+.=.+|..|||||.||+.+-...
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~L  545 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL  545 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHh
Confidence            568999999999999887         3455677789999999999999887544

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=92.80  E-value=0.18  Score=48.30  Aligned_cols=73  Identities=19%  Similarity=0.133  Sum_probs=51.4

Q ss_pred             ccCCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCch
Q 003090          150 ISSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSI  222 (848)
Q Consensus       150 ~~~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~  222 (848)
                      .+.|..-.++||-++.++.+--.-.+.+..-+-|-|+.|+||||-+..+.+..--...=+.+.-...|++-.+
T Consensus        20 KYrP~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGI   92 (333)
T KOG0991|consen   20 KYRPSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGI   92 (333)
T ss_pred             hhCchHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCcccccc
Confidence            3455566789999999988777777889999999999999999987777655432223333444444544333

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=92.66  E-value=0.1  Score=50.65  Aligned_cols=24  Identities=46%  Similarity=0.681  Sum_probs=22.0

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ||+|.|.+|+||||+|+.+.....
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~   24 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILN   24 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            799999999999999999997764

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 ....

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=92.55  E-value=0.28  Score=50.24  Aligned_cols=46  Identities=22%  Similarity=0.142  Sum_probs=33.6

Q ss_pred             ccccchhHHHHHHHHHHh---------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+.+...               ......+-++|..|.||||+|+.+.+..
T Consensus         6 ~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l   66 (261)
T TIGR02881         6 SRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLF   66 (261)
T ss_pred             HHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHH
Confidence            458899888876654422               1233456789999999999999998754

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=92.54  E-value=0.18  Score=54.02  Aligned_cols=51  Identities=16%  Similarity=0.248  Sum_probs=42.3

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.....++|+++.++.+..++.......+-++|..|+||||+|+.+.+..
T Consensus        10 ~P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l   60 (337)
T PRK12402         10 RPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL   60 (337)
T ss_pred             CCCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            344456789999999999998887766677899999999999999988654

>PRK06547 hypothetical protein; Provisional

Probab=92.27  E-value=0.22  Score=47.05  Aligned_cols=35  Identities=26%  Similarity=0.259  Sum_probs=27.8

Q ss_pred             HHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          168 DIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       168 ~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+...+......+|.|.|..|.||||+|+.+.+..
T Consensus         5 ~~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547          5 LIAARLCGGGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             HHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34444556667899999999999999999998753

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.19  E-value=1.8  Score=47.96  Aligned_cols=25  Identities=24%  Similarity=0.446  Sum_probs=21.2

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.++.++|.+|+||||++..+....
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4799999999999999988777543

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=92.11  E-value=1.8  Score=47.05  Aligned_cols=28  Identities=21%  Similarity=0.315  Sum_probs=22.6

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +...+|.++|..|+||||++..+.....
T Consensus        98 ~~~~vi~lvG~~GvGKTTtaaKLA~~l~  125 (429)
T TIGR01425        98 GKQNVIMFVGLQGSGKTTTCTKLAYYYQ  125 (429)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3457999999999999999887765443

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=92.07  E-value=0.19  Score=60.20  Aligned_cols=47  Identities=17%  Similarity=0.357  Sum_probs=40.6

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++||++++..+++.|.......+-++|..|+||||+|+.+....
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i  232 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRI  232 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999999986665666799999999999999988764

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.

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=91.96  E-value=0.86  Score=45.67  Aligned_cols=58  Identities=7%  Similarity=0.063  Sum_probs=49.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHH-HhccccchHHHHHHHHHHHHHHHHHHHHHHHH
Q 003090           37 HYIEALRTEAKKLTDRRNDLQAEIDAA-TRNREVIKDEVKSWIAEVNDIIPKAEKFLEDE   95 (848)
Q Consensus        37 ~~~~~~~~~l~~L~~~l~~i~~~l~~a-~~~~~~~~~~v~~wl~~lk~~~~d~eD~lde~   95 (848)
                      +.+..++.+++.++.++++++.||+.. ++....+++ .+++..++...||++|-++|-.
T Consensus       314 dSlaflKnQiqvIQ~elesLqpFLk~V~ee~~nkh~~-~ed~a~~ii~kAyevEYVVDaC  372 (402)
T PF12061_consen  314 DSLAFLKNQIQVIQTELESLQPFLKHVVEEPHNKHDT-NEDCATQIIRKAYEVEYVVDAC  372 (402)
T ss_pred             chHHHHHHHHHHHHHHHHHhhHHHHHHHhccchhhhh-hhhHHHHHHHHHhheeeeeehh
Confidence            446789999999999999999999997 554455555 9999999999999999999965

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

>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=91.87  E-value=0.15  Score=45.48  Aligned_cols=21  Identities=48%  Similarity=0.841  Sum_probs=19.3

Q ss_pred             EEEEeCCCCchhHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~  201 (848)
                      |.|.|..|+||||+|+.+.+.
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            679999999999999999876

...

>PTZ00301 uridine kinase; Provisional

Probab=91.85  E-value=0.23  Score=48.53  Aligned_cols=25  Identities=32%  Similarity=0.621  Sum_probs=21.9

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|+|.|..|.||||+|+.+.+..
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l   27 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSEL   27 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHH
Confidence            3589999999999999999987654

>TIGR00763 lon ATP-dependent protease La

Probab=91.75  E-value=1.5  Score=52.55  Aligned_cols=46  Identities=28%  Similarity=0.294  Sum_probs=38.1

Q ss_pred             ccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.|.+++.      ...-.++-.+|..|+|||++|+.+.+..
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l  371 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL  371 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999998775      2233578899999999999999998765

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.

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=91.75  E-value=0.34  Score=43.28  Aligned_cols=107  Identities=14%  Similarity=0.261  Sum_probs=46.9

Q ss_pred             cChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCE
Q 003090          270 IPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEI  348 (848)
Q Consensus       270 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~  348 (848)
                      +++..|.++.+|+.+.+..               .+...    -...|..+.+|+.+.+..+ ..... ..+.++.+|+.
T Consensus         3 i~~~~F~~~~~l~~i~~~~---------------~~~~I----~~~~F~~~~~l~~i~~~~~-~~~i~~~~F~~~~~l~~   62 (129)
T PF13306_consen    3 IGNNAFYNCSNLESITFPN---------------TIKKI----GENAFSNCTSLKSINFPNN-LTSIGDNAFSNCKSLES   62 (129)
T ss_dssp             E-TTTTTT-TT--EEEETS---------------T--EE-----TTTTTT-TT-SEEEESST-TSCE-TTTTTT-TT-EE
T ss_pred             ECHHHHhCCCCCCEEEECC---------------CeeEe----Chhhccccccccccccccc-ccccceeeeeccccccc
Confidence            4445566666777776654               12221    1234566666777776664 33322 45566666677


Q ss_pred             EEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEecc
Q 003090          349 LDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS  400 (848)
Q Consensus       349 L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~  400 (848)
                      +.+.. .+..++. .+..+.+|+.+.+..+  ...++...+.+. +|+.+.+.
T Consensus        63 i~~~~-~~~~i~~~~F~~~~~l~~i~~~~~--~~~i~~~~f~~~-~l~~i~~~  111 (129)
T PF13306_consen   63 ITFPN-NLKSIGDNAFSNCTNLKNIDIPSN--ITEIGSSSFSNC-NLKEINIP  111 (129)
T ss_dssp             EEETS-TT-EE-TTTTTT-TTECEEEETTT---BEEHTTTTTT--T--EEE-T
T ss_pred             ccccc-cccccccccccccccccccccCcc--ccEEchhhhcCC-CceEEEEC
Confidence            76654 4443433 3444666666666542  334444445555 66666554

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=91.71  E-value=0.36  Score=48.18  Aligned_cols=42  Identities=14%  Similarity=0.213  Sum_probs=33.4

Q ss_pred             hhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          162 RESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       162 ~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+..++.+.+++..+....+-++|..|+|||++|+.+.+...
T Consensus        22 ~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~   63 (226)
T TIGR03420        22 NAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAE   63 (226)
T ss_pred             cHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            455666777776566667899999999999999999998754

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=91.69  E-value=0.23  Score=58.97  Aligned_cols=46  Identities=17%  Similarity=0.292  Sum_probs=39.9

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.++||+++++.+++.|.......+-++|..|+|||++|+.+....
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~  227 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRI  227 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            5789999999999999986655667799999999999999998765

>PRK05480 uridine/cytidine kinase; Provisional

Probab=91.66  E-value=0.17  Score=49.81  Aligned_cols=27  Identities=37%  Similarity=0.528  Sum_probs=23.4

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+|+|.|..|+|||||++.+....
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            455799999999999999999998754

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

Probab=91.58  E-value=0.81  Score=48.93  Aligned_cols=78  Identities=21%  Similarity=0.180  Sum_probs=56.5

Q ss_pred             ccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHhc
Q 003090          157 YAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGW  232 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  232 (848)
                      ..+.+||++++++...|.    .+....+-|+|..|.|||+.++.|.+..+....=...+.|.--.......+...|++.
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~   96 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNK   96 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHH
Confidence            449999999999998886    3334458899999999999999999877544221114555444455667777888776


Q ss_pred             cC
Q 003090          233 LD  234 (848)
Q Consensus       233 ~~  234 (848)
                      +.
T Consensus        97 ~~   98 (366)
T COG1474          97 LG   98 (366)
T ss_pred             cC
Confidence            64

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=91.57  E-value=0.27  Score=52.07  Aligned_cols=52  Identities=13%  Similarity=0.131  Sum_probs=42.2

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|..-.+++|.++.++.+..++..... .++-++|..|+||||+|+.+++..
T Consensus        15 yrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~   67 (316)
T PHA02544         15 YRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV   67 (316)
T ss_pred             cCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            4444567899999999999999986554 455568999999999999998764

>CHL00181 cbbX CbbX; Provisional

Probab=91.46  E-value=0.5  Score=48.84  Aligned_cols=61  Identities=15%  Similarity=0.134  Sum_probs=38.3

Q ss_pred             ccccchhHHHHHHHHHHh---------c------CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEec
Q 003090          157 YAFKSRESTMKDIMEAMK---------D------ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVS  217 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------~------~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs  217 (848)
                      .+++|.++-+++|.++..         .      ..-..+-++|..|.||||+|+.+.........-....|+.++
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~   98 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVT   98 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEec
Confidence            368888887776655432         0      112246789999999999999998754322222222355555

>PF13173 AAA_14: AAA domain

Probab=91.45  E-value=0.26  Score=44.01  Aligned_cols=38  Identities=29%  Similarity=0.355  Sum_probs=28.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ  218 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~  218 (848)
                      -+++.|.|..|+||||+++.++.+..   .....+++...+
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~   39 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDD   39 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCC
Confidence            46899999999999999999987653   223455555444

>PF05729 NACHT: NACHT domain

Probab=91.36  E-value=0.39  Score=45.01  Aligned_cols=40  Identities=23%  Similarity=0.242  Sum_probs=29.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhcccc----CcEEEEEecc
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMF----DDVAMAVVSQ  218 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F----~~~~wv~vs~  218 (848)
                      +++-|.|.+|+||||+++.+..........    ....|.....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~   44 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRD   44 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehh
Confidence            478899999999999999999877655443    3445555444

>TIGR00235 udk uridine kinase

Probab=91.36  E-value=0.16  Score=49.88  Aligned_cols=25  Identities=44%  Similarity=0.555  Sum_probs=22.2

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+|+|+|..|.||||+++.+....
T Consensus         6 g~vi~I~G~sGsGKSTl~~~l~~~l   30 (207)
T TIGR00235         6 GIIIGIGGGSGSGKTTVARKIYEQL   30 (207)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998754

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK10865 protein disaggregation chaperone; Provisional

Probab=91.31  E-value=0.23  Score=59.70  Aligned_cols=47  Identities=17%  Similarity=0.362  Sum_probs=39.9

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++||+.++..+++.|.......+-++|..|+|||++|+.+-...
T Consensus       177 l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i  223 (857)
T PRK10865        177 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRI  223 (857)
T ss_pred             CCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHh
Confidence            35699999999999999986655566699999999999999887654

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.21  E-value=0.28  Score=54.95  Aligned_cols=51  Identities=20%  Similarity=0.218  Sum_probs=41.9

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHHh
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      |..-.+++|-+.-++.+..++..+.... +-++|..|+||||+|+.+.+...
T Consensus        10 P~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~   61 (504)
T PRK14963         10 PITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVN   61 (504)
T ss_pred             CCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4445679999999999988888776654 48999999999999999987764

>PHA00729 NTP-binding motif containing protein

Probab=91.18  E-value=0.31  Score=47.66  Aligned_cols=36  Identities=28%  Similarity=0.410  Sum_probs=28.9

Q ss_pred             HHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          167 KDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       167 ~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+++.+...+...+.|.|..|+||||+|..+-+..
T Consensus         6 k~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729          6 KKIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             HHHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHH
Confidence            345666666666788999999999999999998764

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=91.07  E-value=0.24  Score=44.83  Aligned_cols=28  Identities=43%  Similarity=0.452  Sum_probs=23.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhcc
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMK  206 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~  206 (848)
                      --|.|.||.|+||||+++.+-+..+.+.
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g   33 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKG   33 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcC
Confidence            3588999999999999999998776544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=90.98  E-value=0.92  Score=52.84  Aligned_cols=78  Identities=18%  Similarity=0.204  Sum_probs=50.9

Q ss_pred             cccccchhHHHHHHHHHHh----cC-CccEEEEEeCCCCchhHHHHHHHHHHhh---ccccCcEEEEEec--cCCchhHH
Q 003090          156 VYAFKSRESTMKDIMEAMK----DE-NVSITGICGMGGVGKTTLVKEIQKQAKE---MKMFDDVAMAVVS--QTPSITKI  225 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----~~-~~~vi~i~G~gG~GKTtla~~v~~~~~~---~~~F~~~~wv~vs--~~~~~~~l  225 (848)
                      ++.++|||+++++|...|.    .. ...++-|+|..|.|||+.++.|.+....   ....+....+.|.  .-.+...+
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sI  833 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAA  833 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHH
Confidence            3578999999999999887    22 2246789999999999999999876532   1122223333332  22344555


Q ss_pred             HHHHHhcc
Q 003090          226 QYEIAGWL  233 (848)
Q Consensus       226 ~~~i~~~~  233 (848)
                      ...|.+.+
T Consensus       834 YqvI~qqL  841 (1164)
T PTZ00112        834 YQVLYKQL  841 (1164)
T ss_pred             HHHHHHHH
Confidence            55565444

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=90.88  E-value=0.47  Score=41.39  Aligned_cols=45  Identities=16%  Similarity=0.265  Sum_probs=35.4

Q ss_pred             ccccchhHHHHHHHHHHh-------cCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK-------DENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~-------~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++|-.-..+.|++.+.       ....-|++..|+.|+|||..++.|-+.
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            568888888888888876       234569999999999999977666554

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

>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=90.87  E-value=0.22  Score=38.71  Aligned_cols=23  Identities=39%  Similarity=0.608  Sum_probs=20.1

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++.|.|..|.||||+++.+-+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999888763

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=90.83  E-value=0.32  Score=56.82  Aligned_cols=48  Identities=27%  Similarity=0.373  Sum_probs=38.2

Q ss_pred             ccccccchhHHHH---HHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMK---DIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~---~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-++++|.+..+.   .+.+.+.......+-++|..|+||||+|+.+.+..
T Consensus        26 tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~   76 (725)
T PRK13341         26 TLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT   76 (725)
T ss_pred             cHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3467889888774   45556667777788899999999999999999765

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

Probab=90.81  E-value=0.61  Score=48.85  Aligned_cols=46  Identities=24%  Similarity=0.288  Sum_probs=33.1

Q ss_pred             ccccchhHHH---HHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTM---KDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~---~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++||-+.-+   .-+-.++....+...-.||..|+||||+|+.|-...
T Consensus        24 de~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~   72 (436)
T COG2256          24 DEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT   72 (436)
T ss_pred             HHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh
Confidence            4555554433   233445556788888899999999999999998754

>PRK08233 hypothetical protein; Provisional

Probab=90.80  E-value=0.2  Score=48.01  Aligned_cols=25  Identities=32%  Similarity=0.492  Sum_probs=21.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|+|.|..|.||||+|+.+....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            3689999999999999999998653

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=90.48  E-value=0.019  Score=54.72  Aligned_cols=86  Identities=20%  Similarity=0.143  Sum_probs=63.0

Q ss_pred             ccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCC
Q 003090          276 QGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD  355 (848)
Q Consensus       276 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~  355 (848)
                      ..++...+||++.              +.+-.     +-..++.++.|..|+++.+.+...+..++.+..++.+++..|.
T Consensus        39 ~~~kr~tvld~~s--------------~r~vn-----~~~n~s~~t~~~rl~~sknq~~~~~~d~~q~~e~~~~~~~~n~   99 (326)
T KOG0473|consen   39 ASFKRVTVLDLSS--------------NRLVN-----LGKNFSILTRLVRLDLSKNQIKFLPKDAKQQRETVNAASHKNN   99 (326)
T ss_pred             hccceeeeehhhh--------------hHHHh-----hccchHHHHHHHHHhccHhhHhhChhhHHHHHHHHHHHhhccc
Confidence            4566777777777              55555     5566777777777777777776677777777777777777777


Q ss_pred             CcccChhhccCCcccEEeccCCccc
Q 003090          356 VSEIPVSFGRLSHLRLLDLTGCYIL  380 (848)
Q Consensus       356 l~~lp~~i~~L~~L~~L~l~~~~~~  380 (848)
                      .+..|.+.+++++++++++.++.+.
T Consensus       100 ~~~~p~s~~k~~~~k~~e~k~~~~~  124 (326)
T KOG0473|consen  100 HSQQPKSQKKEPHPKKNEQKKTEFF  124 (326)
T ss_pred             hhhCCccccccCCcchhhhccCcch
Confidence            7888888888888888877776543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=90.38  E-value=0.38  Score=51.94  Aligned_cols=48  Identities=25%  Similarity=0.316  Sum_probs=38.6

Q ss_pred             ccccccchhHHHHHHHHHHh----c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK----D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~----~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++.|+++.++++.+.+.    .         ....-+-++|..|+|||++|+++.+..
T Consensus       120 ~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l  180 (364)
T TIGR01242       120 SYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET  180 (364)
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC
Confidence            34679999999999988774    1         123458899999999999999998865

Many proteins may score above the trusted cutoff because an internal

>PRK06762 hypothetical protein; Provisional

Probab=90.35  E-value=0.25  Score=46.56  Aligned_cols=24  Identities=38%  Similarity=0.570  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|+|+.|+||||+|+.+.+..
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            578999999999999999998654

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=90.27  E-value=0.35  Score=43.83  Aligned_cols=39  Identities=18%  Similarity=0.330  Sum_probs=26.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ  218 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~  218 (848)
                      ++|.|||..|+||||+++.+.+...-+ .+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            479999999999999999999887533 334444444444

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=90.19  E-value=0.52  Score=46.90  Aligned_cols=51  Identities=24%  Similarity=0.266  Sum_probs=40.2

Q ss_pred             ccccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHHhhc
Q 003090          155 GVYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQAKEM  205 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~  205 (848)
                      .-.+++|-++-++++-=.+.     ...+.-+=++|..|.||||||.-|-+.-.+.
T Consensus        24 ~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn   79 (332)
T COG2255          24 TLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVN   79 (332)
T ss_pred             cHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCC
Confidence            34678999888877665555     4556778899999999999999999876443

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=89.99  E-value=0.54  Score=44.19  Aligned_cols=43  Identities=26%  Similarity=0.463  Sum_probs=33.1

Q ss_pred             ccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          159 FKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       159 ~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++|.+..+.++++.+.   ..+.+|+ |+|-.|.||+.+|+.|++..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVl-I~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVL-ITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EE-EECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEE-EEcCCCCcHHHHHHHHHHhh
Confidence            5788888988888877   4555544 99999999999999999844

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=89.79  E-value=0.43  Score=57.64  Aligned_cols=46  Identities=17%  Similarity=0.347  Sum_probs=39.0

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++||+.++..+++.|....-..+-++|..|+|||++|+.+....
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i  218 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRI  218 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            5699999999999999986555556689999999999999887654

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.

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=89.71  E-value=0.37  Score=44.46  Aligned_cols=29  Identities=34%  Similarity=0.560  Sum_probs=24.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHhhcc
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAKEMK  206 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~~~~  206 (848)
                      ..|++|+|+.|.|||||...+-...+.+.
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G   30 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARG   30 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCC
Confidence            36899999999999999999887665443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=89.69  E-value=0.84  Score=53.74  Aligned_cols=46  Identities=17%  Similarity=0.289  Sum_probs=38.2

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++||++++..+++.|....-..+-++|..|+|||++|+.+....
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            4699999999999998885433445589999999999999998654

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

Probab=89.65  E-value=0.99  Score=46.94  Aligned_cols=74  Identities=19%  Similarity=0.226  Sum_probs=61.4

Q ss_pred             cccccchhHHHHHHHHHHhcCCc---cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHhc
Q 003090          156 VYAFKSRESTMKDIMEAMKDENV---SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGW  232 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~---~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  232 (848)
                      +..+.+|+..+..+..++.+.+.   ++|-|+|-.|.|||.+.+.+++...     -..+|++.-..|....+...|+..
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n-----~~~vw~n~~ecft~~~lle~IL~~   79 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLN-----LENVWLNCVECFTYAILLEKILNK   79 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcC-----CcceeeehHHhccHHHHHHHHHHH
Confidence            46788999999999888875443   3457899999999999999998762     346899999999999999999887


Q ss_pred             cC
Q 003090          233 LD  234 (848)
Q Consensus       233 ~~  234 (848)
                      ..
T Consensus        80 ~~   81 (438)
T KOG2543|consen   80 SQ   81 (438)
T ss_pred             hc
Confidence            74

>PRK10865 protein disaggregation chaperone; Provisional

Probab=89.63  E-value=6.2  Score=47.73  Aligned_cols=46  Identities=20%  Similarity=0.276  Sum_probs=37.1

Q ss_pred             ccccchhHHHHHHHHHHhc---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|-+..++.+...+..         ....++-++|..|+|||++|+.+.+..
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l  622 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM  622 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4688999999888888761         123578899999999999999998654

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=89.51  E-value=0.3  Score=46.50  Aligned_cols=26  Identities=31%  Similarity=0.438  Sum_probs=23.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..+|.|-||=|+||||||+.+-++..
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhC
Confidence            36899999999999999999987764

>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=89.31  E-value=0.26  Score=48.76  Aligned_cols=24  Identities=38%  Similarity=0.502  Sum_probs=21.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|+|.|..|.||||+|+.+.....
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~   24 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLS   24 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHh
Confidence            589999999999999999987653

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=89.23  E-value=0.35  Score=46.73  Aligned_cols=27  Identities=48%  Similarity=0.668  Sum_probs=23.1

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+-+|+|.|-+|.||||+|+.+++...
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~~   33 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQLG   33 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHhC
Confidence            346899999999999999999987653

>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=89.22  E-value=0.39  Score=43.84  Aligned_cols=23  Identities=39%  Similarity=0.693  Sum_probs=19.7

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|-++|+.|+||||+|+.+....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHC
Confidence            57789999999999999987543

...

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.20  E-value=11  Score=40.41  Aligned_cols=25  Identities=28%  Similarity=0.428  Sum_probs=21.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.++.++|..|+||||++..+-...
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999998887654

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=89.14  E-value=0.55  Score=46.21  Aligned_cols=30  Identities=30%  Similarity=0.468  Sum_probs=24.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHhhccc
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAKEMKM  207 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~~~~~  207 (848)
                      ...|-++||.|.||||..|.++.+...++.
T Consensus        19 p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~   48 (366)
T KOG1532|consen   19 PVIILVVGMAGSGKTTFMQRLNSHLHAKKT   48 (366)
T ss_pred             CcEEEEEecCCCCchhHHHHHHHHHhhccC
Confidence            356788999999999999999988765544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.99  E-value=0.63  Score=51.70  Aligned_cols=50  Identities=24%  Similarity=0.323  Sum_probs=40.0

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|.+.-++.+...+....+. .+=++|..|+||||+|+.+.+..
T Consensus        10 P~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l   60 (472)
T PRK14962         10 PKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSL   60 (472)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            334577999998888888877777664 46789999999999999997654

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=88.95  E-value=1.2  Score=46.17  Aligned_cols=61  Identities=15%  Similarity=0.144  Sum_probs=37.4

Q ss_pred             ccccchhHHHHHHHHHHh---------cCCc------cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEec
Q 003090          157 YAFKSRESTMKDIMEAMK---------DENV------SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVS  217 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------~~~~------~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs  217 (848)
                      ..++|.++.++.+.++..         ..++      .-+-++|..|.||||+|+.+..............++.++
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~   97 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVT   97 (284)
T ss_pred             HhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEec
Confidence            357888888877655432         1111      246689999999999998877654322222222355444

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.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=88.87  E-value=0.3  Score=47.57  Aligned_cols=23  Identities=52%  Similarity=0.723  Sum_probs=20.3

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|+|.|..|+||||+++.+....
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999987653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=88.86  E-value=0.55  Score=51.09  Aligned_cols=48  Identities=23%  Similarity=0.300  Sum_probs=38.4

Q ss_pred             ccccccchhHHHHHHHHHHh----c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK----D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~----~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+.|+++.++++.+.+.    .         ...+-|-++|..|.|||++|+++.+..
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~  189 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET  189 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh
Confidence            34578999999999888764    1         233557889999999999999998765

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=88.85  E-value=0.33  Score=46.39  Aligned_cols=22  Identities=50%  Similarity=0.709  Sum_probs=20.0

Q ss_pred             EEEEEeCCCCchhHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +|+|.|..|.||||+|+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999865

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.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=88.75  E-value=0.49  Score=48.63  Aligned_cols=27  Identities=30%  Similarity=0.294  Sum_probs=22.4

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+|+|.|..|+||||+|+.+....
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll   86 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALL   86 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            445799999999999999998776543

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.71  E-value=0.73  Score=49.66  Aligned_cols=49  Identities=18%  Similarity=0.241  Sum_probs=40.4

Q ss_pred             cccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++|-+..++.+.+.+....+. .+-++|..|+||||+|+.+.+..
T Consensus        13 ~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l   62 (363)
T PRK14961         13 QYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSL   62 (363)
T ss_pred             CchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHh
Confidence            34567999999999998888866654 45799999999999999988654

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=88.57  E-value=0.024  Score=54.00  Aligned_cols=88  Identities=15%  Similarity=0.076  Sum_probs=57.5

Q ss_pred             HHHHhccCCCceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCC
Q 003090          227 YEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPL  305 (848)
Q Consensus       227 ~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l  305 (848)
                      .+|..-...+.||++.|++..+...+ -+..+..|+++.|.+..+|.++ +....++.+++..              |..
T Consensus        36 ~ei~~~kr~tvld~~s~r~vn~~~n~s~~t~~~rl~~sknq~~~~~~d~-~q~~e~~~~~~~~--------------n~~  100 (326)
T KOG0473|consen   36 REIASFKRVTVLDLSSNRLVNLGKNFSILTRLVRLDLSKNQIKFLPKDA-KQQRETVNAASHK--------------NNH  100 (326)
T ss_pred             hhhhccceeeeehhhhhHHHhhccchHHHHHHHHHhccHhhHhhChhhH-HHHHHHHHHHhhc--------------cch
Confidence            34444444566777777776666555 5566777777777777777663 5666666677666              566


Q ss_pred             CCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          306 PSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       306 ~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      +.     .|.+++.+++++++++.++.+.
T Consensus       101 ~~-----~p~s~~k~~~~k~~e~k~~~~~  124 (326)
T KOG0473|consen  101 SQ-----QPKSQKKEPHPKKNEQKKTEFF  124 (326)
T ss_pred             hh-----CCccccccCCcchhhhccCcch
Confidence            65     7777777777777777776533

>PRK03839 putative kinase; Provisional

Probab=88.54  E-value=0.4  Score=45.89  Aligned_cols=23  Identities=43%  Similarity=0.608  Sum_probs=20.7

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.++|+.|+||||+++.+.+..
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>COG1084 Predicted GTPase [General function prediction only]

Probab=88.53  E-value=8.4  Score=39.58  Aligned_cols=52  Identities=13%  Similarity=0.269  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHH
Q 003090           39 IEALRTEAKKLTDRRNDLQAEIDAATRNREVIKDEVKSWIAEVNDIIPKAEKF   91 (848)
Q Consensus        39 ~~~~~~~l~~L~~~l~~i~~~l~~a~~~~~~~~~~v~~wl~~lk~~~~d~eD~   91 (848)
                      .+.-.-+..+++..-+.+...++..-++ .-.=+.+--+-.++-|+.||++++
T Consensus        41 ~kar~~e~~rv~t~~~i~~d~l~~iv~~-~P~id~LhpFY~eLidvl~d~d~~   92 (346)
T COG1084          41 VKAREFEIRRVKTASNIVRDRLDKIVER-FPSLDDLHPFYRELIDVLVDIDHL   92 (346)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCccccChHHHHHHHHHhCHHHH
Confidence            4444455677777777788888766544 333345556777888888887665

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=88.52  E-value=0.43  Score=46.03  Aligned_cols=25  Identities=32%  Similarity=0.367  Sum_probs=22.1

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +..+|.|+|..|+||||+|+.+...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~   26 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEK   26 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999988754

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.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=88.49  E-value=0.5  Score=44.27  Aligned_cols=27  Identities=30%  Similarity=0.438  Sum_probs=23.4

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+++|+|..|.|||||++.+.....
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~   31 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALC   31 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHh
Confidence            456899999999999999999987654

>PRK05541 adenylylsulfate kinase; Provisional

Probab=88.43  E-value=0.69  Score=44.05  Aligned_cols=27  Identities=37%  Similarity=0.529  Sum_probs=23.3

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.++|+.|.||||+|+.+++...
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            345899999999999999999997663

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=88.40  E-value=11  Score=44.35  Aligned_cols=24  Identities=33%  Similarity=0.400  Sum_probs=20.9

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      =..|+|+|-.|.|||||+|.+-.-
T Consensus       499 Ge~vaIvG~SGsGKSTL~KLL~gl  522 (709)
T COG2274         499 GEKVAIVGRSGSGKSTLLKLLLGL  522 (709)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            368999999999999999988643

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=88.34  E-value=6  Score=43.41  Aligned_cols=27  Identities=26%  Similarity=0.374  Sum_probs=22.8

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...++-++|..|+||||.+..+.....
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~  120 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFK  120 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            457899999999999999988876554

>cd01878 HflX HflX subfamily

Probab=88.20  E-value=1.6  Score=42.70  Aligned_cols=27  Identities=19%  Similarity=0.402  Sum_probs=22.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .....|.|+|.+|+|||||.+.+.+..
T Consensus        39 ~~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          39 SGIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHhcch
Confidence            455789999999999999998888653

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.19  E-value=0.71  Score=50.64  Aligned_cols=50  Identities=20%  Similarity=0.279  Sum_probs=41.5

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|-+.-+..+..++..+.+. .+=++|..|+||||+|+.+.+..
T Consensus        14 P~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~L   64 (484)
T PRK14956         14 PQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRL   64 (484)
T ss_pred             CCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            344578999999999999998877765 46799999999999999987654

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=88.08  E-value=0.59  Score=45.72  Aligned_cols=48  Identities=27%  Similarity=0.303  Sum_probs=40.2

Q ss_pred             cccccchhHHHH---HHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          156 VYAFKSRESTMK---DIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       156 ~~~~vG~~~~~~---~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -++++|-++.+.   -|++.|.      +|-.+.|=.+|..|.|||.+|+++-|..+
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~k  176 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAK  176 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccC
Confidence            457899988875   4666665      68889999999999999999999998764

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=88.03  E-value=0.88  Score=45.44  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=29.9

Q ss_pred             ccchhHHHHHHH-HHHh-cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          159 FKSRESTMKDIM-EAMK-DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       159 ~vG~~~~~~~i~-~~L~-~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|..+..-..+ ++.. .+....+-++|..|+|||+||+.+++..
T Consensus        21 ~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~   66 (227)
T PRK08903         21 VAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADA   66 (227)
T ss_pred             ccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            346544443333 3323 2444678899999999999999999865

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=88.00  E-value=1.1  Score=39.93  Aligned_cols=40  Identities=25%  Similarity=0.281  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhc--CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          164 STMKDIMEAMKD--ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       164 ~~~~~i~~~L~~--~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++.+++-+.+..  ..-.++.+.|.-|.||||+++.+.+...
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~lg   47 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLG   47 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            344444554442  2335899999999999999999987643

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=87.94  E-value=1.2  Score=46.87  Aligned_cols=59  Identities=22%  Similarity=0.298  Sum_probs=45.2

Q ss_pred             ccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH----hhccccCcEEEEE
Q 003090          157 YAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA----KEMKMFDDVAMAV  215 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~----~~~~~F~~~~wv~  215 (848)
                      .+++|-+.-++.+..++....+. ..-++|..|+||||+|+.+....    ....|+|...|..
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~   67 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKP   67 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecc
Confidence            46889999999999999866654 55789999999999999998753    1235666656654

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=87.89  E-value=0.74  Score=42.60  Aligned_cols=24  Identities=38%  Similarity=0.516  Sum_probs=21.5

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      |++|+|+.|+||||++..+....+
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~   24 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALK   24 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            588999999999999999998764

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=87.79  E-value=0.91  Score=46.35  Aligned_cols=35  Identities=20%  Similarity=0.212  Sum_probs=28.8

Q ss_pred             HHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          168 DIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       168 ~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +..+++...+..++.|+|..|.|||||...+.+..
T Consensus        94 ~~r~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l  128 (290)
T PRK10463         94 RNRARFAARKQLVLNLVSSPGSGKTTLLTETLMRL  128 (290)
T ss_pred             HHHHHHHhcCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34445557788999999999999999999888764

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.75  E-value=0.76  Score=51.73  Aligned_cols=49  Identities=22%  Similarity=0.346  Sum_probs=40.2

Q ss_pred             cccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++|-+..++.+...+..+.+. .+=++|..|+||||+|+.+.+..
T Consensus        13 ~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L   62 (546)
T PRK14957         13 QSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCL   62 (546)
T ss_pred             CcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34567999999999999998876654 35689999999999999998644

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=87.70  E-value=5.1  Score=44.01  Aligned_cols=25  Identities=28%  Similarity=0.457  Sum_probs=20.2

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.++.++|.+|+||||++..+-...
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~  245 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARY  245 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3589999999999999877765433

>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=87.66  E-value=0.28  Score=28.16  Aligned_cols=21  Identities=38%  Similarity=0.618  Sum_probs=14.4

Q ss_pred             cccEEeccCCccccccChhhhhc
Q 003090          368 HLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       368 ~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      +|++|++++|.+. .+|.+ +++
T Consensus         1 ~L~~Ldls~n~l~-~ip~~-~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNNLT-SIPSS-FSN   21 (22)
T ss_dssp             TESEEEETSSEES-EEGTT-TTT
T ss_pred             CccEEECCCCcCE-eCChh-hcC
Confidence            4778888887554 67776 554

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 ....

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=87.56  E-value=0.8  Score=48.34  Aligned_cols=46  Identities=17%  Similarity=0.235  Sum_probs=39.3

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|||-++.+..++-.+.+....-+-|.|..|.||||+++.+-.-.
T Consensus         4 ~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             cccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            5789999999888877777777778899999999999999987544

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PRK04040 adenylate kinase; Provisional

Probab=87.54  E-value=0.53  Score=45.20  Aligned_cols=24  Identities=29%  Similarity=0.537  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|+|+.|+||||+++.+.+..
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l   26 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKL   26 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHh
Confidence            478999999999999999988654

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.49  E-value=0.87  Score=49.73  Aligned_cols=50  Identities=22%  Similarity=0.314  Sum_probs=40.3

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|-+.-++.+..++.+..+.. +=++|..|+||||+|..+-+..
T Consensus        12 P~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l   62 (397)
T PRK14955         12 PKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAV   62 (397)
T ss_pred             CCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHh
Confidence            3345789999999998888887766644 6689999999999999887654

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=87.47  E-value=0.41  Score=53.79  Aligned_cols=74  Identities=27%  Similarity=0.329  Sum_probs=51.4

Q ss_pred             ccccccchhHHHHHHHHHHhcCC----------------------------------ccEEEEEeCCCCchhHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDEN----------------------------------VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~----------------------------------~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      ...+++|.+.--..++.||+.|+                                  -+|.=.+|..|+||||||.-|.+
T Consensus       269 ~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTTLAHViAk  348 (877)
T KOG1969|consen  269 KFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTLAHVIAK  348 (877)
T ss_pred             HHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChhHHHHHHHH
Confidence            34567888888888899988443                                  24566899999999999988876


Q ss_pred             HHhhccccCcEEEEEeccCCchhHHHHHHHhcc
Q 003090          201 QAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWL  233 (848)
Q Consensus       201 ~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~~  233 (848)
                      +..    | .++-+.-|+.-....+-..|...+
T Consensus       349 qaG----Y-sVvEINASDeRt~~~v~~kI~~av  376 (877)
T KOG1969|consen  349 QAG----Y-SVVEINASDERTAPMVKEKIENAV  376 (877)
T ss_pred             hcC----c-eEEEecccccccHHHHHHHHHHHH
Confidence            541    2 355666677666665555555444

>PRK00889 adenylylsulfate kinase; Provisional

Probab=87.45  E-value=0.56  Score=44.62  Aligned_cols=27  Identities=22%  Similarity=0.441  Sum_probs=23.3

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .-.++.++|+.|.||||+|+.+.....
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~   29 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLR   29 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            346899999999999999999997653

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=87.44  E-value=0.74  Score=48.60  Aligned_cols=48  Identities=19%  Similarity=0.227  Sum_probs=41.8

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -..+||-++.+..++..+.+..+.-+-|.|..|.||||+|+.+++-..
T Consensus        16 f~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~   63 (350)
T CHL00081         16 FTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLP   63 (350)
T ss_pred             HHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHh
Confidence            468999999999888888888887777999999999999999987653

>PRK10536 hypothetical protein; Provisional

Probab=87.40  E-value=3.4  Score=41.30  Aligned_cols=46  Identities=17%  Similarity=0.250  Sum_probs=37.8

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +...+.++.......+.++.+.  .++-+.|..|.|||+||.++.-+.
T Consensus        53 ~~~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~   98 (262)
T PRK10536         53 DTSPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEA   98 (262)
T ss_pred             CCccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHH
Confidence            3456788888888899988764  489999999999999998877643

>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=87.39  E-value=0.44  Score=45.42  Aligned_cols=24  Identities=42%  Similarity=0.746  Sum_probs=21.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|+|.|..|.||||+|+.+.....
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~   24 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLR   24 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            589999999999999999987653

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=87.37  E-value=0.87  Score=51.47  Aligned_cols=51  Identities=20%  Similarity=0.268  Sum_probs=41.2

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|.+..++.+.+++....+. .+=++|..|+||||+|+.+-+..
T Consensus        11 RP~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L   62 (605)
T PRK05896         11 RPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAI   62 (605)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3444578999999999999998766554 46689999999999999887654

>smart00369 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily

Probab=87.34  E-value=0.52  Score=28.29  Aligned_cols=21  Identities=38%  Similarity=0.556  Sum_probs=14.3

Q ss_pred             ccCCCEEEccCCCCcccChhh
Q 003090          343 LSGLEILDLSESDVSEIPVSF  363 (848)
Q Consensus       343 l~~L~~L~l~~~~l~~lp~~i  363 (848)
                      +.+|++|++++|.++.+|...
T Consensus         1 L~~L~~L~L~~N~l~~lp~~~   21 (26)
T smart00369        1 LPNLRELDLSNNQLSSLPPGA   21 (26)
T ss_pred             CCCCCEEECCCCcCCcCCHHH
Confidence            356777777777777777653

>smart00370 LRR Leucine-rich repeats, outliers

Probab=87.34  E-value=0.52  Score=28.29  Aligned_cols=21  Identities=38%  Similarity=0.556  Sum_probs=14.3

Q ss_pred             ccCCCEEEccCCCCcccChhh
Q 003090          343 LSGLEILDLSESDVSEIPVSF  363 (848)
Q Consensus       343 l~~L~~L~l~~~~l~~lp~~i  363 (848)
                      +.+|++|++++|.++.+|...
T Consensus         1 L~~L~~L~L~~N~l~~lp~~~   21 (26)
T smart00370        1 LPNLRELDLSNNQLSSLPPGA   21 (26)
T ss_pred             CCCCCEEECCCCcCCcCCHHH
Confidence            356777777777777777653

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=87.29  E-value=0.78  Score=44.44  Aligned_cols=22  Identities=45%  Similarity=0.659  Sum_probs=18.6

Q ss_pred             EEEEEeCCCCchhHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .|+|+|-||+||||+|..+...
T Consensus         2 kIaI~GKGG~GKTtiaalll~~   23 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKR   23 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHH
Confidence            6899999999999999875443

>PRK00625 shikimate kinase; Provisional

Probab=87.13  E-value=0.53  Score=44.44  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=19.8

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|-++||.|+||||+++.+-+..
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l   24 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37799999999999999987654

>PRK08084 DNA replication initiation factor; Provisional

Probab=87.09  E-value=1.1  Score=45.01  Aligned_cols=47  Identities=11%  Similarity=0.238  Sum_probs=32.0

Q ss_pred             ccccchhH-HHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          157 YAFKSRES-TMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       157 ~~~vG~~~-~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..++|... .+..+..+...+....+-++|..|+|||+|++.+.+...
T Consensus        23 ~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~   70 (235)
T PRK08084         23 SFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELS   70 (235)
T ss_pred             ccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            44556322 333333443355556889999999999999999998654

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=87.02  E-value=0.88  Score=54.00  Aligned_cols=47  Identities=28%  Similarity=0.279  Sum_probs=39.7

Q ss_pred             cccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +...+|.++-++.|+++|.      ...-.++.++|..|+||||+|+.+....
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l  373 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT  373 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999887      2345689999999999999999998654

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=86.83  E-value=0.59  Score=44.67  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++.|+|..|+||||+++.+....
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            368999999999999999987654

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.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=86.37  E-value=0.79  Score=44.99  Aligned_cols=31  Identities=19%  Similarity=0.381  Sum_probs=26.2

Q ss_pred             HHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          172 AMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       172 ~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+...++.+|+++|..|.|||||.+++....
T Consensus        16 ~~~~~~~~~i~~~G~~gsGKTTli~~l~~~~   46 (207)
T TIGR00073        16 RLDKHGLVVLNFMSSPGSGKTTLIEKLIDNL   46 (207)
T ss_pred             HhhhcCcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4446789999999999999999999887653

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK10867 signal recognition particle protein; Provisional

Probab=86.21  E-value=7.9  Score=42.42  Aligned_cols=26  Identities=27%  Similarity=0.442  Sum_probs=20.8

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +...+|-++|..|+||||.+..+-..
T Consensus        98 ~~p~vI~~vG~~GsGKTTtaakLA~~  123 (433)
T PRK10867         98 KPPTVIMMVGLQGAGKTTTAGKLAKY  123 (433)
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHH
Confidence            34679999999999999977666543

>PRK03846 adenylylsulfate kinase; Provisional

Probab=86.18  E-value=0.71  Score=44.94  Aligned_cols=27  Identities=19%  Similarity=0.366  Sum_probs=23.4

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++.++|+.|.||||+|+.+....
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~~l   48 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEAL   48 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            455799999999999999999998754

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=86.18  E-value=9.7  Score=40.64  Aligned_cols=36  Identities=25%  Similarity=0.450  Sum_probs=24.2

Q ss_pred             HHHHHHHhcC----CccEEEEEeCCCCchhH-HHHHHHHHH
Q 003090          167 KDIMEAMKDE----NVSITGICGMGGVGKTT-LVKEIQKQA  202 (848)
Q Consensus       167 ~~i~~~L~~~----~~~vi~i~G~gG~GKTt-la~~v~~~~  202 (848)
                      ..+..++..+    +-+++..||.-|||||| ||+....-.
T Consensus       188 ~~~~~~~~~~~~~~~~~vi~LVGPTGVGKTTTlAKLAar~~  228 (407)
T COG1419         188 RKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYV  228 (407)
T ss_pred             HHHHHhhccccccccCcEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3444444433    35899999999999997 666554433

>TIGR03263 guanyl_kin guanylate kinase

Probab=86.17  E-value=0.56  Score=44.84  Aligned_cols=23  Identities=43%  Similarity=0.638  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +++.++|..|+||||+++.+.+.
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHcc
Confidence            47899999999999999999863

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.14  E-value=1.1  Score=51.04  Aligned_cols=50  Identities=18%  Similarity=0.274  Sum_probs=40.9

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|.+..++.+..++....+ ..+=++|..|+||||+|+.+-+..
T Consensus        11 PktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~L   61 (702)
T PRK14960         11 PRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCL   61 (702)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34457899999999999999986665 455789999999999999887654

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=86.04  E-value=1.3  Score=46.08  Aligned_cols=47  Identities=23%  Similarity=0.321  Sum_probs=40.9

Q ss_pred             cccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.+++|.++.++++++.+.      +..-+|+-.+|..|.||+|++..+-+-.
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999997      3455789999999999999999988665

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK06217 hypothetical protein; Validated

Probab=86.00  E-value=0.63  Score=44.62  Aligned_cols=24  Identities=29%  Similarity=0.385  Sum_probs=21.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .|.|.|..|.||||+|+.+.+...
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~   26 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLD   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            488999999999999999987654

>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=85.96  E-value=0.97  Score=41.52  Aligned_cols=25  Identities=28%  Similarity=0.523  Sum_probs=22.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|=+.|..|.||||+|+.+.....
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~   27 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLF   27 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4778999999999999999998764

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 ....

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=85.85  E-value=1.3  Score=50.16  Aligned_cols=47  Identities=26%  Similarity=0.283  Sum_probs=38.7

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|.+..++.+...+......-+=|+|..|+|||++|+.+++..
T Consensus        64 f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        64 FDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             HHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            45799999999988887765544556799999999999999998754

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.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.67  E-value=1.2  Score=52.57  Aligned_cols=49  Identities=18%  Similarity=0.294  Sum_probs=41.2

Q ss_pred             cccccccchhHHHHHHHHHHhcCCccEE-EEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVSIT-GICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~vi-~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+|+|-+.-++.+.+++..+.+.-. =++|..|+||||+|+.+.+..
T Consensus        13 ~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~L   62 (944)
T PRK14949         13 ATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGL   62 (944)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3457899999999999999887777654 689999999999999998765

>PRK00131 aroK shikimate kinase; Reviewed

Probab=85.63  E-value=0.82  Score=43.34  Aligned_cols=25  Identities=24%  Similarity=0.306  Sum_probs=21.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..|-++|+.|.||||+|+.+....
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            3578999999999999999998764

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=85.62  E-value=0.56  Score=42.98  Aligned_cols=23  Identities=39%  Similarity=0.540  Sum_probs=20.3

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|.|+|..|.||||+|+.+-...
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999888654

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.61  E-value=7.9  Score=41.77  Aligned_cols=25  Identities=28%  Similarity=0.347  Sum_probs=21.1

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++.++|..|+||||.+..+....
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999988776544

>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=85.51  E-value=1.9  Score=41.75  Aligned_cols=53  Identities=21%  Similarity=0.287  Sum_probs=34.8

Q ss_pred             cchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEE
Q 003090          160 KSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMA  214 (848)
Q Consensus       160 vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv  214 (848)
                      ..+..+-...++.|.  +..++.+.|..|.|||.||-+.--+.-..+.++..+++
T Consensus         3 ~p~~~~Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~   55 (205)
T PF02562_consen    3 KPKNEEQKFALDALL--NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIIT   55 (205)
T ss_dssp             ---SHHHHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEE
T ss_pred             cCCCHHHHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            344556667778777  55689999999999999987766555445777777665

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=85.47  E-value=1.3  Score=48.64  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=37.3

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|+++.++.+...+....  .+=+.|..|+|||++|+.+-...
T Consensus        20 ~~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~   63 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAF   63 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHh
Confidence            568999999999888887555  46689999999999999998754

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.35  E-value=1.1  Score=49.55  Aligned_cols=49  Identities=18%  Similarity=0.251  Sum_probs=39.4

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .|..-.+++|-+..++.+.+.+....+. .+=++|..|+||||+|+.+-+
T Consensus         8 RP~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk   57 (491)
T PRK14964          8 RPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISL   57 (491)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHH
Confidence            3444578999999888888888766665 577999999999999988765

>PRK13949 shikimate kinase; Provisional

Probab=85.32  E-value=0.74  Score=43.39  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=20.4

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.++|+.|.||||+++.+.+..
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48899999999999999988654

>PRK08727 hypothetical protein; Validated

Probab=84.93  E-value=1.7  Score=43.53  Aligned_cols=56  Identities=14%  Similarity=0.169  Sum_probs=35.2

Q ss_pred             ccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEe
Q 003090          159 FKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVV  216 (848)
Q Consensus       159 ~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~v  216 (848)
                      ++|-......+..+........+-++|..|+|||+|++++.+...-+  .....++..
T Consensus        22 ~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~   77 (233)
T PRK08727         22 IAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPL   77 (233)
T ss_pred             cCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeH
Confidence            44444444444444333333569999999999999999998865432  224455544

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=84.83  E-value=0.76  Score=44.20  Aligned_cols=23  Identities=22%  Similarity=0.499  Sum_probs=20.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .++.|+|+.|+||||+++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            36889999999999999999754

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=84.77  E-value=0.8  Score=41.31  Aligned_cols=24  Identities=33%  Similarity=0.527  Sum_probs=21.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+.++|..|+||||+++.+....
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~   26 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAREL   26 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcc
Confidence            478899999999999999998655

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.

>PRK09087 hypothetical protein; Validated

Probab=84.75  E-value=1.8  Score=43.05  Aligned_cols=28  Identities=21%  Similarity=0.276  Sum_probs=23.2

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+..+.+.|||..|+|||+|++.+.+..
T Consensus        41 ~~~~~~l~l~G~~GsGKThLl~~~~~~~   68 (226)
T PRK09087         41 NWPSPVVVLAGPVGSGKTHLASIWREKS   68 (226)
T ss_pred             cCCCCeEEEECCCCCCHHHHHHHHHHhc
Confidence            4555679999999999999999888653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.71  E-value=1.3  Score=50.28  Aligned_cols=50  Identities=22%  Similarity=0.351  Sum_probs=41.3

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +..-.++||-+.-++.+.+++..+.+.- +=++|..|+||||+|+.+-+..
T Consensus        12 PqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaL   62 (700)
T PRK12323         12 PRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSL   62 (700)
T ss_pred             CCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3345789999999999999998777654 4689999999999998887654

>PRK06893 DNA replication initiation factor; Validated

Probab=84.69  E-value=1.8  Score=43.23  Aligned_cols=41  Identities=20%  Similarity=0.118  Sum_probs=29.7

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEec
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVS  217 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs  217 (848)
                      ++....+-++|..|+|||+|++++.+....+  .....++.+.
T Consensus        36 ~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~   76 (229)
T PRK06893         36 DLQQPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPLS   76 (229)
T ss_pred             ccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeHH
Confidence            4444678999999999999999999875333  2344555553

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=84.65  E-value=0.77  Score=44.81  Aligned_cols=22  Identities=36%  Similarity=0.589  Sum_probs=20.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+++|+|-.|.|||||++.+--
T Consensus        34 e~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          34 ETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhc
Confidence            5899999999999999998874

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=84.65  E-value=1.3  Score=50.76  Aligned_cols=50  Identities=22%  Similarity=0.362  Sum_probs=41.4

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .|..-.+++|.+..++.+.+++....+. .+=++|..|+||||+|+.+-+.
T Consensus        11 RP~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~   61 (709)
T PRK08691         11 RPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKS   61 (709)
T ss_pred             CCCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            3444578999999999999999877654 5678999999999999888764

>TIGR00602 rad24 checkpoint protein rad24

Probab=84.64  E-value=1.3  Score=50.85  Aligned_cols=53  Identities=21%  Similarity=0.266  Sum_probs=43.1

Q ss_pred             ccCCcccccccchhHHHHHHHHHHhcC-----CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          150 ISSSEGVYAFKSRESTMKDIMEAMKDE-----NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       150 ~~~~~~~~~~vG~~~~~~~i~~~L~~~-----~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+.|....+++|-++.++++..|+...     ...++.++|..|.||||+++.+....
T Consensus        77 KyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        77 KYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            445556778999999999999998743     23569999999999999999998754

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK00300 gmk guanylate kinase; Provisional

Probab=84.63  E-value=0.81  Score=44.85  Aligned_cols=24  Identities=33%  Similarity=0.501  Sum_probs=21.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      -.++.|+|..|+||||+++.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            368999999999999999999875

>PRK13695 putative NTPase; Provisional

Probab=84.56  E-value=1.3  Score=41.97  Aligned_cols=24  Identities=54%  Similarity=0.649  Sum_probs=21.0

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+.+.|..|+||||+++.+++...
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~   25 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLK   25 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999987654

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=84.53  E-value=1.4  Score=48.15  Aligned_cols=47  Identities=23%  Similarity=0.301  Sum_probs=37.1

Q ss_pred             cccccchhHHHHHHHHHHh----c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK----D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.|.++.++++.+.+.    .         ....-+-++|..|.|||++|++|.+..
T Consensus       182 ~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el  241 (438)
T PTZ00361        182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET  241 (438)
T ss_pred             HHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            3568899999988888764    1         123457799999999999999999865

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.50  E-value=1.4  Score=49.67  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=41.3

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.++||-+.-++.+.+++....+.- +=++|..|+||||+|+.+-+..
T Consensus        12 P~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l   62 (509)
T PRK14958         12 PRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCL   62 (509)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHh
Confidence            3445789999999999999998776654 5689999999999998887654

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=84.44  E-value=0.89  Score=41.08  Aligned_cols=24  Identities=38%  Similarity=0.562  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+++|+|..|.|||||.+.+....
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~~   35 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGLL   35 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEccCCCccccceeeecccc
Confidence            589999999999999999887543

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=84.44  E-value=1  Score=42.61  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|.++|+.|.||||+++.+-+..
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHc
Confidence            468999999999999999998653

>PRK13975 thymidylate kinase; Provisional

Probab=84.43  E-value=0.9  Score=44.14  Aligned_cols=25  Identities=28%  Similarity=0.383  Sum_probs=22.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..|.|.|+.|+||||+|+.+.+...
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~   27 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLN   27 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999987663

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=84.37  E-value=1.2  Score=41.62  Aligned_cols=24  Identities=38%  Similarity=0.580  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+.+.|..|+||+|+++.++++.
T Consensus         5 ~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           5 LLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhc
Confidence            467899999999999999999764

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.34  E-value=1.6  Score=47.19  Aligned_cols=50  Identities=18%  Similarity=0.377  Sum_probs=40.9

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|.+..++.+..++.+.... .+=++|..|+||||+|+.+-+..
T Consensus        13 P~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l   63 (367)
T PRK14970         13 PQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKI   63 (367)
T ss_pred             CCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            334567899999999999999876654 67799999999999999986654

>PRK06620 hypothetical protein; Validated

Probab=84.31  E-value=1.8  Score=42.63  Aligned_cols=47  Identities=23%  Similarity=0.004  Sum_probs=30.6

Q ss_pred             cccccchhH--HHHHHHHHHhcCCc----cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRES--TMKDIMEAMKDENV----SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~--~~~~i~~~L~~~~~----~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.-++|--.  ....+..|-..|..    ..+-++|..|+|||+|++.+.+..
T Consensus        16 d~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~   68 (214)
T PRK06620         16 DEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLS   68 (214)
T ss_pred             hhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhcc
Confidence            455667622  23344444333432    458899999999999999877654

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=84.25  E-value=0.8  Score=39.34  Aligned_cols=22  Identities=45%  Similarity=0.628  Sum_probs=18.7

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-|+|..|+|||++|+.+..+.
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            3589999999999999977665

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

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=84.17  E-value=0.79  Score=46.83  Aligned_cols=27  Identities=30%  Similarity=0.441  Sum_probs=23.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhc
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEM  205 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~  205 (848)
                      ++++|+|.+|.|||||+..+-....-+
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L~~~   28 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRLSGR   28 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            479999999999999999988766433

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=84.07  E-value=0.91  Score=41.99  Aligned_cols=22  Identities=36%  Similarity=0.448  Sum_probs=19.5

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.++|+.|.||||+|+.+....
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            6789999999999999997654

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=84.06  E-value=0.96  Score=39.57  Aligned_cols=22  Identities=32%  Similarity=0.516  Sum_probs=19.4

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.|+|-.|+|||||.+.+....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            6799999999999999888654

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=84.04  E-value=0.93  Score=38.54  Aligned_cols=21  Identities=38%  Similarity=0.414  Sum_probs=19.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~  199 (848)
                      ..+.|+|..|.|||||++.+.
T Consensus        16 e~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          16 VGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEEEcCCCCCHHHHHHHhh
Confidence            578999999999999998875

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=84.03  E-value=1.6  Score=47.34  Aligned_cols=48  Identities=21%  Similarity=0.252  Sum_probs=37.7

Q ss_pred             ccccccchhHHHHHHHHHHh----------c---CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK----------D---ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~----------~---~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...+|.|.+..++++.+.+.          .   ...+-+-++|..|.|||++|+++.+..
T Consensus       143 ~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l  203 (398)
T PTZ00454        143 TYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT  203 (398)
T ss_pred             CHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            34678999999988877653          1   223567799999999999999998764

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=84.01  E-value=0.8  Score=41.40  Aligned_cols=21  Identities=38%  Similarity=0.650  Sum_probs=19.1

Q ss_pred             EEEEeCCCCchhHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~  201 (848)
                      +.|+|..|+||||+++.+...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            689999999999999999864

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=84.00  E-value=0.84  Score=42.07  Aligned_cols=22  Identities=32%  Similarity=0.566  Sum_probs=19.1

Q ss_pred             EEEEEeCCCCchhHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ++-++|..|+||||+|+.+.+.
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            3678999999999999998765

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=83.95  E-value=0.84  Score=43.77  Aligned_cols=23  Identities=26%  Similarity=0.278  Sum_probs=19.8

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ||-|+|+.|+||||+|+.+....
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            57899999999999999987643

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=83.92  E-value=0.75  Score=42.31  Aligned_cols=23  Identities=22%  Similarity=0.603  Sum_probs=20.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++-|+|..|.||||+|+.+....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l   23 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKL   23 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            47899999999999999988754

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>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=83.92  E-value=1  Score=40.28  Aligned_cols=22  Identities=32%  Similarity=0.433  Sum_probs=19.6

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-++|..|.||||+|+.+.+..
T Consensus         1 ill~G~~G~GKT~l~~~la~~l   22 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL   22 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT
T ss_pred             CEEECcCCCCeeHHHHHHHhhc
Confidence            3589999999999999999875

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 ....

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=83.81  E-value=4  Score=40.34  Aligned_cols=53  Identities=17%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             CcccccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhc
Q 003090          153 SEGVYAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEM  205 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~  205 (848)
                      +.....++|.|..++.+++=..    .....-+=+||..|.|||++++++.+.-..+
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            3456789999999988877543    4445566789999999999999998765433

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=83.79  E-value=1.3  Score=41.16  Aligned_cols=25  Identities=32%  Similarity=0.595  Sum_probs=22.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+++|+|..|.||||++..+.....
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l~   26 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPALS   26 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4799999999999999999987653

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=83.74  E-value=2.2  Score=41.95  Aligned_cols=46  Identities=24%  Similarity=0.225  Sum_probs=34.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQY  227 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  227 (848)
                      +++-|+|.+|.|||+++..+.....  ..-..++|++... ++..++.+
T Consensus        13 ~i~~i~G~~GsGKT~l~~~~~~~~~--~~g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        13 TITQIYGPPGSGKTNICMILAVNAA--RQGKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH--hCCCeEEEEECCC-CCHHHHHH
Confidence            6889999999999999988765442  2245688887765 66655554

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=83.69  E-value=1  Score=42.79  Aligned_cols=24  Identities=21%  Similarity=0.349  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|-+.|..|.||||+|+.+....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            478899999999999999997653

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>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=83.50  E-value=3  Score=40.32  Aligned_cols=25  Identities=32%  Similarity=0.562  Sum_probs=20.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|+.+||..|+||||.+-.+.....
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~   26 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLK   26 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHh
Confidence            6899999999999997666655443

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 ....

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=83.43  E-value=0.94  Score=45.32  Aligned_cols=25  Identities=44%  Similarity=0.550  Sum_probs=22.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|+|..|+|||||.+.+..-.
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g~l   52 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAGLL   52 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccC
Confidence            3689999999999999999998644

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=83.25  E-value=1  Score=41.10  Aligned_cols=24  Identities=42%  Similarity=0.548  Sum_probs=19.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++.|+|..|+||||+.+.+-..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~   27 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKE   27 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHH
Confidence            468999999999999987666543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=83.22  E-value=2  Score=43.12  Aligned_cols=49  Identities=22%  Similarity=0.126  Sum_probs=35.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccc----cCcEEEEEeccCCchhHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKM----FDDVAMAVVSQTPSITKIQY  227 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~l~~  227 (848)
                      .++.|+|..|.|||+++..+.-.......    -..++|++-...++..++..
T Consensus        20 ~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~   72 (235)
T cd01123          20 SITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQ   72 (235)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHH
Confidence            68899999999999999988644322221    25688888777666655543

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 .

>PRK13947 shikimate kinase; Provisional

Probab=83.15  E-value=1  Score=42.58  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=20.1

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.++|+.|+||||+|+.+-+..
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            47899999999999999987654

>CHL00095 clpC Clp protease ATP binding subunit

Probab=83.10  E-value=37  Score=41.14  Aligned_cols=45  Identities=20%  Similarity=0.307  Sum_probs=36.0

Q ss_pred             ccccchhHHHHHHHHHHhc---------CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD---------ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~---------~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..|+|-++.++.+.+.+..         ....++-++|..|+|||++|+.+-+.
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~  562 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASY  562 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHH
Confidence            5689999999999888761         12345668999999999999988754

>TIGR01287 nifH nitrogenase iron protein

Probab=82.96  E-value=0.87  Score=47.06  Aligned_cols=24  Identities=33%  Similarity=0.552  Sum_probs=19.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|+|+|-||+||||++..+--..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~L   24 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAAL   24 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHH
Confidence            368999999999999887665443

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=82.95  E-value=1.8  Score=50.06  Aligned_cols=51  Identities=22%  Similarity=0.318  Sum_probs=40.6

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+..-.+++|.+..++.+.+++...++. .+=++|..|+||||+|+.+-+..
T Consensus        11 RPqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaL   62 (830)
T PRK07003         11 RPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKAL   62 (830)
T ss_pred             CCCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3344578999999999999999876654 44589999999999998776644

>smart00367 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily

Probab=82.95  E-value=0.6  Score=28.05  Aligned_cols=18  Identities=17%  Similarity=0.479  Sum_probs=14.0

Q ss_pred             ccCccEEEeecCcccccc
Q 003090          674 LHNLKKVRVEECDELRQV  691 (848)
Q Consensus       674 l~~L~~L~i~~C~~L~~~  691 (848)
                      +++|+.|+|++|+++++.
T Consensus         1 c~~L~~L~l~~C~~itD~   18 (26)
T smart00367        1 CPNLRELDLSGCTNITDE   18 (26)
T ss_pred             CCCCCEeCCCCCCCcCHH
Confidence            467888888888888763

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=82.94  E-value=2  Score=45.05  Aligned_cols=27  Identities=22%  Similarity=0.373  Sum_probs=22.7

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.-..|.++|+.|.||||+++.+....
T Consensus       131 ~~~~~I~l~G~~GsGKStvg~~La~~L  157 (309)
T PRK08154        131 ARRRRIALIGLRGAGKSTLGRMLAARL  157 (309)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            344689999999999999999987653

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=82.88  E-value=1.7  Score=49.72  Aligned_cols=52  Identities=17%  Similarity=0.313  Sum_probs=42.3

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|..-.+++|.+..++.+..++....+. -+=++|..|+||||+|+.+-+..
T Consensus        18 yRP~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L   70 (598)
T PRK09111         18 YRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARAL   70 (598)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence            34445678999999999999998866654 57789999999999999887654

>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=82.85  E-value=3  Score=37.75  Aligned_cols=41  Identities=24%  Similarity=0.250  Sum_probs=27.8

Q ss_pred             EEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQ  226 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~  226 (848)
                      |-++|..|+|||++|+.+.....     ....-+.++...+...+.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~-----~~~~~i~~~~~~~~~dl~   42 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLG-----RPVIRINCSSDTTEEDLI   42 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHT-----CEEEEEE-TTTSTHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhh-----cceEEEEeccccccccce
Confidence            45899999999999999987651     123334566656655554

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.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.81  E-value=1.8  Score=49.73  Aligned_cols=49  Identities=22%  Similarity=0.320  Sum_probs=39.8

Q ss_pred             cccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++|-+.-++.+.+++....+.. +=++|..|+||||+|+.+-+..
T Consensus        13 ~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L   62 (620)
T PRK14954         13 SKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAV   62 (620)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHh
Confidence            345789999999998888887766644 6789999999999998877654

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=82.80  E-value=2.1  Score=46.17  Aligned_cols=48  Identities=19%  Similarity=0.288  Sum_probs=39.8

Q ss_pred             ccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-.+++|.+..++.+.+++...... .+=++|..|+||||+|+.+....
T Consensus        12 ~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l   60 (355)
T TIGR02397        12 TFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKAL   60 (355)
T ss_pred             cHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3567899999999999999866654 45689999999999998887654

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=82.80  E-value=1.1  Score=42.93  Aligned_cols=34  Identities=21%  Similarity=0.256  Sum_probs=26.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEE
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMA  214 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv  214 (848)
                      -.|+.|+|..|.||||+.+.+..-....   +..+|+
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~LE~~~---~G~I~i   61 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGLEEPD---SGSITV   61 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCcCCC---CceEEE
Confidence            3689999999999999999998655433   346666

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=82.77  E-value=1.1  Score=43.49  Aligned_cols=24  Identities=29%  Similarity=0.509  Sum_probs=21.5

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|.|.|+.|+||||+++.+.+...
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~   25 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLE   25 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999987764

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=82.57  E-value=2.2  Score=45.43  Aligned_cols=25  Identities=36%  Similarity=0.441  Sum_probs=21.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.++|.+|+||||++..+....
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L  265 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQF  265 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHH
Confidence            4789999999999999998887544

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=82.54  E-value=1.7  Score=40.09  Aligned_cols=35  Identities=23%  Similarity=0.509  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          164 STMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       164 ~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +.++++.+++..   +++.++|..|+||+||...+...
T Consensus        24 ~g~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   24 EGIEELKELLKG---KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTHHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCHHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhh
Confidence            346777777754   68899999999999999888754

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=82.48  E-value=1.1  Score=41.37  Aligned_cols=20  Identities=45%  Similarity=0.699  Sum_probs=18.1

Q ss_pred             EEEEEeCCCCchhHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~  199 (848)
                      .|.|.|-.|+||||.++.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58899999999999998876

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=82.38  E-value=1.2  Score=42.28  Aligned_cols=24  Identities=21%  Similarity=0.257  Sum_probs=21.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++.++|..|.||||+++.+....
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l   27 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALF   27 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            478999999999999999999765

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=82.36  E-value=1.7  Score=49.69  Aligned_cols=48  Identities=21%  Similarity=0.348  Sum_probs=38.9

Q ss_pred             cccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..-.++||-+.-++.+.+++..+.+. .+=++|..|+||||+|+.+-+.
T Consensus        13 ~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~   61 (618)
T PRK14951         13 RSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKS   61 (618)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            34567899999888888888877664 4578999999999999888543

>PLN02796 D-glycerate 3-kinase

Probab=82.28  E-value=1.1  Score=46.82  Aligned_cols=27  Identities=33%  Similarity=0.336  Sum_probs=23.0

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..-+|+|.|..|.||||+++.+.....
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~lL~  125 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYLFN  125 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHhc
Confidence            345799999999999999999987653

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=82.13  E-value=3.3  Score=44.17  Aligned_cols=51  Identities=18%  Similarity=0.198  Sum_probs=41.8

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.+...++|-++....+...+...... .+=++|..|+||||+|..+-+..
T Consensus        18 ~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~L   69 (351)
T PRK09112         18 SPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHI   69 (351)
T ss_pred             CCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHH
Confidence            3445678999999999999999866654 47789999999999998887654

>TIGR03689 pup_AAA proteasome ATPase

Probab=82.12  E-value=1.9  Score=48.16  Aligned_cols=48  Identities=19%  Similarity=0.262  Sum_probs=37.8

Q ss_pred             cccccchhHHHHHHHHHHh----------c---CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          156 VYAFKSRESTMKDIMEAMK----------D---ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----------~---~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..+|.|.+..++++.+.+.          .   ...+-+=++|..|.|||++|+++++...
T Consensus       181 ~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~  241 (512)
T TIGR03689       181 YADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLA  241 (512)
T ss_pred             HHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhc
Confidence            4568899999998888764          1   1234577899999999999999998753

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.

>PRK13946 shikimate kinase; Provisional

Probab=81.96  E-value=1.3  Score=42.53  Aligned_cols=24  Identities=21%  Similarity=0.379  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|.++|+.|+||||+++.+.+..
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~L   34 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATML   34 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            468999999999999999998764

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=81.91  E-value=1.2  Score=42.13  Aligned_cols=23  Identities=39%  Similarity=0.476  Sum_probs=20.4

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|-|.|..|.||||+|+.+-+..
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47799999999999999998773

>PRK14490 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional

Probab=81.89  E-value=2  Score=46.49  Aligned_cols=25  Identities=32%  Similarity=0.610  Sum_probs=22.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -+|+|+|..|.|||||+..+....+
T Consensus         6 ~~i~i~G~~gsGKTTl~~~l~~~l~   30 (369)
T PRK14490          6 FEIAFCGYSGSGKTTLITALVRRLS   30 (369)
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHHh
Confidence            4899999999999999999997654

>smart00370 LRR Leucine-rich repeats, outliers

Probab=81.77  E-value=1.1  Score=26.77  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=18.5

Q ss_pred             ccccceeecccCcCcccChHHHc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQ  276 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~  276 (848)
                      +++|++|++++|.+..+|..+|.
T Consensus         1 L~~L~~L~L~~N~l~~lp~~~f~   23 (26)
T smart00370        1 LPNLRELDLSNNQLSSLPPGAFQ   23 (26)
T ss_pred             CCCCCEEECCCCcCCcCCHHHcc
Confidence            36788899999988888887764

>smart00369 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily

Probab=81.77  E-value=1.1  Score=26.77  Aligned_cols=23  Identities=35%  Similarity=0.491  Sum_probs=18.5

Q ss_pred             ccccceeecccCcCcccChHHHc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQ  276 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~  276 (848)
                      +++|++|++++|.+..+|..+|.
T Consensus         1 L~~L~~L~L~~N~l~~lp~~~f~   23 (26)
T smart00369        1 LPNLRELDLSNNQLSSLPPGAFQ   23 (26)
T ss_pred             CCCCCEEECCCCcCCcCCHHHcc
Confidence            36788899999988888887764

>PRK13236 nitrogenase reductase; Reviewed

Probab=81.75  E-value=1.2  Score=46.56  Aligned_cols=25  Identities=36%  Similarity=0.623  Sum_probs=21.1

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHH
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~  199 (848)
                      +.+.+++.+.|=||+||||.|-.+-
T Consensus         3 ~~~~~~~~~~GKGGVGKTt~a~NLA   27 (296)
T PRK13236          3 DENIRQIAFYGKGGIGKSTTSQNTL   27 (296)
T ss_pred             CcCceEEEEECCCcCCHHHHHHHHH
Confidence            5677999999999999999876544

>TIGR00959 ffh signal recognition particle protein

Probab=81.72  E-value=11  Score=41.25  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=20.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ...++-++|..|+||||.|..+...
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            3578999999999999997766554

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.

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=81.69  E-value=1.2  Score=44.20  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+...
T Consensus        31 ~~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          31 EFVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhCC
Confidence            68999999999999999999854

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=81.64  E-value=1.2  Score=39.98  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=20.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|-++|-.|.|||||+|.+....
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            357789999999999999998643

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.63  E-value=3  Score=44.76  Aligned_cols=38  Identities=26%  Similarity=0.304  Sum_probs=29.8

Q ss_pred             cCCccEEEEEeCCCCchhH-HHHHHHHHHhhccccCcEEEE
Q 003090          175 DENVSITGICGMGGVGKTT-LVKEIQKQAKEMKMFDDVAMA  214 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTt-la~~v~~~~~~~~~F~~~~wv  214 (848)
                      .....||.+||-.||||+| ||+-.|.-.  ++.|...+-.
T Consensus       375 ~krPYVi~fvGVNGVGKSTNLAKIayWLl--qNkfrVLIAA  413 (587)
T KOG0781|consen  375 RKRPYVISFVGVNGVGKSTNLAKIAYWLL--QNKFRVLIAA  413 (587)
T ss_pred             cCCCeEEEEEeecCccccchHHHHHHHHH--hCCceEEEEe
Confidence            5678899999999999977 999999876  4556554433

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=81.59  E-value=28  Score=34.21  Aligned_cols=46  Identities=22%  Similarity=0.250  Sum_probs=35.7

Q ss_pred             ccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++-|.|-.+++|.+...             -+..+=|-.+|..|.|||.||++|.|+.
T Consensus       155 ~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t  213 (408)
T KOG0727|consen  155 ADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHT  213 (408)
T ss_pred             cccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhcc
Confidence            467788888888877654             1333456689999999999999999876

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=81.57  E-value=2.3  Score=47.53  Aligned_cols=51  Identities=22%  Similarity=0.287  Sum_probs=40.7

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|-+..+..+...+....+ ..+=++|..|+||||+|+.+.+..
T Consensus        16 RP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~L   67 (507)
T PRK06645         16 RPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAV   67 (507)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            344457899999999888887776554 466789999999999999998765

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=81.57  E-value=1.1  Score=46.25  Aligned_cols=23  Identities=30%  Similarity=0.579  Sum_probs=18.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ++|+|+|-||+||||++..+--.
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~~   24 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAA   24 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH
Confidence            57888899999999988766543

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=81.52  E-value=1.2  Score=43.87  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+...
T Consensus        28 ~~~~l~G~nGsGKSTLl~~l~G~   50 (211)
T cd03225          28 EFVLIVGPNGSGKSTLLRLLNGL   50 (211)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            68999999999999999999854

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of 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.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=81.49  E-value=1.5  Score=42.44  Aligned_cols=24  Identities=38%  Similarity=0.529  Sum_probs=21.1

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++-|.|..|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            358899999999999999988865

>PF06564 YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ protein is encoded immediately upstream of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae, and in several species is clearly part of the bcs operon

Probab=81.48  E-value=1.2  Score=44.27  Aligned_cols=24  Identities=38%  Similarity=0.538  Sum_probs=19.6

Q ss_pred             cEEEEEeC-CCCchhHHHHHHHHHH
Q 003090          179 SITGICGM-GGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~-gG~GKTtla~~v~~~~  202 (848)
                      ++|+|+|. ||+||||++-.+-.-.
T Consensus         2 ~~iai~s~kGGvG~TTltAnLA~aL   26 (243)
T PF06564_consen    2 KVIAIVSPKGGVGKTTLTANLAWAL   26 (243)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHH
Confidence            57999998 8999999987766544

It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm [], based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.

>PRK04182 cytidylate kinase; Provisional

Probab=81.41  E-value=1.4  Score=42.06  Aligned_cols=23  Identities=35%  Similarity=0.512  Sum_probs=20.6

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|.|.|+.|.||||+|+.+.+..
T Consensus         2 ~I~i~G~~GsGKstia~~la~~l   24 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68999999999999999997653

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=81.39  E-value=21  Score=42.03  Aligned_cols=25  Identities=28%  Similarity=0.452  Sum_probs=20.9

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.|+.++|..|+||||.+..+....
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~  209 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARC  209 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhH
Confidence            3699999999999999887777544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.39  E-value=2.3  Score=48.24  Aligned_cols=48  Identities=23%  Similarity=0.369  Sum_probs=40.1

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-.+++|-+.-++.+..++..+.+.. +=++|..|+||||+|+.+-+..
T Consensus        14 ~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l   62 (527)
T PRK14969         14 SFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSL   62 (527)
T ss_pred             cHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            35679999999999999998777654 4689999999999999887654

>PRK14530 adenylate kinase; Provisional

Probab=81.38  E-value=1.4  Score=43.58  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.|+|+.|+||||+|+.+....
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999997554

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=81.38  E-value=1.1  Score=46.37  Aligned_cols=23  Identities=35%  Similarity=0.475  Sum_probs=18.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|+|+|=||+||||++-.+-..
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~   24 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAA   24 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            47899999999999987665543

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=81.35  E-value=2.1  Score=45.17  Aligned_cols=47  Identities=19%  Similarity=0.231  Sum_probs=37.9

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-..++|.++.++.+.-.+.+.+..-+=+.|..|.||||+|+.+-.-
T Consensus         6 ~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~l   52 (334)
T PRK13407          6 PFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAAL   52 (334)
T ss_pred             CHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHH
Confidence            34678999999988776665556566889999999999999988654

>PLN02348 phosphoribulokinase

Probab=81.32  E-value=1.4  Score=46.79  Aligned_cols=27  Identities=19%  Similarity=0.478  Sum_probs=23.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +..-+|+|.|-.|.||||+|+.+.+..
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~L   73 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSVF   73 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            456799999999999999999998765

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=81.31  E-value=1.2  Score=44.01  Aligned_cols=23  Identities=30%  Similarity=0.567  Sum_probs=18.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ++|+|.|-||+||||.+..+-..
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~   23 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAA   23 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHH
Confidence            47899999999999987655433

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=81.29  E-value=1.7  Score=48.66  Aligned_cols=27  Identities=22%  Similarity=0.585  Sum_probs=23.2

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .....+|+|.|..|.||||+|+.+...
T Consensus        62 ~~~riIIGIaGpSGSGKTTLAk~Lagl   88 (656)
T PLN02318         62 NDGIILVGVAGPSGAGKTVFTEKVLNF   88 (656)
T ss_pred             CCCeEEEEEECCCCCcHHHHHHHHHhh
Confidence            345679999999999999999999754

>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=81.26  E-value=1.3  Score=42.24  Aligned_cols=23  Identities=35%  Similarity=0.531  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+...
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          27 EIVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999999743

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.

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=81.21  E-value=1.2  Score=37.19  Aligned_cols=24  Identities=38%  Similarity=0.603  Sum_probs=19.9

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++.+.|.+|+||||++..+-....
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l~   24 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALA   24 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHH
Confidence            467899999999999988876653

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.21  E-value=2.3  Score=48.43  Aligned_cols=50  Identities=14%  Similarity=0.201  Sum_probs=41.1

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|-+.-++.+..++.+..+.. +=++|..|+||||+|+.+-+..
T Consensus         9 P~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l   59 (584)
T PRK14952          9 PATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSL   59 (584)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3345789999999999999998777655 5689999999999998887654

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=81.00  E-value=1  Score=44.56  Aligned_cols=24  Identities=38%  Similarity=0.499  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-|.++|.+|+||||+...+..+.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            358899999999999998888654

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=80.91  E-value=1.5  Score=38.26  Aligned_cols=20  Identities=35%  Similarity=0.566  Sum_probs=18.7

Q ss_pred             EEEEeCCCCchhHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~  200 (848)
                      |.++|..|+||||+...+.+
T Consensus         2 V~iiG~~~~GKSTlin~l~~   21 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTG   21 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999985

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=80.90  E-value=1.3  Score=42.74  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+...
T Consensus        19 e~~~i~G~nGsGKSTLl~~i~G~   41 (190)
T TIGR01166        19 EVLALLGANGAGKSTLLLHLNGL   41 (190)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998754

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=80.89  E-value=1.2  Score=41.59  Aligned_cols=23  Identities=30%  Similarity=0.484  Sum_probs=19.6

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.++|.+|+||||++..+....
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999998888543

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=80.89  E-value=1.3  Score=43.60  Aligned_cols=22  Identities=36%  Similarity=0.570  Sum_probs=19.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      ..|+|+|..|+|||||.+.|--
T Consensus        30 EfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          30 EFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5799999999999999888763

>PRK15453 phosphoribulokinase; Provisional

Probab=80.87  E-value=1.6  Score=44.18  Aligned_cols=27  Identities=26%  Similarity=0.423  Sum_probs=22.7

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+|+|.|-.|.||||+|+.+....
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if   29 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIF   29 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            445799999999999999999887543

>PRK05439 pantothenate kinase; Provisional

Probab=80.87  E-value=1.3  Score=45.83  Aligned_cols=27  Identities=33%  Similarity=0.366  Sum_probs=22.7

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...-+|+|.|..|+||||+|+.+....
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l  110 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALL  110 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            445689999999999999999887644

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=80.73  E-value=1.2  Score=41.76  Aligned_cols=22  Identities=23%  Similarity=0.471  Sum_probs=18.7

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.++|..|+||||+|+.+-...
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4589999999999999887653

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=80.72  E-value=1.2  Score=45.91  Aligned_cols=27  Identities=26%  Similarity=0.402  Sum_probs=22.2

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...++.++|..|+||||++..+.....
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~  219 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFV  219 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            346999999999999999888776543

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=80.65  E-value=2.5  Score=45.42  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=37.3

Q ss_pred             ccccchhHHHHHHHHHHhc--------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD--------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~--------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+..++..              .....+-++|..|+||||+|+.+-...
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l   74 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999988887752              113578899999999999999998764

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=80.60  E-value=3.5  Score=39.92  Aligned_cols=41  Identities=22%  Similarity=0.371  Sum_probs=30.2

Q ss_pred             HHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhc
Q 003090          165 TMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEM  205 (848)
Q Consensus       165 ~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~  205 (848)
                      +-.+.+..+...+-++..|.|.+|.||||+.+.+.......
T Consensus         5 ~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~   45 (196)
T PF13604_consen    5 EQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAA   45 (196)
T ss_dssp             HHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhC
Confidence            34455565554454688899999999999999988766543

>PRK13948 shikimate kinase; Provisional

Probab=80.56  E-value=1.6  Score=41.54  Aligned_cols=26  Identities=23%  Similarity=0.415  Sum_probs=22.1

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....|.++||.|+||||+++.+-+..
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~l   34 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRAL   34 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            34678899999999999999987653

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=80.50  E-value=2.6  Score=40.48  Aligned_cols=37  Identities=22%  Similarity=0.155  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          165 TMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       165 ~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +....++...... ..+.|+|..|.||||+++.+....
T Consensus        13 ~~~~~l~~~v~~g-~~i~I~G~tGSGKTTll~aL~~~i   49 (186)
T cd01130          13 LQAAYLWLAVEAR-KNILISGGTGSGKTTLLNALLAFI   49 (186)
T ss_pred             HHHHHHHHHHhCC-CEEEEECCCCCCHHHHHHHHHhhc
Confidence            3444555544444 689999999999999999887643

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=80.46  E-value=2.4  Score=48.67  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=39.9

Q ss_pred             cccccccchhHHHHHHHHHHhcCCccE-EEEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVSI-TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~v-i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.++||-+.-++.+...+....+.- +=++|..|+||||+|+.+.+..
T Consensus        13 ~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L   62 (647)
T PRK07994         13 QTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGL   62 (647)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            345789999999999888888776654 4689999999999999887654

>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=80.46  E-value=1.4  Score=41.74  Aligned_cols=21  Identities=38%  Similarity=0.553  Sum_probs=19.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~  199 (848)
                      .+++++|..|.|||||.+.+.
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il   42 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGL   42 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            589999999999999999885

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=80.44  E-value=3.3  Score=44.37  Aligned_cols=51  Identities=18%  Similarity=0.240  Sum_probs=41.1

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|....+++|-+..++.+.+.+....+. .+=++|..|+||+|+|..+-+..
T Consensus        14 ~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~L   65 (365)
T PRK07471         14 HPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFL   65 (365)
T ss_pred             CCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3445578999999999999999877665 47799999999999997766543

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=80.41  E-value=1.4  Score=43.97  Aligned_cols=22  Identities=45%  Similarity=0.672  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+++|+|..|.|||||.+.+..
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLG   52 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILG   52 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            6899999999999999999885

>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=80.41  E-value=1.4  Score=41.84  Aligned_cols=25  Identities=44%  Similarity=0.585  Sum_probs=21.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-.+++|+|..|.|||||.+.+...
T Consensus        24 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   48 (177)
T cd03222          24 EGEVIGIVGPNGTGKTTAVKILAGQ   48 (177)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcC
Confidence            3468999999999999999998754

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.

>PRK06761 hypothetical protein; Provisional

Probab=80.32  E-value=1.5  Score=44.69  Aligned_cols=25  Identities=28%  Similarity=0.376  Sum_probs=22.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|.|.|..|.||||+++.+.+...
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L~   28 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDILS   28 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4789999999999999999997653

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=80.26  E-value=2.7  Score=45.20  Aligned_cols=47  Identities=21%  Similarity=0.316  Sum_probs=36.8

Q ss_pred             ccccchhHHHHHHHHHHhcC--------------CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          157 YAFKSRESTMKDIMEAMKDE--------------NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~--------------~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..++|.++.++.+.-.+...              ..+.|-++|..|+|||++|+.+.....
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~   72 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLAN   72 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999998887665521              125678999999999999999987653

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=80.23  E-value=1.4  Score=43.60  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+...
T Consensus        30 e~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        30 EMVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            68999999999999999999864

>PRK05642 DNA replication initiation factor; Validated

Probab=80.18  E-value=3.3  Score=41.46  Aligned_cols=39  Identities=15%  Similarity=0.210  Sum_probs=27.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEe
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVV  216 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~v  216 (848)
                      +....+-|+|-.|+|||.|++++.+....+.  ..++++..
T Consensus        43 ~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~--~~v~y~~~   81 (234)
T PRK05642         43 WTESLIYLWGKDGVGRSHLLQAACLRFEQRG--EPAVYLPL   81 (234)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEeeH
Confidence            3346788999999999999999987653221  23455544

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=80.09  E-value=1.3  Score=45.54  Aligned_cols=24  Identities=29%  Similarity=0.541  Sum_probs=19.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++|+|+|-||+||||++-.+-...
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~L   25 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAAL   25 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHHH
Confidence            478888999999999887665443

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=80.03  E-value=19  Score=37.57  Aligned_cols=55  Identities=18%  Similarity=0.199  Sum_probs=35.7

Q ss_pred             chhHHHHHHHHHHhc----CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEec
Q 003090          161 SRESTMKDIMEAMKD----ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVS  217 (848)
Q Consensus       161 G~~~~~~~i~~~L~~----~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs  217 (848)
                      ++....+...+++..    ....-+-++|..|+|||.||.++.+....+ . -.+.+++++
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~-g-~~v~~~~~~  193 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKK-G-VSSTLLHFP  193 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-C-CCEEEEEHH
Confidence            444445555555552    133568899999999999999999887422 2 234555554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	848
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-23
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	6e-19
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	1e-13
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-19
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	5e-17
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	1e-15
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-15
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-13
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	7e-13
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	8e-08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-05
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-18
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	9e-17
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	2e-15
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-10
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-18
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-14
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	3e-18
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-13
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-11
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	7e-11
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-18
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	6e-18
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	6e-14
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-13
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-04
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-18
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	6e-16
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-12
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	6e-11
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-18
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	9e-18
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-15
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-14
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-12
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	5e-18
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-14
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-11
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	5e-11
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	6e-18
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-15
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-12
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-11
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	1e-10
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	1e-08
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	2e-17
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	5e-14
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	6e-12
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	2e-10
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	2e-08
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	3e-17
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	6e-16
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	4e-05
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	4e-17
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	7e-15
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	2e-04
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	6e-17
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	1e-15
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	2e-14
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	1e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	7e-17
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	2e-14
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	7e-12
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	2e-07
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-15
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-15
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	9e-13
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-15
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-14
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	2e-14
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	6e-14
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	3e-15
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	7e-14
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	2e-13
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	6e-11
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-15
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-14
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-13
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-13
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	3e-11
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-11
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-10
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-09
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	5e-15
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	3e-14
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	2e-10
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	8e-10
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-14
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-14
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-12
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-14
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,	1e-10
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-10
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	2e-14
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	7e-14
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	8e-12
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-10
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-14
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	5e-13
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-10
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-13
1o6v_A	466	Internalin A; bacterial infection, extracellular r	1e-12
1o6v_A	466	Internalin A; bacterial infection, extracellular r	1e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	7e-09
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	3e-13
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	1e-08
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	8e-13
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	2e-12
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	5e-12
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	1e-11
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	3e-10
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	2e-12
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	4e-12
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	1e-10
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	1e-05
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	9e-12
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	1e-11
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	1e-10
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	7e-05
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	1e-11
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	3e-11
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	6e-10
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	1e-06
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	4e-11
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	4e-11
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	5e-11
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	7e-06
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	5e-11
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	6e-11
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	2e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-10
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	4e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-06
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	2e-10
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	6e-09
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	1e-08
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	2e-10
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	3e-09
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	9e-08
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	1e-04
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	3e-10
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	4e-09
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	6e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	5e-10
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	9e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	4e-04
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	5e-10
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	2e-09
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	2e-09
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	2e-09
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	2e-09
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	2e-09
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	2e-09
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	7e-08
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	2e-09
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	3e-08
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	6e-09
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	8e-09
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	2e-08
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	5e-04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-08
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	2e-08
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	2e-07
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	4e-08
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	3e-06
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	8e-04
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	7e-08
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-04
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	4e-04
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	8e-07
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	1e-04
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	1e-06
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	7e-05
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	2e-06
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	2e-05
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	3e-05
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	3e-06
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	4e-05
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	2e-04
3e6j_A	229	Variable lymphocyte receptor diversity region; var	1e-05
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	2e-05
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	2e-05
3m19_A	251	Variable lymphocyte receptor A diversity region; a	4e-05
3m19_A	251	Variable lymphocyte receptor A diversity region; a	2e-04
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	6e-05
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	2e-04
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	2e-04
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	3e-04
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	4e-04
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	4e-04
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	4e-04
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	8e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score =  104 bits (259), Expect = 8e-23
 Identities = 114/807 (14%), Positives = 213/807 (26%), Gaps = 260/807 (32%)

Query: 1   MATETVASVTQPITERIVDVLFNATVRQFGYLCKYKHYIEALRTEAKKLTDRR-NDLQAE 59
           M  ET     Q   + I+ V  +A V  F   CK    ++ +      L+    + +   
Sbjct: 7   MDFET--GEHQYQYKDILSVFEDAFVDNFD--CKD---VQDMPKSI--LSKEEIDHIIMS 57

Query: 60  IDAATRNREVIKDEVKSWIAEVNDIIPK--AEKFLEDEVKVNKKCLGGLCVDLKSRYKLS 117
            DA +    +       W         +   +KF+E+ +++N K L        S  K  
Sbjct: 58  KDAVSGTLRLF------WTLLSK---QEEMVQKFVEEVLRINYKFL-------MSPIK-- 99

Query: 118 REAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEA-MKDE 176
            E  + ++     +   +     ++      +           SR      + +A ++  
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV-----------SRLQPYLKLRQALLELR 148

Query: 177 NVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLT 236
                 I G+ G GKT +  ++    K     D              KI +    WL+  
Sbjct: 149 PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF-------------KI-F----WLN-- 188

Query: 237 GISLMFNDIHEVPDELECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDLGGIRRFSFS 295
                  + +     LE   LQ L  Q +    +  D        +  +    +RR    
Sbjct: 189 -----LKNCNSPETVLE--MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ-AELRRL--- 237

Query: 296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD 355
                   P  +    LL                                  +L     +
Sbjct: 238 ----LKSKPYENC---LL----------------------------------VLL----N 252

Query: 356 VSEIPVSFGRLSHLRLLDLTGCYILELIPR--GVLSRLRKLEELYMSHSFRHWQF-ESES 412
           V                +L  C IL L  R   V   L      ++S           E 
Sbjct: 253 VQN-------AKAWNAFNL-SCKIL-LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 413 EEDSSSNAKFIELGALSRLTSLHIHIPE--GKIMPSDMSFQNLTSFSIAIGDLEERPLSD 470
           +       K+++     R   L    P       P            ++I          
Sbjct: 304 KSLL---LKYLDC----RPQDL----PREVLTTNP----------RRLSI---------- 332

Query: 471 FIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEV-NYFENIVSDLAN 529
            I   ++             + +    L + I++ L    +L  AE    F+        
Sbjct: 333 -IAESIRDGLATWDN----WKHVNCDKLTTIIESSL---NVLEPAEYRKMFDR------- 377

Query: 530 DGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLE--WLFI--RENQNFVEICHGQLPA 585
                   L +F  +              +    L   W  +   +    V   H     
Sbjct: 378 --------LSVFPPS------------AHIPTILLSLIWFDVIKSDVMVVVNKLH----- 412

Query: 586 GCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETE 645
                 K S               LV+       + + S  L + V       + +   +
Sbjct: 413 ------KYS---------------LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD 451

Query: 646 LFSSLEKLTLWDLPRMTDIWKGDT---QFVSLHNLKKVR-VEECDELRQVFPANFGKKAA 701
            ++  +     DL         D      +  H LK +   E     R VF  +F     
Sbjct: 452 HYNIPKTFDSDDLIPPYL----DQYFYSHIGHH-LKNIEHPERMTLFRMVF-LDFR---- 501

Query: 702 AEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSIT-----IRGCGKLRNLFTTSMVKSL 756
                L +K R     H +T+ ++    L  L  +      I            +++  L
Sbjct: 502 ----FLEQKIR-----HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552

Query: 757 VRLESLEVRS--CPTLQEIIMDDEGEV 781
            ++E   + S     L+  +M ++  +
Sbjct: 553 PKIEENLICSKYTDLLRIALMAEDEAI 579

>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 = 87.4 bits (217), Expect = 6e-19
 Identities = 37/181 (20%), Positives = 57/181 (31%), Gaps = 17/181 (9%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRR 291
             T I      +  VP  +       L L+ N   ++P   F  +  L  L L    +  
Sbjct: 8   SGTEIRCNSKGLTSVPTGIP-SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSF 66

Query: 292 FSFSVRFPFLFPPLPS-SPLFL-------LPSSLSFLINLRTLRLHDRRIQ--GDLSLIG 341
                          S   L L       + S+   L  L  L      ++   + S+  
Sbjct: 67  KGCC---SQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFL 123

Query: 342 ELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS 400
            L  L  LD+S +         F  LS L +L + G    E     + + LR L  L +S
Sbjct: 124 SLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLS 183

Query: 401 H 401
            
Sbjct: 184 Q 184

>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 = 71.6 bits (176), Expect = 1e-13
 Identities = 34/217 (15%), Positives = 71/217 (32%), Gaps = 36/217 (16%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDE---LECPKLQALFLQENSPLAIPDRFFQGM 278
           +  +     G   L  +    +++ ++ +    L    L  L +         +  F G+
Sbjct: 90  VITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGL 149

Query: 279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ--GD 336
             L+VL + G                        LP   + L NL  L L   +++    
Sbjct: 150 SSLEVLKMAGNSFQEN-----------------FLPDIFTELRNLTFLDLSQCQLEQLSP 192

Query: 337 LSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRL-RKL 394
            +    LS L++L++S ++   +    +  L+ L++LD +  +I     +  L      L
Sbjct: 193 TAFNS-LSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHI-MTSKKQELQHFPSSL 250

Query: 395 EELYMSH----------SFRHWQFESESEEDSSSNAK 421
             L ++           SF  W  +           +
Sbjct: 251 AFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERME 287

>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 = 90.5 bits (225), Expect = 6e-19
 Identities = 85/469 (18%), Positives = 145/469 (30%), Gaps = 92/469 (19%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
               +   FN +  + +        L  L L       I +  FQ    L  L L    +
Sbjct: 34  STECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQIYWIHEDTFQSQHRLDTLVLTANPL 93

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEI 348
              +                     ++LS    L+ L      I   D   +     LE 
Sbjct: 94  IFMA--------------------ETALSGPKALKHLFFIQTGISSIDFIPLHNQKTLES 133

Query: 349 LDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQ 407
           L L  + +S I +        L++LD     I  L     +S L++   L +        
Sbjct: 134 LYLGSNHISSIKLPKGFPTEKLKVLDFQNNAIHYLSK-EDMSSLQQATNLSL-------- 184

Query: 408 FESESEEDSSSNA-KFIELGA--LSRLTSLHI-HIPEGKIMPSDMSFQNLTSFSIAIGDL 463
                  + + N    IE GA   +   SL+        ++   +    +   S+ +G  
Sbjct: 185 -------NLNGNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQ--SLWLGTF 235

Query: 464 EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENI 523
           E+    D      +   +    ++ L        + S   +     + L L    +   +
Sbjct: 236 EDMDDEDISPAVFEGLCEMSVESINLQ-KHYFFNISSNTFHCFSGLQELDLTA-THLSEL 293

Query: 524 VSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQL 583
            S L     + L  LV+           +L +        L  L I+ N   +E+     
Sbjct: 294 PSGLVG--LSTLKKLVLSANK-----FENLCQISASNFPSLTHLSIKGNTKRLEL----- 341

Query: 584 PAGCLSNVKRSDVVDCGSILKIL-LSH--------LVQSFQNLQRLRVYSCGLLVSVFEI 634
             GCL N++          L+ L LSH             +NL  L+     L +S  E 
Sbjct: 342 GTGCLENLEN---------LRELDLSHDDIETSDCCNLQLRNLSHLQS----LNLSYNEP 388

Query: 635 ERVNIAKEETELFSSLEKLTLWDLP--RMTDIWKGDTQFVSLHNLKKVR 681
             +     +TE F    +L L DL   R+       + F +LH LK + 
Sbjct: 389 LSL-----KTEAFKECPQLELLDLAFTRLKVKDA-QSPFQNLHLLKVLN 431

>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 = 84.7 bits (210), Expect = 5e-17
 Identities = 52/244 (21%), Positives = 78/244 (31%), Gaps = 40/244 (16%)

Query: 221 SITKIQYEIAGWL-DLTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPDRFFQGM 278
               I          L  + L    + E+P  L     L+ L L  N    +        
Sbjct: 265 YFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNF 324

Query: 279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
             L  L + G  +                  L L    L  L NLR L L    I+    
Sbjct: 325 PSLTHLSIKGNTKR-----------------LELGTGCLENLENLRELDLSHDDIETSDC 367

Query: 339 LIGELSG---LEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL 394
              +L     L+ L+LS ++   +   +F     L LLDL    +     +     L  L
Sbjct: 368 CNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLL 427

Query: 395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI---HIPEGKIMPSDMSFQ 451
           + L +SHS      +  SE+             L  L  L++   H P+G I  ++ S Q
Sbjct: 428 KVLNLSHS----LLDISSEQ---------LFDGLPALQHLNLQGNHFPKGNIQKTN-SLQ 473

Query: 452 NLTS 455
            L  
Sbjct: 474 TLGR 477

>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 = 79.7 bits (197), Expect = 1e-15
 Identities = 31/188 (16%), Positives = 58/188 (30%), Gaps = 25/188 (13%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDE----LECPKLQALFLQENSPLAIPDRFFQ 276
            I  I+           ++        V  +         L     ++     I    F+
Sbjct: 190 DIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDMDDEDISPAVFE 249

Query: 277 GMKD--LQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ 334
           G+ +  ++ ++L     F+                  +  ++      L+ L L    + 
Sbjct: 250 GLCEMSVESINLQKHYFFN------------------ISSNTFHCFSGLQELDLTATHLS 291

Query: 335 GDLSLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK 393
              S +  LS L+ L LS +    +  +S      L  L + G      +  G L  L  
Sbjct: 292 ELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLEN 351

Query: 394 LEELYMSH 401
           L EL +SH
Sbjct: 352 LRELDLSH 359

>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 = 79.3 bits (196), Expect = 2e-15
 Identities = 44/231 (19%), Positives = 77/231 (33%), Gaps = 45/231 (19%)

Query: 233 LDLTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
           LDL+   +          +L     LQ+L L  N PL++    F+    L++LDL     
Sbjct: 355 LDLSHDDIET--SDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAF--- 409

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILD 350
                R                 S    L  L+ L L    +      L   L  L+ L+
Sbjct: 410 ----TRLKVKDAQ----------SPFQNLHLLKVLNLSHSLLDISSEQLFDGLPALQHLN 455

Query: 351 LSESDVSEIPV----SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW 406
           L  +   +  +    S   L  L +L L+ C +   I +   + L+ +  + +SH     
Sbjct: 456 LQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSS-IDQHAFTSLKMMNHVDLSH----- 509

Query: 407 QFESESEEDSSSNA-KFIELGALSRLTSLHIHIPEGKI-MPSDMSFQNLTS 455
                       N      + ALS L  +++++    I +        L+ 
Sbjct: 510 ------------NRLTSSSIEALSHLKGIYLNLASNHISIILPSLLPILSQ 548

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 71.2 bits (175), Expect = 6e-13
 Identities = 39/186 (20%), Positives = 68/186 (36%), Gaps = 26/186 (13%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENS-PLAIPDRFFQGMKDLQVLDLGG--I 289
           L  ++L +N+   +  E   ECP+L+ L L      +      FQ +  L+VL+L    +
Sbjct: 378 LQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLNLSHSLL 437

Query: 290 RRFSFSVRFPFLFPPLPS------------SPLFLLPSSLSFLINLRTLRLHDRRIQG-D 336
              S       LF  LP+                   +SL  L  L  L L    +   D
Sbjct: 438 DISS-----EQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSSID 492

Query: 337 LSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE 395
                 L  +  +DLS + ++   +     L  + L +L   +I  +I   +L  L +  
Sbjct: 493 QHAFTSLKMMNHVDLSHNRLTSSSIEALSHLKGIYL-NLASNHI-SIILPSLLPILSQQR 550

Query: 396 ELYMSH 401
            + +  
Sbjct: 551 TINLRQ 556

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 71.2 bits (175), Expect = 7e-13
 Identities = 79/479 (16%), Positives = 145/479 (30%), Gaps = 120/479 (25%)

Query: 233 LDLTGISLMFNDIHEVPDEL-ECPKLQALFLQ--ENSPLAIPDRFFQGMKDLQVLDLGGI 289
                ++L  NDI  +     +    Q+L     +N  +         ++ L +     +
Sbjct: 179 ATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDM 238

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS-LIGELSGLEI 348
                S   P +F  L                ++ ++ L         S      SGL+ 
Sbjct: 239 DDEDIS---PAVFEGLCEM-------------SVESINLQKHYFFNISSNTFHCFSGLQE 282

Query: 349 LDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
           LDL+ + +SE+P     LS L+ L L+     E + +   S    L  L +         
Sbjct: 283 LDLTATHLSELPSGLVGLSTLKKLVLSANKF-ENLCQISASNFPSLTHLSIKG------- 334

Query: 409 ESESEEDSSSNAKFIEL--GALSRLTSL------HIHIPEGKIMPSDMSFQNLTSFSIAI 460
                     N K +EL  G L  L +L      H  I        ++  +NL+      
Sbjct: 335 ----------NTKRLELGTGCLENLENLRELDLSHDDI--ETSDCCNLQLRNLSH----- 377

Query: 461 GDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYF 520
             L+         L L                    +L +       + E+L LA     
Sbjct: 378 --LQS--------LNLS--------------YNEPLSLKTEAFKECPQLELLDLAF-TRL 412

Query: 521 ENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICH 580
           +   +       + L  L +         L+     L   L  L+ L ++ N  F +   
Sbjct: 413 KVKDAQSPFQNLHLLKVLNLSHSL-----LDISSEQLFDGLPALQHLNLQGNH-FPKG-- 464

Query: 581 GQLPAGCLSNVKRSDVVDCGSILKIL------LSHL-VQSFQNLQRLRVYSCGLLVSVFE 633
                  L  + R         L+IL      LS +   +F +L+ +      + +S   
Sbjct: 465 NIQKTNSLQTLGR---------LEILVLSFCDLSSIDQHAFTSLKMMNH----VDLS--- 508

Query: 634 IERVNIAKEETELFSSLEKLTLWDLP--RMTDIWKGDTQFVSLHNLKKVRVE----ECD 686
                +     E  S L+ + L +L    ++ I    +    L   + + +     +C 
Sbjct: 509 --HNRLTSSSIEALSHLKGIYL-NLASNHISII--LPSLLPILSQQRTINLRQNPLDCT 562

>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 = 55.0 bits (133), Expect = 8e-08
 Identities = 42/326 (12%), Positives = 88/326 (26%), Gaps = 62/326 (19%)

Query: 324 RTLRLHDRRIQGDLSLIGEL-SGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILE 381
           +T    +  +     + G L +  E L+ S + +  I   +F RL +L  LDLT C I  
Sbjct: 15  KTYNCENLGLN---EIPGTLPNSTECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQIYW 71

Query: 382 LIPRGVLSRLRKLEELYMSHSFRHWQFESESEE-----------DSSSNA-KFIELGALS 429
            I         +L+ L ++ +         +E                     I+   L 
Sbjct: 72  -IHEDTFQSQHRLDTLVLTAN----PLIFMAETALSGPKALKHLFFIQTGISSIDFIPLH 126

Query: 430 RLTSL-HIHIPEGKIM-PSDMSFQNLTSFSI------AIGDLEERPLSDFIGLFLQKFKK 481
              +L  +++    I               +      AI  L +  +S            
Sbjct: 127 NQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDFQNNAIHYLSKEDMSSLQQATNLSLN- 185

Query: 482 RCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIF 541
                        I+ +     +     + L          I   L N     L     F
Sbjct: 186 --------LNGNDIAGIEPGAFD-SAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGT-F 235

Query: 542 RCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGS 601
              + + +  ++   L      +E + ++++          + +                
Sbjct: 236 EDMDDEDISPAVFEGL--CEMSVESINLQKHY------FFNISSNTFHC--------FSG 279

Query: 602 ILKILLSH-----LVQSFQNLQRLRV 622
           + ++ L+      L      L  L+ 
Sbjct: 280 LQELDLTATHLSELPSGLVGLSTLKK 305

>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 = 2e-05
 Identities = 33/158 (20%), Positives = 51/158 (32%), Gaps = 22/158 (13%)

Query: 232 WLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
            L+L G      +I +        +L+ L L      +I    F  +K +  +DL    +
Sbjct: 453 HLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSSIDQHAFTSLKMMNHVDLSHNRL 512

Query: 290 RRFSFSVRFPFLFPPLPSSPLFL--------LPSSLSFLINLRTLRLHDRRIQGDLSLIG 341
              S           L    L L        LPS L  L   RT+ L    +    S I 
Sbjct: 513 TSSS-----IEALSHLKGIYLNLASNHISIILPSLLPILSQQRTINLRQNPLDCTCSNIY 567

Query: 342 ELSGLEILDLSESDVSEIP----VSFGRLSHLRLLDLT 375
               LE    +   + +       +   L  +RL D+T
Sbjct: 568 F---LEWYKENMQKLEDTEDTLCENPPLLRGVRLSDVT 602

>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 = 89.4 bits (222), Expect = 1e-18
 Identities = 72/450 (16%), Positives = 139/450 (30%), Gaps = 80/450 (17%)

Query: 239 SLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF 298
                    +P  L    +++L L  N    I     +   +LQVL L            
Sbjct: 11  DGRSRSFTSIPSGL-TAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS---------- 59

Query: 299 PFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVS 357
                   S    +   +   L +L  L L D  +     S  G LS L+ L+L  +   
Sbjct: 60  --------SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQ 111

Query: 358 EIPVS--FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED 415
            + V+  F  L++L+ L +        I R   + L  L EL +          +   + 
Sbjct: 112 TLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKAL----SLRNYQSQS 167

Query: 416 SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERPLSDFIG 473
                    L ++  +  L +H+ E   +         ++    +   +L     S    
Sbjct: 168 ---------LKSIRDIHHLTLHLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPV 218

Query: 474 LFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFN 533
             +    K+ +    +  D   + L   ++ +L  SE+             +   +D  +
Sbjct: 219 DEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVS 278

Query: 534 ELMFL--VIFRCNEMKYL-LNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSN 590
           EL  +  V  R   +    L     T+   L K++ + +  ++ F       +P     +
Sbjct: 279 ELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVF------LVPCSFSQH 332

Query: 591 VKRSDVVDCGSILKIL-LSHLVQSFQN-LQRLRVYSCGLLVSVFEIERVNIAKEETELFS 648
           +K          L+ L LS       N +    + +                      + 
Sbjct: 333 LKS---------LEFLDLSE------NLMVEEYLKNSACK----------------GAWP 361

Query: 649 SLEKLTLWDLPRMTDIWKGDTQFVSLHNLK 678
           SL+ L L     +  + K     ++L NL 
Sbjct: 362 SLQTLVLSQN-HLRSMQKTGEILLTLKNLT 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 = 83.6 bits (207), Expect = 9e-17
 Identities = 75/466 (16%), Positives = 131/466 (28%), Gaps = 101/466 (21%)

Query: 234 DLTGISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
            +  + L FN I  +       C  LQ L L+ +    I    F  +  L+ LDL    +
Sbjct: 27  AMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHL 86

Query: 290 RRFSFSVRFPFLFPPLPS-SPLFL-------LPSSLSF--LINLRTLRLHDRRIQGDLS- 338
              S        F PL S   L L       L  +  F  L NL+TLR+ +     ++  
Sbjct: 87  SSLS-----SSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRR 141

Query: 339 -LIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
                L+ L  L++    +      S   +  +  L L        +       L  +  
Sbjct: 142 IDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTLHLSES-AFLLEIFADILSSVRY 200

Query: 397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSF 456
           L +  +       S                  S +  L         + +D SF  L   
Sbjct: 201 LELRDTNLARFQFSP----------LPVDEVSSPMKKLAFRG----SVLTDESFNELLKL 246

Query: 457 SIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMR-------------ISALHSWIK 503
              I +L E    D     L  F    S  +     +              +    S + 
Sbjct: 247 LRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVY 306

Query: 504 NLLLRSEILALA-------EVNYFENIVS----DLANDGFNELMFLVIFRCNEMKYL--- 549
           +LL + + + +          ++ +++ S    DL+    N ++   +            
Sbjct: 307 SLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSE---NLMVEEYLKNSACKGAWPSL 363

Query: 550 ---------LNSLERTLRVT--LHKLEWLFIRENQ--NFVEICHG--------------- 581
                    L S+++T  +   L  L  L I  N      + C                 
Sbjct: 364 QTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSSTGIR 423

Query: 582 QLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGL 627
            +       ++  DV +        L         LQ L +    L
Sbjct: 424 VVKTCIPQTLEVLDVSNNN------LDSFSLFLPRLQELYISRNKL 463

>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 = 79.0 bits (195), Expect = 2e-15
 Identities = 38/243 (15%), Positives = 77/243 (31%), Gaps = 57/243 (23%)

Query: 233 LDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG-- 288
           + +  + +    +      +     K++ + ++ +    +P  F Q +K L+ LDL    
Sbjct: 286 VTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENL 345

Query: 289 IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ---GDLSLIGELSG 345
           +                         +      +L+TL L    ++       ++  L  
Sbjct: 346 M-----------------VEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEILLTLKN 388

Query: 346 LEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRH 405
           L  LD+S +    +P S      +R L+L+    + ++   +   L  L           
Sbjct: 389 LTSLDISRNTFHPMPDSCQWPEKMRFLNLSSTG-IRVVKTCIPQTLEVL----------- 436

Query: 406 WQFESESEEDSSSNAKFIELGA-LSRLTSLHI------HIPEGKIMPS----DMSFQNLT 454
                    D S+N         L RL  L+I       +P+  + P      +S   L 
Sbjct: 437 ---------DVSNN-NLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMKISRNQLK 486

Query: 455 SFS 457
           S  
Sbjct: 487 SVP 489

>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 = 63.6 bits (155), Expect = 1e-10
 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 43/191 (22%)

Query: 232 WLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD--RFFQGMKDLQVLDLGGI 289
           +LDL+   ++   +     +   P LQ L L +N   ++         +K+L  LD+   
Sbjct: 338 FLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISR- 396

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEIL 349
                             +    +P S  +   +R L L    I+   + I     LE+L
Sbjct: 397 ------------------NTFHPMPDSCQWPEKMRFLNLSSTGIRVVKTCI--PQTLEVL 436

Query: 350 DLSESDVSEIPVSFGRLSHLRL-------------------LDLTGCYILELIPRGVLSR 390
           D+S +++    +   RL  L +                   + ++   + + +P G+  R
Sbjct: 437 DVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMKISRNQL-KSVPDGIFDR 495

Query: 391 LRKLEELYMSH 401
           L  L+++++  
Sbjct: 496 LTSLQKIWLHT 506

>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 = 86.5 bits (215), Expect = 2e-18
 Identities = 40/186 (21%), Positives = 67/186 (36%), Gaps = 20/186 (10%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMK 279
            + +   +      L  +++    + E+PD + +   L+ L L  N   A+P      + 
Sbjct: 92  PLPQFPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPLRALPASIAS-LN 150

Query: 280 DLQVLDLGGIRRFSFSVRFPFLFPPLPSS-PLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
            L+ L +      +           LP              L+NL++LRL    I+   S
Sbjct: 151 RLRELSIRACPELTE----------LPEPLASTDASGEHQGLVNLQSLRLEWTGIR---S 197

Query: 339 L---IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE 395
           L   I  L  L+ L +  S +S +  +   L  L  LDL GC  L   P         L+
Sbjct: 198 LPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPI-FGGRAPLK 256

Query: 396 ELYMSH 401
            L +  
Sbjct: 257 RLILKD 262

>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 = 74.6 bits (184), Expect = 2e-14
 Identities = 65/401 (16%), Positives = 108/401 (26%), Gaps = 112/401 (27%)

Query: 233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           L   G       +    D L   + Q  +  + +      R      + Q+    G    
Sbjct: 17  LYFQGS----TALRPYHDVLS--QWQRHYNADRNRWHSAWRQ-ANSNNPQIETRTGRALK 69

Query: 293 SFSVRFPFLFPP------LPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL---IGEL 343
           + +        P      L S PL   P     L +L+ + +    +     L   + + 
Sbjct: 70  ATADLLEDATQPGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGLM---ELPDTMQQF 126

Query: 344 SGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGV--------LSRLRKLE 395
           +GLE L L+ + +  +P S   L+ LR L +  C  L  +P  +           L  L+
Sbjct: 127 AGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQ 186

Query: 396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTS 455
            L +  +       S              +  L  L SL             +    L++
Sbjct: 187 SLRLEWT----GIRSLPA----------SIANLQNLKSL------------KIRNSPLSA 220

Query: 456 FSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALA 515
              AI  L                                         L    E L L 
Sbjct: 221 LGPAIHHL---------------------------------------PKL----EELDLR 237

Query: 516 EVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNF 575
                 N            L  L++  C+ +  L   + R     L +LE L +R   N 
Sbjct: 238 GCTALRNYPPIFGG--RAPLKRLILKDCSNLLTLPLDIHR-----LTQLEKLDLRGCVNL 290

Query: 576 VEICHGQLPA--GCLSNVKRSDVVDCGSILKILLSHLVQSF 614
                 +LP+    L       V     +   L  H   + 
Sbjct: 291 -----SRLPSLIAQLPANCIILVPPH--LQAQLDQHRPVAR 324

>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 = 89.1 bits (221), Expect = 3e-18
 Identities = 73/430 (16%), Positives = 135/430 (31%), Gaps = 82/430 (19%)

Query: 240 LMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFP 299
             F ++ +VP  L     + L L  N    +    F  ++ LQ+L+LG            
Sbjct: 11  YRFCNLTQVPQVL--NTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQY--------- 59

Query: 300 FLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSE---SD 355
                   +PL +   +   L NLR L L   +I          L  L  L L     SD
Sbjct: 60  --------TPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRLYFCGLSD 111

Query: 356 VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED 415
                  F  L  L  LDL+   I  L       +L  L+ +  S +    Q        
Sbjct: 112 AVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSN----QIFL----- 162

Query: 416 SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLF 475
                  +    L  L    +           ++  +L S    +     + ++ F  + 
Sbjct: 163 -------VCEHELEPLQGKTLSFF-------SLAANSLYSR---VSVDWGKCMNPFRNMV 205

Query: 476 LQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNEL 535
           L+      +           +A+       L+ +    +    +  + + D   + F  L
Sbjct: 206 LEILDVSGNGWTVDITGNFSNAISKSQAFSLILAHH--IMGAGFGFHNIKDPDQNTFAGL 263

Query: 536 MFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSD 595
               +   +     + SL   +  TL  L+ L +  N+        ++       +    
Sbjct: 264 ARSSVRHLDLSHGFVFSLNSRVFETLKDLKVLNLAYNKIN------KIADEAFYGLDN-- 315

Query: 596 VVDCGSILKIL-LSHL------VQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFS 648
                  L++L LS+         +F  L ++            ++++ +IA  + + F 
Sbjct: 316 -------LQVLNLSYNLLGELYSSNFYGLPKVA---------YIDLQKNHIAIIQDQTFK 359

Query: 649 SLEKLTLWDL 658
            LEKL   DL
Sbjct: 360 FLEKLQTLDL 369

>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 = 73.3 bits (180), Expect = 2e-13
 Identities = 46/252 (18%), Positives = 94/252 (37%), Gaps = 40/252 (15%)

Query: 221 SITKIQYEIAGWL-DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQG 277
            +  +   +   L DL  ++L +N I+++ DE       LQ L L  N    +    F G
Sbjct: 277 FVFSLNSRVFETLKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYNLLGELYSSNFYG 336

Query: 278 MKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL------PSSLSFLINLRTLRLHDR 331
           +  +  +DL        ++     F  L    L  L       +++ F+ ++  + L   
Sbjct: 337 LPKVAYIDLQK---NHIAIIQDQTFKFLEK--LQTLDLRDNALTTIHFIPSIPDIFLSGN 391

Query: 332 RIQGDLSLIGELSGLEILDLSESDVSEIPVS--FGRLSHLRLLDLTGCYILELIPRGVLS 389
           ++   ++L        ++ LSE+ +  + +     R+ HL++L L              S
Sbjct: 392 KL---VTLPKINLTANLIHLSENRLENLDILYFLLRVPHLQILILNQNRFSSCSGDQTPS 448

Query: 390 RLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH------IPEGKI 443
               LE+L++  +      +   E +   +        LS L  L+++      +P G  
Sbjct: 449 ENPSLEQLFLGEN----MLQLAWETELCWDV----FEGLSHLQVLYLNHNYLNSLPPG-- 498

Query: 444 MPSDMSFQNLTS 455
                 F +LT+
Sbjct: 499 -----VFSHLTA 505

>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 = 66.8 bits (163), Expect = 2e-11
 Identities = 34/247 (13%), Positives = 64/247 (25%), Gaps = 35/247 (14%)

Query: 221 SITKIQYEI-AGWLDLTGISLMFNDI-HEVPDEL--ECPKLQALFLQENSPLAIPDRFFQ 276
            I  +          L  + L        +  E     P L+ L L  +    +    FQ
Sbjct: 35  YIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQ 94

Query: 277 GMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ-- 334
           G+  L  L L                     S   L       L  L  L L   +I+  
Sbjct: 95  GLFHLFELRLYFCG----------------LSDAVLKDGYFRNLKALTRLDLSKNQIRSL 138

Query: 335 GDLSLIGELSGLEILDLSESDVSEIPV-SFGRLS--HLRLLDLTGCYILELIPRGVLSRL 391
                 G+L+ L+ +D S + +  +       L    L    L    +   +       +
Sbjct: 139 YLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAANSLYSRVSVDWGKCM 198

Query: 392 RKLEELYMSH-SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSF 450
                + +         +  +   + S+     +  +L     +         M +   F
Sbjct: 199 NPFRNMVLEILDVSGNGWTVDITGNFSNAISKSQAFSLILAHHI---------MGAGFGF 249

Query: 451 QNLTSFS 457
            N+    
Sbjct: 250 HNIKDPD 256

>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 = 65.2 bits (159), Expect = 7e-11
 Identities = 57/352 (16%), Positives = 115/352 (32%), Gaps = 47/352 (13%)

Query: 343 LSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           L+  E L LS + +  +   SF  L  L+LL+L   Y    I +     L  L  L +  
Sbjct: 23  LNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGS 82

Query: 402 SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSI--- 458
           S + +    ++         F  L  L  L      + +  +      F+NL + +    
Sbjct: 83  S-KIYFLHPDA---------FQGLFHLFELRLYFCGLSDAVLKDG--YFRNLKALTRLDL 130

Query: 459 ---AIGDLEERP----LSDFIGLFLQ--KFKKRCSRAMGLSQDMRISALHSWIKNLLLRS 509
               I  L   P    L+    +     +    C   +   Q   +S       +L  R 
Sbjct: 131 SKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAANSLYSRV 190

Query: 510 EILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFI 569
            +     +N F N+V ++ +   N     +    +     ++  +    +  H +     
Sbjct: 191 SVDWGKCMNPFRNMVLEILDVSGNGWTVDITGNFSN---AISKSQAFSLILAHHIMGAGF 247

Query: 570 RENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLV 629
             + N  +           S+V+  D+      +  L S + ++ ++L+ L +       
Sbjct: 248 GFH-NIKDPDQNTFAGLARSSVRHLDLSHGF--VFSLNSRVFETLKDLKVLNLAYN---- 300

Query: 630 SVFEIERVNIAKEETELFSSLEKLTLWDL--PRMTDIWKGDTQFVSLHNLKK 679
                    I K   E F  L+ L + +L    + ++    + F  L  +  
Sbjct: 301 --------KINKIADEAFYGLDNLQVLNLSYNLLGEL--YSSNFYGLPKVAY 342

>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 = 88.5 bits (220), Expect = 3e-18
 Identities = 71/491 (14%), Positives = 156/491 (31%), Gaps = 77/491 (15%)

Query: 234 DLTGISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           ++T ++L  N +  +P        +L +L +  N+   +     Q +  L+VL+L    +
Sbjct: 26  NITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQHNEL 85

Query: 290 RRFSFSVRFPFLFPPLPS-SPLFL--------LPSSLSFLINLRTLRLHDRRIQG-DLSL 339
            + S        F    + + L L          +      NL TL L    +    L  
Sbjct: 86  SQLS-----DKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGT 140

Query: 340 IGELSGLEILDLSE---SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
             +L  L+ L LS      +    +     S L+ L+L+   I E  P G    + +L  
Sbjct: 141 QVQLENLQELLLSNNKIQALKSEELDIFANSSLKKLELSSNQIKEFSP-GCFHAIGRLFG 199

Query: 397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH------IPEGKIMPSDMSF 450
           L++++               S   K     A + + +L +                  +F
Sbjct: 200 LFLNNVQLG----------PSLTEKLCLELANTSIRNLSLSNSQLSTTSNT-------TF 242

Query: 451 QNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSE 510
             L   ++ + DL    L+           +       L     I  L S   + L    
Sbjct: 243 LGLKWTNLTMLDLSYNNLNVVGNDSFAWLPQ--LEYFFLE-YNNIQHLFSHSLHGLFNVR 299

Query: 511 ILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYL------LNSLERTLRVTLHKL 564
            L L   ++ +     ++     ++          +++L      +  ++  +   L  L
Sbjct: 300 YLNLKR-SFTK---QSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSNMFTGLINL 355

Query: 565 EWLFIRENQ-NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVY 623
           ++L +  +  +   + +    +   S +   ++      +  + S       +L+ L + 
Sbjct: 356 KYLSLSNSFTSLRTLTNETFVSLAHSPLHILNLTKNK--ISKIESDAFSWLGHLEVLDLG 413

Query: 624 SCGL-----------LVSVFE--IERVNIAKEETELFSSLEKLTLWDLP--RMTDIWKGD 668
              +           L ++FE  +      +     F+ +  L    L    + ++    
Sbjct: 414 LNEIGQELTGQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSLQRLMLRRVALKNVDSSP 473

Query: 669 TQFVSLHNLKK 679
           + F  L NL  
Sbjct: 474 SPFQPLRNLTI 484

>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 = 87.7 bits (218), Expect = 6e-18
 Identities = 73/451 (16%), Positives = 134/451 (29%), Gaps = 81/451 (17%)

Query: 235 LTGISLMFNDIHEVPDE----LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
           L  + L  N I  +  E         L+ L L  N         F  +  L  L L  + 
Sbjct: 147 LQELLLSNNKIQALKSEELDIFANSSLKKLELSSNQIKEFSPGCFHAIGRLFGLFLNNV- 205

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG--DLSLIG-ELSGLE 347
                     L P L       L ++     ++R L L + ++    + + +G + + L 
Sbjct: 206 ---------QLGPSLTEKLCLELANT-----SIRNLSLSNSQLSTTSNTTFLGLKWTNLT 251

Query: 348 ILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW 406
           +LDLS ++++ +   SF  L  L    L    I  L     L  L  +  L +  SF   
Sbjct: 252 MLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFS-HSLHGLFNVRYLNLKRSFTKQ 310

Query: 407 QFESESEEDSSSNAKFIELGALSRLTSLHIH------IPEGKIMPSDMSFQNLTSF---- 456
                S       +       L  L  L++       I           F  L +     
Sbjct: 311 SISLASLPKIDDFS----FQWLKCLEHLNMEDNDIPGIKSN-------MFTGLINLKYLS 359

Query: 457 ----SIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALH----SWIKNLLLR 508
                 ++  L            L            L+   +IS +     SW+ +L   
Sbjct: 360 LSNSFTSLRTLTNETFVSLAHSPLHILN--------LT-KNKISKIESDAFSWLGHL--- 407

Query: 509 SEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLF 568
            E+L L   N     ++     G   +  + +            L R     +  L+ L 
Sbjct: 408 -EVLDLGL-NEIGQELTGQEWRGLENIFEIYLSYNK-----YLQLTRNSFALVPSLQRLM 460

Query: 569 IRENQ-NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGL 627
           +R      V+          L N+   D+ +    +  +   +++  + L+ L +    L
Sbjct: 461 LRRVALKNVDSSPSPF--QPLRNLTILDLSNNN--IANINDDMLEGLEKLEILDLQHNNL 516

Query: 628 LVSVFEIERVNIAKEETELFSSLEKLTLWDL 658
                 + +             L  L + +L
Sbjct: 517 A----RLWKHANPGGPIYFLKGLSHLHILNL 543

>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 = 74.7 bits (184), Expect = 6e-14
 Identities = 39/188 (20%), Positives = 64/188 (34%), Gaps = 20/188 (10%)

Query: 224 KIQYEIAGWLD----LTGISLMFNDIHEVPDELE----CPKLQALFLQENSPLAIPDRFF 275
           K              L  + L    +  V            L  L L  N+   I D   
Sbjct: 441 KYLQLTRNSFALVPSLQRLMLRRVALKNVDSSPSPFQPLRNLTILDLSNNNIANINDDML 500

Query: 276 QGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG 335
           +G++ L++LDL        +  +    P  P          L  L +L  L L       
Sbjct: 501 EGLEKLEILDLQHNN---LARLWKHANPGGP-------IYFLKGLSHLHILNLESNGFDE 550

Query: 336 -DLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRK 393
             + +  +L  L+I+DL  ++++ +P S F     L+ L+L    I  +  +      R 
Sbjct: 551 IPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQKNLITSVEKKVFGPAFRN 610

Query: 394 LEELYMSH 401
           L EL M  
Sbjct: 611 LTELDMRF 618

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 72.3 bits (178), Expect = 3e-13
 Identities = 36/186 (19%), Positives = 61/186 (32%), Gaps = 36/186 (19%)

Query: 233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD--LQVLDLGG-- 288
           L L  + L  +   ++  EL    ++ L L  +      +  F G+K   L +LDL    
Sbjct: 200 LFLNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNN 259

Query: 289 IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLE 347
           +                          S ++L  L    L    IQ      +  L  + 
Sbjct: 260 LNVVG--------------------NDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVR 299

Query: 348 ILDLSESDVSE----------IPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEEL 397
            L+L  S   +             SF  L  L  L++    I  +    + + L  L+ L
Sbjct: 300 YLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKS-NMFTGLINLKYL 358

Query: 398 YMSHSF 403
            +S+SF
Sbjct: 359 SLSNSF 364

>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 = 56.5 bits (137), Expect = 2e-08
 Identities = 24/143 (16%), Positives = 52/143 (36%), Gaps = 32/143 (22%)

Query: 321 INLRTLRLHDRRIQGDLSLIGEL-SGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCY 378
           ++         ++     +  +L + + +L+L+ + +  +P  +F R S L  LD+    
Sbjct: 4   VSHEVADCSHLKLT---QVPDDLPTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNT 60

Query: 379 ILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI-- 436
           I +L P  +  +L  L+ L + H+    +    S++              + LT LH+  
Sbjct: 61  ISKLEP-ELCQKLPMLKVLNLQHN----ELSQLSDK---------TFAFCTNLTELHLMS 106

Query: 437 ----HIPEGKIMPSDMSFQNLTS 455
                I           F    +
Sbjct: 107 NSIQKIKNN-------PFVKQKN 122

>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 = 44.6 bits (106), Expect = 1e-04
 Identities = 28/151 (18%), Positives = 51/151 (33%), Gaps = 26/151 (17%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           L  ++L  N   E+P E+  +  +L+ + L  N+   +P   F     L+ L+L   ++ 
Sbjct: 538 LHILNLESNGFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNL---QKN 594

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGEL------SGL 346
             +     +F P                 NL  L +           I         +  
Sbjct: 595 LITSVEKKVFGPAFR--------------NLTELDMRFNPFDCTCESIAWFVNWINETHT 640

Query: 347 EILDLSESDVSEIPVSFGRLSHLRLLDLTGC 377
            I +LS   +   P  +     +RL D + C
Sbjct: 641 NIPELSSHYLCNTPPHYHGFP-VRLFDTSSC 670

>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 = 88.2 bits (219), Expect = 4e-18
 Identities = 41/287 (14%), Positives = 79/287 (27%), Gaps = 53/287 (18%)

Query: 235 LTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG----- 288
           L  +  ++N +           KL +L L  N    IP  F    + ++ L         
Sbjct: 332 LGMLECLYNQLEGKLPAFGSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLKY 391

Query: 289 IRRFSFSVRFPFL---------FPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-S 338
           I     +     +            +       L  +    IN+ ++ L + +I      
Sbjct: 392 IPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSINLSNNQISKFPKE 451

Query: 339 LIGELSGLEILDLSE--------SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSR 390
           L    S L  ++L          + + +   +F     L  +DL    + +L      + 
Sbjct: 452 LFSTGSPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDFRATT 511

Query: 391 LRKLEELYMSH--------SFRHWQ----FESESEEDSSSNAKF----IELGALSRLTSL 434
           L  L  + +S+           +      F   ++ D+  N         +     LT L
Sbjct: 512 LPYLVGIDLSYNSFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQL 571

Query: 435 HI------HIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLF 475
            I       + E           N++   I         LS      
Sbjct: 572 QIGSNDIRKVNEK-------ITPNISVLDIKDNPNISIDLSYVCPYI 611

>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 = 81.2 bits (201), Expect = 6e-16
 Identities = 28/253 (11%), Positives = 71/253 (28%), Gaps = 61/253 (24%)

Query: 220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGM 278
           P    I+      L  T I  + N+I  V   +    KL+  ++  +  +A         
Sbjct: 170 PQQKSIKKSSRITLKDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNSPFVAENICEAWEN 229

Query: 279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL- 337
           ++ +                                     L +L  + +++      L 
Sbjct: 230 ENSEYAQQYKT-----------------------EDLKWDNLKDLTDVEVYNCPNLTKLP 266

Query: 338 SLIGELSGLEILDLSE---------SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVL 388
           + +  L  +++++++           D  +          ++++ +    +        L
Sbjct: 267 TFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVETSL 326

Query: 389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI------HIPEGK 442
            +++KL  L   ++    Q E +              G+  +L SL++       IP   
Sbjct: 327 QKMKKLGMLECLYN----QLEGKLP----------AFGSEIKLASLNLAYNQITEIPAN- 371

Query: 443 IMPSDMSFQNLTS 455
                        
Sbjct: 372 ------FCGFTEQ 378

>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 = 70.5 bits (173), Expect = 1e-12
 Identities = 33/191 (17%), Positives = 57/191 (29%), Gaps = 46/191 (24%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGM 278
           +   +       ++++ I+L  N I + P EL      L ++ L  N             
Sbjct: 421 NFDPLDPTPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNM------------ 468

Query: 279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG--D 336
                  L  I                P + L     +      L ++ L   ++    D
Sbjct: 469 -------LTEI----------------PKNSLKDENENFKNTYLLTSIDLRFNKLTKLSD 505

Query: 337 LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLL------DLTGCYILELIPRGVLSR 390
                 L  L  +DLS +  S+ P      S L+        D  G   L   P G ++ 
Sbjct: 506 DFRATTLPYLVGIDLSYNSFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEG-ITL 564

Query: 391 LRKLEELYMSH 401
              L +L +  
Sbjct: 565 CPSLTQLQIGS 575

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 65.1 bits (159), Expect = 6e-11
 Identities = 31/276 (11%), Positives = 77/276 (27%), Gaps = 43/276 (15%)

Query: 228 EIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDL 286
           E+  W    G+SL               ++  L L+       +PD   Q + +L+VL L
Sbjct: 65  ELDMWGAQPGVSL-----------NSNGRVTGLSLEGFGASGRVPDAIGQ-LTELEVLAL 112

Query: 287 GG-IRRFSFSVRFPFLFPPLPS------SPLFLLPSSLSFLINLRTLRLHDRRIQGD--- 336
           G    + +  +  P       S        +    + + +        L    I  D   
Sbjct: 113 GSHGEKVNERLFGPKGISANMSDEQKQKMRMHYQKTFVDYDPREDFSDLIKDCINSDPQQ 172

Query: 337 ---LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK 393
                          +    ++++ +  +  RL+ LR   +     +             
Sbjct: 173 KSIKKSSRITLKDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNSPFVAENIC-EAWENEN 231

Query: 394 LEELYMSHSF--RHWQFESESEEDSSSNAKF----IELGALSRLTSLHIH---------- 437
            E      +   +    +  ++ +  +          L AL  +  +++           
Sbjct: 232 SEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQL 291

Query: 438 IPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIG 473
             + + +      + +    I   +L+  P+   + 
Sbjct: 292 KDDWQALADAPVGEKIQIIYIGYNNLKTFPVETSLQ 327

>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 = 88.2 bits (219), Expect = 4e-18
 Identities = 48/271 (17%), Positives = 76/271 (28%), Gaps = 57/271 (21%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRF------ 274
            +  I        +++  SL+   I  V D       Q L L        P         
Sbjct: 270 YLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKR 329

Query: 275 -------------FQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPS--------SPLFLL 313
                           +  L+ LDL      SF            S        + +  +
Sbjct: 330 LTFTSNKGGNAFSEVDLPSLEFLDLSRNG-LSFKGCCSQSDFGTTSLKYLDLSFNGVITM 388

Query: 314 PSSLSFLINLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDVSEI-PVSFGRLSHLR 370
            S+   L  L  L      ++   + S+   L  L  LD+S +         F  LS L 
Sbjct: 389 SSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLE 448

Query: 371 LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR 430
           +L + G    E     + + LR L  L +S      Q E  S              +LS 
Sbjct: 449 VLKMAGNSFQENFLPDIFTELRNLTFLDLSQC----QLEQLSPT---------AFNSLSS 495

Query: 431 LTSLHI------HIPEGKIMPSDMSFQNLTS 455
           L  L++       +           ++ L S
Sbjct: 496 LQVLNMSHNNFFSLDTF-------PYKCLNS 519

>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 = 86.6 bits (215), Expect = 9e-18
 Identities = 81/415 (19%), Positives = 135/415 (32%), Gaps = 58/415 (13%)

Query: 239 SLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF 298
             M  + +++PD L     + L L  N    +    F    +LQVLDL            
Sbjct: 13  QCMELNFYKIPDNL-PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSR---------- 61

Query: 299 PFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVS 357
                        +   +   L +L TL L    IQ   L     LS L+ L   E++++
Sbjct: 62  --------CEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLA 113

Query: 358 E-IPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH-SFRHWQFES----- 410
                  G L  L+ L++    I         S L  LE L +S    +           
Sbjct: 114 SLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLH 173

Query: 411 -----ESEEDSSSNA-KFIELGALS--RLTSLHIH--IPEGKIMPSDM-SFQNLTSFSIA 459
                    D S N   FI+ GA    RL  L +        +M + +     L    + 
Sbjct: 174 QMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLV 233

Query: 460 IGDLE-ERPLSDFIGLFLQKFKKRCSRAMGLSQ----DMRISALHSWIKNL----LLRSE 510
           +G+   E  L  F    L+           L+        I  L + + N+    L+   
Sbjct: 234 LGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVT 293

Query: 511 ILALAEVNYFENIVS-DLANDGFNELMFLVIFRCNEMKYLLNSLERTLR-VTLHKLEWLF 568
           I  + + +Y       +L N  F +   L +     + +  N        V L  LE+L 
Sbjct: 294 IERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLD 353

Query: 569 IRENQ-NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRV 622
           +  N  +F   C         +++K  D+   G      +  +  +F  L++L  
Sbjct: 354 LSRNGLSFKGCCSQSD--FGTTSLKYLDLSFNG------VITMSSNFLGLEQLEH 400

>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 = 78.9 bits (195), Expect = 3e-15
 Identities = 36/173 (20%), Positives = 59/173 (34%), Gaps = 8/173 (4%)

Query: 233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
             L  +    +DI ++ + L    + +  L   +   + D  F      Q L+L   +  
Sbjct: 262 FRLAYLDYYLDDIIDLFNCL--TNVSSFSLVSVTIERVKD--FSYNFGWQHLELVNCKFG 317

Query: 293 SFSVRFPFLFPPL-PSSPLFLLPSSLSFLINLRTLRLHDRRIQGD---LSLIGELSGLEI 348
            F          L  +S       S   L +L  L L    +             + L+ 
Sbjct: 318 QFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKY 377

Query: 349 LDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           LDLS + V  +  +F  L  L  LD     + ++    V   LR L  L +SH
Sbjct: 378 LDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISH 430

>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 = 76.6 bits (189), Expect = 2e-14
 Identities = 37/186 (19%), Positives = 70/186 (37%), Gaps = 27/186 (14%)

Query: 235 LTGISLMFNDIHEVPDE-LECPKLQALFLQEN--SPLAIPDRFFQGMKDLQVLDLGGIRR 291
           L  + L FN +  +    L   +L+ L  Q +    +      F  +++L  LD+     
Sbjct: 375 LKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQM-SEFSVFLSLRNLIYLDISHTH- 432

Query: 292 FSFSVRFPFLFPPLPSSPL------------FLLPSSLSFLINLRTLRLHDRRIQG-DLS 338
               V F  +F  L S  L              LP   + L NL  L L   +++    +
Sbjct: 433 --TRVAFNGIFNGLSS--LEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPT 488

Query: 339 LIGELSGLEILDLSE---SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE 395
               LS L++L++S      +      +  L+ L++LD +  +I+    + +      L 
Sbjct: 489 AFNSLSSLQVLNMSHNNFFSL--DTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLA 546

Query: 396 ELYMSH 401
            L ++ 
Sbjct: 547 FLNLTQ 552

>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 = 69.3 bits (170), Expect = 3e-12
 Identities = 73/440 (16%), Positives = 132/440 (30%), Gaps = 80/440 (18%)

Query: 224 KIQYEIAGWLD----LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIP-DRFFQ 276
            IQ    G       L  +  +  ++  + +        L+ L +  N   +     +F 
Sbjct: 87  PIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFS 146

Query: 277 GMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSF------------LINLR 324
            + +L+ LDL   +       +      L   PL  L   LS              I L 
Sbjct: 147 NLTNLEHLDLSSNK---IQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLH 203

Query: 325 TLRLHDRRIQGDL--SLIGELSGLEILDLSESDVSE-------IPVSFGRLSHLRLLDLT 375
            L L +     ++  + I  L+GLE+  L   +             +   L +L + +  
Sbjct: 204 KLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFR 263

Query: 376 GCYI--LELIPRGVLSRLRKLEELYMSH----SFRHWQFESESEEDSSSNAKF--IELGA 427
             Y+         + + L  +    +        + + +    +     N KF       
Sbjct: 264 LAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLK 323

Query: 428 LSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAM 487
           L  L  L     +G    S++   +L        DL    LS F G   Q          
Sbjct: 324 LKSLKRLTFTSNKGGNAFSEVDLPSLEFL-----DLSRNGLS-FKGCCSQSDF------- 370

Query: 488 GLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMK 547
           G +           +K L L          N    + S+       +L  L     N   
Sbjct: 371 GTTS----------LKYLDLSF--------NGVITMSSNFLG--LEQLEHLDFQHSN--- 407

Query: 548 YLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILL 607
            L    E ++ ++L  L +L I    +     +G      LS+++   +    S  +  L
Sbjct: 408 -LKQMSEFSVFLSLRNLIYLDISHT-HTRVAFNGIF--NGLSSLEVLKMAGN-SFQENFL 462

Query: 608 SHLVQSFQNLQRLRVYSCGL 627
             +    +NL  L +  C L
Sbjct: 463 PDIFTELRNLTFLDLSQCQL 482

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 88.0 bits (218), Expect = 5e-18
 Identities = 26/197 (13%), Positives = 58/197 (29%), Gaps = 35/197 (17%)

Query: 217 SQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFF 275
           ++ P +  I+ +    L  T I  + N I  +   +    KLQ ++   +          
Sbjct: 409 NRNPEMKPIKKDSRISLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVD 468

Query: 276 QGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG 335
               +                                   S S L +L  + L++     
Sbjct: 469 WEDANSDYAKQYEN-----------------------EELSWSNLKDLTDVELYNCPNMT 505

Query: 336 DL-SLIGELSGLEILDLSE----------SDVSEIPVSFGRLSHLRLLDLTGCYILELIP 384
            L   + +L  L+ L+++           +D + +         +++  +    + E   
Sbjct: 506 QLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPA 565

Query: 385 RGVLSRLRKLEELYMSH 401
              L ++ KL  L   H
Sbjct: 566 SASLQKMVKLGLLDCVH 582

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 77.6 bits (191), Expect = 1e-14
 Identities = 34/233 (14%), Positives = 63/233 (27%), Gaps = 46/233 (19%)

Query: 215 VVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELE--------------------- 253
                   T++  +      +    + +N++ E P                         
Sbjct: 530 AAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHNKVRHLE 589

Query: 254 ----CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG-----IRRFSFSVRFPFLFP- 303
                 KL  L L  N    IP+ F      ++ L         I     +     +   
Sbjct: 590 AFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVYVMGSV 649

Query: 304 -----PLPSSPLFLLPSSLSF-LINLRTLRLHDRRIQG-DLSLIGELSGLEILDLS---- 352
                 + S    +  S   +  IN  T+ L    IQ     L    S +  + LS    
Sbjct: 650 DFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPISTIILSNNLM 709

Query: 353 ----ESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
               E+ +     ++     L  +DL    +  L      + L  L  + +S+
Sbjct: 710 TSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSY 762

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 66.1 bits (161), Expect = 4e-11
 Identities = 63/476 (13%), Positives = 133/476 (27%), Gaps = 92/476 (19%)

Query: 228 EIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG 287
           E+  W D  G+ L               ++  L L               + +L+VL  G
Sbjct: 307 ELDMWGDQPGVDL-----------DNNGRVTGLSLAGFGAKGRVPDAIGQLTELKVLSFG 355

Query: 288 -----GIRRFSFSVRFPFLFPPLPSS--PLFLLPSSLSFLINLRTLRLHDRRIQGDLSLI 340
                   R                    +      L +   L    L    I      +
Sbjct: 356 THSETVSGRLFGDEELTPDMSEERKHRIRMHYKKMFLDYDQRLNLSDLLQDAIN-RNPEM 414

Query: 341 GELSGLEILDLSESDV-------SEIPVSFGRLSHLRLLDLTGCYILELIPR-------- 385
             +     + L ++ +       + I  +  RL+ L+++                     
Sbjct: 415 KPIKKDSRISLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANS 474

Query: 386 ----------GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLH 435
                        S L+ L ++ + +     Q                 L  L  L SL+
Sbjct: 475 DYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPD-------------FLYDLPELQSLN 521

Query: 436 IH------IPE-----GKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCS 484
           I         +      ++   + +   +  F +   +LEE P S  +   + K      
Sbjct: 522 IACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQK-MVKLGL--- 577

Query: 485 RAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCN 544
             +      ++  L ++  N+ L    L L   N  E I  D      +++  L  F  N
Sbjct: 578 --LDCV-HNKVRHLEAFGTNVKLT--DLKLDY-NQIEEIPEDFCA-FTDQVEGL-GFSHN 629

Query: 545 EMKYLLNSLERTLRVTLHKLEWLFIRENQ--NFVEICHGQLPAGCLSNVKRSDVVDCGSI 602
           ++KY+ N        +++ +  +    N+  +        +      N     +      
Sbjct: 630 KLKYIPNIFNAK---SVYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNE-- 684

Query: 603 LKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDL 658
           ++   + L  +   +  + + +  +      I   N  K +   + +   LT  DL
Sbjct: 685 IQKFPTELFATGSPISTIILSNNLMT----SIPE-NSLKPKDGNYKNTYLLTTIDL 735

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 65.3 bits (159), Expect = 5e-11
 Identities = 32/210 (15%), Positives = 67/210 (31%), Gaps = 38/210 (18%)

Query: 222 ITKIQYEIAGWLD------LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPD- 272
           I      I+  +D       + ++L +N+I + P EL      +  + L  N   +IP+ 
Sbjct: 656 IGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPISTIILSNNLMTSIPEN 715

Query: 273 ------RFFQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPS-SPLFL-------LPSS 316
                   ++    L  +DL    +   S      F    LP  S + +        P+ 
Sbjct: 716 SLKPKDGNYKNTYLLTTIDLRFNKLTSLSDD----FRATTLPYLSNMDVSYNCFSSFPTQ 771

Query: 317 LSFLINLRTLRLHDRRIQGDLSL-------IGELSGLEILDLSESDVSEIPVSFGRLSHL 369
                 L+   +  +R      +       I     L  L +  +D+ ++         L
Sbjct: 772 PLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSNDIRKVDEKL--TPQL 829

Query: 370 RLLDLTGCYILELIPRGVLSRLRKLEELYM 399
            +LD+     + +    V   +     + +
Sbjct: 830 YILDIADNPNISIDVTSVCPYIEAGMYVLL 859

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 85.9 bits (213), Expect = 6e-18
 Identities = 43/174 (24%), Positives = 69/174 (39%), Gaps = 18/174 (10%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IR 290
           LT + L  ND+  +P  +    PKL  L +  N+   I D  FQ    LQ L L    + 
Sbjct: 119 LTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLT 178

Query: 291 RFSFSVRFPFLFPPLPSSPLFL---LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE 347
               S     L P L      +   L S+L+  I +  L      I   +        L 
Sbjct: 179 HVDLS-----LIPSLFH--ANVSYNLLSTLAIPIAVEELDASHNSIN-VVR-GPVNVELT 229

Query: 348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           IL L  +++++          L  +DL+   + E I      ++++LE LY+S+
Sbjct: 230 ILKLQHNNLTDTA-WLLNYPGLVEVDLSYNEL-EKIMYHPFVKMQRLERLYISN 281

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 77.4 bits (191), Expect = 3e-15
 Identities = 29/232 (12%), Positives = 67/232 (28%), Gaps = 43/232 (18%)

Query: 238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFS 295
           I +   D++   +++     + +  + ++   +P       + +++L+L    I      
Sbjct: 28  IDMQTQDVYFGFEDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEID-- 85

Query: 296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSES 354
                               + ++   ++ L +    I+     +   +  L +L L  +
Sbjct: 86  ------------------TYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERN 127

Query: 355 DVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH----SFRHWQFE 409
           D+S +P   F     L  L ++   + E I          L+ L +S             
Sbjct: 128 DLSSLPRGIFHNTPKLTTLSMSNNNL-ERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIP 186

Query: 410 SESEEDSSSNAKFIELGALSRLTSLHI------HIPEGKIMPSDMSFQNLTS 455
           S    + S N     L     +  L         +              LT 
Sbjct: 187 SLFHANVSYN-LLSTLAIPIAVEELDASHNSINVVRGP-------VNVELTI 230

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 68.5 bits (168), Expect = 3e-12
 Identities = 26/169 (15%), Positives = 53/169 (31%), Gaps = 26/169 (15%)

Query: 228 EIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG 287
            +A  + +  +    N I+ V   +   +L  L LQ N+       +      L  +DL 
Sbjct: 200 TLAIPIAVEELDASHNSINVVRGPV-NVELTILKLQHNNLTDTA--WLLNYPGLVEVDLS 256

Query: 288 G--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSG 345
              + +                            +  L  L + + R+         +  
Sbjct: 257 YNELEKIM--------------------YHPFVKMQRLERLYISNNRLVALNLYGQPIPT 296

Query: 346 LEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL 394
           L++LDLS + +  +  +  +   L  L L    I+  +       L+ L
Sbjct: 297 LKVLDLSHNHLLHVERNQPQFDRLENLYLDHNSIVT-LKLSTHHTLKNL 344

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 65.5 bits (160), Expect = 2e-11
 Identities = 37/242 (15%), Positives = 80/242 (33%), Gaps = 47/242 (19%)

Query: 221 SITKIQYEIAGWL-DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQG 277
            ++ +   I      LT +S+  N++  + D+       LQ L L  N    +       
Sbjct: 128 DLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIPS 187

Query: 278 MKDLQVLDLGG--IRRFSFSVRFPFL---------FPPLPSSPLFLL---------PSSL 317
              L   ++    +   +  +    L              +  L +L          + L
Sbjct: 188 ---LFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTDTAWL 244

Query: 318 SFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTG 376
                L  + L    ++        ++  LE L +S + +  + +    +  L++LDL+ 
Sbjct: 245 LNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVALNLYGQPIPTLKVLDLSH 304

Query: 377 CYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA-KFIELGALSRLTSLH 435
            ++L  + R    +  +LE LY+ H                 N+   ++L     L +L 
Sbjct: 305 NHLLH-VERN-QPQFDRLENLYLDH-----------------NSIVTLKLSTHHTLKNLT 345

Query: 436 IH 437
           + 
Sbjct: 346 LS 347

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 63.1 bits (154), Expect = 1e-10
 Identities = 27/143 (18%), Positives = 45/143 (31%), Gaps = 21/143 (14%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
           +LT + L  N++ +    L  P L  + L  N    I    F  M+ L+ L +   R   
Sbjct: 227 ELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNR--- 283

Query: 294 FSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSE 353
                           L  L      +  L+ L L    +        +   LE L L  
Sbjct: 284 ----------------LVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQFDRLENLYLDH 327

Query: 354 SDVSEIPVSFGRLSHLRLLDLTG 376
           + +  +         L+ L L+ 
Sbjct: 328 NSIVTLK--LSTHHTLKNLTLSH 348

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 57.4 bits (139), Expect = 1e-08
 Identities = 62/413 (15%), Positives = 127/413 (30%), Gaps = 115/413 (27%)

Query: 310 LFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIP-VSFGRLS 367
           ++     ++ L N + +   +  ++    +L+     +E+L+L++  + EI   +F    
Sbjct: 35  VYFGFEDIT-LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAH 93

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA-KFIELG 426
            ++ L +    I   +P  V   +  L  L +                   N    +  G
Sbjct: 94  TIQKLYMGFNAI-RYLPPHVFQNVPLLTVLVLER-----------------NDLSSLPRG 135

Query: 427 ALSRLTSLHI---------HIPEGKIMPSDMSFQNLTSFSI------AIGDLEERPLSDF 471
                  L            I +        +FQ  TS          +  +    LS  
Sbjct: 136 IFHNTPKLTTLSMSNNNLERIEDD-------TFQATTSLQNLQLSSNRLTHV---DLSLI 185

Query: 472 IGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDG 531
             LF                    +  ++ +  L   +  +A+ E++   N ++ +    
Sbjct: 186 PSLF------------------HANVSYNLLSTL---AIPIAVEELDASHNSINVVRGPV 224

Query: 532 FNELMFLVIFRCNEMKYLLNSLERT-LRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSN 590
             EL  L +          N+L  T   +    L  + +  N+    +    +       
Sbjct: 225 NVELTILKLQH--------NNLTDTAWLLNYPGLVEVDLSYNE----LEK--IMYHPFVK 270

Query: 591 VKRSDVVDCGSILKIL------LSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEET 644
           ++R         L+ L      L  L    Q +  L+V    L +S   +  V       
Sbjct: 271 MQR---------LERLYISNNRLVALNLYGQPIPTLKV----LDLSHNHLLHVE---RNQ 314

Query: 645 ELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVE----ECDELRQVFP 693
             F  LE L L     +  +     +  + H LK + +     +C+ LR +F 
Sbjct: 315 PQFDRLENLYLDHN-SIVTL-----KLSTHHTLKNLTLSHNDWDCNSLRALFR 361

>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 = 82.3 bits (204), Expect = 2e-17
 Identities = 48/182 (26%), Positives = 63/182 (34%), Gaps = 18/182 (9%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
               I L  N I  VP      C  L  L+L  N    I    F G+  L+ LDL    +
Sbjct: 33  ASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQ 92

Query: 292 FSFSVRFPFLFPPLPS-SPLFL-------LPS-SLSFLINLRTLRLHDRRIQG--DLSLI 340
              SV  P  F  L     L L       L       L  L+ L L D  +Q   D +  
Sbjct: 93  LR-SVD-PATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFR 150

Query: 341 GELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
             L  L  L L  + +S +P  +F  L  L  L L    +   +       L +L  LY+
Sbjct: 151 D-LGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRV-AHVHPHAFRDLGRLMTLYL 208

Query: 400 SH 401
             
Sbjct: 209 FA 210

>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 = 72.3 bits (178), Expect = 5e-14
 Identities = 43/207 (20%), Positives = 68/207 (32%), Gaps = 39/207 (18%)

Query: 243 NDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFSVRFPF 300
             +  VP  +     Q +FL  N    +P   F+  ++L +L L    + R         
Sbjct: 21  QGLQAVPVGIP-AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARID-----AA 74

Query: 301 LFPPLPS-SPLFLL---------PSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEIL 349
            F  L     L L          P++   L  L TL L    +Q     L   L+ L+ L
Sbjct: 75  AFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYL 134

Query: 350 DLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
            L ++ +  +P  +F  L +L  L L G   +  +P      L  L+ L +         
Sbjct: 135 YLQDNALQALPDDTFRDLGNLTHLFLHG-NRISSVPERAFRGLHSLDRLLLHQ------- 186

Query: 409 ESESEEDSSSNA-KFIELGALSRLTSL 434
                     N    +   A   L  L
Sbjct: 187 ----------NRVAHVHPHAFRDLGRL 203

>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 = 66.2 bits (162), Expect = 6e-12
 Identities = 36/166 (21%), Positives = 57/166 (34%), Gaps = 29/166 (17%)

Query: 243 NDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFSVRF 298
             +  V         +L  L L       +    F+G+  LQ L L    ++        
Sbjct: 91  AQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALP----- 145

Query: 299 PFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDV 356
                            +   L NL  L LH  RI    + +  G L  L+ L L ++ V
Sbjct: 146 ---------------DDTFRDLGNLTHLFLHGNRISSVPERAFRG-LHSLDRLLLHQNRV 189

Query: 357 SEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           + +   +F  L  L  L L     L  +P   L+ LR L+ L ++ 
Sbjct: 190 AHVHPHAFRDLGRLMTLYLFANN-LSALPTEALAPLRALQYLRLND 234

>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 = 61.9 bits (151), Expect = 2e-10
 Identities = 37/160 (23%), Positives = 57/160 (35%), Gaps = 32/160 (20%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IR 290
           L  + L    + E+   L      LQ L+LQ+N+  A+PD  F+ + +L  L L G  I 
Sbjct: 107 LHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRIS 166

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEIL 349
                                +   +   L +L  L LH  R+         +L  L  L
Sbjct: 167 S--------------------VPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTL 206

Query: 350 DLSESDVSEIPVS-FGRLSHLRLLDLTG------CYILEL 382
            L  +++S +P      L  L+ L L        C    L
Sbjct: 207 YLFANNLSALPTEALAPLRALQYLRLNDNPWVCDCRARPL 246

>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 = 55.4 bits (134), Expect = 2e-08
 Identities = 26/157 (16%), Positives = 49/157 (31%), Gaps = 42/157 (26%)

Query: 313 LPSSLSFLINLRTLRLHDRRI----QGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLS 367
           +P  +      + + LH  RI                L IL L  + ++ I   +F  L+
Sbjct: 26  VPVGIP--AASQRIFLHGNRISHVPAASFR---ACRNLTILWLHSNVLARIDAAAFTGLA 80

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA 427
            L  LDL+    L  +       L +L  L++         +             +  G 
Sbjct: 81  LLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRC----GLQE------------LGPGL 124

Query: 428 LSRLTSLHI---------HIPEGKIMPSDMSFQNLTS 455
              L +L            +P+        +F++L +
Sbjct: 125 FRGLAALQYLYLQDNALQALPDD-------TFRDLGN 154

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 84.4 bits (209), Expect = 3e-17
 Identities = 50/218 (22%), Positives = 78/218 (35%), Gaps = 42/218 (19%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           +   ++L  N I  +          L+ L L  N    I    F G+ +L  L+L    +
Sbjct: 65  NTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRL 124

Query: 290 RRFSFSVRFPFLFPPLPS-SPLFL--------LPSSLSFLINLRTLRLHD----RRIQGD 336
                       F  L     L+L           + + + +LR L L +      I   
Sbjct: 125 TTIP-----NGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEG 179

Query: 337 LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
            +  G LS L  L+L+  ++ EIP +   L  L  LDL+G ++   I  G    L  L++
Sbjct: 180 -AFEG-LSNLRYLNLAMCNLREIP-NLTPLIKLDELDLSGNHL-SAIRPGSFQGLMHLQK 235

Query: 397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL 434
           L+M                  S  + IE  A   L SL
Sbjct: 236 LWMIQ----------------SQIQVIERNAFDNLQSL 257

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 80.2 bits (198), Expect = 6e-16
 Identities = 53/235 (22%), Positives = 78/235 (33%), Gaps = 59/235 (25%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRR 291
             + +  +  ++ EVPD +     + L L EN    I    F+ ++ L++L L    IR 
Sbjct: 44  QFSKVICVRKNLREVPDGIS-TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRT 102

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILD 350
                               +   + + L NL TL L D R+          LS L+ L 
Sbjct: 103 --------------------IEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELW 142

Query: 351 LSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFE 409
           L  + +  IP  +F R+  LR LDL     L  I  G    L  L  L ++         
Sbjct: 143 LRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAM-------- 194

Query: 410 SESEEDSSSNAKFIELGALSRLTSLHI---------HIPEGKIMPSDMSFQNLTS 455
                         E+  L+ L  L            I  G       SFQ L  
Sbjct: 195 ---------C-NLREIPNLTPLIKLDELDLSGNHLSAIRPG-------SFQGLMH 232

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 45.9 bits (109), Expect = 4e-05
 Identities = 28/107 (26%), Positives = 41/107 (38%), Gaps = 16/107 (14%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           L  ++L   ++ E+P+     KL  L L  N   AI    FQG+  LQ L +    I+  
Sbjct: 187 LRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQGLMHLQKLWMIQSQIQVI 246

Query: 293 SFSVRFPFLFPPLPS-SPLFL-------LPSS-LSFLINLRTLRLHD 330
                    F  L S   + L       LP    + L +L  + LH 
Sbjct: 247 E-----RNAFDNLQSLVEINLAHNNLTLLPHDLFTPLHHLERIHLHH 288

>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 = 84.0 bits (208), Expect = 4e-17
 Identities = 45/219 (20%), Positives = 78/219 (35%), Gaps = 42/219 (19%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           +   ++LM N+I  +  +       L+ L L  NS   I    F G+  L  L+L    +
Sbjct: 76  NTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWL 135

Query: 290 RRFSFSVRFPFLFPPLPS-SPLFL--------LPSSLSFLINLRTLRLHD----RRIQGD 336
                       F  L     L+L           + + + +L  L L +      I   
Sbjct: 136 TVIP-----SGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEG 190

Query: 337 LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
            +  G L  L+ L+L   ++ ++P +   L  L  L+++G +    I  G    L  L++
Sbjct: 191 -AFEG-LFNLKYLNLGMCNIKDMP-NLTPLVGLEELEMSGNHF-PEIRPGSFHGLSSLKK 246

Query: 397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLH 435
           L++ +                S    IE  A   L SL 
Sbjct: 247 LWVMN----------------SQVSLIERNAFDGLASLV 269

>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 = 77.1 bits (190), Expect = 7e-15
 Identities = 51/239 (21%), Positives = 75/239 (31%), Gaps = 67/239 (28%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRR 291
             + +      + EVP  +     + L L EN+   I    F+ +  L+VL LG   IR+
Sbjct: 55  QFSKVVCTRRGLSEVPQGIP-SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQ 113

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILD 350
                               +   + + L +L TL L D  +          LS L  L 
Sbjct: 114 --------------------IEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELW 153

Query: 351 LSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH-------S 402
           L  + +  IP  +F R+  L  LDL     LE I  G    L  L+ L +         +
Sbjct: 154 LRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDMPN 213

Query: 403 FRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH------IPEGKIMPSDMSFQNLTS 455
                                    L  L  L +       I  G       SF  L+S
Sbjct: 214 LTP----------------------LVGLEELEMSGNHFPEIRPG-------SFHGLSS 243

>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 = 43.6 bits (103), Expect = 2e-04
 Identities = 24/107 (22%), Positives = 37/107 (34%), Gaps = 16/107 (14%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           L  ++L   +I ++P+      L+ L +  N    I    F G+  L+ L +    +   
Sbjct: 198 LKYLNLGMCNIKDMPNLTPLVGLEELEMSGNHFPEIRPGSFHGLSSLKKLWVMNSQVSLI 257

Query: 293 SFSVRFPFLFPPLPS-SPLFL-------LPSS-LSFLINLRTLRLHD 330
                    F  L S   L L       LP    + L  L  L LH 
Sbjct: 258 E-----RNAFDGLASLVELNLAHNNLSSLPHDLFTPLRYLVELHLHH 299

>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 = 83.6 bits (207), Expect = 6e-17
 Identities = 51/249 (20%), Positives = 84/249 (33%), Gaps = 61/249 (24%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IR 290
           L  + L  N +  +P  +      L  L + EN  + + D  FQ + +L+ L++G   + 
Sbjct: 82  LRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLV 141

Query: 291 RFSFSVRFPFLFPPLPSSPLFLL-----------PSSLSFLINLRTLRLHDRRIQ--GDL 337
             S        F  L S  L  L             +LS L  L  LRL    I    D 
Sbjct: 142 YIS-----HRAFSGLNS--LEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNINAIRDY 194

Query: 338 SLIGELSGLEILDLSESD-VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
           S    L  L++L++S    +  +  +     +L  L +T C +   +P   +  L  L  
Sbjct: 195 SFKR-LYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTA-VPYLAVRHLVYLRF 252

Query: 397 LYMSHSFRHWQFESESEEDSSSNA-KFIELGA---LSRLTSLHIH------IPEGKIMPS 446
           L +S+                 N    IE      L RL  + +       +        
Sbjct: 253 LNLSY-----------------NPISTIEGSMLHELLRLQEIQLVGGQLAVVEPY----- 290

Query: 447 DMSFQNLTS 455
             +F+ L  
Sbjct: 291 --AFRGLNY 297

>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 = 79.8 bits (197), Expect = 1e-15
 Identities = 48/257 (18%), Positives = 79/257 (30%), Gaps = 51/257 (19%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           +   + L  N I  +  +     P L+ L L EN   A+    F  + +L+ L L    +
Sbjct: 33  ETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRL 92

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLL-----------PSSLSFLINLRTLRLHDRRIQ--GD 336
           +          +F  L +  L  L                 L NL++L + D  +     
Sbjct: 93  KLIP-----LGVFTGLSN--LTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISH 145

Query: 337 LSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE 395
            +  G L+ LE L L + +++ IP  +   L  L +L L    I   I      RL +L+
Sbjct: 146 RAFSG-LNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNI-NAIRDYSFKRLYRLK 203

Query: 396 ELYMSHSFRHWQFESESEEDS-------SSNA-KFIELGALSRLTSLHI---------HI 438
            L +SH                      +      +   A+  L  L            I
Sbjct: 204 VLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSYNPISTI 263

Query: 439 PEGKIMPSDMSFQNLTS 455
                         L  
Sbjct: 264 EGS-------MLHELLR 273

>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 = 75.9 bits (187), Expect = 2e-14
 Identities = 41/218 (18%), Positives = 84/218 (38%), Gaps = 26/218 (11%)

Query: 222 ITKIQYEI-AGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGM 278
           +  I +   +G   L  ++L   ++  +P E       L  L L+  +  AI D  F+ +
Sbjct: 140 LVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNINAIRDYSFKRL 199

Query: 279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL-------LPS-SLSFLINLRTLRLHD 330
             L+VL++            P     L  + L +       +P  ++  L+ LR L L  
Sbjct: 200 YRLKVLEISHWPYLDTM--TPNCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSY 257

Query: 331 RRIQG-DLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVL 388
             I   + S++ EL  L+ + L    ++ +   +F  L++LR+L+++G  +   +   V 
Sbjct: 258 NPISTIEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVLNVSGNQL-TTLEESVF 316

Query: 389 SRLRKLEELYMSHS----------FRHWQFESESEEDS 416
             +  LE L +  +              ++        
Sbjct: 317 HSVGNLETLILDSNPLACDCRLLWVFRRRWRLNFNRQQ 354

>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 = 1e-04
 Identities = 27/141 (19%), Positives = 45/141 (31%), Gaps = 25/141 (17%)

Query: 217 SQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRF 274
           S  P +  +       L+LT +S+   ++  VP         L+ L L  N    I    
Sbjct: 208 SHWPYLDTMTPNCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLRFLNLSYNPISTIEGSM 267

Query: 275 FQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR 332
              +  LQ + L G  +                        P +   L  LR L +   +
Sbjct: 268 LHELLRLQEIQLVGGQLAVVE--------------------PYAFRGLNYLRVLNVSGNQ 307

Query: 333 IQG-DLSLIGELSGLEILDLS 352
           +   + S+   +  LE L L 
Sbjct: 308 LTTLEESVFHSVGNLETLILD 328

>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 = 83.8 bits (207), Expect = 7e-17
 Identities = 43/174 (24%), Positives = 69/174 (39%), Gaps = 18/174 (10%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IR 290
           LT + L  ND+  +P  +    PKL  L +  N+   I D  FQ    LQ L L    + 
Sbjct: 125 LTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLT 184

Query: 291 RFSFSVRFPFLFPPLPSSPLFL---LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE 347
               S     L P L      +   L S+L+  I +  L      I   +        L 
Sbjct: 185 HVDLS-----LIPSLFH--ANVSYNLLSTLAIPIAVEELDASHNSIN-VVRG-PVNVELT 235

Query: 348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           IL L  +++++          L  +DL+   + E I      ++++LE LY+S+
Sbjct: 236 ILKLQHNNLTDTA-WLLNYPGLVEVDLSYNEL-EKIMYHPFVKMQRLERLYISN 287

>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 = 76.1 bits (187), Expect = 2e-14
 Identities = 29/232 (12%), Positives = 67/232 (28%), Gaps = 43/232 (18%)

Query: 238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFS 295
           I +   D++   +++     + +  + ++   +P       + +++L+L    I      
Sbjct: 34  IDMQTQDVYFGFEDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEID-- 91

Query: 296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSES 354
                               + ++   ++ L +    I+     +   +  L +L L  +
Sbjct: 92  ------------------TYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERN 133

Query: 355 DVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH----SFRHWQFE 409
           D+S +P   F     L  L ++   + E I          L+ L +S             
Sbjct: 134 DLSSLPRGIFHNTPKLTTLSMSNNNL-ERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIP 192

Query: 410 SESEEDSSSNAKFIELGALSRLTSLHI------HIPEGKIMPSDMSFQNLTS 455
           S    + S N     L     +  L         +              LT 
Sbjct: 193 SLFHANVSYN-LLSTLAIPIAVEELDASHNSINVVRGP-------VNVELTI 236

>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 = 68.0 bits (166), Expect = 7e-12
 Identities = 25/162 (15%), Positives = 49/162 (30%), Gaps = 26/162 (16%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           +  +    N I+ V   +   +L  L LQ N+              L  +DL    + + 
Sbjct: 213 VEELDASHNSINVVRGPV-NVELTILKLQHNNLTDTAW--LLNYPGLVEVDLSYNELEKI 269

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
                                      +  L  L + + R+         +  L++LDLS
Sbjct: 270 M--------------------YHPFVKMQRLERLYISNNRLVALNLYGQPIPTLKVLDLS 309

Query: 353 ESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL 394
            + +  +  +  +   L  L L    I+  +       L+ L
Sbjct: 310 HNHLLHVERNQPQFDRLENLYLDHNSIVT-LKLSTHHTLKNL 350

>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 = 53.8 bits (129), Expect = 2e-07
 Identities = 58/413 (14%), Positives = 124/413 (30%), Gaps = 115/413 (27%)

Query: 310 LFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIP-VSFGRLS 367
           ++     ++ L N + +   +  ++    +L+     +E+L+L++  + EI   +F    
Sbjct: 41  VYFGFEDIT-LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAH 99

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA-KFIELG 426
            ++ L +    I   +P  V   +  L  L +                   N    +  G
Sbjct: 100 TIQKLYMGFNAI-RYLPPHVFQNVPLLTVLVLER-----------------NDLSSLPRG 141

Query: 427 ALSRLTSLHI---------HIPEGKIMPSDMSFQNLTSFSI------AIGDLEERPLSDF 471
                  L            I +        +FQ  TS          +  ++   +   
Sbjct: 142 IFHNTPKLTTLSMSNNNLERIEDD-------TFQATTSLQNLQLSSNRLTHVDLSLIPSL 194

Query: 472 IGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDG 531
               +                  +S L          +  +A+ E++   N ++ +    
Sbjct: 195 FHANVS--------------YNLLSTL----------AIPIAVEELDASHNSINVVRGPV 230

Query: 532 FNELMFLVIFRCNEMKYLLNSL-ERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSN 590
             EL  L +          N+L +    +    L  + +  N+    +    +       
Sbjct: 231 NVELTILKLQH--------NNLTDTAWLLNYPGLVEVDLSYNE----LEK--IMYHPFVK 276

Query: 591 VKRSDVVDCGSILKIL------LSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEET 644
           ++R         L+ L      L  L    Q +  L+V    L +S   +  V   +   
Sbjct: 277 MQR---------LERLYISNNRLVALNLYGQPIPTLKV----LDLSHNHLLHV---ERNQ 320

Query: 645 ELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEE----CDELRQVFP 693
             F  LE L L     +  +     +  + H LK + +      C+ LR +F 
Sbjct: 321 PQFDRLENLYLDHN-SIVTL-----KLSTHHTLKNLTLSHNDWDCNSLRALFR 367

>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 = 79.0 bits (195), Expect = 2e-15
 Identities = 88/485 (18%), Positives = 150/485 (30%), Gaps = 71/485 (14%)

Query: 240 LMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFP 299
            M  + +++PD L     + L L  N    +    F    +LQVLDL             
Sbjct: 14  CMELNFYKIPDNLP-FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSR----------- 61

Query: 300 FLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSE 358
                       +   +   L +L TL L    IQ   L     LS L+ L   E++++ 
Sbjct: 62  -------CEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLAS 114

Query: 359 IP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH------------SFRH 405
           +     G L  L+ L++    I         S L  LE L +S                 
Sbjct: 115 LENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174

Query: 406 WQFESESEEDSSSNAKFIELGALS--RLTSLHIHIPEGKIMPSDMSFQNLTSFSIA---- 459
               + S + S +   FI+ GA    RL  L +      +       Q L    +     
Sbjct: 175 MPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVL 234

Query: 460 --------IGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEI 511
                   +   ++  L     L +++F+               + L +     L+   I
Sbjct: 235 GEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTI 294

Query: 512 LALAEVNYFENIVS-DLANDGFNELMFLVIFRCNEMKYLLNSLERTLR-VTLHKLEWLFI 569
             + + +Y       +L N  F +   L +     + +  N        V L  LE+L +
Sbjct: 295 ERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDL 354

Query: 570 RENQ-NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLL 628
             N  +F   C         +++K    +D      I +S      + L+ L      L 
Sbjct: 355 SRNGLSFKGCCSQSD--FGTTSLK---YLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLK 409

Query: 629 ----VSVFE---------IERVNIAKEETELFSSLEKLTLWDLP--RMTDIWKGDTQFVS 673
                SVF          I   +       +F+ L  L +  +      + +  D  F  
Sbjct: 410 QMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDI-FTE 468

Query: 674 LHNLK 678
           L NL 
Sbjct: 469 LRNLT 473

>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 = 78.2 bits (193), Expect = 4e-15
 Identities = 35/174 (20%), Positives = 71/174 (40%), Gaps = 28/174 (16%)

Query: 235 LTGISLMFNDIHEVPDE-LECPKLQALFLQENSPLAIPDR-FFQGMKDLQVLDLGG--IR 290
           L  + L FN +  +    L   +L+ L  Q ++   + +   F  +++L  LD+     R
Sbjct: 375 LKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTR 434

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS--LIGELSGLEI 348
                                      + L +L  L++     Q +    +  EL  L  
Sbjct: 435 --------------------VAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTF 474

Query: 349 LDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           LDLS+  + ++  + F  LS L++L++     L+ +P G+  RL  L+++++  
Sbjct: 475 LDLSQCQLEQLSPTAFNSLSSLQVLNMASNQ-LKSVPDGIFDRLTSLQKIWLHT 527

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 70.9 bits (174), Expect = 9e-13
 Identities = 35/171 (20%), Positives = 53/171 (30%), Gaps = 26/171 (15%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
           +++  SL+   I  V D       Q L L        P      +K L+ L     +  +
Sbjct: 283 NVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFP---TLKLKSLKRLTFTSNKGGN 339

Query: 294 FSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD---RRIQGDLSLIGELSGLEILD 350
                                 S   L +L  L L                  + L+ LD
Sbjct: 340 AF--------------------SEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLD 379

Query: 351 LSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           LS + V  +  +F  L  L  LD     + ++    V   LR L  L +SH
Sbjct: 380 LSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISH 430

>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 = 78.9 bits (195), Expect = 3e-15
 Identities = 49/339 (14%), Positives = 95/339 (28%), Gaps = 61/339 (17%)

Query: 238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR 297
              M   + +VPD++     + + L  N    +    F    +LQ LDL           
Sbjct: 16  YQCMDQKLSKVPDDIP-SSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSR--------- 65

Query: 298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDV 356
                         +   +   L +L  L L    IQ         L+ LE L   E+ +
Sbjct: 66  ---------CEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKL 116

Query: 357 SEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED 415
           + +     G+L  L+ L++   +I         S L  L  + +S++      ++ +  D
Sbjct: 117 ASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYN----YIQTITVND 172

Query: 416 SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLF 475
                    L  L     +++ +        DMS   +                 F G+ 
Sbjct: 173 ---------LQFLRENPQVNLSL--------DMSLNPIDFI----------QDQAFQGIK 205

Query: 476 LQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFE-NIVSDLANDGFNE 534
           L +          L  +   S +       L    +  L    + +   +          
Sbjct: 206 LHELT--------LRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEG 257

Query: 535 LMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQ 573
           L  + I           S +      L  +  + +    
Sbjct: 258 LCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVS 296

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 77.0 bits (190), Expect = 1e-14
 Identities = 39/179 (21%), Positives = 66/179 (36%), Gaps = 35/179 (19%)

Query: 232 WLDLTGISLMFNDIHEVPD----ELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG 287
           +LDL+      N +         +L    L+ L L  N    I    F G+++LQ LD  
Sbjct: 354 YLDLSR-----NALSFSGCCSYSDLGTNSLRHLDLSFNG-AIIMSANFMGLEELQHLDFQ 407

Query: 288 G--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELS 344
              ++R +                     S+   L  L  L +     +     +   L+
Sbjct: 408 HSTLKRVTE-------------------FSAFLSLEKLLYLDISYTNTKIDFDGIFLGLT 448

Query: 345 GLEILDLSESDVSEI--PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            L  L ++ +   +      F   ++L  LDL+ C + + I  GV   L +L+ L MSH
Sbjct: 449 SLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQ-ISWGVFDTLHRLQLLNMSH 506

>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 = 76.2 bits (188), Expect = 2e-14
 Identities = 30/171 (17%), Positives = 52/171 (30%), Gaps = 26/171 (15%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
           +++ +SL    I  + D  +  K Q+L +        P      +  L+ L L       
Sbjct: 286 NVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFP---TLDLPFLKSLTL------- 335

Query: 294 FSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD---RRIQGDLSLIGELSGLEILD 350
                        +     +      L +L  L L                  + L  LD
Sbjct: 336 -------------TMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLD 382

Query: 351 LSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           LS +    +  +F  L  L+ LD     +  +        L KL  L +S+
Sbjct: 383 LSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISY 433

>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 = 74.7 bits (184), Expect = 6e-14
 Identities = 30/186 (16%), Positives = 62/186 (33%), Gaps = 23/186 (12%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDE---LECPKLQALFLQENSPLAIPDRFFQG 277
               +     G  +L  +    + +  V +    L   KL  L +   +     D  F G
Sbjct: 387 GAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLG 446

Query: 278 MKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-D 336
           +  L  L + G                        L +  +   NL  L L   +++   
Sbjct: 447 LTSLNTLKMAGNSFKDN-----------------TLSNVFANTTNLTFLDLSKCQLEQIS 489

Query: 337 LSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE 395
             +   L  L++L++S +++  +  S + +L  L  LD +   I E     +    + L 
Sbjct: 490 WGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRI-ETSKGILQHFPKSLA 548

Query: 396 ELYMSH 401
              +++
Sbjct: 549 FFNLTN 554

>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 = 76.6 bits (189), Expect = 3e-15
 Identities = 48/241 (19%), Positives = 90/241 (37%), Gaps = 42/241 (17%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           L  + L  N + E+P+++    LQ L + EN    +    F G+  + V++LG   ++  
Sbjct: 102 LERLYLSKNQLKELPEKM-PKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSS 160

Query: 293 SFSVRFPFLFPPLPS-SPLFL-------LPSSLSFLINLRTLRLHDRRIQ--GDLSLIGE 342
                    F  +   S + +       +P  L    +L  L L   +I      SL G 
Sbjct: 161 GIENG---AFQGMKKLSYIRIADTNITTIPQGL--PPSLTELHLDGNKITKVDAASLKG- 214

Query: 343 LSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           L+ L  L LS + +S +   S     HLR L L     L  +P G L+  + ++ +Y+ +
Sbjct: 215 LNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNK-LVKVPGG-LADHKYIQVVYLHN 272

Query: 402 ----SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH---IPEGKIMPSDMSFQNLT 454
               +     F                    +  + + +    +   +I PS  +F+ + 
Sbjct: 273 NNISAIGSNDFCPPGYNTK-----------KASYSGVSLFSNPVQYWEIQPS--TFRCVY 319

Query: 455 S 455
            
Sbjct: 320 V 320

>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 = 72.7 bits (179), Expect = 7e-14
 Identities = 36/185 (19%), Positives = 61/185 (32%), Gaps = 29/185 (15%)

Query: 234 DLTGISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           D   + L  N I E+ D        L  L L  N    I    F  +  L+ L L    +
Sbjct: 53  DTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQL 112

Query: 290 RRFSFSVRFPFLFPPLPSSPLFL--------LPSSLSFLINLRTLRLHDRRIQGDLSLIG 341
           +          +   L    L +          S  + L  +  + L    ++   S I 
Sbjct: 113 KELP-----EKMPKTLQE--LRVHENEITKVRKSVFNGLNQMIVVELGTNPLK--SSGIE 163

Query: 342 E-----LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
                 +  L  + +++++++ IP   G    L  L L G  I   +    L  L  L +
Sbjct: 164 NGAFQGMKKLSYIRIADTNITTIPQ--GLPPSLTELHLDGNKI-TKVDAASLKGLNNLAK 220

Query: 397 LYMSH 401
           L +S 
Sbjct: 221 LGLSF 225

>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 = 71.6 bits (176), Expect = 2e-13
 Identities = 40/236 (16%), Positives = 76/236 (32%), Gaps = 64/236 (27%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRR 291
            L  +      + +VP +L  P    L LQ N    I D  F+ +K+L  L L    I  
Sbjct: 32  HLRVVQCSDLGLEKVPKDLP-PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKIS- 89

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD---RRIQGDLSLIGELSGLEI 348
                               + P + + L+ L  L L     + +   +        L+ 
Sbjct: 90  -------------------KISPGAFAPLVKLERLYLSKNQLKELPEKM-----PKTLQE 125

Query: 349 LDLSESDVSEIPV-SFGRLSHLRLLDLTG-CYILELIPRGVLSRLRKLEELYMSHSFRHW 406
           L + E++++++    F  L+ + +++L         I  G    ++KL  + ++      
Sbjct: 126 LRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIAD----- 180

Query: 407 QFESESEEDSSSNA-KFIELGALSRLTSLHIH------IPEGKIMPSDMSFQNLTS 455
                            I  G    LT LH+       +          S + L +
Sbjct: 181 ------------TNITTIPQGLPPSLTELHLDGNKITKVDAA-------SLKGLNN 217

>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 = 63.9 bits (156), Expect = 6e-11
 Identities = 26/170 (15%), Positives = 47/170 (27%), Gaps = 38/170 (22%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           LT + L  N I +V          L  L L  NS  A+ +        L+ L L      
Sbjct: 194 LTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNN---- 249

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
                          + L  +P  L+    ++ + LH+  I              I    
Sbjct: 250 ---------------NKLVKVPGGLADHKYIQVVYLHNNNIS------------AI---- 278

Query: 353 ESDVSEIPVSFGRLSHLRLLDLTGCYI-LELIPRGVLSRLRKLEELYMSH 401
            S+    P    + +    + L    +    I       +     + + +
Sbjct: 279 GSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQLGN 328

>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 = 78.8 bits (195), Expect = 4e-15
 Identities = 41/242 (16%), Positives = 84/242 (34%), Gaps = 47/242 (19%)

Query: 233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENS---PLAIPDRFFQGMKDLQVLDLGGI 289
           L+++  +L  +   +V   L+   L+ L L  NS      +      G  +L+ L + G 
Sbjct: 131 LNVSSNTL--DFPGKVSGGLKLNSLEVLDLSANSISGANVVGWVLSDGCGELKHLAISGN 188

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEIL 349
                S                     +S  +NL  L +        +  +G+ S L+ L
Sbjct: 189 ---KISGDVD-----------------VSRCVNLEFLDVSSNNFSTGIPFLGDCSALQHL 228

Query: 350 DLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
           D+S + +S +   +    + L+LL+++    +  IP      L+ L+ L ++ +    + 
Sbjct: 229 DISGNKLSGDFSRAISTCTELKLLNISSNQFVGPIPP---LPLKSLQYLSLAENKFTGEI 285

Query: 409 ESESEEDSS-------SNAKFI-----ELGALSRLTSLHI---HIPEGKIMPSDMSFQNL 453
                           S   F        G+ S L SL +   +   G++     +   +
Sbjct: 286 PDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNF-SGELPMD--TLLKM 342

Query: 454 TS 455
             
Sbjct: 343 RG 344

>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 = 74.9 bits (185), Expect = 6e-14
 Identities = 42/208 (20%), Positives = 70/208 (33%), Gaps = 49/208 (23%)

Query: 235 LTGISLMFNDIH-EVPDELE----CPKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLG 287
           L  + L  N I             C +L+ L +  N  +   +         +L+ LD+ 
Sbjct: 153 LEVLDLSANSISGANVVGWVLSDGCGELKHLAISGNK-ISGDVD---VSRCVNLEFLDVS 208

Query: 288 GIRRFSFSVRFPFLFP----------------PLPSSPLFLLPS----SLSF-------- 319
                +FS   PFL                      + +         ++S         
Sbjct: 209 S---NNFSTGIPFLGDCSALQHLDISGNKLSGDFSRA-ISTCTELKLLNISSNQFVGPIP 264

Query: 320 ---LINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLD 373
              L +L+ L L + +  G++   L G    L  LDLS +     +P  FG  S L  L 
Sbjct: 265 PLPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLA 324

Query: 374 LTGCYILELIPRGVLSRLRKLEELYMSH 401
           L+       +P   L ++R L+ L +S 
Sbjct: 325 LSSNNFSGELPMDTLLKMRGLKVLDLSF 352

>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 = 73.0 bits (180), Expect = 2e-13
 Identities = 32/171 (18%), Positives = 56/171 (32%), Gaps = 31/171 (18%)

Query: 307 SSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS-EIP--VSF 363
           +     + SSL  L  L +L L +  I G +S     + L  LDLS + +S  +    S 
Sbjct: 63  NVGFSAVSSSLLSLTGLESLFLSNSHINGSVSGFKCSASLTSLDLSRNSLSGPVTTLTSL 122

Query: 364 GRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSS------ 417
           G  S L+ L+++   +          +L  LE L +S +                     
Sbjct: 123 GSCSGLKFLNVSSNTLDFPGKVSGGLKLNSLEVLDLSANSISGANVVGWVLSDGCGELKH 182

Query: 418 ---SNAKF---IELGALSRLTSLHIH-------IPEGKIMPSDMSFQNLTS 455
              S  K    +++     L  L +        IP            + ++
Sbjct: 183 LAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGIP---------FLGDCSA 224

>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 = 71.9 bits (177), Expect = 5e-13
 Identities = 53/185 (28%), Positives = 76/185 (41%), Gaps = 23/185 (12%)

Query: 235 LTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLGGIR 290
           LTG+ L  N  +  VP     C  L++L L  N+     +P      M+ L+VLDL    
Sbjct: 296 LTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNN-FSGELPMDTLLKMRGLKVLDLSFN- 353

Query: 291 RFSFSVRFPFLFPPLPSSPLFL----------LPSSL--SFLINLRTLRLHDRRIQGDL- 337
              FS   P     L +S L L          +  +L  +    L+ L L +    G + 
Sbjct: 354 --EFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNGFTGKIP 411

Query: 338 SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
             +   S L  L LS + +S  IP S G LS LR L L    +   IP+  L  ++ LE 
Sbjct: 412 PTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQE-LMYVKTLET 470

Query: 397 LYMSH 401
           L +  
Sbjct: 471 LILDF 475

>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 = 66.5 bits (163), Expect = 3e-11
 Identities = 54/237 (22%), Positives = 78/237 (32%), Gaps = 36/237 (15%)

Query: 235 LTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLGGIR 290
           L  + L FN +   +P  L    KL+ L L  N  L   IP      +K L+ L L    
Sbjct: 420 LVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNM-LEGEIPQELMY-VKTLETLILDF-N 476

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEIL 349
             +                   +PS LS   NL  + L + R+ G++   IG L  L IL
Sbjct: 477 DLTGE-----------------IPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAIL 519

Query: 350 DLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPR--GVLSRLRKLEELYMSHSFRHW 406
            LS +  S  IP   G    L  LDL        IP      S       +         
Sbjct: 520 KLSNNSFSGNIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIK 579

Query: 407 QFESESEEDSSSNAKFI------ELGALSRLTSLHIH--IPEGKIMPSDMSFQNLTS 455
               + E   + N          +L  LS     +I   +  G   P+  +  ++  
Sbjct: 580 NDGMKKECHGAGNLLEFQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSMMF 636

>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 = 65.3 bits (160), Expect = 6e-11
 Identities = 48/184 (26%), Positives = 75/184 (40%), Gaps = 22/184 (11%)

Query: 235 LTGISLMFNDIH-EVPDELE--CPKLQALFLQENSPL--AIPDRFFQG-MKDLQVLDLGG 288
           L  + L FN+   E+P+ L      L  L L  N+     I     Q     LQ L L  
Sbjct: 345 LKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNN-FSGPILPNLCQNPKNTLQELYLQN 403

Query: 289 IRRFSFSVRFPFLFPPLPS-SPLFL--------LPSSLSFLINLRTLRLHDRRIQGDL-S 338
                F+ + P           L L        +PSSL  L  LR L+L    ++G++  
Sbjct: 404 N---GFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQ 460

Query: 339 LIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEEL 397
            +  +  LE L L  +D++ EIP      ++L  + L+   +   IP+  + RL  L  L
Sbjct: 461 ELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKW-IGRLENLAIL 519

Query: 398 YMSH 401
            +S+
Sbjct: 520 KLSN 523

>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 = 62.2 bits (152), Expect = 5e-10
 Identities = 47/205 (22%), Positives = 67/205 (32%), Gaps = 45/205 (21%)

Query: 235 LTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLGGIR 290
           L  + L  N     +P EL +C  L  L L  N      IP   F+    +    + G R
Sbjct: 516 LAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNL-FNGTIPAAMFKQSGKIAANFIAGKR 574

Query: 291 RFSFSVRFPFLFPPLPSSPLFL---LPSSLSFLINLRTLRLHDRRIQG------------ 335
                            + L         L+ L       +  R   G            
Sbjct: 575 YVYIKNDGMKKECHGAGNLLEFQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSM 634

Query: 336 ---DLSL----------IGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLD-----LTG 376
              D+S           IG +  L IL+L  +D+S  IP   G L  L +LD     L G
Sbjct: 635 MFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDG 694

Query: 377 CYILELIPRGVLSRLRKLEELYMSH 401
                 IP+  +S L  L E+ +S+
Sbjct: 695 -----RIPQA-MSALTMLTEIDLSN 713

>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 = 58.8 bits (143), Expect = 6e-09
 Identities = 43/274 (15%), Positives = 74/274 (27%), Gaps = 75/274 (27%)

Query: 228 EIAGWLDLTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIPDRFFQGMKDLQV 283
            +     L  + L  N +  E+P EL     L+ L L  N  L   IP        +L  
Sbjct: 437 SLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFND-LTGEIP-SGLSNCTNLNW 494

Query: 284 LDLGGIRRFSFSVRFPFLFPPLPS-SPLFL--------LPSSLSFLINLRTLRLHDRRIQ 334
           + L   R    +   P     L + + L L        +P+ L    +L  L L+     
Sbjct: 495 ISLSNNR---LTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNLFN 551

Query: 335 GDL---------------------SLIGELSGLEILDLSESDVS---EIPVSFGRLSHLR 370
           G +                       I      +    + + +           RLS   
Sbjct: 552 GTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGNLLEFQGIRSEQLNRLSTRN 611

Query: 371 LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI--ELGAL 428
             ++T                  +  L MS++                    I  E+G++
Sbjct: 612 PCNITSRVYGGHTSPT-FDNNGSMMFLDMSYN----MLSGY-----------IPKEIGSM 655

Query: 429 SRLTSLHI-------HIPEGKIMPSDMSFQNLTS 455
             L  L++        IP+           +L  
Sbjct: 656 PYLFILNLGHNDISGSIPD--------EVGDLRG 681

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 76.2 bits (188), Expect = 5e-15
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 27/233 (11%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           L  + +  N + E+P  L    L  L + +N    +P   F G++++  +++GG  +   
Sbjct: 104 LQKLYISKNHLVEIPPNL-PSSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENS 162

Query: 293 SFSVRFPFLFPPLPSSPLFL-------LPSSLSFLINLRTLRLHDRRIQ--GDLSLIGEL 343
            F    P  F  L  + L +       +P  L     L  L L   +IQ      L+   
Sbjct: 163 GFE---PGAFDGLKLNYLRISEAKLTGIPKDL--PETLNELHLDHNKIQAIELEDLLR-Y 216

Query: 344 SGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
           S L  L L  + +  I   S   L  LR L L     L  +P G L  L+ L+ +Y+  +
Sbjct: 217 SKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNK-LSRVPAG-LPDLKLLQVVYLHTN 274

Query: 403 FRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTS 455
                       D       ++    + ++  +  +P  ++ P+  +F+ +T 
Sbjct: 275 ----NITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPA--TFRCVTD 321

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 73.9 bits (182), Expect = 3e-14
 Identities = 43/182 (23%), Positives = 64/182 (35%), Gaps = 24/182 (13%)

Query: 234 DLTGISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--I 289
           D T + L  NDI E+  +       L AL L  N    I ++ F  ++ LQ L +    +
Sbjct: 55  DTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQKLYISKNHL 114

Query: 290 RRFSFSVRFPFLFPPLPSSPLFL--------LPSSLSFLINLRTLRLHDRRIQGDLSLIG 341
                    P L   L    L +             S L N+  + +    ++      G
Sbjct: 115 VEIP-----PNLPSSLVE--LRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPG 167

Query: 342 ELSG--LEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
              G  L  L +SE+ ++ IP        L  L L    I + I    L R  KL  L +
Sbjct: 168 AFDGLKLNYLRISEAKLTGIPK--DLPETLNELHLDHNKI-QAIELEDLLRYSKLYRLGL 224

Query: 400 SH 401
            H
Sbjct: 225 GH 226

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 62.3 bits (152), Expect = 2e-10
 Identities = 39/235 (16%), Positives = 67/235 (28%), Gaps = 63/235 (26%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRR 291
            L  +      +  VP E+  P    L LQ N    +    F+G++ L  L L    I  
Sbjct: 34  HLRVVQCSDLGLKAVPKEIS-PDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKIS- 91

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD---RRIQGDLSLIGELSGLEI 348
                               +   + S L  L+ L +       I  +L      S L  
Sbjct: 92  -------------------KIHEKAFSPLRKLQKLYISKNHLVEIPPNL-----PSSLVE 127

Query: 349 LDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILEL-IPRGVLSRLRKLEELYMSHSFRHW 406
           L + ++ + ++P   F  L ++  +++ G  +       G    L KL  L +S      
Sbjct: 128 LRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-KLNYLRISE----- 181

Query: 407 QFESESEEDSSSNAKFIELGALSRLTSLHI------HIPEGKIMPSDMSFQNLTS 455
                      +    I       L  LH+       I               + 
Sbjct: 182 -----------AKLTGIPKDLPETLNELHLDHNKIQAIELE-------DLLRYSK 218

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 60.4 bits (147), Expect = 8e-10
 Identities = 23/170 (13%), Positives = 46/170 (27%), Gaps = 38/170 (22%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           L  + L  N I  +  E      KL  L L  N    I +     +  L+ L L      
Sbjct: 195 LNELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDN---- 250

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
                          + L  +P+ L  L  L+ + LH   I        ++   +   + 
Sbjct: 251 ---------------NKLSRVPAGLPDLKLLQVVYLHTNNIT-------KVGVNDFCPVG 288

Query: 353 ESDVSEIPVSFGRLSHLRLLDLTGCYI-LELIPRGVLSRLRKLEELYMSH 401
                       + ++   + L    +    +       +     +   +
Sbjct: 289 ---------FGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFGN 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 = 74.9 bits (185), Expect = 2e-14
 Identities = 41/227 (18%), Positives = 80/227 (35%), Gaps = 40/227 (17%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
            I +I    A   +     L    + +V  + E   +  L +      +I     + + +
Sbjct: 11  PINQIF-PDADLAEGIRAVLQKASVTDVVTQEELESITKLVVAGEKVASIQG--IEYLTN 67

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFL------LPSSLSFLINLRTLRLHDRR 332
           L+ L+L G  I   S       L      + L++        S+L  L NLR L L++  
Sbjct: 68  LEYLNLNGNQITDISPLSNLVKL------TNLYIGTNKITDISALQNLTNLRELYLNEDN 121

Query: 333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR 392
           I  D+S +  L+ +  L+L  +           ++ L  L +T   + ++ P   ++ L 
Sbjct: 122 IS-DISPLANLTKMYSLNLGANHNLSDLSPLSNMTGLNYLTVTESKVKDVTP---IANLT 177

Query: 393 KLEELYMSHSFRHWQFESESEEDSSSN--AKFIELGALSRLTSLHIH 437
            L  L +++                 N       L +L+ L     +
Sbjct: 178 DLYSLSLNY-----------------NQIEDISPLASLTSLHYFTAY 207

>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 = 74.1 bits (183), Expect = 3e-14
 Identities = 46/220 (20%), Positives = 74/220 (33%), Gaps = 50/220 (22%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +  IQ  I    +L  ++L  N I ++       KL  L++  N    I     Q + +L
Sbjct: 56  VASIQ-GIEYLTNLEYLNLNGNQITDISPLSNLVKLTNLYIGTNKITDIS--ALQNLTNL 112

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
           + L L    I   S                       L+ L  + +L L       DLS 
Sbjct: 113 RELYLNEDNISDIS----------------------PLANLTKMYSLNLGANHNLSDLSP 150

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
           +  ++GL  L ++ES V ++      L+ L  L L    I ++ P   L+ L  L     
Sbjct: 151 LSNMTGLNYLTVTESKVKDVT-PIANLTDLYSLSLNYNQIEDISP---LASLTSLHYFTA 206

Query: 400 SHSFRHWQFESESEEDSSSN--AKFIELGALSRLTSLHIH 437
                              N       +  ++RL SL I 
Sbjct: 207 YV-----------------NQITDITPVANMTRLNSLKIG 229

>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 = 69.1 bits (170), Expect = 1e-12
 Identities = 34/183 (18%), Positives = 69/183 (37%), Gaps = 32/183 (17%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           I  I   +A    L   +   N I ++       +L +L +  N    +       +  L
Sbjct: 189 IEDIS-PLASLTSLHYFTAYVNQITDITPVANMTRLNSLKIGNNKITDLS--PLANLSQL 245

Query: 282 QVLDLG--GIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
             L++G   I                         +++  L  L+ L +   +I  D+S+
Sbjct: 246 TWLEIGTNQISD----------------------INAVKDLTKLKMLNVGSNQIS-DISV 282

Query: 340 IGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           +  LS L  L L+ + +    +   G L++L  L L+  +I ++ P   L+ L K++   
Sbjct: 283 LNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNHITDIRP---LASLSKMDSAD 339

Query: 399 MSH 401
            ++
Sbjct: 340 FAN 342

>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 = 68.3 bits (168), Expect = 2e-12
 Identities = 38/182 (20%), Positives = 64/182 (35%), Gaps = 30/182 (16%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +  +   IA   DL  +SL +N I ++        L       N    I       M  L
Sbjct: 167 VKDVT-PIANLTDLYSLSLNYNQIEDISPLASLTSLHYFTAYVNQITDITP--VANMTRL 223

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
             L +G   I                         S L+ L  L  L +   +I  D++ 
Sbjct: 224 NSLKIGNNKITDL----------------------SPLANLSQLTWLEIGTNQIS-DINA 260

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
           + +L+ L++L++  + +S+I      LS L  L L    +       V+  L  L  L++
Sbjct: 261 VKDLTKLKMLNVGSNQISDIS-VLNNLSQLNSLFLNNNQLGNEDME-VIGGLTNLTTLFL 318

Query: 400 SH 401
           S 
Sbjct: 319 SQ 320

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 74.3 bits (183), Expect = 2e-14
 Identities = 27/178 (15%), Positives = 57/178 (32%), Gaps = 22/178 (12%)

Query: 235 LTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IR 290
                +  + + +    L      ++ L L  N    I          L++L+L    + 
Sbjct: 12  YKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLY 71

Query: 291 RFSFSVRFPFLFPPLPSSPLFLL------PSSLSFLINLRTLRLHDRRIQGDLSLIGELS 344
                         L +  L  L         L    ++ TL   +  I   +S      
Sbjct: 72  ETLD-------LESLST--LRTLDLNNNYVQELLVGPSIETLHAANNNIS-RVSC-SRGQ 120

Query: 345 GLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           G + + L+ + ++ +  +  G  S ++ LDL    I  +    + +    LE L + +
Sbjct: 121 GKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQY 178

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 72.3 bits (178), Expect = 7e-14
 Identities = 33/240 (13%), Positives = 75/240 (31%), Gaps = 49/240 (20%)

Query: 245 IHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFSVRFPFLF 302
           IHE+       + +   + ++S         Q   +++ LDL G  + + S         
Sbjct: 2   IHEIKQNGN--RYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQIS-----AADL 54

Query: 303 PPLPSSPLFLL---------PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSE 353
            P     L LL            L  L  LRTL L++  +      +     +E L  + 
Sbjct: 55  APFTK--LELLNLSSNVLYETLDLESLSTLRTLDLNNNYV----QELLVGPSIETLHAAN 108

Query: 354 SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE 413
           +++S +     R    + + L    I   +         +++ L +  +    + ++ + 
Sbjct: 109 NNISRVS--CSRGQGKKNIYLANNKITM-LRDLDEGCRSRVQYLDLKLN----EIDTVNF 161

Query: 414 EDSSSNAKFIELGALSRLTSLHIH------IPEGKIMPS----DMSFQNLTSFSIAIGDL 463
            + +++           L  L++       +    +       D+S   L          
Sbjct: 162 AELAAS--------SDTLEHLNLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGPEFQSA 213

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 66.2 bits (162), Expect = 8e-12
 Identities = 30/184 (16%), Positives = 55/184 (29%), Gaps = 26/184 (14%)

Query: 222 ITKIQYE--IAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMK 279
           I  + +    A    L  ++L +N I++V  ++   KL+ L L  N    +   F Q   
Sbjct: 156 IDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGPEF-QSAA 214

Query: 280 DLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL 337
            +  + L    +                       +  +L F  NL    L         
Sbjct: 215 GVTWISLRNNKLVL---------------------IEKALRFSQNLEHFDLRGNGFHCGT 253

Query: 338 SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEEL 397
                     +  +++  V ++         +  L   G Y  E +P     RL  L   
Sbjct: 254 LRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLIALGHH 313

Query: 398 YMSH 401
           +  H
Sbjct: 314 HHHH 317

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 61.5 bits (150), Expect = 3e-10
 Identities = 39/265 (14%), Positives = 80/265 (30%), Gaps = 47/265 (17%)

Query: 222 ITKIQYE-IAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
           +++I    +A +  L  ++L  N ++E  D      L+ L L  N    +          
Sbjct: 46  LSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLRTLDLNNNYVQELL-----VGPS 100

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFL-------LPS-SLSFLINLRTLRLHD 330
           ++ L      I R S S           +  ++L       L          ++ L L  
Sbjct: 101 IETLHAANNNISRVSCS-----RGQGKKN--IYLANNKITMLRDLDEGCRSRVQYLDLKL 153

Query: 331 RRIQG--DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVL 388
             I       L      LE L+L  + + ++       + L+ LDL+   +  + P    
Sbjct: 154 NEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSNKLAFMGP--EF 210

Query: 389 SRLRKLEELYMSH--------SFRHW-----------QFESESEEDSSSNAKFIELGALS 429
                +  + + +        + R              F   +  D  S  + ++  A  
Sbjct: 211 QSAAGVTWISLRNNKLVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQ 270

Query: 430 RLTSLHIHIPEGKIMPSDMSFQNLT 454
            +  L     E   +P+   +    
Sbjct: 271 TVKKLTGQNEEECTVPTLGHYGAYC 295

>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 = 75.7 bits (186), Expect = 2e-14
 Identities = 32/218 (14%), Positives = 66/218 (30%), Gaps = 24/218 (11%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           +  +    N+I  V         + ++L  N    + D        +Q LDL    I   
Sbjct: 101 IETLHAANNNISRVSCSR-GQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEID-- 157

Query: 293 SFSVRFPFLFPPLPS-SPLFL-------LPSSLSFLINLRTLRLHDRRIQGDLSLIGELS 344
             +V F  L     +   L L       +   +     L+TL L   ++          +
Sbjct: 158 --TVNFAELAASSDTLEHLNLQYNFIYDVKGQV-VFAKLKTLDLSSNKLAFMGPEFQSAA 214

Query: 345 GLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS---- 400
           G+  + L  + +  I  +     +L   DL G        R   S+ ++++ +       
Sbjct: 215 GVTWISLRNNKLVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKK 274

Query: 401 ---HSFRHWQFESESEEDSSSNAKFIELGALSRLTSLH 435
               +       +      +   + +      RL +L 
Sbjct: 275 LTGQNEEECTVPTLGHY-GAYCCEDLPAPFADRLIALK 311

>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 = 71.4 bits (175), Expect = 5e-13
 Identities = 32/238 (13%), Positives = 75/238 (31%), Gaps = 45/238 (18%)

Query: 245 IHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFSVRFPFLF 302
           IHE+       + +   + ++S         Q   +++ LDL G  + + S         
Sbjct: 2   IHEIKQNG--NRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQIS-----AADL 54

Query: 303 PPLPS-SPLFL------LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD 355
            P      L L          L  L  LRTL L++  +      +     +E L  + ++
Sbjct: 55  APFTKLELLNLSSNVLYETLDLESLSTLRTLDLNNNYV----QELLVGPSIETLHAANNN 110

Query: 356 VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED 415
           +S +     R    + + L    I  ++         +++ L +  +    + ++ +  +
Sbjct: 111 ISRVS--CSRGQGKKNIYLANNKI-TMLRDLDEGCRSRVQYLDLKLN----EIDTVNFAE 163

Query: 416 SSSNAKFIELGALSRLTSLHIH------IPEGKIMPS----DMSFQNLTSFSIAIGDL 463
            +++           L  L++       +    +       D+S   L          
Sbjct: 164 LAAS--------SDTLEHLNLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGPEFQSA 213

>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 = 62.9 bits (153), Expect = 2e-10
 Identities = 53/462 (11%), Positives = 122/462 (26%), Gaps = 76/462 (16%)

Query: 222 ITKIQYE-IAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
           +++I    +A +  L  ++L  N ++E  D      L+ L L  N    +          
Sbjct: 46  LSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLRTLDLNNNYVQELL-----VGPS 100

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFL--------LPSSLSFLINLRTLRLHD 330
           ++ L      I R S S           +  ++L                  ++ L L  
Sbjct: 101 IETLHAANNNISRVSCS-----RGQGKKN--IYLANNKITMLRDLDEGCRSRVQYLDLKL 153

Query: 331 RRIQG--DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVL 388
             I       L      LE L+L  + + ++       + L+ LDL+   +  + P    
Sbjct: 154 NEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSNKLAFMGP--EF 210

Query: 389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH---IPEGKIMP 445
                +  + + ++    +     +           L     L    +       G +  
Sbjct: 211 QSAAGVTWISLRNN----KLVLIEK----------ALRFSQNLEHFDLRGNGFHCGTLRD 256

Query: 446 SDMSFQNLTSFSI-AIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKN 504
                Q + + +   +  L  +   +     L  +   C        D+        I  
Sbjct: 257 FFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCCE------DLPAPFADRLIAL 310

Query: 505 LLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKL 564
                 +L+  + +  E +  +  N        +   +         ++   + +     
Sbjct: 311 KRKEHALLSG-QGSETERLECEREN--QARQREIDALKEQ-----YRTVIDQVTLRKQAK 362

Query: 565 EWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYS 624
             L  ++          +  +         D     ++ +I L H  +    LQ LR   
Sbjct: 363 ITLEQKKKALD------EQVSNGRRAHAELDGTLQQAVGQIELQHATEEQSPLQLLRA-- 414

Query: 625 CGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWK 666
                    ++R      E +   +                 
Sbjct: 415 --------IVKRYEEMYVEQQSVQNNAIRDWDMYQHKETQLA 448

>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 = 51.0 bits (122), Expect = 1e-06
 Identities = 25/229 (10%), Positives = 57/229 (24%), Gaps = 17/229 (7%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQAL-FLQENSPLAIPDRFFQGMK 279
            +  I+  +    +L    L  N  H         K Q +  + + +   +  +  +   
Sbjct: 225 KLVLIEKALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECT 284

Query: 280 DLQVLDLGGIR----RFSFSVRFPFL------FPPLPSSPLFLLPSSLSFLINLRTLRLH 329
              +   G          F+ R   L            S    L          R +   
Sbjct: 285 VPTLGHYGAYCCEDLPAPFADRLIALKRKEHALLSGQGSETERLECERENQARQREIDAL 344

Query: 330 DRRIQGDLSLIGE-LSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGV 387
             + +  +  +         L+  +  + E         + L          +EL  +  
Sbjct: 345 KEQYRTVIDQVTLRKQAKITLEQKKKALDEQVSNGRRAHAELDGTLQQAVGQIEL--QHA 402

Query: 388 LSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI 436
                 L+ L      + ++     ++   +NA         + T L  
Sbjct: 403 TEEQSPLQLL--RAIVKRYEEMYVEQQSVQNNAIRDWDMYQHKETQLAE 449

>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 = 72.7 bits (179), Expect = 2e-13
 Identities = 49/216 (22%), Positives = 82/216 (37%), Gaps = 44/216 (20%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           IT I   +    +L  + L  N I ++        LQ L    N    +       +  L
Sbjct: 124 ITDID-PLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFG-NQVTDLKP--LANLTTL 179

Query: 282 QVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIG 341
           + LD+   +                        S L+ L NL +L   + +I  D++ +G
Sbjct: 180 ERLDISSNK--------------------VSDISVLAKLTNLESLIATNNQIS-DITPLG 218

Query: 342 ELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            L+ L+ L L+ + + +I  +   L++L  LDL    I  L P   LS L KL EL +  
Sbjct: 219 ILTNLDELSLNGNQLKDIG-TLASLTNLTDLDLANNQISNLAP---LSGLTKLTELKLGA 274

Query: 402 SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH 437
           +    Q  +              L  L+ LT+L ++
Sbjct: 275 N----QISN-----------ISPLAGLTALTNLELN 295

>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 = 70.4 bits (173), Expect = 1e-12
 Identities = 47/223 (21%), Positives = 84/223 (37%), Gaps = 38/223 (17%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +T I   +     L  I +  N I ++        L  L L  N    I     + + +L
Sbjct: 80  LTDIT-PLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDP--LKNLTNL 136

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPS-SPLFL-----LPSSLSFLINLRTLRLHDRRI 333
             L+L    I   S           L S   L           L+ L  L  L +   ++
Sbjct: 137 NRLELSSNTISDISA-------LSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKV 189

Query: 334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK 393
             D+S++ +L+ LE L  + + +S+I    G L++L  L L G  + ++     L+ L  
Sbjct: 190 S-DISVLAKLTNLESLIATNNQISDIT-PLGILTNLDELSLNGNQLKDIGT---LASLTN 244

Query: 394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI 436
           L +L ++++    Q  +              L  L++LT L +
Sbjct: 245 LTDLDLANN----QISN-----------LAPLSGLTKLTELKL 272

>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 = 66.5 bits (163), Expect = 1e-11
 Identities = 33/226 (14%), Positives = 75/226 (33%), Gaps = 48/226 (21%)

Query: 214 AVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDR 273
           A ++Q   I +I        +     L   ++ +   + +  ++  L       +   D 
Sbjct: 6   ATITQDTPINQIF-TDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLG-IKSID- 62

Query: 274 FFQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDR 331
             + + +L  ++     +                         + L  L  L  + +++ 
Sbjct: 63  GVEYLNNLTQINFSNNQLTDI----------------------TPLKNLTKLVDILMNNN 100

Query: 332 RIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL 391
           +I  D++ +  L+ L  L L  + +++I      L++L  L+L+   I ++     LS L
Sbjct: 101 QIA-DITPLANLTNLTGLTLFNNQITDID-PLKNLTNLNRLELSSNTISDISA---LSGL 155

Query: 392 RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH 437
             L++L   +                       L  L+ L  L I 
Sbjct: 156 TSLQQLSFGNQVT----------------DLKPLANLTTLERLDIS 185

>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 = 66.1 bits (162), Expect = 2e-11
 Identities = 41/183 (22%), Positives = 68/183 (37%), Gaps = 32/183 (17%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
            +  I   +A   +LT + L  N I  +       KL  L L  N    I      G+  
Sbjct: 232 QLKDIG-TLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISP--LAGLTA 288

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
           L  L+L    +                         S +S L NL  L L+   I  D+S
Sbjct: 289 LTNLELNENQLEDI----------------------SPISNLKNLTYLTLYFNNIS-DIS 325

Query: 339 LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
            +  L+ L+ L    + VS++  S   L+++  L      I +L P   L+ L ++ +L 
Sbjct: 326 PVSSLTKLQRLFFYNNKVSDVS-SLANLTNINWLSAGHNQISDLTP---LANLTRITQLG 381

Query: 399 MSH 401
           ++ 
Sbjct: 382 LND 384

>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 = 65.4 bits (160), Expect = 3e-11
 Identities = 43/175 (24%), Positives = 70/175 (40%), Gaps = 22/175 (12%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           LT I+   N + ++       KL  + +  N    I       + +L  L L    I   
Sbjct: 70  LTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITP--LANLTNLTGLTLFNNQITDI 127

Query: 293 SFSVRFPFLFPPLPSSPLFL------LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGL 346
                   L      + L L        S+LS L +L+ L   ++    DL  +  L+ L
Sbjct: 128 DPLKNLTNL------NRLELSSNTISDISALSGLTSLQQLSFGNQVT--DLKPLANLTTL 179

Query: 347 EILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           E LD+S + VS+I     +L++L  L  T   I ++ P   L  L  L+EL ++ 
Sbjct: 180 ERLDISSNKVSDIS-VLAKLTNLESLIATNNQISDITP---LGILTNLDELSLNG 230

>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 = 58.1 bits (141), Expect = 7e-09
 Identities = 32/179 (17%), Positives = 59/179 (32%), Gaps = 30/179 (16%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           I+ +   ++G   LT + L  N I  +        L  L L EN    I       +K+L
Sbjct: 255 ISNLA-PLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISP--ISNLKNL 311

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
             L L    I                         S +S L  L+ L  ++ ++  D+S 
Sbjct: 312 TYLTLYFNNISDI----------------------SPVSSLTKLQRLFFYNNKVS-DVSS 348

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           +  L+ +  L    + +S++      L+ +  L L         P    + +     + 
Sbjct: 349 LANLTNINWLSAGHNQISDLT-PLANLTRITQLGLNDQAW-TNAPVNYKANVSIPNTVK 405

>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 = 72.2 bits (177), Expect = 3e-13
 Identities = 53/381 (13%), Positives = 116/381 (30%), Gaps = 44/381 (11%)

Query: 312 LLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLR 370
           L  S +  L  LR L +   RIQ  D+S+      LE LDLS + + +I        +L+
Sbjct: 36  LWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHNKLVKIS--CHPTVNLK 93

Query: 371 LLDLTGCYILELIPRGVLSRLRKLEELYMSH---------SFRHWQFESESEEDSSSNAK 421
            LDL+      L        + +L+ L +S             H            +  +
Sbjct: 94  HLDLSFNAFDALPICKEFGNMSQLKFLGLSTTHLEKSSVLPIAHLNISKVLLVLGETYGE 153

Query: 422 FIELGALSRL--TSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKF 479
             +   L      SLHI  P  K     +     T  ++ + +++     +    FL   
Sbjct: 154 KEDPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVANLELSNIKCVLEDNKCSYFLSIL 213

Query: 480 KKRCSRAMGLSQDMRIS-----ALHSWIKNLLLRS-EILALAEVNYFENIVSDLANDGFN 533
            K  +     +  +        +    ++ +   +    +++ V     +     +    
Sbjct: 214 AKLQTNPKLSNLTLNNIETTWNSFIRILQLVWHTTVWYFSISNVKLQGQLDFRDFDYSGT 273

Query: 534 ELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKR 593
            L  L I +      +    +  +      +       +          +   C S +  
Sbjct: 274 SLKALSIHQVVS--DVFGFPQSYIYEIFSNMNIKNFTVSGT------RMVHMLCPSKISP 325

Query: 594 SDVVDCGS-ILKILLSHLVQSFQNLQRLRVYSCGL-----LVSVF---------EIERVN 638
              +D  + +L   +         L+ L +    L     +  +          +I + +
Sbjct: 326 FLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNS 385

Query: 639 IAKEE-TELFSSLEKLTLWDL 658
           ++ +E     S  + L   ++
Sbjct: 386 VSYDEKKGDCSWTKSLLSLNM 406

>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 = 57.6 bits (139), Expect = 1e-08
 Identities = 41/257 (15%), Positives = 76/257 (29%), Gaps = 46/257 (17%)

Query: 233 LDLTGISLMFNDIHEVPD-----ELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG 287
           L L  I   +N    +        +    +  + LQ        D     +K L +  + 
Sbjct: 225 LTLNNIETTWNSFIRILQLVWHTTVWYFSISNVKLQGQLDFRDFDYSGTSLKALSIHQVV 284

Query: 288 GIRRFSFSVRFPFLFPP------LPSSPLFLLPS-SLSFLINLRTLRLHDRRIQGDLS-L 339
               F F   + +             S   ++     S +     L   +  +   +   
Sbjct: 285 -SDVFGFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDFSNNLLTDTVFEN 343

Query: 340 IGELSGLEILDLSESDVSEIPVS---FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE 396
            G L+ LE L L  + + E+        ++  L+ LD++   +     +G  S  + L  
Sbjct: 344 CGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTKSLLS 403

Query: 397 LYMSHSFRHWQFESESEEDSSSNAKFIELG------------ALSRLTSLHIH------I 438
           L MS +                  K ++L              L  L  L++       +
Sbjct: 404 LNMSSN----ILTDTIFRCLPPRIKVLDLHSNKIKSIPKQVVKLEALQELNVASNQLKSV 459

Query: 439 PEGKIMPSDMSFQNLTS 455
           P+G        F  LTS
Sbjct: 460 PDG-------IFDRLTS 469

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A* Length = 276

 Score = 68.8 bits (169), Expect = 8e-13
 Identities = 49/235 (20%), Positives = 80/235 (34%), Gaps = 51/235 (21%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
               + L FN +  +        P+LQ L L       I D  +Q +  L  L L G   
Sbjct: 29  STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNP- 87

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILD 350
                        + S        + S L +L+ L   +  +   +   IG L  L+ L+
Sbjct: 88  -------------IQSLA----LGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELN 130

Query: 351 LSESDVSEIPVS--FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
           ++ + +    +   F  L++L  LDL+   I + I    L  L ++  L +S        
Sbjct: 131 VAHNLIQSFKLPEYFSNLTNLEHLDLSSNKI-QSIYCTDLRVLHQMPLLNLSLDLSLNPM 189

Query: 409 ESESEEDSSSNAKFIELGALS--RLTSLHIH------IPEGKIMPSDMSFQNLTS 455
                         I+ GA    RL  L +       +P+G        F  LTS
Sbjct: 190 NF------------IQPGAFKEIRLKELALDTNQLKSVPDG-------IFDRLTS 225

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 68.3 bits (168), Expect = 2e-12
 Identities = 44/259 (16%), Positives = 86/259 (33%), Gaps = 59/259 (22%)

Query: 217 SQTPSIT-KIQYEIAGWLDLTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIP 271
               ++   I   IA    L  + +   ++   +PD L +   L  L    N+ L   +P
Sbjct: 84  GGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNA-LSGTLP 142

Query: 272 DRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRT-LRLHD 330
                 + +L  +   G  R S +                 +P S      L T + +  
Sbjct: 143 PSISS-LPNLVGITFDG-NRISGA-----------------IPDSYGSFSKLFTSMTISR 183

Query: 331 RRIQGDL-SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVL 388
            R+ G +      L+ L  +DLS + +  +  V FG   + + + L    +   + +  +
Sbjct: 184 NRLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLGK--V 240

Query: 389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKF-----IELGALSRLTSLHI---HIPE 440
              + L  L + +                 N +        L  L  L SL++   ++  
Sbjct: 241 GLSKNLNGLDLRN-----------------N-RIYGTLPQGLTQLKFLHSLNVSFNNL-C 281

Query: 441 GKIMPSDMSFQNLTSFSIA 459
           G+I P   + Q     + A
Sbjct: 282 GEI-PQGGNLQRFDVSAYA 299

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 66.8 bits (164), Expect = 5e-12
 Identities = 34/192 (17%), Positives = 62/192 (32%), Gaps = 43/192 (22%)

Query: 235 LTGISLMFNDIH-EVPDEL-ECPKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLGGIR 290
           L  +   +N +   +P  +   P L  +    N  +  AIPD +    K    + +   R
Sbjct: 127 LVTLDFSYNALSGTLPPSISSLPNLVGITFDGNR-ISGAIPDSYGSFSKLFTSMTISRNR 185

Query: 291 RFSFSVRFPFLFPPLPSS-------PLFL--------LPSSLSFLINLRTLRLHDRRIQG 335
                     L   +P +        + L                 N + + L    +  
Sbjct: 186 ----------LTGKIPPTFANLNLAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAF 235

Query: 336 DLSLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLD-----LTGCYILELIPRGVLS 389
           DL  +G    L  LDL  + +   +P    +L  L  L+     L G      IP+G   
Sbjct: 236 DLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCG-----EIPQG--G 288

Query: 390 RLRKLEELYMSH 401
            L++ +    ++
Sbjct: 289 NLQRFDVSAYAN 300

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 66.0 bits (162), Expect = 1e-11
 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 4/92 (4%)

Query: 313 LPSSLSFLINLRTLRLHDR-RIQGDL-SLIGELSGLEILDLSESDVS-EIPVSFGRLSHL 369
           +PSSL+ L  L  L +     + G +   I +L+ L  L ++ ++VS  IP    ++  L
Sbjct: 68  IPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTL 127

Query: 370 RLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
             LD +   +   +P   +S L  L  +    
Sbjct: 128 VTLDFSYNALSGTLPPS-ISSLPNLVGITFDG 158

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 61.4 bits (150), Expect = 3e-10
 Identities = 25/157 (15%), Positives = 51/157 (32%), Gaps = 38/157 (24%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSL---IGELSGLEILDLSESD--VSEIPVSFGRLS 367
           L  + +    +  L L    +     +   +  L  L  L +   +  V  IP +  +L+
Sbjct: 42  LCDTDTQTYRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLT 101

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI--EL 425
            L  L +T   +   IP   LS+++ L  L  S++                    +   +
Sbjct: 102 QLHYLYITHTNVSGAIPDF-LSQIKTLVTLDFSYN----ALSGT-----------LPPSI 145

Query: 426 GALSRLTSLHIH-------IPEGKIMPSDMSFQNLTS 455
            +L  L  +          IP+        S+ + + 
Sbjct: 146 SSLPNLVGITFDGNRISGAIPD--------SYGSFSK 174

>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 = 69.8 bits (170), Expect = 2e-12
 Identities = 41/198 (20%), Positives = 72/198 (36%), Gaps = 42/198 (21%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD-RFFQGMKD 280
           I +I      + +    +L    + +   + E   +  +    +    I   +  Q + +
Sbjct: 11  IKQIF-PDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSD---IKSVQGIQYLPN 66

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLP---------------SSLSFLINL 323
           +  L L G  +                   PL  L                SSL  L  L
Sbjct: 67  VTKLFLNGNKLTDI---------------KPLTNLKNLGWLFLDENKIKDLSSLKDLKKL 111

Query: 324 RTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELI 383
           ++L L    I  D++ +  L  LE L L  + +++I     RL+ L  L L    I +++
Sbjct: 112 KSLSLEHNGIS-DINGLVHLPQLESLYLGNNKITDIT-VLSRLTKLDTLSLEDNQISDIV 169

Query: 384 PRGVLSRLRKLEELYMSH 401
           P   L+ L KL+ LY+S 
Sbjct: 170 P---LAGLTKLQNLYLSK 184

>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 = 68.6 bits (167), Expect = 4e-12
 Identities = 42/183 (22%), Positives = 75/183 (40%), Gaps = 34/183 (18%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD-RFFQGMKD 280
           I  +Q  I    ++T + L  N + ++        L  LFL EN    I D    + +K 
Sbjct: 55  IKSVQ-GIQYLPNVTKLFLNGNKLTDIKPLTNLKNLGWLFLDENK---IKDLSSLKDLKK 110

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
           L+ L L    I                         + L  L  L +L L + +I  D++
Sbjct: 111 LKSLSLEHNGISDI----------------------NGLVHLPQLESLYLGNNKIT-DIT 147

Query: 339 LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           ++  L+ L+ L L ++ +S+I      L+ L+ L L+  +I +L     L+ L+ L+ L 
Sbjct: 148 VLSRLTKLDTLSLEDNQISDIV-PLAGLTKLQNLYLSKNHISDLRA---LAGLKNLDVLE 203

Query: 399 MSH 401
           +  
Sbjct: 204 LFS 206

>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 = 64.4 bits (156), Expect = 1e-10
 Identities = 26/169 (15%), Positives = 56/169 (33%), Gaps = 31/169 (18%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           +     +   I ++  +    +     L++ S           +  +  +      I+  
Sbjct: 1   MGETITVSTPIKQIFPDDAFAETIKDNLKKKSVTDAV--TQNELNSIDQIIANNSDIKSV 58

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
                                   + +L N+  L L+  ++  D+  +  L  L  L L 
Sbjct: 59  QG----------------------IQYLPNVTKLFLNGNKLT-DIKPLTNLKNLGWLFLD 95

Query: 353 ESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           E+ + ++  S   L  L+ L L    I ++     L  L +LE LY+ +
Sbjct: 96  ENKIKDLS-SLKDLKKLKSLSLEHNGISDING---LVHLPQLESLYLGN 140

>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 = 1e-05
 Identities = 40/221 (18%), Positives = 76/221 (34%), Gaps = 31/221 (14%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +T I+  +    +L  + L  N I ++    +  KL++L L+ N    I       +  L
Sbjct: 77  LTDIK-PLTNLKNLGWLFLDENKIKDLSSLKDLKKLKSLSLEHNGISDIN--GLVHLPQL 133

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLP---------SSLSFLINLRTLRLHD 330
           + L LG   I   +           L    L  L            L+ L  L+ L L  
Sbjct: 134 ESLYLGNNKITDITV-------LSRLTK--LDTLSLEDNQISDIVPLAGLTKLQNLYLSK 184

Query: 331 RRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGR----LSHLRLLDLTGCYILELIPRG 386
             I  DL  +  L  L++L+L   +    P++        + ++  D +      +   G
Sbjct: 185 NHIS-DLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDG 243

Query: 387 VLSRL---RKLEELYMSHSFRHWQFESESEEDSSSNAKFIE 424
              +      L E     SF  +Q  +  +  +  + +  +
Sbjct: 244 DYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQ 284

>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 = 65.9 bits (161), Expect = 9e-12
 Identities = 32/190 (16%), Positives = 69/190 (36%), Gaps = 32/190 (16%)

Query: 214 AVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDR 273
             ++Q  +I  I        +   I+   +++ +   + +   +  L         I   
Sbjct: 1   GSITQPTAINVIF-PDPALANAIKIAAGKSNVTDTVTQADLDGITTLSAFGTGVTTIE-- 57

Query: 274 FFQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDR 331
             Q + +L  L+L    I                         + L  L  +  L L   
Sbjct: 58  GVQYLNNLIGLELKDNQITDL----------------------APLKNLTKITELELSGN 95

Query: 332 RIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL 391
            ++ ++S I  L  ++ LDL+ + ++++      LS+L++L L    I  + P   L+ L
Sbjct: 96  PLK-NVSAIAGLQSIKTLDLTSTQITDVT-PLAGLSNLQVLYLDLNQITNISP---LAGL 150

Query: 392 RKLEELYMSH 401
             L+ L + +
Sbjct: 151 TNLQYLSIGN 160

>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 = 65.5 bits (160), Expect = 1e-11
 Identities = 36/182 (19%), Positives = 67/182 (36%), Gaps = 32/182 (17%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           IT +   +     +T + L  N +  V        ++ L L       +      G+ +L
Sbjct: 75  ITDLA-PLKNLTKITELELSGNPLKNVSAIAGLQSIKTLDLTSTQITDVTP--LAGLSNL 131

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
           QVL L    I   S                       L+ L NL+ L + + ++  DL+ 
Sbjct: 132 QVLYLDLNQITNIS----------------------PLAGLTNLQYLSIGNAQVS-DLTP 168

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
           +  LS L  L   ++ +S+I      L +L  + L    I ++ P   L+    L  + +
Sbjct: 169 LANLSKLTTLKADDNKISDIS-PLASLPNLIEVHLKNNQISDVSP---LANTSNLFIVTL 224

Query: 400 SH 401
           ++
Sbjct: 225 TN 226

>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 = 62.8 bits (153), Expect = 1e-10
 Identities = 32/169 (18%), Positives = 67/169 (39%), Gaps = 31/169 (18%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           +T +S     +  +        L  L L++N    +     + +  +  L+L G  ++  
Sbjct: 43  ITTLSAFGTGVTTIEGVQYLNNLIGLELKDNQITDLAP--LKNLTKITELELSGNPLKNV 100

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
                                 S+++ L +++TL L   +I  D++ +  LS L++L L 
Sbjct: 101 ----------------------SAIAGLQSIKTLDLTSTQIT-DVTPLAGLSNLQVLYLD 137

Query: 353 ESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            + ++ I      L++L+ L +    + +L P   L+ L KL  L    
Sbjct: 138 LNQITNIS-PLAGLTNLQYLSIGNAQVSDLTP---LANLSKLTTLKADD 182

>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 = 44.7 bits (106), Expect = 7e-05
 Identities = 37/176 (21%), Positives = 66/176 (37%), Gaps = 20/176 (11%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +  +   IAG   +  + L    I +V        LQ L+L  N    I      G+ +L
Sbjct: 97  LKNVS-AIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLYLDLNQITNISP--LAGLTNL 153

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFL------LPSSLSFLINLRTLRLHDRRI 333
           Q L +G   +   +       L      + L          S L+ L NL  + L + +I
Sbjct: 154 QYLSIGNAQVSDLTPLANLSKL------TTLKADDNKISDISPLASLPNLIEVHLKNNQI 207

Query: 334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLS 389
             D+S +   S L I+ L+   ++  PV +   ++L + ++        I    +S
Sbjct: 208 S-DVSPLANTSNLFIVTLTNQTITNQPVFY--NNNLVVPNVVKGPSGAPIAPATIS 260

>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 = 66.3 bits (162), Expect = 1e-11
 Identities = 41/221 (18%), Positives = 69/221 (31%), Gaps = 56/221 (25%)

Query: 248 VPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPS 307
           +P  L    +++L L  N    I +   Q   +LQ L L                    S
Sbjct: 46  IPSGL-TEAVKSLDLSNNRITYISNSDLQRCVNLQALVLT-------------------S 85

Query: 308 SPLFLLPS-SLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIPVS--F 363
           + +  +   S S L +L  L L    +     S    LS L  L+L  +    +  +  F
Sbjct: 86  NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF 145

Query: 364 GRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI 423
             L+ L++L +        I R   + L  LEEL +  S      +S             
Sbjct: 146 SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDAS----DLQS------------Y 189

Query: 424 ELGALSRLTSLHI---------HIPEGKIMPSDMSFQNLTS 455
           E  +L  + ++            + E             +S
Sbjct: 190 EPKSLKSIQNVSHLILHMKQHILLLEI-------FVDVTSS 223

>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 = 64.0 bits (156), Expect = 3e-11
 Identities = 34/146 (23%), Positives = 54/146 (36%), Gaps = 22/146 (15%)

Query: 257 LQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSS 316
              L L EN               L  L+L                  L    +      
Sbjct: 33  TTILHLSENLLYTFSLATLMPYTRLTQLNLDRAE--------------LTKLQVD----- 73

Query: 317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLT 375
              L  L TL L   ++Q    L   L  L +LD+S + ++ +P+     L  L+ L L 
Sbjct: 74  -GTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLK 132

Query: 376 GCYILELIPRGVLSRLRKLEELYMSH 401
           G   L+ +P G+L+   KLE+L +++
Sbjct: 133 GN-ELKTLPPGLLTPTPKLEKLSLAN 157

>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 = 60.1 bits (146), Expect = 6e-10
 Identities = 33/154 (21%), Positives = 53/154 (34%), Gaps = 36/154 (23%)

Query: 312 LLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRL 371
              ++L     L  L L    +   L + G L  L  LDLS + +  +P+    L  L +
Sbjct: 46  FSLATLMPYTRLTQLNLDRAELT-KLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTV 104

Query: 372 LDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA-KFIELGALSR 430
           LD++   +   +P G L  L +L+ELY+                   N  K +  G L+ 
Sbjct: 105 LDVSFNRL-TSLPLGALRGLGELQELYLKG-----------------NELKTLPPGLLTP 146

Query: 431 LTSLHI---------HIPEGKIMPSDMSFQNLTS 455
              L            +P G           L +
Sbjct: 147 TPKLEKLSLANNNLTELPAG-------LLNGLEN 173

>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 = 50.5 bits (121), Expect = 1e-06
 Identities = 37/188 (19%), Positives = 66/188 (35%), Gaps = 34/188 (18%)

Query: 222 ITKIQYEI-AGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
           +          +  LT ++L   ++ ++  +   P L  L L  N   ++P    Q +  
Sbjct: 43  LYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQSLPL-LGQTLPA 101

Query: 281 LQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSF--LINLRTLRLHDRRIQGDLS 338
           L VLD+                     + L  LP       L  L+ L L    ++   +
Sbjct: 102 LTVLDVS-------------------FNRLTSLPLGA-LRGLGELQELYLKGNELK---T 138

Query: 339 L----IGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRK 393
           L    +     LE L L+ ++++E+P      L +L  L L     L  IP+G       
Sbjct: 139 LPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQE-NSLYTIPKGFFGSH-L 196

Query: 394 LEELYMSH 401
           L   ++  
Sbjct: 197 LPFAFLHG 204

>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 = 65.4 bits (159), Expect = 4e-11
 Identities = 30/236 (12%), Positives = 67/236 (28%), Gaps = 17/236 (7%)

Query: 54  NDLQAEIDAATRNREVIKDEV--KSWIAEVNDIIPKAEKFLEDEVKVNKKCLGGLCVDLK 111
             L+ +      + E+I         IA    I  +    L   +            D  
Sbjct: 28  TYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFL 87

Query: 112 SRYKLSREAEEKTLAMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIME 171
             Y +     E  L    ++A     + + R      +       Y  +     +   ++
Sbjct: 88  EDY-IDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMT-CYIREYHVDRVIKKLD 145

Query: 172 AMKDENVSITGICGMGGVGKTTLVKEIQKQAKEM--KMFDDVAMAVVSQTPSITKIQYEI 229
            M D +     + G  G GK+ +  +   ++ ++    +D +     S T   +      
Sbjct: 146 EMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKS----TF 201

Query: 230 AGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLD 285
             + D+  +    +D+   P       +    +  N+ +            L V D
Sbjct: 202 DLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALI-------DRPNTLFVFD 250

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 65.2 bits (159), Expect = 4e-11
 Identities = 42/205 (20%), Positives = 74/205 (36%), Gaps = 35/205 (17%)

Query: 208 FDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDE----LECPKLQALFLQ 263
           F +          + TKIQ  I       G S    +  +  +     LE   ++   L 
Sbjct: 224 FKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLS 283

Query: 264 ENSPLAIPDRFFQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLI 321
           ++   A+    F    DL+ L L    I +             +         ++   L 
Sbjct: 284 KSKIFALLKSVFSHFTDLEQLTLAQNEINK-------------ID-------DNAFWGLT 323

Query: 322 NLRTLRLHDRRIQGDLSLIGE----LSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTG 376
           +L  L L    +    S+       L  LE+LDLS + +  +   SF  L +L+ L L  
Sbjct: 324 HLLKLNLSQNFLG---SIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDT 380

Query: 377 CYILELIPRGVLSRLRKLEELYMSH 401
              L+ +P G+  RL  L+++++  
Sbjct: 381 NQ-LKSVPDGIFDRLTSLQKIWLHT 404

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 64.8 bits (158), Expect = 5e-11
 Identities = 50/325 (15%), Positives = 106/325 (32%), Gaps = 50/325 (15%)

Query: 255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP 314
             +  + L  NS   + +  F  ++DLQ L +                  +         
Sbjct: 30  AHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQT----------PGLVIR-------N 72

Query: 315 SSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIPV---SFGRLSHLR 370
           ++   L +L  L+L   +    +      L+ LE+L L++ ++    +    F  L+ L 
Sbjct: 73  NTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLE 132

Query: 371 LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR 430
           +L L    I ++ P      +R+   L ++ +    +   E +  +     F  L  LS 
Sbjct: 133 MLVLRDNNIKKIQPASFFLNMRRFHVLDLTFN--KVKSICEEDLLNFQGKHFTLLR-LSS 189

Query: 431 LTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLS 490
           +T   ++           +    TS +                L L     + S A    
Sbjct: 190 ITLQDMNEYWLGWEK-CGNPFKNTSITT---------------LDLSGNGFKESMAKRFF 233

Query: 491 QDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMF--LVIFRCNEMKY 548
             +  + + S I +             ++      D  N  F  L    +     ++ K 
Sbjct: 234 DAIAGTKIQSLILSN------SYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSK- 286

Query: 549 LLNSLERTLRVTLHKLEWLFIRENQ 573
            + +L +++      LE L + +N+
Sbjct: 287 -IFALLKSVFSHFTDLEQLTLAQNE 310

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 48.6 bits (116), Expect = 7e-06
 Identities = 56/353 (15%), Positives = 108/353 (30%), Gaps = 90/353 (25%)

Query: 344 SGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
           + +  +DLS + ++E+   SF RL  L+ L +       +I       L  L  L + ++
Sbjct: 30  AHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYN 89

Query: 403 FRHWQFESESEEDSSSNAKFIELGALSRLTSLH-----------IHIPEGKIMPSDMSFQ 451
               QF              +E GA + L +L              +           F+
Sbjct: 90  ----QFLQ------------LETGAFNGLANLEVLTLTQCNLDGAVLSGN-------FFK 126

Query: 452 NLTSFSIAIGDLEERPLSD-------FIGLF--LQKFKKRCSRAMGLSQDMRISALHSWI 502
            LTS       LE   L D           F  +++F       + L+ + ++ ++    
Sbjct: 127 PLTS-------LEMLVLRDNNIKKIQPASFFLNMRRFHV-----LDLTFN-KVKSICE-- 171

Query: 503 KNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLL---NSLERTL-- 557
              LL  +      +      + D+             F+   +  L    N  + ++  
Sbjct: 172 -EDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAK 230

Query: 558 ----RVTLHKLEWLFIRENQNFVEICHG----QLPAGCLSNVKRSDV--VDCGS-ILKIL 606
                +   K++ L +  + N                    ++ S V   D     +  L
Sbjct: 231 RFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKSKIFAL 290

Query: 607 LSHLVQSFQNLQRLRVYSCGLLVSVFEIERVN-IAKEETELFSSLEKLTLWDL 658
           L  +   F +L++L +               N I K +   F  L  L   +L
Sbjct: 291 LKSVFSHFTDLEQLTLAQ-------------NEINKIDDNAFWGLTHLLKLNL 330

>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 = 63.5 bits (155), Expect = 5e-11
 Identities = 41/209 (19%), Positives = 75/209 (35%), Gaps = 42/209 (20%)

Query: 211 VAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAI 270
           +    ++    I +I      + +    +L    + +   + E   +  +    +    I
Sbjct: 3   LGSETITVPTPIKQIF-SDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSD---I 58

Query: 271 PD-RFFQGMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLP------------- 314
              +  Q + ++  L L G  +                   PL  L              
Sbjct: 59  KSVQGIQYLPNVTKLFLNGNKLTDI---------------KPLANLKNLGWLFLDENKVK 103

Query: 315 --SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLL 372
             SSL  L  L++L L    I  D++ +  L  LE L L  + +++I     RL+ L  L
Sbjct: 104 DLSSLKDLKKLKSLSLEHNGIS-DINGLVHLPQLESLYLGNNKITDIT-VLSRLTKLDTL 161

Query: 373 DLTGCYILELIPRGVLSRLRKLEELYMSH 401
            L    I +++P   L+ L KL+ LY+S 
Sbjct: 162 SLEDNQISDIVP---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 = 63.1 bits (154), Expect = 6e-11
 Identities = 41/183 (22%), Positives = 75/183 (40%), Gaps = 34/183 (18%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD-RFFQGMKD 280
           I  +Q  I    ++T + L  N + ++        L  LFL EN    + D    + +K 
Sbjct: 58  IKSVQ-GIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENK---VKDLSSLKDLKK 113

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
           L+ L L    I                         + L  L  L +L L + +I  D++
Sbjct: 114 LKSLSLEHNGISDI----------------------NGLVHLPQLESLYLGNNKIT-DIT 150

Query: 339 LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           ++  L+ L+ L L ++ +S+I      L+ L+ L L+  +I +L     L+ L+ L+ L 
Sbjct: 151 VLSRLTKLDTLSLEDNQISDIV-PLAGLTKLQNLYLSKNHISDLRA---LAGLKNLDVLE 206

Query: 399 MSH 401
           +  
Sbjct: 207 LFS 209

>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 = 55.8 bits (135), Expect = 2e-08
 Identities = 41/179 (22%), Positives = 71/179 (39%), Gaps = 30/179 (16%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDL 281
           +T I+  +A   +L  + L  N + ++    +  KL++L L+ N    I       +  L
Sbjct: 80  LTDIK-PLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDIN--GLVHLPQL 136

Query: 282 QVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
           + L LG   I                         + LS L  L TL L D +I  D+  
Sbjct: 137 ESLYLGNNKITDI----------------------TVLSRLTKLDTLSLEDNQIS-DIVP 173

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           +  L+ L+ L LS++ +S++  +   L +L +L+L     L   P    S L     + 
Sbjct: 174 LAGLTKLQNLYLSKNHISDLR-ALAGLKNLDVLELFSQECLN-KPINHQSNLVVPNTVK 230

>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 = 63.9 bits (156), Expect = 1e-10
 Identities = 49/355 (13%), Positives = 91/355 (25%), Gaps = 90/355 (25%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMK 279
            ++ +         L  +    N + E+P+       L        +   +P        
Sbjct: 82  GLSSLPELPP---HLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPL------ 132

Query: 280 DLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL 339
            L+ L +   +                   L  LP  L     L+ + + +  ++    L
Sbjct: 133 -LEYLGVSNNQ-------------------LEKLP-ELQNSSFLKIIDVDNNSLK---KL 168

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
                 LE +    + + E+P     L  L  +      + +L           LE +  
Sbjct: 169 PDLPPSLEFIAAGNNQLEELP-ELQNLPFLTAIYADNNSLKKLPD-----LPLSLESIVA 222

Query: 400 SHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA 459
            ++      E              EL  L  LT+++                 L +    
Sbjct: 223 GNN----ILEE-----------LPELQNLPFLTTIYA------------DNNLLKTLPDL 255

Query: 460 IGDLEERPLSDFIGLFLQKFKKRCSRAMGLS-QDMRISALHSWIKNLLLRSEILALAEVN 518
              LE   + D    +L    +       L   +   S L     NL      L  +  N
Sbjct: 256 PPSLEALNVRD---NYLTDLPELPQSLTFLDVSENIFSGLSELPPNL----YYLNASS-N 307

Query: 519 YFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQ 573
              ++     +        L     +      N L   L     +LE L    N 
Sbjct: 308 EIRSLCDLPPS--------LEELNVSN-----NKLI-ELPALPPRLERLIASFNH 348

>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 = 57.3 bits (139), Expect = 1e-08
 Identities = 47/240 (19%), Positives = 80/240 (33%), Gaps = 53/240 (22%)

Query: 228 EIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG 287
           E+     LT I    N +  +PD    P L+AL +++N    +P+   Q +  L V +  
Sbjct: 232 ELQNLPFLTTIYADNNLLKTLPDLP--PSLEALNVRDNYLTDLPE-LPQSLTFLDVSENI 288

Query: 288 GIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE 347
                                    L        NL  L      I+   SL      LE
Sbjct: 289 FSG----------------------LSELPP---NLYYLNASSNEIR---SLCDLPPSLE 320

Query: 348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH-SFRHW 406
            L++S + + E+P    R   L  L  +  ++ E+         + L++L++ +   R +
Sbjct: 321 ELNVSNNKLIELPALPPR---LERLIASFNHLAEVPE-----LPQNLKQLHVEYNPLREF 372

Query: 407 QFESESEEDSSSNAKFIELGA-LSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEE 465
               ES ED   N+   E+      L  L             +    L  F      +E+
Sbjct: 373 PDIPESVEDLRMNSHLAEVPELPQNLKQL------------HVETNPLREFPDIPESVED 420

>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 = 55.4 bits (134), Expect = 4e-08
 Identities = 31/214 (14%), Positives = 63/214 (29%), Gaps = 40/214 (18%)

Query: 249 PDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSS 308
           P  +    LQ      ++   +P      +K                  +    PP    
Sbjct: 5   PRNVSNTFLQEPLRHSSNLTEMPVEAEN-VKSKTEYYNA-------WSEWERNAPPGNGE 56

Query: 309 PLFLLPSSLSFLI--NLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRL 366
              +  S L   +      L L++  +    SL      LE L  S + ++E+P     L
Sbjct: 57  QREMAVSRLRDCLDRQAHELELNNLGLS---SLPELPPHLESLVASCNSLTELPELPQSL 113

Query: 367 SHLRLLDLTGCYILELIPR--------------GVLSRLRKLEELYMSHSFRHWQFESES 412
             L + +     + +L P                 L     L+ + + ++      +   
Sbjct: 114 KSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDNN----SLKKLP 169

Query: 413 EE-------DSSSN--AKFIELGALSRLTSLHIH 437
           +         + +N   +  EL  L  LT+++  
Sbjct: 170 DLPPSLEFIAAGNNQLEELPELQNLPFLTAIYAD 203

>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 = 50.8 bits (122), Expect = 1e-06
 Identities = 30/190 (15%), Positives = 54/190 (28%), Gaps = 37/190 (19%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
             + +         L  ++   N+I  + D    P L+ L +  N  + +P         
Sbjct: 288 IFSGLSELPPN---LYYLNASSNEIRSLCDLP--PSLEELNVSNNKLIELPA----LPPR 338

Query: 281 LQVLDLGGIRRFSFSVRFPFLFPPLPSS---------PLFLLPSSLSFLINLRTLRLHDR 331
           L+ L                  P LP +         PL   P       ++  LR++  
Sbjct: 339 LERLIASFNHLAEV--------PELPQNLKQLHVEYNPLREFPDIPE---SVEDLRMNSH 387

Query: 332 RIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL 391
                  +      L+ L +  + + E P     +  LR+         E          
Sbjct: 388 LA----EVPELPQNLKQLHVETNPLREFPDIPESVEDLRMNSERVVDPYEFAH----ETT 439

Query: 392 RKLEELYMSH 401
            KLE+    H
Sbjct: 440 DKLEDDVFEH 449

>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 = 63.4 bits (154), Expect = 2e-10
 Identities = 56/366 (15%), Positives = 107/366 (29%), Gaps = 41/366 (11%)

Query: 312 LLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLR 370
           L    +SFL  LR LRL   RI+  D  +      LE LD+S + +  I      ++ LR
Sbjct: 67  LRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHNRLQNIS--CCPMASLR 124

Query: 371 LLDLTGCYILELIPRGVLSRLRKLEELYMSH---------SFRHWQFESESEEDSSSNAK 421
            LDL+      L        L KL  L +S             H        +  S + K
Sbjct: 125 HLDLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQLDLLPVAHLHLSCILLDLVSYHIK 184

Query: 422 FIELGALSRLTSLHIHIPEGKI----MPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQ 477
             E  +L    +  +H+         +  +MS   L    ++   L +      +    +
Sbjct: 185 GGETESLQIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDENCQRLMTFLSE 244

Query: 478 KFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEI--LALAEVNYFENIVSDLANDGFNEL 535
             +      + L            +        +  L +  +   E I  +        L
Sbjct: 245 LTRGPTLLNVTLQHIETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETAL 304

Query: 536 MFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSD 595
             L+I   +    +    +  L     ++    +  +          +   C  +     
Sbjct: 305 KSLMIE--HVKNQVFLFSKEALYSVFAEMNIKMLSISDT------PFIHMVCPPSPSSFT 356

Query: 596 VVDCGS-ILKILLSHLVQSFQNLQRLRVYSCGL--LVSVFEIERVNIAKEETELFSSLEK 652
            ++    +    +     + + LQ L +   GL     V  +              ++  
Sbjct: 357 FLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALM------------TKNMSS 404

Query: 653 LTLWDL 658
           L   D+
Sbjct: 405 LETLDV 410

>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 = 58.3 bits (141), Expect = 6e-09
 Identities = 64/447 (14%), Positives = 126/447 (28%), Gaps = 67/447 (14%)

Query: 234 DLTGISLMFNDIHEVPDE--LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
               +SL  N I E+         +L+ L L  N   ++    F   +DL+ LD+   R 
Sbjct: 53  RTKALSLSQNSISELRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHNR- 111

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSF--LINLRTLRLHDRRIQ--GDLSLIGELSGLE 347
                    L              ++S   + +LR L L              G L+ L 
Sbjct: 112 ---------L-------------QNISCCPMASLRHLDLSFNDFDVLPVCKEFGNLTKLT 149

Query: 348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQ 407
            L LS +   ++      ++HL L  +    +   I  G    L+      +   F    
Sbjct: 150 FLGLSAAKFRQLD--LLPVAHLHLSCILLDLVSYHIKGGETESLQIPNTTVLHLVFHPNS 207

Query: 408 FESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-DMSFQNLTSFSIAIGDLEER 466
             S     S +    ++L  +         +       +   +  N+T   I        
Sbjct: 208 LFSVQVNMSVNALGHLQLSNIKLNDENCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSV 267

Query: 467 PLSDFIGL-FLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVS 525
            L  F     ++                  +   + +K+L++    +      + +  + 
Sbjct: 268 KLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEH--VKNQVFLFSKEALY 325

Query: 526 D---------LANDGFNELMFLVIFRCNEMKYL------LNSLERTLRVTLHKLEWLFIR 570
                     L+      +  +     +   +L                TL +L+ L ++
Sbjct: 326 SVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQ 385

Query: 571 ENQNFVEICHGQLPAGCLSNVKRSDVVDCG--SILKILLSHLVQSFQNLQRLRVYSCGLL 628
            N            A    N+   + +D    S+            +++  L + S  L 
Sbjct: 386 RNG-LKNF---FKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAESILVLNLSSNMLT 441

Query: 629 VSVFEIERVNIAKEETELFSSLEKLTL 655
            SVF             L   ++ L L
Sbjct: 442 GSVFR-----------CLPPKVKVLDL 457

>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 = 57.6 bits (139), Expect = 1e-08
 Identities = 30/171 (17%), Positives = 57/171 (33%), Gaps = 23/171 (13%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
             T ++   N   +   +      +LQ L LQ N             K++  L+   +  
Sbjct: 354 SFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALM-TKNMSSLETLDVSL 412

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL--SLIGELSGLEIL 349
            S                            ++  L L    + G +   L      +++L
Sbjct: 413 NSL--------NSHAYDRTCAWAE------SILVLNLSSNMLTGSVFRCL---PPKVKVL 455

Query: 350 DLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS 400
           DL  + +  IP     L  L+ L++     L+ +P GV  RL  L+ +++ 
Sbjct: 456 DLHNNRIMSIPKDVTHLQALQELNVAS-NQLKSVPDGVFDRLTSLQYIWLH 505

>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 = 60.4 bits (147), Expect = 2e-10
 Identities = 29/170 (17%), Positives = 58/170 (34%), Gaps = 28/170 (16%)

Query: 235 LTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPD-RFFQGMKDLQVLDLGGIRRF 292
           LT I+L   ++ ++   +E    ++ L +         +     G+ +L+ L + G    
Sbjct: 46  LTYITLANINVTDL-TGIEYAHNIKDLTINNIH---ATNYNPISGLSNLERLRIMGKDVT 101

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEILDL 351
           S                      +LS L +L  L +         L+ I  L  +  +DL
Sbjct: 102 S------------------DKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDL 143

Query: 352 SESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           S +      +    L  L+ L++    + +      +    KL +LY   
Sbjct: 144 SYNGAITDIMPLKTLPELKSLNIQFDGVHDYRG---IEDFPKLNQLYAFS 190

>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 = 56.9 bits (138), Expect = 3e-09
 Identities = 29/159 (18%), Positives = 58/159 (36%), Gaps = 30/159 (18%)

Query: 315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLD 373
           + + +  N++ L +++     + + I  LS LE L +   DV+   +     L+ L LLD
Sbjct: 60  TGIEYAHNIKDLTINNIHAT-NYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLD 118

Query: 374 LTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTS 433
           ++     + I    ++ L K+  + +S+                 N    ++  L  L  
Sbjct: 119 ISHSAHDDSILTK-INTLPKVNSIDLSY-----------------NGAITDIMPLKTLPE 160

Query: 434 L-HIHIPEGKIMPSDMS----FQNLTSFSIA---IGDLE 464
           L  ++I    +   D      F  L         IG  +
Sbjct: 161 LKSLNIQFDGV--HDYRGIEDFPKLNQLYAFSQTIGGKK 197

>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 = 52.3 bits (126), Expect = 9e-08
 Identities = 31/166 (18%), Positives = 62/166 (37%), Gaps = 28/166 (16%)

Query: 316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLT 375
           + + + +L  + L +  +  DL+ I     ++ L ++    +        LS+L  L + 
Sbjct: 39  TEAQMNSLTYITLANINVT-DLTGIEYAHNIKDLTINNIHATNYN-PISGLSNLERLRIM 96

Query: 376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLH 435
           G  +        LS L  L  L +SHS             +  ++   ++  L ++ S+ 
Sbjct: 97  GKDVTSDKIPN-LSGLTSLTLLDISHS-------------AHDDSILTKINTLPKVNSID 142

Query: 436 IHIPEGKIMPSDMS----FQNLTSFSIA---IGDLEERPLSDFIGL 474
           +    G I  +D+        L S +I    + D     + DF  L
Sbjct: 143 LSY-NGAI--TDIMPLKTLPELKSLNIQFDGVHDYR--GIEDFPKL 183

>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 = 42.6 bits (101), Expect = 1e-04
 Identities = 16/127 (12%), Positives = 33/127 (25%), Gaps = 22/127 (17%)

Query: 235 LTGISLMFNDIH-EVPDELE-CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF 292
           L  + +M  D+  +    L     L  L +  ++           +  +  +DL      
Sbjct: 90  LERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAI 149

Query: 293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
           +                       L  L  L++L +    +  D   I +   L  L   
Sbjct: 150 T-------------------DIMPLKTLPELKSLNIQFDGVH-DYRGIEDFPKLNQLYAF 189

Query: 353 ESDVSEI 359
              +   
Sbjct: 190 SQTIGGK 196

>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 = 60.4 bits (147), Expect = 3e-10
 Identities = 26/222 (11%), Positives = 61/222 (27%), Gaps = 37/222 (16%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDLGGIR 290
               + L+   +  +P       P +  +++  +  L  +    F  +  +  +++   R
Sbjct: 32  STQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTR 91

Query: 291 RFSFSVRFPFLFPPLPS--------SPLFLLPSSLSF--LINLRTLRLHD----RRIQGD 336
             +  +  P     LP         + L + P             L + D      I  +
Sbjct: 92  NLT-YID-PDALKELPLLKFLGIFNTGLKMFPDLTKVYSTDIFFILEITDNPYMTSIPVN 149

Query: 337 LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR-KLE 395
            +  G  +    L L  +  + +       + L  + L     L +I +     +     
Sbjct: 150 -AFQGLCNETLTLKLYNNGFTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPS 208

Query: 396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH 437
            L +S +       +            +    L  L  L   
Sbjct: 209 LLDVSQT----SVTA------------LPSKGLEHLKELIAR 234

>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 = 56.9 bits (138), Expect = 4e-09
 Identities = 27/167 (16%), Positives = 49/167 (29%), Gaps = 30/167 (17%)

Query: 243 NDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLF 302
            DI  +P     P  Q L L E     IP   F  + ++  + +                
Sbjct: 21  KDIQRIPSLP--PSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQ--------- 69

Query: 303 PPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGE-----LSGLEILDLSESDVS 357
                    L   S   L  +  + + + R   +L+ I       L  L+ L +  + + 
Sbjct: 70  --------QLESHSFYNLSKVTHIEIRNTR---NLTYIDPDALKELPLLKFLGIFNTGLK 118

Query: 358 EIP--VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK-LEELYMSH 401
             P            +L++T    +  IP      L      L + +
Sbjct: 119 MFPDLTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYN 165

>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 = 50.4 bits (121), Expect = 6e-07
 Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 23/140 (16%)

Query: 343 LSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
               + L L E+ +  IP  +F  L ++  + ++    L+ +       L K+  + + +
Sbjct: 30  PPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRN 89

Query: 402 SFRHWQFESESEEDSSSNAKFIELGA---LSRLTSLHIHIPEGKIMPSDMSFQNLTS-FS 457
                          + N  +I+  A   L  L  L I     K+ P      +    F 
Sbjct: 90  ---------------TRNLTYIDPDALKELPLLKFLGIFNTGLKMFPDLTKVYSTDIFFI 134

Query: 458 IAIGD---LEERPLSDFIGL 474
           + I D   +   P++ F GL
Sbjct: 135 LEITDNPYMTSIPVNAFQGL 154

>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 = 62.2 bits (151), Expect = 5e-10
 Identities = 42/232 (18%), Positives = 71/232 (30%), Gaps = 42/232 (18%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
            +  +    +   +L  +    N +  +P       LQ L + +N   ++P        +
Sbjct: 152 QLASLPALPS---ELCKLWAYNNQLTSLPMLP--SGLQELSVSDNQLASLPT----LPSE 202

Query: 281 LQVLDLGGIRRFSFSVRFPFLFPPLPSS---------PLFLLPSSLSFLINLRTLRLHDR 331
           L  L     R  S         P LPS           L  LP   S    L+ L +   
Sbjct: 203 LYKLWAYNNRLTSL--------PALPSGLKELIVSGNRLTSLPVLPS---ELKELMVSGN 251

Query: 332 RIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL 391
           R+    SL    SGL  L +  + ++ +P S   LS    ++L G  + E      L  +
Sbjct: 252 RLT---SLPMLPSGLLSLSVYRNQLTRLPESLIHLSSETTVNLEGNPLSER-TLQALREI 307

Query: 392 RKLEEL---------YMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL 434
                            + + R  +    +  D    A+  E     R    
Sbjct: 308 TSAPGYSGPIIRFDMAGASAPRETRALHLAAADWLVPAREGEPAPADRWHMF 359

>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 = 48.4 bits (115), Expect = 9e-06
 Identities = 30/160 (18%), Positives = 51/160 (31%), Gaps = 36/160 (22%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLL 372
           LP  L    ++ TL + D  +    SL      L  L++S + ++ +PV    L  L + 
Sbjct: 55  LPDCL--PAHITTLVIPDNNLT---SLPALPPELRTLEVSGNQLTSLPVLPPGLLELSIF 109

Query: 373 DLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSS------SNAKFIEL- 425
                ++  L           L +L++  +    Q  S             S+ +   L 
Sbjct: 110 SNPLTHLPALPS--------GLCKLWIFGN----QLTSLPVLPPGLQELSVSDNQLASLP 157

Query: 426 GALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEE 465
              S L  L                  LTS  +    L+E
Sbjct: 158 ALPSELCKL------------WAYNNQLTSLPMLPSGLQE 185

>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 = 43.0 bits (101), Expect = 4e-04
 Identities = 25/133 (18%), Positives = 47/133 (35%), Gaps = 26/133 (19%)

Query: 343 LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
            +G  +L++ ES ++ +P      +H+  L +    +  L P    +   +L  L +S +
Sbjct: 39  NNGNAVLNVGESGLTTLPDCLP--AHITTLVIPDNNLTSL-P----ALPPELRTLEVSGN 91

Query: 403 FRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-----DMSFQNLTSFS 457
               Q  S                 L  L+     +     +PS      +    LTS  
Sbjct: 92  ----QLTSLPV----------LPPGLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLP 137

Query: 458 IAIGDLEERPLSD 470
           +    L+E  +SD
Sbjct: 138 VLPPGLQELSVSD 150

>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 = 61.0 bits (148), Expect = 5e-10
 Identities = 38/178 (21%), Positives = 59/178 (33%), Gaps = 31/178 (17%)

Query: 243 NDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG---IRRFSFSVR 297
           N++  +  E     P LQ L +       +PD          +LD+     I        
Sbjct: 90  NNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIE---- 145

Query: 298 FPFLFPPLPSSPLFL---------LPSSLSFLINLRTLRLHD----RRIQGDLSLIGELS 344
               F  L    + L         + +S      L  L L D      +  D    G  S
Sbjct: 146 -RNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNNNLEELPND-VFHG-AS 202

Query: 345 GLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
           G  ILD+S + +  +P      L  LR       Y L+ +P   L +L  L E  +++
Sbjct: 203 GPVILDISRTRIHSLPSYGLENLKKLRARST---YNLKKLP--TLEKLVALMEASLTY 255

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 59.5 bits (144), Expect = 2e-09
 Identities = 34/236 (14%), Positives = 66/236 (27%), Gaps = 50/236 (21%)

Query: 243 NDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLF 302
           + + E+P +L       L         I    F G  DL+ +++                
Sbjct: 19  SKVTEIPSDL-PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLE--------- 68

Query: 303 PPLPSSPLFLLPSSLSFLINLRTLRL-HDRRIQG-DLSLIGELSGLEILDLSESDVSEIP 360
                    +     S L  L  +R+     +   +      L  L+ L +S + +  +P
Sbjct: 69  --------VIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLP 120

Query: 361 -VSFGRLSHLRLLDLTGCYILELIPRGVLSRLR-KLEELYMSH---------SFRHWQFE 409
            V         LLD+     +  I R     L  +   L+++          +F   Q  
Sbjct: 121 DVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQ-- 178

Query: 410 SESEEDSSSNA-KFIELGALSRLTSLHI---------HIPEGKIMPSDMSFQNLTS 455
            +    S +N  + +        +   I          +P           +NL  
Sbjct: 179 LDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSY-------GLENLKK 227

>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 = 59.1 bits (143), Expect = 2e-09
 Identities = 50/267 (18%), Positives = 91/267 (34%), Gaps = 47/267 (17%)

Query: 322 NLRTLRLHDRRIQ---GDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGC 377
           + R     + ++     DL           L    + +  I   +F     L  ++++  
Sbjct: 10  SNRVFLCQESKVTEIPSDLP-----RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQN 64

Query: 378 YILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA---LSRLTSL 434
            +LE+I   V S L KL E+ +                 ++N  +I   A   L  L  L
Sbjct: 65  DVLEVIEADVFSNLPKLHEIRIEK---------------ANNLLYINPEAFQNLPNLQYL 109

Query: 435 HIHIPEGKIMPSDMSFQNLTSFSIAIGD---LEERPLSDFIGLFLQKFKKRCSRAMGLSQ 491
            I     K +P      +L    + I D   +     + F+GL  +      S  + L+ 
Sbjct: 110 LISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFE------SVILWLN- 162

Query: 492 DMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLN 551
              I  +H+   N   + + L L++ N  E + +D    G +  + L I R         
Sbjct: 163 KNGIQEIHNSAFN-GTQLDELNLSDNNNLEELPND-VFHGASGPVILDISR--------T 212

Query: 552 SLERTLRVTLHKLEWLFIRENQNFVEI 578
            +       L  L+ L  R   N  ++
Sbjct: 213 RIHSLPSYGLENLKKLRARSTYNLKKL 239

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 58.5 bits (142), Expect = 2e-09
 Identities = 31/183 (16%), Positives = 63/183 (34%), Gaps = 33/183 (18%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
            I ++     G  +    +L    + ++  + E   +Q      ++  ++     Q   +
Sbjct: 8   PINQVF-PDPGLANAVKQNLGKQSVTDLVSQKELSGVQNFNGDNSNIQSLAG--MQFFTN 64

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
           L+ L L    I                         S L  L  L  L ++  R++ +L+
Sbjct: 65  LKELHLSHNQISDL----------------------SPLKDLTKLEELSVNRNRLK-NLN 101

Query: 339 LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
            I     L  L L  +++ +   S   L +L +L +    +  ++    L  L KLE L 
Sbjct: 102 GIPSAC-LSRLFLDNNELRDTD-SLIHLKNLEILSIRNNKLKSIVM---LGFLSKLEVLD 156

Query: 399 MSH 401
           +  
Sbjct: 157 LHG 159

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 58.5 bits (142), Expect = 2e-09
 Identities = 37/180 (20%), Positives = 73/180 (40%), Gaps = 34/180 (18%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD-RFFQGMKDLQVLDLGG--IRR 291
           +   +   ++I  +        L+ L L  N    I D    + +  L+ L +    ++ 
Sbjct: 43  VQNFNGDNSNIQSLAGMQFFTNLKELHLSHNQ---ISDLSPLKDLTKLEELSVNRNRLKN 99

Query: 292 FSFSVRFPFLFPPLPSSPLFLL---------PSSLSFLINLRTLRLHDRRIQGDLSLIGE 342
            +           +PS+ L  L           SL  L NL  L + + +++  + ++G 
Sbjct: 100 LN----------GIPSACLSRLFLDNNELRDTDSLIHLKNLEILSIRNNKLK-SIVMLGF 148

Query: 343 LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
           LS LE+LDL  ++++       RL  +  +DLTG          V   ++   ELY++++
Sbjct: 149 LSKLEVLDLHGNEITNTG-GLTRLKKVNWIDLTGQKC-------VNEPVKYQPELYITNT 200

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 59.5 bits (144), Expect = 2e-09
 Identities = 34/161 (21%), Positives = 61/161 (37%), Gaps = 18/161 (11%)

Query: 313 LPSSLSF--LINLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDVSEIPV-SFGRLS 367
           L +  +   L NL +L L    +      + +  +  L  LDLS + +  +    F  L 
Sbjct: 54  LRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVP-VPNLRYLDLSSNHLHTLDEFLFSDLQ 112

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA 427
            L +L L   +I  ++ R     + +L++LY+S +    Q      E         +   
Sbjct: 113 ALEVLLLYNNHI-VVVDRNAFEDMAQLQKLYLSQN----QISRFPVE------LIKDGNK 161

Query: 428 LSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPL 468
           L +L  L +   + K +P     Q L ++      L   PL
Sbjct: 162 LPKLMLLDLSSNKLKKLPLTD-LQKLPAWVKNGLYLHNNPL 201

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 59.1 bits (143), Expect = 2e-09
 Identities = 35/175 (20%), Positives = 61/175 (34%), Gaps = 31/175 (17%)

Query: 234 DLTGISLMFNDIHEVPDEL---ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG-- 288
               + L  N++  +  E        L +L L  N    I    F  + +L+ LDL    
Sbjct: 40  YTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSSNH 99

Query: 289 IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLE 347
           +                            S L  L  L L++  I   D +   +++ L+
Sbjct: 100 LHTLD--------------------EFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQ 139

Query: 348 ILDLSESDVSEIP----VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
            L LS++ +S  P        +L  L LLDL+   + + +P   L +L    +  
Sbjct: 140 KLYLSQNQISRFPVELIKDGNKLPKLMLLDLSSNKL-KKLPLTDLQKLPAWVKNG 193

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 54.5 bits (131), Expect = 7e-08
 Identities = 27/127 (21%), Positives = 48/127 (37%), Gaps = 26/127 (20%)

Query: 313 LPSSLSFLINLRTLRLHD---RRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSH 368
           +P SL        L L      R++ + +    L+ L  L LS + ++ I   +F  + +
Sbjct: 33  VPQSLP--SYTALLDLSHNNLSRLRAEWTPTR-LTNLHSLLLSHNHLNFISSEAFVPVPN 89

Query: 369 LRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA-KFIELGA 427
           LR LDL+    L  +   + S L+ LE L + +                 N    ++  A
Sbjct: 90  LRYLDLSSN-HLHTLDEFLFSDLQALEVLLLYN-----------------NHIVVVDRNA 131

Query: 428 LSRLTSL 434
              +  L
Sbjct: 132 FEDMAQL 138

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 59.1 bits (143), Expect = 2e-09
 Identities = 33/191 (17%), Positives = 53/191 (27%), Gaps = 21/191 (10%)

Query: 232 WLDLTGISLMFNDIHEVPDELECPKLQALFLQEN--SPLAIPDRFFQGMKDLQVLDLGGI 289
            L +    +    +      L    LQ L L+    +  A P        DL +L+L  +
Sbjct: 72  RLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNV 131

Query: 290 RRFSFSVRFPFLFPPLPSS---------PLFLLPSSLSF-LINLRTLRLHDRRIQGDLSL 339
              +       L   L                           L TL L D    G+  L
Sbjct: 132 SWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGL 191

Query: 340 I-----GELSGLEILDLS----ESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSR 390
           I      +   L++L L     E+              L+ LDL+   + +         
Sbjct: 192 ISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDW 251

Query: 391 LRKLEELYMSH 401
             +L  L +S 
Sbjct: 252 PSQLNSLNLSF 262

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 55.3 bits (133), Expect = 3e-08
 Identities = 33/193 (17%), Positives = 59/193 (30%), Gaps = 37/193 (19%)

Query: 233 LDLTGISL--MFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
           L+L  +S       + E+   L+ P L+ L + +   L       +    L  LDL    
Sbjct: 126 LNLRNVSWATRDAWLAELQQWLK-PGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNP 184

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEIL 349
                                L P     L  L           G   +L      L+ L
Sbjct: 185 ELG-----------ERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGL 233

Query: 350 DLSESDVSEIP--VSFGRLSHLRLLDLTGCYILELIPRGVLSRLR--------------- 392
           DLS + + +     S    S L  L+L+   + ++ P+G+ ++L                
Sbjct: 234 DLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQV-PKGLPAKLSVLDLSYNRLDRNPSP 292

Query: 393 ----KLEELYMSH 401
               ++  L +  
Sbjct: 293 DELPQVGNLSLKG 305

>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 = 58.2 bits (141), Expect = 6e-09
 Identities = 32/168 (19%), Positives = 64/168 (38%), Gaps = 12/168 (7%)

Query: 312 LLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRL 371
               S   L  L +L  H+  I  D++ I +L+GL  L  + ++++ + +S  + ++L  
Sbjct: 33  TDTISEEQLATLTSLDCHNSSIT-DMTGIEKLTGLTKLICTSNNITTLDLS--QNTNLTY 89

Query: 372 LDLTGCYILELIPRGVLSRLRKLEELYMSH----SFRHWQFESESEEDSSSNA-KFIELG 426
           L      +  L     ++ L KL  L             Q    +  + + N    I++ 
Sbjct: 90  LACDSNKLTNLD----VTPLTKLTYLNCDTNKLTKLDVSQNPLLTYLNCARNTLTEIDVS 145

Query: 427 ALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGL 474
             ++LT L  H+ +            LT+   +   + E  +S    L
Sbjct: 146 HNTQLTELDCHLNKKITKLDVTPQTQLTTLDCSFNKITELDVSQNKLL 193

>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 = 57.8 bits (140), Expect = 8e-09
 Identities = 41/268 (15%), Positives = 75/268 (27%), Gaps = 62/268 (23%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG--IRRF 292
           LT +    + I ++    +   L  L    N+   +         +L  L      +   
Sbjct: 44  LTSLDCHNSSITDMTGIEKLTGLTKLICTSNNITTLD---LSQNTNLTYLACDSNKLTNL 100

Query: 293 SFSVRFPFL------FPPLPSSPLFLLPS--------------SLSFLINLRTLRLHDRR 332
             +     L         L    +   P                +S    L  L  H  +
Sbjct: 101 DVT-PLTKLTYLNCDTNKLTKLDVSQNPLLTYLNCARNTLTEIDVSHNTQLTELDCHLNK 159

Query: 333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR 392
                  +   + L  LD S + ++E+ VS  +   L  L+     I +L     L++  
Sbjct: 160 KI-TKLDVTPQTQLTTLDCSFNKITELDVS--QNKLLNRLNCDTNNITKLD----LNQNI 212

Query: 393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH------IPEGKIMPS 446
           +L  L  S +    +               I++  L++LT           +        
Sbjct: 213 QLTFLDCSSN----KLTE------------IDVTPLTQLTYFDCSVNPLTELDVST---- 252

Query: 447 DMSFQNLTSFSIAIGDLEERPLSDFIGL 474
                 LT+      DL E  L+    L
Sbjct: 253 ---LSKLTTLHCIQTDLLEIDLTHNTQL 277

>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 = 56.6 bits (137), Expect = 2e-08
 Identities = 39/263 (14%), Positives = 81/263 (30%), Gaps = 26/263 (9%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
           +IT +  +++   +LT ++   N +  +       KL  L    N    +          
Sbjct: 75  NITTL--DLSQNTNLTYLACDSNKLTNLDVT-PLTKLTYLNCDTNKLTKLD---VSQNPL 128

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLS 338
           L  L+     +     S     L          +    ++    L TL     +I  +L 
Sbjct: 129 LTYLNCARNTLTEIDVS-HNTQLTELDCHLNKKITKLDVTPQTQLTTLDCSFNKIT-ELD 186

Query: 339 LIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
            + +   L  L+   ++++++ ++  +   L  LD +   + E I    ++ L +L    
Sbjct: 187 -VSQNKLLNRLNCDTNNITKLDLN--QNIQLTFLDCSSNKLTE-ID---VTPLTQLTYFD 239

Query: 399 MSH----SFRHWQFESESEEDSSSNA-KFIELGALSRLTSLHI-HIPEGKIMPSDMS-FQ 451
            S               +           I+L   ++L           KI   D++   
Sbjct: 240 CSVNPLTELDVSTLSKLTTLHCIQTDLLEIDLTHNTQLIYFQAEGCR--KIKELDVTHNT 297

Query: 452 NLTSFSIAIGDLEERPLSDFIGL 474
            L         + E  LS    L
Sbjct: 298 QLYLLDCQAAGITELDLSQNPKL 320

>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 = 42.4 bits (100), Expect = 5e-04
 Identities = 28/165 (16%), Positives = 48/165 (29%), Gaps = 38/165 (23%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSF 294
           LT +  +  D+ E+ D     +L     +    +   D        L +LD         
Sbjct: 256 LTTLHCIQTDLLEI-DLTHNTQLIYFQAEGCRKIKELD--VTHNTQLYLLDCQAAG---- 308

Query: 295 SVRFPFLFPPLPSSPLFLLPS--------------SLSFLINLRTLRLHDRRIQGDLSLI 340
                     +    L   P                +S    L++L   +  IQ D S +
Sbjct: 309 ----------ITELDLSQNPKLVYLYLNNTELTELDVSHNTKLKSLSCVNAHIQ-DFSSV 357

Query: 341 GELSGLEILDLSESDVSEIPVSFGRLSHL------RLLDLTGCYI 379
           G++  L     +E     +P      + L       LLD  G  +
Sbjct: 358 GKIPALNNNFEAEGQTITMPKETLTNNSLTIAVSPDLLDQFGNPM 402

>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 = 56.8 bits (137), Expect = 2e-08
 Identities = 23/192 (11%), Positives = 51/192 (26%), Gaps = 6/192 (3%)

Query: 68  EVIKDEVKSWIAEVNDIIPKAEKFLED-EVKVNKKCLGGLCVDLKSRYK-LSREAEEKTL 125
             +    +  +        +A   ++    K N   +      L   YK L+    +   
Sbjct: 33  GFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIP 92

Query: 126 AMSALMAVGNFGKGVSRPAPPPAIISSSEGVYAFKSRESTMKDIMEAMK--DENVSITGI 183
            +S+     +     S            +    F +R+  +  I + +           I
Sbjct: 93  VVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTI 152

Query: 184 CGMGGVGKTTLVKEIQKQAKEMKMFDDVAMA--VVSQTPSITKIQYEIAGWLDLTGISLM 241
            GM G GK+ L  E  +    ++      +    V +      +         L      
Sbjct: 153 HGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESF 212

Query: 242 FNDIHEVPDELE 253
              +    +E +
Sbjct: 213 SQRLPLNIEEAK 224

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri} Length = 270

 Score = 55.0 bits (133), Expect = 2e-08
 Identities = 44/178 (24%), Positives = 70/178 (39%), Gaps = 37/178 (20%)

Query: 235 LTGISLMFNDIHEVP----DELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
           L  + L  N +  +P     EL    L+ L++ +N   A+P   F  + +L  L L    
Sbjct: 63  LRLLYLNDNKLQTLPAGIFKEL--KNLETLWVTDNKLQALPIGVFDQLVNLAELRLD--- 117

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSF--LINLRTLRLHDRRIQGDLSL-IG---ELS 344
                            + L  LP  + F  L  L  L L    +Q   SL  G   +L+
Sbjct: 118 ----------------RNQLKSLPPRV-FDSLTKLTYLSLGYNELQ---SLPKGVFDKLT 157

Query: 345 GLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            L+ L L  + +  +P   F +L+ L+ L L     L+ +P G    L KL+ L +  
Sbjct: 158 SLKELRLYNNQLKRVPEGAFDKLTELKTLKLDNNQ-LKRVPEGAFDSLEKLKMLQLQE 214

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri} Length = 270

 Score = 52.7 bits (127), Expect = 2e-07
 Identities = 47/215 (21%), Positives = 84/215 (39%), Gaps = 52/215 (24%)

Query: 234 DLTGISLMFNDIHEVP----DELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGI 289
           D   + L  N +  +P      L   KL+ L+L +N    +P   F+ +K+L+ L +   
Sbjct: 38  DTKKLDLQSNKLSSLPSKAFHRL--TKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDN 95

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSL-SFLINLRTLRLHDRRIQGDLSL----IGELS 344
           +              L +     LP  +   L+NL  LRL   +++   SL       L+
Sbjct: 96  K--------------LQA-----LPIGVFDQLVNLAELRLDRNQLK---SLPPRVFDSLT 133

Query: 345 GLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF 403
            L  L L  +++  +P   F +L+ L+ L L     L+ +P G   +L +L+ L + +  
Sbjct: 134 KLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNN-QLKRVPEGAFDKLTELKTLKLDN-- 190

Query: 404 RHWQFESESEEDSSSNAKFIELGALSRLTSL-HIH 437
                         +  K +  GA   L  L  + 
Sbjct: 191 --------------NQLKRVPEGAFDSLEKLKMLQ 211

>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 = 55.9 bits (134), Expect = 4e-08
 Identities = 36/215 (16%), Positives = 71/215 (33%), Gaps = 20/215 (9%)

Query: 227 YEIAGWLDLTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPDRFFQGMKDLQVLD 285
            + A    L    L       +  ELE C +LQ L  +    L       + +  L    
Sbjct: 343 RDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEK 402

Query: 286 --LGGIRRFSFSVRFPFLFPPLPSSP-LFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGE 342
             L               +     S  L           ++R L L  + +   L  + +
Sbjct: 403 ETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLT-VLCHLEQ 461

Query: 343 LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
           L  +  LDLS + +  +P +   L  L +L  +   +  +     ++ L +L+EL + ++
Sbjct: 462 LLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDG---VANLPRLQELLLCNN 518

Query: 403 FRHWQFESESEEDSSSNAKFIELGALSRLTSLHIH 437
               + +  +            L +  RL  L++ 
Sbjct: 519 ----RLQQSAA--------IQPLVSCPRLVLLNLQ 541

>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 = 49.8 bits (118), Expect = 3e-06
 Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDL 374
             L  L+ +  L L   R++     +  L  LE+L  S++ +  +      L  L+ L L
Sbjct: 457 CHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLL 515

Query: 375 TGCYILELIPRGVLSRLRKLEELYMSH 401
               + +      L    +L  L +  
Sbjct: 516 CNNRLQQSAAIQPLVSCPRLVLLNLQG 542

>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 = 42.1 bits (98), Expect = 8e-04
 Identities = 22/165 (13%), Positives = 52/165 (31%), Gaps = 31/165 (18%)

Query: 217 SQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQ 276
            ++  + +       + D+  + L   D+  +    +   +  L L  N   A+P     
Sbjct: 425 LRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPP-ALA 483

Query: 277 GMKDLQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ 334
            ++ L+VL      +                           ++ L  L+ L L + R+Q
Sbjct: 484 ALRCLEVLQASDNALENV----------------------DGVANLPRLQELLLCNNRLQ 521

Query: 335 G--DLSLIGELSGLEILDLSESDVSEIPVSFGR----LSHLRLLD 373
               +  +     L +L+L  + + +      R    L  +  + 
Sbjct: 522 QSAAIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSIL 566

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 55.0 bits (132), Expect = 7e-08
 Identities = 30/215 (13%), Positives = 65/215 (30%), Gaps = 48/215 (22%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSF 294
            + + L   ++  +PD L  P++  L + +N+ +++P+        L+ LD    R  + 
Sbjct: 61  FSELQLNRLNLSSLPDNL-PPQITVLEITQNALISLPELP----ASLEYLDACDNRLSTL 115

Query: 295 SVRFPFL------------FPPLPSS---------PLFLLPSSLS--------------- 318
                 L             P LP+           L +LP   +               
Sbjct: 116 PELPASLKHLDVDNNQLTMLPELPALLEYINADNNQLTMLPELPTSLEVLSVRNNQLTFL 175

Query: 319 --FLINLRTLRLHDRRIQGDLSLIGELSGLE----ILDLSESDVSEIPVSFGRLSHLRLL 372
                +L  L +    ++   ++       E         E+ ++ IP +   L     +
Sbjct: 176 PELPESLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENRITHIPENILSLDPTCTI 235

Query: 373 DLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQ 407
            L    +     R  LS+     + +    +    
Sbjct: 236 ILEDNPLSSR-IRESLSQQTAQPDYHGPRIYFSMS 269

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 32/214 (14%), Positives = 62/214 (28%), Gaps = 21/214 (9%)

Query: 235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSF 294
           L  I+   N +  +P+      L+ L ++ N    +P+      + L+ LD+      S 
Sbjct: 142 LEYINADNNQLTMLPELP--TSLEVLSVRNNQLTFLPE----LPESLEALDVSTNLLESL 195

Query: 295 SVRFPFLFPPLPSSPLFL---------LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSG 345
               P        + +F          +P ++  L    T+ L D  +   +        
Sbjct: 196 P-AVPVRNHHSEETEIFFRCRENRITHIPENILSLDPTCTIILEDNPLSSRIRESLSQQT 254

Query: 346 LEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRH 405
            +           +        H  L D    +  E     V       E    +++F  
Sbjct: 255 AQPDYHGPRIYFSMSDGQQNTLHRPLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSA 314

Query: 406 WQFESESEEDSSSNAKFIE-----LGALSRLTSL 434
           +         + + + F E     L  LS    L
Sbjct: 315 FLDRLSDTVSARNTSGFREQVAAWLEKLSASAEL 348

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 31/181 (17%), Positives = 53/181 (29%), Gaps = 50/181 (27%)

Query: 238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR 297
           IS  + D     D+ E  K        N  +++       +     L L  +        
Sbjct: 22  ISGTYADYFSAWDKWE--KQALPGENRNEAVSLLKECL--INQFSELQLNRLN------- 70

Query: 298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS 357
                  L S P  L P        +  L +    +    SL    + LE LD  ++ +S
Sbjct: 71  -------LSSLPDNLPP-------QITVLEITQNALI---SLPELPASLEYLDACDNRLS 113

Query: 358 EIPVSFGRLSHLRL-----------------LDLTGCYILELIPRGVLSRLRKLEELYMS 400
            +P     L HL +                 ++      L ++P         LE L + 
Sbjct: 114 TLPELPASLKHLDVDNNQLTMLPELPALLEYINADNNQ-LTMLP----ELPTSLEVLSVR 168

Query: 401 H 401
           +
Sbjct: 169 N 169

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A Length = 220

 Score = 49.6 bits (119), Expect = 8e-07
 Identities = 31/131 (23%), Positives = 51/131 (38%), Gaps = 18/131 (13%)

Query: 322 NLRTLRLHDRRIQ----GDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTG 376
            +  +RL    I+    G  S       L  +DLS + +SE+   +F  L  L  L L G
Sbjct: 33  TITEIRLEQNTIKVIPPGAFS---PYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYG 89

Query: 377 CYILELIPRGVLSRLRKLEELYMSH----SFRHWQFES----ESEEDSSSNAKFIELGAL 428
             I EL P+ +   L  L+ L ++       R   F+            +  + I  G  
Sbjct: 90  NKITEL-PKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQTIAKGTF 148

Query: 429 SRLTSL-HIHI 438
           S L ++  +H+
Sbjct: 149 SPLRAIQTMHL 159

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A Length = 220

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 37/171 (21%), Positives = 61/171 (35%), Gaps = 51/171 (29%)

Query: 234 DLTGISLMFNDIHEVP----DELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGI 289
            +T I L  N I  +P          KL+ + L  N    +    FQG            
Sbjct: 33  TITEIRLEQNTIKVIPPGAFSPY--KKLRRIDLSNNQISELAPDAFQG------------ 78

Query: 290 RRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG-DLSLIGELSGLEI 348
                                         L +L +L L+  +I     SL   L  L++
Sbjct: 79  ------------------------------LRSLNSLVLYGNKITELPKSLFEGLFSLQL 108

Query: 349 LDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           L L+ + ++ + V +F  L +L LL L     L+ I +G  S LR ++ ++
Sbjct: 109 LLLNANKINCLRVDAFQDLHNLNLLSLYDNK-LQTIAKGTFSPLRAIQTMH 158

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens} Length = 220

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 23/146 (15%), Positives = 49/146 (33%), Gaps = 36/146 (24%)

Query: 322 NLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCY 378
               LRL++          +  +L  L  ++ S + +++I   +F   S +  + LT   
Sbjct: 33  YTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTS-N 91

Query: 379 ILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA---LSRLTSLH 435
            LE +   +   L  L+ L +  +    +               +   +   LS +  L 
Sbjct: 92  RLENVQHKMFKGLESLKTLMLRSN----RITC------------VGNDSFIGLSSVRLLS 135

Query: 436 IH------IPEGKIMPSDMSFQNLTS 455
           ++      +  G       +F  L S
Sbjct: 136 LYDNQITTVAPG-------AFDTLHS 154

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens} Length = 220

 Score = 43.9 bits (104), Expect = 7e-05
 Identities = 27/169 (15%), Positives = 49/169 (28%), Gaps = 46/169 (27%)

Query: 234 DLTGISLMFNDIHEVPDE---LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIR 290
               + L  N+   +       + P+L+ +    N    I +  F+G   +  + L    
Sbjct: 33  YTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTS-- 90

Query: 291 RFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILD 350
                            + L  +   + F                       L  L+ L 
Sbjct: 91  -----------------NRLENVQHKM-F----------KG-----------LESLKTLM 111

Query: 351 LSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           L  + ++ +   SF  LS +RLL L     +  +  G    L  L  L 
Sbjct: 112 LRSNRITCVGNDSFIGLSSVRLLSLYDNQ-ITTVAPGAFDTLHSLSTLN 159

>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 = 49.7 bits (118), Expect = 2e-06
 Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 5/95 (5%)

Query: 310 LFLLPSSLSFLINLRTLRL-HDRRIQG-DLSLIGELSGLEILDLSESDVSEIPV-SFGRL 366
                  L    NL  L + + + +Q  +L  +  L  L  L + +S +  +   +F   
Sbjct: 20  ALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFT 79

Query: 367 SHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
             L  L+L+    LE +    +  L  L+EL +S 
Sbjct: 80  PRLSRLNLSFNA-LESLSWKTVQGL-SLQELVLSG 112

>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 = 46.7 bits (110), Expect = 2e-05
 Identities = 15/97 (15%), Positives = 28/97 (28%), Gaps = 19/97 (19%)

Query: 344 SGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF 403
            G   L  +     +         +L  L +     L+ +    L  L +L  L +    
Sbjct: 8   HGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVK-- 65

Query: 404 RHWQFESESEEDSSSNAKFIELGA---LSRLTSLHIH 437
                         S  +F+   A     RL+ L++ 
Sbjct: 66  --------------SGLRFVAPDAFHFTPRLSRLNLS 88

>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 = 45.9 bits (108), Expect = 3e-05
 Identities = 12/80 (15%), Positives = 22/80 (27%), Gaps = 3/80 (3%)

Query: 324 RTLRLHDRRIQGDLSLIGELSGLEILDLS-ESDVSEIP-VSFGRLSHLRLLDLTGCYILE 381
             LR         L  +     L  L +  +  +  +       L  LR L +    +  
Sbjct: 11  SGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGL-R 69

Query: 382 LIPRGVLSRLRKLEELYMSH 401
            +         +L  L +S 
Sbjct: 70  FVAPDAFHFTPRLSRLNLSF 89

>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 = 47.8 bits (114), Expect = 3e-06
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLL 372
           + ++LS L   + L L    I+  +S +  +  L IL L  + + +I         L  L
Sbjct: 40  MDATLSTLKACKHLALSTNNIE-KISSLSGMENLRILSLGRNLIKKIENLDAVADTLEEL 98

Query: 373 DLTGCYILELIPRGVLSRLRKLEELYMSH 401
            ++   I  L     + +L  L  LYMS+
Sbjct: 99  WISYNQIASLSG---IEKLVNLRVLYMSN 124

>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 = 44.3 bits (105), Expect = 4e-05
 Identities = 38/192 (19%), Positives = 67/192 (34%), Gaps = 42/192 (21%)

Query: 222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELE-CPKLQALFLQENSPLAIPDRFFQGMKD 280
             + +  +A   +   +  M   I ++   L      + L L  N+   I      GM++
Sbjct: 14  FEERKSVVATEAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKI--SSLSGMEN 71

Query: 281 LQVLDLGG--IRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLIN-LRTLRLHDRRIQGDL 337
           L++L LG   I++                        +L  + + L  L +   +I   L
Sbjct: 72  LRILSLGRNLIKKI----------------------ENLDAVADTLEELWISYNQIA-SL 108

Query: 338 SLIGELSGLEILDLSE---SDVSEIPVSFGRLSHLRLLDLTGCYILELIPRG-------- 386
           S I +L  L +L +S    ++  EI      L  L  L L G  +               
Sbjct: 109 SGIEKLVNLRVLYMSNNKITNWGEI-DKLAALDKLEDLLLAGNPLYNDYKENNATSEYRI 167

Query: 387 -VLSRLRKLEEL 397
            V+ RL  L++L
Sbjct: 168 EVVKRLPNLKKL 179

>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 = 2e-04
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTG 376
           LS + NLR L L    I+   +L      LE L +S + ++ +     +L +LR+L ++ 
Sbjct: 66  LSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLS-GIEKLVNLRVLYMSN 124

Query: 377 CYILELIPRGVLSRLRKLEELYMSH 401
             I        L+ L KLE+L ++ 
Sbjct: 125 NKITNWGEIDKLAALDKLEDLLLAG 149

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus} Length = 229

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 37/147 (25%), Positives = 55/147 (37%), Gaps = 30/147 (20%)

Query: 258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL 317
           Q L+L +N    +    F  + +L+ L LG  +                   L  LP  +
Sbjct: 43  QILYLHDNQITKLEPGVFDSLINLKELYLGSNQ-------------------LGALPVGV 83

Query: 318 SF--LINLRTLRLHDRRIQGDLSL----IGELSGLEILDLSESDVSEIPVSFGRLSHLRL 371
            F  L  L  L L   ++     L       L  L+ L +  + ++E+P    RL+HL  
Sbjct: 84  -FDSLTQLTVLDLGTNQLT---VLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTH 139

Query: 372 LDLTGCYILELIPRGVLSRLRKLEELY 398
           L L     L+ IP G   RL  L   Y
Sbjct: 140 LALDQNQ-LKSIPHGAFDRLSSLTHAY 165

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A Length = 272

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 46/174 (26%), Positives = 75/174 (43%), Gaps = 35/174 (20%)

Query: 234 DLTGISLMFNDIHEVP--DELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
           ++  ++L  N +H++    EL    L  L L  N   ++P+  F  + +L+ L L   + 
Sbjct: 64  NVRYLALGGNKLHDISALKEL--TNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQ- 120

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSL-IG---ELSGLE 347
                        L S P          L NL  L L   ++Q   SL  G   +L+ L 
Sbjct: 121 -------------LQSLP----DGVFDKLTNLTYLNLAHNQLQ---SLPKGVFDKLTNLT 160

Query: 348 ILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILEL--IPRGVLSRLRKLEELY 398
            LDLS + +  +P   F +L+ L+ L L   Y  +L  +P GV  RL  L+ ++
Sbjct: 161 ELDLSYNQLQSLPEGVFDKLTQLKDLRL---YQNQLKSVPDGVFDRLTSLQYIW 211

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A Length = 272

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 48/218 (22%), Positives = 91/218 (41%), Gaps = 42/218 (19%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
           +    +L    + +   + E   +  +    +   ++     Q + +++ L LGG +   
Sbjct: 20  ETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQG--IQYLPNVRYLALGGNKLHD 77

Query: 294 FSVRFPFLFPPLPS-SPLFLLPSSLS------F--LINLRTLRLHDRRIQGDLSL----I 340
            S         L + + L L  + L       F  L NL+ L L + ++Q   SL     
Sbjct: 78  ISA-----LKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQ---SLPDGVF 129

Query: 341 GELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
            +L+ L  L+L+ + +  +P   F +L++L  LDL     L+ +P GV  +L +L++L +
Sbjct: 130 DKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDL-SYNQLQSLPEGVFDKLTQLKDLRL 188

Query: 400 SHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL-HI 436
             +    Q +S            +  G   RLTSL +I
Sbjct: 189 YQN----QLKS------------VPDGVFDRLTSLQYI 210

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A Length = 251

 Score = 45.1 bits (107), Expect = 4e-05
 Identities = 42/174 (24%), Positives = 67/174 (38%), Gaps = 33/174 (18%)

Query: 234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
           D   + L    +  + D       KL  L L  N    +    F  + +L  L L   + 
Sbjct: 36  DTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQ- 94

Query: 292 FSFSVRFPFLFPPLPSSPLFLLPSSLSF--LINLRTLRLHDRRIQGDLSL-IG---ELSG 345
                        L S     LP  + F  L  L  L L   +++   SL  G    L+ 
Sbjct: 95  -------------LAS-----LPLGV-FDHLTQLDKLYLGGNQLK---SLPSGVFDRLTK 132

Query: 346 LEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY 398
           L+ L L+ + +  IP   F +L++L+ L L+    L+ +P G   RL KL+ + 
Sbjct: 133 LKELRLNTNQLQSIPAGAFDKLTNLQTLSLSTNQ-LQSVPHGAFDRLGKLQTIT 185

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A Length = 251

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 45/201 (22%), Positives = 70/201 (34%), Gaps = 61/201 (30%)

Query: 258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL 317
           + L LQ      + D  F+G+  L  L+L   +              L +          
Sbjct: 38  EKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQ--------------LQTLS----AGVF 79

Query: 318 SFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGC 377
             L  L TL L + ++    SL                V      F  L+ L  L L G 
Sbjct: 80  DDLTELGTLGLANNQLA---SL-------------PLGV------FDHLTQLDKLYLGGN 117

Query: 378 YILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA---LSRLTSL 434
             L+ +P GV  RL KL+EL ++ +    Q +S            I  GA   L+ L +L
Sbjct: 118 Q-LKSLPSGVFDRLTKLKELRLNTN----QLQS------------IPAGAFDKLTNLQTL 160

Query: 435 HIHIPEGKIMPSDMSFQNLTS 455
            +   + + +P   +F  L  
Sbjct: 161 SLSTNQLQSVP-HGAFDRLGK 180

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis} Length = 362

 Score = 45.3 bits (106), Expect = 6e-05
 Identities = 24/163 (14%), Positives = 51/163 (31%), Gaps = 23/163 (14%)

Query: 229 IAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQEN--SPLAIPDRFFQGMKDLQVLDL 286
           +     L  + +   +   +      P L++L +         + D     + +L+ L L
Sbjct: 168 LDAMPLLNNLKIKGTNNLSIGK-KPRPNLKSLEIISGGLPDSVVEDILGSDLPNLEKLVL 226

Query: 287 -GGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD----LSLIG 341
             G+  + F        P                  NL+ L + D   Q           
Sbjct: 227 YVGVEDYGFDGDMNVFRPLFSKDRFP----------NLKWLGIVDAEEQNVVVEMFLESD 276

Query: 342 ELSGLEILDLS-----ESDVSEIPVSFGRLSHLRLLDLTGCYI 379
            L  LE +D+S     +     +     ++ HL+ +++   Y+
Sbjct: 277 ILPQLETMDISAGVLTDEGARLLLDHVDKIKHLKFINMKYNYL 319

>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 = 44.2 bits (104), Expect = 2e-04
 Identities = 29/166 (17%), Positives = 52/166 (31%), Gaps = 17/166 (10%)

Query: 254 CPKLQALFLQENSPLAIPDR----FFQGMKDLQVLDLGGIRRFSFSVR-FPFLFPPLPS- 307
           C K++ L ++E+S      +      Q    L+VL+         S +    +     S 
Sbjct: 163 CRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSL 222

Query: 308 -------SPLFLLPSSLSFLINLRTLRL----HDRRIQGDLSLIGELSGLEILDLSESDV 356
                    +  L        NL          D  +      +     L  L LS    
Sbjct: 223 VSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGP 282

Query: 357 SEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS 402
           +E+P+ F   + +R LDL    +       ++ +   LE L   + 
Sbjct: 283 NEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCPNLEVLETRNV 328

>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 = 44.0 bits (104), Expect = 2e-04
 Identities = 60/431 (13%), Positives = 115/431 (26%), Gaps = 68/431 (15%)

Query: 159 FKSRESTMKDIMEAM--KDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVV 216
           F +R+  +  I + +   +       I GM G GK+ L  E  +    ++     +  V 
Sbjct: 126 FVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLE--GCFSGGVH 183

Query: 217 ------SQTPSITKIQYEIAGWLD--LTGISLMFNDIHEVPDELECPKLQALFLQENSPL 268
                      +      +   LD   +    +  +I E  D L       +  +    L
Sbjct: 184 WVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRL----RVLMLRKHPRSL 239

Query: 269 AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTL-R 327
            I D          V D   ++ F    +   L   L +    +  S +     +     
Sbjct: 240 LILD---------DVWDPWVLKAFDNQCQ--IL---LTTRDKSVTDSVMGPKHVVPVESG 285

Query: 328 LHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLS----HLRLLDLTGCYILELI 383
           L   +    LSL   +   ++   + S + E   S   +S     LR       Y L  +
Sbjct: 286 LGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQL 345

Query: 384 PRGVLSRLRKLEELYMSHSFR--HWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEG 441
                 R+RK                 E   E+                 T L I     
Sbjct: 346 QNKQFKRIRKSSSYDYEALDEAMSISVEMLRED------------IKDYYTDLSI----- 388

Query: 442 KIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSW 501
                    Q        +  +     ++ +   LQ+F  +       +       LH  
Sbjct: 389 --------LQKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDL 440

Query: 502 IKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERT----- 556
             + L       L +++  + +         + L            +L   +        
Sbjct: 441 QVDFLTEKNRSQLQDLH-RKMVTQFQRYYQPHTLSPDQEDCMYWYNFLAYHMASANMHKE 499

Query: 557 LRVTLHKLEWL 567
           L   +  L+W+
Sbjct: 500 LCALMFSLDWI 510

>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 = 41.6 bits (98), Expect = 3e-04
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDL 374
           +  +  +  R L L   +I    +L   L   + +D S++++ ++   F  L  L+ L +
Sbjct: 13  AQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLV 71

Query: 375 TGCYILELIPRGVLSRLRKLEELYMSH 401
               I   I  G+   L  L EL +++
Sbjct: 72  NNNRI-CRIGEGLDQALPDLTELILTN 97

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A Length = 168

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 20/86 (23%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLT 375
            +  +NL  L L +  +   +S + +L  L+ L+LSE+ +     +   +L +L  L+L+
Sbjct: 45  TAEFVNLEFLSLINVGLI-SVSNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLNLS 103

Query: 376 GCYILELIPRGVLSRLRKLEELYMSH 401
           G  + ++     L +L  L+ L + +
Sbjct: 104 GNKLKDISTLEPLKKLECLKSLDLFN 129

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri} Length = 208

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 38/146 (26%), Positives = 63/146 (43%), Gaps = 27/146 (18%)

Query: 258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL 317
             L L+ NS  ++P+  F  +  L  L LGG +              L S P        
Sbjct: 31  TYLDLETNSLKSLPNGVFDELTSLTQLYLGGNK--------------LQSLP----NGVF 72

Query: 318 SFLINLRTLRLHDRRIQGDLSL----IGELSGLEILDLSESDVSEIPV-SFGRLSHLRLL 372
           + L +L  L L   ++Q   SL      +L+ L+ L L+ + +  +P   F +L+ L+ L
Sbjct: 73  NKLTSLTYLNLSTNQLQ---SLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDL 129

Query: 373 DLTGCYILELIPRGVLSRLRKLEELY 398
            L     L+ +P GV  RL  L+ ++
Sbjct: 130 RLYQNQ-LKSVPDGVFDRLTSLQYIW 154

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A Length = 149

 Score = 40.4 bits (95), Expect = 4e-04
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 322 NLRTLRLHDRRIQ--GDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYI 379
           +++ L L + R        L  E   LE L      ++ I     +L+ L+ L+L+   +
Sbjct: 18  DVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIAN-LPKLNKLKKLELSDNRV 76

Query: 380 LELIPRGVLSRLRKLEELYMSH 401
                  +  +   L  L +S 
Sbjct: 77  -SGGLEVLAEKCPNLTHLNLSG 97

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A Length = 149

 Score = 39.7 bits (93), Expect = 8e-04
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 15/85 (17%)

Query: 315 SSLSFLINLRTLRLHDRRIQGDLSLIGE-LSGLEILDLSE---SDVSEIPVSFGRLSHLR 370
           ++L  L  L+ L L D R+ G L ++ E    L  L+LS     D+S I     +L +L+
Sbjct: 58  ANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTI-EPLKKLENLK 116

Query: 371 LLDLTGC----------YILELIPR 385
            LDL  C           + +L+P+
Sbjct: 117 SLDLFNCEVTNLNDYRENVFKLLPQ 141

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	848
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	100.0
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	100.0
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	100.0
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.98
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.97
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.97
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.97
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.97
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.97
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.97
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.97
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.97
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.96
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.96
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.96
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.96
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.95
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.95
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.95
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.95
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.94
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.94
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.93
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.93
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.93
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.93
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.92
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.92
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.91
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.91
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.9
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.9
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.9
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.89
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.89
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.89
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.89
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.89
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.88
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	99.87
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.86
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	99.84
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.84
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.83
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.83
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	99.83
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.83
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.82
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.82
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.82
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.81
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.8
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.79
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.79
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.78
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.78
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.78
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	99.78
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.76
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.76
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.75
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.75
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.74
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.73
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.73
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.73
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.72
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.71
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.7
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.7
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.7
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.69
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.68
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.68
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.67
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.67
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.67
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.67
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.66
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.66
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.66
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.64
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.64
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.61
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.61
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.6
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.59
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.58
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.58
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.57
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.57
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.56
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.56
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.56
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.55
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.54
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.54
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.54
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.54
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.54
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.53
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.53
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.53
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.52
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.5
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.5
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.49
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.49
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.49
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.49
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.48
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.47
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.45
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.44
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.43
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.42
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.39
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.38
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.37
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.37
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.33
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.31
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.29
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.29
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.27
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.27
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.27
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.26
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.26
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.22
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.22
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.22
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.2
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.14
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.13
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.13
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	99.12
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	99.03
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	99.0
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.96
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.95
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.91
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.79
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	98.75
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.6
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.55
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.53
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.49
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.46
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.44
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	98.4
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.38
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.29
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	98.24
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	98.13
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	98.1
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.06
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.83
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.77
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	97.64
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.57
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	97.52
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.52
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	96.7
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	96.63
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.53
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.45
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.44
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.43
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	96.4
2fna_A	357	Conserved hypothetical protein; structural genomic	96.35
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.1
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.82
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.81
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.71
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.39
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.83
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.63
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	94.58
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.26
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	93.96
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	93.82
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	93.68
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	93.55
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	93.48
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	93.47
2chq_A	319	Replication factor C small subunit; DNA-binding pr	93.2
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	93.12
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	92.89
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	92.78
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	92.67
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	92.55
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	92.45
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	92.43
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	92.33
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	92.16
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	91.91
3pvs_A	447	Replication-associated recombination protein A; ma	91.85
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	91.82
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	91.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	91.76
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	91.7
3bos_A	242	Putative DNA replication factor; P-loop containing	91.65
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	91.64
3co5_A	143	Putative two-component system transcriptional RES	91.56
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	91.19
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.11
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	91.06
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	90.87
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	90.78
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	90.77
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	90.66
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	90.61
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	90.57
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	90.42
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	90.34
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	90.31
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	90.05
2hf9_A	226	Probable hydrogenase nickel incorporation protein	90.04
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	90.03
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	89.98
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	89.89
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	89.88
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.84
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	89.76
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	89.36
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	89.32
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	89.28
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	88.94
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	88.89
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	88.86
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	88.79
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	88.78
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	88.77
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	88.6
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	88.44
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	88.32
2xxa_A	433	Signal recognition particle protein; protein trans	88.29
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	88.13
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.1
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	88.1
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	87.68
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	87.66
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	87.65
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	87.64
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	87.63
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	87.55
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	87.45
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	87.4
3fwy_A	314	Light-independent protochlorophyllide reductase I	87.36
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	87.29
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	87.29
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	87.07
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	86.97
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	86.97
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	86.95
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	86.88
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	86.83
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	86.63
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	86.51
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	86.47
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	86.34
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	86.32
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	86.28
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	86.17
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.08
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	86.04
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	85.75
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	85.68
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	85.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	85.56
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	85.47
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	85.46
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	85.39
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	85.37
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	85.31
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	85.29
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.29
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	85.18
1via_A	175	Shikimate kinase; structural genomics, transferase	85.13
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	85.02
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	84.9
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	84.87
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	84.79
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	84.7
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	84.69
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	84.62
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	84.56
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	84.56
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	84.45
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	84.33
2r44_A	331	Uncharacterized protein; putative ATPase, structur	84.32
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	84.26
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	84.18
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	84.14
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	84.1
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	83.99
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	83.91
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	83.87
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	83.81
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	83.69
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	83.62
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	83.61
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	83.61
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	83.6
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	83.59
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	83.58
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	83.58
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	83.51
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	83.48
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	83.44
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	83.43
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	83.31
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	83.29
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	83.28
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	83.21
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	83.18
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	83.17
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	83.16
2vli_A	183	Antibiotic resistance protein; transferase, tunica	83.12
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	83.06
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	83.03
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	83.0
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	82.91
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	82.88
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	82.85
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	82.62
2cvh_A	220	DNA repair and recombination protein RADB; filamen	82.61
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	82.58
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	82.58
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	82.35
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	82.32
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	82.24
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	82.18
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	82.17
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	82.11
1b0u_A	262	Histidine permease; ABC transporter, transport pro	81.98
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	81.9
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	81.75
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	81.64
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	81.62
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	81.6
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	81.56
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	81.49
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	81.45
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	81.43
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	81.39
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	81.35
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.33
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	81.31
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	81.28
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	81.24
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	81.23
1sgw_A	214	Putative ABC transporter; structural genomics, P p	81.19
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	81.15
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	81.13
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	81.12
1g6h_A	257	High-affinity branched-chain amino acid transport	81.08
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	81.0
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	80.98
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	80.94
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	80.86
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	80.85
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	80.83
4a74_A	231	DNA repair and recombination protein RADA; hydrola	80.81
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	80.55
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	80.52
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	80.38
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.33
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	80.32
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	80.28
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	80.25
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	80.17
2ghi_A	260	Transport protein; multidrug resistance protein, M	80.05

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=100.00  E-value=4.3e-33  Score=324.27  Aligned_cols=477  Identities=19%  Similarity=0.184  Sum_probs=230.4

Q ss_pred             CCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ++.|++++|.+..++.. + ++++|++|++++|.+..+++..|.++++|++|++++              +.+...    
T Consensus        34 l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~i~~~~~~~l~~L~~L~Ls~--------------n~l~~~----   95 (606)
T 3vq2_A           34 TKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTG--------------NPIQSF----   95 (606)
T ss_dssp             CCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTT--------------CCCCCC----
T ss_pred             cCEEECCCCCcCEeChhhccCCccCcEEeCCCCcccccCHHHhhchhhcCEeECCC--------------Cccccc----
Confidence            44555555555544442 2 455555555555555554444445555555555555              444442    


Q ss_pred             CCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCc--ccChhhccCCcccEEeccCCccccccChhhhh
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                      .|..++++++|++|++++|.+...+ ..++++++|++|++++|.+.  .+|..++++++|++|++++|...+..|.. ++
T Consensus        96 ~p~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~-~~  174 (606)
T 3vq2_A           96 SPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVND-LQ  174 (606)
T ss_dssp             CTTSSTTCTTCCEEECTTSCCCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSSCCCEECTTT-TH
T ss_pred             ChhhcCCcccCCEEEccCCccccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCCcceecChhh-hh
Confidence            2445555555555555555444443 34555555555555555554  34555555555555555554443322222 44


Q ss_pred             cccccc----EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC--CCCCCC-ccCCCCeEEEEeCC
Q 003090          390 RLRKLE----ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK--IMPSDM-SFQNLTSFSIAIGD  462 (848)
Q Consensus       390 ~l~~L~----~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~--~~~~~~-~~~~L~~L~l~~~~  462 (848)
                      .+++|+    +|++++|.+...              +.......+|+.|++++|.+.  ..+..+ .+++|+.+.+..+.
T Consensus       175 ~l~~L~~~l~~L~l~~n~l~~~--------------~~~~~~~~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~l~l~~~~  240 (606)
T 3vq2_A          175 FLRENPQVNLSLDMSLNPIDFI--------------QDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGE  240 (606)
T ss_dssp             HHHHCTTCCCEEECTTCCCCEE--------------CTTTTTTCEEEEEEEESCCSCHHHHHHHHHTTTTCEEEEEEEEC
T ss_pred             hhhccccccceeeccCCCccee--------------CcccccCceeeeeeccCCccchhHHHHHhccccccccccccccc
Confidence            444433    455555544332              111112224555555555432  112222 34444444443222


Q ss_pred             CCC---------CCCCcccceEEecccc-cccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCC
Q 003090          463 LEE---------RPLSDFIGLFLQKFKK-RCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGF  532 (848)
Q Consensus       463 ~~~---------~~~~~l~~l~l~~~~~-~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l  532 (848)
                      ...         .....+..+.+....- .+..+.        ..+|.  ...+++|+.|.+.++... .++ .+  ..+
T Consensus       241 ~~~~~~l~~~~~~~~~~l~~l~l~~l~l~~~~~~~--------~~~~~--~~~l~~L~~L~l~~~~~~-~l~-~l--~~~  306 (606)
T 3vq2_A          241 FKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFS--------DDIVK--FHCLANVSAMSLAGVSIK-YLE-DV--PKH  306 (606)
T ss_dssp             CTTSCCCSCCCGGGGTTGGGSEEEEEEECCCTTCC--------GGGGS--CGGGTTCSEEEEESCCCC-CCC-CC--CTT
T ss_pred             cccCCcccccChHHhhhhhhccHhheecccccccc--------ccccc--cccCCCCCEEEecCccch-hhh-hc--ccc
Confidence            100         0001111111111110 000010        01111  122578888888877653 333 22  567


Q ss_pred             CCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhh---hHH
Q 003090          533 NELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKIL---LSH  609 (848)
Q Consensus       533 ~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l---~~~  609 (848)
                      ++|++|++.+|.. +.++      .. .+++|++|+++++..+..     .+.+.+++|+.|++++|. + ..+   |. 
T Consensus       307 ~~L~~L~l~~n~l-~~lp------~~-~l~~L~~L~l~~n~~~~~-----~~~~~l~~L~~L~ls~n~-l-~~~~~~~~-  370 (606)
T 3vq2_A          307 FKWQSLSIIRCQL-KQFP------TL-DLPFLKSLTLTMNKGSIS-----FKKVALPSLSYLDLSRNA-L-SFSGCCSY-  370 (606)
T ss_dssp             CCCSEEEEESCCC-SSCC------CC-CCSSCCEEEEESCSSCEE-----CCCCCCTTCCEEECCSSC-E-EEEEECCH-
T ss_pred             ccCCEEEcccccC-cccc------cC-CCCccceeeccCCcCccc-----hhhccCCCCCEEECcCCc-c-CCCcchhh-
Confidence            8899999998865 4432      22 688888888888865443     244568888888888864 3 333   33 


Q ss_pred             HHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccc
Q 003090          610 LVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELR  689 (848)
Q Consensus       610 ~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~  689 (848)
                      ....+++|++|++++|. ++.++         ..+..+++|++|+++++.-....+..  .+..+++|+.|++++|. ++
T Consensus       371 ~~~~~~~L~~L~L~~n~-l~~~~---------~~~~~l~~L~~L~l~~n~l~~~~~~~--~~~~l~~L~~L~l~~n~-l~  437 (606)
T 3vq2_A          371 SDLGTNSLRHLDLSFNG-AIIMS---------ANFMGLEELQHLDFQHSTLKRVTEFS--AFLSLEKLLYLDISYTN-TK  437 (606)
T ss_dssp             HHHCCSCCCEEECCSCS-EEEEC---------CCCTTCTTCCEEECTTSEEESTTTTT--TTTTCTTCCEEECTTSC-CE
T ss_pred             hhccCCcccEeECCCCc-cccch---------hhccCCCCCCeeECCCCccCCccChh--hhhccccCCEEECcCCC-CC
Confidence            33778888888888876 44443         23445566666666655322221111  13445555555555543 22


Q ss_pred             ccccCccccccccceee-----------------eccccccceeeeecC---CCCCCCCCCCCccEEEEecCCCCceecc
Q 003090          690 QVFPANFGKKAAAEEMV-----------------LYRKRRDQIHIHATT---STSSPTPSLGNLVSITIRGCGKLRNLFT  749 (848)
Q Consensus       690 ~~~p~~~~~~~~~~~l~-----------------l~~l~~~~l~i~~c~---~~~~~~~~l~~L~~L~i~~C~~L~~l~~  749 (848)
                      ...|..+......+.+.                 +++|  +.+++.+|.   ..+..+..+++|++|++++| +++.+++
T Consensus       438 ~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L--~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~  514 (606)
T 3vq2_A          438 IDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNL--TFLDLSKCQLEQISWGVFDTLHRLQLLNMSHN-NLLFLDS  514 (606)
T ss_dssp             ECCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTC--CEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCSCEEG
T ss_pred             ccchhhhcCCCCCCEEECCCCcCCCcchHHhhccCCCC--CEEECCCCcCCccChhhhcccccCCEEECCCC-cCCCcCH
Confidence            22232222110001111                 2223  333343331   12334555666666666665 4444433


Q ss_pred             cchhhccccccEEEEecccccceeecCCcccccccCCCccceecc-ccccccccccc
Q 003090          750 TSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFP-SLFGIKLCDLD  805 (848)
Q Consensus       750 ~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~-sL~~L~i~~cp  805 (848)
                       ..+.++++|++|++++|. ++.++..      +..       ++ +|++|++.++|
T Consensus       515 -~~~~~l~~L~~L~l~~N~-l~~~p~~------~~~-------l~~~L~~l~l~~N~  556 (606)
T 3vq2_A          515 -SHYNQLYSLSTLDCSFNR-IETSKGI------LQH-------FPKSLAFFNLTNNS  556 (606)
T ss_dssp             -GGTTTCTTCCEEECTTSC-CCCEESC------GGG-------SCTTCCEEECCSCC
T ss_pred             -HHccCCCcCCEEECCCCc-CcccCHh------Hhh-------hcccCcEEEccCCC
Confidence             345566666666666664 4444221      111       33 57777777766

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=100.00  E-value=4.7e-32  Score=322.53  Aligned_cols=197  Identities=21%  Similarity=0.265  Sum_probs=129.2

Q ss_pred             ccCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          232 WLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       232 ~~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      ...++.|++++|.+....+...+++|++|++++|.+...++. +.++++|++|++++              +.+.+.   
T Consensus       177 l~~L~~L~Ls~n~l~~~~~~~~l~~L~~L~Ls~n~l~~~~~~-l~~l~~L~~L~Ls~--------------n~l~~~---  238 (768)
T 3rgz_A          177 CGELKHLAISGNKISGDVDVSRCVNLEFLDVSSNNFSTGIPF-LGDCSALQHLDISG--------------NKLSGD---  238 (768)
T ss_dssp             CTTCCEEECCSSEEESCCBCTTCTTCCEEECCSSCCCSCCCB-CTTCCSCCEEECCS--------------SCCCSC---
T ss_pred             CCCCCEEECCCCcccccCCcccCCcCCEEECcCCcCCCCCcc-cccCCCCCEEECcC--------------CcCCCc---
Confidence            344666666666665444444666677777776655443333 56667777777776              666654   


Q ss_pred             CCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCc-ccChhhccC-CcccEEeccCCccccccChhhhh
Q 003090          312 LLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS-EIPVSFGRL-SHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       312 ~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L-~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                       .|..++.+++|++|++++|.+.+..+.. .+++|++|++++|.++ .+|..+..+ ++|++|++++|...+.+|.. ++
T Consensus       239 -~~~~l~~l~~L~~L~Ls~n~l~~~~~~~-~l~~L~~L~L~~n~l~~~ip~~~~~~~~~L~~L~Ls~n~l~~~~p~~-~~  315 (768)
T 3rgz_A          239 -FSRAISTCTELKLLNISSNQFVGPIPPL-PLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPF-FG  315 (768)
T ss_dssp             -HHHHTTTCSSCCEEECCSSCCEESCCCC-CCTTCCEEECCSSEEEESCCCCSCTTCTTCSEEECCSSEEEECCCGG-GG
T ss_pred             -ccHHHhcCCCCCEEECCCCcccCccCcc-ccCCCCEEECcCCccCCccCHHHHhhcCcCCEEECcCCcCCCccchH-Hh
Confidence             6667777777777777777665544333 6777777777777776 667666664 77777777777766666666 67


Q ss_pred             ccccccEEeccccccccccccccccccCcccchh-hhcccCCCcEEEeeccCCC-CCCCCC-ccC-CCCeEEEEeCC
Q 003090          390 RLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI-ELGALSRLTSLHIHIPEGK-IMPSDM-SFQ-NLTSFSIAIGD  462 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~-~L~~l~~L~~L~l~~~~~~-~~~~~~-~~~-~L~~L~l~~~~  462 (848)
                      ++++|++|++++|.+.+.             .+. .++++++|+.|++++|.+. .+|..+ .+. +|+.|++..+.
T Consensus       316 ~l~~L~~L~L~~n~l~~~-------------ip~~~l~~l~~L~~L~Ls~n~l~~~~p~~l~~l~~~L~~L~Ls~N~  379 (768)
T 3rgz_A          316 SCSLLESLALSSNNFSGE-------------LPMDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNN  379 (768)
T ss_dssp             GCTTCCEEECCSSEEEEE-------------CCHHHHTTCTTCCEEECCSSEEEECCCTTHHHHTTTCSEEECCSSE
T ss_pred             cCCCccEEECCCCcccCc-------------CCHHHHhcCCCCCEEeCcCCccCccccHHHHhhhcCCcEEEccCCC
Confidence            777777777777766544             233 3777777777777777765 566655 454 77777776443

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=100.00  E-value=9e-32  Score=320.12  Aligned_cols=95  Identities=13%  Similarity=-0.017  Sum_probs=57.0

Q ss_pred             cCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcccccccc
Q 003090          587 CLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWK  666 (848)
Q Consensus       587 ~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~  666 (848)
                      .+++|+.|++.+|.-. ..+|..+ ..+++|++|++++|.-...+|         ..+..+++|++|++++|.-...+|.
T Consensus       464 ~l~~L~~L~L~~N~l~-~~~p~~l-~~l~~L~~L~L~~N~l~~~~p---------~~~~~l~~L~~L~L~~N~l~~~~p~  532 (768)
T 3rgz_A          464 YVKTLETLILDFNDLT-GEIPSGL-SNCTNLNWISLSNNRLTGEIP---------KWIGRLENLAILKLSNNSFSGNIPA  532 (768)
T ss_dssp             GCTTCCEEECCSSCCC-SCCCGGG-GGCTTCCEEECCSSCCCSCCC---------GGGGGCTTCCEEECCSSCCEEECCG
T ss_pred             CCCCceEEEecCCccc-CcCCHHH-hcCCCCCEEEccCCccCCcCC---------hHHhcCCCCCEEECCCCcccCcCCH
Confidence            4566666666665433 3444432 556666666666665443443         4566778888888887765445544


Q ss_pred             CCCccccccCccEEEeecCccccccccCcc
Q 003090          667 GDTQFVSLHNLKKVRVEECDELRQVFPANF  696 (848)
Q Consensus       667 ~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~  696 (848)
                      .   +..+++|+.|++++|+-... +|..+
T Consensus       533 ~---l~~l~~L~~L~Ls~N~l~g~-ip~~~  558 (768)
T 3rgz_A          533 E---LGDCRSLIWLDLNTNLFNGT-IPAAM  558 (768)
T ss_dssp             G---GGGCTTCCEEECCSSEEESB-CCGGG
T ss_pred             H---HcCCCCCCEEECCCCccCCc-CChHH
Confidence            3   56788888888888753333 34433

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=99.98  E-value=4.1e-31  Score=307.58  Aligned_cols=465  Identities=16%  Similarity=0.123  Sum_probs=317.4

Q ss_pred             EEEEEeccCCchhHHHH-HHHhccCCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEcc
Q 003090          211 VAMAVVSQTPSITKIQY-EIAGWLDLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG  287 (848)
Q Consensus       211 ~~wv~vs~~~~~~~l~~-~i~~~~~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~  287 (848)
                      ...+.++. ..+..+.. .+.....++.|++++|.+..+++. + .+++|++|++++|.+..+++..|.++++|++|+++
T Consensus        34 l~~L~Ls~-n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~i~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~L~  112 (606)
T 3vq2_A           34 TKNIDLSF-NPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAV  112 (606)
T ss_dssp             CCEEECTT-SCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCCCCTTSSTTCTTCCEEECT
T ss_pred             cCEEECCC-CCcCEeChhhccCCccCcEEeCCCCcccccCHHHhhchhhcCEeECCCCcccccChhhcCCcccCCEEEcc
Confidence            33445555 33444443 455566799999999999988654 4 89999999999999988866667999999999999


Q ss_pred             CcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccC--CchhhccccCCCEEEccCCCCccc-Chhhc
Q 003090          288 GIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDVSEI-PVSFG  364 (848)
Q Consensus       288 ~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~--~~~~i~~l~~L~~L~l~~~~l~~l-p~~i~  364 (848)
                      +              +.+...    .|..++++++|++|++++|.+..  .+..++++++|++|++++|.++.+ |..++
T Consensus       113 ~--------------n~l~~~----~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~~~  174 (606)
T 3vq2_A          113 E--------------TKLASL----ESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQ  174 (606)
T ss_dssp             T--------------SCCCCS----SSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSSCCCEECTTTTH
T ss_pred             C--------------Cccccc----cccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCCcceecChhhhh
Confidence            9              888773    34779999999999999998875  468899999999999999999966 44577


Q ss_pred             cCCccc----EEeccCCccccccChhhhhccccccEEecccccccccccc-----cc----------------c------
Q 003090          365 RLSHLR----LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFES-----ES----------------E------  413 (848)
Q Consensus       365 ~L~~L~----~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~-----~~----------------~------  413 (848)
                      .+.+|+    +|++++|.. ..+|... ....+|+.|++++|.+.+....     ..                .      
T Consensus       175 ~l~~L~~~l~~L~l~~n~l-~~~~~~~-~~~~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~l~l~~~~~~~~~~l~~~~~  252 (606)
T 3vq2_A          175 FLRENPQVNLSLDMSLNPI-DFIQDQA-FQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEP  252 (606)
T ss_dssp             HHHHCTTCCCEEECTTCCC-CEECTTT-TTTCEEEEEEEESCCSCHHHHHHHHHTTTTCEEEEEEEECCTTSCCCSCCCG
T ss_pred             hhhccccccceeeccCCCc-ceeCccc-ccCceeeeeeccCCccchhHHHHHhccccccccccccccccccCCcccccCh
Confidence            777665    899999866 4567663 4445999999999876421000     00                0      


Q ss_pred             -----------------cccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeCCCCCCCCCcccceE
Q 003090          414 -----------------EDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIGDLEERPLSDFIGLF  475 (848)
Q Consensus       414 -----------------~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~  475 (848)
                                       ...........+..+++|+.|+++++.+..++ .+ .+++|+.|.+..+..            
T Consensus       253 ~~~~~l~~l~l~~l~l~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l~-~l~~~~~L~~L~l~~n~l------------  319 (606)
T 3vq2_A          253 SIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLE-DVPKHFKWQSLSIIRCQL------------  319 (606)
T ss_dssp             GGGTTGGGSEEEEEEECCCTTCCGGGGSCGGGTTCSEEEEESCCCCCCC-CCCTTCCCSEEEEESCCC------------
T ss_pred             HHhhhhhhccHhheeccccccccccccccccCCCCCEEEecCccchhhh-hccccccCCEEEcccccC------------
Confidence                             00011111222556667777777777766666 33 666777777765443            


Q ss_pred             EecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccc
Q 003090          476 LQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLER  555 (848)
Q Consensus       476 l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~  555 (848)
                                          ..+|.+   .+++|+.|++.++......    ....+++|++|+++++.. +.+..  ..
T Consensus       320 --------------------~~lp~~---~l~~L~~L~l~~n~~~~~~----~~~~l~~L~~L~ls~n~l-~~~~~--~~  369 (606)
T 3vq2_A          320 --------------------KQFPTL---DLPFLKSLTLTMNKGSISF----KKVALPSLSYLDLSRNAL-SFSGC--CS  369 (606)
T ss_dssp             --------------------SSCCCC---CCSSCCEEEEESCSSCEEC----CCCCCTTCCEEECCSSCE-EEEEE--CC
T ss_pred             --------------------cccccC---CCCccceeeccCCcCccch----hhccCCCCCEEECcCCcc-CCCcc--hh
Confidence                                111100   1477888888887655433    234778899999888743 22100  01


Q ss_pred             cccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecc
Q 003090          556 TLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIE  635 (848)
Q Consensus       556 ~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~  635 (848)
                      .....+++|++|+++++. +..+.   .....+++|+.|++.+|.-. ...|...+..+++|++|++++|.-....+   
T Consensus       370 ~~~~~~~~L~~L~L~~n~-l~~~~---~~~~~l~~L~~L~l~~n~l~-~~~~~~~~~~l~~L~~L~l~~n~l~~~~~---  441 (606)
T 3vq2_A          370 YSDLGTNSLRHLDLSFNG-AIIMS---ANFMGLEELQHLDFQHSTLK-RVTEFSAFLSLEKLLYLDISYTNTKIDFD---  441 (606)
T ss_dssp             HHHHCCSCCCEEECCSCS-EEEEC---CCCTTCTTCCEEECTTSEEE-STTTTTTTTTCTTCCEEECTTSCCEECCT---
T ss_pred             hhhccCCcccEeECCCCc-cccch---hhccCCCCCCeeECCCCccC-CccChhhhhccccCCEEECcCCCCCccch---
Confidence            234567889999998884 44432   22346888999999887544 33332334678889999998887544343   


Q ss_pred             ccccccccccccCCcCEEecCCCccccc-cccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccc
Q 003090          636 RVNIAKEETELFSSLEKLTLWDLPRMTD-IWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQ  714 (848)
Q Consensus       636 ~~~~~~~~~~~l~~L~~L~l~~c~~L~~-l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~  714 (848)
                            ..+..+++|++|++++|.-... ++.   .+..+++|++|++++| +++.+.|..+..        +++|  +.
T Consensus       442 ------~~~~~l~~L~~L~l~~n~l~~~~~~~---~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~--------l~~L--~~  501 (606)
T 3vq2_A          442 ------GIFLGLTSLNTLKMAGNSFKDNTLSN---VFANTTNLTFLDLSKC-QLEQISWGVFDT--------LHRL--QL  501 (606)
T ss_dssp             ------TTTTTCTTCCEEECTTCEEGGGEECS---CCTTCTTCCEEECTTS-CCCEECTTTTTT--------CTTC--CE
T ss_pred             ------hhhcCCCCCCEEECCCCcCCCcchHH---hhccCCCCCEEECCCC-cCCccChhhhcc--------cccC--CE
Confidence                  4567788899999988753332 232   2567888999999887 455555554433        3334  45


Q ss_pred             eeeeecC---CCCCCCCCCCCccEEEEecCCCCceecccchhhccc-cccEEEEeccccc
Q 003090          715 IHIHATT---STSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLV-RLESLEVRSCPTL  770 (848)
Q Consensus       715 l~i~~c~---~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~-~L~~L~i~~C~~L  770 (848)
                      +++.+|.   ..+..+..+++|++|++++| +++.+|..  +..++ +|++|+++++|-.
T Consensus       502 L~Ls~N~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~p~~--~~~l~~~L~~l~l~~N~~~  558 (606)
T 3vq2_A          502 LNMSHNNLLFLDSSHYNQLYSLSTLDCSFN-RIETSKGI--LQHFPKSLAFFNLTNNSVA  558 (606)
T ss_dssp             EECCSSCCSCEEGGGTTTCTTCCEEECTTS-CCCCEESC--GGGSCTTCCEEECCSCCCC
T ss_pred             EECCCCcCCCcCHHHccCCCcCCEEECCCC-cCcccCHh--HhhhcccCcEEEccCCCcc
Confidence            5555541   12456788999999999997 58888753  77786 6999999998743

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.97  E-value=1.8e-30  Score=300.03  Aligned_cols=493  Identities=19%  Similarity=0.231  Sum_probs=289.7

Q ss_pred             CCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ++.|++++|.+..++.. + .+++|++|++++|.+..+++..|.++++|++|++++              +.+...    
T Consensus        30 l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~--------------n~l~~~----   91 (570)
T 2z63_A           30 TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG--------------NPIQSL----   91 (570)
T ss_dssp             CCEEECCSCCCCEECTTTTTTCSSCCEEECTTCCCCEECTTTTTTCTTCCEEECTT--------------CCCCEE----
T ss_pred             ccEEEccCCccCccChhHhhCCCCceEEECCCCcCCccCcccccCchhCCEEeCcC--------------CcCCcc----
Confidence            45566666666655442 2 566666666666666555555556666666666666              555542    


Q ss_pred             CCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcc--cChhhccCCcccEEeccCCccccccChhhhh
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSE--IPVSFGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~--lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                      .|..++.+++|++|++++|.+...+ ..++++++|++|++++|.+..  +|..++++++|++|++++|......|.. ++
T Consensus        92 ~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n~l~~~~~~~-~~  170 (570)
T 2z63_A           92 ALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTD-LR  170 (570)
T ss_dssp             CTTTTTTCTTCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTSCCCEECGGG-GH
T ss_pred             CHhhhcCccccccccccccccccCCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcCCccceecHHH-cc
Confidence            2345666666666666666555444 245666666666666666553  4566666666666666665443322333 55


Q ss_pred             ccccc----cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC--CCCCCC-ccCCCCeEEEEeCC
Q 003090          390 RLRKL----EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK--IMPSDM-SFQNLTSFSIAIGD  462 (848)
Q Consensus       390 ~l~~L----~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~--~~~~~~-~~~~L~~L~l~~~~  462 (848)
                      .+++|    +.|++++|.+...             .+..+..+ +|+.|++++|...  .++..+ .+++++.+.+..+.
T Consensus       171 ~l~~L~~~~~~L~l~~n~l~~~-------------~~~~~~~~-~L~~L~l~~n~~~~~~~~~~~~~l~~l~~~~l~~~~  236 (570)
T 2z63_A          171 VLHQMPLLNLSLDLSLNPMNFI-------------QPGAFKEI-RLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGE  236 (570)
T ss_dssp             HHHTCTTCCCEEECTTCCCCEE-------------CTTTTTTC-EEEEEEEESCCSCTTHHHHHHHTTTTCEEEEEEEEE
T ss_pred             chhccchhhhhcccCCCCceec-------------CHHHhccC-cceeEecccccccccchhhhhcCccccceeeecccc
Confidence            55555    5666666655443             12222222 4666666655321  111111 34444443333211


Q ss_pred             CC---------CCCCCcccceEEeccc-ccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCC
Q 003090          463 LE---------ERPLSDFIGLFLQKFK-KRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGF  532 (848)
Q Consensus       463 ~~---------~~~~~~l~~l~l~~~~-~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l  532 (848)
                      ..         ......+..+.+.... ..+..+.        ...+.++. .+++|+.|++.++... .++..+  ..+
T Consensus       237 ~~~~~~l~~~~~~~~~~l~~l~l~~l~l~~~~~~~--------~~~~~~~~-~l~~L~~L~l~~~~l~-~l~~~~--~~~  304 (570)
T 2z63_A          237 FRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYL--------DDIIDLFN-CLTNVSSFSLVSVTIE-RVKDFS--YNF  304 (570)
T ss_dssp             CCCCSSCEECCTTTTGGGGGSEEEEEEEEETTEEE--------SCSTTTTG-GGTTCSEEEEESCEEC-SCCBCC--SCC
T ss_pred             ccCchhhhhcchhhhccccccchhhhhhhcchhhh--------hhchhhhc-CcCcccEEEecCccch-hhhhhh--ccC
Confidence            10         0001111111111111 0000000        11111111 2578999999887644 344444  345


Q ss_pred             CCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhh---hHH
Q 003090          533 NELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKIL---LSH  609 (848)
Q Consensus       533 ~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l---~~~  609 (848)
                       +|+.|++.+|... .+       +...+++|++|++.++....     ..+...+++|+.|++++|. + ...   |. 
T Consensus       305 -~L~~L~l~~n~~~-~l-------~~~~l~~L~~L~l~~n~~~~-----~~~~~~~~~L~~L~l~~n~-l-~~~~~~~~-  367 (570)
T 2z63_A          305 -GWQHLELVNCKFG-QF-------PTLKLKSLKRLTFTSNKGGN-----AFSEVDLPSLEFLDLSRNG-L-SFKGCCSQ-  367 (570)
T ss_dssp             -CCSEEEEESCBCS-SC-------CBCBCSSCCEEEEESCBSCC-----BCCCCBCTTCCEEECCSSC-C-BEEEEEEH-
T ss_pred             -CccEEeeccCccc-cc-------CcccccccCEEeCcCCcccc-----ccccccCCCCCEEeCcCCc-c-Cccccccc-
Confidence             8999999988543 22       22568999999999986322     2334679999999999975 3 333   33 


Q ss_pred             HHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccc
Q 003090          610 LVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELR  689 (848)
Q Consensus       610 ~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~  689 (848)
                      ....+++|++|++++|. +..++         ..+..+++|++|+++++.-....+..  .+..+++|++|++++|. +.
T Consensus       368 ~~~~~~~L~~L~l~~n~-l~~~~---------~~~~~l~~L~~L~l~~n~l~~~~~~~--~~~~l~~L~~L~l~~n~-l~  434 (570)
T 2z63_A          368 SDFGTTSLKYLDLSFNG-VITMS---------SNFLGLEQLEHLDFQHSNLKQMSEFS--VFLSLRNLIYLDISHTH-TR  434 (570)
T ss_dssp             HHHTCSCCCEEECCSCS-EEEEE---------EEEETCTTCCEEECTTSEEESCTTSC--TTTTCTTCCEEECTTSC-CE
T ss_pred             cccccCccCEEECCCCc-ccccc---------ccccccCCCCEEEccCCccccccchh--hhhcCCCCCEEeCcCCc-cc
Confidence            34789999999999986 44444         23678999999999997633322222  36789999999999985 44


Q ss_pred             ccccCccccccccceeeeccccccceeeeecC----CCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEe
Q 003090          690 QVFPANFGKKAAAEEMVLYRKRRDQIHIHATT----STSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVR  765 (848)
Q Consensus       690 ~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~----~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~  765 (848)
                      ...|..+..        +++|  +.+++.+|.    ..|..+..+++|+.|++++| +++.+++ ..+.++++|++|+++
T Consensus       435 ~~~~~~~~~--------l~~L--~~L~l~~n~l~~~~~p~~~~~l~~L~~L~l~~n-~l~~~~~-~~~~~l~~L~~L~l~  502 (570)
T 2z63_A          435 VAFNGIFNG--------LSSL--EVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC-QLEQLSP-TAFNSLSSLQVLNMA  502 (570)
T ss_dssp             ECCTTTTTT--------CTTC--CEEECTTCEEGGGEECSCCTTCTTCCEEECTTS-CCCEECT-TTTTTCTTCCEEECC
T ss_pred             ccchhhhhc--------CCcC--cEEECcCCcCccccchhhhhcccCCCEEECCCC-ccccCCh-hhhhcccCCCEEeCC
Confidence            444544433        2334  555555551    35677889999999999997 5777744 467899999999999


Q ss_pred             cccccceeecCCcccccccCCCccceecccccccccccccccccccCCCccc-cccccccceee
Q 003090          766 SCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFCSTAHHF-NFVFHLGQKIR  828 (848)
Q Consensus       766 ~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~~~~~~~~~-~~~~i~~~~~~  828 (848)
                      +|. +..++.  .   .+..       +++|++|+++++| +...|+....+ .|++.....+.
T Consensus       503 ~n~-l~~~~~--~---~~~~-------l~~L~~L~l~~N~-~~~~~~~~~~~~~wl~~~~~~~~  552 (570)
T 2z63_A          503 SNQ-LKSVPD--G---IFDR-------LTSLQKIWLHTNP-WDCSCPRIDYLSRWLNKNSQKEQ  552 (570)
T ss_dssp             SSC-CSCCCT--T---TTTT-------CTTCCEEECCSSC-BCCCTTTTHHHHHHHHHTGGGEE
T ss_pred             CCc-CCCCCH--H---Hhhc-------ccCCcEEEecCCc-ccCCCcchHHHHHHHHhccccCC
Confidence            994 555521  1   2222       7999999999988 66666666555 66655544443

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=99.97  E-value=2.2e-31  Score=309.82  Aligned_cols=500  Identities=17%  Similarity=0.110  Sum_probs=315.4

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCC-cc-cccccceeecccCcCcccChHHHccCCceeEEEccCccccccccc
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPD-EL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~-~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      .++..++..+..  .++.|++++|.++.+++ .+ ++++|++|++++|.+..+++..|.++++|++|++++         
T Consensus        22 ~~l~~iP~~l~~--~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~---------   90 (606)
T 3t6q_A           22 LGLNEIPGTLPN--STECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQIYWIHEDTFQSQHRLDTLVLTA---------   90 (606)
T ss_dssp             SCCSSCCTTSCT--TCCEEECTTCCCSEECTTTSTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTT---------
T ss_pred             CCcccCcCCCCC--cCcEEEccCCccCcCChhHhccCccceEEECCCCccceeChhhccCccccCeeeCCC---------
Confidence            344555555544  46889999999998854 44 899999999999988888776688999999999999         


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCcccC-hhhccCCcccEEecc
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLT  375 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~  375 (848)
                           +.+...    .|..++.+++|++|++++|.+... +..++++++|++|++++|.+..++ ..+..+++|++|+++
T Consensus        91 -----n~l~~~----~~~~~~~l~~L~~L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~  161 (606)
T 3t6q_A           91 -----NPLIFM----AETALSGPKALKHLFFIQTGISSIDFIPLHNQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDFQ  161 (606)
T ss_dssp             -----CCCSEE----CTTTTSSCTTCCEEECTTSCCSCGGGSCCTTCTTCCEEECCSSCCCCCCCCTTCCCTTCCEEECC
T ss_pred             -----Cccccc----ChhhhcccccccEeeccccCcccCCcchhccCCcccEEECCCCcccccCcccccCCcccCEEEcc
Confidence                 777774    577889999999999999987776 367889999999999999988652 234458999999999


Q ss_pred             CCccccccChhhhhcccccc--EEeccccccccccccccccc--------------------------------------
Q 003090          376 GCYILELIPRGVLSRLRKLE--ELYMSHSFRHWQFESESEED--------------------------------------  415 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~--~L~l~~~~~~~~~~~~~~~~--------------------------------------  415 (848)
                      +|.... ++...++.+++|+  .|++++|.+....++.-...                                      
T Consensus       162 ~n~l~~-~~~~~~~~l~~L~~l~L~l~~n~l~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~l~~~~~~~~~~  240 (606)
T 3t6q_A          162 NNAIHY-LSKEDMSSLQQATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDMDD  240 (606)
T ss_dssp             SSCCCE-ECHHHHHTTTTCCSEEEECTTCCCCEECTTTTTTCEEEEEECTTCSCHHHHHHHTTTCEEEEEECCCCTTSCC
T ss_pred             cCcccc-cChhhhhhhcccceeEEecCCCccCccChhHhhhccccccccCCchhHHHHhhhccccchhheechhhccccc
Confidence            986654 4444488899998  88888888766533210000                                      


Q ss_pred             -cCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccc
Q 003090          416 -SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQD  492 (848)
Q Consensus       416 -~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~  492 (848)
                       .-....+..+..+ +|+.|++++|.+..++...  .+++|+.|++..+...                            
T Consensus       241 ~~i~~~~~~~l~~~-~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~----------------------------  291 (606)
T 3t6q_A          241 EDISPAVFEGLCEM-SVESINLQKHYFFNISSNTFHCFSGLQELDLTATHLS----------------------------  291 (606)
T ss_dssp             CCCCGGGGGGGGGS-EEEEEECTTCCCSSCCTTTTTTCTTCSEEECTTSCCS----------------------------
T ss_pred             cccChhHhchhhcC-ceeEEEeecCccCccCHHHhccccCCCEEeccCCccC----------------------------
Confidence             0000111111111 6778888888877777653  7788888887754431                            


Q ss_pred             cchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccc
Q 003090          493 MRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIREN  572 (848)
Q Consensus       493 ~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~  572 (848)
                          .+|.++. .+++|++|+++++......+..+  ..+++|++|++.++.....++    ......+++|++|+++++
T Consensus       292 ----~lp~~l~-~l~~L~~L~l~~n~l~~~~~~~~--~~l~~L~~L~l~~n~~~~~~~----~~~~~~l~~L~~L~l~~n  360 (606)
T 3t6q_A          292 ----ELPSGLV-GLSTLKKLVLSANKFENLCQISA--SNFPSLTHLSIKGNTKRLELG----TGCLENLENLRELDLSHD  360 (606)
T ss_dssp             ----CCCSSCC-SCTTCCEEECTTCCCSBGGGGCG--GGCTTCSEEECCSCSSCCBCC----SSTTTTCTTCCEEECCSS
T ss_pred             ----CCChhhc-ccccCCEEECccCCcCcCchhhh--hccCcCCEEECCCCCcccccc----hhhhhccCcCCEEECCCC
Confidence                0110000 03567777777665443323222  456777777777775432221    112445677777777776


Q ss_pred             cccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCE
Q 003090          573 QNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEK  652 (848)
Q Consensus       573 ~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~  652 (848)
                      . ++.+.......+.+++|++|++++|. + ..+++..+..+++|++|++++|.-....+.        ..+..+++|++
T Consensus       361 ~-l~~~~~~~~~~~~l~~L~~L~l~~n~-l-~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~--------~~~~~l~~L~~  429 (606)
T 3t6q_A          361 D-IETSDCCNLQLRNLSHLQSLNLSYNE-P-LSLKTEAFKECPQLELLDLAFTRLKVKDAQ--------SPFQNLHLLKV  429 (606)
T ss_dssp             C-CCEEEESTTTTTTCTTCCEEECCSCS-C-EEECTTTTTTCTTCSEEECTTCCEECCTTC--------CTTTTCTTCCE
T ss_pred             c-cccccCcchhcccCCCCCEEECCCCc-C-CcCCHHHhcCCccCCeEECCCCcCCCcccc--------hhhhCcccCCE
Confidence            3 33321111223457777777777764 3 233332335677777777777643222211        23556777777


Q ss_pred             EecCCCccccccccCCCccccccCccEEEeecCccccccccC--ccccccccceeeeccccccceeeeecC---CCCCCC
Q 003090          653 LTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPA--NFGKKAAAEEMVLYRKRRDQIHIHATT---STSSPT  727 (848)
Q Consensus       653 L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~--~~~~~~~~~~l~l~~l~~~~l~i~~c~---~~~~~~  727 (848)
                      |++++|. +......  .+..+++|++|++++|.--...+|.  .+..        +++|  +.+++++|.   ..+..+
T Consensus       430 L~l~~n~-l~~~~~~--~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~--------l~~L--~~L~Ls~n~l~~~~~~~~  496 (606)
T 3t6q_A          430 LNLSHSL-LDISSEQ--LFDGLPALQHLNLQGNHFPKGNIQKTNSLQT--------LGRL--EILVLSFCDLSSIDQHAF  496 (606)
T ss_dssp             EECTTCC-CBTTCTT--TTTTCTTCCEEECTTCBCGGGEECSSCGGGG--------CTTC--CEEECTTSCCCEECTTTT
T ss_pred             EECCCCc-cCCcCHH--HHhCCCCCCEEECCCCCCCccccccchhhcc--------CCCc--cEEECCCCccCccChhhh
Confidence            7777764 3322221  2456777777777776522211111  1111        2333  444444441   124567


Q ss_pred             CCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccccccccccc
Q 003090          728 PSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSL  807 (848)
Q Consensus       728 ~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L  807 (848)
                      ..+++|+.|++++| +++..++ ..+.++++| +|++++|. +..++.  .   .+.       .+++|+.|+++++| +
T Consensus       497 ~~l~~L~~L~Ls~N-~l~~~~~-~~l~~l~~L-~L~L~~N~-l~~~~~--~---~~~-------~l~~L~~L~l~~N~-~  559 (606)
T 3t6q_A          497 TSLKMMNHVDLSHN-RLTSSSI-EALSHLKGI-YLNLASNH-ISIILP--S---LLP-------ILSQQRTINLRQNP-L  559 (606)
T ss_dssp             TTCTTCCEEECCSS-CCCGGGG-GGGTTCCSC-EEECCSSC-CCCCCG--G---GHH-------HHHTSSEEECTTCC-E
T ss_pred             ccccCCCEEECCCC-ccCcCCh-hHhCccccc-EEECcCCc-ccccCH--h---hcc-------cCCCCCEEeCCCCC-c
Confidence            78899999999996 5766644 567889999 99999985 333311  1   121       27899999999998 6


Q ss_pred             ccccCCCccccccc
Q 003090          808 ACFCSTAHHFNFVF  821 (848)
Q Consensus       808 ~~~~~~~~~~~~~~  821 (848)
                      ...|.....+.|++
T Consensus       560 ~c~c~~~~~~~w~~  573 (606)
T 3t6q_A          560 DCTCSNIYFLEWYK  573 (606)
T ss_dssp             ECSGGGHHHHHHHH
T ss_pred             cccCCcHHHHHHHH
Confidence            66665444444544

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.97  E-value=4.2e-30  Score=303.25  Aligned_cols=147  Identities=22%  Similarity=0.242  Sum_probs=65.3

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchh
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL  317 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~  317 (848)
                      ++.+++.++.+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+...    .|..+
T Consensus         9 ~~cs~~~L~~ip~~~~-~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~--------------n~l~~~----~~~~~   69 (680)
T 1ziw_A            9 ADCSHLKLTQVPDDLP-TNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGF--------------NTISKL----EPELC   69 (680)
T ss_dssp             EECCSSCCSSCCSCSC-TTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCS--------------SCCCCC----CTTHH
T ss_pred             eECCCCCccccccccC-CCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCC--------------CccCcc----CHHHH
Confidence            3444444444444332 3444444444444444444344444444444444              344432    33444


Q ss_pred             hhcccCcEEEccCccccCCch-hhccccCCCEEEccCCCCcccC-hhhccCCcccEEeccCCccccccChhhhhcccccc
Q 003090          318 SFLINLRTLRLHDRRIQGDLS-LIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE  395 (848)
Q Consensus       318 ~~l~~L~~L~L~~~~~~~~~~-~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~  395 (848)
                      +++++|++|++++|.+...++ .++++++|++|++++|.+..+| ..++++++|++|++++|...+..|.. ++++++|+
T Consensus        70 ~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~-~~~l~~L~  148 (680)
T 1ziw_A           70 QKLPMLKVLNLQHNELSQLSDKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGT-QVQLENLQ  148 (680)
T ss_dssp             HHCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCS-SSCCTTCC
T ss_pred             hcccCcCEEECCCCccCccChhhhccCCCCCEEECCCCccCccChhHccccCCCCEEECCCCcccccCchh-hcccccCC
Confidence            444444444444444443332 3444444444444444444333 23444444444444444433332322 34444444


Q ss_pred             EEecccccc
Q 003090          396 ELYMSHSFR  404 (848)
Q Consensus       396 ~L~l~~~~~  404 (848)
                      +|++++|.+
T Consensus       149 ~L~L~~n~l  157 (680)
T 1ziw_A          149 ELLLSNNKI  157 (680)
T ss_dssp             EEECCSSCC
T ss_pred             EEEccCCcc
Confidence            444444443

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=99.97  E-value=3.4e-30  Score=299.79  Aligned_cols=192  Identities=17%  Similarity=0.125  Sum_probs=162.6

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ..++.++..+..+|..+. +.+++|++++|.+..+++..|.++++|++|++++              +.+...    .|.
T Consensus        15 ~~~~c~~~~l~~iP~~l~-~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~--------------n~i~~~----~~~   75 (606)
T 3t6q_A           15 KTYNCENLGLNEIPGTLP-NSTECLEFSFNVLPTIQNTTFSRLINLTFLDLTR--------------CQIYWI----HED   75 (606)
T ss_dssp             TEEECTTSCCSSCCTTSC-TTCCEEECTTCCCSEECTTTSTTCTTCSEEECTT--------------CCCCEE----CTT
T ss_pred             ceEECCCCCcccCcCCCC-CcCcEEEccCCccCcCChhHhccCccceEEECCC--------------Ccccee----Chh
Confidence            356777888999998774 4799999999999999777789999999999999              788774    688


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCcccc-ccChhhhhccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILE-LIPRGVLSRLR  392 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~-~~p~~~l~~l~  392 (848)
                      .|+++++|++|++++|.+...+ ..++++++|++|++++|.++.+ |..++++++|++|++++|...+ ..|.  +..++
T Consensus        76 ~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~--~~~l~  153 (606)
T 3t6q_A           76 TFQSQHRLDTLVLTANPLIFMAETALSGPKALKHLFFIQTGISSIDFIPLHNQKTLESLYLGSNHISSIKLPK--GFPTE  153 (606)
T ss_dssp             TTTTCTTCCEEECTTCCCSEECTTTTSSCTTCCEEECTTSCCSCGGGSCCTTCTTCCEEECCSSCCCCCCCCT--TCCCT
T ss_pred             hccCccccCeeeCCCCcccccChhhhcccccccEeeccccCcccCCcchhccCCcccEEECCCCcccccCccc--ccCCc
Confidence            8999999999999999887764 7899999999999999999977 5679999999999999987765 2344  55699


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCc--EEEeeccCCCCCCCCC-ccCCCCeEEEEeC
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLT--SLHIHIPEGKIMPSDM-SFQNLTSFSIAIG  461 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~--~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~  461 (848)
                      +|++|++++|.+...             .+..++.+++|+  .|++++|.+..++... ...+|+.|++..+
T Consensus       154 ~L~~L~L~~n~l~~~-------------~~~~~~~l~~L~~l~L~l~~n~l~~~~~~~~~~~~L~~L~l~~~  212 (606)
T 3t6q_A          154 KLKVLDFQNNAIHYL-------------SKEDMSSLQQATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFGGT  212 (606)
T ss_dssp             TCCEEECCSSCCCEE-------------CHHHHHTTTTCCSEEEECTTCCCCEECTTTTTTCEEEEEECTTC
T ss_pred             ccCEEEcccCccccc-------------ChhhhhhhcccceeEEecCCCccCccChhHhhhccccccccCCc
Confidence            999999999988765             567788899999  8999999988776655 6667888877644

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.97  E-value=3.1e-29  Score=295.77  Aligned_cols=524  Identities=17%  Similarity=0.152  Sum_probs=255.0

Q ss_pred             CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.|++++|.+..+|.. + .+++|++|++++|.+..+++..|.++++|++|++++              +.+..    
T Consensus        26 ~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~--------------n~l~~----   87 (680)
T 1ziw_A           26 NITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQH--------------NELSQ----   87 (680)
T ss_dssp             TCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSSCCCCCCTTHHHHCTTCCEEECCS--------------SCCCC----
T ss_pred             CCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCCccCccCHHHHhcccCcCEEECCC--------------CccCc----
Confidence            466777777777776654 3 677777777777777666666667777777777777              66665    


Q ss_pred             CCCc-hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhh
Q 003090          312 LLPS-SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       312 ~lp~-~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                       +|. .++++++|++|++++|.+...+ ..++++++|++|++++|.++.. |..++++++|++|++++|...+ ++...+
T Consensus        88 -l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~  165 (680)
T 1ziw_A           88 -LSDKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNKIQA-LKSEEL  165 (680)
T ss_dssp             -CCTTTTTTCTTCSEEECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSCCCC-BCHHHH
T ss_pred             -cChhhhccCCCCCEEECCCCccCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCCcccc-cCHHHh
Confidence             554 4677777777777777665555 4567777777777777766633 4456667777777777765443 333223


Q ss_pred             h--ccccccEEeccccccccccccc----ccc----------------------------------ccCcccchhhhccc
Q 003090          389 S--RLRKLEELYMSHSFRHWQFESE----SEE----------------------------------DSSSNAKFIELGAL  428 (848)
Q Consensus       389 ~--~l~~L~~L~l~~~~~~~~~~~~----~~~----------------------------------~~~~~~~~~~L~~l  428 (848)
                      .  .+++|++|++++|.+....+..    ...                                  ..-....+..+..+
T Consensus       166 ~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~~~l~~~~~~~~~~~l~~~~L~~L~L~~n~l~~~~~~~~~~l  245 (680)
T 1ziw_A          166 DIFANSSLKKLELSSNQIKEFSPGCFHAIGRLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGL  245 (680)
T ss_dssp             GGGTTCEESEEECTTCCCCCBCTTGGGGSSEECEEECTTCCCHHHHHHHHHHHHTTSCCCEEECTTSCCCEECTTTTGGG
T ss_pred             hccccccccEEECCCCcccccChhhhhhhhhhhhhhccccccChhhHHHHHHHhhhccccEEEccCCcccccChhHhhcc
Confidence            3  3466777777766554432210    000                                  00000112233333


Q ss_pred             C--CCcEEEeeccCCCCCCCC-C-ccCCCCeEEEEeCCC------CCCCCCcccceEEeccc-ccccccccCccccchhh
Q 003090          429 S--RLTSLHIHIPEGKIMPSD-M-SFQNLTSFSIAIGDL------EERPLSDFIGLFLQKFK-KRCSRAMGLSQDMRISA  497 (848)
Q Consensus       429 ~--~L~~L~l~~~~~~~~~~~-~-~~~~L~~L~l~~~~~------~~~~~~~l~~l~l~~~~-~~c~~~~~l~~~~~l~~  497 (848)
                      +  +|+.|++++|.+..++.. + .+++|+.|++..+..      +....+.++.+.+.... .....+..+      ..
T Consensus       246 ~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~l------p~  319 (680)
T 1ziw_A          246 KWTNLTMLDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASL------PK  319 (680)
T ss_dssp             GGSCCCEEECTTSCCCEECTTTTTTCTTCCEEECCSCCBSEECTTTTTTCTTCCEEECTTCBCCC------C------CE
T ss_pred             CcCCCCEEECCCCCcCccCcccccCcccccEeeCCCCccCccChhhhcCCCCccEEeccchhhhcccccccc------cc
Confidence            2  366666666665544332 2 556666666654433      22233344444443210 000000000      00


Q ss_pred             HHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCC-ceeecccccccccccCCCccEEecccccccc
Q 003090          498 LHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNE-MKYLLNSLERTLRVTLHKLEWLFIRENQNFV  576 (848)
Q Consensus       498 l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~-l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~  576 (848)
                      ++......+++|++|+++++.........+  ..+++|++|++.+|.. ...++.. .+ .....++|+.|+++++. +.
T Consensus       320 i~~~~~~~l~~L~~L~l~~n~l~~~~~~~~--~~l~~L~~L~Ls~n~~~~~~l~~~-~f-~~~~~~~L~~L~L~~n~-l~  394 (680)
T 1ziw_A          320 IDDFSFQWLKCLEHLNMEDNDIPGIKSNMF--TGLINLKYLSLSNSFTSLRTLTNE-TF-VSLAHSPLHILNLTKNK-IS  394 (680)
T ss_dssp             ECTTTTTTCTTCCEEECCSCCBCCCCTTTT--TTCTTCCEEECTTCBSCCCEECTT-TT-GGGTTSCCCEEECTTSC-CC
T ss_pred             cChhhcccCCCCCEEECCCCccCCCChhHh--ccccCCcEEECCCCchhhhhcchh-hh-cccccCcCceEECCCCC-CC
Confidence            000001114667777777665443222222  3567777777776641 2221100 00 00112456666666653 33


Q ss_pred             cccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecc------------------ccc
Q 003090          577 EICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIE------------------RVN  638 (848)
Q Consensus       577 ~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~------------------~~~  638 (848)
                      .+..  .....+++|+.|++++|.-. ..+|...+..+++|++|++++|. +..++...                  ...
T Consensus       395 ~~~~--~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~~~~L~~L~l~~n~l~~~~  470 (680)
T 1ziw_A          395 KIES--DAFSWLGHLEVLDLGLNEIG-QELTGQEWRGLENIFEIYLSYNK-YLQLTRNSFALVPSLQRLMLRRVALKNVD  470 (680)
T ss_dssp             EECT--TTTTTCTTCCEEECCSSCCE-EECCSGGGTTCTTCCEEECCSCS-EEECCTTTTTTCTTCCEEECTTSCCBCTT
T ss_pred             eECh--hhhhCCCCCCEEeCCCCcCc-cccCcccccCcccccEEecCCCC-cceeChhhhhcCcccccchhccccccccc
Confidence            3211  11224666666666665433 33443333556666666666654 22221100                  000


Q ss_pred             cccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeee
Q 003090          639 IAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIH  718 (848)
Q Consensus       639 ~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~  718 (848)
                      .....+..+++|++|+++++. ++.++...  +..+++|+.|+++++. ++.+.+..........--.+.+|  +.+++.
T Consensus       471 ~~p~~~~~l~~L~~L~Ls~N~-l~~i~~~~--~~~l~~L~~L~Ls~N~-l~~~~~~~~~~~~~~~~~~l~~L--~~L~L~  544 (680)
T 1ziw_A          471 SSPSPFQPLRNLTILDLSNNN-IANINDDM--LEGLEKLEILDLQHNN-LARLWKHANPGGPIYFLKGLSHL--HILNLE  544 (680)
T ss_dssp             CSSCTTTTCTTCCEEECCSSC-CCCCCTTT--TTTCTTCCEEECCSSC-CGGGGSTTSTTSCCCTTTTCTTC--CEEECC
T ss_pred             cCCcccccCCCCCEEECCCCC-CCcCChhh--hccccccCEEeCCCCC-ccccchhhccCCcchhhcCCCCC--CEEECC
Confidence            001233444555555555432 33333221  3445555555555542 22221100000000000001223  333333


Q ss_pred             ec--CCCCC-CCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccc
Q 003090          719 AT--TSTSS-PTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPS  795 (848)
Q Consensus       719 ~c--~~~~~-~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~s  795 (848)
                      ++  ...+. .+..+++|+.|++++ ++++.+|+ ..+.++++|++|+++++ .+..+...     .+.      ..+++
T Consensus       545 ~N~l~~i~~~~~~~l~~L~~L~Ls~-N~l~~l~~-~~~~~l~~L~~L~L~~N-~l~~~~~~-----~~~------~~~~~  610 (680)
T 1ziw_A          545 SNGFDEIPVEVFKDLFELKIIDLGL-NNLNTLPA-SVFNNQVSLKSLNLQKN-LITSVEKK-----VFG------PAFRN  610 (680)
T ss_dssp             SSCCCCCCTTTTTTCTTCCEEECCS-SCCCCCCT-TTTTTCTTCCEEECTTS-CCCBCCHH-----HHH------HHHTT
T ss_pred             CCCCCCCCHHHcccccCcceeECCC-CCCCcCCH-hHhCCCCCCCEEECCCC-cCCccChh-----Hhc------ccccc
Confidence            33  12222 345666777777765 45666644 34566677777777776 34443110     000      02688


Q ss_pred             ccccccccccccccccCC
Q 003090          796 LFGIKLCDLDSLACFCST  813 (848)
Q Consensus       796 L~~L~i~~cp~L~~~~~~  813 (848)
                      |+.|++.++| +...|..
T Consensus       611 L~~l~l~~N~-~~c~c~~  627 (680)
T 1ziw_A          611 LTELDMRFNP-FDCTCES  627 (680)
T ss_dssp             CSEEECTTCC-CCBCCCC
T ss_pred             cCEEEccCCC-cccCCcc
Confidence            9999998877 5555553

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.97  E-value=2.7e-30  Score=296.96  Aligned_cols=478  Identities=15%  Similarity=0.131  Sum_probs=268.5

Q ss_pred             eecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhh
Q 003090          240 LMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSF  319 (848)
Q Consensus       240 l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~  319 (848)
                      .+++.++.+|..+. ++|++|++++|.+..+++..|.++++|++|++++              +.+...    .|..++.
T Consensus        12 ~~~~~l~~ip~~~~-~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~--------------n~i~~~----~~~~~~~   72 (549)
T 2z81_A           12 GRSRSFTSIPSGLT-AAMKSLDLSFNKITYIGHGDLRACANLQVLILKS--------------SRINTI----EGDAFYS   72 (549)
T ss_dssp             CTTSCCSSCCSCCC-TTCCEEECCSSCCCEECSSTTSSCTTCCEEECTT--------------SCCCEE----CTTTTTT
T ss_pred             CCCCccccccccCC-CCccEEECcCCccCccChhhhhcCCcccEEECCC--------------CCcCcc----Chhhccc
Confidence            34455555555443 4555555555555555443345555555555555              444442    3344555


Q ss_pred             cccCcEEEccCccccCCch-hhccccCCCEEEccCCCCcc--cChhhccCCcccEEeccCCccccccChhhhhccccccE
Q 003090          320 LINLRTLRLHDRRIQGDLS-LIGELSGLEILDLSESDVSE--IPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEE  396 (848)
Q Consensus       320 l~~L~~L~L~~~~~~~~~~-~i~~l~~L~~L~l~~~~l~~--lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~  396 (848)
                      +++|++|++++|.+...++ .++++++|++|++++|.++.  .|..++++++|++|++++|...+.+|...+.++++|++
T Consensus        73 l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~  152 (549)
T 2z81_A           73 LGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNE  152 (549)
T ss_dssp             CTTCCEEECTTSCCCSCCHHHHTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEE
T ss_pred             cccCCEEECCCCccCccCHHHhccCCCCcEEECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCe
Confidence            5555555555555555442 35555555555555555552  34455555555555555555444454333555555555


Q ss_pred             EeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCCCC---------
Q 003090          397 LYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEE---------  465 (848)
Q Consensus       397 L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~~~---------  465 (848)
                      |++++|.+...             .+..++.+++|++|+++++....++...  .+++|+.|++..+....         
T Consensus       153 L~L~~n~l~~~-------------~~~~l~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~  219 (549)
T 2z81_A          153 LEIKALSLRNY-------------QSQSLKSIRDIHHLTLHLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVD  219 (549)
T ss_dssp             EEEEETTCCEE-------------CTTTTTTCSEEEEEEEECSBSTTHHHHHHHSTTTBSEEEEESCBCTTCCCCCCSSC
T ss_pred             eeccCCccccc-------------ChhhhhccccCceEecccCcccccchhhHhhcccccEEEccCCccccccccccchh
Confidence            55555555443             3344555555555555555544443332  34555555555433211         


Q ss_pred             CCCCcccceEEecccccccccccCccccchhhHHHHHH---HHHhhcceeeecccccccc--ccc--cccccCCCCCcEE
Q 003090          466 RPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIK---NLLLRSEILALAEVNYFEN--IVS--DLANDGFNELMFL  538 (848)
Q Consensus       466 ~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~---~~~~~L~~L~l~~~~~~~~--~~~--~l~~~~l~~L~~L  538 (848)
                      .....++.+.+.+..     +        -...+..+.   ..+++|+.+.+.+|.....  +..  .-....+++|+.|
T Consensus       220 ~~~~~L~~L~l~~n~-----l--------~~~~~~~l~~~~~~~~~L~~l~l~~~~~~~~~~~~~~~~~~~~~l~~L~~L  286 (549)
T 2z81_A          220 EVSSPMKKLAFRGSV-----L--------TDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETV  286 (549)
T ss_dssp             CCCCCCCEEEEESCE-----E--------EHHHHHHHHGGGGGCTTCCEEEEESCEEECCSCCCCCTTTCCCCCTTCCEE
T ss_pred             hhhhcccceeccccc-----c--------chhHHHHHHHHhhhhccccccccccccccccccccccchhhhhhhcccccc
Confidence            012223333333221     0        011111111   1246788888887764321  100  0012457888999


Q ss_pred             EEecCCCceeeccccccc-ccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHH--HHhhc
Q 003090          539 VIFRCNEMKYLLNSLERT-LRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHL--VQSFQ  615 (848)
Q Consensus       539 ~l~~~~~l~~l~~~~~~~-~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~--~~~l~  615 (848)
                      .+.++..-... ...... ....+++|++|+++++. ++.+....  ...+++|+.|++++|.-. ..+|...  ...++
T Consensus       287 ~l~~~~i~~~~-~~~~l~~~~~~~~~L~~L~l~~n~-l~~ip~~~--~~~l~~L~~L~Ls~N~l~-~~~~~~~~~~~~l~  361 (549)
T 2z81_A          287 TIRRLHIPQFY-LFYDLSTVYSLLEKVKRITVENSK-VFLVPCSF--SQHLKSLEFLDLSENLMV-EEYLKNSACKGAWP  361 (549)
T ss_dssp             EEESCBCSCGG-GSCCCCHHHHHSTTCCEEEEESSC-CCCCCHHH--HHHCTTCCEEECCSSCCC-HHHHHHHTCTTSST
T ss_pred             cccccccchhh-hcccchhhhhhcccceEEEeccCc-cccCCHHH--HhcCccccEEEccCCccc-cccccchhhhhccc
Confidence            98877432110 000000 12345789999999874 54331110  124889999999998655 5554321  25678


Q ss_pred             cCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCc
Q 003090          616 NLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPAN  695 (848)
Q Consensus       616 ~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~  695 (848)
                      +|++|++++|. ++.++..      ...+..+++|++|++++| +++.+|..   +..+++|+.|++++|. ++.+ |..
T Consensus       362 ~L~~L~Ls~N~-l~~~~~~------~~~~~~l~~L~~L~Ls~N-~l~~lp~~---~~~~~~L~~L~Ls~N~-l~~l-~~~  428 (549)
T 2z81_A          362 SLQTLVLSQNH-LRSMQKT------GEILLTLKNLTSLDISRN-TFHPMPDS---CQWPEKMRFLNLSSTG-IRVV-KTC  428 (549)
T ss_dssp             TCCEEECTTSC-CCCHHHH------HHHGGGCTTCCEEECTTC-CCCCCCSC---CCCCTTCCEEECTTSC-CSCC-CTT
T ss_pred             cCcEEEccCCc-ccccccc------hhhhhcCCCCCEEECCCC-CCccCChh---hcccccccEEECCCCC-cccc-cch
Confidence            99999999874 4433210      023668899999999997 57777654   5678999999999985 5442 322


Q ss_pred             cccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeec
Q 003090          696 FGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIM  775 (848)
Q Consensus       696 ~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~  775 (848)
                      ..          .++  +.+++.+| .+......+++|++|++++| +++.+|.   ...+++|++|++++|. ++.++.
T Consensus       429 ~~----------~~L--~~L~Ls~N-~l~~~~~~l~~L~~L~Ls~N-~l~~ip~---~~~l~~L~~L~Ls~N~-l~~~~~  490 (549)
T 2z81_A          429 IP----------QTL--EVLDVSNN-NLDSFSLFLPRLQELYISRN-KLKTLPD---ASLFPVLLVMKISRNQ-LKSVPD  490 (549)
T ss_dssp             SC----------TTC--SEEECCSS-CCSCCCCCCTTCCEEECCSS-CCSSCCC---GGGCTTCCEEECCSSC-CCCCCT
T ss_pred             hc----------CCc--eEEECCCC-ChhhhcccCChhcEEECCCC-ccCcCCC---cccCccCCEEecCCCc-cCCcCH
Confidence            21          233  55666665 23333468899999999996 7888864   3578999999999984 555421


Q ss_pred             CCcccccccCCCccceeccccccccccccccccccc
Q 003090          776 DDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFC  811 (848)
Q Consensus       776 ~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~~~  811 (848)
                        .   .+..       +++|+.|++.++| +...|
T Consensus       491 --~---~~~~-------l~~L~~L~l~~N~-~~~~~  513 (549)
T 2z81_A          491 --G---IFDR-------LTSLQKIWLHTNP-WDCSC  513 (549)
T ss_dssp             --T---GGGG-------CTTCCEEECCSSC-BCCCH
T ss_pred             --H---HHhc-------CcccCEEEecCCC-ccCCC
Confidence              1   1222       7899999999988 44433

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.97  E-value=1.4e-30  Score=300.93  Aligned_cols=171  Identities=23%  Similarity=0.287  Sum_probs=138.3

Q ss_pred             EEEEEeccCCchhHHHH-HHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEcc
Q 003090          211 VAMAVVSQTPSITKIQY-EIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLG  287 (848)
Q Consensus       211 ~~wv~vs~~~~~~~l~~-~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~  287 (848)
                      ...+.++.. .+..+.. .+.....++.|++++|.+..++...  .+++|++|++++|.+..+++..|.++++|++|+++
T Consensus        30 l~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~  108 (570)
T 2z63_A           30 TKNLDLSFN-PLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAV  108 (570)
T ss_dssp             CCEEECCSC-CCCEECTTTTTTCSSCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECT
T ss_pred             ccEEEccCC-ccCccChhHhhCCCCceEEECCCCcCCccCcccccCchhCCEEeCcCCcCCccCHhhhcCcccccccccc
Confidence            344556553 3444432 4555667999999999999887653  89999999999999999987778999999999999


Q ss_pred             CcccccccccCCCCCCCCCCCCCCCCCc-hhhhcccCcEEEccCccccC--CchhhccccCCCEEEccCCCCcccC-hhh
Q 003090          288 GIRRFSFSVRFPFLFPPLPSSPLFLLPS-SLSFLINLRTLRLHDRRIQG--DLSLIGELSGLEILDLSESDVSEIP-VSF  363 (848)
Q Consensus       288 ~~~~~~~~~~~~~~~~~l~~~~~~~lp~-~~~~l~~L~~L~L~~~~~~~--~~~~i~~l~~L~~L~l~~~~l~~lp-~~i  363 (848)
                      +              +.+..     +|. .++.+++|++|++++|.+..  .+..++++++|++|++++|.++.++ ..+
T Consensus       109 ~--------------n~l~~-----l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n~l~~~~~~~~  169 (570)
T 2z63_A          109 E--------------TNLAS-----LENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDL  169 (570)
T ss_dssp             T--------------SCCCC-----STTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTSCCCEECGGGG
T ss_pred             c--------------ccccc-----CCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcCCccceecHHHc
Confidence            9              88887     554 68999999999999998876  3688999999999999999999664 568


Q ss_pred             ccCCcc----cEEeccCCccccccChhhhhccccccEEeccccc
Q 003090          364 GRLSHL----RLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       364 ~~L~~L----~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~  403 (848)
                      +.+.+|    ++|++++|.... ++.+.+..+ +|+.|++++|.
T Consensus       170 ~~l~~L~~~~~~L~l~~n~l~~-~~~~~~~~~-~L~~L~l~~n~  211 (570)
T 2z63_A          170 RVLHQMPLLNLSLDLSLNPMNF-IQPGAFKEI-RLHKLTLRNNF  211 (570)
T ss_dssp             HHHHTCTTCCCEEECTTCCCCE-ECTTTTTTC-EEEEEEEESCC
T ss_pred             cchhccchhhhhcccCCCCcee-cCHHHhccC-cceeEeccccc
Confidence            888888    899999987655 444435544 89999998874

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.97  E-value=3.4e-29  Score=287.83  Aligned_cols=467  Identities=17%  Similarity=0.193  Sum_probs=330.1

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCC-cc-cccccceeecccCcCcccChHHHccCCceeEEEccCccccccccc
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPD-EL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~-~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      ..+..++..+.  ..++.|++++|.+..+++ .+ .+++|++|++++|.+..+++..|.++++|++|++++         
T Consensus        15 ~~l~~ip~~~~--~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~---------   83 (549)
T 2z81_A           15 RSFTSIPSGLT--AAMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSD---------   83 (549)
T ss_dssp             SCCSSCCSCCC--TTCCEEECCSSCCCEECSSTTSSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTT---------
T ss_pred             CccccccccCC--CCccEEECcCCccCccChhhhhcCCcccEEECCCCCcCccChhhccccccCCEEECCC---------
Confidence            34444444433  357999999999998864 44 899999999999999998877789999999999999         


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC--chhhccccCCCEEEccCCC-CcccC-hhhccCCcccEEe
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD--LSLIGELSGLEILDLSESD-VSEIP-VSFGRLSHLRLLD  373 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~--~~~i~~l~~L~~L~l~~~~-l~~lp-~~i~~L~~L~~L~  373 (848)
                           +.+.+.    .|..++.+++|++|++++|.+...  +..++++++|++|++++|. +..+| ..++++++|++|+
T Consensus        84 -----n~l~~~----~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~  154 (549)
T 2z81_A           84 -----NHLSSL----SSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELE  154 (549)
T ss_dssp             -----SCCCSC----CHHHHTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEE
T ss_pred             -----CccCcc----CHHHhccCCCCcEEECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeee
Confidence                 888883    344599999999999999988753  4789999999999999997 66777 5799999999999


Q ss_pred             ccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCC---CCC--
Q 003090          374 LTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMP---SDM--  448 (848)
Q Consensus       374 l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~---~~~--  448 (848)
                      +++|...+..|.. ++++++|++|++++|.....             ....++.+++|+.|++++|.+...+   ..+  
T Consensus       155 L~~n~l~~~~~~~-l~~l~~L~~L~l~~n~~~~~-------------~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~  220 (549)
T 2z81_A          155 IKALSLRNYQSQS-LKSIRDIHHLTLHLSESAFL-------------LEIFADILSSVRYLELRDTNLARFQFSPLPVDE  220 (549)
T ss_dssp             EEETTCCEECTTT-TTTCSEEEEEEEECSBSTTH-------------HHHHHHSTTTBSEEEEESCBCTTCCCCCCSSCC
T ss_pred             ccCCcccccChhh-hhccccCceEecccCccccc-------------chhhHhhcccccEEEccCCccccccccccchhh
Confidence            9999888778877 89999999999998876432             1123456899999999999987653   222  


Q ss_pred             ccCCCCeEEEEeCCC----------CCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeecccc
Q 003090          449 SFQNLTSFSIAIGDL----------EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVN  518 (848)
Q Consensus       449 ~~~~L~~L~l~~~~~----------~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~  518 (848)
                      .+++|+.|.+..+..          .......++.+.+....  -.....+... ...     ....+++++.|.+.++.
T Consensus       221 ~~~~L~~L~l~~n~l~~~~~~~l~~~~~~~~~L~~l~l~~~~--~~~~~~~~~~-~~~-----~~~~l~~L~~L~l~~~~  292 (549)
T 2z81_A          221 VSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEVEFDDCT--LNGLGDFNPS-ESD-----VVSELGKVETVTIRRLH  292 (549)
T ss_dssp             CCCCCCEEEEESCEEEHHHHHHHHGGGGGCTTCCEEEEESCE--EECCSCCCCC-TTT-----CCCCCTTCCEEEEESCB
T ss_pred             hhhcccceeccccccchhHHHHHHHHhhhhcccccccccccc--cccccccccc-chh-----hhhhhcccccccccccc
Confidence            578899999885543          11223445555554432  0000000000 000     00114678888887765


Q ss_pred             cccccc-cccc--ccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEE
Q 003090          519 YFENIV-SDLA--NDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSD  595 (848)
Q Consensus       519 ~~~~~~-~~l~--~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~  595 (848)
                      ...... ..+.  ...+++|+.|++.++. ++.++.    .....+++|++|+++++.-...+.......+.+++|+.|+
T Consensus       293 i~~~~~~~~l~~~~~~~~~L~~L~l~~n~-l~~ip~----~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~l~~L~~L~  367 (549)
T 2z81_A          293 IPQFYLFYDLSTVYSLLEKVKRITVENSK-VFLVPC----SFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLV  367 (549)
T ss_dssp             CSCGGGSCCCCHHHHHSTTCCEEEEESSC-CCCCCH----HHHHHCTTCCEEECCSSCCCHHHHHHHTCTTSSTTCCEEE
T ss_pred             cchhhhcccchhhhhhcccceEEEeccCc-cccCCH----HHHhcCccccEEEccCCccccccccchhhhhccccCcEEE
Confidence            322110 0000  1234789999999985 444321    1224689999999999953222111111235789999999


Q ss_pred             EecCchhhHhhhH--HHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCcccc
Q 003090          596 VVDCGSILKILLS--HLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVS  673 (848)
Q Consensus       596 l~~c~~l~~~l~~--~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~  673 (848)
                      +++|. + ..++.  .....+++|++|++++| .++.+|         ..+..+++|++|+++++. ++.++...     
T Consensus       368 Ls~N~-l-~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~lp---------~~~~~~~~L~~L~Ls~N~-l~~l~~~~-----  429 (549)
T 2z81_A          368 LSQNH-L-RSMQKTGEILLTLKNLTSLDISRN-TFHPMP---------DSCQWPEKMRFLNLSSTG-IRVVKTCI-----  429 (549)
T ss_dssp             CTTSC-C-CCHHHHHHHGGGCTTCCEEECTTC-CCCCCC---------SCCCCCTTCCEEECTTSC-CSCCCTTS-----
T ss_pred             ccCCc-c-cccccchhhhhcCCCCCEEECCCC-CCccCC---------hhhcccccccEEECCCCC-cccccchh-----
Confidence            99974 5 55553  33578999999999998 556665         456788999999999975 66665432     


Q ss_pred             ccCccEEEeecCccccccccCccccccccceeeeccccccceeeeec--CCCCCCCCCCCCccEEEEecCCCCceecccc
Q 003090          674 LHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT--TSTSSPTPSLGNLVSITIRGCGKLRNLFTTS  751 (848)
Q Consensus       674 l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c--~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~  751 (848)
                      .++|++|++++| +++.+ +..           +++|  +.+++.+|  ..+|. ...+++|+.|++++| +++.+++ .
T Consensus       430 ~~~L~~L~Ls~N-~l~~~-~~~-----------l~~L--~~L~Ls~N~l~~ip~-~~~l~~L~~L~Ls~N-~l~~~~~-~  491 (549)
T 2z81_A          430 PQTLEVLDVSNN-NLDSF-SLF-----------LPRL--QELYISRNKLKTLPD-ASLFPVLLVMKISRN-QLKSVPD-G  491 (549)
T ss_dssp             CTTCSEEECCSS-CCSCC-CCC-----------CTTC--CEEECCSSCCSSCCC-GGGCTTCCEEECCSS-CCCCCCT-T
T ss_pred             cCCceEEECCCC-Chhhh-ccc-----------CChh--cEEECCCCccCcCCC-cccCccCCEEecCCC-ccCCcCH-H
Confidence            379999999998 45553 211           3344  55555555  23343 357899999999995 7888865 5


Q ss_pred             hhhccccccEEEEecccc
Q 003090          752 MVKSLVRLESLEVRSCPT  769 (848)
Q Consensus       752 ~~~~l~~L~~L~i~~C~~  769 (848)
                      .+..+++|++|++++|+-
T Consensus       492 ~~~~l~~L~~L~l~~N~~  509 (549)
T 2z81_A          492 IFDRLTSLQKIWLHTNPW  509 (549)
T ss_dssp             GGGGCTTCCEEECCSSCB
T ss_pred             HHhcCcccCEEEecCCCc
Confidence            678999999999999974

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.96  E-value=1.8e-28  Score=294.81  Aligned_cols=154  Identities=27%  Similarity=0.364  Sum_probs=90.1

Q ss_pred             CCCceeeecCCCcccCC-cc-cccccceeecccC-cCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPD-EL-ECPKLQALFLQEN-SPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~-~~-~~~~L~~L~l~~~-~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      .++.|++++|.++.++. .+ .+++|++|++++| ....+++..|.++++|++|+|++              +.+...  
T Consensus        25 ~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~--------------N~l~~~--   88 (844)
T 3j0a_A           25 TTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGS--------------SKIYFL--   88 (844)
T ss_dssp             TCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTT--------------CCCCEE--
T ss_pred             CcCEEECCCCcCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCC--------------CcCccc--
Confidence            35666666666665532 23 6666666666666 44455444456666666666666              555553  


Q ss_pred             CCCCchhhhcccCcEEEccCccccCC-ch--hhccccCCCEEEccCCCCccc--ChhhccCCcccEEeccCCccccccCh
Q 003090          311 FLLPSSLSFLINLRTLRLHDRRIQGD-LS--LIGELSGLEILDLSESDVSEI--PVSFGRLSHLRLLDLTGCYILELIPR  385 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~~~~~-~~--~i~~l~~L~~L~l~~~~l~~l--p~~i~~L~~L~~L~l~~~~~~~~~p~  385 (848)
                        .|..++++++|++|++++|.+... +.  .++++++|++|++++|.+..+  +..++++++|++|++++|.+....+.
T Consensus        89 --~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~  166 (844)
T 3j0a_A           89 --HPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEH  166 (844)
T ss_dssp             --CTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCCCCSG
T ss_pred             --CHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCeeCHH
Confidence              356666666666666666655543 22  256666666666666666543  23566666666666666655554444


Q ss_pred             hhhhcc--ccccEEecccccccc
Q 003090          386 GVLSRL--RKLEELYMSHSFRHW  406 (848)
Q Consensus       386 ~~l~~l--~~L~~L~l~~~~~~~  406 (848)
                      . +..+  ++|+.|++++|.+..
T Consensus       167 ~-l~~l~~~~L~~L~L~~n~l~~  188 (844)
T 3j0a_A          167 E-LEPLQGKTLSFFSLAANSLYS  188 (844)
T ss_dssp             G-GHHHHHCSSCCCEECCSBSCC
T ss_pred             H-cccccCCccceEECCCCcccc
Confidence            4 4555  566666666665544

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.96  E-value=4e-29  Score=294.40  Aligned_cols=285  Identities=15%  Similarity=0.113  Sum_probs=141.3

Q ss_pred             CCchhhhcccCcEEEccCccccC------------------Cchhhc--cccCCCEEEccCCCCc-ccChhhccCCcccE
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQG------------------DLSLIG--ELSGLEILDLSESDVS-EIPVSFGRLSHLRL  371 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~------------------~~~~i~--~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~  371 (848)
                      +|..++++++|++|+|++|.+.+                  .|..++  ++++|++|++++|.+. .+|..++++++|++
T Consensus       440 IP~~l~~L~~L~~L~Ls~N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~  519 (876)
T 4ecn_A          440 ISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQS  519 (876)
T ss_dssp             ECGGGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCSCCGGGGGCSSCCE
T ss_pred             hhHHHhcCCCCCEEECcCCcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCccChHHHhCCCCCCE
Confidence            55556666666666666665555                  444444  5666666666665543 55555666666666


Q ss_pred             EeccCCc-ccc-ccChhhhhccc-------cccEEeccccccccccccccccccCcccchh--hhcccCCCcEEEeeccC
Q 003090          372 LDLTGCY-ILE-LIPRGVLSRLR-------KLEELYMSHSFRHWQFESESEEDSSSNAKFI--ELGALSRLTSLHIHIPE  440 (848)
Q Consensus       372 L~l~~~~-~~~-~~p~~~l~~l~-------~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~--~L~~l~~L~~L~l~~~~  440 (848)
                      |++++|. +.+ .+|.. +++++       +|++|++++|.+. .             .+.  .++++++|+.|++++|.
T Consensus       520 L~Ls~N~~lsg~~iP~~-i~~L~~~~~~l~~L~~L~Ls~N~L~-~-------------ip~~~~l~~L~~L~~L~Ls~N~  584 (876)
T 4ecn_A          520 LNIACNRGISAAQLKAD-WTRLADDEDTGPKIQIFYMGYNNLE-E-------------FPASASLQKMVKLGLLDCVHNK  584 (876)
T ss_dssp             EECTTCTTSCHHHHHHH-HHHHHHCTTTTTTCCEEECCSSCCC-B-------------CCCHHHHTTCTTCCEEECTTSC
T ss_pred             EECcCCCCcccccchHH-HHhhhhcccccCCccEEEeeCCcCC-c-------------cCChhhhhcCCCCCEEECCCCC
Confidence            6666654 333 45554 44444       5666666665554 2             333  45556666666666665


Q ss_pred             CCCCCCCC-ccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccc
Q 003090          441 GKIMPSDM-SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNY  519 (848)
Q Consensus       441 ~~~~~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~  519 (848)
                      +..+| .+ .+++|+.|                                                        .++++..
T Consensus       585 l~~lp-~~~~L~~L~~L--------------------------------------------------------~Ls~N~l  607 (876)
T 4ecn_A          585 VRHLE-AFGTNVKLTDL--------------------------------------------------------KLDYNQI  607 (876)
T ss_dssp             CCBCC-CCCTTSEESEE--------------------------------------------------------ECCSSCC
T ss_pred             cccch-hhcCCCcceEE--------------------------------------------------------ECcCCcc
Confidence            55555 22 44444444                                                        4444432


Q ss_pred             cccccccccccCCCC-CcEEEEecCCCceeecccccccccccCCCccEEeccccccccccccc---ccccccCCCcceEE
Q 003090          520 FENIVSDLANDGFNE-LMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHG---QLPAGCLSNVKRSD  595 (848)
Q Consensus       520 ~~~~~~~l~~~~l~~-L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~---~~~~~~l~~L~~L~  595 (848)
                      . .++..+  ..+++ |+.|+++++. ++.++.   .......++|+.|+++++. +......   ....-.+++|+.|+
T Consensus       608 ~-~lp~~l--~~l~~~L~~L~Ls~N~-L~~lp~---~~~~~~~~~L~~L~Ls~N~-l~g~ip~l~~~l~~~~~~~L~~L~  679 (876)
T 4ecn_A          608 E-EIPEDF--CAFTDQVEGLGFSHNK-LKYIPN---IFNAKSVYVMGSVDFSYNK-IGSEGRNISCSMDDYKGINASTVT  679 (876)
T ss_dssp             S-CCCTTS--CEECTTCCEEECCSSC-CCSCCS---CCCTTCSSCEEEEECCSSC-TTTTSSSCSSCTTTCCCCCEEEEE
T ss_pred             c-cchHHH--hhccccCCEEECcCCC-CCcCch---hhhccccCCCCEEECcCCc-CCCccccchhhhccccCCCcCEEE
Confidence            2 222222  34455 6666666654 223211   1111122346666666663 2111000   00001234666777


Q ss_pred             EecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccc--c
Q 003090          596 VVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFV--S  673 (848)
Q Consensus       596 l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~--~  673 (848)
                      +++|. + ..+|......+++|+.|++++| .++.++... ..........+++|++|++++| +++.+|..   +.  .
T Consensus       680 Ls~N~-L-~~lp~~~~~~l~~L~~L~Ls~N-~L~~ip~~~-~~~~~~~l~nl~~L~~L~Ls~N-~L~~lp~~---l~~~~  751 (876)
T 4ecn_A          680 LSYNE-I-QKFPTELFATGSPISTIILSNN-LMTSIPENS-LKPKDGNYKNTYLLTTIDLRFN-KLTSLSDD---FRATT  751 (876)
T ss_dssp             CCSSC-C-CSCCHHHHHTTCCCSEEECCSC-CCSCCCTTS-SSCTTSCCTTGGGCCEEECCSS-CCCCCCGG---GSTTT
T ss_pred             ccCCc-C-CccCHHHHccCCCCCEEECCCC-cCCccChHH-hccccccccccCCccEEECCCC-CCccchHH---hhhcc
Confidence            66653 4 4566655556667777777665 333443210 0000000122346777777665 45555433   22  5


Q ss_pred             ccCccEEEeecC
Q 003090          674 LHNLKKVRVEEC  685 (848)
Q Consensus       674 l~~L~~L~i~~C  685 (848)
                      +++|+.|++++|
T Consensus       752 l~~L~~L~Ls~N  763 (876)
T 4ecn_A          752 LPYLSNMDVSYN  763 (876)
T ss_dssp             CTTCCEEECCSS
T ss_pred             CCCcCEEEeCCC
Confidence            667777777665

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.96  E-value=6.4e-29  Score=288.53  Aligned_cols=401  Identities=11%  Similarity=0.097  Sum_probs=248.9

Q ss_pred             CcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCC-----CCC--------CCCchhh--hcccCcEEEcc
Q 003090          265 NSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSS-----PLF--------LLPSSLS--FLINLRTLRLH  329 (848)
Q Consensus       265 ~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~-----~~~--------~lp~~~~--~l~~L~~L~L~  329 (848)
                      |.+..+|.. ++++++|++|++++              +.+.+.     ...        .+|..++  ++++|++|+++
T Consensus       193 n~l~~ip~~-l~~l~~L~~L~Ls~--------------n~l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~  257 (636)
T 4eco_A          193 NNITFVSKA-VMRLTKLRQFYMGN--------------SPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVY  257 (636)
T ss_dssp             CEEEEECGG-GGGCTTCCEEEEES--------------CCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEE
T ss_pred             CCCccCCHH-HhcccCCCEEECcC--------------CccccccccccccccccchhcccCchhhhhcccCCCCEEEec
Confidence            344458876 68999999999999              556551     000        0678888  99999999999


Q ss_pred             CccccCCc-hhhccccCCCEEEccCCC-Cc--ccChhhccC------CcccEEeccCCccccccCh--hhhhccccccEE
Q 003090          330 DRRIQGDL-SLIGELSGLEILDLSESD-VS--EIPVSFGRL------SHLRLLDLTGCYILELIPR--GVLSRLRKLEEL  397 (848)
Q Consensus       330 ~~~~~~~~-~~i~~l~~L~~L~l~~~~-l~--~lp~~i~~L------~~L~~L~l~~~~~~~~~p~--~~l~~l~~L~~L  397 (848)
                      +|.+.+.. ..++++++|++|++++|+ ++  .+|..++++      ++|++|++++|... .+|.  . ++++++|++|
T Consensus       258 ~n~l~~~~p~~l~~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~-~ip~~~~-l~~l~~L~~L  335 (636)
T 4eco_A          258 NCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLK-TFPVETS-LQKMKKLGML  335 (636)
T ss_dssp             CCTTCSSCCTTTTTCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSCCS-SCCCHHH-HTTCTTCCEE
T ss_pred             CCcCCccChHHHhcCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCcCC-ccCchhh-hccCCCCCEE
Confidence            99877754 789999999999999998 88  499999887      99999999998776 8998  6 8999999999


Q ss_pred             eccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCC-CCeEEEEeCCCCCCCCCcccceE
Q 003090          398 YMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQN-LTSFSIAIGDLEERPLSDFIGLF  475 (848)
Q Consensus       398 ~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~-L~~L~l~~~~~~~~~~~~l~~l~  475 (848)
                      ++++|.+.+.             .+ .++.+++|+.|++++|.+..+|..+ .+++ |+.|++..+...           
T Consensus       336 ~L~~N~l~g~-------------ip-~~~~l~~L~~L~L~~N~l~~lp~~l~~l~~~L~~L~Ls~N~l~-----------  390 (636)
T 4eco_A          336 ECLYNQLEGK-------------LP-AFGSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLK-----------  390 (636)
T ss_dssp             ECCSCCCEEE-------------CC-CCEEEEEESEEECCSSEEEECCTTSEEECTTCCEEECCSSCCS-----------
T ss_pred             eCcCCcCccc-------------hh-hhCCCCCCCEEECCCCccccccHhhhhhcccCcEEEccCCcCc-----------
Confidence            9999998754             44 7889999999999999988888877 7777 888887644331           


Q ss_pred             EecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeeccccc-
Q 003090          476 LQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLE-  554 (848)
Q Consensus       476 l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~-  554 (848)
                                                                    .++..+....+++|+.|+++++.....++.... 
T Consensus       391 ----------------------------------------------~lp~~~~~~~l~~L~~L~Ls~N~l~~~~p~~l~~  424 (636)
T 4eco_A          391 ----------------------------------------------YIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDP  424 (636)
T ss_dssp             ----------------------------------------------SCCSCCCTTCSSCEEEEECCSSCTTTTTTCSSCT
T ss_pred             ----------------------------------------------ccchhhhhcccCccCEEECcCCcCCCcchhhhcc
Confidence                                                          111111111233444444444432211100000 


Q ss_pred             -ccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHH-------hhccCcEEEEeccC
Q 003090          555 -RTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQ-------SFQNLQRLRVYSCG  626 (848)
Q Consensus       555 -~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~-------~l~~L~~L~l~~c~  626 (848)
                       ......+++|++|+++++. ++.+....  ...+++|+.|++++|. + ..+|.....       .+++|++|++++|.
T Consensus       425 ~~~~~~~~~~L~~L~Ls~N~-l~~lp~~~--~~~l~~L~~L~Ls~N~-l-~~i~~~~~~~~~~~~~~l~~L~~L~Ls~N~  499 (636)
T 4eco_A          425 LDPTPFKGINVSSINLSNNQ-ISKFPKEL--FSTGSPLSSINLMGNM-L-TEIPKNSLKDENENFKNTYLLTSIDLRFNK  499 (636)
T ss_dssp             TCSSCCCCCCEEEEECCSSC-CCSCCTHH--HHTTCCCSEEECCSSC-C-SBCCSSSSEETTEECTTGGGCCEEECCSSC
T ss_pred             cccccccCCCCCEEECcCCc-cCcCCHHH--HccCCCCCEEECCCCC-C-CCcCHHHhccccccccccCCccEEECcCCc
Confidence             0000023455555555542 22210000  0124555555555542 3 344432211       22377777777764


Q ss_pred             Cceeeeecccccccccccc--ccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccce
Q 003090          627 LLVSVFEIERVNIAKEETE--LFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEE  704 (848)
Q Consensus       627 ~l~~~~~~~~~~~~~~~~~--~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~  704 (848)
                       ++.++         ..+.  .+++|++|+++++. ++.+|..   +..+++|+.|+++++..+..-             
T Consensus       500 -l~~lp---------~~~~~~~l~~L~~L~Ls~N~-l~~ip~~---~~~l~~L~~L~Ls~N~~ls~N-------------  552 (636)
T 4eco_A          500 -LTKLS---------DDFRATTLPYLVGIDLSYNS-FSKFPTQ---PLNSSTLKGFGIRNQRDAQGN-------------  552 (636)
T ss_dssp             -CCBCC---------GGGSTTTCTTCCEEECCSSC-CSSCCCG---GGGCSSCCEEECCSCBCTTCC-------------
T ss_pred             -CCccC---------hhhhhccCCCcCEEECCCCC-CCCcChh---hhcCCCCCEEECCCCcccccC-------------
Confidence             33554         2343  67788888888764 4445443   566788888888765422110             


Q ss_pred             eeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCccccccc
Q 003090          705 MVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQ  784 (848)
Q Consensus       705 l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~  784 (848)
                              .   +  ....|..+..+++|++|++++|. +..+|.. .   .++|++|++++|+-. .+.....    ..
T Consensus       553 --------~---l--~~~~p~~l~~l~~L~~L~Ls~N~-l~~ip~~-~---~~~L~~L~Ls~N~l~-~~~~~~~----~~  609 (636)
T 4eco_A          553 --------R---T--LREWPEGITLCPSLTQLQIGSND-IRKVNEK-I---TPNISVLDIKDNPNI-SIDLSYV----CP  609 (636)
T ss_dssp             --------B---C--CCCCCTTGGGCSSCCEEECCSSC-CCBCCSC-C---CTTCCEEECCSCTTC-EEECTTT----HH
T ss_pred             --------c---c--cccChHHHhcCCCCCEEECCCCc-CCccCHh-H---hCcCCEEECcCCCCc-cccHHhc----ch
Confidence                    0   0  01224455667888888888854 5777542 2   268888888888633 3211100    00


Q ss_pred             CCCccceecccccccccccccccc
Q 003090          785 GASTKKITFPSLFGIKLCDLDSLA  808 (848)
Q Consensus       785 ~~~~~~~~~~sL~~L~i~~cp~L~  808 (848)
                      ........+...+..+|++||.|.
T Consensus       610 ~~~~~~~~l~~~~~~~i~~C~~L~  633 (636)
T 4eco_A          610 YIEAGMYMLFYDKTQDIRGCDALD  633 (636)
T ss_dssp             HHHTTCCEEECCTTSEEESCGGGC
T ss_pred             hhhcccceeecCCccccCCCcccc
Confidence            001112224556777888888875

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.96  E-value=4.4e-28  Score=276.40  Aligned_cols=457  Identities=15%  Similarity=0.093  Sum_probs=299.9

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.+++++|.++.+|..+. ++|++|++++|.+..+++..|.++++|++|++++              +.+.+.    .|.
T Consensus         3 ~~l~ls~n~l~~ip~~~~-~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~--------------n~l~~~----~~~   63 (520)
T 2z7x_B            3 FLVDRSKNGLIHVPKDLS-QKTTILNISQNYISELWTSDILSLSKLRILIISH--------------NRIQYL----DIS   63 (520)
T ss_dssp             CEEECTTSCCSSCCCSCC-TTCSEEECCSSCCCCCCHHHHTTCTTCCEEECCS--------------SCCCEE----EGG
T ss_pred             ceEecCCCCccccccccc-ccccEEECCCCcccccChhhccccccccEEecCC--------------CccCCc----ChH
Confidence            468999999999998776 8999999999999999887789999999999999              888874    478


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcc--cChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSE--IPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~--lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .++.+++|++|++++|.+...+..  .+++|++|++++|.++.  +|..++++++|++|++++|....   .. +..+++
T Consensus        64 ~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n~l~~---~~-~~~l~~  137 (520)
T 2z7x_B           64 VFKFNQELEYLDLSHNKLVKISCH--PTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTTHLEK---SS-VLPIAH  137 (520)
T ss_dssp             GGTTCTTCCEEECCSSCCCEEECC--CCCCCSEEECCSSCCSSCCCCGGGGGCTTCCEEEEEESSCCG---GG-GGGGTT
T ss_pred             HhhcccCCCEEecCCCceeecCcc--ccCCccEEeccCCccccccchhhhccCCcceEEEecCcccch---hh-cccccc
Confidence            999999999999999988765544  89999999999999985  67899999999999999987654   23 678888


Q ss_pred             c--cEEecccccc--ccccccccccccCcccchhhhcccCC-CcEEEeeccCCCC-CCCCC--ccCCCCeEEEEeCCC--
Q 003090          394 L--EELYMSHSFR--HWQFESESEEDSSSNAKFIELGALSR-LTSLHIHIPEGKI-MPSDM--SFQNLTSFSIAIGDL--  463 (848)
Q Consensus       394 L--~~L~l~~~~~--~~~~~~~~~~~~~~~~~~~~L~~l~~-L~~L~l~~~~~~~-~~~~~--~~~~L~~L~l~~~~~--  463 (848)
                      |  ++|++++|.+  ...             .+..+..+.. .-.+++++|.... ++...  .+++|+.|++..+..  
T Consensus       138 L~L~~L~l~~n~l~~~~~-------------~~~~l~~l~~~~l~l~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~~~~  204 (520)
T 2z7x_B          138 LNISKVLLVLGETYGEKE-------------DPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVANLELSNIKCVLEDN  204 (520)
T ss_dssp             SCEEEEEEEECTTTTSSC-------------CTTTTTTCCEEEEEEECCSSSCCCCCCCCCCTTCSEEEECCEEECCSTT
T ss_pred             ceeeEEEeeccccccccc-------------ccccccccccceEEEEeccCcchhhhhhhhhhcccceeecccccccccc
Confidence            8  9999999987  433             3344554442 2234455555432 22222  567777777776531  


Q ss_pred             ----------CCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeecccccccccccccc---cc
Q 003090          464 ----------EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLA---ND  530 (848)
Q Consensus       464 ----------~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~---~~  530 (848)
                                .....+.++.+.+....-..         ..+..++.+.  ..++|++|+++++......+..+.   ..
T Consensus       205 ~~~~~~~~~~~l~~l~~L~~L~l~~~~l~~---------~~~~~~~~~~--~~~~L~~L~l~~n~l~~~~p~~~~~~~~~  273 (520)
T 2z7x_B          205 KCSYFLSILAKLQTNPKLSNLTLNNIETTW---------NSFIRILQLV--WHTTVWYFSISNVKLQGQLDFRDFDYSGT  273 (520)
T ss_dssp             TTHHHHHHHHGGGGCTTCCEEEEEEEEEEH---------HHHHHHHHHH--HTSSCSEEEEEEEEEESCCCCCCCCCCSC
T ss_pred             ccceeecchhhhccccchhhccccccccCH---------HHHHHHHHHh--hhCcccEEEeecccccCccccchhhcccc
Confidence                      12233444555444321000         0011111111  134788888888765544443331   14


Q ss_pred             CCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHH
Q 003090          531 GFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHL  610 (848)
Q Consensus       531 ~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~  610 (848)
                      .+++|+.+++.++..  .++.. .......-++|+.|+++++. +..+   .. ...+++|++|++++|.-- ..+|..+
T Consensus       274 ~l~~L~~l~l~~n~~--~~p~~-~~~~~~~~~~L~~L~l~~n~-l~~~---~~-~~~l~~L~~L~Ls~n~l~-~~~~~~~  344 (520)
T 2z7x_B          274 SLKALSIHQVVSDVF--GFPQS-YIYEIFSNMNIKNFTVSGTR-MVHM---LC-PSKISPFLHLDFSNNLLT-DTVFENC  344 (520)
T ss_dssp             CCCEEEEEEEEECCC--CSCTH-HHHHHHHTCCCSEEEEESSC-CCCC---CC-CSSCCCCCEEECCSSCCC-TTTTTTC
T ss_pred             cCceeEeccccccce--ecchh-hhhcccccCceeEEEcCCCc-cccc---cc-hhhCCcccEEEeECCccC-hhhhhhh
Confidence            567777777777653  22100 00011111568888888874 3222   11 146888888888887543 4344433


Q ss_pred             HHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccc
Q 003090          611 VQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQ  690 (848)
Q Consensus       611 ~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~  690 (848)
                       ..+++|++|++++|.- +.++..      ...+..+++|++|+++++.-...++...  +..+++|++|++++|. ++.
T Consensus       345 -~~l~~L~~L~L~~N~l-~~l~~~------~~~~~~l~~L~~L~Ls~N~l~~~l~~~~--~~~l~~L~~L~Ls~N~-l~~  413 (520)
T 2z7x_B          345 -GHLTELETLILQMNQL-KELSKI------AEMTTQMKSLQQLDISQNSVSYDEKKGD--CSWTKSLLSLNMSSNI-LTD  413 (520)
T ss_dssp             -CCCSSCCEEECCSSCC-CBHHHH------HHHHTTCTTCCEEECCSSCCBCCGGGCS--CCCCTTCCEEECCSSC-CCG
T ss_pred             -ccCCCCCEEEccCCcc-Cccccc------hHHHhhCCCCCEEECCCCcCCcccccch--hccCccCCEEECcCCC-CCc
Confidence             6788888888888753 222110      0345678888888888875333365542  5667888888888875 322


Q ss_pred             cccCccccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEeccccc
Q 003090          691 VFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTL  770 (848)
Q Consensus       691 ~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L  770 (848)
                      ..|..                               +  .++|+.|++++| +++.+|.  .+..+++|++|++++| .+
T Consensus       414 ~~~~~-------------------------------l--~~~L~~L~Ls~N-~l~~ip~--~~~~l~~L~~L~L~~N-~l  456 (520)
T 2z7x_B          414 TIFRC-------------------------------L--PPRIKVLDLHSN-KIKSIPK--QVVKLEALQELNVASN-QL  456 (520)
T ss_dssp             GGGGS-------------------------------C--CTTCCEEECCSS-CCCCCCG--GGGGCTTCCEEECCSS-CC
T ss_pred             chhhh-------------------------------h--cccCCEEECCCC-cccccch--hhhcCCCCCEEECCCC-cC
Confidence            21211                               1  167888888886 6777754  3458888888888888 45


Q ss_pred             ceeecCCcccccccCCCccceeccccccccccccccccccc
Q 003090          771 QEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACFC  811 (848)
Q Consensus       771 ~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~~~  811 (848)
                      +.++.  .   .+..       +++|++|++.++| +...|
T Consensus       457 ~~l~~--~---~~~~-------l~~L~~L~l~~N~-~~c~c  484 (520)
T 2z7x_B          457 KSVPD--G---IFDR-------LTSLQKIWLHTNP-WDCSC  484 (520)
T ss_dssp             CCCCT--T---TTTT-------CTTCCEEECCSSC-BCCCH
T ss_pred             CccCH--H---Hhcc-------CCcccEEECcCCC-CcccC
Confidence            55532  1   1222       6888888888877 55443

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.95  E-value=4.3e-28  Score=285.59  Aligned_cols=354  Identities=14%  Similarity=0.131  Sum_probs=198.2

Q ss_pred             cCCcc-cccccceeecccCcCcc------------------cChHH-HccCCceeEEEccCcccccccccCCCCCCCCCC
Q 003090          248 VPDEL-ECPKLQALFLQENSPLA------------------IPDRF-FQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPS  307 (848)
Q Consensus       248 lp~~~-~~~~L~~L~l~~~~~~~------------------~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~  307 (848)
                      +|..+ .+++|++|++++|.+..                  +|+.+ |.++++|++|++++              +.+.+
T Consensus       440 IP~~l~~L~~L~~L~Ls~N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~--------------N~l~~  505 (876)
T 4ecn_A          440 ISKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYN--------------CPNMT  505 (876)
T ss_dssp             ECGGGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEES--------------CTTCC
T ss_pred             hhHHHhcCCCCCEEECcCCcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcC--------------CCCCc
Confidence            45444 55666666666665544                  55543 23566666666666              44444


Q ss_pred             CCCCCCCchhhhcccCcEEEccCcc-ccC--Cchhhcccc-------CCCEEEccCCCCcccCh--hhccCCcccEEecc
Q 003090          308 SPLFLLPSSLSFLINLRTLRLHDRR-IQG--DLSLIGELS-------GLEILDLSESDVSEIPV--SFGRLSHLRLLDLT  375 (848)
Q Consensus       308 ~~~~~lp~~~~~l~~L~~L~L~~~~-~~~--~~~~i~~l~-------~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~  375 (848)
                      .    +|..++++++|++|++++|+ +.+  .|..++++.       +|++|++++|.++.+|.  .++++++|++|+++
T Consensus       506 ~----iP~~l~~L~~L~~L~Ls~N~~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~~~~l~~L~~L~~L~Ls  581 (876)
T 4ecn_A          506 Q----LPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCV  581 (876)
T ss_dssp             S----CCGGGGGCSSCCEEECTTCTTSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCCHHHHTTCTTCCEEECT
T ss_pred             c----ChHHHhCCCCCCEEECcCCCCcccccchHHHHhhhhcccccCCccEEEeeCCcCCccCChhhhhcCCCCCEEECC
Confidence            4    66666666666666666665 443  234444444       66666666666666666  56666666666666


Q ss_pred             CCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCC-CcEEEeeccCCCCCCCCC-c--cC
Q 003090          376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR-LTSLHIHIPEGKIMPSDM-S--FQ  451 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~-L~~L~l~~~~~~~~~~~~-~--~~  451 (848)
                      +|.+. .+| . ++++++|+.|++++|.+. .             .+..+..+++ |+.|++++|.+..+|..+ .  .+
T Consensus       582 ~N~l~-~lp-~-~~~L~~L~~L~Ls~N~l~-~-------------lp~~l~~l~~~L~~L~Ls~N~L~~lp~~~~~~~~~  644 (876)
T 4ecn_A          582 HNKVR-HLE-A-FGTNVKLTDLKLDYNQIE-E-------------IPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVY  644 (876)
T ss_dssp             TSCCC-BCC-C-CCTTSEESEEECCSSCCS-C-------------CCTTSCEECTTCCEEECCSSCCCSCCSCCCTTCSS
T ss_pred             CCCcc-cch-h-hcCCCcceEEECcCCccc-c-------------chHHHhhccccCCEEECcCCCCCcCchhhhccccC
Confidence            65544 566 3 566666666666666554 2             3344566666 666666666666665544 2  22


Q ss_pred             CCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccC
Q 003090          452 NLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDG  531 (848)
Q Consensus       452 ~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~  531 (848)
                      +|+.|++..+..... .+.+. ..+..                +         ..++|+.|+++++... .++..+ ...
T Consensus       645 ~L~~L~Ls~N~l~g~-ip~l~-~~l~~----------------~---------~~~~L~~L~Ls~N~L~-~lp~~~-~~~  695 (876)
T 4ecn_A          645 VMGSVDFSYNKIGSE-GRNIS-CSMDD----------------Y---------KGINASTVTLSYNEIQ-KFPTEL-FAT  695 (876)
T ss_dssp             CEEEEECCSSCTTTT-SSSCS-SCTTT----------------C---------CCCCEEEEECCSSCCC-SCCHHH-HHT
T ss_pred             CCCEEECcCCcCCCc-cccch-hhhcc----------------c---------cCCCcCEEEccCCcCC-ccCHHH-Hcc
Confidence            356666554332110 00000 00000                0         0246777777776544 223222 125


Q ss_pred             CCCCcEEEEecCCCceeecccccccc---cccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhH
Q 003090          532 FNELMFLVIFRCNEMKYLLNSLERTL---RVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLS  608 (848)
Q Consensus       532 l~~L~~L~l~~~~~l~~l~~~~~~~~---~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~  608 (848)
                      +++|+.|+++++. ++.++.......   ...+++|++|+|++| +++.+... +....+++|+.|++++|. + ..+|.
T Consensus       696 l~~L~~L~Ls~N~-L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N-~L~~lp~~-l~~~~l~~L~~L~Ls~N~-L-~~lp~  770 (876)
T 4ecn_A          696 GSPISTIILSNNL-MTSIPENSLKPKDGNYKNTYLLTTIDLRFN-KLTSLSDD-FRATTLPYLSNMDVSYNC-F-SSFPT  770 (876)
T ss_dssp             TCCCSEEECCSCC-CSCCCTTSSSCTTSCCTTGGGCCEEECCSS-CCCCCCGG-GSTTTCTTCCEEECCSSC-C-SSCCC
T ss_pred             CCCCCEEECCCCc-CCccChHHhccccccccccCCccEEECCCC-CCccchHH-hhhccCCCcCEEEeCCCC-C-Cccch
Confidence            6788888888774 333322111000   123347888888887 45543211 111257888888888764 4 44665


Q ss_pred             HHHHhhccCcEEEEeccC------CceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEe
Q 003090          609 HLVQSFQNLQRLRVYSCG------LLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRV  682 (848)
Q Consensus       609 ~~~~~l~~L~~L~l~~c~------~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i  682 (848)
                      .+ ..+++|+.|++++|+      -...+|         ..+..+++|++|++++|. +..+|...     +++|+.|+|
T Consensus       771 ~l-~~L~~L~~L~Ls~N~~ls~N~l~~~ip---------~~l~~L~~L~~L~Ls~N~-L~~Ip~~l-----~~~L~~LdL  834 (876)
T 4ecn_A          771 QP-LNSSQLKAFGIRHQRDAEGNRILRQWP---------TGITTCPSLIQLQIGSND-IRKVDEKL-----TPQLYILDI  834 (876)
T ss_dssp             GG-GGCTTCCEEECCCCBCTTCCBCCCCCC---------TTGGGCSSCCEEECCSSC-CCBCCSCC-----CSSSCEEEC
T ss_pred             hh-hcCCCCCEEECCCCCCcccccccccCh---------HHHhcCCCCCEEECCCCC-CCccCHhh-----cCCCCEEEC
Confidence            44 577888888887643      222333         456678888888888875 46666542     368888888


Q ss_pred             ecCc
Q 003090          683 EECD  686 (848)
Q Consensus       683 ~~C~  686 (848)
                      ++|+
T Consensus       835 s~N~  838 (876)
T 4ecn_A          835 ADNP  838 (876)
T ss_dssp             CSCT
T ss_pred             CCCC
Confidence            8876

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.95  E-value=6.7e-27  Score=281.11  Aligned_cols=470  Identities=15%  Similarity=0.113  Sum_probs=260.9

Q ss_pred             HHHhccCCCceeeecC-CCccc-CCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCC
Q 003090          228 EIAGWLDLTGISLMFN-DIHEV-PDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPP  304 (848)
Q Consensus       228 ~i~~~~~l~~l~l~~n-~l~~l-p~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~  304 (848)
                      .+.....++.|++++| .+..+ |..+ .+++|++|++++|.+..+++..|.++++|++|++++              +.
T Consensus        43 ~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~Ls~--------------n~  108 (844)
T 3j0a_A           43 SFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRLYF--------------CG  108 (844)
T ss_dssp             SCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSCCCEECTT--------------CC
T ss_pred             HCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCcccCEeeCcC--------------CC
Confidence            3445556888999888 44466 4444 888999999999988887666678899999999998              77


Q ss_pred             CCCCCCCCCCch--hhhcccCcEEEccCccccCCc--hhhccccCCCEEEccCCCCc-ccChhhccC--CcccEEeccCC
Q 003090          305 LPSSPLFLLPSS--LSFLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESDVS-EIPVSFGRL--SHLRLLDLTGC  377 (848)
Q Consensus       305 l~~~~~~~lp~~--~~~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L--~~L~~L~l~~~  377 (848)
                      +.+.    .|..  ++++++|++|++++|.+....  ..++++++|++|++++|.++ ..|..+..+  ++|+.|++++|
T Consensus       109 l~~~----~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~~~l~~l~~~~L~~L~L~~n  184 (844)
T 3j0a_A          109 LSDA----VLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAAN  184 (844)
T ss_dssp             CSSC----CSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCCCCSGGGHHHHHCSSCCCEECCS
T ss_pred             CCcc----cccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCeeCHHHcccccCCccceEECCCC
Confidence            7654    4544  888899999999998877654  56889999999999998887 456667766  78888888888


Q ss_pred             ccccccChhhhhcccc------ccEEeccccccccccccccc-c----------------------ccCcccchhhhcc-
Q 003090          378 YILELIPRGVLSRLRK------LEELYMSHSFRHWQFESESE-E----------------------DSSSNAKFIELGA-  427 (848)
Q Consensus       378 ~~~~~~p~~~l~~l~~------L~~L~l~~~~~~~~~~~~~~-~----------------------~~~~~~~~~~L~~-  427 (848)
                      ...+..|.. ++.+.+      |+.|++++|.+....+..-. .                      ..-.......+.. 
T Consensus       185 ~l~~~~~~~-~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~~l~~~~l~~L~l~~~~~~~~~~~~~l~~~~~~~f~~l  263 (844)
T 3j0a_A          185 SLYSRVSVD-WGKCMNPFRNMVLEILDVSGNGWTVDITGNFSNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAGL  263 (844)
T ss_dssp             BSCCCCCCC-CCSSSCTTTTCCBSEEBCSSCCSSTTTTSGGGGTSCSCCBSEEECCSSCCBCSSSCSSSTTGGGTTTTTT
T ss_pred             ccccccccc-hhhcCCccccCceeEEecCCCcCchhHHHHHHhhcCcccccceecccccccccccccccCCCChhhhhcc
Confidence            777766665 555554      88888888865543221000 0                      0000011112222 


Q ss_pred             -cCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHH
Q 003090          428 -LSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKN  504 (848)
Q Consensus       428 -l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~  504 (848)
                       .++|+.|++++|.+..++...  .+++|+.|++..+......+...                                .
T Consensus       264 ~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~--------------------------------~  311 (844)
T 3j0a_A          264 ARSSVRHLDLSHGFVFSLNSRVFETLKDLKVLNLAYNKINKIADEAF--------------------------------Y  311 (844)
T ss_dssp             TTSCCCEEECTTCCCCEECSCCSSSCCCCCEEEEESCCCCEECTTTT--------------------------------T
T ss_pred             ccCCccEEECCCCcccccChhhhhcCCCCCEEECCCCcCCCCChHHh--------------------------------c
Confidence             268999999999887665443  78999999998665410000000                                0


Q ss_pred             HHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccc
Q 003090          505 LLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLP  584 (848)
Q Consensus       505 ~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~  584 (848)
                      .+++|++|+++++......+..+  ..+++|+.|++.++. +..++    ......+++|++|+++++. ++.+     +
T Consensus       312 ~l~~L~~L~Ls~N~l~~~~~~~~--~~l~~L~~L~L~~N~-i~~~~----~~~~~~l~~L~~L~Ls~N~-l~~i-----~  378 (844)
T 3j0a_A          312 GLDNLQVLNLSYNLLGELYSSNF--YGLPKVAYIDLQKNH-IAIIQ----DQTFKFLEKLQTLDLRDNA-LTTI-----H  378 (844)
T ss_dssp             TCSSCCEEEEESCCCSCCCSCSC--SSCTTCCEEECCSCC-CCCCC----SSCSCSCCCCCEEEEETCC-SCCC-----S
T ss_pred             CCCCCCEEECCCCCCCccCHHHh--cCCCCCCEEECCCCC-CCccC----hhhhcCCCCCCEEECCCCC-CCcc-----c
Confidence            02455666665554332222222  345666666666553 22221    1123445666666666552 2221     1


Q ss_pred             cccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcccccc
Q 003090          585 AGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDI  664 (848)
Q Consensus       585 ~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l  664 (848)
                        .+++|+.|.+.+|. + ..+|..    ..+++.|+++++. ++.++..       ..+..+++|++|+++++. +..+
T Consensus       379 --~~~~L~~L~l~~N~-l-~~l~~~----~~~l~~L~ls~N~-l~~l~~~-------~~~~~l~~L~~L~Ls~N~-l~~~  441 (844)
T 3j0a_A          379 --FIPSIPDIFLSGNK-L-VTLPKI----NLTANLIHLSENR-LENLDIL-------YFLLRVPHLQILILNQNR-FSSC  441 (844)
T ss_dssp             --SCCSCSEEEEESCC-C-CCCCCC----CTTCCEEECCSCC-CCSSTTH-------HHHTTCTTCCEEEEESCC-CCCC
T ss_pred             --CCCCcchhccCCCC-c-cccccc----ccccceeecccCc-cccCchh-------hhhhcCCccceeeCCCCc-cccc
Confidence              25556666665542 3 333321    2345555554432 1111100       112244555555555432 2222


Q ss_pred             ccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeec--CC-CCCCCCCCCCccEEEEecC
Q 003090          665 WKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT--TS-TSSPTPSLGNLVSITIRGC  741 (848)
Q Consensus       665 ~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c--~~-~~~~~~~l~~L~~L~i~~C  741 (848)
                      +... .+..+++|+.|+++++. ++...+.......   --.+++|  +.+++.+|  .. .+..+..+++|+.|+++++
T Consensus       442 ~~~~-~~~~~~~L~~L~Ls~N~-l~~~~~~~~~~~~---~~~l~~L--~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N  514 (844)
T 3j0a_A          442 SGDQ-TPSENPSLEQLFLGENM-LQLAWETELCWDV---FEGLSHL--QVLYLNHNYLNSLPPGVFSHLTALRGLSLNSN  514 (844)
T ss_dssp             CSSS-SSCSCTTCCBCEEESCC-CSSSCCSCCCSSC---SSCBCCE--ECCCCCHHHHTTCCTTSSSSCCSCSEEEEESC
T ss_pred             cccc-ccccCCccccccCCCCc-cccccccccchhh---hcCcccc--cEEECCCCcccccChhHccchhhhheeECCCC
Confidence            1111 12234455555555432 2111000000000   0001222  23333332  11 2234567788888888884


Q ss_pred             CCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceeccccccccccccc
Q 003090          742 GKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIKLCDLD  805 (848)
Q Consensus       742 ~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp  805 (848)
                       +|+.+++... .  ++|+.|+++++. +..+. ++.              +++|+.|++.+.|
T Consensus       515 -~l~~l~~~~~-~--~~L~~L~Ls~N~-l~~~~-~~~--------------~~~L~~l~l~~Np  558 (844)
T 3j0a_A          515 -RLTVLSHNDL-P--ANLEILDISRNQ-LLAPN-PDV--------------FVSLSVLDITHNK  558 (844)
T ss_dssp             -CCSSCCCCCC-C--SCCCEEEEEEEC-CCCCC-SCC--------------CSSCCEEEEEEEC
T ss_pred             -CCCccChhhh-h--ccccEEECCCCc-CCCCC-hhH--------------hCCcCEEEecCCC
Confidence             6777765332 2  778888888874 32221 111              5677777776655

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.95  E-value=6.1e-28  Score=280.29  Aligned_cols=360  Identities=14%  Similarity=0.150  Sum_probs=267.6

Q ss_pred             CcccCCcc-cccccceeecccCcCcc------------------cChHHHc--cCCceeEEEccCcccccccccCCCCCC
Q 003090          245 IHEVPDEL-ECPKLQALFLQENSPLA------------------IPDRFFQ--GMKDLQVLDLGGIRRFSFSVRFPFLFP  303 (848)
Q Consensus       245 l~~lp~~~-~~~~L~~L~l~~~~~~~------------------~~~~~~~--~~~~Lr~L~l~~~~~~~~~~~~~~~~~  303 (848)
                      ++.+|..+ .+++|++|++++|.+..                  +|..+ .  ++++|++|++++              +
T Consensus       195 l~~ip~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~~~~~~~~~~~ip~~l-~~~~l~~L~~L~L~~--------------n  259 (636)
T 4eco_A          195 ITFVSKAVMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKTEDL-KWDNLKDLTDVEVYN--------------C  259 (636)
T ss_dssp             EEEECGGGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCC-CGGGCTTCCEEEEEC--------------C
T ss_pred             CccCCHHHhcccCCCEEECcCCccccccccccccccccchhcccCchhh-hhcccCCCCEEEecC--------------C
Confidence            33577777 89999999999998877                  88874 6  899999999999              7


Q ss_pred             CCCCCCCCCCCchhhhcccCcEEEccCcc-ccC--Cchhhccc------cCCCEEEccCCCCcccCh--hhccCCcccEE
Q 003090          304 PLPSSPLFLLPSSLSFLINLRTLRLHDRR-IQG--DLSLIGEL------SGLEILDLSESDVSEIPV--SFGRLSHLRLL  372 (848)
Q Consensus       304 ~l~~~~~~~lp~~~~~l~~L~~L~L~~~~-~~~--~~~~i~~l------~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L  372 (848)
                      .+.+.    +|..++++++|++|++++|. +.+  .|..++++      ++|++|++++|.++.+|.  .++++++|++|
T Consensus       260 ~l~~~----~p~~l~~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~~ip~~~~l~~l~~L~~L  335 (636)
T 4eco_A          260 PNLTK----LPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGML  335 (636)
T ss_dssp             TTCSS----CCTTTTTCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSCCSSCCCHHHHTTCTTCCEE
T ss_pred             cCCcc----ChHHHhcCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCcCCccCchhhhccCCCCCEE
Confidence            77776    99999999999999999998 665  45777776      999999999999999999  89999999999


Q ss_pred             eccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCC-CcEEEeeccCCCCCCCCC-c-
Q 003090          373 DLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR-LTSLHIHIPEGKIMPSDM-S-  449 (848)
Q Consensus       373 ~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~-L~~L~l~~~~~~~~~~~~-~-  449 (848)
                      ++++|...+.+| . ++++++|++|++++|.+. .             .+..+..+++ |+.|++++|.+..+|..+ . 
T Consensus       336 ~L~~N~l~g~ip-~-~~~l~~L~~L~L~~N~l~-~-------------lp~~l~~l~~~L~~L~Ls~N~l~~lp~~~~~~  399 (636)
T 4eco_A          336 ECLYNQLEGKLP-A-FGSEIKLASLNLAYNQIT-E-------------IPANFCGFTEQVENLSFAHNKLKYIPNIFDAK  399 (636)
T ss_dssp             ECCSCCCEEECC-C-CEEEEEESEEECCSSEEE-E-------------CCTTSEEECTTCCEEECCSSCCSSCCSCCCTT
T ss_pred             eCcCCcCccchh-h-hCCCCCCCEEECCCCccc-c-------------ccHhhhhhcccCcEEEccCCcCcccchhhhhc
Confidence            999998887899 5 899999999999999887 3             5667999999 999999999999999876 3 


Q ss_pred             -cCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeecccccccccccccc
Q 003090          450 -FQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLA  528 (848)
Q Consensus       450 -~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~  528 (848)
                       +++|+.|++..+......+..+.......+.                         .++|+.|+++++... .++..+ 
T Consensus       400 ~l~~L~~L~Ls~N~l~~~~p~~l~~~~~~~~~-------------------------~~~L~~L~Ls~N~l~-~lp~~~-  452 (636)
T 4eco_A          400 SVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFK-------------------------GINVSSINLSNNQIS-KFPKEL-  452 (636)
T ss_dssp             CSSCEEEEECCSSCTTTTTTCSSCTTCSSCCC-------------------------CCCEEEEECCSSCCC-SCCTHH-
T ss_pred             ccCccCEEECcCCcCCCcchhhhccccccccc-------------------------CCCCCEEECcCCccC-cCCHHH-
Confidence             4489999988665422111111100000000                         257888888877654 333322 


Q ss_pred             ccCCCCCcEEEEecCCCceeecccccccc---cccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHh
Q 003090          529 NDGFNELMFLVIFRCNEMKYLLNSLERTL---RVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKI  605 (848)
Q Consensus       529 ~~~l~~L~~L~l~~~~~l~~l~~~~~~~~---~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~  605 (848)
                      ...+++|++|+++++... .++.......   ...+++|++|+++++ +++.+... +....+++|+.|++++|. + ..
T Consensus       453 ~~~l~~L~~L~Ls~N~l~-~i~~~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~lp~~-~~~~~l~~L~~L~Ls~N~-l-~~  527 (636)
T 4eco_A          453 FSTGSPLSSINLMGNMLT-EIPKNSLKDENENFKNTYLLTSIDLRFN-KLTKLSDD-FRATTLPYLVGIDLSYNS-F-SK  527 (636)
T ss_dssp             HHTTCCCSEEECCSSCCS-BCCSSSSEETTEECTTGGGCCEEECCSS-CCCBCCGG-GSTTTCTTCCEEECCSSC-C-SS
T ss_pred             HccCCCCCEEECCCCCCC-CcCHHHhccccccccccCCccEEECcCC-cCCccChh-hhhccCCCcCEEECCCCC-C-CC
Confidence            134789999999988543 4432111100   122348999999988 45544211 111268999999999975 4 45


Q ss_pred             hhHHHHHhhccCcEEEEeccC------CceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccE
Q 003090          606 LLSHLVQSFQNLQRLRVYSCG------LLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKK  679 (848)
Q Consensus       606 l~~~~~~~l~~L~~L~l~~c~------~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~  679 (848)
                      +|..+ ..+++|++|++++|.      -...+|         ..+..+++|++|+++++. +..+|...     +++|+.
T Consensus       528 ip~~~-~~l~~L~~L~Ls~N~~ls~N~l~~~~p---------~~l~~l~~L~~L~Ls~N~-l~~ip~~~-----~~~L~~  591 (636)
T 4eco_A          528 FPTQP-LNSSTLKGFGIRNQRDAQGNRTLREWP---------EGITLCPSLTQLQIGSND-IRKVNEKI-----TPNISV  591 (636)
T ss_dssp             CCCGG-GGCSSCCEEECCSCBCTTCCBCCCCCC---------TTGGGCSSCCEEECCSSC-CCBCCSCC-----CTTCCE
T ss_pred             cChhh-hcCCCCCEEECCCCcccccCcccccCh---------HHHhcCCCCCEEECCCCc-CCccCHhH-----hCcCCE
Confidence            77654 678999999997643      233343         567789999999999976 47776652     389999


Q ss_pred             EEeecCcc
Q 003090          680 VRVEECDE  687 (848)
Q Consensus       680 L~i~~C~~  687 (848)
                      |++++|+-
T Consensus       592 L~Ls~N~l  599 (636)
T 4eco_A          592 LDIKDNPN  599 (636)
T ss_dssp             EECCSCTT
T ss_pred             EECcCCCC
Confidence            99999863

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.95  E-value=2.1e-26  Score=269.90  Aligned_cols=149  Identities=18%  Similarity=0.198  Sum_probs=87.3

Q ss_pred             ccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecC--
Q 003090          644 TELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATT--  721 (848)
Q Consensus       644 ~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~--  721 (848)
                      +..+++++.++++.+. +..+...  .+..+++|+.|+++++.....+.|..+..        +++|  +.+++.+|.  
T Consensus       441 ~~~l~~l~~l~ls~n~-l~~~~~~--~~~~~~~L~~L~Ls~N~~~~~~~~~~~~~--------l~~L--~~L~Ls~N~L~  507 (635)
T 4g8a_A          441 FLSLRNLIYLDISHTH-TRVAFNG--IFNGLSSLEVLKMAGNSFQENFLPDIFTE--------LRNL--TFLDLSQCQLE  507 (635)
T ss_dssp             TTTCTTCCEEECTTSC-CEECCTT--TTTTCTTCCEEECTTCEEGGGEECSCCTT--------CTTC--CEEECTTSCCC
T ss_pred             cccccccccccccccc-ccccccc--ccccchhhhhhhhhhcccccccCchhhhh--------cccc--CEEECCCCccC
Confidence            3445555555555432 2222222  13556677777777666555544443332        2233  334444431  


Q ss_pred             -CCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecccccceeecCCcccccccCCCccceecccccccc
Q 003090          722 -STSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEIIMDDEGEVGLQGASTKKITFPSLFGIK  800 (848)
Q Consensus       722 -~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~~~~~~sL~~L~  800 (848)
                       -.+..+..+++|++|+++++ +|+.+++ ..+.++++|++|+++++. +..+.  ..   .+..+      +++|+.|+
T Consensus       508 ~l~~~~f~~l~~L~~L~Ls~N-~l~~l~~-~~~~~l~~L~~L~Ls~N~-l~~~~--~~---~l~~l------~~~L~~L~  573 (635)
T 4g8a_A          508 QLSPTAFNSLSSLQVLNMSHN-NFFSLDT-FPYKCLNSLQVLDYSLNH-IMTSK--KQ---ELQHF------PSSLAFLN  573 (635)
T ss_dssp             EECTTTTTTCTTCCEEECTTS-CCCBCCC-GGGTTCTTCCEEECTTSC-CCBCC--SS---CTTCC------CTTCCEEE
T ss_pred             CcChHHHcCCCCCCEEECCCC-cCCCCCh-hHHhCCCCCCEEECCCCc-CCCCC--HH---HHHhh------hCcCCEEE
Confidence             12456778899999999984 7888865 457889999999999885 44441  11   22221      47899999


Q ss_pred             cccccccccccCCCcccccc
Q 003090          801 LCDLDSLACFCSTAHHFNFV  820 (848)
Q Consensus       801 i~~cp~L~~~~~~~~~~~~~  820 (848)
                      +.+.| +...|.......|+
T Consensus       574 L~~Np-~~C~C~~~~~~~wl  592 (635)
T 4g8a_A          574 LTQND-FACTCEHQSFLQWI  592 (635)
T ss_dssp             CTTCC-BCCSGGGHHHHHHH
T ss_pred             eeCCC-CcccCCcHHHHHHH
Confidence            98877 66655543334444

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=99.94  E-value=7.9e-26  Score=259.86  Aligned_cols=457  Identities=19%  Similarity=0.168  Sum_probs=280.6

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.+++++|.++.+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+.+.    .|.
T Consensus        34 ~~l~ls~~~L~~ip~~~~-~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~--------------N~l~~~----~~~   94 (562)
T 3a79_B           34 SMVDYSNRNLTHVPKDLP-PRTKALSLSQNSISELRMPDISFLSELRVLRLSH--------------NRIRSL----DFH   94 (562)
T ss_dssp             CEEECTTSCCCSCCTTSC-TTCCEEECCSSCCCCCCGGGTTTCTTCCEEECCS--------------CCCCEE----CTT
T ss_pred             cEEEcCCCCCccCCCCCC-CCcCEEECCCCCccccChhhhccCCCccEEECCC--------------CCCCcC----CHH
Confidence            679999999999998765 8999999999999999877789999999999999              888874    478


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccC--hhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIP--VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp--~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+..+++|++|++++|.+...+..  .+++|++|++++|.++.+|  ..++++++|++|++++|.....   . +..+++
T Consensus        95 ~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~L~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n~l~~~---~-~~~l~~  168 (562)
T 3a79_B           95 VFLFNQDLEYLDVSHNRLQNISCC--PMASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQL---D-LLPVAH  168 (562)
T ss_dssp             TTTTCTTCCEEECTTSCCCEECSC--CCTTCSEEECCSSCCSBCCCCGGGGGCTTCCEEEEECSBCCTT---T-TGGGTT
T ss_pred             HhCCCCCCCEEECCCCcCCccCcc--ccccCCEEECCCCCccccCchHhhcccCcccEEecCCCccccC---c-hhhhhh
Confidence            899999999999999987765544  8999999999999998654  7899999999999999876542   2 556666


Q ss_pred             c--cEEecccccc--ccccccccccccCcccchhhhcccC--CCcEEEeeccCCCCCCCCC---ccCCCCeEEEEeCCC-
Q 003090          394 L--EELYMSHSFR--HWQFESESEEDSSSNAKFIELGALS--RLTSLHIHIPEGKIMPSDM---SFQNLTSFSIAIGDL-  463 (848)
Q Consensus       394 L--~~L~l~~~~~--~~~~~~~~~~~~~~~~~~~~L~~l~--~L~~L~l~~~~~~~~~~~~---~~~~L~~L~l~~~~~-  463 (848)
                      |  ++|++++|.+  ...             .+..+..+.  .| .++++.|.+.......   .+++|+.+++..+.. 
T Consensus       169 L~L~~L~L~~n~l~~~~~-------------~~~~l~~l~~~~l-~l~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~~~  234 (562)
T 3a79_B          169 LHLSCILLDLVSYHIKGG-------------ETESLQIPNTTVL-HLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDEN  234 (562)
T ss_dssp             SCEEEEEEEESSCCCCSS-------------SCCEEEECCEEEE-EEEECSSSCCCCCCEEEESSEEEEEEEEEECCSTT
T ss_pred             ceeeEEEeeccccccccc-------------CcccccccCcceE-EEEecCccchhhhhhhcccccceEEEecccccccc
Confidence            6  9999999887  443             233344433  12 3455555544322221   456666666664321 


Q ss_pred             ---------CCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCC
Q 003090          464 ---------EERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNE  534 (848)
Q Consensus       464 ---------~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~  534 (848)
                               .....+.++.+.+....-.         ...+..++.+..  .++|++|+++++.....++..+.....++
T Consensus       235 ~~~l~~~~~~l~~l~~L~~L~L~~~~l~---------~~~~~~~~~~~~--~~~L~~L~l~~n~l~~~ip~~~~~~~~~~  303 (562)
T 3a79_B          235 CQRLMTFLSELTRGPTLLNVTLQHIETT---------WKCSVKLFQFFW--PRPVEYLNIYNLTITERIDREEFTYSETA  303 (562)
T ss_dssp             HHHHHHHHHHHHSCSSCEEEEEEEEEEC---------HHHHHHHHHHHT--TSSEEEEEEEEEEECSCCCCCCCCCCSCS
T ss_pred             cchHHHHHHHHhccCcceEEEecCCcCc---------HHHHHHHHHhhh--cccccEEEEeccEeeccccchhhhccccc
Confidence                     0112233333333322100         001112222211  24788888887765544443321111255


Q ss_pred             CcEEEEecCCCce-eecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHh
Q 003090          535 LMFLVIFRCNEMK-YLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQS  613 (848)
Q Consensus       535 L~~L~l~~~~~l~-~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~  613 (848)
                      |+.|.+.+..... .++.. ........++|++|+++++. +..+    ...+.+++|+.|++++|.-- ...|.. +..
T Consensus       304 L~~L~~~~~~~~~~~~p~~-~~~~~~~~~~L~~L~l~~n~-~~~~----~~~~~l~~L~~L~l~~n~l~-~~~~~~-~~~  375 (562)
T 3a79_B          304 LKSLMIEHVKNQVFLFSKE-ALYSVFAEMNIKMLSISDTP-FIHM----VCPPSPSSFTFLNFTQNVFT-DSVFQG-CST  375 (562)
T ss_dssp             CCEEEEEEEEECCCSSCHH-HHHHHHHTCCCSEEEEESSC-CCCC----CCCSSCCCCCEEECCSSCCC-TTTTTT-CCS
T ss_pred             chheehhhcccceeecChh-hhhhhhccCcceEEEccCCC-cccc----cCccCCCCceEEECCCCccc-cchhhh-hcc
Confidence            5555555443221 11000 00011112568888888874 3222    11145788888888887533 334433 267


Q ss_pred             hccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccccccc
Q 003090          614 FQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFP  693 (848)
Q Consensus       614 l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p  693 (848)
                      +++|++|++++|. ++.++..      ...+..+++|++|+++++.--..++...  +..+++|+.|++++|. ++...|
T Consensus       376 l~~L~~L~L~~N~-l~~~~~~------~~~~~~l~~L~~L~l~~N~l~~~~~~~~--~~~l~~L~~L~l~~n~-l~~~~~  445 (562)
T 3a79_B          376 LKRLQTLILQRNG-LKNFFKV------ALMTKNMSSLETLDVSLNSLNSHAYDRT--CAWAESILVLNLSSNM-LTGSVF  445 (562)
T ss_dssp             CSSCCEEECCSSC-CCBTTHH------HHTTTTCTTCCEEECTTSCCBSCCSSCC--CCCCTTCCEEECCSSC-CCGGGG
T ss_pred             cCCCCEEECCCCC-cCCcccc------hhhhcCCCCCCEEECCCCcCCCccChhh--hcCcccCCEEECCCCC-CCcchh
Confidence            7888888888863 4433210      0335678888888888875333355432  5667888888888874 332222


Q ss_pred             CccccccccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEeccccccee
Q 003090          694 ANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPTLQEI  773 (848)
Q Consensus       694 ~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~L~~l  773 (848)
                      ..+                               .  ++|+.|++++| +++.+|.  .+.++++|++|+++++. ++.+
T Consensus       446 ~~l-------------------------------~--~~L~~L~L~~N-~l~~ip~--~~~~l~~L~~L~L~~N~-l~~l  488 (562)
T 3a79_B          446 RCL-------------------------------P--PKVKVLDLHNN-RIMSIPK--DVTHLQALQELNVASNQ-LKSV  488 (562)
T ss_dssp             SSC-------------------------------C--TTCSEEECCSS-CCCCCCT--TTTSSCCCSEEECCSSC-CCCC
T ss_pred             hhh-------------------------------c--CcCCEEECCCC-cCcccCh--hhcCCCCCCEEECCCCC-CCCC
Confidence            111                               1  56777777775 6676653  23377777777777764 4444


Q ss_pred             ecCCcccccccCCCccceecccccccccccccccccc
Q 003090          774 IMDDEGEVGLQGASTKKITFPSLFGIKLCDLDSLACF  810 (848)
Q Consensus       774 ~~~~~~~~~l~~~~~~~~~~~sL~~L~i~~cp~L~~~  810 (848)
                      +..     .+..       +++|+.|++.++| +...
T Consensus       489 ~~~-----~~~~-------l~~L~~L~l~~N~-~~c~  512 (562)
T 3a79_B          489 PDG-----VFDR-------LTSLQYIWLHDNP-WDCT  512 (562)
T ss_dssp             CTT-----STTT-------CTTCCCEECCSCC-BCCC
T ss_pred             CHH-----HHhc-------CCCCCEEEecCCC-cCCC
Confidence            221     1111       5777777777766 4443

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.94  E-value=4.6e-26  Score=259.63  Aligned_cols=446  Identities=15%  Similarity=0.159  Sum_probs=273.1

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      ++|++++|.+..+|..++   ++|++|++++              +.+...    .|..+..+++|++|++++|.+....
T Consensus         3 ~~l~ls~n~l~~ip~~~~---~~L~~L~Ls~--------------n~i~~~----~~~~~~~l~~L~~L~Ls~n~l~~~~   61 (520)
T 2z7x_B            3 FLVDRSKNGLIHVPKDLS---QKTTILNISQ--------------NYISEL----WTSDILSLSKLRILIISHNRIQYLD   61 (520)
T ss_dssp             CEEECTTSCCSSCCCSCC---TTCSEEECCS--------------SCCCCC----CHHHHTTCTTCCEEECCSSCCCEEE
T ss_pred             ceEecCCCCccccccccc---ccccEEECCC--------------Cccccc----ChhhccccccccEEecCCCccCCcC
Confidence            578999999999998653   8999999999              888883    4478999999999999999888774


Q ss_pred             -hhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcccc-ccChhhhhccccccEEeccccccccccccccccc
Q 003090          338 -SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE-LIPRGVLSRLRKLEELYMSHSFRHWQFESESEED  415 (848)
Q Consensus       338 -~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~-~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  415 (848)
                       ..++++++|++|++++|.++.+|..  .+++|++|++++|...+ .+|.. ++++++|++|++++|.+..         
T Consensus        62 ~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~L~L~~N~l~~~~~p~~-~~~l~~L~~L~L~~n~l~~---------  129 (520)
T 2z7x_B           62 ISVFKFNQELEYLDLSHNKLVKISCH--PTVNLKHLDLSFNAFDALPICKE-FGNMSQLKFLGLSTTHLEK---------  129 (520)
T ss_dssp             GGGGTTCTTCCEEECCSSCCCEEECC--CCCCCSEEECCSSCCSSCCCCGG-GGGCTTCCEEEEEESSCCG---------
T ss_pred             hHHhhcccCCCEEecCCCceeecCcc--ccCCccEEeccCCccccccchhh-hccCCcceEEEecCcccch---------
Confidence             7899999999999999999999987  89999999999998766 46777 8999999999999998754         


Q ss_pred             cCcccchhhhcccCCC--cEEEeeccCC--C-CCCCCCccCCC--CeEEEEeCCCCCCCCCcccceEEeccccccccccc
Q 003090          416 SSSNAKFIELGALSRL--TSLHIHIPEG--K-IMPSDMSFQNL--TSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMG  488 (848)
Q Consensus       416 ~~~~~~~~~L~~l~~L--~~L~l~~~~~--~-~~~~~~~~~~L--~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~  488 (848)
                             ..+..+++|  +.|++++|.+  . ..|..+  .+|  +.+.+.........  ......+.           
T Consensus       130 -------~~~~~l~~L~L~~L~l~~n~l~~~~~~~~~l--~~l~~~~l~l~l~~n~~~~--~~~~~~~~-----------  187 (520)
T 2z7x_B          130 -------SSVLPIAHLNISKVLLVLGETYGEKEDPEGL--QDFNTESLHIVFPTNKEFH--FILDVSVK-----------  187 (520)
T ss_dssp             -------GGGGGGTTSCEEEEEEEECTTTTSSCCTTTT--TTCCEEEEEEECCSSSCCC--CCCCCCCT-----------
T ss_pred             -------hhccccccceeeEEEeecccccccccccccc--cccccceEEEEeccCcchh--hhhhhhhh-----------
Confidence                   245666777  9999999987  3 333333  333  34444322211000  00000000           


Q ss_pred             CccccchhhHHHHHHHHHhhcceeeecccc------ccccccccccccCCCCCcEEEEecCCCceeecccccccccccCC
Q 003090          489 LSQDMRISALHSWIKNLLLRSEILALAEVN------YFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLH  562 (848)
Q Consensus       489 l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~------~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p  562 (848)
                                      .+++|+.|+++++.      ........+  ..+++|+.|++.++.......  .........+
T Consensus       188 ----------------~l~~L~~L~l~~n~~~~~~~~~~~~~~~l--~~l~~L~~L~l~~~~l~~~~~--~~~~~~~~~~  247 (520)
T 2z7x_B          188 ----------------TVANLELSNIKCVLEDNKCSYFLSILAKL--QTNPKLSNLTLNNIETTWNSF--IRILQLVWHT  247 (520)
T ss_dssp             ----------------TCSEEEECCEEECCSTTTTHHHHHHHHGG--GGCTTCCEEEEEEEEEEHHHH--HHHHHHHHTS
T ss_pred             ----------------cccceeeccccccccccccceeecchhhh--ccccchhhccccccccCHHHH--HHHHHHhhhC
Confidence                            02455566665543      011111122  356777777777653211000  0001111245


Q ss_pred             CccEEecccccccc-cccccccc--cccCCCcceEEEecCchhhHhhhHHHHHhh---ccCcEEEEeccCCceeeeeccc
Q 003090          563 KLEWLFIRENQNFV-EICHGQLP--AGCLSNVKRSDVVDCGSILKILLSHLVQSF---QNLQRLRVYSCGLLVSVFEIER  636 (848)
Q Consensus       563 ~L~~L~l~~~~~L~-~~~~~~~~--~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l---~~L~~L~l~~c~~l~~~~~~~~  636 (848)
                      +|++|+++++. +. .+....+.  .+.+++|+.+++.++..   .+|......+   ++|+.|++++|.-. ..+    
T Consensus       248 ~L~~L~l~~n~-l~~~~p~~~~~~~~~~l~~L~~l~l~~n~~---~~p~~~~~~~~~~~~L~~L~l~~n~l~-~~~----  318 (520)
T 2z7x_B          248 TVWYFSISNVK-LQGQLDFRDFDYSGTSLKALSIHQVVSDVF---GFPQSYIYEIFSNMNIKNFTVSGTRMV-HML----  318 (520)
T ss_dssp             SCSEEEEEEEE-EESCCCCCCCCCCSCCCCEEEEEEEEECCC---CSCTHHHHHHHHTCCCSEEEEESSCCC-CCC----
T ss_pred             cccEEEeeccc-ccCccccchhhcccccCceeEeccccccce---ecchhhhhcccccCceeEEEcCCCccc-ccc----
Confidence            77777777764 22 21110000  03466677777766542   3442222333   45777777776532 111    


Q ss_pred             cccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccccc--ccCccccccccceeeeccccccc
Q 003090          637 VNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQV--FPANFGKKAAAEEMVLYRKRRDQ  714 (848)
Q Consensus       637 ~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~--~p~~~~~~~~~~~l~l~~l~~~~  714 (848)
                            ....+++|++|+++++.--..++..   +..+++|+.|++++|. ++.+  +|..+..        +++|  +.
T Consensus       319 ------~~~~l~~L~~L~Ls~n~l~~~~~~~---~~~l~~L~~L~L~~N~-l~~l~~~~~~~~~--------l~~L--~~  378 (520)
T 2z7x_B          319 ------CPSKISPFLHLDFSNNLLTDTVFEN---CGHLTELETLILQMNQ-LKELSKIAEMTTQ--------MKSL--QQ  378 (520)
T ss_dssp             ------CCSSCCCCCEEECCSSCCCTTTTTT---CCCCSSCCEEECCSSC-CCBHHHHHHHHTT--------CTTC--CE
T ss_pred             ------chhhCCcccEEEeECCccChhhhhh---hccCCCCCEEEccCCc-cCccccchHHHhh--------CCCC--CE
Confidence                  1146677777777776432223322   4567777777777764 3321  1221211        2333  44


Q ss_pred             eeeeecC--C-CCC-CCCCCCCccEEEEecCCCCceecccchhhcc-ccccEEEEecccccceeecCCcccccccCCCcc
Q 003090          715 IHIHATT--S-TSS-PTPSLGNLVSITIRGCGKLRNLFTTSMVKSL-VRLESLEVRSCPTLQEIIMDDEGEVGLQGASTK  789 (848)
Q Consensus       715 l~i~~c~--~-~~~-~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l-~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~~  789 (848)
                      +++.+|.  . .+. .+..+++|++|++++|.--..+|     ..+ ++|++|++++| .+..++.  .           
T Consensus       379 L~Ls~N~l~~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~-----~~l~~~L~~L~Ls~N-~l~~ip~--~-----------  439 (520)
T 2z7x_B          379 LDISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIF-----RCLPPRIKVLDLHSN-KIKSIPK--Q-----------  439 (520)
T ss_dssp             EECCSSCCBCCGGGCSCCCCTTCCEEECCSSCCCGGGG-----GSCCTTCCEEECCSS-CCCCCCG--G-----------
T ss_pred             EECCCCcCCcccccchhccCccCCEEECcCCCCCcchh-----hhhcccCCEEECCCC-cccccch--h-----------
Confidence            4444441  1 222 35678999999999975323332     223 79999999999 4555522  1           


Q ss_pred             ceecccccccccccccccccccCC-Cc---ccccccccccee
Q 003090          790 KITFPSLFGIKLCDLDSLACFCST-AH---HFNFVFHLGQKI  827 (848)
Q Consensus       790 ~~~~~sL~~L~i~~cp~L~~~~~~-~~---~~~~~~i~~~~~  827 (848)
                      ...+++|++|++++|. ++.++.. +.   .+..+.+.+-.+
T Consensus       440 ~~~l~~L~~L~L~~N~-l~~l~~~~~~~l~~L~~L~l~~N~~  480 (520)
T 2z7x_B          440 VVKLEALQELNVASNQ-LKSVPDGIFDRLTSLQKIWLHTNPW  480 (520)
T ss_dssp             GGGCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCB
T ss_pred             hhcCCCCCEEECCCCc-CCccCHHHhccCCcccEEECcCCCC
Confidence            1127999999999985 7776654 33   344455555444

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.93  E-value=5.4e-25  Score=257.92  Aligned_cols=473  Identities=19%  Similarity=0.162  Sum_probs=261.7

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      ++..|+..+..  .++.|+|++|.|+.+|+. + ++++|++|+|++|.+..+++..|.++++|++|+|++          
T Consensus        42 ~l~~vP~~lp~--~~~~LdLs~N~i~~l~~~~f~~l~~L~~L~Ls~N~i~~i~~~~f~~L~~L~~L~Ls~----------  109 (635)
T 4g8a_A           42 NFYKIPDNLPF--STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG----------  109 (635)
T ss_dssp             CCSSCCSSSCT--TCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTT----------
T ss_pred             CcCccCCCCCc--CCCEEEeeCCCCCCCCHHHHhCCCCCCEEECCCCcCCCcChhHhcCCCCCCEEEccC----------
Confidence            45556655543  468899999999999864 3 899999999999999999988889999999999999          


Q ss_pred             CCCCCCCCCCCCCCCC-chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCc--ccChhhccCCcccEEec
Q 003090          299 PFLFPPLPSSPLFLLP-SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVS--EIPVSFGRLSHLRLLDL  374 (848)
Q Consensus       299 ~~~~~~l~~~~~~~lp-~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~--~lp~~i~~L~~L~~L~l  374 (848)
                          |.++.     +| ..|.++++|++|++++|.+...+ ..++++++|++|++++|.++  .+|..++.+++|++|++
T Consensus       110 ----N~l~~-----l~~~~f~~L~~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L  180 (635)
T 4g8a_A          110 ----NPIQS-----LALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDL  180 (635)
T ss_dssp             ----CCCCE-----ECGGGGTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEEC
T ss_pred             ----CcCCC-----CCHHHhcCCCCCCEEECCCCcCCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhcc
Confidence                88887     66 45899999999999999888776 46899999999999999887  46788899999999999


Q ss_pred             cCCccccccChhhhhcccccc----EEecccccccccccccccc-----------ccCcccchhhhcccCCCcEEEee--
Q 003090          375 TGCYILELIPRGVLSRLRKLE----ELYMSHSFRHWQFESESEE-----------DSSSNAKFIELGALSRLTSLHIH--  437 (848)
Q Consensus       375 ~~~~~~~~~p~~~l~~l~~L~----~L~l~~~~~~~~~~~~~~~-----------~~~~~~~~~~L~~l~~L~~L~l~--  437 (848)
                      ++|...+..|.. +..+.+++    .++++.|.+....++....           ..........+..+..++...+.  
T Consensus       181 ~~N~l~~~~~~~-l~~L~~l~~~~~~~~ls~n~l~~i~~~~~~~~~~~~l~l~~n~~~~~~~~~~~~~l~~l~~~~l~~~  259 (635)
T 4g8a_A          181 SSNKIQSIYCTD-LRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLG  259 (635)
T ss_dssp             CSSCCCEECGGG-GHHHHTCTTCCCEEECTTCCCCEECTTTTTTCEEEEEEEESCCSSHHHHHHHHHTTTTCEEEEEEEE
T ss_pred             cCcccccccccc-ccchhhhhhhhhhhhcccCcccccCcccccchhhhhhhhhcccccccccchhhcCCccccccccccc
Confidence            998765544444 66665544    4556665554322110000           00000111223334444433332  


Q ss_pred             ----------------------------ccCCC----CCCCCC-ccCCCCeEEEEeCCC----CCCCCCcccceEEeccc
Q 003090          438 ----------------------------IPEGK----IMPSDM-SFQNLTSFSIAIGDL----EERPLSDFIGLFLQKFK  480 (848)
Q Consensus       438 ----------------------------~~~~~----~~~~~~-~~~~L~~L~l~~~~~----~~~~~~~l~~l~l~~~~  480 (848)
                                                  .+...    ...... ...+++.+.+.....    .......++.+.+....
T Consensus       260 ~~~~~~~l~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~L~~L~l~~~~  339 (635)
T 4g8a_A          260 EFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDGIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCK  339 (635)
T ss_dssp             CCTTSCCCSCCCTTTTGGGGGSEEEEEEEECCCSCEEECTTTTGGGTTCSEEEEESCEEEECGGGGSCCCCSEEEEESCE
T ss_pred             ccccccccccccccccccccchhhhhhhhhhhcccccchhhhhhhhcccccccccccccccccccccchhhhhhhccccc
Confidence                                        11111    011111 344566665543322    11122233444443321


Q ss_pred             ccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeeccccccccccc
Q 003090          481 KRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVT  560 (848)
Q Consensus       481 ~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~  560 (848)
                           ...+..            ..++.|+.+.+.++..... .   ....+++|+.|.++++......   ........
T Consensus       340 -----~~~~~~------------~~l~~L~~l~l~~n~~~~~-~---~~~~l~~L~~L~ls~n~l~~~~---~~~~~~~~  395 (635)
T 4g8a_A          340 -----FGQFPT------------LKLKSLKRLTFTSNKGGNA-F---SEVDLPSLEFLDLSRNGLSFKG---CCSQSDFG  395 (635)
T ss_dssp             -----ESSCCC------------CBCTTCCEEEEESCCSCCB-C---CCCBCTTCCEEECCSSCCBEEE---ECCHHHHS
T ss_pred             -----ccCcCc------------ccchhhhhcccccccCCCC-c---ccccccccccchhhcccccccc---ccccchhh
Confidence                 000000            0024555555554443221 1   1124566777766655432110   00012223


Q ss_pred             CCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccc
Q 003090          561 LHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIA  640 (848)
Q Consensus       561 ~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~  640 (848)
                      .++|+.|++..+... ..   ......+++|+.+++..+... ...+......+++|+.++++++.--...+        
T Consensus       396 ~~~L~~L~~~~~~~~-~~---~~~~~~l~~L~~l~l~~~~~~-~~~~~~~~~~l~~l~~l~ls~n~l~~~~~--------  462 (635)
T 4g8a_A          396 TISLKYLDLSFNGVI-TM---SSNFLGLEQLEHLDFQHSNLK-QMSEFSVFLSLRNLIYLDISHTHTRVAFN--------  462 (635)
T ss_dssp             CSCCCEEECCSCSEE-EE---CSCCTTCTTCCEEECTTSEEE-STTSSCTTTTCTTCCEEECTTSCCEECCT--------
T ss_pred             hhhhhhhhccccccc-cc---cccccccccccchhhhhcccc-ccccccccccccccccccccccccccccc--------
Confidence            455666665554311 11   011224555555555554433 33332222445555555555543222111        


Q ss_pred             cccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeec
Q 003090          641 KEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHAT  720 (848)
Q Consensus       641 ~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c  720 (848)
                       ..+..+++|+.|+++++.....+....  +..+++|+.|++++| +++.+.|..+..        +++|  +.+.+.++
T Consensus       463 -~~~~~~~~L~~L~Ls~N~~~~~~~~~~--~~~l~~L~~L~Ls~N-~L~~l~~~~f~~--------l~~L--~~L~Ls~N  528 (635)
T 4g8a_A          463 -GIFNGLSSLEVLKMAGNSFQENFLPDI--FTELRNLTFLDLSQC-QLEQLSPTAFNS--------LSSL--QVLNMSHN  528 (635)
T ss_dssp             -TTTTTCTTCCEEECTTCEEGGGEECSC--CTTCTTCCEEECTTS-CCCEECTTTTTT--------CTTC--CEEECTTS
T ss_pred             -cccccchhhhhhhhhhcccccccCchh--hhhccccCEEECCCC-ccCCcChHHHcC--------CCCC--CEEECCCC
Confidence             233445555555555554444332221  344555555555555 344443333322        1222  22222222


Q ss_pred             --CCC-CCCCCCCCCccEEEEecCCCCceecccchhhcc-ccccEEEEeccc
Q 003090          721 --TST-SSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSL-VRLESLEVRSCP  768 (848)
Q Consensus       721 --~~~-~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l-~~L~~L~i~~C~  768 (848)
                        ... +..+..+++|+.|++++ ++|+.+++ ..+.++ ++|++|+++++|
T Consensus       529 ~l~~l~~~~~~~l~~L~~L~Ls~-N~l~~~~~-~~l~~l~~~L~~L~L~~Np  578 (635)
T 4g8a_A          529 NFFSLDTFPYKCLNSLQVLDYSL-NHIMTSKK-QELQHFPSSLAFLNLTQND  578 (635)
T ss_dssp             CCCBCCCGGGTTCTTCCEEECTT-SCCCBCCS-SCTTCCCTTCCEEECTTCC
T ss_pred             cCCCCChhHHhCCCCCCEEECCC-CcCCCCCH-HHHHhhhCcCCEEEeeCCC
Confidence              011 23456789999999999 57888866 455666 789999998755

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.93  E-value=9e-25  Score=244.69  Aligned_cols=342  Identities=18%  Similarity=0.215  Sum_probs=192.7

Q ss_pred             ccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      +++++.|+++++.+..+|.  +..+++|++|++++              +.+..     +|. +..+++|++|++++|.+
T Consensus        45 l~~l~~L~l~~~~i~~l~~--~~~l~~L~~L~Ls~--------------n~l~~-----~~~-~~~l~~L~~L~l~~n~l  102 (466)
T 1o6v_A           45 LDQVTTLQADRLGIKSIDG--VEYLNNLTQINFSN--------------NQLTD-----ITP-LKNLTKLVDILMNNNQI  102 (466)
T ss_dssp             HHTCCEEECCSSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GTTCTTCCEEECCSSCC
T ss_pred             hccccEEecCCCCCccCcc--hhhhcCCCEEECCC--------------CccCC-----chh-hhccccCCEEECCCCcc
Confidence            4566666666666666654  45666667777666              55655     444 66666677777766655


Q ss_pred             cCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccc
Q 003090          334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       334 ~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                      ...++ ++++++|++|++++|.++.+|. +.++++|++|++++|... .++.  ++++++|++|++.++ +.        
T Consensus       103 ~~~~~-~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~l~~n~l~-~~~~--~~~l~~L~~L~l~~~-~~--------  168 (466)
T 1o6v_A          103 ADITP-LANLTNLTGLTLFNNQITDIDP-LKNLTNLNRLELSSNTIS-DISA--LSGLTSLQQLSFGNQ-VT--------  168 (466)
T ss_dssp             CCCGG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEEEEEEEC-CCGG--GTTCTTCSEEEEEES-CC--------
T ss_pred             ccChh-hcCCCCCCEEECCCCCCCCChH-HcCCCCCCEEECCCCccC-CChh--hccCCcccEeecCCc-cc--------
Confidence            55444 6666677777776666666654 666667777777665433 3443  566666776666422 11        


Q ss_pred             cccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCcccc
Q 003090          414 EDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDM  493 (848)
Q Consensus       414 ~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~  493 (848)
                             ....+.++++|+.|++++|.+..++....+++|+.|++.                                  
T Consensus       169 -------~~~~~~~l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~----------------------------------  207 (466)
T 1o6v_A          169 -------DLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIAT----------------------------------  207 (466)
T ss_dssp             -------CCGGGTTCTTCCEEECCSSCCCCCGGGGGCTTCSEEECC----------------------------------
T ss_pred             -------CchhhccCCCCCEEECcCCcCCCChhhccCCCCCEEEec----------------------------------
Confidence                   112366666667777666665544321144444444443                                  


Q ss_pred             chhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccccc
Q 003090          494 RISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQ  573 (848)
Q Consensus       494 ~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~  573 (848)
                                            ++..... ..   ...+++|+.|++.+|. ++.+      .....+++|++|++++|.
T Consensus       208 ----------------------~n~l~~~-~~---~~~l~~L~~L~l~~n~-l~~~------~~l~~l~~L~~L~l~~n~  254 (466)
T 1o6v_A          208 ----------------------NNQISDI-TP---LGILTNLDELSLNGNQ-LKDI------GTLASLTNLTDLDLANNQ  254 (466)
T ss_dssp             ----------------------SSCCCCC-GG---GGGCTTCCEEECCSSC-CCCC------GGGGGCTTCSEEECCSSC
T ss_pred             ----------------------CCccccc-cc---ccccCCCCEEECCCCC-cccc------hhhhcCCCCCEEECCCCc
Confidence                                  2211110 00   1234556666665553 2221      233445666666666653


Q ss_pred             ccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEE
Q 003090          574 NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKL  653 (848)
Q Consensus       574 ~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L  653 (848)
                       +..+    .+...+++|+.|++++|. + ..+++  ...+++|++|++++|. ++.++          .+..+++|++|
T Consensus       255 -l~~~----~~~~~l~~L~~L~l~~n~-l-~~~~~--~~~l~~L~~L~L~~n~-l~~~~----------~~~~l~~L~~L  314 (466)
T 1o6v_A          255 -ISNL----APLSGLTKLTELKLGANQ-I-SNISP--LAGLTALTNLELNENQ-LEDIS----------PISNLKNLTYL  314 (466)
T ss_dssp             -CCCC----GGGTTCTTCSEEECCSSC-C-CCCGG--GTTCTTCSEEECCSSC-CSCCG----------GGGGCTTCSEE
T ss_pred             -cccc----hhhhcCCCCCEEECCCCc-c-Ccccc--ccCCCccCeEEcCCCc-ccCch----------hhcCCCCCCEE
Confidence             3222    223456666777666653 3 34444  2566777777777653 33331          24566777777


Q ss_pred             ecCCCccccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecCCCCCCCCCCCCc
Q 003090          654 TLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNL  733 (848)
Q Consensus       654 ~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L  733 (848)
                      ++++|. +..++    ++..+++|+.|++++|. ++.+                                 ..+..+++|
T Consensus       315 ~L~~n~-l~~~~----~~~~l~~L~~L~l~~n~-l~~~---------------------------------~~l~~l~~L  355 (466)
T 1o6v_A          315 TLYFNN-ISDIS----PVSSLTKLQRLFFYNNK-VSDV---------------------------------SSLANLTNI  355 (466)
T ss_dssp             ECCSSC-CSCCG----GGGGCTTCCEEECCSSC-CCCC---------------------------------GGGTTCTTC
T ss_pred             ECcCCc-CCCch----hhccCccCCEeECCCCc-cCCc---------------------------------hhhccCCCC
Confidence            777763 33332    24567777777777762 3321                                 123456777


Q ss_pred             cEEEEecCCCCceecccchhhccccccEEEEeccc
Q 003090          734 VSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCP  768 (848)
Q Consensus       734 ~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~  768 (848)
                      +.|++++| .+..+++   +..+++|++|++++|+
T Consensus       356 ~~L~l~~n-~l~~~~~---~~~l~~L~~L~l~~n~  386 (466)
T 1o6v_A          356 NWLSAGHN-QISDLTP---LANLTRITQLGLNDQA  386 (466)
T ss_dssp             CEEECCSS-CCCBCGG---GTTCTTCCEEECCCEE
T ss_pred             CEEeCCCC-ccCccch---hhcCCCCCEEeccCCc
Confidence            77887775 4555543   5677778888887775

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.93  E-value=1.1e-24  Score=244.01  Aligned_cols=340  Identities=20%  Similarity=0.209  Sum_probs=260.8

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.++++++.+..+|....+++|++|++++|.+..++.  +.++++|++|++++              +.+..     +
T Consensus        47 ~l~~L~l~~~~i~~l~~~~~l~~L~~L~Ls~n~l~~~~~--~~~l~~L~~L~l~~--------------n~l~~-----~  105 (466)
T 1o6v_A           47 QVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITP--LKNLTKLVDILMNN--------------NQIAD-----I  105 (466)
T ss_dssp             TCCEEECCSSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----C
T ss_pred             cccEEecCCCCCccCcchhhhcCCCEEECCCCccCCchh--hhccccCCEEECCC--------------Ccccc-----C
Confidence            467899999999998875589999999999999888887  68999999999999              88887     6


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      +. +.++++|++|++++|.+...++ +.++++|++|++++|.+..+| .++.+++|++|++++ .. ..++.  +.++++
T Consensus       106 ~~-~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~l~~n~l~~~~-~~~~l~~L~~L~l~~-~~-~~~~~--~~~l~~  178 (466)
T 1o6v_A          106 TP-LANLTNLTGLTLFNNQITDIDP-LKNLTNLNRLELSSNTISDIS-ALSGLTSLQQLSFGN-QV-TDLKP--LANLTT  178 (466)
T ss_dssp             GG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEEEEEEECCCG-GGTTCTTCSEEEEEE-SC-CCCGG--GTTCTT
T ss_pred             hh-hcCCCCCCEEECCCCCCCCChH-HcCCCCCCEEECCCCccCCCh-hhccCCcccEeecCC-cc-cCchh--hccCCC
Confidence            65 9999999999999997666544 899999999999999998887 489999999999974 33 33444  789999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccc
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIG  473 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~  473 (848)
                      |++|++++|.+..               +..+..+++|+.|++++|.+..++....+++|+.|++..+....  .+    
T Consensus       179 L~~L~l~~n~l~~---------------~~~l~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~--~~----  237 (466)
T 1o6v_A          179 LERLDISSNKVSD---------------ISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKD--IG----  237 (466)
T ss_dssp             CCEEECCSSCCCC---------------CGGGGGCTTCSEEECCSSCCCCCGGGGGCTTCCEEECCSSCCCC--CG----
T ss_pred             CCEEECcCCcCCC---------------ChhhccCCCCCEEEecCCcccccccccccCCCCEEECCCCCccc--ch----
Confidence            9999999998753               24588899999999999998877653378889999887544310  00    


Q ss_pred             eEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccc
Q 003090          474 LFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSL  553 (848)
Q Consensus       474 l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~  553 (848)
                          .                       + ..+++|+.|+++++...... .   ...+++|+.|++.+|.. ..+    
T Consensus       238 ----~-----------------------l-~~l~~L~~L~l~~n~l~~~~-~---~~~l~~L~~L~l~~n~l-~~~----  280 (466)
T 1o6v_A          238 ----T-----------------------L-ASLTNLTDLDLANNQISNLA-P---LSGLTKLTELKLGANQI-SNI----  280 (466)
T ss_dssp             ----G-----------------------G-GGCTTCSEEECCSSCCCCCG-G---GTTCTTCSEEECCSSCC-CCC----
T ss_pred             ----h-----------------------h-hcCCCCCEEECCCCccccch-h---hhcCCCCCEEECCCCcc-Ccc----
Confidence                0                       0 01478888888887654322 1   35778999999988853 322    


Q ss_pred             cccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeee
Q 003090          554 ERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFE  633 (848)
Q Consensus       554 ~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~  633 (848)
                        .....+++|++|+++++. ++.+    .+.+.+++|+.|++++|. + ..+++  ...+++|++|++++| .++.+  
T Consensus       281 --~~~~~l~~L~~L~L~~n~-l~~~----~~~~~l~~L~~L~L~~n~-l-~~~~~--~~~l~~L~~L~l~~n-~l~~~--  346 (466)
T 1o6v_A          281 --SPLAGLTALTNLELNENQ-LEDI----SPISNLKNLTYLTLYFNN-I-SDISP--VSSLTKLQRLFFYNN-KVSDV--  346 (466)
T ss_dssp             --GGGTTCTTCSEEECCSSC-CSCC----GGGGGCTTCSEEECCSSC-C-SCCGG--GGGCTTCCEEECCSS-CCCCC--
T ss_pred             --ccccCCCccCeEEcCCCc-ccCc----hhhcCCCCCCEEECcCCc-C-CCchh--hccCccCCEeECCCC-ccCCc--
Confidence              235678999999999884 5443    335578999999999885 4 45554  278899999999988 44444  


Q ss_pred             ccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCc
Q 003090          634 IERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECD  686 (848)
Q Consensus       634 ~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~  686 (848)
                              ..+..+++|+.|++++|. +..+.    ++..+++|+.|++++|+
T Consensus       347 --------~~l~~l~~L~~L~l~~n~-l~~~~----~~~~l~~L~~L~l~~n~  386 (466)
T 1o6v_A          347 --------SSLANLTNINWLSAGHNQ-ISDLT----PLANLTRITQLGLNDQA  386 (466)
T ss_dssp             --------GGGTTCTTCCEEECCSSC-CCBCG----GGTTCTTCCEEECCCEE
T ss_pred             --------hhhccCCCCCEEeCCCCc-cCccc----hhhcCCCCCEEeccCCc
Confidence                    346688999999999885 44332    36778999999999875

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=99.93  E-value=1.1e-24  Score=243.85  Aligned_cols=365  Identities=15%  Similarity=0.159  Sum_probs=258.0

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC-C
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL-P  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l-p  314 (848)
                      +.++.+++.++.+|. + .++|++|++++|.+..+++..|.++++|++|++++              +.+...    + |
T Consensus        13 ~~~~c~~~~l~~lp~-l-~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~~~~~----i~~   72 (455)
T 3v47_A           13 YNAICINRGLHQVPE-L-PAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQ--------------QTPGLV----IRN   72 (455)
T ss_dssp             TEEECCSSCCSSCCC-C-CTTCCEEECCSSCCCEECTTTTSSCTTCCEEECCC--------------CSTTCE----ECT
T ss_pred             cccCcCCCCcccCCC-C-CCccCEEEecCCccCcCChhHhccCccccEEECcC--------------Ccccce----ECc
Confidence            346677788888887 3 37899999999988888666678899999999998              666532    3 5


Q ss_pred             chhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCcc-cChh--hccCCcccEEeccCCccccccChhhhhc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVSE-IPVS--FGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~~-lp~~--i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      ..+..+++|++|++++|.+... +..++++++|++|++++|.++. +|..  ++++++|++|++++|...+..|...+.+
T Consensus        73 ~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~  152 (455)
T 3v47_A           73 NTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLN  152 (455)
T ss_dssp             TTTTTCTTCCEEECTTCTTCEECTTTTTTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGGG
T ss_pred             ccccccccCCEEeCCCCccCccChhhccCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccCC
Confidence            6688899999999999987766 4678899999999999998884 4444  8889999999999987776667665788


Q ss_pred             cccccEEeccccccccccccccccccCcccchhhhccc--CCCcEEEeeccCCCCCCCCC----------ccCCCCeEEE
Q 003090          391 LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGAL--SRLTSLHIHIPEGKIMPSDM----------SFQNLTSFSI  458 (848)
Q Consensus       391 l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l--~~L~~L~l~~~~~~~~~~~~----------~~~~L~~L~l  458 (848)
                      +++|++|++++|.+...             .+..+..+  .+|+.|+++++.+..++...          .+++|+.|++
T Consensus       153 l~~L~~L~L~~n~l~~~-------------~~~~l~~l~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~~~~~~~L~~L~L  219 (455)
T 3v47_A          153 MRRFHVLDLTFNKVKSI-------------CEEDLLNFQGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDL  219 (455)
T ss_dssp             CTTCCEEECTTCCBSCC-------------CTTTSGGGTTCEEEEEECTTCBCTTCSTTCTTHHHHCCTTTTCEEEEEEC
T ss_pred             CCcccEEeCCCCccccc-------------ChhhhhccccccccccccccCcccccchhhccccccccccccceeeeEec
Confidence            99999999999887765             33344444  57888899888877665432          3356666666


Q ss_pred             EeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHH--Hhhcceeeeccccccccccc----------c
Q 003090          459 AIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNL--LLRSEILALAEVNYFENIVS----------D  526 (848)
Q Consensus       459 ~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~--~~~L~~L~l~~~~~~~~~~~----------~  526 (848)
                      ..+..                               ....+.++...  .++|+.|.+.++........          .
T Consensus       220 s~n~l-------------------------------~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~  268 (455)
T 3v47_A          220 SGNGF-------------------------------KESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFT  268 (455)
T ss_dssp             TTSCC-------------------------------CHHHHHHHHHHTTTCCEEEEECTTCTTTSCCTTCCSSCCCCTTT
T ss_pred             CCCcc-------------------------------cccchhhhhccccccceeeEeeccccccccccchhhhccCcccc
Confidence            53322                               12344444333  26788888877643322110          1


Q ss_pred             ccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhh
Q 003090          527 LANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKIL  606 (848)
Q Consensus       527 l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l  606 (848)
                      +..-..++|+.|++.++......     ......+++|++|+++++. ++.+..  ...+.+++|+.|++++|. + ..+
T Consensus       269 ~~~~~~~~L~~L~l~~n~l~~~~-----~~~~~~l~~L~~L~Ls~n~-l~~~~~--~~~~~l~~L~~L~Ls~N~-l-~~~  338 (455)
T 3v47_A          269 FKGLEASGVKTCDLSKSKIFALL-----KSVFSHFTDLEQLTLAQNE-INKIDD--NAFWGLTHLLKLNLSQNF-L-GSI  338 (455)
T ss_dssp             TGGGTTSCCCEEECCSSCCCEEC-----TTTTTTCTTCCEEECTTSC-CCEECT--TTTTTCTTCCEEECCSSC-C-CEE
T ss_pred             cccccccCceEEEecCccccccc-----hhhcccCCCCCEEECCCCc-ccccCh--hHhcCcccCCEEECCCCc-c-CCc
Confidence            11113478999999988644321     1234568999999999884 444311  123468899999999874 5 555


Q ss_pred             hHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCc
Q 003090          607 LSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECD  686 (848)
Q Consensus       607 ~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~  686 (848)
                      ++..+..+++|++|++++|.- +.++.        ..+..+++|++|+++++ .++.++...  +..+++|+.|++++++
T Consensus       339 ~~~~~~~l~~L~~L~Ls~N~l-~~~~~--------~~~~~l~~L~~L~L~~N-~l~~~~~~~--~~~l~~L~~L~l~~N~  406 (455)
T 3v47_A          339 DSRMFENLDKLEVLDLSYNHI-RALGD--------QSFLGLPNLKELALDTN-QLKSVPDGI--FDRLTSLQKIWLHTNP  406 (455)
T ss_dssp             CGGGGTTCTTCCEEECCSSCC-CEECT--------TTTTTCTTCCEEECCSS-CCSCCCTTT--TTTCTTCCEEECCSSC
T ss_pred             ChhHhcCcccCCEEECCCCcc-cccCh--------hhccccccccEEECCCC-ccccCCHhH--hccCCcccEEEccCCC
Confidence            444447889999999999854 44422        45778899999999986 577766543  5778999999999876

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=99.92  E-value=3.2e-24  Score=246.47  Aligned_cols=439  Identities=13%  Similarity=0.117  Sum_probs=248.6

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+...+++++++|.+..+|..+   .++|++|++++              +.+...    .|..+.++++|++|++++|.
T Consensus        29 ~~~~~~~l~ls~~~L~~ip~~~---~~~L~~L~Ls~--------------N~i~~~----~~~~~~~l~~L~~L~Ls~N~   87 (562)
T 3a79_B           29 SNELESMVDYSNRNLTHVPKDL---PPRTKALSLSQ--------------NSISEL----RMPDISFLSELRVLRLSHNR   87 (562)
T ss_dssp             ----CCEEECTTSCCCSCCTTS---CTTCCEEECCS--------------SCCCCC----CGGGTTTCTTCCEEECCSCC
T ss_pred             ccCCCcEEEcCCCCCccCCCCC---CCCcCEEECCC--------------CCcccc----ChhhhccCCCccEEECCCCC
Confidence            4555689999999999999865   38999999999              888883    44789999999999999998


Q ss_pred             ccCCc-hhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcccc-ccChhhhhccccccEEecccccccccccc
Q 003090          333 IQGDL-SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE-LIPRGVLSRLRKLEELYMSHSFRHWQFES  410 (848)
Q Consensus       333 ~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~-~~p~~~l~~l~~L~~L~l~~~~~~~~~~~  410 (848)
                      +.... ..++++++|++|++++|.++.+|..  .+++|++|++++|.... .+|.. ++++++|++|++++|.+...   
T Consensus        88 l~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~L~Ls~N~l~~l~~p~~-~~~l~~L~~L~L~~n~l~~~---  161 (562)
T 3a79_B           88 IRSLDFHVFLFNQDLEYLDVSHNRLQNISCC--PMASLRHLDLSFNDFDVLPVCKE-FGNLTKLTFLGLSAAKFRQL---  161 (562)
T ss_dssp             CCEECTTTTTTCTTCCEEECTTSCCCEECSC--CCTTCSEEECCSSCCSBCCCCGG-GGGCTTCCEEEEECSBCCTT---
T ss_pred             CCcCCHHHhCCCCCCCEEECCCCcCCccCcc--ccccCCEEECCCCCccccCchHh-hcccCcccEEecCCCccccC---
Confidence            88764 7799999999999999999999987  89999999999987655 34456 89999999999999987642   


Q ss_pred             ccccccCcccchhhhcccCCCcEEEeeccCC--CCC-CCCC-ccCCCCeEEEEeCCCCCCCCCcccceEEeccccccccc
Q 003090          411 ESEEDSSSNAKFIELGALSRLTSLHIHIPEG--KIM-PSDM-SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRA  486 (848)
Q Consensus       411 ~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~--~~~-~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~  486 (848)
                                .+..+..+ +|+.|++++|.+  ... +..+ .+. .+.+.+.........  .........        
T Consensus       162 ----------~~~~l~~L-~L~~L~L~~n~l~~~~~~~~~l~~l~-~~~l~l~l~~n~~~~--~~~~~~~~~--------  219 (562)
T 3a79_B          162 ----------DLLPVAHL-HLSCILLDLVSYHIKGGETESLQIPN-TTVLHLVFHPNSLFS--VQVNMSVNA--------  219 (562)
T ss_dssp             ----------TTGGGTTS-CEEEEEEEESSCCCCSSSCCEEEECC-EEEEEEEECSSSCCC--CCCEEEESS--------
T ss_pred             ----------chhhhhhc-eeeEEEeecccccccccCcccccccC-cceEEEEecCccchh--hhhhhcccc--------
Confidence                      23334444 449999999987  433 3332 221 134444322221000  000000100        


Q ss_pred             ccCccccchhhHHHHHHHHHhhcceeeecccc----ccccccccccccCCCCCcEEEEecCCCceeecccccccccccCC
Q 003090          487 MGLSQDMRISALHSWIKNLLLRSEILALAEVN----YFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLH  562 (848)
Q Consensus       487 ~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~----~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p  562 (848)
                                         +++|+.|+++++.    ........+  ..+++|+.|.+.++..-..-  -.........+
T Consensus       220 -------------------l~~L~~L~l~~n~~~~~~l~~~~~~l--~~l~~L~~L~L~~~~l~~~~--~~~~~~~~~~~  276 (562)
T 3a79_B          220 -------------------LGHLQLSNIKLNDENCQRLMTFLSEL--TRGPTLLNVTLQHIETTWKC--SVKLFQFFWPR  276 (562)
T ss_dssp             -------------------EEEEEEEEEECCSTTHHHHHHHHHHH--HSCSSCEEEEEEEEEECHHH--HHHHHHHHTTS
T ss_pred             -------------------cceEEEecccccccccchHHHHHHHH--hccCcceEEEecCCcCcHHH--HHHHHHhhhcc
Confidence                               2344455444431    111111111  23455666665544211000  00000111224


Q ss_pred             CccEEeccccccccccccccccccc----CCCcceEEEecCchhhHhhhHHHHHhh---ccCcEEEEeccCCceeeeecc
Q 003090          563 KLEWLFIRENQNFVEICHGQLPAGC----LSNVKRSDVVDCGSILKILLSHLVQSF---QNLQRLRVYSCGLLVSVFEIE  635 (848)
Q Consensus       563 ~L~~L~l~~~~~L~~~~~~~~~~~~----l~~L~~L~l~~c~~l~~~l~~~~~~~l---~~L~~L~l~~c~~l~~~~~~~  635 (848)
                      +|++|+++++. +.    +.+|...    .++|+.|.+.++..-.-.+|......+   .+|++|++++|.-. .+    
T Consensus       277 ~L~~L~l~~n~-l~----~~ip~~~~~~~~~~L~~L~~~~~~~~~~~~p~~~~~~~~~~~~L~~L~l~~n~~~-~~----  346 (562)
T 3a79_B          277 PVEYLNIYNLT-IT----ERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFI-HM----  346 (562)
T ss_dssp             SEEEEEEEEEE-EC----SCCCCCCCCCCSCSCCEEEEEEEEECCCSSCHHHHHHHHHTCCCSEEEEESSCCC-CC----
T ss_pred             cccEEEEeccE-ee----ccccchhhhcccccchheehhhcccceeecChhhhhhhhccCcceEEEccCCCcc-cc----
Confidence            66666666663 21    1122111    134444443332211002222111111   45666666665421 11    


Q ss_pred             ccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCcccccc--ccCccccccccceeeecccccc
Q 003090          636 RVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQV--FPANFGKKAAAEEMVLYRKRRD  713 (848)
Q Consensus       636 ~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~--~p~~~~~~~~~~~l~l~~l~~~  713 (848)
                            .....+++|++|+++++.--..++.   .+..+++|+.|+++++ +++.+  .|..+..        +.+|  +
T Consensus       347 ------~~~~~l~~L~~L~l~~n~l~~~~~~---~~~~l~~L~~L~L~~N-~l~~~~~~~~~~~~--------l~~L--~  406 (562)
T 3a79_B          347 ------VCPPSPSSFTFLNFTQNVFTDSVFQ---GCSTLKRLQTLILQRN-GLKNFFKVALMTKN--------MSSL--E  406 (562)
T ss_dssp             ------CCCSSCCCCCEEECCSSCCCTTTTT---TCCSCSSCCEEECCSS-CCCBTTHHHHTTTT--------CTTC--C
T ss_pred             ------cCccCCCCceEEECCCCccccchhh---hhcccCCCCEEECCCC-CcCCcccchhhhcC--------CCCC--C
Confidence                  0113556666666666532222222   1455666666666664 33332  1111111        2222  3


Q ss_pred             ceeeeecC--C-CCC-CCCCCCCccEEEEecCCCCceecccchhhcc-ccccEEEEecccccceeecCCcccccccCCCc
Q 003090          714 QIHIHATT--S-TSS-PTPSLGNLVSITIRGCGKLRNLFTTSMVKSL-VRLESLEVRSCPTLQEIIMDDEGEVGLQGAST  788 (848)
Q Consensus       714 ~l~i~~c~--~-~~~-~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l-~~L~~L~i~~C~~L~~l~~~~~~~~~l~~~~~  788 (848)
                      .+++.++.  . .+. .+..+++|+.|++++|. ++..    ....+ ++|++|++++| .++.++.  .    +     
T Consensus       407 ~L~l~~N~l~~~~~~~~~~~l~~L~~L~l~~n~-l~~~----~~~~l~~~L~~L~L~~N-~l~~ip~--~----~-----  469 (562)
T 3a79_B          407 TLDVSLNSLNSHAYDRTCAWAESILVLNLSSNM-LTGS----VFRCLPPKVKVLDLHNN-RIMSIPK--D----V-----  469 (562)
T ss_dssp             EEECTTSCCBSCCSSCCCCCCTTCCEEECCSSC-CCGG----GGSSCCTTCSEEECCSS-CCCCCCT--T----T-----
T ss_pred             EEECCCCcCCCccChhhhcCcccCCEEECCCCC-CCcc----hhhhhcCcCCEEECCCC-cCcccCh--h----h-----
Confidence            33333331  1 222 35678999999999975 5432    12334 69999999999 5766632  1    1     


Q ss_pred             cceecccccccccccccccccccCC
Q 003090          789 KKITFPSLFGIKLCDLDSLACFCST  813 (848)
Q Consensus       789 ~~~~~~sL~~L~i~~cp~L~~~~~~  813 (848)
                        ..+++|++|+++++. ++.++..
T Consensus       470 --~~l~~L~~L~L~~N~-l~~l~~~  491 (562)
T 3a79_B          470 --THLQALQELNVASNQ-LKSVPDG  491 (562)
T ss_dssp             --TSSCCCSEEECCSSC-CCCCCTT
T ss_pred             --cCCCCCCEEECCCCC-CCCCCHH
Confidence              127899999998875 6666554

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.92  E-value=1.3e-23  Score=226.10  Aligned_cols=173  Identities=22%  Similarity=0.295  Sum_probs=124.4

Q ss_pred             cccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcE
Q 003090          246 HEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRT  325 (848)
Q Consensus       246 ~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~  325 (848)
                      ..++....+++|++|+++++.+..++.  +..+++|++|++++              +.+..     +|. +..+++|++
T Consensus        35 ~~~~~~~~l~~L~~L~l~~~~i~~~~~--~~~~~~L~~L~l~~--------------n~i~~-----~~~-~~~l~~L~~   92 (347)
T 4fmz_A           35 TDVVTQEELESITKLVVAGEKVASIQG--IEYLTNLEYLNLNG--------------NQITD-----ISP-LSNLVKLTN   92 (347)
T ss_dssp             TSEECHHHHTTCSEEECCSSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GTTCTTCCE
T ss_pred             CCcccchhcccccEEEEeCCccccchh--hhhcCCccEEEccC--------------Ccccc-----chh-hhcCCcCCE
Confidence            333333366778888888887777765  56788888888888              66766     555 778888888


Q ss_pred             EEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccc
Q 003090          326 LRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRH  405 (848)
Q Consensus       326 L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~  405 (848)
                      |++++|.+.. ++.+.++++|++|++++|.+..+|. +..+++|++|++++|.....++.  +..+++|++|++++|.+.
T Consensus        93 L~L~~n~i~~-~~~~~~l~~L~~L~l~~n~i~~~~~-~~~l~~L~~L~l~~n~~~~~~~~--~~~l~~L~~L~l~~~~~~  168 (347)
T 4fmz_A           93 LYIGTNKITD-ISALQNLTNLRELYLNEDNISDISP-LANLTKMYSLNLGANHNLSDLSP--LSNMTGLNYLTVTESKVK  168 (347)
T ss_dssp             EECCSSCCCC-CGGGTTCTTCSEEECTTSCCCCCGG-GTTCTTCCEEECTTCTTCCCCGG--GTTCTTCCEEECCSSCCC
T ss_pred             EEccCCcccC-chHHcCCCcCCEEECcCCcccCchh-hccCCceeEEECCCCCCcccccc--hhhCCCCcEEEecCCCcC
Confidence            8888885544 4567888888888888888887765 77888888888888766665554  678888888888887765


Q ss_pred             cccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          406 WQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       406 ~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      ..               ..+..+++|+.|++++|.+..++....+++|+.|.+.
T Consensus       169 ~~---------------~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~  207 (347)
T 4fmz_A          169 DV---------------TPIANLTDLYSLSLNYNQIEDISPLASLTSLHYFTAY  207 (347)
T ss_dssp             CC---------------GGGGGCTTCSEEECTTSCCCCCGGGGGCTTCCEEECC
T ss_pred             Cc---------------hhhccCCCCCEEEccCCcccccccccCCCccceeecc
Confidence            32               2267778888888888877766552266666666665

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=99.91  E-value=8.6e-24  Score=236.67  Aligned_cols=155  Identities=18%  Similarity=0.201  Sum_probs=124.3

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      +.++.+++.+..+|.    -.++|++|++++              +.+...    .|..++++++|++|++++|.+....
T Consensus        13 ~~~~c~~~~l~~lp~----l~~~l~~L~Ls~--------------n~i~~~----~~~~~~~l~~L~~L~L~~n~~~~~i   70 (455)
T 3v47_A           13 YNAICINRGLHQVPE----LPAHVNYVDLSL--------------NSIAEL----NETSFSRLQDLQFLKVEQQTPGLVI   70 (455)
T ss_dssp             TEEECCSSCCSSCCC----CCTTCCEEECCS--------------SCCCEE----CTTTTSSCTTCCEEECCCCSTTCEE
T ss_pred             cccCcCCCCcccCCC----CCCccCEEEecC--------------CccCcC----ChhHhccCccccEEECcCCcccceE
Confidence            345666777788886    237899999999              888874    5788999999999999999776443


Q ss_pred             --hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccCh-hhhhccccccEEeccccccccccccccc
Q 003090          338 --SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       338 --~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                        ..+.++++|++|++++|.+..+ |..++++++|++|++++|...+..|. ..+.++++|++|++++|.+...      
T Consensus        71 ~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~------  144 (455)
T 3v47_A           71 RNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKI------  144 (455)
T ss_dssp             CTTTTTTCTTCCEEECTTCTTCEECTTTTTTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSC------
T ss_pred             CcccccccccCCEEeCCCCccCccChhhccCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCccCcc------
Confidence              6789999999999999999865 77899999999999999877654433 2368899999999999988764      


Q ss_pred             cccCcccchhh-hcccCCCcEEEeeccCCCCCCCC
Q 003090          414 EDSSSNAKFIE-LGALSRLTSLHIHIPEGKIMPSD  447 (848)
Q Consensus       414 ~~~~~~~~~~~-L~~l~~L~~L~l~~~~~~~~~~~  447 (848)
                             .+.. ++++++|+.|++++|.+...+..
T Consensus       145 -------~~~~~~~~l~~L~~L~L~~n~l~~~~~~  172 (455)
T 3v47_A          145 -------QPASFFLNMRRFHVLDLTFNKVKSICEE  172 (455)
T ss_dssp             -------CCCGGGGGCTTCCEEECTTCCBSCCCTT
T ss_pred             -------CcccccCCCCcccEEeCCCCcccccChh
Confidence                   2333 78899999999999987765443

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.91  E-value=1.3e-23  Score=229.89  Aligned_cols=173  Identities=10%  Similarity=0.166  Sum_probs=138.1

Q ss_pred             CCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEc
Q 003090          249 PDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRL  328 (848)
Q Consensus       249 p~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L  328 (848)
                      +..+.+++++.|+++++.+..+|..+|..+++|++|++++              +.+...    .+..+..+++|++|++
T Consensus        39 ~~~~~l~~l~~l~l~~~~l~~l~~~~~~~l~~L~~L~L~~--------------n~i~~~----~~~~~~~l~~L~~L~L  100 (390)
T 3o6n_A           39 FEDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLND--------------LQIEEI----DTYAFAYAHTIQKLYM  100 (390)
T ss_dssp             CSSGGGCCCSEEEEESCEESEECTHHHHHCCCCSEEECTT--------------SCCCEE----CTTTTTTCTTCCEEEC
T ss_pred             ccccccCCceEEEecCCchhhCChhHhcccccCcEEECCC--------------Cccccc----ChhhccCCCCcCEEEC
Confidence            3445778999999999999999998888999999999999              777773    3457889999999999


Q ss_pred             cCccccCCc-hhhccccCCCEEEccCCCCcccChhh-ccCCcccEEeccCCccccccChhhhhccccccEEecccccccc
Q 003090          329 HDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVSF-GRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       329 ~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i-~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      ++|.+...+ ..++++++|++|++++|.++.+|..+ +++++|++|++++|......|.. +.++++|++|++++|.+..
T Consensus       101 ~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~-~~~l~~L~~L~l~~n~l~~  179 (390)
T 3o6n_A          101 GFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDT-FQATTSLQNLQLSSNRLTH  179 (390)
T ss_dssp             CSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTT-TSSCTTCCEEECCSSCCSB
T ss_pred             CCCCCCcCCHHHhcCCCCCCEEECCCCccCcCCHHHhcCCCCCcEEECCCCccCccChhh-ccCCCCCCEEECCCCcCCc
Confidence            999888776 56889999999999999999888774 88999999999998765544444 7899999999999988764


Q ss_pred             ccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          407 QFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      .                .++.+++|+.|++++|.+..++   ...+|+.|++.
T Consensus       180 ~----------------~~~~l~~L~~L~l~~n~l~~~~---~~~~L~~L~l~  213 (390)
T 3o6n_A          180 V----------------DLSLIPSLFHANVSYNLLSTLA---IPIAVEELDAS  213 (390)
T ss_dssp             C----------------CGGGCTTCSEEECCSSCCSEEE---CCSSCSEEECC
T ss_pred             c----------------ccccccccceeecccccccccC---CCCcceEEECC
Confidence            2                3667788999999888766443   23456666665

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=99.90  E-value=2.1e-23  Score=231.22  Aligned_cols=324  Identities=17%  Similarity=0.096  Sum_probs=193.4

Q ss_pred             hccCCCceeeecCCCcccCCcc-cccccceeecccCcCc-ccChHHHccCCce-------------eEEEccCccccccc
Q 003090          231 GWLDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPL-AIPDRFFQGMKDL-------------QVLDLGGIRRFSFS  295 (848)
Q Consensus       231 ~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~-~~~~~~~~~~~~L-------------r~L~l~~~~~~~~~  295 (848)
                      ....++.+++++|.+..+|..+ .+++|++|++++|.+. .+|.. ++.+++|             ++|++++       
T Consensus         9 ~~~~L~~L~l~~n~l~~iP~~i~~L~~L~~L~l~~n~~~~~~p~~-~~~l~~L~~l~l~~c~~~~l~~L~l~~-------   80 (454)
T 1jl5_A            9 SNTFLQEPLRHSSNLTEMPVEAENVKSKTEYYNAWSEWERNAPPG-NGEQREMAVSRLRDCLDRQAHELELNN-------   80 (454)
T ss_dssp             -------------------------CCHHHHHHHHHHHHHTSCTT-SCCCHHHHHHHHHHHHHHTCSEEECTT-------
T ss_pred             ccccchhhhcccCchhhCChhHhcccchhhhhccCCcccccCCcc-cccchhcchhhhhhhhccCCCEEEecC-------
Confidence            3456778888888888888877 8889999999888543 56665 3566654             8888888       


Q ss_pred             ccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEecc
Q 003090          296 VRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLT  375 (848)
Q Consensus       296 ~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~  375 (848)
                             +.+.+     +|..   .++|++|++++|.+.+.+..   +.+|++|++++|.++.+|..   .++|++|+++
T Consensus        81 -------~~l~~-----lp~~---~~~L~~L~l~~n~l~~lp~~---~~~L~~L~l~~n~l~~l~~~---~~~L~~L~L~  139 (454)
T 1jl5_A           81 -------LGLSS-----LPEL---PPHLESLVASCNSLTELPEL---PQSLKSLLVDNNNLKALSDL---PPLLEYLGVS  139 (454)
T ss_dssp             -------SCCSC-----CCSC---CTTCSEEECCSSCCSSCCCC---CTTCCEEECCSSCCSCCCSC---CTTCCEEECC
T ss_pred             -------Ccccc-----CCCC---cCCCCEEEccCCcCCccccc---cCCCcEEECCCCccCcccCC---CCCCCEEECc
Confidence                   67776     6652   36788999998877775532   47888999998888877642   2688899998


Q ss_pred             CCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCe
Q 003090          376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTS  455 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~  455 (848)
                      +|...+ +| + ++++++|++|++++|.+... +.                ...+|+.|++++|.+..+|....+++|+.
T Consensus       140 ~n~l~~-lp-~-~~~l~~L~~L~l~~N~l~~l-p~----------------~~~~L~~L~L~~n~l~~l~~~~~l~~L~~  199 (454)
T 1jl5_A          140 NNQLEK-LP-E-LQNSSFLKIIDVDNNSLKKL-PD----------------LPPSLEFIAAGNNQLEELPELQNLPFLTA  199 (454)
T ss_dssp             SSCCSS-CC-C-CTTCTTCCEEECCSSCCSCC-CC----------------CCTTCCEEECCSSCCSSCCCCTTCTTCCE
T ss_pred             CCCCCC-Cc-c-cCCCCCCCEEECCCCcCccc-CC----------------CcccccEEECcCCcCCcCccccCCCCCCE
Confidence            876654 77 4 78889999999988877642 11                12488889998888888774227888888


Q ss_pred             EEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCC
Q 003090          456 FSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNEL  535 (848)
Q Consensus       456 L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L  535 (848)
                      |++..+...                                .+|.    .+++|++|+++++... .++. +  ..+++|
T Consensus       200 L~l~~N~l~--------------------------------~l~~----~~~~L~~L~l~~n~l~-~lp~-~--~~l~~L  239 (454)
T 1jl5_A          200 IYADNNSLK--------------------------------KLPD----LPLSLESIVAGNNILE-ELPE-L--QNLPFL  239 (454)
T ss_dssp             EECCSSCCS--------------------------------SCCC----CCTTCCEEECCSSCCS-SCCC-C--TTCTTC
T ss_pred             EECCCCcCC--------------------------------cCCC----CcCcccEEECcCCcCC-cccc-c--CCCCCC
Confidence            887644321                                0000    0246777777766433 3332 2  467778


Q ss_pred             cEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhc
Q 003090          536 MFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQ  615 (848)
Q Consensus       536 ~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~  615 (848)
                      ++|++.++. ++.++        ..+++|++|+++++. ++.+     +. .+++|+.|++++|. + ..+|..    .+
T Consensus       240 ~~L~l~~N~-l~~l~--------~~~~~L~~L~l~~N~-l~~l-----~~-~~~~L~~L~ls~N~-l-~~l~~~----~~  297 (454)
T 1jl5_A          240 TTIYADNNL-LKTLP--------DLPPSLEALNVRDNY-LTDL-----PE-LPQSLTFLDVSENI-F-SGLSEL----PP  297 (454)
T ss_dssp             CEEECCSSC-CSSCC--------SCCTTCCEEECCSSC-CSCC-----CC-CCTTCCEEECCSSC-C-SEESCC----CT
T ss_pred             CEEECCCCc-CCccc--------ccccccCEEECCCCc-cccc-----Cc-ccCcCCEEECcCCc-c-CcccCc----CC
Confidence            888887763 22221        124777888887773 4332     22 24677788877764 4 344321    25


Q ss_pred             cCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecC
Q 003090          616 NLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEEC  685 (848)
Q Consensus       616 ~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C  685 (848)
                      +|++|++++|. ++.++.            ..++|++|+++++ .++.++..      +++|+.|++++|
T Consensus       298 ~L~~L~l~~N~-l~~i~~------------~~~~L~~L~Ls~N-~l~~lp~~------~~~L~~L~L~~N  347 (454)
T 1jl5_A          298 NLYYLNASSNE-IRSLCD------------LPPSLEELNVSNN-KLIELPAL------PPRLERLIASFN  347 (454)
T ss_dssp             TCCEEECCSSC-CSEECC------------CCTTCCEEECCSS-CCSCCCCC------CTTCCEEECCSS
T ss_pred             cCCEEECcCCc-CCcccC------------CcCcCCEEECCCC-cccccccc------CCcCCEEECCCC
Confidence            77777777663 333321            1247777777774 35544332      467777777776

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.90  E-value=7.6e-23  Score=230.24  Aligned_cols=191  Identities=21%  Similarity=0.248  Sum_probs=154.8

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.++.+++.+..+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+...    .|.
T Consensus        14 ~~v~c~~~~l~~ip~~~~-~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~--------------n~i~~~----~~~   74 (477)
T 2id5_A           14 RAVLCHRKRFVAVPEGIP-TETRLLDLGKNRIKTLNQDEFASFPHLEELELNE--------------NIVSAV----EPG   74 (477)
T ss_dssp             TEEECCSCCCSSCCSCCC-TTCSEEECCSSCCCEECTTTTTTCTTCCEEECTT--------------SCCCEE----CTT
T ss_pred             CEEEeCCCCcCcCCCCCC-CCCcEEECCCCccceECHhHccCCCCCCEEECCC--------------CccCEe----Chh
Confidence            357777888888988764 6899999999999888777788999999999999              778774    578


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+.++++|++|++++|.+...+ ..+.++++|++|++++|.+..+ |..+.++++|++|++++|......+.. +.++++
T Consensus        75 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~-~~~l~~  153 (477)
T 2id5_A           75 AFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRA-FSGLNS  153 (477)
T ss_dssp             TTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTS-STTCTT
T ss_pred             hhhCCccCCEEECCCCcCCccCcccccCCCCCCEEECCCCccccCChhHccccccCCEEECCCCccceeChhh-ccCCCC
Confidence            8999999999999999888777 4578999999999999998855 567889999999999998765544545 889999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEE
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIA  459 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~  459 (848)
                      |++|++++|.+...             ....+..+++|+.|++++|.+..++...  .+++|+.|++.
T Consensus       154 L~~L~l~~n~l~~~-------------~~~~l~~l~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~  208 (477)
T 2id5_A          154 LEQLTLEKCNLTSI-------------PTEALSHLHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEIS  208 (477)
T ss_dssp             CCEEEEESCCCSSC-------------CHHHHTTCTTCCEEEEESCCCCEECTTCSCSCTTCCEEEEE
T ss_pred             CCEEECCCCcCccc-------------ChhHhcccCCCcEEeCCCCcCcEeChhhcccCcccceeeCC
Confidence            99999999987654             4456888999999999998877665432  55666666665

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.90  E-value=2.8e-23  Score=230.42  Aligned_cols=179  Identities=15%  Similarity=0.086  Sum_probs=107.0

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.|++++|.+..+|....+++|++|++++|.+..+|   +..+++|++|++++              +.+.+     
T Consensus        42 ~~L~~L~Ls~n~l~~~~~l~~l~~L~~L~Ls~n~l~~~~---~~~l~~L~~L~Ls~--------------N~l~~-----   99 (457)
T 3bz5_A           42 ATLTSLDCHNSSITDMTGIEKLTGLTKLICTSNNITTLD---LSQNTNLTYLACDS--------------NKLTN-----   99 (457)
T ss_dssp             TTCCEEECCSSCCCCCTTGGGCTTCSEEECCSSCCSCCC---CTTCTTCSEEECCS--------------SCCSC-----
T ss_pred             CCCCEEEccCCCcccChhhcccCCCCEEEccCCcCCeEc---cccCCCCCEEECcC--------------CCCce-----
Confidence            345666666666666653336666666666666666654   45666666666666              55555     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      +|  ++.+++|++|++++|.+...+  ++.+++|++|++++|.++.+|  ++++++|++|++++|...+.++   ++.++
T Consensus       100 ~~--~~~l~~L~~L~L~~N~l~~l~--~~~l~~L~~L~l~~N~l~~l~--l~~l~~L~~L~l~~n~~~~~~~---~~~l~  170 (457)
T 3bz5_A          100 LD--VTPLTKLTYLNCDTNKLTKLD--VSQNPLLTYLNCARNTLTEID--VSHNTQLTELDCHLNKKITKLD---VTPQT  170 (457)
T ss_dssp             CC--CTTCTTCCEEECCSSCCSCCC--CTTCTTCCEEECTTSCCSCCC--CTTCTTCCEEECTTCSCCCCCC---CTTCT
T ss_pred             ee--cCCCCcCCEEECCCCcCCeec--CCCCCcCCEEECCCCccceec--cccCCcCCEEECCCCCcccccc---cccCC
Confidence            43  566666666666666555532  666666666666666666654  5666666666666665555442   45666


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      +|++|++++|.+...              +  +..+++|+.|++++|.++.++ ...+++|+.|++.
T Consensus       171 ~L~~L~ls~n~l~~l--------------~--l~~l~~L~~L~l~~N~l~~~~-l~~l~~L~~L~Ls  220 (457)
T 3bz5_A          171 QLTTLDCSFNKITEL--------------D--VSQNKLLNRLNCDTNNITKLD-LNQNIQLTFLDCS  220 (457)
T ss_dssp             TCCEEECCSSCCCCC--------------C--CTTCTTCCEEECCSSCCSCCC-CTTCTTCSEEECC
T ss_pred             cCCEEECCCCcccee--------------c--cccCCCCCEEECcCCcCCeec-cccCCCCCEEECc
Confidence            666666666655431              1  555666666666666655542 1144555555544

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.89  E-value=7.9e-23  Score=236.02  Aligned_cols=309  Identities=14%  Similarity=0.186  Sum_probs=209.5

Q ss_pred             CcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEcc
Q 003090          250 DELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLH  329 (848)
Q Consensus       250 ~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~  329 (848)
                      ..+.+.+++.+++++|.++.+|..+|.++++|++|++++              +.+...    .|..++.+++|++|+++
T Consensus        46 ~~l~l~~l~~l~l~~~~l~~lp~~~~~~l~~L~~L~L~~--------------n~l~~~----~~~~~~~l~~L~~L~L~  107 (597)
T 3oja_B           46 EDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLND--------------LQIEEI----DTYAFAYAHTIQKLYMG  107 (597)
T ss_dssp             SSGGGCCCSEEEESSCEESEECTHHHHHCCCCSEEECTT--------------SCCCEE----CTTTTTTCTTCCEEECC
T ss_pred             ccccCCCceEEEeeCCCCCCcCHHHHccCCCCcEEECCC--------------CCCCCC----ChHHhcCCCCCCEEECC
Confidence            345678899999999999999999889999999999999              778773    44588999999999999


Q ss_pred             CccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccc
Q 003090          330 DRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQ  407 (848)
Q Consensus       330 ~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~  407 (848)
                      +|.+...+ ..++++++|++|++++|.++.+|.. ++++++|++|++++|.+.+..|.. ++++++|++|++++|.+...
T Consensus       108 ~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~-~~~l~~L~~L~L~~N~l~~~  186 (597)
T 3oja_B          108 FNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDT-FQATTSLQNLQLSSNRLTHV  186 (597)
T ss_dssp             SSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTT-TTTCTTCCEEECTTSCCSBC
T ss_pred             CCcCCCCCHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCCEEEeeCCcCCCCChhh-hhcCCcCcEEECcCCCCCCc
Confidence            99888877 5678999999999999999988876 488999999999998776544544 88999999999999987643


Q ss_pred             cccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccc
Q 003090          408 FESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAM  487 (848)
Q Consensus       408 ~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~  487 (848)
                                      .++.+++|+.|++++|.+..++   ...+|+.|++..+...        .  +..         
T Consensus       187 ----------------~~~~l~~L~~L~l~~n~l~~l~---~~~~L~~L~ls~n~l~--------~--~~~---------  228 (597)
T 3oja_B          187 ----------------DLSLIPSLFHANVSYNLLSTLA---IPIAVEELDASHNSIN--------V--VRG---------  228 (597)
T ss_dssp             ----------------CGGGCTTCSEEECCSSCCSEEE---CCTTCSEEECCSSCCC--------E--EEC---------
T ss_pred             ----------------ChhhhhhhhhhhcccCcccccc---CCchhheeeccCCccc--------c--ccc---------
Confidence                            3567788999999988776443   3356777776533320        0  000         


Q ss_pred             cCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEE
Q 003090          488 GLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWL  567 (848)
Q Consensus       488 ~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L  567 (848)
                                   .   .+++|+.|.++++.....  ..+  ..+++|+.|+++++......     ......+++|++|
T Consensus       229 -------------~---~~~~L~~L~L~~n~l~~~--~~l--~~l~~L~~L~Ls~N~l~~~~-----~~~~~~l~~L~~L  283 (597)
T 3oja_B          229 -------------P---VNVELTILKLQHNNLTDT--AWL--LNYPGLVEVDLSYNELEKIM-----YHPFVKMQRLERL  283 (597)
T ss_dssp             -------------S---CCSCCCEEECCSSCCCCC--GGG--GGCTTCSEEECCSSCCCEEE-----SGGGTTCSSCCEE
T ss_pred             -------------c---cCCCCCEEECCCCCCCCC--hhh--ccCCCCCEEECCCCccCCCC-----HHHhcCccCCCEE
Confidence                         0   024566666666543321  222  35677777777776432221     1234456777777


Q ss_pred             ecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecccccccccccccc
Q 003090          568 FIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELF  647 (848)
Q Consensus       568 ~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l  647 (848)
                      +++++ .+..+.   ...+.+|+|+.|++++|. + ..+|..+ ..+++|++|++++|.- ..+           .+..+
T Consensus       284 ~Ls~N-~l~~l~---~~~~~l~~L~~L~Ls~N~-l-~~i~~~~-~~l~~L~~L~L~~N~l-~~~-----------~~~~~  344 (597)
T 3oja_B          284 YISNN-RLVALN---LYGQPIPTLKVLDLSHNH-L-LHVERNQ-PQFDRLENLYLDHNSI-VTL-----------KLSTH  344 (597)
T ss_dssp             ECTTS-CCCEEE---CSSSCCTTCCEEECCSSC-C-CCCGGGH-HHHTTCSEEECCSSCC-CCC-----------CCCTT
T ss_pred             ECCCC-CCCCCC---cccccCCCCcEEECCCCC-C-CccCccc-ccCCCCCEEECCCCCC-CCc-----------Chhhc
Confidence            77766 344331   112346677777777653 4 4555443 5666777777766542 222           13455


Q ss_pred             CCcCEEecCCCc
Q 003090          648 SSLEKLTLWDLP  659 (848)
Q Consensus       648 ~~L~~L~l~~c~  659 (848)
                      ++|+.|++++++
T Consensus       345 ~~L~~L~l~~N~  356 (597)
T 3oja_B          345 HTLKNLTLSHND  356 (597)
T ss_dssp             CCCSEEECCSSC
T ss_pred             CCCCEEEeeCCC
Confidence            666666666554

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.89  E-value=3.1e-22  Score=218.86  Aligned_cols=303  Identities=17%  Similarity=0.159  Sum_probs=227.7

Q ss_pred             ccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCC
Q 003090          232 WLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSP  309 (848)
Q Consensus       232 ~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~  309 (848)
                      ...++.+++++|.+..+|...  .+++|++|++++|.+..++...|..+++|++|++++              +.+... 
T Consensus        44 l~~l~~l~l~~~~l~~l~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~-  108 (390)
T 3o6n_A           44 LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGF--------------NAIRYL-  108 (390)
T ss_dssp             GCCCSEEEEESCEESEECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCS--------------SCCCCC-
T ss_pred             cCCceEEEecCCchhhCChhHhcccccCcEEECCCCcccccChhhccCCCCcCEEECCC--------------CCCCcC-
Confidence            345788999999999999875  799999999999999999887789999999999999              888884 


Q ss_pred             CCCCCchhhhcccCcEEEccCccccCCchh-hccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhh
Q 003090          310 LFLLPSSLSFLINLRTLRLHDRRIQGDLSL-IGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGV  387 (848)
Q Consensus       310 ~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~-i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~  387 (848)
                         .|..++.+++|++|++++|.+...+.. ++++++|++|++++|.+..++. .++.+++|++|++++|.... ++   
T Consensus       109 ---~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~-~~---  181 (390)
T 3o6n_A          109 ---PPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTH-VD---  181 (390)
T ss_dssp             ---CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSSCCSB-CC---
T ss_pred             ---CHHHhcCCCCCCEEECCCCccCcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCCcCCc-cc---
Confidence               566789999999999999988877754 6899999999999999997754 58999999999999986644 43   


Q ss_pred             hhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCC
Q 003090          388 LSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERP  467 (848)
Q Consensus       388 l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~  467 (848)
                      ++.+++|+.|++++|.+..                  +....+|+.|++++|.+..++.. ..++|+.|++.        
T Consensus       182 ~~~l~~L~~L~l~~n~l~~------------------~~~~~~L~~L~l~~n~l~~~~~~-~~~~L~~L~l~--------  234 (390)
T 3o6n_A          182 LSLIPSLFHANVSYNLLST------------------LAIPIAVEELDASHNSINVVRGP-VNVELTILKLQ--------  234 (390)
T ss_dssp             GGGCTTCSEEECCSSCCSE------------------EECCSSCSEEECCSSCCCEEECC-CCSSCCEEECC--------
T ss_pred             cccccccceeecccccccc------------------cCCCCcceEEECCCCeeeecccc-ccccccEEECC--------
Confidence            5789999999999987653                  34456899999999988766543 23455555554        


Q ss_pred             CCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCce
Q 003090          468 LSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMK  547 (848)
Q Consensus       468 ~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~  547 (848)
                                                                      ++.....  ..+  ..+++|++|+++++....
T Consensus       235 ------------------------------------------------~n~l~~~--~~l--~~l~~L~~L~Ls~n~l~~  262 (390)
T 3o6n_A          235 ------------------------------------------------HNNLTDT--AWL--LNYPGLVEVDLSYNELEK  262 (390)
T ss_dssp             ------------------------------------------------SSCCCCC--GGG--GGCTTCSEEECCSSCCCE
T ss_pred             ------------------------------------------------CCCCccc--HHH--cCCCCccEEECCCCcCCC
Confidence                                                            3322111  111  466888888888875332


Q ss_pred             eecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCC
Q 003090          548 YLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGL  627 (848)
Q Consensus       548 ~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~  627 (848)
                      ..     ......+++|++|+++++ .++.+.   .....+++|+.|++++| .+ ..+|..+ ..+++|++|++++|. 
T Consensus       263 ~~-----~~~~~~l~~L~~L~L~~n-~l~~~~---~~~~~l~~L~~L~L~~n-~l-~~~~~~~-~~l~~L~~L~L~~N~-  329 (390)
T 3o6n_A          263 IM-----YHPFVKMQRLERLYISNN-RLVALN---LYGQPIPTLKVLDLSHN-HL-LHVERNQ-PQFDRLENLYLDHNS-  329 (390)
T ss_dssp             EE-----SGGGTTCSSCCEEECCSS-CCCEEE---CSSSCCTTCCEEECCSS-CC-CCCGGGH-HHHTTCSEEECCSSC-
T ss_pred             cC-----hhHccccccCCEEECCCC-cCcccC---cccCCCCCCCEEECCCC-cc-eecCccc-cccCcCCEEECCCCc-
Confidence            21     124456788888888887 455441   12235788888888887 45 5666543 677888888888875 


Q ss_pred             ceeeeeccccccccccccccCCcCEEecCCCc
Q 003090          628 LVSVFEIERVNIAKEETELFSSLEKLTLWDLP  659 (848)
Q Consensus       628 l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~  659 (848)
                      ++.+           .+..+++|++|++++++
T Consensus       330 i~~~-----------~~~~~~~L~~L~l~~N~  350 (390)
T 3o6n_A          330 IVTL-----------KLSTHHTLKNLTLSHND  350 (390)
T ss_dssp             CCCC-----------CCCTTCCCSEEECCSSC
T ss_pred             ccee-----------CchhhccCCEEEcCCCC
Confidence            3333           24467777777777754

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=99.89  E-value=8e-23  Score=226.50  Aligned_cols=310  Identities=17%  Similarity=0.064  Sum_probs=176.0

Q ss_pred             CCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhccc------
Q 003090          249 PDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLIN------  322 (848)
Q Consensus       249 p~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~------  322 (848)
                      |+.+..+.|++|++++|.++.+|+++ +++++|++|++++              +.+.+.    +|.+++++.+      
T Consensus         5 p~~~~~~~L~~L~l~~n~l~~iP~~i-~~L~~L~~L~l~~--------------n~~~~~----~p~~~~~l~~L~~l~l   65 (454)
T 1jl5_A            5 PRNVSNTFLQEPLRHSSNLTEMPVEA-ENVKSKTEYYNAW--------------SEWERN----APPGNGEQREMAVSRL   65 (454)
T ss_dssp             ------------------------------CCHHHHHHHH--------------HHHHHT----SCTTSCCCHHHHHHHH
T ss_pred             ccccccccchhhhcccCchhhCChhH-hcccchhhhhccC--------------Cccccc----CCcccccchhcchhhh
Confidence            44556789999999999999999874 8999999999999              555544    6777776665      


Q ss_pred             -------CcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccccc
Q 003090          323 -------LRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE  395 (848)
Q Consensus       323 -------L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~  395 (848)
                             +++|++++|.+.+.+..   .++|++|++++|.++.+|..   +.+|++|++++|... .+|..    .++|+
T Consensus        66 ~~c~~~~l~~L~l~~~~l~~lp~~---~~~L~~L~l~~n~l~~lp~~---~~~L~~L~l~~n~l~-~l~~~----~~~L~  134 (454)
T 1jl5_A           66 RDCLDRQAHELELNNLGLSSLPEL---PPHLESLVASCNSLTELPEL---PQSLKSLLVDNNNLK-ALSDL----PPLLE  134 (454)
T ss_dssp             HHHHHHTCSEEECTTSCCSCCCSC---CTTCSEEECCSSCCSSCCCC---CTTCCEEECCSSCCS-CCCSC----CTTCC
T ss_pred             hhhhccCCCEEEecCCccccCCCC---cCCCCEEEccCCcCCccccc---cCCCcEEECCCCccC-cccCC----CCCCC
Confidence                   48888888876665442   36788888888888888753   478888888887553 34431    16888


Q ss_pred             EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceE
Q 003090          396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLF  475 (848)
Q Consensus       396 ~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~  475 (848)
                      +|++++|.+..              .+ .++++++|++|++++|.++.+|..  ..+|+.|++..+....  .+.+    
T Consensus       135 ~L~L~~n~l~~--------------lp-~~~~l~~L~~L~l~~N~l~~lp~~--~~~L~~L~L~~n~l~~--l~~~----  191 (454)
T 1jl5_A          135 YLGVSNNQLEK--------------LP-ELQNSSFLKIIDVDNNSLKKLPDL--PPSLEFIAAGNNQLEE--LPEL----  191 (454)
T ss_dssp             EEECCSSCCSS--------------CC-CCTTCTTCCEEECCSSCCSCCCCC--CTTCCEEECCSSCCSS--CCCC----
T ss_pred             EEECcCCCCCC--------------Cc-ccCCCCCCCEEECCCCcCcccCCC--cccccEEECcCCcCCc--Cccc----
Confidence            88888887653              22 478888888888888888777654  3577777776443311  0000    


Q ss_pred             EecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccc
Q 003090          476 LQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLER  555 (848)
Q Consensus       476 l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~  555 (848)
                       .                           .+++|+.|+++++.... ++.     ..++|++|++.+|. ++.++     
T Consensus       192 -~---------------------------~l~~L~~L~l~~N~l~~-l~~-----~~~~L~~L~l~~n~-l~~lp-----  231 (454)
T 1jl5_A          192 -Q---------------------------NLPFLTAIYADNNSLKK-LPD-----LPLSLESIVAGNNI-LEELP-----  231 (454)
T ss_dssp             -T---------------------------TCTTCCEEECCSSCCSS-CCC-----CCTTCCEEECCSSC-CSSCC-----
T ss_pred             -c---------------------------CCCCCCEEECCCCcCCc-CCC-----CcCcccEEECcCCc-CCccc-----
Confidence             0                           13667777777665332 111     22577777777773 33321     


Q ss_pred             cccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeecc
Q 003090          556 TLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIE  635 (848)
Q Consensus       556 ~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~  635 (848)
                       ....+++|++|+++++. ++.+     +. .+++|+.|++++|. + ..+|..    +++|++|++++|. ++.++.  
T Consensus       232 -~~~~l~~L~~L~l~~N~-l~~l-----~~-~~~~L~~L~l~~N~-l-~~l~~~----~~~L~~L~ls~N~-l~~l~~--  294 (454)
T 1jl5_A          232 -ELQNLPFLTTIYADNNL-LKTL-----PD-LPPSLEALNVRDNY-L-TDLPEL----PQSLTFLDVSENI-FSGLSE--  294 (454)
T ss_dssp             -CCTTCTTCCEEECCSSC-CSSC-----CS-CCTTCCEEECCSSC-C-SCCCCC----CTTCCEEECCSSC-CSEESC--
T ss_pred             -ccCCCCCCCEEECCCCc-CCcc-----cc-cccccCEEECCCCc-c-cccCcc----cCcCCEEECcCCc-cCcccC--
Confidence             24456777777777763 3332     22 35677777777754 4 445432    3677777777764 333321  


Q ss_pred             ccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecC
Q 003090          636 RVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEEC  685 (848)
Q Consensus       636 ~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C  685 (848)
                                ..++|++|+++++. ++.++..      .++|+.|+++++
T Consensus       295 ----------~~~~L~~L~l~~N~-l~~i~~~------~~~L~~L~Ls~N  327 (454)
T 1jl5_A          295 ----------LPPNLYYLNASSNE-IRSLCDL------PPSLEELNVSNN  327 (454)
T ss_dssp             ----------CCTTCCEEECCSSC-CSEECCC------CTTCCEEECCSS
T ss_pred             ----------cCCcCCEEECcCCc-CCcccCC------cCcCCEEECCCC
Confidence                      12577777777653 4443221      147777777765

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.89  E-value=4.1e-22  Score=214.33  Aligned_cols=301  Identities=16%  Similarity=0.156  Sum_probs=233.8

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.++++++.+..++....+++|++|++++|.+..++.  +..+++|++|++++              +.+..     
T Consensus        44 ~~L~~L~l~~~~i~~~~~~~~~~~L~~L~l~~n~i~~~~~--~~~l~~L~~L~L~~--------------n~i~~-----  102 (347)
T 4fmz_A           44 ESITKLVVAGEKVASIQGIEYLTNLEYLNLNGNQITDISP--LSNLVKLTNLYIGT--------------NKITD-----  102 (347)
T ss_dssp             TTCSEEECCSSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----
T ss_pred             ccccEEEEeCCccccchhhhhcCCccEEEccCCccccchh--hhcCCcCCEEEccC--------------CcccC-----
Confidence            4578899999999999875589999999999999988887  78999999999999              77877     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      +| .+..+++|++|++++|.+...+. +..+++|++|++++|.....+..+..+++|++|++++|... .++.  +..++
T Consensus       103 ~~-~~~~l~~L~~L~l~~n~i~~~~~-~~~l~~L~~L~l~~n~~~~~~~~~~~l~~L~~L~l~~~~~~-~~~~--~~~l~  177 (347)
T 4fmz_A          103 IS-ALQNLTNLRELYLNEDNISDISP-LANLTKMYSLNLGANHNLSDLSPLSNMTGLNYLTVTESKVK-DVTP--IANLT  177 (347)
T ss_dssp             CG-GGTTCTTCSEEECTTSCCCCCGG-GTTCTTCCEEECTTCTTCCCCGGGTTCTTCCEEECCSSCCC-CCGG--GGGCT
T ss_pred             ch-HHcCCCcCCEEECcCCcccCchh-hccCCceeEEECCCCCCcccccchhhCCCCcEEEecCCCcC-Cchh--hccCC
Confidence            65 59999999999999997766555 89999999999999965544456999999999999998654 4554  78999


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCccc
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFI  472 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~  472 (848)
                      +|++|++++|.+...               ..+..+++|+.|++++|.+..++....+++|+.|++.             
T Consensus       178 ~L~~L~l~~n~l~~~---------------~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~L~~L~l~-------------  229 (347)
T 4fmz_A          178 DLYSLSLNYNQIEDI---------------SPLASLTSLHYFTAYVNQITDITPVANMTRLNSLKIG-------------  229 (347)
T ss_dssp             TCSEEECTTSCCCCC---------------GGGGGCTTCCEEECCSSCCCCCGGGGGCTTCCEEECC-------------
T ss_pred             CCCEEEccCCccccc---------------ccccCCCccceeecccCCCCCCchhhcCCcCCEEEcc-------------
Confidence            999999999987643               2388999999999999988766542255666666654             


Q ss_pred             ceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeeccc
Q 003090          473 GLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNS  552 (848)
Q Consensus       473 ~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~  552 (848)
                                                                 ++.... ...   ...+++|++|++.+|. ++.+   
T Consensus       230 -------------------------------------------~n~l~~-~~~---~~~l~~L~~L~l~~n~-l~~~---  258 (347)
T 4fmz_A          230 -------------------------------------------NNKITD-LSP---LANLSQLTWLEIGTNQ-ISDI---  258 (347)
T ss_dssp             -------------------------------------------SSCCCC-CGG---GTTCTTCCEEECCSSC-CCCC---
T ss_pred             -------------------------------------------CCccCC-Ccc---hhcCCCCCEEECCCCc-cCCC---
Confidence                                                       322111 111   2467888999998874 3332   


Q ss_pred             ccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeee
Q 003090          553 LERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVF  632 (848)
Q Consensus       553 ~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~  632 (848)
                         .....+++|++|++++| .++.+    .....+++|+.|++++|. + ...++..+..+++|++|++++|+ ++.++
T Consensus       259 ---~~~~~l~~L~~L~l~~n-~l~~~----~~~~~l~~L~~L~L~~n~-l-~~~~~~~l~~l~~L~~L~L~~n~-l~~~~  327 (347)
T 4fmz_A          259 ---NAVKDLTKLKMLNVGSN-QISDI----SVLNNLSQLNSLFLNNNQ-L-GNEDMEVIGGLTNLTTLFLSQNH-ITDIR  327 (347)
T ss_dssp             ---GGGTTCTTCCEEECCSS-CCCCC----GGGGGCTTCSEEECCSSC-C-CGGGHHHHHTCTTCSEEECCSSS-CCCCG
T ss_pred             ---hhHhcCCCcCEEEccCC-ccCCC----hhhcCCCCCCEEECcCCc-C-CCcChhHhhccccCCEEEccCCc-ccccc
Confidence               34567899999999988 45554    224468999999999985 4 44444455889999999999987 55543


Q ss_pred             eccccccccccccccCCcCEEecCCCc
Q 003090          633 EIERVNIAKEETELFSSLEKLTLWDLP  659 (848)
Q Consensus       633 ~~~~~~~~~~~~~~l~~L~~L~l~~c~  659 (848)
                                .+..+++|++|++++++
T Consensus       328 ----------~~~~l~~L~~L~l~~N~  344 (347)
T 4fmz_A          328 ----------PLASLSKMDSADFANQV  344 (347)
T ss_dssp             ----------GGGGCTTCSEESSSCC-
T ss_pred             ----------Chhhhhccceeehhhhc
Confidence                      36689999999999876

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.89  E-value=6.6e-22  Score=219.36  Aligned_cols=160  Identities=16%  Similarity=0.147  Sum_probs=132.6

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+++|++|++++|.+..+|.  +..+++|++|++++              +.+.+     +|  ++.+++|++|++++|.
T Consensus        40 ~l~~L~~L~Ls~n~l~~~~~--l~~l~~L~~L~Ls~--------------n~l~~-----~~--~~~l~~L~~L~Ls~N~   96 (457)
T 3bz5_A           40 QLATLTSLDCHNSSITDMTG--IEKLTGLTKLICTS--------------NNITT-----LD--LSQNTNLTYLACDSNK   96 (457)
T ss_dssp             HHTTCCEEECCSSCCCCCTT--GGGCTTCSEEECCS--------------SCCSC-----CC--CTTCTTCSEEECCSSC
T ss_pred             HcCCCCEEEccCCCcccChh--hcccCCCCEEEccC--------------CcCCe-----Ec--cccCCCCCEEECcCCC
Confidence            68899999999998888873  68999999999999              88887     65  8899999999999998


Q ss_pred             ccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccc
Q 003090          333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESES  412 (848)
Q Consensus       333 ~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~  412 (848)
                      +.+.+  ++++++|++|++++|.++.+|  ++++++|++|++++|...+ ++   ++++++|++|++++|.....     
T Consensus        97 l~~~~--~~~l~~L~~L~L~~N~l~~l~--~~~l~~L~~L~l~~N~l~~-l~---l~~l~~L~~L~l~~n~~~~~-----  163 (457)
T 3bz5_A           97 LTNLD--VTPLTKLTYLNCDTNKLTKLD--VSQNPLLTYLNCARNTLTE-ID---VSHNTQLTELDCHLNKKITK-----  163 (457)
T ss_dssp             CSCCC--CTTCTTCCEEECCSSCCSCCC--CTTCTTCCEEECTTSCCSC-CC---CTTCTTCCEEECTTCSCCCC-----
T ss_pred             Cceee--cCCCCcCCEEECCCCcCCeec--CCCCCcCCEEECCCCccce-ec---cccCCcCCEEECCCCCcccc-----
Confidence            77753  889999999999999999886  8899999999999987655 43   68899999999999854432     


Q ss_pred             ccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          413 EEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       413 ~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                              .  .++.+++|+.|++++|.++.++ ...+++|+.|.+.
T Consensus       164 --------~--~~~~l~~L~~L~ls~n~l~~l~-l~~l~~L~~L~l~  199 (457)
T 3bz5_A          164 --------L--DVTPQTQLTTLDCSFNKITELD-VSQNKLLNRLNCD  199 (457)
T ss_dssp             --------C--CCTTCTTCCEEECCSSCCCCCC-CTTCTTCCEEECC
T ss_pred             --------c--ccccCCcCCEEECCCCccceec-cccCCCCCEEECc
Confidence                    1  4778899999999999888776 1166667766665

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.88  E-value=4.1e-22  Score=224.24  Aligned_cols=314  Identities=17%  Similarity=0.178  Sum_probs=210.4

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      +.++.+++.+..+|..+   .+++++|++++              +.+...    .|..+.++++|++|++++|.+....
T Consensus        14 ~~v~c~~~~l~~ip~~~---~~~l~~L~L~~--------------n~l~~~----~~~~~~~l~~L~~L~L~~n~i~~~~   72 (477)
T 2id5_A           14 RAVLCHRKRFVAVPEGI---PTETRLLDLGK--------------NRIKTL----NQDEFASFPHLEELELNENIVSAVE   72 (477)
T ss_dssp             TEEECCSCCCSSCCSCC---CTTCSEEECCS--------------SCCCEE----CTTTTTTCTTCCEEECTTSCCCEEC
T ss_pred             CEEEeCCCCcCcCCCCC---CCCCcEEECCC--------------CccceE----CHhHccCCCCCCEEECCCCccCEeC
Confidence            56677777888888754   46889999999              888873    4678999999999999999877764


Q ss_pred             -hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccc
Q 003090          338 -SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED  415 (848)
Q Consensus       338 -~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  415 (848)
                       ..++++++|++|++++|.++.+|.. +.++++|++|++++|......|.. +.++++|++|++++|.+...        
T Consensus        73 ~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~-~~~l~~L~~L~l~~n~l~~~--------  143 (477)
T 2id5_A           73 PGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYM-FQDLYNLKSLEVGDNDLVYI--------  143 (477)
T ss_dssp             TTTTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCCEEECTTSCCCEECTTT-TTTCTTCCEEEECCTTCCEE--------
T ss_pred             hhhhhCCccCCEEECCCCcCCccCcccccCCCCCCEEECCCCccccCChhH-ccccccCCEEECCCCcccee--------
Confidence             7889999999999999999988865 688999999999998776655555 89999999999999988765        


Q ss_pred             cCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCcccc
Q 003090          416 SSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDM  493 (848)
Q Consensus       416 ~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~  493 (848)
                           .+..+..+++|+.|++++|.+..++...  .+++|+.|++..+..                              
T Consensus       144 -----~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n~i------------------------------  188 (477)
T 2id5_A          144 -----SHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNI------------------------------  188 (477)
T ss_dssp             -----CTTSSTTCTTCCEEEEESCCCSSCCHHHHTTCTTCCEEEEESCCC------------------------------
T ss_pred             -----ChhhccCCCCCCEEECCCCcCcccChhHhcccCCCcEEeCCCCcC------------------------------
Confidence                 4456888999999999999888777543  677777777764332                              


Q ss_pred             chhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccccc
Q 003090          494 RISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQ  573 (848)
Q Consensus       494 ~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~  573 (848)
                                                .......+  ..+++|+.|++.+|..+..++.     .....++|++|+++++ 
T Consensus       189 --------------------------~~~~~~~~--~~l~~L~~L~l~~~~~~~~~~~-----~~~~~~~L~~L~l~~n-  234 (477)
T 2id5_A          189 --------------------------NAIRDYSF--KRLYRLKVLEISHWPYLDTMTP-----NCLYGLNLTSLSITHC-  234 (477)
T ss_dssp             --------------------------CEECTTCS--CSCTTCCEEEEECCTTCCEECT-----TTTTTCCCSEEEEESS-
T ss_pred             --------------------------cEeChhhc--ccCcccceeeCCCCccccccCc-----ccccCccccEEECcCC-
Confidence                                      10001111  3456666666666655544321     1112236666666665 


Q ss_pred             ccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEE
Q 003090          574 NFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKL  653 (848)
Q Consensus       574 ~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L  653 (848)
                      +++.+...  ....+++|+.|++++|. + ..++...+..+++|++|++++|. ++.+..        ..+..+++|++|
T Consensus       235 ~l~~~~~~--~~~~l~~L~~L~Ls~n~-l-~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~--------~~~~~l~~L~~L  301 (477)
T 2id5_A          235 NLTAVPYL--AVRHLVYLRFLNLSYNP-I-STIEGSMLHELLRLQEIQLVGGQ-LAVVEP--------YAFRGLNYLRVL  301 (477)
T ss_dssp             CCCSCCHH--HHTTCTTCCEEECCSSC-C-CEECTTSCTTCTTCCEEECCSSC-CSEECT--------TTBTTCTTCCEE
T ss_pred             cccccCHH--HhcCccccCeeECCCCc-C-CccChhhccccccCCEEECCCCc-cceECH--------HHhcCcccCCEE
Confidence            33332110  12345666666666653 3 34444333556667777776653 233321        345566777777


Q ss_pred             ecCCCccccccccCCCccccccCccEEEeecCc
Q 003090          654 TLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECD  686 (848)
Q Consensus       654 ~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~  686 (848)
                      +++++ .++.++...  +..+++|++|++++++
T Consensus       302 ~L~~N-~l~~~~~~~--~~~l~~L~~L~l~~N~  331 (477)
T 2id5_A          302 NVSGN-QLTTLEESV--FHSVGNLETLILDSNP  331 (477)
T ss_dssp             ECCSS-CCSCCCGGG--BSCGGGCCEEECCSSC
T ss_pred             ECCCC-cCceeCHhH--cCCCcccCEEEccCCC
Confidence            77765 455554432  4556777777776654

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=99.87  E-value=3.3e-23  Score=240.26  Aligned_cols=219  Identities=14%  Similarity=0.010  Sum_probs=100.7

Q ss_pred             HhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEeccc----------cccc
Q 003090          506 LLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRE----------NQNF  575 (848)
Q Consensus       506 ~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~----------~~~L  575 (848)
                      +++|++|++++|.........+ ...+++|+.|++.++..-..     .......+++|++|++.+          |..+
T Consensus       292 ~~~L~~L~Ls~~~l~~~~~~~~-~~~~~~L~~L~L~~~~~~~~-----l~~~~~~~~~L~~L~L~~g~~~~~~~~~~~~~  365 (592)
T 3ogk_B          292 AAQIRKLDLLYALLETEDHCTL-IQKCPNLEVLETRNVIGDRG-----LEVLAQYCKQLKRLRIERGADEQGMEDEEGLV  365 (592)
T ss_dssp             GGGCCEEEETTCCCCHHHHHHH-HTTCTTCCEEEEEGGGHHHH-----HHHHHHHCTTCCEEEEECCCCSSTTSSTTCCC
T ss_pred             cCCCcEEecCCCcCCHHHHHHH-HHhCcCCCEEeccCccCHHH-----HHHHHHhCCCCCEEEeecCccccccccccCcc
Confidence            3566666666665211111111 13556677776663311110     011223456666666663          4443


Q ss_pred             ccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEec---cCCceeeeeccccccccccccccCCcCE
Q 003090          576 VEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYS---CGLLVSVFEIERVNIAKEETELFSSLEK  652 (848)
Q Consensus       576 ~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~---c~~l~~~~~~~~~~~~~~~~~~l~~L~~  652 (848)
                      +......+ ...+++|++|++ .|..++...+..+...+++|++|++++   |+.++..|..+.   ....+..+++|++
T Consensus       366 ~~~~~~~l-~~~~~~L~~L~l-~~~~l~~~~~~~l~~~~~~L~~L~l~~~~~~n~l~~~p~~~~---~~~~~~~~~~L~~  440 (592)
T 3ogk_B          366 SQRGLIAL-AQGCQELEYMAV-YVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNG---VRSLLIGCKKLRR  440 (592)
T ss_dssp             CHHHHHHH-HHHCTTCSEEEE-EESCCCHHHHHHHHHHCCSCCEEEEEECSCCSCCSSCCCHHH---HHHHHHHCTTCCE
T ss_pred             CHHHHHHH-HhhCccCeEEEe-ecCCccHHHHHHHHhhCCCCcEEEEeecCCCccccCchHHHH---HHHHHHhCCCCCE
Confidence            32100000 113566666666 344442333333334466666666663   334443321000   0011334666666


Q ss_pred             EecCCCcc-ccccccCCCccccccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecCCCCCCCCCCC
Q 003090          653 LTLWDLPR-MTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLG  731 (848)
Q Consensus       653 L~l~~c~~-L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~  731 (848)
                      |+++.|.+ +....... -...+++|+.|++++|. +++.                              ..+.....++
T Consensus       441 L~L~~~~~~l~~~~~~~-~~~~~~~L~~L~L~~n~-l~~~------------------------------~~~~~~~~~~  488 (592)
T 3ogk_B          441 FAFYLRQGGLTDLGLSY-IGQYSPNVRWMLLGYVG-ESDE------------------------------GLMEFSRGCP  488 (592)
T ss_dssp             EEEECCGGGCCHHHHHH-HHHSCTTCCEEEECSCC-SSHH------------------------------HHHHHHTCCT
T ss_pred             EEEecCCCCccHHHHHH-HHHhCccceEeeccCCC-CCHH------------------------------HHHHHHhcCc
Confidence            66665543 11110000 01235666666666553 2221                              0011123457


Q ss_pred             CccEEEEecCCCCceecccchhhccccccEEEEeccc
Q 003090          732 NLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCP  768 (848)
Q Consensus       732 ~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~  768 (848)
                      +|++|+|++|+ +..-........+++|++|++++|.
T Consensus       489 ~L~~L~l~~n~-l~~~~~~~~~~~l~~L~~L~ls~n~  524 (592)
T 3ogk_B          489 NLQKLEMRGCC-FSERAIAAAVTKLPSLRYLWVQGYR  524 (592)
T ss_dssp             TCCEEEEESCC-CBHHHHHHHHHHCSSCCEEEEESCB
T ss_pred             ccCeeeccCCC-CcHHHHHHHHHhcCccCeeECcCCc
Confidence            77777777776 5433222345567777777777776

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.86  E-value=6.5e-21  Score=220.00  Aligned_cols=302  Identities=14%  Similarity=0.118  Sum_probs=237.4

Q ss_pred             cCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      ..++.+++++|.+..+|...  .+++|++|++++|.+..+++..|..+++|++|++++              +.+...  
T Consensus        51 ~~l~~l~l~~~~l~~lp~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~--  114 (597)
T 3oja_B           51 NNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGF--------------NAIRYL--  114 (597)
T ss_dssp             CCCSEEEESSCEESEECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCS--------------SCCCCC--
T ss_pred             CCceEEEeeCCCCCCcCHHHHccCCCCcEEECCCCCCCCCChHHhcCCCCCCEEECCC--------------CcCCCC--
Confidence            45678999999999999876  789999999999999999887789999999999999              888884  


Q ss_pred             CCCCchhhhcccCcEEEccCccccCCchh-hccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhh
Q 003090          311 FLLPSSLSFLINLRTLRLHDRRIQGDLSL-IGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~~~~~~~~-i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                        .|..++.+++|++|++++|.+...++. ++++++|++|++++|.+..+|. .++.+++|++|++++|.... ++   +
T Consensus       115 --~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~-~~---~  188 (597)
T 3oja_B          115 --PPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTH-VD---L  188 (597)
T ss_dssp             --CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECTTSCCSB-CC---G
T ss_pred             --CHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCCEEEeeCCcCCCCChhhhhcCCcCcEEECcCCCCCC-cC---h
Confidence              556679999999999999988887754 6999999999999999996654 69999999999999986644 44   5


Q ss_pred             hccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCC
Q 003090          389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPL  468 (848)
Q Consensus       389 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~  468 (848)
                      +.+++|+.|++++|.+..                  +....+|+.|++++|.+..++... .++|+.|++..+....  .
T Consensus       189 ~~l~~L~~L~l~~n~l~~------------------l~~~~~L~~L~ls~n~l~~~~~~~-~~~L~~L~L~~n~l~~--~  247 (597)
T 3oja_B          189 SLIPSLFHANVSYNLLST------------------LAIPIAVEELDASHNSINVVRGPV-NVELTILKLQHNNLTD--T  247 (597)
T ss_dssp             GGCTTCSEEECCSSCCSE------------------EECCTTCSEEECCSSCCCEEECSC-CSCCCEEECCSSCCCC--C
T ss_pred             hhhhhhhhhhcccCcccc------------------ccCCchhheeeccCCccccccccc-CCCCCEEECCCCCCCC--C
Confidence            779999999999987653                  345568999999999988776653 4689998887554310  0


Q ss_pred             CcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCcee
Q 003090          469 SDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKY  548 (848)
Q Consensus       469 ~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~  548 (848)
                      +                               ++ ..+++|+.|+++++......+..+  ..+++|+.|+++++. ++.
T Consensus       248 ~-------------------------------~l-~~l~~L~~L~Ls~N~l~~~~~~~~--~~l~~L~~L~Ls~N~-l~~  292 (597)
T 3oja_B          248 A-------------------------------WL-LNYPGLVEVDLSYNELEKIMYHPF--VKMQRLERLYISNNR-LVA  292 (597)
T ss_dssp             G-------------------------------GG-GGCTTCSEEECCSSCCCEEESGGG--TTCSSCCEEECTTSC-CCE
T ss_pred             h-------------------------------hh-ccCCCCCEEECCCCccCCCCHHHh--cCccCCCEEECCCCC-CCC
Confidence            0                               00 114789999999887655444444  578999999999985 443


Q ss_pred             ecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccC
Q 003090          549 LLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCG  626 (848)
Q Consensus       549 l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~  626 (848)
                      ++     .....+|+|++|++++|. +..+.   ...+.+++|+.|++++|. + ..+|   ...+++|+.|++++|+
T Consensus       293 l~-----~~~~~l~~L~~L~Ls~N~-l~~i~---~~~~~l~~L~~L~L~~N~-l-~~~~---~~~~~~L~~L~l~~N~  356 (597)
T 3oja_B          293 LN-----LYGQPIPTLKVLDLSHNH-LLHVE---RNQPQFDRLENLYLDHNS-I-VTLK---LSTHHTLKNLTLSHND  356 (597)
T ss_dssp             EE-----CSSSCCTTCCEEECCSSC-CCCCG---GGHHHHTTCSEEECCSSC-C-CCCC---CCTTCCCSEEECCSSC
T ss_pred             CC-----cccccCCCCcEEECCCCC-CCccC---cccccCCCCCEEECCCCC-C-CCcC---hhhcCCCCEEEeeCCC
Confidence            32     123558999999999984 54432   123468999999999975 4 4554   2678999999999986

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=99.84  E-value=1.8e-21  Score=225.72  Aligned_cols=406  Identities=14%  Similarity=0.057  Sum_probs=240.8

Q ss_pred             cccccceeecccCcCcccChHHHcc-CCc-eeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccC
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQG-MKD-LQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD  330 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~-~~~-Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~  330 (848)
                      .+++|++|++++|.+.......+.. ++. |++|++++|..             +...   .++..+..+++|++|++++
T Consensus       110 ~~~~L~~L~L~~~~i~~~~~~~l~~~~~~~L~~L~L~~~~~-------------~~~~---~l~~~~~~~~~L~~L~L~~  173 (592)
T 3ogk_B          110 NLRQLKSVHFRRMIVSDLDLDRLAKARADDLETLKLDKCSG-------------FTTD---GLLSIVTHCRKIKTLLMEE  173 (592)
T ss_dssp             HCTTCCEEEEESCBCCHHHHHHHHHHHGGGCCEEEEESCEE-------------EEHH---HHHHHHHHCTTCSEEECTT
T ss_pred             hCCCCCeEEeeccEecHHHHHHHHHhccccCcEEECcCCCC-------------cCHH---HHHHHHhhCCCCCEEECcc
Confidence            4678888888877554322222223 334 88888887421             1110   0333445778888888888


Q ss_pred             ccccCC----c-hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecc
Q 003090          331 RRIQGD----L-SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS  400 (848)
Q Consensus       331 ~~~~~~----~-~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~  400 (848)
                      |.+...    + ..+..+++|++|++++|.++     .++..+.++++|++|++++|... .+|.. +.++++|++|+++
T Consensus       174 ~~~~~~~~~~l~~~~~~~~~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~-~l~~~-~~~~~~L~~L~l~  251 (592)
T 3ogk_B          174 SSFSEKDGKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEIL-ELVGF-FKAAANLEEFCGG  251 (592)
T ss_dssp             CEEECCCSHHHHHHHHHCCCCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECSSCBGG-GGHHH-HHHCTTCCEEEEC
T ss_pred             ccccCcchhHHHHHHhcCCCccEEEeeccCCCccCHHHHHHHHhhCCCCcEEeccCccHH-HHHHH-HhhhhHHHhhccc
Confidence            865443    2 24466788888888887765     44555667888888888886554 36654 7788888888876


Q ss_pred             ccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeCCCCCCCCCcccceEEecc
Q 003090          401 HSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIGDLEERPLSDFIGLFLQKF  479 (848)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~  479 (848)
                      .......          .......+..+++|+.|+++.+....++..+ .+++|++|++..+..                
T Consensus       252 ~~~~~~~----------~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~~~l----------------  305 (592)
T 3ogk_B          252 SLNEDIG----------MPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALL----------------  305 (592)
T ss_dssp             BCCCCTT----------CTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGGGGCCEEEETTCCC----------------
T ss_pred             ccccccc----------hHHHHHHhhccccccccCccccchhHHHHHHhhcCCCcEEecCCCcC----------------
Confidence            5322111          1123456677778888888776555555555 677788887763331                


Q ss_pred             cccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEec----------CCCceee
Q 003090          480 KKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFR----------CNEMKYL  549 (848)
Q Consensus       480 ~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~----------~~~l~~l  549 (848)
                                    .-..+. .+...+++|+.|++.++.....+...  ...+++|++|++.+          |..++..
T Consensus       306 --------------~~~~~~-~~~~~~~~L~~L~L~~~~~~~~l~~~--~~~~~~L~~L~L~~g~~~~~~~~~~~~~~~~  368 (592)
T 3ogk_B          306 --------------ETEDHC-TLIQKCPNLEVLETRNVIGDRGLEVL--AQYCKQLKRLRIERGADEQGMEDEEGLVSQR  368 (592)
T ss_dssp             --------------CHHHHH-HHHTTCTTCCEEEEEGGGHHHHHHHH--HHHCTTCCEEEEECCCCSSTTSSTTCCCCHH
T ss_pred             --------------CHHHHH-HHHHhCcCCCEEeccCccCHHHHHHH--HHhCCCCCEEEeecCccccccccccCccCHH
Confidence                          001111 11223578888888743322222111  13578999999995          6655431


Q ss_pred             cccccccccccCCCccEEecccccccccccccccccccCCCcceEEEec---CchhhHh------hhHHHHHhhccCcEE
Q 003090          550 LNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVD---CGSILKI------LLSHLVQSFQNLQRL  620 (848)
Q Consensus       550 ~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~---c~~l~~~------l~~~~~~~l~~L~~L  620 (848)
                         ........+|+|++|.+ .|.+++.-....+. ..+++|+.|++.+   |+.+ ..      ++. ....+++|++|
T Consensus       369 ---~~~~l~~~~~~L~~L~l-~~~~l~~~~~~~l~-~~~~~L~~L~l~~~~~~n~l-~~~p~~~~~~~-~~~~~~~L~~L  441 (592)
T 3ogk_B          369 ---GLIALAQGCQELEYMAV-YVSDITNESLESIG-TYLKNLCDFRLVLLDREERI-TDLPLDNGVRS-LLIGCKKLRRF  441 (592)
T ss_dssp             ---HHHHHHHHCTTCSEEEE-EESCCCHHHHHHHH-HHCCSCCEEEEEECSCCSCC-SSCCCHHHHHH-HHHHCTTCCEE
T ss_pred             ---HHHHHHhhCccCeEEEe-ecCCccHHHHHHHH-hhCCCCcEEEEeecCCCccc-cCchHHHHHHH-HHHhCCCCCEE
Confidence               01112345899999999 44444432111111 1388999999984   5566 54      333 34678999999


Q ss_pred             EEeccCC-ceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeecCccccccccCccccc
Q 003090          621 RVYSCGL-LVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEECDELRQVFPANFGKK  699 (848)
Q Consensus       621 ~l~~c~~-l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~C~~L~~~~p~~~~~~  699 (848)
                      ++++|.. +.....       ......+++|++|++++|. +...... ..+..+++|++|+|++|+ +++...      
T Consensus       442 ~L~~~~~~l~~~~~-------~~~~~~~~~L~~L~L~~n~-l~~~~~~-~~~~~~~~L~~L~l~~n~-l~~~~~------  505 (592)
T 3ogk_B          442 AFYLRQGGLTDLGL-------SYIGQYSPNVRWMLLGYVG-ESDEGLM-EFSRGCPNLQKLEMRGCC-FSERAI------  505 (592)
T ss_dssp             EEECCGGGCCHHHH-------HHHHHSCTTCCEEEECSCC-SSHHHHH-HHHTCCTTCCEEEEESCC-CBHHHH------
T ss_pred             EEecCCCCccHHHH-------HHHHHhCccceEeeccCCC-CCHHHHH-HHHhcCcccCeeeccCCC-CcHHHH------
Confidence            9988764 221100       0112347899999999875 4321000 013568999999999998 543200      


Q ss_pred             cccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEecc
Q 003090          700 AAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSC  767 (848)
Q Consensus       700 ~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C  767 (848)
                                              +.....+++|+.|++++|+ ++..........++.|....+...
T Consensus       506 ------------------------~~~~~~l~~L~~L~ls~n~-it~~~~~~l~~~~p~l~~~~~~~~  548 (592)
T 3ogk_B          506 ------------------------AAAVTKLPSLRYLWVQGYR-ASMTGQDLMQMARPYWNIELIPSR  548 (592)
T ss_dssp             ------------------------HHHHHHCSSCCEEEEESCB-CCTTCTTGGGGCCTTEEEEEECCC
T ss_pred             ------------------------HHHHHhcCccCeeECcCCc-CCHHHHHHHHHhCCCcEEEEecCc
Confidence                                    0111346889999999987 655433234456677766665543

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.84  E-value=7.5e-21  Score=201.61  Aligned_cols=239  Identities=20%  Similarity=0.247  Sum_probs=169.0

Q ss_pred             EEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHHhccCCCceeeecCCCcccCCcc-ccccccee
Q 003090          182 GICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL-ECPKLQAL  260 (848)
Q Consensus       182 ~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~-~~~~L~~L  260 (848)
                      .++.|.|++.+..+..+...     .+.....+.++. ..+..++..+.....++.|++++|.+..+|..+ .+++|++|
T Consensus        59 ~~~~~~g~~~~~~~~~l~~~-----~~~~l~~L~L~~-n~l~~lp~~l~~l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L  132 (328)
T 4fcg_A           59 QIETRTGRALKATADLLEDA-----TQPGRVALELRS-VPLPQFPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETL  132 (328)
T ss_dssp             TSCCSHHHHHHHHHHHHHHH-----TSTTCCEEEEES-SCCSSCCSCGGGGTTCSEEEEESSCCCCCCSCGGGGTTCSEE
T ss_pred             cccccCCcchhhhHHHHhcc-----cccceeEEEccC-CCchhcChhhhhCCCCCEEECCCCCccchhHHHhccCCCCEE
Confidence            34566676666555444332     234444555554 344566666666667788888888888787766 77888888


Q ss_pred             ecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhh---------hcccCcEEEccCc
Q 003090          261 FLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS---------FLINLRTLRLHDR  331 (848)
Q Consensus       261 ~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~---------~l~~L~~L~L~~~  331 (848)
                      ++++|.+..+|.. +.++++|++|++++|              .+.+.    +|..+.         .+++|++|++++|
T Consensus       133 ~Ls~n~l~~lp~~-l~~l~~L~~L~L~~n--------------~~~~~----~p~~~~~~~~~~~~~~l~~L~~L~L~~n  193 (328)
T 4fcg_A          133 TLARNPLRALPAS-IASLNRLRELSIRAC--------------PELTE----LPEPLASTDASGEHQGLVNLQSLRLEWT  193 (328)
T ss_dssp             EEESCCCCCCCGG-GGGCTTCCEEEEEEE--------------TTCCC----CCSCSEEEC-CCCEEESTTCCEEEEEEE
T ss_pred             ECCCCccccCcHH-HhcCcCCCEEECCCC--------------CCccc----cChhHhhccchhhhccCCCCCEEECcCC
Confidence            8888877777765 467888888888873              33332    555444         4788888888888


Q ss_pred             cccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccc
Q 003090          332 RIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESE  411 (848)
Q Consensus       332 ~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~  411 (848)
                      .+...+..++++++|++|++++|.++.+|..++.+++|++|++++|...+.+|.. ++.+++|++|++++|.+...    
T Consensus       194 ~l~~lp~~l~~l~~L~~L~L~~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~-~~~l~~L~~L~L~~n~~~~~----  268 (328)
T 4fcg_A          194 GIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPI-FGGRAPLKRLILKDCSNLLT----  268 (328)
T ss_dssp             CCCCCCGGGGGCTTCCEEEEESSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCCC-TTCCCCCCEEECTTCTTCCB----
T ss_pred             CcCcchHhhcCCCCCCEEEccCCCCCcCchhhccCCCCCEEECcCCcchhhhHHH-hcCCCCCCEEECCCCCchhh----
Confidence            7776667788888888888888888888877888888888888888777777776 67888888888888776654    


Q ss_pred             cccccCcccchhhhcccCCCcEEEeeccC-CCCCCCCC-ccCCCCeEEEE
Q 003090          412 SEEDSSSNAKFIELGALSRLTSLHIHIPE-GKIMPSDM-SFQNLTSFSIA  459 (848)
Q Consensus       412 ~~~~~~~~~~~~~L~~l~~L~~L~l~~~~-~~~~~~~~-~~~~L~~L~l~  459 (848)
                               .+..++++++|+.|++++|. ...+|..+ .+++|+.+.+.
T Consensus       269 ---------~p~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~l~  309 (328)
T 4fcg_A          269 ---------LPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILVP  309 (328)
T ss_dssp             ---------CCTTGGGCTTCCEEECTTCTTCCCCCGGGGGSCTTCEEECC
T ss_pred             ---------cchhhhcCCCCCEEeCCCCCchhhccHHHhhccCceEEeCC
Confidence                     45567778888888888866 45667666 77777777654

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.83  E-value=3.7e-20  Score=197.43  Aligned_cols=148  Identities=21%  Similarity=0.280  Sum_probs=74.0

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ++.++++++.+..+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+...    .|
T Consensus        35 l~~l~~~~~~l~~ip~~~~-~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~----~~   95 (332)
T 2ft3_A           35 LRVVQCSDLGLKAVPKEIS-PDTTLLDLQNNDISELRKDDFKGLQHLYALVLVN--------------NKISKI----HE   95 (332)
T ss_dssp             TTEEECCSSCCSSCCSCCC-TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS--------------SCCCEE----CG
T ss_pred             CCEEECCCCCccccCCCCC-CCCeEEECCCCcCCccCHhHhhCCCCCcEEECCC--------------CccCcc----CH
Confidence            4555555555555554442 4555555555555555444445555555555555              444442    24


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCcccc--ccChhhhhcc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILE--LIPRGVLSRL  391 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~--~~p~~~l~~l  391 (848)
                      ..++.+++|++|++++|.+...+..+.  ++|++|++++|.+..+|.. +.++++|++|++++|....  ..|.. +..+
T Consensus        96 ~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~-~~~l  172 (332)
T 2ft3_A           96 KAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGA-FDGL  172 (332)
T ss_dssp             GGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCEEECCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTS-SCSC
T ss_pred             hHhhCcCCCCEEECCCCcCCccCcccc--ccCCEEECCCCccCccCHhHhCCCccCCEEECCCCccccCCCCccc-ccCC
Confidence            455555555555555555444443332  4555555555555544432 4555555555555544321  22222 3444


Q ss_pred             ccccEEeccccccc
Q 003090          392 RKLEELYMSHSFRH  405 (848)
Q Consensus       392 ~~L~~L~l~~~~~~  405 (848)
                       +|++|++++|.+.
T Consensus       173 -~L~~L~l~~n~l~  185 (332)
T 2ft3_A          173 -KLNYLRISEAKLT  185 (332)
T ss_dssp             -CCSCCBCCSSBCS
T ss_pred             -ccCEEECcCCCCC
Confidence             5555555555443

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.83  E-value=9.6e-20  Score=194.18  Aligned_cols=293  Identities=16%  Similarity=0.147  Sum_probs=211.8

Q ss_pred             ccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccC
Q 003090          256 KLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQG  335 (848)
Q Consensus       256 ~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~  335 (848)
                      +++.++++++.+..+|..+   .++|++|++++              +.+...    .|..+.++++|++|++++|.+..
T Consensus        34 ~l~~l~~~~~~l~~ip~~~---~~~l~~L~l~~--------------n~i~~~----~~~~~~~l~~L~~L~L~~n~l~~   92 (332)
T 2ft3_A           34 HLRVVQCSDLGLKAVPKEI---SPDTTLLDLQN--------------NDISEL----RKDDFKGLQHLYALVLVNNKISK   92 (332)
T ss_dssp             ETTEEECCSSCCSSCCSCC---CTTCCEEECCS--------------SCCCEE----CTTTTTTCTTCCEEECCSSCCCE
T ss_pred             cCCEEECCCCCccccCCCC---CCCCeEEECCC--------------CcCCcc----CHhHhhCCCCCcEEECCCCccCc
Confidence            7899999999998998764   46899999999              778773    35689999999999999998877


Q ss_pred             Cc-hhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccccc
Q 003090          336 DL-SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE  414 (848)
Q Consensus       336 ~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  414 (848)
                      .. ..++++++|++|++++|.++.+|..+.  ++|++|++++|... .+|...+.++++|++|++++|.+...       
T Consensus        93 ~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~L~l~~n~i~-~~~~~~~~~l~~L~~L~l~~n~l~~~-------  162 (332)
T 2ft3_A           93 IHEKAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVELRIHDNRIR-KVPKGVFSGLRNMNCIEMGGNPLENS-------  162 (332)
T ss_dssp             ECGGGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCEEECCSSCCC-CCCSGGGSSCSSCCEEECCSCCCBGG-------
T ss_pred             cCHhHhhCcCCCCEEECCCCcCCccCcccc--ccCCEEECCCCccC-ccCHhHhCCCccCCEEECCCCccccC-------
Confidence            64 789999999999999999999998766  89999999998665 56665589999999999999987531       


Q ss_pred             ccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEecccccccccccCccccc
Q 003090          415 DSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMR  494 (848)
Q Consensus       415 ~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~  494 (848)
                          +..+..+..+ +|+.|++++|.++.+|..+. ++|+.|++..+..-......+.                      
T Consensus       163 ----~~~~~~~~~l-~L~~L~l~~n~l~~l~~~~~-~~L~~L~l~~n~i~~~~~~~l~----------------------  214 (332)
T 2ft3_A          163 ----GFEPGAFDGL-KLNYLRISEAKLTGIPKDLP-ETLNELHLDHNKIQAIELEDLL----------------------  214 (332)
T ss_dssp             ----GSCTTSSCSC-CCSCCBCCSSBCSSCCSSSC-SSCSCCBCCSSCCCCCCTTSST----------------------
T ss_pred             ----CCCcccccCC-ccCEEECcCCCCCccCcccc-CCCCEEECCCCcCCccCHHHhc----------------------
Confidence                1134556666 89999999999998887653 7888888875543111110000                      


Q ss_pred             hhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccccc
Q 003090          495 ISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQN  574 (848)
Q Consensus       495 l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~  574 (848)
                                .+++|+.|+++++.........+  ..+++|++|++.++. ++.++.     ....+++|++|+++++ .
T Consensus       215 ----------~l~~L~~L~L~~N~l~~~~~~~~--~~l~~L~~L~L~~N~-l~~lp~-----~l~~l~~L~~L~l~~N-~  275 (332)
T 2ft3_A          215 ----------RYSKLYRLGLGHNQIRMIENGSL--SFLPTLRELHLDNNK-LSRVPA-----GLPDLKLLQVVYLHTN-N  275 (332)
T ss_dssp             ----------TCTTCSCCBCCSSCCCCCCTTGG--GGCTTCCEEECCSSC-CCBCCT-----TGGGCTTCCEEECCSS-C
T ss_pred             ----------CCCCCCEEECCCCcCCcCChhHh--hCCCCCCEEECCCCc-CeecCh-----hhhcCccCCEEECCCC-C
Confidence                      13678888888776543322233  467899999999884 444321     2456899999999988 4


Q ss_pred             ccccccccccc----ccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccC
Q 003090          575 FVEICHGQLPA----GCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCG  626 (848)
Q Consensus       575 L~~~~~~~~~~----~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~  626 (848)
                      ++.+....+..    ..++.|+.|++.+++.....+++..+..+++|+.|++++|.
T Consensus       276 l~~~~~~~~~~~~~~~~~~~l~~L~l~~N~~~~~~~~~~~~~~l~~L~~l~l~~n~  331 (332)
T 2ft3_A          276 ITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFGNYK  331 (332)
T ss_dssp             CCBCCTTSSSCSSCCSSSCCBSEEECCSSSSCGGGSCGGGGTTBCCSTTEEC----
T ss_pred             CCccChhHccccccccccccccceEeecCcccccccCcccccccchhhhhhccccc
Confidence            55542222211    12677899999988743124454445778899999988875

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=99.83  E-value=7.2e-22  Score=229.18  Aligned_cols=217  Identities=15%  Similarity=0.036  Sum_probs=115.7

Q ss_pred             HhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccccccccccCCCccEEecccc--------ccccc
Q 003090          506 LLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIREN--------QNFVE  577 (848)
Q Consensus       506 ~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~--------~~L~~  577 (848)
                      +++|++|+++++......... ....+++|++|.+.+|.  ..   .........+++|++|++.+|        ..+..
T Consensus       288 ~~~L~~L~L~~~~l~~~~l~~-~~~~~~~L~~L~l~~~~--~~---~~l~~l~~~~~~L~~L~L~~~~~~g~~~~~~l~~  361 (594)
T 2p1m_B          288 CSRLTTLNLSYATVQSYDLVK-LLCQCPKLQRLWVLDYI--ED---AGLEVLASTCKDLRELRVFPSEPFVMEPNVALTE  361 (594)
T ss_dssp             HTTCCEEECTTCCCCHHHHHH-HHTTCTTCCEEEEEGGG--HH---HHHHHHHHHCTTCCEEEEECSCTTCSSCSSCCCH
T ss_pred             hCCCCEEEccCCCCCHHHHHH-HHhcCCCcCEEeCcCcc--CH---HHHHHHHHhCCCCCEEEEecCcccccccCCCCCH
Confidence            467777777777622111111 12366888888888772  11   000112234788888888442        23322


Q ss_pred             ccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEe-----ccCCceeeeeccccccccccccccCCcCE
Q 003090          578 ICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVY-----SCGLLVSVFEIERVNIAKEETELFSSLEK  652 (848)
Q Consensus       578 ~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~-----~c~~l~~~~~~~~~~~~~~~~~~l~~L~~  652 (848)
                      .....+. ..+++|+.|.+ +|..++...+..+...+++|++|++.     +|..++..+..+.   ....+..+++|++
T Consensus       362 ~~l~~l~-~~~~~L~~L~~-~~~~l~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~---~~~l~~~~~~L~~  436 (594)
T 2p1m_B          362 QGLVSVS-MGCPKLESVLY-FCRQMTNAALITIARNRPNMTRFRLCIIEPKAPDYLTLEPLDIG---FGAIVEHCKDLRR  436 (594)
T ss_dssp             HHHHHHH-HHCTTCCEEEE-EESCCCHHHHHHHHHHCTTCCEEEEEESSTTCCCTTTCCCTHHH---HHHHHHHCTTCCE
T ss_pred             HHHHHHH-HhchhHHHHHH-hcCCcCHHHHHHHHhhCCCcceeEeecccCCCcccccCCchhhH---HHHHHhhCCCccE
Confidence            1000000 13778888844 45555233334444567888888888     5666664431100   0011446778888


Q ss_pred             EecCCCccccccccCCCccc-cccCccEEEeecCccccccccCccccccccceeeeccccccceeeeecCCCCCCCCCCC
Q 003090          653 LTLWDLPRMTDIWKGDTQFV-SLHNLKKVRVEECDELRQVFPANFGKKAAAEEMVLYRKRRDQIHIHATTSTSSPTPSLG  731 (848)
Q Consensus       653 L~l~~c~~L~~l~~~~~~l~-~l~~L~~L~i~~C~~L~~~~p~~~~~~~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~  731 (848)
                      |++++  .+......  .+. .+++|+.|++++|. +++..+..                              ....++
T Consensus       437 L~L~~--~l~~~~~~--~l~~~~~~L~~L~L~~~~-i~~~~~~~------------------------------l~~~~~  481 (594)
T 2p1m_B          437 LSLSG--LLTDKVFE--YIGTYAKKMEMLSVAFAG-DSDLGMHH------------------------------VLSGCD  481 (594)
T ss_dssp             EECCS--SCCHHHHH--HHHHHCTTCCEEEEESCC-SSHHHHHH------------------------------HHHHCT
T ss_pred             EeecC--cccHHHHH--HHHHhchhccEeeccCCC-CcHHHHHH------------------------------HHhcCC
Confidence            88865  33321110  112 36778888888775 33210000                              012367


Q ss_pred             CccEEEEecCCCCceecccchhhccccccEEEEecccc
Q 003090          732 NLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVRSCPT  769 (848)
Q Consensus       732 ~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~~C~~  769 (848)
                      +|++|++++|+. ...........+++|++|++++|+.
T Consensus       482 ~L~~L~L~~n~~-~~~~~~~~~~~l~~L~~L~l~~~~~  518 (594)
T 2p1m_B          482 SLRKLEIRDCPF-GDKALLANASKLETMRSLWMSSCSV  518 (594)
T ss_dssp             TCCEEEEESCSC-CHHHHHHTGGGGGGSSEEEEESSCC
T ss_pred             CcCEEECcCCCC-cHHHHHHHHHhCCCCCEEeeeCCCC
Confidence            788888888774 4332223455678888888888864

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.83  E-value=1.1e-19  Score=193.50  Aligned_cols=187  Identities=19%  Similarity=0.262  Sum_probs=117.1

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ++.++++++.+..+|..+. +.+++|++++|.+..++...|.++++|++|++++              +.+...    .|
T Consensus        33 l~~l~~~~~~l~~lp~~~~-~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~----~~   93 (330)
T 1xku_A           33 LRVVQCSDLGLEKVPKDLP-PDTALLDLQNNKITEIKDGDFKNLKNLHTLILIN--------------NKISKI----SP   93 (330)
T ss_dssp             TTEEECTTSCCCSCCCSCC-TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS--------------SCCCCB----CT
T ss_pred             CeEEEecCCCccccCccCC-CCCeEEECCCCcCCEeChhhhccCCCCCEEECCC--------------CcCCee----CH
Confidence            4567777777777776543 5677777777777777665567777777777777              666663    36


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCcccc--ccChhhhhcc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILE--LIPRGVLSRL  391 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~--~~p~~~l~~l  391 (848)
                      ..++.+++|++|++++|.+...+..+.  ++|++|++++|.++.++. .+.++++|++|++++|....  ..+.. +.++
T Consensus        94 ~~~~~l~~L~~L~Ls~n~l~~l~~~~~--~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~-~~~l  170 (330)
T 1xku_A           94 GAFAPLVKLERLYLSKNQLKELPEKMP--KTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGA-FQGM  170 (330)
T ss_dssp             TTTTTCTTCCEEECCSSCCSBCCSSCC--TTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTG-GGGC
T ss_pred             HHhcCCCCCCEEECCCCcCCccChhhc--ccccEEECCCCcccccCHhHhcCCccccEEECCCCcCCccCcChhh-ccCC
Confidence            667777777777777776665554433  567777777777775554 36667777777777765532  23333 6667


Q ss_pred             ccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC-CC-ccCCCCeEEEE
Q 003090          392 RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-DM-SFQNLTSFSIA  459 (848)
Q Consensus       392 ~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~-~~-~~~~L~~L~l~  459 (848)
                      ++|++|++++|.+...              +..+  .++|+.|++++|.+..++. .+ .+++|+.|++.
T Consensus       171 ~~L~~L~l~~n~l~~l--------------~~~~--~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls  224 (330)
T 1xku_A          171 KKLSYIRIADTNITTI--------------PQGL--PPSLTELHLDGNKITKVDAASLKGLNNLAKLGLS  224 (330)
T ss_dssp             TTCCEEECCSSCCCSC--------------CSSC--CTTCSEEECTTSCCCEECTGGGTTCTTCCEEECC
T ss_pred             CCcCEEECCCCccccC--------------Cccc--cccCCEEECCCCcCCccCHHHhcCCCCCCEEECC
Confidence            7777777777665432              1111  1567777777766655432 22 55556665554

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.82  E-value=2.9e-20  Score=195.90  Aligned_cols=176  Identities=19%  Similarity=0.299  Sum_probs=135.7

Q ss_pred             CCCceeeecCCCc---ccCCcc-cccccceeeccc-CcCc-ccChHHHccCCceeEEEccCcccccccccCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIH---EVPDEL-ECPKLQALFLQE-NSPL-AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPS  307 (848)
Q Consensus       234 ~l~~l~l~~n~l~---~lp~~~-~~~~L~~L~l~~-~~~~-~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~  307 (848)
                      .++.+++++|.+.   .+|..+ .+++|++|++++ |.+. .+|.. +.++++|++|++++              +.+.+
T Consensus        51 ~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n~l~~~~p~~-l~~l~~L~~L~Ls~--------------n~l~~  115 (313)
T 1ogq_A           51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPA-IAKLTQLHYLYITH--------------TNVSG  115 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGG-GGGCTTCSEEEEEE--------------ECCEE
T ss_pred             eEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCCcccccCChh-HhcCCCCCEEECcC--------------CeeCC
Confidence            4567888888887   477766 788888888884 5444 56655 57888888888888              67764


Q ss_pred             CCCCCCCchhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCc-ccChhhccCC-cccEEeccCCccccccC
Q 003090          308 SPLFLLPSSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVS-EIPVSFGRLS-HLRLLDLTGCYILELIP  384 (848)
Q Consensus       308 ~~~~~lp~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~-~L~~L~l~~~~~~~~~p  384 (848)
                      .    +|..+..+++|++|++++|.+.+. +..++.+++|++|++++|.++ .+|..++++. +|++|++++|...+.+|
T Consensus       116 ~----~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~~~~~  191 (313)
T 1ogq_A          116 A----IPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIP  191 (313)
T ss_dssp             E----CCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECC
T ss_pred             c----CCHHHhCCCCCCEEeCCCCccCCcCChHHhcCCCCCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeeeccCC
Confidence            4    788888888888888888877744 477888888888888888888 7888888887 88888888887777777


Q ss_pred             hhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCC
Q 003090          385 RGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKI  443 (848)
Q Consensus       385 ~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~  443 (848)
                      .. +..+. |+.|++++|.+...             .+..+..+++|+.|++++|.+..
T Consensus       192 ~~-~~~l~-L~~L~Ls~N~l~~~-------------~~~~~~~l~~L~~L~L~~N~l~~  235 (313)
T 1ogq_A          192 PT-FANLN-LAFVDLSRNMLEGD-------------ASVLFGSDKNTQKIHLAKNSLAF  235 (313)
T ss_dssp             GG-GGGCC-CSEEECCSSEEEEC-------------CGGGCCTTSCCSEEECCSSEECC
T ss_pred             hH-HhCCc-ccEEECcCCcccCc-------------CCHHHhcCCCCCEEECCCCceee
Confidence            76 67776 88888888877654             45667788888888888876653

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.82  E-value=3.2e-19  Score=189.99  Aligned_cols=169  Identities=18%  Similarity=0.218  Sum_probs=139.4

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      .+++.++++++.+..+|..+   .+++++|++++              +.+...    .+..+.++++|++|++++|.+.
T Consensus        31 c~l~~l~~~~~~l~~lp~~~---~~~l~~L~L~~--------------n~i~~~----~~~~~~~l~~L~~L~L~~n~l~   89 (330)
T 1xku_A           31 CHLRVVQCSDLGLEKVPKDL---PPDTALLDLQN--------------NKITEI----KDGDFKNLKNLHTLILINNKIS   89 (330)
T ss_dssp             EETTEEECTTSCCCSCCCSC---CTTCCEEECCS--------------SCCCCB----CTTTTTTCTTCCEEECCSSCCC
T ss_pred             CCCeEEEecCCCccccCccC---CCCCeEEECCC--------------CcCCEe----ChhhhccCCCCCEEECCCCcCC
Confidence            37899999999888898753   46899999999              888883    3347999999999999999888


Q ss_pred             CC-chhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccc
Q 003090          335 GD-LSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       335 ~~-~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                      .. +..++++++|++|++++|.++.+|..+.  ++|++|++++|... .++...+.++++|++|++++|.+...      
T Consensus        90 ~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~--~~L~~L~l~~n~l~-~~~~~~~~~l~~L~~L~l~~n~l~~~------  160 (330)
T 1xku_A           90 KISPGAFAPLVKLERLYLSKNQLKELPEKMP--KTLQELRVHENEIT-KVRKSVFNGLNQMIVVELGTNPLKSS------  160 (330)
T ss_dssp             CBCTTTTTTCTTCCEEECCSSCCSBCCSSCC--TTCCEEECCSSCCC-BBCHHHHTTCTTCCEEECCSSCCCGG------
T ss_pred             eeCHHHhcCCCCCCEEECCCCcCCccChhhc--ccccEEECCCCccc-ccCHhHhcCCccccEEECCCCcCCcc------
Confidence            77 4789999999999999999999998765  79999999998665 56665589999999999999987532      


Q ss_pred             cccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          414 EDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       414 ~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                           +..+..+..+++|+.|++++|.+..+|..+. ++|+.|++.
T Consensus       161 -----~~~~~~~~~l~~L~~L~l~~n~l~~l~~~~~-~~L~~L~l~  200 (330)
T 1xku_A          161 -----GIENGAFQGMKKLSYIRIADTNITTIPQGLP-PSLTELHLD  200 (330)
T ss_dssp             -----GBCTTGGGGCTTCCEEECCSSCCCSCCSSCC-TTCSEEECT
T ss_pred             -----CcChhhccCCCCcCEEECCCCccccCCcccc-ccCCEEECC
Confidence                 1245678899999999999999988876643 666666665

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.82  E-value=1.9e-19  Score=190.78  Aligned_cols=136  Identities=23%  Similarity=0.330  Sum_probs=109.9

Q ss_pred             cCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCC
Q 003090          277 GMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDV  356 (848)
Q Consensus       277 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l  356 (848)
                      ...+++.|++++              +.+..     +|..+.++++|++|++++|.+...+..++++++|++|++++|.+
T Consensus        79 ~~~~l~~L~L~~--------------n~l~~-----lp~~l~~l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~n~l  139 (328)
T 4fcg_A           79 TQPGRVALELRS--------------VPLPQ-----FPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPL  139 (328)
T ss_dssp             TSTTCCEEEEES--------------SCCSS-----CCSCGGGGTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEESCCC
T ss_pred             cccceeEEEccC--------------CCchh-----cChhhhhCCCCCEEECCCCCccchhHHHhccCCCCEEECCCCcc
Confidence            467899999999              88886     99999999999999999998886678899999999999999999


Q ss_pred             cccChhhccCCcccEEeccCCccccccChhhhhc---------cccccEEeccccccccccccccccccCcccchhhhcc
Q 003090          357 SEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSR---------LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGA  427 (848)
Q Consensus       357 ~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~---------l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~  427 (848)
                      +.+|..++++++|++|++++|...+.+|.. ++.         +++|++|++++|.+. .             .+..++.
T Consensus       140 ~~lp~~l~~l~~L~~L~L~~n~~~~~~p~~-~~~~~~~~~~~~l~~L~~L~L~~n~l~-~-------------lp~~l~~  204 (328)
T 4fcg_A          140 RALPASIASLNRLRELSIRACPELTELPEP-LASTDASGEHQGLVNLQSLRLEWTGIR-S-------------LPASIAN  204 (328)
T ss_dssp             CCCCGGGGGCTTCCEEEEEEETTCCCCCSC-SEEEC-CCCEEESTTCCEEEEEEECCC-C-------------CCGGGGG
T ss_pred             ccCcHHHhcCcCCCEEECCCCCCccccChh-HhhccchhhhccCCCCCEEECcCCCcC-c-------------chHhhcC
Confidence            999999999999999999999888888886 443         666666666666554 2             3445666


Q ss_pred             cCCCcEEEeeccCCCCCCC
Q 003090          428 LSRLTSLHIHIPEGKIMPS  446 (848)
Q Consensus       428 l~~L~~L~l~~~~~~~~~~  446 (848)
                      +++|+.|++++|.+..+|.
T Consensus       205 l~~L~~L~L~~N~l~~l~~  223 (328)
T 4fcg_A          205 LQNLKSLKIRNSPLSALGP  223 (328)
T ss_dssp             CTTCCEEEEESSCCCCCCG
T ss_pred             CCCCCEEEccCCCCCcCch
Confidence            6666666666665554443

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.81  E-value=6.3e-20  Score=197.44  Aligned_cols=192  Identities=20%  Similarity=0.180  Sum_probs=151.8

Q ss_pred             ceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCch
Q 003090          237 GISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSS  316 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~  316 (848)
                      ..+.+++.++.+|..+. ++|++|++++|.+..++...|.++++|++|++++              +.+...    .|..
T Consensus        35 ~c~~~~~~l~~iP~~~~-~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~----~~~~   95 (353)
T 2z80_A           35 ICKGSSGSLNSIPSGLT-EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS--------------NGINTI----EEDS   95 (353)
T ss_dssp             EEECCSTTCSSCCTTCC-TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTT--------------SCCCEE----CTTT
T ss_pred             EeeCCCCCccccccccc-ccCcEEECCCCcCcccCHHHhccCCCCCEEECCC--------------CccCcc----CHhh
Confidence            36777888888887664 5899999999988888886678899999999998              777773    4567


Q ss_pred             hhhcccCcEEEccCccccCCch-hhccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          317 LSFLINLRTLRLHDRRIQGDLS-LIGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~~-~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      +..+++|++|++++|.+...+. .++++++|++|++++|.++.+|.  .+.++++|++|++++|.....++...++++++
T Consensus        96 ~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~  175 (353)
T 2z80_A           96 FSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTF  175 (353)
T ss_dssp             TTTCTTCCEEECCSSCCSSCCHHHHTTCTTCSEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCE
T ss_pred             cCCCCCCCEEECCCCcCCcCCHhHhCCCccCCEEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCC
Confidence            8889999999999998887774 48889999999999999988886  68889999999999886566665544788999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEe
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAI  460 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~  460 (848)
                      |++|++++|.+...             .+..++.+++|++|++++|.+..++...  .+++|+.|++..
T Consensus       176 L~~L~l~~n~l~~~-------------~~~~l~~l~~L~~L~l~~n~l~~~~~~~~~~~~~L~~L~L~~  231 (353)
T 2z80_A          176 LEELEIDASDLQSY-------------EPKSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRD  231 (353)
T ss_dssp             EEEEEEEETTCCEE-------------CTTTTTTCSEEEEEEEECSCSTTHHHHHHHHTTTEEEEEEES
T ss_pred             CCEEECCCCCcCcc-------------CHHHHhccccCCeecCCCCccccchhhhhhhcccccEEECCC
Confidence            99999998887654             4567788888888888888766555433  355666666653

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=99.80  E-value=1e-20  Score=212.00  Aligned_cols=164  Identities=16%  Similarity=0.108  Sum_probs=107.2

Q ss_pred             cccceeecccCcCcccC-hHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          255 PKLQALFLQENSPLAIP-DRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      ++|++|++++|.+...+ ..++..+++|++|++++              +.+.......++..+..+++|++|++++|.+
T Consensus         3 ~~l~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~~--------------~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l   68 (461)
T 1z7x_W            3 LDIQSLDIQCEELSDARWAELLPLLQQCQVVRLDD--------------CGLTEARCKDISSALRVNPALAELNLRSNEL   68 (461)
T ss_dssp             EEEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEES--------------SCCCHHHHHHHHHHHHTCTTCCEEECTTCCC
T ss_pred             ccceehhhhhcccCchhHHHHHhhcCCccEEEccC--------------CCCCHHHHHHHHHHHHhCCCcCEEeCCCCcC
Confidence            56788888888765543 23467788888888888              5555310001566677778888888888865


Q ss_pred             cCCc-hhh-cccc----CCCEEEccCCCCc-----ccChhhccCCcccEEeccCCccccccChhh----hhccccccEEe
Q 003090          334 QGDL-SLI-GELS----GLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILELIPRGV----LSRLRKLEELY  398 (848)
Q Consensus       334 ~~~~-~~i-~~l~----~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~----l~~l~~L~~L~  398 (848)
                      .... ..+ ..+.    +|++|++++|.++     .+|..+.++++|++|++++|......+..+    ....++|++|+
T Consensus        69 ~~~~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~  148 (461)
T 1z7x_W           69 GDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQ  148 (461)
T ss_dssp             HHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEE
T ss_pred             ChHHHHHHHHHHhhCCCceeEEEccCCCCCHHHHHHHHHHHccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcceEEE
Confidence            5432 222 3344    6888888888877     457778888888888888876543323321    12245688888


Q ss_pred             ccccccccccccccccccCcccchhhhcccCCCcEEEeeccCC
Q 003090          399 MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       399 l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~  441 (848)
                      +++|.+...         ........+..+++|++|++++|.+
T Consensus       149 L~~n~l~~~---------~~~~l~~~l~~~~~L~~L~L~~n~i  182 (461)
T 1z7x_W          149 LEYCSLSAA---------SCEPLASVLRAKPDFKELTVSNNDI  182 (461)
T ss_dssp             CTTSCCBGG---------GHHHHHHHHHHCTTCCEEECCSSBC
T ss_pred             CCCCCCCHH---------HHHHHHHHHhhCCCCCEEECcCCCc
Confidence            888876543         1112345666778888888877754

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.79  E-value=1.1e-19  Score=191.39  Aligned_cols=194  Identities=21%  Similarity=0.152  Sum_probs=157.8

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ++++.+++.++.+|..+. +++++|++++|.+..+|..+|.++++|++|++++              +.+...  ...|.
T Consensus        10 ~~l~c~~~~l~~ip~~~~-~~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~--------------n~l~~~--~~~~~   72 (306)
T 2z66_A           10 TEIRCNSKGLTSVPTGIP-SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSS--------------NGLSFK--GCCSQ   72 (306)
T ss_dssp             TEEECCSSCCSSCCSCCC-TTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCS--------------SCCCEE--EEEEH
T ss_pred             CEEEcCCCCcccCCCCCC-CCCCEEECCCCccCccCHhHhhccccCCEEECCC--------------CccCcc--cCccc
Confidence            567888889999998664 6899999999999999998889999999999999              777641  00267


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+..+++|++|++++|.+...+..+..+++|++|++++|.++.++.  .+..+++|++|++++|......+.. +..+++
T Consensus        73 ~~~~~~~L~~L~Ls~n~i~~l~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~-~~~l~~  151 (306)
T 2z66_A           73 SDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGI-FNGLSS  151 (306)
T ss_dssp             HHHSCSCCCEEECCSCSEEEEEEEEETCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTT-TTTCTT
T ss_pred             ccccccccCEEECCCCccccChhhcCCCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCccchhh-cccCcC
Confidence            7888999999999999888777778999999999999999997764  7889999999999998776655555 789999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC-CC-ccCCCCeEEEE
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-DM-SFQNLTSFSIA  459 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~-~~-~~~~L~~L~l~  459 (848)
                      |++|++++|.+...            ..+..+..+++|+.|++++|.+..++. .+ .+++|+.|++.
T Consensus       152 L~~L~l~~n~l~~~------------~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~  207 (306)
T 2z66_A          152 LEVLKMAGNSFQEN------------FLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMS  207 (306)
T ss_dssp             CCEEECTTCEEGGG------------EECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECT
T ss_pred             CCEEECCCCccccc------------cchhHHhhCcCCCEEECCCCCcCCcCHHHhcCCCCCCEEECC
Confidence            99999999987652            134567889999999999998876643 33 55666666654

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.79  E-value=3e-19  Score=188.14  Aligned_cols=172  Identities=20%  Similarity=0.244  Sum_probs=132.0

Q ss_pred             cccceeecccCcCc---ccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCc
Q 003090          255 PKLQALFLQENSPL---AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDR  331 (848)
Q Consensus       255 ~~L~~L~l~~~~~~---~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~  331 (848)
                      .+++.|++++|.+.   .+|.. +.++++|++|+++++             +.+.+.    +|..++++++|++|++++|
T Consensus        50 ~~l~~L~L~~~~l~~~~~~~~~-l~~l~~L~~L~L~~~-------------n~l~~~----~p~~l~~l~~L~~L~Ls~n  111 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPKPYPIPSS-LANLPYLNFLYIGGI-------------NNLVGP----IPPAIAKLTQLHYLYITHT  111 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGG-GGGCTTCSEEEEEEE-------------TTEESC----CCGGGGGCTTCSEEEEEEE
T ss_pred             ceEEEEECCCCCccCCcccChh-HhCCCCCCeeeCCCC-------------Cccccc----CChhHhcCCCCCEEECcCC
Confidence            57888888888766   46665 578889999999832             566654    8888888999999999988


Q ss_pred             cccC-CchhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCccccccChhhhhccc-cccEEecccccccccc
Q 003090          332 RIQG-DLSLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR-KLEELYMSHSFRHWQF  408 (848)
Q Consensus       332 ~~~~-~~~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~-~L~~L~l~~~~~~~~~  408 (848)
                      .+.+ .+..++++++|++|++++|.++ .+|..++++++|++|++++|...+.+|.. +++++ +|++|++++|.+.+. 
T Consensus       112 ~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~-l~~l~~~L~~L~L~~N~l~~~-  189 (313)
T 1ogq_A          112 NVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDS-YGSFSKLFTSMTISRNRLTGK-  189 (313)
T ss_dssp             CCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGG-GGCCCTTCCEEECCSSEEEEE-
T ss_pred             eeCCcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCCCCCeEECcCCcccCcCCHH-HhhhhhcCcEEECcCCeeecc-
Confidence            8774 4577888899999999998888 78888888999999999888877778887 78887 889999988887755 


Q ss_pred             ccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC-CC-ccCCCCeEEEE
Q 003090          409 ESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-DM-SFQNLTSFSIA  459 (848)
Q Consensus       409 ~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~-~~-~~~~L~~L~l~  459 (848)
                                  .+..+..++ |+.|++++|.+...+. .+ .+++|+.|++.
T Consensus       190 ------------~~~~~~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~  229 (313)
T 1ogq_A          190 ------------IPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLA  229 (313)
T ss_dssp             ------------CCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEECC
T ss_pred             ------------CChHHhCCc-ccEEECcCCcccCcCCHHHhcCCCCCEEECC
Confidence                        445666666 8888888887664332 22 55556555554

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.78  E-value=8.3e-19  Score=188.66  Aligned_cols=194  Identities=22%  Similarity=0.278  Sum_probs=162.4

Q ss_pred             cCCchhHHHHHHHhccCCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCccccccc
Q 003090          218 QTPSITKIQYEIAGWLDLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFS  295 (848)
Q Consensus       218 ~~~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~  295 (848)
                      ....+..++..+..  .++.|++++|.+..+|.. + .+++|++|++++|.+..++...|.++++|++|++++       
T Consensus        39 ~~~~l~~iP~~~~~--~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~-------  109 (353)
T 2z80_A           39 SSGSLNSIPSGLTE--AVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSY-------  109 (353)
T ss_dssp             CSTTCSSCCTTCCT--TCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCS-------
T ss_pred             CCCCcccccccccc--cCcEEECCCCcCcccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCC-------
Confidence            34556666665543  679999999999999873 4 899999999999999998877789999999999999       


Q ss_pred             ccCCCCCCCCCCCCCCCCCch-hhhcccCcEEEccCccccCCch--hhccccCCCEEEccCC-CCccc-ChhhccCCccc
Q 003090          296 VRFPFLFPPLPSSPLFLLPSS-LSFLINLRTLRLHDRRIQGDLS--LIGELSGLEILDLSES-DVSEI-PVSFGRLSHLR  370 (848)
Q Consensus       296 ~~~~~~~~~l~~~~~~~lp~~-~~~l~~L~~L~L~~~~~~~~~~--~i~~l~~L~~L~l~~~-~l~~l-p~~i~~L~~L~  370 (848)
                             +.+..     +|.. ++.+++|++|++++|.+...+.  .+.++++|++|++++| .+..+ |..++++++|+
T Consensus       110 -------n~l~~-----~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~  177 (353)
T 2z80_A          110 -------NYLSN-----LSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLE  177 (353)
T ss_dssp             -------SCCSS-----CCHHHHTTCTTCSEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEE
T ss_pred             -------CcCCc-----CCHhHhCCCccCCEEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCC
Confidence                   88887     6665 8999999999999998887665  7899999999999999 57766 45789999999


Q ss_pred             EEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC
Q 003090          371 LLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS  446 (848)
Q Consensus       371 ~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~  446 (848)
                      +|++++|...+..|.. +.++++|++|++++|.+...             ....+..+++|+.|++++|.+..++.
T Consensus       178 ~L~l~~n~l~~~~~~~-l~~l~~L~~L~l~~n~l~~~-------------~~~~~~~~~~L~~L~L~~n~l~~~~~  239 (353)
T 2z80_A          178 ELEIDASDLQSYEPKS-LKSIQNVSHLILHMKQHILL-------------LEIFVDVTSSVECLELRDTDLDTFHF  239 (353)
T ss_dssp             EEEEEETTCCEECTTT-TTTCSEEEEEEEECSCSTTH-------------HHHHHHHTTTEEEEEEESCBCTTCCC
T ss_pred             EEECCCCCcCccCHHH-HhccccCCeecCCCCccccc-------------hhhhhhhcccccEEECCCCccccccc
Confidence            9999998877666766 89999999999999987543             22335568999999999999876553

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=192.42  Aligned_cols=241  Identities=23%  Similarity=0.284  Sum_probs=191.4

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ..++.+++.+..+|..+. ++++.|++++|.+..++...|.++++|++|++++              +.+...    .+.
T Consensus        46 ~~v~c~~~~l~~iP~~~~-~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~--------------n~i~~i----~~~  106 (440)
T 3zyj_A           46 SKVICVRKNLREVPDGIS-TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSR--------------NHIRTI----EIG  106 (440)
T ss_dssp             CEEECCSCCCSSCCSCCC-TTCSEEECCSCCCCEECTTTTSSCSSCCEEECCS--------------SCCCEE----CGG
T ss_pred             CEEEeCCCCcCcCCCCCC-CCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCC--------------CcCCcc----Chh
Confidence            467788889999998775 7899999999999999877789999999999999              888873    457


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+..+++|++|+|++|.+...+ ..+..+++|++|++++|.++.+|. .+.++++|++|++++|.....++...+.++++
T Consensus       107 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~  186 (440)
T 3zyj_A          107 AFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSN  186 (440)
T ss_dssp             GGTTCSSCCEEECCSSCCSSCCTTTSCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSS
T ss_pred             hccCCccCCEEECCCCcCCeeCHhHhhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccc
Confidence            7999999999999999888777 578999999999999999998776 68899999999999988888888877899999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC-C-ccCCCCeEEEEeCCCCCCCCCcc
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD-M-SFQNLTSFSIAIGDLEERPLSDF  471 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~-~-~~~~L~~L~l~~~~~~~~~~~~l  471 (848)
                      |++|++++|.+...               ..+..+++|+.|++++|.+..++.. + .+++|+.|++.            
T Consensus       187 L~~L~L~~n~l~~~---------------~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~------------  239 (440)
T 3zyj_A          187 LRYLNLAMCNLREI---------------PNLTPLIKLDELDLSGNHLSAIRPGSFQGLMHLQKLWMI------------  239 (440)
T ss_dssp             CCEEECTTSCCSSC---------------CCCTTCSSCCEEECTTSCCCEECTTTTTTCTTCCEEECT------------
T ss_pred             cCeecCCCCcCccc---------------cccCCCcccCEEECCCCccCccChhhhccCccCCEEECC------------
Confidence            99999999987632               3478899999999999988866443 3 56666666554            


Q ss_pred             cceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecc
Q 003090          472 IGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLN  551 (848)
Q Consensus       472 ~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~  551 (848)
                                                                  ++.........+  ..+++|+.|+++++. ++.++ 
T Consensus       240 --------------------------------------------~n~l~~~~~~~~--~~l~~L~~L~L~~N~-l~~~~-  271 (440)
T 3zyj_A          240 --------------------------------------------QSQIQVIERNAF--DNLQSLVEINLAHNN-LTLLP-  271 (440)
T ss_dssp             --------------------------------------------TCCCCEECTTSS--TTCTTCCEEECTTSC-CCCCC-
T ss_pred             --------------------------------------------CCceeEEChhhh--cCCCCCCEEECCCCC-CCccC-
Confidence                                                        222211112222  466888999998874 33321 


Q ss_pred             cccccccccCCCccEEeccccc
Q 003090          552 SLERTLRVTLHKLEWLFIRENQ  573 (848)
Q Consensus       552 ~~~~~~~~~~p~L~~L~l~~~~  573 (848)
                         ......+++|+.|+|++++
T Consensus       272 ---~~~~~~l~~L~~L~L~~Np  290 (440)
T 3zyj_A          272 ---HDLFTPLHHLERIHLHHNP  290 (440)
T ss_dssp             ---TTTTSSCTTCCEEECCSSC
T ss_pred             ---hhHhccccCCCEEEcCCCC
Confidence               1234567899999999886

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.78  E-value=1.4e-18  Score=193.42  Aligned_cols=241  Identities=23%  Similarity=0.233  Sum_probs=190.3

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ..++.+++.+..+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+...    .|.
T Consensus        57 ~~v~c~~~~l~~iP~~~~-~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~--------------n~i~~~----~~~  117 (452)
T 3zyi_A           57 SKVVCTRRGLSEVPQGIP-SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGR--------------NSIRQI----EVG  117 (452)
T ss_dssp             CEEECCSSCCSSCCSCCC-TTCSEEECCSSCCCEECTTTTTTCTTCCEEECCS--------------SCCCEE----CTT
T ss_pred             cEEEECCCCcCccCCCCC-CCccEEECcCCcCceECHHHcCCCCCCCEEECCC--------------CccCCc----Chh
Confidence            457778888999998764 6899999999999988877789999999999999              888774    557


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+..+++|++|+|++|.+...+ ..+..+++|++|++++|.++.+|. .+.++++|++|++++|...+.++...+.++++
T Consensus       118 ~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~  197 (452)
T 3zyi_A          118 AFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFN  197 (452)
T ss_dssp             TTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTT
T ss_pred             hccCcccCCEEECCCCcCCccChhhhcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCC
Confidence            8999999999999999888777 558899999999999999998876 68899999999999988888898877899999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC-C-ccCCCCeEEEEeCCCCCCCCCcc
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD-M-SFQNLTSFSIAIGDLEERPLSDF  471 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~-~-~~~~L~~L~l~~~~~~~~~~~~l  471 (848)
                      |++|++++|.+...               ..+..+++|+.|++++|.+..++.. + .+++|+.|++.            
T Consensus       198 L~~L~L~~n~l~~~---------------~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~------------  250 (452)
T 3zyi_A          198 LKYLNLGMCNIKDM---------------PNLTPLVGLEELEMSGNHFPEIRPGSFHGLSSLKKLWVM------------  250 (452)
T ss_dssp             CCEEECTTSCCSSC---------------CCCTTCTTCCEEECTTSCCSEECGGGGTTCTTCCEEECT------------
T ss_pred             CCEEECCCCccccc---------------ccccccccccEEECcCCcCcccCcccccCccCCCEEEeC------------
Confidence            99999999987642               3478889999999999988766443 2 55555555554            


Q ss_pred             cceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecc
Q 003090          472 IGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLN  551 (848)
Q Consensus       472 ~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~  551 (848)
                                                                  ++......+..+  ..+++|+.|+++++. ++.++ 
T Consensus       251 --------------------------------------------~n~l~~~~~~~~--~~l~~L~~L~L~~N~-l~~~~-  282 (452)
T 3zyi_A          251 --------------------------------------------NSQVSLIERNAF--DGLASLVELNLAHNN-LSSLP-  282 (452)
T ss_dssp             --------------------------------------------TSCCCEECTTTT--TTCTTCCEEECCSSC-CSCCC-
T ss_pred             --------------------------------------------CCcCceECHHHh--cCCCCCCEEECCCCc-CCccC-
Confidence                                                        332222112222  467889999998884 44331 


Q ss_pred             cccccccccCCCccEEeccccc
Q 003090          552 SLERTLRVTLHKLEWLFIRENQ  573 (848)
Q Consensus       552 ~~~~~~~~~~p~L~~L~l~~~~  573 (848)
                         ......+++|++|++++++
T Consensus       283 ---~~~~~~l~~L~~L~L~~Np  301 (452)
T 3zyi_A          283 ---HDLFTPLRYLVELHLHHNP  301 (452)
T ss_dssp             ---TTSSTTCTTCCEEECCSSC
T ss_pred             ---hHHhccccCCCEEEccCCC
Confidence               1234567899999999886

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=99.78  E-value=7.6e-20  Score=212.15  Aligned_cols=404  Identities=16%  Similarity=0.131  Sum_probs=225.8

Q ss_pred             cccccceeecccCcCccc-ChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCc
Q 003090          253 ECPKLQALFLQENSPLAI-PDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDR  331 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~-~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~  331 (848)
                      .+++|++|++++|.+... +..+...+++|++|++++|.             .+....   ++..+..+++|++|++++|
T Consensus       103 ~~~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~-------------~~~~~~---l~~~~~~~~~L~~L~L~~~  166 (594)
T 2p1m_B          103 SYTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCE-------------GFSTDG---LAAIAATCRNLKELDLRES  166 (594)
T ss_dssp             HCTTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCE-------------EEEHHH---HHHHHHHCTTCCEEECTTC
T ss_pred             hCCCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcC-------------CCCHHH---HHHHHHhCCCCCEEeCcCC
Confidence            467788888887754432 22333367788888888741             222110   3344457788888888887


Q ss_pred             cccCCc-hhh----ccccCCCEEEccCCC--Cc--ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccc
Q 003090          332 RIQGDL-SLI----GELSGLEILDLSESD--VS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS  402 (848)
Q Consensus       332 ~~~~~~-~~i----~~l~~L~~L~l~~~~--l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~  402 (848)
                      .+.... ..+    ..+++|++|++++|.  +.  .++.-+.++++|++|++++|.....+|.. +.++++|++|++..+
T Consensus       167 ~i~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~-~~~~~~L~~L~l~~~  245 (594)
T 2p1m_B          167 DVDDVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATL-LQRAPQLEELGTGGY  245 (594)
T ss_dssp             EEECCCGGGGGGSCTTCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHH-HHHCTTCSEEECSBC
T ss_pred             ccCCcchHHHHHHhhcCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHH-HhcCCcceEcccccc
Confidence            644422 222    356688888888775  32  33333455788888888887555556555 677888888876654


Q ss_pred             ccccccccccccccCcccchhhhcccCCCcEE-EeeccCCCCCCCCC-ccCCCCeEEEEeCCCCCCCCCcccceEEeccc
Q 003090          403 FRHWQFESESEEDSSSNAKFIELGALSRLTSL-HIHIPEGKIMPSDM-SFQNLTSFSIAIGDLEERPLSDFIGLFLQKFK  480 (848)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L-~l~~~~~~~~~~~~-~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~~~  480 (848)
                      ...-.       .......+..+.++++|+.| .+.......++... .+++|+.|++..+...                
T Consensus       246 ~~~~~-------~~~~~~l~~~l~~~~~L~~Ls~~~~~~~~~l~~~~~~~~~L~~L~L~~~~l~----------------  302 (594)
T 2p1m_B          246 TAEVR-------PDVYSGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQ----------------  302 (594)
T ss_dssp             CCCCC-------HHHHHHHHHHHHTCTTCCEEECCBTCCGGGGGGGHHHHTTCCEEECTTCCCC----------------
T ss_pred             cCccc-------hhhHHHHHHHHhcCCCcccccCCcccchhhHHHHHHhhCCCCEEEccCCCCC----------------
Confidence            32100       00111244466777777777 33333333333333 5677777777533210                


Q ss_pred             ccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecC--------CCceeeccc
Q 003090          481 KRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRC--------NEMKYLLNS  552 (848)
Q Consensus       481 ~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~--------~~l~~l~~~  552 (848)
                                    -..+. .+...+++|+.|.+.++.....+. .+ ...+++|++|++.+|        ..+..   .
T Consensus       303 --------------~~~l~-~~~~~~~~L~~L~l~~~~~~~~l~-~l-~~~~~~L~~L~L~~~~~~g~~~~~~l~~---~  362 (594)
T 2p1m_B          303 --------------SYDLV-KLLCQCPKLQRLWVLDYIEDAGLE-VL-ASTCKDLRELRVFPSEPFVMEPNVALTE---Q  362 (594)
T ss_dssp             --------------HHHHH-HHHTTCTTCCEEEEEGGGHHHHHH-HH-HHHCTTCCEEEEECSCTTCSSCSSCCCH---H
T ss_pred             --------------HHHHH-HHHhcCCCcCEEeCcCccCHHHHH-HH-HHhCCCCCEEEEecCcccccccCCCCCH---H
Confidence                          00111 111224778888888773211111 11 124788999999654        22221   1


Q ss_pred             ccccccccCCCccEEecccccccccccccccccccCCCcceEEEe-----cCchhhHh------hhHHHHHhhccCcEEE
Q 003090          553 LERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVV-----DCGSILKI------LLSHLVQSFQNLQRLR  621 (848)
Q Consensus       553 ~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~-----~c~~l~~~------l~~~~~~~l~~L~~L~  621 (848)
                      ........+|+|++|.+ +|.+++......+ ...+|+|+.|++.     +|..+ ..      ++. ++..+++|++|+
T Consensus       363 ~l~~l~~~~~~L~~L~~-~~~~l~~~~~~~l-~~~~~~L~~L~L~~~~~~~~~~l-~~~~~~~~~~~-l~~~~~~L~~L~  438 (594)
T 2p1m_B          363 GLVSVSMGCPKLESVLY-FCRQMTNAALITI-ARNRPNMTRFRLCIIEPKAPDYL-TLEPLDIGFGA-IVEHCKDLRRLS  438 (594)
T ss_dssp             HHHHHHHHCTTCCEEEE-EESCCCHHHHHHH-HHHCTTCCEEEEEESSTTCCCTT-TCCCTHHHHHH-HHHHCTTCCEEE
T ss_pred             HHHHHHHhchhHHHHHH-hcCCcCHHHHHHH-HhhCCCcceeEeecccCCCcccc-cCCchhhHHHH-HHhhCCCccEEe
Confidence            11112234799999955 4445543211111 1147899999999     67777 52      222 347789999999


Q ss_pred             EeccCCceeeeecccccccccccc-ccCCcCEEecCCCccccccccCCCcc-ccccCccEEEeecCccccccccCccccc
Q 003090          622 VYSCGLLVSVFEIERVNIAKEETE-LFSSLEKLTLWDLPRMTDIWKGDTQF-VSLHNLKKVRVEECDELRQVFPANFGKK  699 (848)
Q Consensus       622 l~~c~~l~~~~~~~~~~~~~~~~~-~l~~L~~L~l~~c~~L~~l~~~~~~l-~~l~~L~~L~i~~C~~L~~~~p~~~~~~  699 (848)
                      +++  .++....        ..+. .+++|++|++++|. +.....  ..+ ..+++|++|++++|+. ++..+      
T Consensus       439 L~~--~l~~~~~--------~~l~~~~~~L~~L~L~~~~-i~~~~~--~~l~~~~~~L~~L~L~~n~~-~~~~~------  498 (594)
T 2p1m_B          439 LSG--LLTDKVF--------EYIGTYAKKMEMLSVAFAG-DSDLGM--HHVLSGCDSLRKLEIRDCPF-GDKAL------  498 (594)
T ss_dssp             CCS--SCCHHHH--------HHHHHHCTTCCEEEEESCC-SSHHHH--HHHHHHCTTCCEEEEESCSC-CHHHH------
T ss_pred             ecC--cccHHHH--------HHHHHhchhccEeeccCCC-CcHHHH--HHHHhcCCCcCEEECcCCCC-cHHHH------
Confidence            966  3332210        1222 37899999999886 322111  011 5589999999999974 33100      


Q ss_pred             cccceeeeccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEEEe
Q 003090          700 AAAEEMVLYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLEVR  765 (848)
Q Consensus       700 ~~~~~l~l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~i~  765 (848)
                                              ......+++|+.|++++|+. +.-........++.|+...+.
T Consensus       499 ------------------------~~~~~~l~~L~~L~l~~~~~-~~~~~~~l~~~lp~l~i~~~~  539 (594)
T 2p1m_B          499 ------------------------LANASKLETMRSLWMSSCSV-SFGACKLLGQKMPKLNVEVID  539 (594)
T ss_dssp             ------------------------HHTGGGGGGSSEEEEESSCC-BHHHHHHHHHHCTTEEEEEEC
T ss_pred             ------------------------HHHHHhCCCCCEEeeeCCCC-CHHHHHHHHHhCCCCEEEEec
Confidence                                    01123568999999999975 221111122445566544443

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=99.76  E-value=6.6e-20  Score=205.48  Aligned_cols=179  Identities=16%  Similarity=0.130  Sum_probs=102.6

Q ss_pred             CCceeeecCCCcccCCc--c-cccccceeecccCcCcc-----cChHHHccCCceeEEEccCcccccccccCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDE--L-ECPKLQALFLQENSPLA-----IPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLP  306 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~--~-~~~~L~~L~l~~~~~~~-----~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~  306 (848)
                      ++.|++++|++...+..  + .+++|++|++++|.+..     ++. .+..+++|++|++++              +.+.
T Consensus         5 l~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~-~l~~~~~L~~L~Ls~--------------n~l~   69 (461)
T 1z7x_W            5 IQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISS-ALRVNPALAELNLRS--------------NELG   69 (461)
T ss_dssp             EEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHH-HHHTCTTCCEEECTT--------------CCCH
T ss_pred             ceehhhhhcccCchhHHHHHhhcCCccEEEccCCCCCHHHHHHHHH-HHHhCCCcCEEeCCC--------------CcCC
Confidence            45677777777643321  2 56777777777776552     233 345677777777777              5554


Q ss_pred             CCCCCCCCchh-hhcc----cCcEEEccCccccCC-----chhhccccCCCEEEccCCCCccc-Chhhc-----cCCccc
Q 003090          307 SSPLFLLPSSL-SFLI----NLRTLRLHDRRIQGD-----LSLIGELSGLEILDLSESDVSEI-PVSFG-----RLSHLR  370 (848)
Q Consensus       307 ~~~~~~lp~~~-~~l~----~L~~L~L~~~~~~~~-----~~~i~~l~~L~~L~l~~~~l~~l-p~~i~-----~L~~L~  370 (848)
                      ..    .+..+ ..+.    +|++|++++|.+...     +..+..+++|++|++++|.+... +..+.     ..++|+
T Consensus        70 ~~----~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~  145 (461)
T 1z7x_W           70 DV----GVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLE  145 (461)
T ss_dssp             HH----HHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCC
T ss_pred             hH----HHHHHHHHHhhCCCceeEEEccCCCCCHHHHHHHHHHHccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcce
Confidence            32    12222 2344    577777777765531     35667777777777777776521 22222     245677


Q ss_pred             EEeccCCccccc----cChhhhhccccccEEeccccccccccccccccccCcccchhhhc-ccCCCcEEEeeccCCC
Q 003090          371 LLDLTGCYILEL----IPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELG-ALSRLTSLHIHIPEGK  442 (848)
Q Consensus       371 ~L~l~~~~~~~~----~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~-~l~~L~~L~l~~~~~~  442 (848)
                      +|++++|.....    ++.. +..+++|++|++++|.+.....         ......+. ..++|+.|++++|.++
T Consensus       146 ~L~L~~n~l~~~~~~~l~~~-l~~~~~L~~L~L~~n~i~~~~~---------~~l~~~l~~~~~~L~~L~L~~n~l~  212 (461)
T 1z7x_W          146 KLQLEYCSLSAASCEPLASV-LRAKPDFKELTVSNNDINEAGV---------RVLCQGLKDSPCQLEALKLESCGVT  212 (461)
T ss_dssp             EEECTTSCCBGGGHHHHHHH-HHHCTTCCEEECCSSBCHHHHH---------HHHHHHHHHSCCCCCEEECTTSCCB
T ss_pred             EEECCCCCCCHHHHHHHHHH-HhhCCCCCEEECcCCCcchHHH---------HHHHHHHhcCCCCceEEEccCCCCc
Confidence            777777755442    2333 5666777777777776543200         00111121 2457777777777654

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.76  E-value=3.8e-18  Score=177.53  Aligned_cols=195  Identities=26%  Similarity=0.326  Sum_probs=121.6

Q ss_pred             CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCC-CCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPP-LPSSPL  310 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~-l~~~~~  310 (848)
                      .++.|++++|.+..++.. + .+++|++|++++|.+..++...|.++++|++|++++              +. +...  
T Consensus        33 ~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~--------------n~~l~~~--   96 (285)
T 1ozn_A           33 ASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSD--------------NAQLRSV--   96 (285)
T ss_dssp             TCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS--------------CTTCCCC--
T ss_pred             CceEEEeeCCcCCccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCC--------------CCCcccc--
Confidence            456667777776666643 2 566777777777666666544456667777777776              44 5542  


Q ss_pred             CCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhh
Q 003090          311 FLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                        .|..+..+++|++|++++|.+...+ ..+.++++|++|++++|.++.+|.. ++++++|++|++++|... .+|...+
T Consensus        97 --~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-~~~~~~~  173 (285)
T 1ozn_A           97 --DPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRIS-SVPERAF  173 (285)
T ss_dssp             --CTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-EECTTTT
T ss_pred             --CHHHhcCCcCCCEEECCCCcCCEECHhHhhCCcCCCEEECCCCcccccCHhHhccCCCccEEECCCCccc-ccCHHHh
Confidence              2556666677777777777666553 4566677777777777766655543 566677777777765443 3444335


Q ss_pred             hccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEe
Q 003090          389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAI  460 (848)
Q Consensus       389 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~  460 (848)
                      ..+++|++|++++|.+...             .+..+..+++|+.|++++|.+..++...  .+++|+.|++..
T Consensus       174 ~~l~~L~~L~l~~n~l~~~-------------~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~  234 (285)
T 1ozn_A          174 RGLHSLDRLLLHQNRVAHV-------------HPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQYLRLND  234 (285)
T ss_dssp             TTCTTCCEEECCSSCCCEE-------------CTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTCCEEECCS
T ss_pred             cCccccCEEECCCCccccc-------------CHhHccCcccccEeeCCCCcCCcCCHHHcccCcccCEEeccC
Confidence            6667777777777666543             3445666667777777777666655432  556666666653

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.75  E-value=8.1e-19  Score=185.42  Aligned_cols=126  Identities=20%  Similarity=0.125  Sum_probs=67.2

Q ss_pred             ccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      +++|++|++++|.+..++...|.++++|++|++++              +.+.+     .+. +..+++|++|++++|.+
T Consensus        33 ~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~--------------n~l~~-----~~~-~~~l~~L~~L~Ls~n~l   92 (317)
T 3o53_A           33 AWNVKELDLSGNPLSQISAADLAPFTKLELLNLSS--------------NVLYE-----TLD-LESLSTLRTLDLNNNYV   92 (317)
T ss_dssp             GGGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTT--------------SCCEE-----EEE-ETTCTTCCEEECCSSEE
T ss_pred             CCCCCEEECcCCccCcCCHHHhhCCCcCCEEECCC--------------CcCCc-----chh-hhhcCCCCEEECcCCcc
Confidence            44566666666655555554455666666666666              55544     332 55556666666666544


Q ss_pred             cCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccc
Q 003090          334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       334 ~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      ...    ...++|++|++++|.++.++..  .+++|++|++++|......+.. ++.+++|++|++++|.+..
T Consensus        93 ~~l----~~~~~L~~L~l~~n~l~~~~~~--~~~~L~~L~l~~N~l~~~~~~~-~~~l~~L~~L~Ls~N~l~~  158 (317)
T 3o53_A           93 QEL----LVGPSIETLHAANNNISRVSCS--RGQGKKNIYLANNKITMLRDLD-EGCRSRVQYLDLKLNEIDT  158 (317)
T ss_dssp             EEE----EECTTCCEEECCSSCCSEEEEC--CCSSCEEEECCSSCCCSGGGBC-TGGGSSEEEEECTTSCCCE
T ss_pred             ccc----cCCCCcCEEECCCCccCCcCcc--ccCCCCEEECCCCCCCCccchh-hhccCCCCEEECCCCCCCc
Confidence            322    2335566666666655544422  2455666666665443322222 4555666666666655543

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=99.75  E-value=2.7e-17  Score=187.58  Aligned_cols=262  Identities=17%  Similarity=0.120  Sum_probs=192.4

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.+++++|.++.+|..+. ++|++|++++|.+..+|.    .+++|++|++++              |.++.     +
T Consensus        41 ~l~~L~ls~n~L~~lp~~l~-~~L~~L~L~~N~l~~lp~----~l~~L~~L~Ls~--------------N~l~~-----l   96 (622)
T 3g06_A           41 GNAVLNVGESGLTTLPDCLP-AHITTLVIPDNNLTSLPA----LPPELRTLEVSG--------------NQLTS-----L   96 (622)
T ss_dssp             CCCEEECCSSCCSCCCSCCC-TTCSEEEECSCCCSCCCC----CCTTCCEEEECS--------------CCCSC-----C
T ss_pred             CCcEEEecCCCcCccChhhC-CCCcEEEecCCCCCCCCC----cCCCCCEEEcCC--------------CcCCc-----C
Confidence            47889999999999998776 899999999999998886    578999999999              88887     7


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      |.   .+++|++|++++|.+...+.   .+.+|++|++++|.++.+|..   +++|++|++++|... .+|.    .+.+
T Consensus        97 p~---~l~~L~~L~Ls~N~l~~l~~---~l~~L~~L~L~~N~l~~lp~~---l~~L~~L~Ls~N~l~-~l~~----~~~~  162 (622)
T 3g06_A           97 PV---LPPGLLELSIFSNPLTHLPA---LPSGLCKLWIFGNQLTSLPVL---PPGLQELSVSDNQLA-SLPA----LPSE  162 (622)
T ss_dssp             CC---CCTTCCEEEECSCCCCCCCC---CCTTCCEEECCSSCCSCCCCC---CTTCCEEECCSSCCS-CCCC----CCTT
T ss_pred             CC---CCCCCCEEECcCCcCCCCCC---CCCCcCEEECCCCCCCcCCCC---CCCCCEEECcCCcCC-CcCC----ccCC
Confidence            77   77899999999998777655   678999999999999999874   489999999998654 4664    3568


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccc
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIG  473 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~  473 (848)
                      |+.|++++|.+...              +   ..+++|+.|++++|.+..+|..  +++|+.|.+..+..          
T Consensus       163 L~~L~L~~N~l~~l--------------~---~~~~~L~~L~Ls~N~l~~l~~~--~~~L~~L~L~~N~l----------  213 (622)
T 3g06_A          163 LCKLWAYNNQLTSL--------------P---MLPSGLQELSVSDNQLASLPTL--PSELYKLWAYNNRL----------  213 (622)
T ss_dssp             CCEEECCSSCCSCC--------------C---CCCTTCCEEECCSSCCSCCCCC--CTTCCEEECCSSCC----------
T ss_pred             CCEEECCCCCCCCC--------------c---ccCCCCcEEECCCCCCCCCCCc--cchhhEEECcCCcc----------
Confidence            99999999987643              2   4568999999999999887764  47788887764432          


Q ss_pred             eEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecccc
Q 003090          474 LFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSL  553 (848)
Q Consensus       474 l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~  553 (848)
                                            ..+|.    .+++|+.|+++++... .++     ..+++|+.|+++++. ++.++   
T Consensus       214 ----------------------~~l~~----~~~~L~~L~Ls~N~L~-~lp-----~~l~~L~~L~Ls~N~-L~~lp---  257 (622)
T 3g06_A          214 ----------------------TSLPA----LPSGLKELIVSGNRLT-SLP-----VLPSELKELMVSGNR-LTSLP---  257 (622)
T ss_dssp             ----------------------SSCCC----CCTTCCEEECCSSCCS-CCC-----CCCTTCCEEECCSSC-CSCCC---
T ss_pred             ----------------------cccCC----CCCCCCEEEccCCccC-cCC-----CCCCcCcEEECCCCC-CCcCC---
Confidence                                  11110    0256777777766432 222     355778888887773 33331   


Q ss_pred             cccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhH
Q 003090          554 ERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLS  608 (848)
Q Consensus       554 ~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~  608 (848)
                         .  .+++|++|++++| +++.+.   .....+++|+.|++++|+-- ...|.
T Consensus       258 ---~--~~~~L~~L~Ls~N-~L~~lp---~~l~~l~~L~~L~L~~N~l~-~~~~~  302 (622)
T 3g06_A          258 ---M--LPSGLLSLSVYRN-QLTRLP---ESLIHLSSETTVNLEGNPLS-ERTLQ  302 (622)
T ss_dssp             ---C--CCTTCCEEECCSS-CCCSCC---GGGGGSCTTCEEECCSCCCC-HHHHH
T ss_pred             ---c--ccccCcEEeCCCC-CCCcCC---HHHhhccccCEEEecCCCCC-CcCHH
Confidence               1  4677788888777 455431   12345777778888776543 44433

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.74  E-value=1.3e-17  Score=173.48  Aligned_cols=193  Identities=20%  Similarity=0.249  Sum_probs=160.9

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.++.+++.+..+|..+ .+++++|++++|.+..++...|..+++|++|++++              +.+...    .|.
T Consensus        14 ~~~~c~~~~l~~ip~~~-~~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~--------------n~l~~~----~~~   74 (285)
T 1ozn_A           14 VTTSCPQQGLQAVPVGI-PAASQRIFLHGNRISHVPAASFRACRNLTILWLHS--------------NVLARI----DAA   74 (285)
T ss_dssp             CEEECCSSCCSSCCTTC-CTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCS--------------SCCCEE----CTT
T ss_pred             eEEEcCcCCcccCCcCC-CCCceEEEeeCCcCCccCHHHcccCCCCCEEECCC--------------Ccccee----CHh
Confidence            46788888999998765 47899999999999999987789999999999999              888773    478


Q ss_pred             hhhhcccCcEEEccCcc-ccCC-chhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          316 SLSFLINLRTLRLHDRR-IQGD-LSLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~-~~~~-~~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      .+..+++|++|++++|. +... +..+..+++|++|++++|.++.+ |..+.++++|++|++++|... .++...+++++
T Consensus        75 ~~~~l~~L~~L~l~~n~~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-~~~~~~~~~l~  153 (285)
T 1ozn_A           75 AFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQ-ALPDDTFRDLG  153 (285)
T ss_dssp             TTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCT
T ss_pred             hcCCccCCCEEeCCCCCCccccCHHHhcCCcCCCEEECCCCcCCEECHhHhhCCcCCCEEECCCCccc-ccCHhHhccCC
Confidence            89999999999999997 5555 37889999999999999999976 566899999999999998765 45655488999


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCC-CCCC-ccCCCCeEEEEeC
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIM-PSDM-SFQNLTSFSIAIG  461 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~-~~~~-~~~~L~~L~l~~~  461 (848)
                      +|++|++++|.+...             ....+..+++|+.|++++|.+..+ +..+ .+++|+.|++..+
T Consensus       154 ~L~~L~l~~n~l~~~-------------~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n  211 (285)
T 1ozn_A          154 NLTHLFLHGNRISSV-------------PERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFAN  211 (285)
T ss_dssp             TCCEEECCSSCCCEE-------------CTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             CccEEECCCCccccc-------------CHHHhcCccccCEEECCCCcccccCHhHccCcccccEeeCCCC
Confidence            999999999988754             334588899999999999998766 4444 6777777777643

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.73  E-value=1.3e-17  Score=175.53  Aligned_cols=196  Identities=21%  Similarity=0.234  Sum_probs=166.4

Q ss_pred             CCCceeeecCCCcccCCcc--cccccceeecccCcCccc---ChHHHccCCceeEEEccCcccccccccCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAI---PDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSS  308 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~---~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~  308 (848)
                      .++.|++++|.+..+|...  .+++|++|++++|.+..+   +..+ ..+++|++|++++              +.+.. 
T Consensus        29 ~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~-~~~~~L~~L~Ls~--------------n~i~~-   92 (306)
T 2z66_A           29 SATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSD-FGTTSLKYLDLSF--------------NGVIT-   92 (306)
T ss_dssp             TCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHH-HSCSCCCEEECCS--------------CSEEE-
T ss_pred             CCCEEECCCCccCccCHhHhhccccCCEEECCCCccCcccCccccc-ccccccCEEECCC--------------Ccccc-
Confidence            5789999999999999864  899999999999987655   4554 5799999999999              77777 


Q ss_pred             CCCCCCchhhhcccCcEEEccCccccCCc--hhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCcccc-ccC
Q 003090          309 PLFLLPSSLSFLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILE-LIP  384 (848)
Q Consensus       309 ~~~~lp~~~~~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~-~~p  384 (848)
                          +|..+..+++|++|++++|.+...+  ..+..+++|++|++++|.+. ..|..+..+++|++|++++|...+ .+|
T Consensus        93 ----l~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~  168 (306)
T 2z66_A           93 ----MSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP  168 (306)
T ss_dssp             ----EEEEEETCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCEEECTTCEEGGGEEC
T ss_pred             ----ChhhcCCCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCEEECCCCccccccch
Confidence                8888999999999999999887765  47899999999999999988 455668899999999999987765 466


Q ss_pred             hhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCC
Q 003090          385 RGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       385 ~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~  462 (848)
                      .. +..+++|++|++++|.+...             .+..+..+++|+.|++++|.+..++...  .+++|+.|++..+.
T Consensus       169 ~~-~~~l~~L~~L~Ls~n~l~~~-------------~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  234 (306)
T 2z66_A          169 DI-FTELRNLTFLDLSQCQLEQL-------------SPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNH  234 (306)
T ss_dssp             SC-CTTCTTCCEEECTTSCCCEE-------------CTTTTTTCTTCCEEECTTSCCSBCCSGGGTTCTTCCEEECTTSC
T ss_pred             hH-HhhCcCCCEEECCCCCcCCc-------------CHHHhcCCCCCCEEECCCCccCccChhhccCcccCCEeECCCCC
Confidence            66 89999999999999988764             4567888999999999999988877643  78899999998665


Q ss_pred             C
Q 003090          463 L  463 (848)
Q Consensus       463 ~  463 (848)
                      .
T Consensus       235 l  235 (306)
T 2z66_A          235 I  235 (306)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=99.73  E-value=8e-17  Score=183.74  Aligned_cols=150  Identities=21%  Similarity=0.173  Sum_probs=101.9

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      .+++.|++++|.+..+|..++   ++|++|++++              +.++.     +|.   .+++|++|++++|.+.
T Consensus        40 ~~l~~L~ls~n~L~~lp~~l~---~~L~~L~L~~--------------N~l~~-----lp~---~l~~L~~L~Ls~N~l~   94 (622)
T 3g06_A           40 NGNAVLNVGESGLTTLPDCLP---AHITTLVIPD--------------NNLTS-----LPA---LPPELRTLEVSGNQLT   94 (622)
T ss_dssp             HCCCEEECCSSCCSCCCSCCC---TTCSEEEECS--------------CCCSC-----CCC---CCTTCCEEEECSCCCS
T ss_pred             CCCcEEEecCCCcCccChhhC---CCCcEEEecC--------------CCCCC-----CCC---cCCCCCEEEcCCCcCC
Confidence            357788888888878877542   6788888888              77776     666   4677888888888766


Q ss_pred             CCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccccc
Q 003090          335 GDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE  414 (848)
Q Consensus       335 ~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  414 (848)
                      ..+.   .+++|++|++++|.++.+|.   .+.+|++|++++|.. ..+|..    +++|++|++++|.+...       
T Consensus        95 ~lp~---~l~~L~~L~Ls~N~l~~l~~---~l~~L~~L~L~~N~l-~~lp~~----l~~L~~L~Ls~N~l~~l-------  156 (622)
T 3g06_A           95 SLPV---LPPGLLELSIFSNPLTHLPA---LPSGLCKLWIFGNQL-TSLPVL----PPGLQELSVSDNQLASL-------  156 (622)
T ss_dssp             CCCC---CCTTCCEEEECSCCCCCCCC---CCTTCCEEECCSSCC-SCCCCC----CTTCCEEECCSSCCSCC-------
T ss_pred             cCCC---CCCCCCEEECcCCcCCCCCC---CCCCcCEEECCCCCC-CcCCCC----CCCCCEEECcCCcCCCc-------
Confidence            5444   67788888888888887776   567788888887654 346653    37777888877766532       


Q ss_pred             ccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          415 DSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       415 ~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                             +   ..+.+|+.|++++|.++.+|.  .+++|+.|++.
T Consensus       157 -------~---~~~~~L~~L~L~~N~l~~l~~--~~~~L~~L~Ls  189 (622)
T 3g06_A          157 -------P---ALPSELCKLWAYNNQLTSLPM--LPSGLQELSVS  189 (622)
T ss_dssp             -------C---CCCTTCCEEECCSSCCSCCCC--CCTTCCEEECC
T ss_pred             -------C---CccCCCCEEECCCCCCCCCcc--cCCCCcEEECC
Confidence                   1   123567777777777666552  33444444443

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.73  E-value=7e-17  Score=166.26  Aligned_cols=194  Identities=23%  Similarity=0.361  Sum_probs=163.9

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      .+.++++++.++.+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+..     +|
T Consensus        18 ~~~l~~~~~~l~~ip~~~~-~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~--------------n~l~~-----i~   77 (270)
T 2o6q_A           18 KNSVDCSSKKLTAIPSNIP-ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLND--------------NKLQT-----LP   77 (270)
T ss_dssp             TTEEECTTSCCSSCCSCCC-TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCS--------------SCCSC-----CC
T ss_pred             CCEEEccCCCCCccCCCCC-CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCC--------------CccCe-----eC
Confidence            3568899999999998765 6899999999999999887788999999999999              78877     55


Q ss_pred             ch-hhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhcc
Q 003090          315 SS-LSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       315 ~~-~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                      .. +..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|. .++.+++|++|++++|.. ..+|...+..+
T Consensus        78 ~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l-~~~~~~~~~~l  156 (270)
T 2o6q_A           78 AGIFKELKNLETLWVTDNKLQALPIGVFDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNEL-QSLPKGVFDKL  156 (270)
T ss_dssp             TTTTSSCTTCCEEECCSSCCCCCCTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCC-CCCCTTTTTTC
T ss_pred             hhhhcCCCCCCEEECCCCcCCcCCHhHcccccCCCEEECCCCccCeeCHHHhCcCcCCCEEECCCCcC-CccCHhHccCC
Confidence            54 588999999999999888777 567899999999999999997765 478999999999999865 45676657899


Q ss_pred             ccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCC
Q 003090          392 RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       392 ~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~  462 (848)
                      ++|++|++++|.+...             .+..+..+++|+.|++++|.+..++...  .+++|+.|++..+.
T Consensus       157 ~~L~~L~L~~n~l~~~-------------~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~  216 (270)
T 2o6q_A          157 TSLKELRLYNNQLKRV-------------PEGAFDKLTELKTLKLDNNQLKRVPEGAFDSLEKLKMLQLQENP  216 (270)
T ss_dssp             TTCCEEECCSSCCSCC-------------CTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             cccceeEecCCcCcEe-------------ChhHhccCCCcCEEECCCCcCCcCCHHHhccccCCCEEEecCCC
Confidence            9999999999988754             3345788999999999999999888764  78899999887443

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.72  E-value=5.6e-17  Score=168.37  Aligned_cols=195  Identities=22%  Similarity=0.206  Sum_probs=169.4

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.++++++.++.+|..+. ++++.|++++|.+..++...|..+++|++|++++              +.+..     
T Consensus        10 ~~l~~l~~~~~~l~~ip~~~~-~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~--------------n~l~~-----   69 (290)
T 1p9a_G           10 ASHLEVNCDKRNLTALPPDLP-KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDR--------------AELTK-----   69 (290)
T ss_dssp             TTCCEEECTTSCCSSCCSCCC-TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTT--------------SCCCE-----
T ss_pred             CCccEEECCCCCCCcCCCCCC-CCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCC--------------CccCc-----
Confidence            346789999999999998775 7899999999999988877789999999999999              88877     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccC-hhhccCCcccEEeccCCccccccChhhhhcc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                      ++.. +.+++|++|++++|.+...+..+..+++|++|++++|.++.+| ..+..+++|++|++++|... .+|.+.+..+
T Consensus        70 ~~~~-~~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~l  147 (290)
T 1p9a_G           70 LQVD-GTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELK-TLPPGLLTPT  147 (290)
T ss_dssp             EECC-SCCTTCCEEECCSSCCSSCCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCC-CCCTTTTTTC
T ss_pred             ccCC-CCCCcCCEEECCCCcCCcCchhhccCCCCCEEECCCCcCcccCHHHHcCCCCCCEEECCCCCCC-ccChhhcccc
Confidence            6554 7899999999999998888888899999999999999999887 46899999999999998664 5777768899


Q ss_pred             ccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeCC
Q 003090          392 RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIGD  462 (848)
Q Consensus       392 ~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~  462 (848)
                      ++|+.|++++|.+...             ....+..+++|+.|++++|.+..+|..+ ...+|+.+.+..+.
T Consensus       148 ~~L~~L~L~~N~l~~l-------------~~~~~~~l~~L~~L~L~~N~l~~ip~~~~~~~~L~~l~L~~Np  206 (290)
T 1p9a_G          148 PKLEKLSLANNNLTEL-------------PAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNP  206 (290)
T ss_dssp             TTCCEEECTTSCCSCC-------------CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCCCSEEECCSCC
T ss_pred             cCCCEEECCCCcCCcc-------------CHHHhcCcCCCCEEECCCCcCCccChhhcccccCCeEEeCCCC
Confidence            9999999999998754             2345678999999999999999999888 77889999887443

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.71  E-value=5.6e-17  Score=180.56  Aligned_cols=195  Identities=26%  Similarity=0.306  Sum_probs=100.2

Q ss_pred             CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.|++++|.+..++.. + .+++|++|++++|.+..++...|.++++|++|++++              +.+...   
T Consensus        76 ~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~---  138 (452)
T 3zyi_A           76 NTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFD--------------NWLTVI---  138 (452)
T ss_dssp             TCSEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS--------------SCCSBC---
T ss_pred             CccEEECcCCcCceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCC--------------CcCCcc---
Confidence            345566666666655433 2 566666666666666665555556666666666666              445441   


Q ss_pred             CCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCC-CCcccCh-hhccCCcccEEeccCCccccccChhhh
Q 003090          312 LLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSES-DVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       312 ~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~-~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                       .+..+..+++|++|++++|.+...+ ..+.++++|++|++++| .+..+|. .+..+++|++|++++|... .+|.  +
T Consensus       139 -~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~-~~~~--~  214 (452)
T 3zyi_A          139 -PSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIK-DMPN--L  214 (452)
T ss_dssp             -CTTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCCS-SCCC--C
T ss_pred             -ChhhhcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCccc-cccc--c
Confidence             2223555555555555555544433 34555555555555552 4444443 2455555555555554332 3343  4


Q ss_pred             hccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCC
Q 003090          389 SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       389 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~  462 (848)
                      ..+++|++|++++|.+...             .+..+.++++|+.|++++|.+..++...  .+++|+.|++..+.
T Consensus       215 ~~l~~L~~L~Ls~N~l~~~-------------~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~  277 (452)
T 3zyi_A          215 TPLVGLEELEMSGNHFPEI-------------RPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHNN  277 (452)
T ss_dssp             TTCTTCCEEECTTSCCSEE-------------CGGGGTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             cccccccEEECcCCcCccc-------------CcccccCccCCCEEEeCCCcCceECHHHhcCCCCCCEEECCCCc
Confidence            5555555555555554433             2334455555555555555544433222  44555555554443

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.70  E-value=2.4e-17  Score=170.53  Aligned_cols=145  Identities=26%  Similarity=0.261  Sum_probs=73.8

Q ss_pred             cCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcc
Q 003090          242 FNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLI  321 (848)
Q Consensus       242 ~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~  321 (848)
                      +..+..+|..+. +++++|++++|.+..++...|.++++|++|++++              +.+...    .+..+..++
T Consensus        16 ~~~l~~ip~~l~-~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~--------------n~l~~~----~~~~~~~l~   76 (276)
T 2z62_A           16 ELNFYKIPDNLP-FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSR--------------CEIQTI----EDGAYQSLS   76 (276)
T ss_dssp             TSCCSSCCSSSC-TTCCEEECTTCCCCEECTTTTTTCTTCSEEECTT--------------CCCCEE----CTTTTTTCT
T ss_pred             CCCccccCCCCC-CCccEEECCCCcccccCHhHhccccCCcEEECCC--------------CcCCcc----CHHHccCCc
Confidence            334444554432 3455555555555555544445555555555555              444441    223455555


Q ss_pred             cCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCcccc-ccChhhhhccccccEEe
Q 003090          322 NLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILE-LIPRGVLSRLRKLEELY  398 (848)
Q Consensus       322 ~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~-~~p~~~l~~l~~L~~L~  398 (848)
                      +|++|++++|.+...+ ..+.++++|++|++++|.+..++. .++++++|++|++++|.... .+|.. ++++++|++|+
T Consensus        77 ~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~-~~~l~~L~~L~  155 (276)
T 2z62_A           77 HLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEY-FSNLTNLEHLD  155 (276)
T ss_dssp             TCCEEECTTCCCCEECTTTTTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGG-GGGCTTCCEEE
T ss_pred             CCCEEECCCCccCccChhhhcCCccccEEECCCCCccccCchhcccCCCCCEEECcCCccceecCchh-hccCCCCCEEE
Confidence            5555555555544433 445555555555555555554443 35555555555555554433 23444 45555555555


Q ss_pred             cccccccc
Q 003090          399 MSHSFRHW  406 (848)
Q Consensus       399 l~~~~~~~  406 (848)
                      +++|.+..
T Consensus       156 Ls~N~l~~  163 (276)
T 2z62_A          156 LSSNKIQS  163 (276)
T ss_dssp             CCSSCCCE
T ss_pred             CCCCCCCc
Confidence            55555443

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.70  E-value=8.7e-17  Score=166.33  Aligned_cols=196  Identities=23%  Similarity=0.266  Sum_probs=165.6

Q ss_pred             CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.|++++|.+..++.. + .+++|++|++++|.+..++...|.++++|++|++++              +.+...   
T Consensus        29 ~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~---   91 (276)
T 2z62_A           29 STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTG--------------NPIQSL---   91 (276)
T ss_dssp             TCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTT--------------CCCCEE---
T ss_pred             CccEEECCCCcccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCC--------------CccCcc---
Confidence            578999999999988863 4 899999999999999999887789999999999999              888873   


Q ss_pred             CCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcc--cChhhccCCcccEEeccCCccccccChhhh
Q 003090          312 LLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSE--IPVSFGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       312 ~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~--lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                       .|..+..+++|++|++++|.+.... ..++++++|++|++++|.+..  +|..++++++|++|++++|.... ++...+
T Consensus        92 -~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls~N~l~~-~~~~~~  169 (276)
T 2z62_A           92 -ALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQS-IYCTDL  169 (276)
T ss_dssp             -CTTTTTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSCCCE-ECGGGG
T ss_pred             -ChhhhcCCccccEEECCCCCccccCchhcccCCCCCEEECcCCccceecCchhhccCCCCCEEECCCCCCCc-CCHHHh
Confidence             4577999999999999999888776 479999999999999999985  78999999999999999987655 444337


Q ss_pred             hcccccc----EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCC
Q 003090          389 SRLRKLE----ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       389 ~~l~~L~----~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~  462 (848)
                      ..+++|+    .|++++|.+...              +.......+|+.|++++|.++.++...  .+++|+.|++..+.
T Consensus       170 ~~l~~L~~l~l~L~ls~n~l~~~--------------~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~N~  235 (276)
T 2z62_A          170 RVLHQMPLLNLSLDLSLNPMNFI--------------QPGAFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNP  235 (276)
T ss_dssp             HHHHTCTTCCEEEECCSSCCCEE--------------CTTSSCSCCEEEEECCSSCCSCCCTTTTTTCCSCCEEECCSSC
T ss_pred             hhhhhccccceeeecCCCccccc--------------CccccCCCcccEEECCCCceeecCHhHhcccccccEEEccCCc
Confidence            7777777    899999988754              222333448999999999999988775  78999999987544

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.70  E-value=6.8e-17  Score=179.20  Aligned_cols=222  Identities=25%  Similarity=0.332  Sum_probs=143.2

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      ++..++..+.  ..++.|++++|.+..++...  .+++|++|++++|.+..++...|.++++|++|++++          
T Consensus        54 ~l~~iP~~~~--~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~----------  121 (440)
T 3zyj_A           54 NLREVPDGIS--TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFD----------  121 (440)
T ss_dssp             CCSSCCSCCC--TTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCS----------
T ss_pred             CcCcCCCCCC--CCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCC----------
Confidence            4444444443  24577888888888776433  778888888888888887777778888888888888          


Q ss_pred             CCCCCCCCCCCCCCCCc-hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCC-CCcccCh-hhccCCcccEEec
Q 003090          299 PFLFPPLPSSPLFLLPS-SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSES-DVSEIPV-SFGRLSHLRLLDL  374 (848)
Q Consensus       299 ~~~~~~l~~~~~~~lp~-~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~-~l~~lp~-~i~~L~~L~~L~l  374 (848)
                          |.+..     +|. .+..+++|++|++++|.+...+ ..+.++++|++|++++| .+..+|. .+.++++|++|++
T Consensus       122 ----n~l~~-----~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L  192 (440)
T 3zyj_A          122 ----NRLTT-----IPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNL  192 (440)
T ss_dssp             ----SCCSS-----CCTTTSCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEEC
T ss_pred             ----CcCCe-----eCHhHhhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecC
Confidence                66666     443 5677777777777777666554 45667777777777763 4555554 4666777777777


Q ss_pred             cCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCC
Q 003090          375 TGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQN  452 (848)
Q Consensus       375 ~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~  452 (848)
                      ++|.. ..+|.  +..+++|++|++++|.+...             .+..+.++++|+.|++++|.+..++...  .+++
T Consensus       193 ~~n~l-~~~~~--~~~l~~L~~L~Ls~N~l~~~-------------~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~  256 (440)
T 3zyj_A          193 AMCNL-REIPN--LTPLIKLDELDLSGNHLSAI-------------RPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQS  256 (440)
T ss_dssp             TTSCC-SSCCC--CTTCSSCCEEECTTSCCCEE-------------CTTTTTTCTTCCEEECTTCCCCEECTTSSTTCTT
T ss_pred             CCCcC-ccccc--cCCCcccCEEECCCCccCcc-------------ChhhhccCccCCEEECCCCceeEEChhhhcCCCC
Confidence            77644 34554  56777777777777766544             3445666667777777766666554433  5666


Q ss_pred             CCeEEEEeCCC------CCCCCCcccceEEecc
Q 003090          453 LTSFSIAIGDL------EERPLSDFIGLFLQKF  479 (848)
Q Consensus       453 L~~L~l~~~~~------~~~~~~~l~~l~l~~~  479 (848)
                      |+.|++..+..      .....+.++.+.+.+.
T Consensus       257 L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N  289 (440)
T 3zyj_A          257 LVEINLAHNNLTLLPHDLFTPLHHLERIHLHHN  289 (440)
T ss_dssp             CCEEECTTSCCCCCCTTTTSSCTTCCEEECCSS
T ss_pred             CCEEECCCCCCCccChhHhccccCCCEEEcCCC
Confidence            66666665544      1223344555555443

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.69  E-value=5.3e-18  Score=178.70  Aligned_cols=194  Identities=18%  Similarity=0.182  Sum_probs=142.6

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCc--ccChHHH------ccCCceeEEEccCcccccccccCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPL--AIPDRFF------QGMKDLQVLDLGGIRRFSFSVRFPFLFPPL  305 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~--~~~~~~~------~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l  305 (848)
                      .++.+++++|.+ .+|..+. ..|+.|++++|.+.  .+|..+.      .++++|++|++++              +.+
T Consensus        44 ~L~~l~l~~n~l-~~p~~~~-~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~~l~~L~~L~L~~--------------n~l  107 (312)
T 1wwl_A           44 SLEYLLKRVDTE-ADLGQFT-DIIKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLEN--------------LEV  107 (312)
T ss_dssp             ECTTHHHHCCTT-CCCHHHH-HHHHHCCCCEEEEEEEECBHHHHHHHHHHHTTSCCCEEEEEE--------------EBC
T ss_pred             CceeEeeccccc-ccHHHHH-HHHhhcccccccccCCCcCHHHHHHHHHhcCcCCccEEEccC--------------Ccc
Confidence            367788888888 7777662 12888899988664  3555432      2688999999999              777


Q ss_pred             CCCCCCCCCchh--hhcccCcEEEccCccccCCchhhccc-----cCCCEEEccCCCCcccC-hhhccCCcccEEeccCC
Q 003090          306 PSSPLFLLPSSL--SFLINLRTLRLHDRRIQGDLSLIGEL-----SGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGC  377 (848)
Q Consensus       306 ~~~~~~~lp~~~--~~l~~L~~L~L~~~~~~~~~~~i~~l-----~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~  377 (848)
                      .+.    .|..+  ..+++|++|++++|.+...+..++.+     ++|++|++++|.+..+| ..++++++|++|++++|
T Consensus       108 ~~~----~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N  183 (312)
T 1wwl_A          108 TGT----APPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDN  183 (312)
T ss_dssp             BSC----CCCCSSSCCSCCCSEEEEESCBCSSSSSHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCCCCSSCCEEECCSC
T ss_pred             cch----hHHHHHHhcCCCccEEEccCCCCcchhHHHHHHHHhhcCCCcEEEeeCCCCccchHHHhccCCCCCEEECCCC
Confidence            755    77766  88999999999999888877777777     89999999999999776 67889999999999998


Q ss_pred             ccccc--cChhhh--hccccccEEeccccccccccccccccccCcccch-hhhcccCCCcEEEeeccCCCCCCC-C-C-c
Q 003090          378 YILEL--IPRGVL--SRLRKLEELYMSHSFRHWQFESESEEDSSSNAKF-IELGALSRLTSLHIHIPEGKIMPS-D-M-S  449 (848)
Q Consensus       378 ~~~~~--~p~~~l--~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~-~~L~~l~~L~~L~l~~~~~~~~~~-~-~-~  449 (848)
                      ...+.  +|.. +  +++++|++|++++|.+...           ...+ ..+..+++|+.|++++|.+...+. . . .
T Consensus       184 ~l~~~~~~~~~-~~~~~l~~L~~L~L~~N~l~~~-----------~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~  251 (312)
T 1wwl_A          184 PELGERGLISA-LCPLKFPTLQVLALRNAGMETP-----------SGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDW  251 (312)
T ss_dssp             TTCHHHHHHHH-SCTTSCTTCCEEECTTSCCCCH-----------HHHHHHHHHTTCCCSEEECTTSCCCSSCCCSCCCC
T ss_pred             CcCcchHHHHH-HHhccCCCCCEEECCCCcCcch-----------HHHHHHHHhcCCCCCEEECCCCcCCcccchhhhhh
Confidence            76654  2333 3  7889999999999987632           0122 334577899999999998876542 1 1 3


Q ss_pred             cCCCCeEEEE
Q 003090          450 FQNLTSFSIA  459 (848)
Q Consensus       450 ~~~L~~L~l~  459 (848)
                      +++|+.|+++
T Consensus       252 l~~L~~L~Ls  261 (312)
T 1wwl_A          252 PSQLNSLNLS  261 (312)
T ss_dssp             CTTCCEEECT
T ss_pred             cCCCCEEECC
Confidence            4455555443

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.68  E-value=4.3e-16  Score=160.32  Aligned_cols=177  Identities=22%  Similarity=0.367  Sum_probs=153.4

Q ss_pred             CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.|++++|.+..++.. + .+++|++|++++|.+..++..+|.++++|++|++++              +.+...   
T Consensus        38 ~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~--------------n~l~~~---  100 (270)
T 2o6q_A           38 DTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTD--------------NKLQAL---  100 (270)
T ss_dssp             TCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCS--------------SCCCCC---
T ss_pred             CCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEECCC--------------CcCCcC---
Confidence            578999999999999874 3 899999999999999999998889999999999999              888873   


Q ss_pred             CCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhh
Q 003090          312 LLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       312 ~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                       .+..+..+++|++|++++|.+...+ ..++.+++|++|++++|.++.+|.. +..+++|++|++++|... .+|...+.
T Consensus       101 -~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~-~~~~~~~~  178 (270)
T 2o6q_A          101 -PIGVFDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLK-RVPEGAFD  178 (270)
T ss_dssp             -CTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCS-CCCTTTTT
T ss_pred             -CHhHcccccCCCEEECCCCccCeeCHHHhCcCcCCCEEECCCCcCCccCHhHccCCcccceeEecCCcCc-EeChhHhc
Confidence             3355789999999999999888877 5689999999999999999988875 789999999999998665 46655588


Q ss_pred             ccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          390 RLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      ++++|++|++++|.+...             ....+..+++|+.|++++|...
T Consensus       179 ~l~~L~~L~L~~N~l~~~-------------~~~~~~~l~~L~~L~l~~N~~~  218 (270)
T 2o6q_A          179 KLTELKTLKLDNNQLKRV-------------PEGAFDSLEKLKMLQLQENPWD  218 (270)
T ss_dssp             TCTTCCEEECCSSCCSCC-------------CTTTTTTCTTCCEEECCSSCBC
T ss_pred             cCCCcCEEECCCCcCCcC-------------CHHHhccccCCCEEEecCCCee
Confidence            999999999999988754             2345788999999999999754

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.68  E-value=7e-16  Score=161.85  Aligned_cols=189  Identities=19%  Similarity=0.254  Sum_probs=160.9

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.|++++|.+..+|....+++|++|++++|.+..++.  +..+++|++|++++              +.+..     
T Consensus        41 ~~L~~L~l~~~~i~~l~~~~~l~~L~~L~L~~n~i~~~~~--~~~l~~L~~L~L~~--------------n~l~~-----   99 (308)
T 1h6u_A           41 DGITTLSAFGTGVTTIEGVQYLNNLIGLELKDNQITDLAP--LKNLTKITELELSG--------------NPLKN-----   99 (308)
T ss_dssp             HTCCEEECTTSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCCSCCEEECCS--------------CCCSC-----
T ss_pred             CCcCEEEeeCCCccCchhhhccCCCCEEEccCCcCCCChh--HccCCCCCEEEccC--------------CcCCC-----
Confidence            3578899999999998855589999999999999988887  68999999999999              78877     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      ++ .+..+++|++|++++|.+... +.+..+++|++|++++|.++.+|. ++.+++|++|++++|... .++.  +..++
T Consensus       100 ~~-~~~~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~l~-~~~~--l~~l~  173 (308)
T 1h6u_A          100 VS-AIAGLQSIKTLDLTSTQITDV-TPLAGLSNLQVLYLDLNQITNISP-LAGLTNLQYLSIGNAQVS-DLTP--LANLS  173 (308)
T ss_dssp             CG-GGTTCTTCCEEECTTSCCCCC-GGGTTCTTCCEEECCSSCCCCCGG-GGGCTTCCEEECCSSCCC-CCGG--GTTCT
T ss_pred             ch-hhcCCCCCCEEECCCCCCCCc-hhhcCCCCCCEEECCCCccCcCcc-ccCCCCccEEEccCCcCC-CChh--hcCCC
Confidence            65 688999999999999977664 458999999999999999998876 899999999999998654 4665  78999


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCC
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL  463 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~  463 (848)
                      +|+.|++++|.+...               ..+..+++|+.|++++|.+..++....+++|+.|++..+..
T Consensus       174 ~L~~L~l~~n~l~~~---------------~~l~~l~~L~~L~L~~N~l~~~~~l~~l~~L~~L~l~~N~i  229 (308)
T 1h6u_A          174 KLTTLKADDNKISDI---------------SPLASLPNLIEVHLKNNQISDVSPLANTSNLFIVTLTNQTI  229 (308)
T ss_dssp             TCCEEECCSSCCCCC---------------GGGGGCTTCCEEECTTSCCCBCGGGTTCTTCCEEEEEEEEE
T ss_pred             CCCEEECCCCccCcC---------------hhhcCCCCCCEEEccCCccCccccccCCCCCCEEEccCCee
Confidence            999999999987643               23888999999999999998887533889999999986553

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.67  E-value=1.5e-16  Score=160.72  Aligned_cols=191  Identities=14%  Similarity=0.249  Sum_probs=160.9

Q ss_pred             CCCceeeecCCCcccCCcc--cccccceeecccCc-CcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENS-PLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~-~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      .++.|++++|.++.+|...  .+++|++|++++|. +..++...|.++++|++|++++|             +.+..   
T Consensus        32 ~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~-------------n~l~~---   95 (239)
T 2xwt_C           32 STQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNT-------------RNLTY---   95 (239)
T ss_dssp             TCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEE-------------TTCCE---
T ss_pred             cccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCC-------------CCeeE---
Confidence            6789999999999998843  89999999999996 89999877899999999999974             56766   


Q ss_pred             CCCC-chhhhcccCcEEEccCccccCCchhhccccCCC---EEEccCC-CCcccChh-hccCCccc-EEeccCCcccccc
Q 003090          311 FLLP-SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE---ILDLSES-DVSEIPVS-FGRLSHLR-LLDLTGCYILELI  383 (848)
Q Consensus       311 ~~lp-~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~---~L~l~~~-~l~~lp~~-i~~L~~L~-~L~l~~~~~~~~~  383 (848)
                        +| ..+..+++|++|++++|.+...+. ++.+.+|+   +|++++| .++.+|.. +..+++|+ +|++++|... .+
T Consensus        96 --i~~~~f~~l~~L~~L~l~~n~l~~lp~-~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l~-~i  171 (239)
T 2xwt_C           96 --IDPDALKELPLLKFLGIFNTGLKMFPD-LTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFT-SV  171 (239)
T ss_dssp             --ECTTSEECCTTCCEEEEEEECCCSCCC-CTTCCBCCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCCC-EE
T ss_pred             --cCHHHhCCCCCCCEEeCCCCCCccccc-cccccccccccEEECCCCcchhhcCcccccchhcceeEEEcCCCCCc-cc
Confidence              44 568899999999999998877555 88888888   9999999 99988864 88999999 9999998665 78


Q ss_pred             ChhhhhccccccEEeccccc-cccccccccccccCcccchhhhccc-CCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          384 PRGVLSRLRKLEELYMSHSF-RHWQFESESEEDSSSNAKFIELGAL-SRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       384 p~~~l~~l~~L~~L~l~~~~-~~~~~~~~~~~~~~~~~~~~~L~~l-~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      |...+.. ++|+.|++++|. +...             ....+..+ ++|+.|++++|.++.+|.. .+++|+.|.+.
T Consensus       172 ~~~~~~~-~~L~~L~L~~n~~l~~i-------------~~~~~~~l~~~L~~L~l~~N~l~~l~~~-~~~~L~~L~l~  234 (239)
T 2xwt_C          172 QGYAFNG-TKLDAVYLNKNKYLTVI-------------DKDAFGGVYSGPSLLDVSQTSVTALPSK-GLEHLKELIAR  234 (239)
T ss_dssp             CTTTTTT-CEEEEEECTTCTTCCEE-------------CTTTTTTCSBCCSEEECTTCCCCCCCCT-TCTTCSEEECT
T ss_pred             CHhhcCC-CCCCEEEcCCCCCcccC-------------CHHHhhccccCCcEEECCCCccccCChh-HhccCceeecc
Confidence            8874444 899999999995 7643             33567788 9999999999999988877 78889988875

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.67  E-value=5.8e-16  Score=157.49  Aligned_cols=175  Identities=21%  Similarity=0.298  Sum_probs=137.7

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      .+.++++++.+..+|..+. ++++.|++++|.+..++...|.++++|++|++++              +.+...    .|
T Consensus        16 ~~~l~~~~~~l~~~p~~~~-~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~--------------n~l~~~----~~   76 (251)
T 3m19_A           16 KKEVDCQGKSLDSVPSGIP-ADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDY--------------NQLQTL----SA   76 (251)
T ss_dssp             GTEEECTTCCCSSCCSCCC-TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTT--------------SCCCCC----CT
T ss_pred             CeEEecCCCCccccCCCCC-CCCCEEEccCCCcCccCHhHhcCcccCCEEECCC--------------CcCCcc----CH
Confidence            3568888888888887765 6888899999888888777778888999999988              777774    55


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      ..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|.. +..+++|++|++++|... .+|...++.++
T Consensus        77 ~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~-~~~~~~~~~l~  155 (251)
T 3m19_A           77 GVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQ-SIPAGAFDKLT  155 (251)
T ss_dssp             TTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCT
T ss_pred             hHhccCCcCCEEECCCCcccccChhHhcccCCCCEEEcCCCcCCCcChhHhccCCcccEEECcCCcCC-ccCHHHcCcCc
Confidence            56788888999999988877766 5678888889999988888877765 577888888888887554 45554478888


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      +|++|++++|.+...             .+..+..+++|+.|++++|.+.
T Consensus       156 ~L~~L~L~~N~l~~~-------------~~~~~~~l~~L~~L~l~~N~~~  192 (251)
T 3m19_A          156 NLQTLSLSTNQLQSV-------------PHGAFDRLGKLQTITLFGNQFD  192 (251)
T ss_dssp             TCCEEECCSSCCSCC-------------CTTTTTTCTTCCEEECCSCCBC
T ss_pred             CCCEEECCCCcCCcc-------------CHHHHhCCCCCCEEEeeCCcee
Confidence            888888888877654             3345777888888888887654

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.67  E-value=1.8e-17  Score=174.67  Aligned_cols=202  Identities=17%  Similarity=0.187  Sum_probs=157.1

Q ss_pred             HHHHHhccCCCceeeecCCCcc--cCCcc--------cccccceeecccCcCc-ccChHHH-ccCCceeEEEccCccccc
Q 003090          226 QYEIAGWLDLTGISLMFNDIHE--VPDEL--------ECPKLQALFLQENSPL-AIPDRFF-QGMKDLQVLDLGGIRRFS  293 (848)
Q Consensus       226 ~~~i~~~~~l~~l~l~~n~l~~--lp~~~--------~~~~L~~L~l~~~~~~-~~~~~~~-~~~~~Lr~L~l~~~~~~~  293 (848)
                      +..+...  ++.+++++|.+..  +|...        .+++|++|++++|.+. .+|..+| ..+++|++|++++     
T Consensus        58 p~~~~~~--L~~L~L~~n~l~~~~~~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls~-----  130 (312)
T 1wwl_A           58 LGQFTDI--IKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRN-----  130 (312)
T ss_dssp             CHHHHHH--HHHCCCCEEEEEEEECBHHHHHHHHHHHTTSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEES-----
T ss_pred             HHHHHHH--HhhcccccccccCCCcCHHHHHHHHHhcCcCCccEEEccCCcccchhHHHHHHhcCCCccEEEccC-----
Confidence            4444444  6778888888753  45443        4889999999999876 5776653 7899999999999     


Q ss_pred             ccccCCCCCCCCCCCCCCCCCchhhhc-----ccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcc---cChhh-
Q 003090          294 FSVRFPFLFPPLPSSPLFLLPSSLSFL-----INLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSE---IPVSF-  363 (848)
Q Consensus       294 ~~~~~~~~~~~l~~~~~~~lp~~~~~l-----~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~---lp~~i-  363 (848)
                               +.+.+     .|..++.+     ++|++|++++|.+...+ ..++++++|++|++++|.+..   +|..+ 
T Consensus       131 ---------N~l~~-----~~~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~  196 (312)
T 1wwl_A          131 ---------VSWAT-----RDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALC  196 (312)
T ss_dssp             ---------CBCSS-----SSSHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCCCCSSCCEEECCSCTTCHHHHHHHHSC
T ss_pred             ---------CCCcc-----hhHHHHHHHHhhcCCCcEEEeeCCCCccchHHHhccCCCCCEEECCCCCcCcchHHHHHHH
Confidence                     88888     78888888     89999999999888877 789999999999999998763   45555 


Q ss_pred             -ccCCcccEEeccCCcccc--ccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccC
Q 003090          364 -GRLSHLRLLDLTGCYILE--LIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE  440 (848)
Q Consensus       364 -~~L~~L~~L~l~~~~~~~--~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~  440 (848)
                       +++++|++|++++|....  .++...+.++++|++|++++|.+....+            ...+..+++|+.|++++|.
T Consensus       197 ~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~------------~~~~~~l~~L~~L~Ls~N~  264 (312)
T 1wwl_A          197 PLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAG------------APSCDWPSQLNSLNLSFTG  264 (312)
T ss_dssp             TTSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTSCCCSSCC------------CSCCCCCTTCCEEECTTSC
T ss_pred             hccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCCcCCcccc------------hhhhhhcCCCCEEECCCCc
Confidence             889999999999987652  4455546788999999999998876421            1345567899999999999


Q ss_pred             CCCCCCCCccCCCCeEEEEeC
Q 003090          441 GKIMPSDMSFQNLTSFSIAIG  461 (848)
Q Consensus       441 ~~~~~~~~~~~~L~~L~l~~~  461 (848)
                      ++.+|..+. ++|+.|+++.+
T Consensus       265 l~~ip~~~~-~~L~~L~Ls~N  284 (312)
T 1wwl_A          265 LKQVPKGLP-AKLSVLDLSYN  284 (312)
T ss_dssp             CSSCCSSCC-SEEEEEECCSS
T ss_pred             cChhhhhcc-CCceEEECCCC
Confidence            988887655 66666666533

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.67  E-value=9.3e-17  Score=169.57  Aligned_cols=201  Identities=18%  Similarity=0.162  Sum_probs=131.5

Q ss_pred             CchhHHHHHHHhcc-CCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccc
Q 003090          220 PSITKIQYEIAGWL-DLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSV  296 (848)
Q Consensus       220 ~~~~~l~~~i~~~~-~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~  296 (848)
                      ..+..+...+.... .++.|++++|.+..++.. + .+++|++|++++|.+..+++  +..+++|++|++++        
T Consensus        20 ~~l~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~--~~~l~~L~~L~Ls~--------   89 (317)
T 3o53_A           20 SSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD--LESLSTLRTLDLNN--------   89 (317)
T ss_dssp             TTHHHHHHHHHTTGGGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTTSCCEEEEE--ETTCTTCCEEECCS--------
T ss_pred             cchhhhHHHHhccCCCCCEEECcCCccCcCCHHHhhCCCcCCEEECCCCcCCcchh--hhhcCCCCEEECcC--------
Confidence            44555555555444 588899999998887743 3 78899999999998776665  67888999999998        


Q ss_pred             cCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh-hhccCCcccEEecc
Q 003090          297 RFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLT  375 (848)
Q Consensus       297 ~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~  375 (848)
                            +.+..     +|    ..++|++|++++|.+...+.  ..+++|++|++++|.++.++. .++.+++|++|+++
T Consensus        90 ------n~l~~-----l~----~~~~L~~L~l~~n~l~~~~~--~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls  152 (317)
T 3o53_A           90 ------NYVQE-----LL----VGPSIETLHAANNNISRVSC--SRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLK  152 (317)
T ss_dssp             ------SEEEE-----EE----ECTTCCEEECCSSCCSEEEE--CCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECT
T ss_pred             ------Ccccc-----cc----CCCCcCEEECCCCccCCcCc--cccCCCCEEECCCCCCCCccchhhhccCCCCEEECC
Confidence                  55544     33    23667777777776555442  225667777777777765543 56667777777777


Q ss_pred             CCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCCCC
Q 003090          376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQNLT  454 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~  454 (848)
                      +|......+..+...+++|++|++++|.+...               .....+++|+.|++++|.+..++..+ .+++|+
T Consensus       153 ~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~~---------------~~~~~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~  217 (317)
T 3o53_A          153 LNEIDTVNFAELAASSDTLEHLNLQYNFIYDV---------------KGQVVFAKLKTLDLSSNKLAFMGPEFQSAAGVT  217 (317)
T ss_dssp             TSCCCEEEGGGGGGGTTTCCEEECTTSCCCEE---------------ECCCCCTTCCEEECCSSCCCEECGGGGGGTTCS
T ss_pred             CCCCCcccHHHHhhccCcCCEEECCCCcCccc---------------ccccccccCCEEECCCCcCCcchhhhcccCccc
Confidence            76555544444234667777777777766532               12234666777777777766666555 666677


Q ss_pred             eEEEEeCC
Q 003090          455 SFSIAIGD  462 (848)
Q Consensus       455 ~L~l~~~~  462 (848)
                      .|++..+.
T Consensus       218 ~L~L~~N~  225 (317)
T 3o53_A          218 WISLRNNK  225 (317)
T ss_dssp             EEECTTSC
T ss_pred             EEECcCCc
Confidence            66665443

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.66  E-value=7e-16  Score=158.90  Aligned_cols=188  Identities=21%  Similarity=0.308  Sum_probs=138.9

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchh
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL  317 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~  317 (848)
                      +++..+.+..+.....+++|+.|++++|.+..++.  +..+++|++|++++              +.+..     ++ .+
T Consensus        24 l~l~~~~~~~~~~~~~l~~L~~L~l~~~~i~~~~~--l~~l~~L~~L~l~~--------------n~l~~-----~~-~l   81 (272)
T 3rfs_A           24 ANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQG--IQYLPNVRYLALGG--------------NKLHD-----IS-AL   81 (272)
T ss_dssp             HHHTCSCTTSEECHHHHTTCCEEECTTSCCCCCTT--GGGCTTCCEEECTT--------------SCCCC-----CG-GG
T ss_pred             HHhcCcccccccccccccceeeeeeCCCCcccccc--cccCCCCcEEECCC--------------CCCCC-----ch-hh
Confidence            44455555555444477888888888887777664  56788888888888              67766     43 67


Q ss_pred             hhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhcccccc
Q 003090          318 SFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE  395 (848)
Q Consensus       318 ~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~  395 (848)
                      ..+++|++|++++|.+...+ ..++++++|++|++++|.++.+|.. ++.+++|++|++++|... .+|...++++++|+
T Consensus        82 ~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~-~~~~~~~~~l~~L~  160 (272)
T 3rfs_A           82 KELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQ-SLPKGVFDKLTNLT  160 (272)
T ss_dssp             TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCTTCC
T ss_pred             cCCCCCCEEECCCCccCccChhHhcCCcCCCEEECCCCcCCccCHHHhccCCCCCEEECCCCccC-ccCHHHhccCccCC
Confidence            78888888888888777666 4468888888888888888876654 678888888888887554 45555467888888


Q ss_pred             EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeC
Q 003090          396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIG  461 (848)
Q Consensus       396 ~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~  461 (848)
                      +|++++|.+...             .+..++.+++|+.|++++|.+..++...  .+++|+.|++..+
T Consensus       161 ~L~l~~n~l~~~-------------~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N  215 (272)
T 3rfs_A          161 ELDLSYNQLQSL-------------PEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDN  215 (272)
T ss_dssp             EEECCSSCCCCC-------------CTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSS
T ss_pred             EEECCCCCcCcc-------------CHHHhcCCccCCEEECCCCcCCccCHHHHhCCcCCCEEEccCC
Confidence            888888877653             3344677888888888888887776653  6788888887644

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.66  E-value=1.2e-16  Score=178.71  Aligned_cols=166  Identities=19%  Similarity=0.173  Sum_probs=107.0

Q ss_pred             ccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      +++|++|++++|.+..+++..|..+++|++|++++              |.+.+     .+. ++.+++|++|++++|.+
T Consensus        33 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~--------------N~l~~-----~~~-l~~l~~L~~L~Ls~N~l   92 (487)
T 3oja_A           33 AWNVKELDLSGNPLSQISAADLAPFTKLELLNLSS--------------NVLYE-----TLD-LESLSTLRTLDLNNNYV   92 (487)
T ss_dssp             GGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTT--------------SCCEE-----EEE-CTTCTTCCEEECCSSEE
T ss_pred             CCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeC--------------CCCCC-----Ccc-cccCCCCCEEEecCCcC
Confidence            34677777777777666655567777777777777              66655     333 67777777777777755


Q ss_pred             cCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccc
Q 003090          334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       334 ~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                      ...+    ..++|++|++++|.++.+|.  ..+++|++|++++|...+..|.. ++++++|+.|++++|.+...      
T Consensus        93 ~~l~----~~~~L~~L~L~~N~l~~~~~--~~l~~L~~L~L~~N~l~~~~~~~-~~~l~~L~~L~Ls~N~l~~~------  159 (487)
T 3oja_A           93 QELL----VGPSIETLHAANNNISRVSC--SRGQGKKNIYLANNKITMLRDLD-EGCRSRVQYLDLKLNEIDTV------  159 (487)
T ss_dssp             EEEE----ECTTCCEEECCSSCCCCEEE--CCCSSCEEEECCSSCCCSGGGBC-GGGGSSEEEEECTTSCCCEE------
T ss_pred             CCCC----CCCCcCEEECcCCcCCCCCc--cccCCCCEEECCCCCCCCCCchh-hcCCCCCCEEECCCCCCCCc------
Confidence            4433    23677777777777776554  24567777777777665544444 67777777777777776654      


Q ss_pred             cccCcccchhhhc-ccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          414 EDSSSNAKFIELG-ALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       414 ~~~~~~~~~~~L~-~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                             .+..+. .+++|+.|++++|.++.++....+++|+.|+++
T Consensus       160 -------~~~~l~~~l~~L~~L~Ls~N~l~~~~~~~~l~~L~~L~Ls  199 (487)
T 3oja_A          160 -------NFAELAASSDTLEHLNLQYNFIYDVKGQVVFAKLKTLDLS  199 (487)
T ss_dssp             -------EGGGGGGGTTTCCEEECTTSCCCEEECCCCCTTCCEEECC
T ss_pred             -------ChHHHhhhCCcccEEecCCCccccccccccCCCCCEEECC
Confidence                   333443 567777777777776655444345555555554

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.66  E-value=1.8e-16  Score=160.08  Aligned_cols=173  Identities=17%  Similarity=0.235  Sum_probs=129.4

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCC-CCCCCCCCCCc-
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPP-LPSSPLFLLPS-  315 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~-l~~~~~~~lp~-  315 (848)
                      +.+..+.++.+|. + .+++++|++++|.+..++...|.++++|++|++++              +. +..     +|. 
T Consensus        16 ~~v~c~~l~~ip~-~-~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~--------------n~~l~~-----i~~~   74 (239)
T 2xwt_C           16 FRVTCKDIQRIPS-L-PPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSI--------------DVTLQQ-----LESH   74 (239)
T ss_dssp             TEEEECSCSSCCC-C-CTTCCEEEEESCCCSEECTTTTTTCTTCCEEEEEC--------------CSSCCE-----ECTT
T ss_pred             ceeEccCccccCC-C-CCcccEEEEeCCcceEECHHHccCCCCCcEEeCCC--------------CCCcce-----eCHh
Confidence            4444555778887 3 34889999999988888887788899999999998              65 766     543 


Q ss_pred             hhhhcccCcEEEccC-ccccCCc-hhhccccCCCEEEccCCCCcccChhhccCCccc---EEeccCCccccccChhhhhc
Q 003090          316 SLSFLINLRTLRLHD-RRIQGDL-SLIGELSGLEILDLSESDVSEIPVSFGRLSHLR---LLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~-~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~---~L~l~~~~~~~~~p~~~l~~  390 (848)
                      .+..+++|++|++++ |.+...+ ..+..+++|++|++++|.++.+|. +..+++|+   +|++++|.....+|...+.+
T Consensus        75 ~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~~L~l~~n~l~~lp~-~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~  153 (239)
T 2xwt_C           75 SFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFLGIFNTGLKMFPD-LTKVYSTDIFFILEITDNPYMTSIPVNAFQG  153 (239)
T ss_dssp             TEESCTTCCEEEEEEETTCCEECTTSEECCTTCCEEEEEEECCCSCCC-CTTCCBCCSEEEEEEESCTTCCEECTTTTTT
T ss_pred             HcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCCEEeCCCCCCccccc-cccccccccccEEECCCCcchhhcCcccccc
Confidence            678888999999988 7666655 567888899999999998888886 77788887   88888874455677665788


Q ss_pred             ccccc-EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccC-CCCCCC
Q 003090          391 LRKLE-ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE-GKIMPS  446 (848)
Q Consensus       391 l~~L~-~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~-~~~~~~  446 (848)
                      +++|+ +|++++|.+... +            ...+.. ++|+.|++++|. ++.++.
T Consensus       154 l~~L~~~L~l~~n~l~~i-~------------~~~~~~-~~L~~L~L~~n~~l~~i~~  197 (239)
T 2xwt_C          154 LCNETLTLKLYNNGFTSV-Q------------GYAFNG-TKLDAVYLNKNKYLTVIDK  197 (239)
T ss_dssp             TBSSEEEEECCSCCCCEE-C------------TTTTTT-CEEEEEECTTCTTCCEECT
T ss_pred             hhcceeEEEcCCCCCccc-C------------HhhcCC-CCCCEEEcCCCCCcccCCH
Confidence            88888 888888877632 1            112223 678888888773 665544

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.64  E-value=3.4e-15  Score=153.69  Aligned_cols=176  Identities=23%  Similarity=0.290  Sum_probs=150.2

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.+++++|.+..++....+++|++|++++|.+..++  .+..+++|++|++++              +.+...    
T Consensus        41 ~~L~~L~l~~~~i~~~~~l~~l~~L~~L~l~~n~l~~~~--~l~~l~~L~~L~L~~--------------n~l~~~----  100 (272)
T 3rfs_A           41 NSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDIS--ALKELTNLTYLILTG--------------NQLQSL----  100 (272)
T ss_dssp             TTCCEEECTTSCCCCCTTGGGCTTCCEEECTTSCCCCCG--GGTTCTTCCEEECTT--------------SCCCCC----
T ss_pred             cceeeeeeCCCCcccccccccCCCCcEEECCCCCCCCch--hhcCCCCCCEEECCC--------------CccCcc----
Confidence            457889999999998887668999999999999888875  368999999999999              888873    


Q ss_pred             CCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      .+..+..+++|++|++++|.+...+ ..++.+++|++|++++|.++.+|.. ++.+++|++|++++|... .+|...++.
T Consensus       101 ~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~-~~~~~~~~~  179 (272)
T 3rfs_A          101 PNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQ-SLPEGVFDK  179 (272)
T ss_dssp             CTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTT
T ss_pred             ChhHhcCCcCCCEEECCCCcCCccCHHHhccCCCCCEEECCCCccCccCHHHhccCccCCEEECCCCCcC-ccCHHHhcC
Confidence            4455799999999999999888777 4579999999999999999988765 689999999999998765 566655789


Q ss_pred             cccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          391 LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       391 l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      +++|++|++++|.+...             .+..+..+++|+.|++++|.+.
T Consensus       180 l~~L~~L~L~~N~l~~~-------------~~~~~~~l~~L~~L~l~~N~~~  218 (272)
T 3rfs_A          180 LTQLKDLRLYQNQLKSV-------------PDGVFDRLTSLQYIWLHDNPWD  218 (272)
T ss_dssp             CTTCCEEECCSSCCSCC-------------CTTTTTTCTTCCEEECCSSCBC
T ss_pred             CccCCEEECCCCcCCcc-------------CHHHHhCCcCCCEEEccCCCcc
Confidence            99999999999988764             3456788999999999999754

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.64  E-value=2.2e-15  Score=158.05  Aligned_cols=177  Identities=21%  Similarity=0.248  Sum_probs=134.6

Q ss_pred             ecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhc
Q 003090          241 MFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFL  320 (848)
Q Consensus       241 ~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l  320 (848)
                      ..+.+.++.....+++|++|++++|.+..++.  +..+++|++|++++              +.+..     ++. +..+
T Consensus        27 ~~~~~~~~~~~~~l~~L~~L~l~~~~i~~l~~--~~~l~~L~~L~L~~--------------n~i~~-----~~~-~~~l   84 (308)
T 1h6u_A           27 GKSNVTDTVTQADLDGITTLSAFGTGVTTIEG--VQYLNNLIGLELKD--------------NQITD-----LAP-LKNL   84 (308)
T ss_dssp             TCSSTTSEECHHHHHTCCEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GTTC
T ss_pred             CCCCcCceecHHHcCCcCEEEeeCCCccCchh--hhccCCCCEEEccC--------------CcCCC-----Chh-HccC
Confidence            34444444444467889999999998888874  57899999999998              77877     666 8889


Q ss_pred             ccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecc
Q 003090          321 INLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS  400 (848)
Q Consensus       321 ~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~  400 (848)
                      ++|++|++++|.+.. ++.+..+++|++|++++|.++.+|. +..+++|++|++++|... .++.  ++.+++|+.|+++
T Consensus        85 ~~L~~L~L~~n~l~~-~~~~~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~l~-~~~~--l~~l~~L~~L~l~  159 (308)
T 1h6u_A           85 TKITELELSGNPLKN-VSAIAGLQSIKTLDLTSTQITDVTP-LAGLSNLQVLYLDLNQIT-NISP--LAGLTNLQYLSIG  159 (308)
T ss_dssp             CSCCEEECCSCCCSC-CGGGTTCTTCCEEECTTSCCCCCGG-GTTCTTCCEEECCSSCCC-CCGG--GGGCTTCCEEECC
T ss_pred             CCCCEEEccCCcCCC-chhhcCCCCCCEEECCCCCCCCchh-hcCCCCCCEEECCCCccC-cCcc--ccCCCCccEEEcc
Confidence            999999999997554 4578889999999999999888775 888999999999987654 4555  7888999999999


Q ss_pred             ccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          401 HSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       401 ~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      +|.+...               ..+..+++|+.|++++|.+..++....+++|+.|++.
T Consensus       160 ~n~l~~~---------------~~l~~l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~L~  203 (308)
T 1h6u_A          160 NAQVSDL---------------TPLANLSKLTTLKADDNKISDISPLASLPNLIEVHLK  203 (308)
T ss_dssp             SSCCCCC---------------GGGTTCTTCCEEECCSSCCCCCGGGGGCTTCCEEECT
T ss_pred             CCcCCCC---------------hhhcCCCCCCEEECCCCccCcChhhcCCCCCCEEEcc
Confidence            8877642               2278888999999988887766542244445544443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.61  E-value=1.3e-15  Score=170.29  Aligned_cols=201  Identities=18%  Similarity=0.179  Sum_probs=145.2

Q ss_pred             CchhHHHHHHHhcc----CCCceeeecCCCcccCC-cc-cccccceeecccCcCcccChHHHccCCceeEEEccCccccc
Q 003090          220 PSITKIQYEIAGWL----DLTGISLMFNDIHEVPD-EL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS  293 (848)
Q Consensus       220 ~~~~~l~~~i~~~~----~l~~l~l~~n~l~~lp~-~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~  293 (848)
                      .....++..+....    .++.|++++|.+..+++ .+ .+++|++|++++|.+...++  +..+++|++|++++     
T Consensus        17 ~~~~~l~~~l~~l~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~--l~~l~~L~~L~Ls~-----   89 (487)
T 3oja_A           17 VTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD--LESLSTLRTLDLNN-----   89 (487)
T ss_dssp             CCTTTHHHHHHTTSTTGGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTTSCCEEEEE--CTTCTTCCEEECCS-----
T ss_pred             CchhhhHHHHHHhcccCCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeCCCCCCCcc--cccCCCCCEEEecC-----
Confidence            34456666666665    68999999999998875 44 89999999999998877665  68999999999999     


Q ss_pred             ccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCccc-ChhhccCCcccEE
Q 003090          294 FSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLL  372 (848)
Q Consensus       294 ~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L  372 (848)
                               |.+.+     +|.    .++|++|++++|.+...+.  ..+++|++|++++|.++.+ |..++.+++|++|
T Consensus        90 ---------N~l~~-----l~~----~~~L~~L~L~~N~l~~~~~--~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L  149 (487)
T 3oja_A           90 ---------NYVQE-----LLV----GPSIETLHAANNNISRVSC--SRGQGKKNIYLANNKITMLRDLDEGCRSRVQYL  149 (487)
T ss_dssp             ---------SEEEE-----EEE----CTTCCEEECCSSCCCCEEE--CCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEE
T ss_pred             ---------CcCCC-----CCC----CCCcCEEECcCCcCCCCCc--cccCCCCEEECCCCCCCCCCchhhcCCCCCCEE
Confidence                     65555     442    2677888888876665543  2456778888888877755 4467777788888


Q ss_pred             eccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccC
Q 003090          373 DLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQ  451 (848)
Q Consensus       373 ~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~  451 (848)
                      ++++|.+.+..|..+...+++|++|++++|.+...               .....+++|+.|++++|.++.+|..+ .++
T Consensus       150 ~Ls~N~l~~~~~~~l~~~l~~L~~L~Ls~N~l~~~---------------~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~  214 (487)
T 3oja_A          150 DLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDV---------------KGQVVFAKLKTLDLSSNKLAFMGPEFQSAA  214 (487)
T ss_dssp             ECTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCEE---------------ECCCCCTTCCEEECCSSCCCEECGGGGGGT
T ss_pred             ECCCCCCCCcChHHHhhhCCcccEEecCCCccccc---------------cccccCCCCCEEECCCCCCCCCCHhHcCCC
Confidence            88877766656665333677888888887776543               22335777777777777777776666 677


Q ss_pred             CCCeEEEEeCC
Q 003090          452 NLTSFSIAIGD  462 (848)
Q Consensus       452 ~L~~L~l~~~~  462 (848)
                      +|+.|+++.+.
T Consensus       215 ~L~~L~Ls~N~  225 (487)
T 3oja_A          215 GVTWISLRNNK  225 (487)
T ss_dssp             TCSEEECTTSC
T ss_pred             CccEEEecCCc
Confidence            77777776544

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.61  E-value=3.3e-15  Score=155.03  Aligned_cols=175  Identities=22%  Similarity=0.242  Sum_probs=151.1

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .++++++++++++.+..+|..+   .+++++|++++              +.+...    .|..+..+++|++|++++|.
T Consensus         8 ~l~~l~~l~~~~~~l~~ip~~~---~~~l~~L~L~~--------------N~l~~~----~~~~~~~l~~L~~L~L~~n~   66 (290)
T 1p9a_G            8 KVASHLEVNCDKRNLTALPPDL---PKDTTILHLSE--------------NLLYTF----SLATLMPYTRLTQLNLDRAE   66 (290)
T ss_dssp             CSTTCCEEECTTSCCSSCCSCC---CTTCCEEECTT--------------SCCSEE----EGGGGTTCTTCCEEECTTSC
T ss_pred             ccCCccEEECCCCCCCcCCCCC---CCCCCEEEcCC--------------CcCCcc----CHHHhhcCCCCCEEECCCCc
Confidence            5788999999999999999764   36899999999              888774    46789999999999999997


Q ss_pred             ccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccc
Q 003090          333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESES  412 (848)
Q Consensus       333 ~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~  412 (848)
                      +...+. .+.+++|++|++++|.++.+|..+..+++|++|++++|.+. .+|.+.+.++++|++|++++|.+...     
T Consensus        67 l~~~~~-~~~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~~L~l~~N~l~-~l~~~~~~~l~~L~~L~L~~N~l~~~-----  139 (290)
T 1p9a_G           67 LTKLQV-DGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLT-SLPLGALRGLGELQELYLKGNELKTL-----  139 (290)
T ss_dssp             CCEEEC-CSCCTTCCEEECCSSCCSSCCCCTTTCTTCCEEECCSSCCC-CCCSSTTTTCTTCCEEECTTSCCCCC-----
T ss_pred             cCcccC-CCCCCcCCEEECCCCcCCcCchhhccCCCCCEEECCCCcCc-ccCHHHHcCCCCCCEEECCCCCCCcc-----
Confidence            766544 38999999999999999999999999999999999998765 56655589999999999999988754     


Q ss_pred             ccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCC
Q 003090          413 EEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDL  463 (848)
Q Consensus       413 ~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~  463 (848)
                              .+..+..+++|+.|++++|.++.++...  .+++|+.|++..+..
T Consensus       140 --------~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~l  184 (290)
T 1p9a_G          140 --------PPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSL  184 (290)
T ss_dssp             --------CTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCCEEECCSSCC
T ss_pred             --------ChhhcccccCCCEEECCCCcCCccCHHHhcCcCCCCEEECCCCcC
Confidence                    3345788999999999999999998876  789999999986655

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.60  E-value=1e-14  Score=151.49  Aligned_cols=143  Identities=29%  Similarity=0.374  Sum_probs=67.9

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ++.+++++|.+..++....+++|++|++++|.+..++.  +.++++|++|++++              +.+..     +|
T Consensus        48 L~~L~l~~~~i~~~~~~~~l~~L~~L~L~~n~l~~~~~--l~~l~~L~~L~l~~--------------n~l~~-----~~  106 (291)
T 1h6t_A           48 IDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKP--LANLKNLGWLFLDE--------------NKVKD-----LS  106 (291)
T ss_dssp             CCEEECTTSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----GG
T ss_pred             ccEEEccCCCcccChhHhcCCCCCEEEccCCccCCCcc--cccCCCCCEEECCC--------------CcCCC-----Ch
Confidence            34455555555544432244555555555554444443  34555555555555              44443     33


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      . +..+++|++|++++|.+.. ++.+..+++|++|++++|.++.+ ..++.+++|++|++++|.... ++.  +..+++|
T Consensus       107 ~-l~~l~~L~~L~L~~n~i~~-~~~l~~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~L~~N~l~~-~~~--l~~l~~L  180 (291)
T 1h6t_A          107 S-LKDLKKLKSLSLEHNGISD-INGLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDNQISD-IVP--LAGLTKL  180 (291)
T ss_dssp             G-GTTCTTCCEEECTTSCCCC-CGGGGGCTTCCEEECCSSCCCCC-GGGGGCTTCSEEECCSSCCCC-CGG--GTTCTTC
T ss_pred             h-hccCCCCCEEECCCCcCCC-ChhhcCCCCCCEEEccCCcCCcc-hhhccCCCCCEEEccCCcccc-chh--hcCCCcc
Confidence            2 4455555555555553333 23444555555555555555444 244455555555555543322 222  4455555


Q ss_pred             cEEecccccc
Q 003090          395 EELYMSHSFR  404 (848)
Q Consensus       395 ~~L~l~~~~~  404 (848)
                      +.|++++|.+
T Consensus       181 ~~L~L~~N~i  190 (291)
T 1h6t_A          181 QNLYLSKNHI  190 (291)
T ss_dssp             CEEECCSSCC
T ss_pred             CEEECCCCcC
Confidence            5555555544

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.59  E-value=1.1e-14  Score=151.17  Aligned_cols=183  Identities=22%  Similarity=0.270  Sum_probs=154.5

Q ss_pred             eeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhh
Q 003090          239 SLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS  318 (848)
Q Consensus       239 ~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~  318 (848)
                      .+..+.+..+.....+++|+.|++++|.+..++.  +..+++|++|++++              +.+..     ++. +.
T Consensus        30 ~l~~~~~~~~~~~~~l~~L~~L~l~~~~i~~~~~--~~~l~~L~~L~L~~--------------n~l~~-----~~~-l~   87 (291)
T 1h6t_A           30 NLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQG--IQYLPNVTKLFLNG--------------NKLTD-----IKP-LA   87 (291)
T ss_dssp             HTTCSCTTSEECHHHHHTCCEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GT
T ss_pred             HhcCCCcccccchhhcCcccEEEccCCCcccChh--HhcCCCCCEEEccC--------------CccCC-----Ccc-cc
Confidence            3445555555544578999999999999988875  68899999999999              88888     666 99


Q ss_pred             hcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEe
Q 003090          319 FLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY  398 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~  398 (848)
                      .+++|++|++++|.+.. ++.+..+++|++|++++|.++.++ .+..+++|++|++++|.... ++ . ++.+++|++|+
T Consensus        88 ~l~~L~~L~l~~n~l~~-~~~l~~l~~L~~L~L~~n~i~~~~-~l~~l~~L~~L~l~~n~l~~-~~-~-l~~l~~L~~L~  162 (291)
T 1h6t_A           88 NLKNLGWLFLDENKVKD-LSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKITD-IT-V-LSRLTKLDTLS  162 (291)
T ss_dssp             TCTTCCEEECCSSCCCC-GGGGTTCTTCCEEECTTSCCCCCG-GGGGCTTCCEEECCSSCCCC-CG-G-GGGCTTCSEEE
T ss_pred             cCCCCCEEECCCCcCCC-ChhhccCCCCCEEECCCCcCCCCh-hhcCCCCCCEEEccCCcCCc-ch-h-hccCCCCCEEE
Confidence            99999999999997655 566999999999999999999885 68999999999999987654 54 3 89999999999


Q ss_pred             ccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCC
Q 003090          399 MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL  463 (848)
Q Consensus       399 l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~  463 (848)
                      +++|.+...              + .+..+++|+.|++++|.++.++....+++|+.|++..+..
T Consensus       163 L~~N~l~~~--------------~-~l~~l~~L~~L~L~~N~i~~l~~l~~l~~L~~L~l~~n~i  212 (291)
T 1h6t_A          163 LEDNQISDI--------------V-PLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQEC  212 (291)
T ss_dssp             CCSSCCCCC--------------G-GGTTCTTCCEEECCSSCCCBCGGGTTCTTCSEEEEEEEEE
T ss_pred             ccCCccccc--------------h-hhcCCCccCEEECCCCcCCCChhhccCCCCCEEECcCCcc
Confidence            999988653              2 2889999999999999999887633899999999986654

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.58  E-value=1.5e-15  Score=159.73  Aligned_cols=87  Identities=15%  Similarity=0.120  Sum_probs=39.8

Q ss_pred             hhcccCcEEEccCccccCCc-----hhhccccCCCEEEccCCCCcccC-hhhccCCcccEEeccCCccccc--cC-hhhh
Q 003090          318 SFLINLRTLRLHDRRIQGDL-----SLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGCYILEL--IP-RGVL  388 (848)
Q Consensus       318 ~~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~~~~~~--~p-~~~l  388 (848)
                      ..+++|++|++++|.+....     ..+..+++|++|++++|.+..+| ..++.+++|++|++++|...+.  ++ ...+
T Consensus       114 ~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~  193 (310)
T 4glp_A          114 ATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCP  193 (310)
T ss_dssp             CCCBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHHTTSCT
T ss_pred             ccCCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccchhhhHHHhh
Confidence            45555555555555444321     12234555555555555555333 3444555555555555543321  11 1112


Q ss_pred             hccccccEEecccccc
Q 003090          389 SRLRKLEELYMSHSFR  404 (848)
Q Consensus       389 ~~l~~L~~L~l~~~~~  404 (848)
                      +.+++|++|++++|.+
T Consensus       194 ~~l~~L~~L~Ls~N~l  209 (310)
T 4glp_A          194 HKFPAIQNLALRNTGM  209 (310)
T ss_dssp             TSSCCCCSCBCCSSCC
T ss_pred             hcCCCCCEEECCCCCC
Confidence            3455555555555544

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.58  E-value=4e-15  Score=156.54  Aligned_cols=196  Identities=15%  Similarity=0.083  Sum_probs=155.5

Q ss_pred             ccCCCceeeecCCCccc-CCc---ccccccceeecccCcCccc----ChHHHccCCceeEEEccCcccccccccCCCCCC
Q 003090          232 WLDLTGISLMFNDIHEV-PDE---LECPKLQALFLQENSPLAI----PDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFP  303 (848)
Q Consensus       232 ~~~l~~l~l~~n~l~~l-p~~---~~~~~L~~L~l~~~~~~~~----~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~  303 (848)
                      ...++.|++++|.+... |..   ..+++|++|++++|.+...    +...+..+++|++|++++              +
T Consensus        90 ~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~--------------n  155 (310)
T 4glp_A           90 YSRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQ--------------A  155 (310)
T ss_dssp             HSCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEEC--------------C
T ss_pred             cCceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeC--------------C
Confidence            34589999999999844 444   4689999999999977652    223345799999999999              8


Q ss_pred             CCCCCCCCCCCchhhhcccCcEEEccCccccCC---c--hhhccccCCCEEEccCCCCcccChh----hccCCcccEEec
Q 003090          304 PLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD---L--SLIGELSGLEILDLSESDVSEIPVS----FGRLSHLRLLDL  374 (848)
Q Consensus       304 ~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~---~--~~i~~l~~L~~L~l~~~~l~~lp~~----i~~L~~L~~L~l  374 (848)
                      .+...    .|..++.+++|++|++++|.+.+.   +  ..++.+++|++|++++|.++.+|..    ++.+++|++|++
T Consensus       156 ~l~~~----~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~l~~~l~~L~~L~L  231 (310)
T 4glp_A          156 HSPAF----SCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETPTGVCAALAAAGVQPHSLDL  231 (310)
T ss_dssp             SSCCC----CTTSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCCHHHHHHHHHHHTCCCSSEEC
T ss_pred             Ccchh----hHHHhccCCCCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCCCCCchHHHHHHHHhcCCCCCEEEC
Confidence            88774    557889999999999999986542   2  3347899999999999999877653    578899999999


Q ss_pred             cCCccccccChhhhhcc---ccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccC
Q 003090          375 TGCYILELIPRGVLSRL---RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQ  451 (848)
Q Consensus       375 ~~~~~~~~~p~~~l~~l---~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~  451 (848)
                      ++|......|.. +..+   ++|++|++++|.+..              .+..+.  ++|+.|++++|.++.+|....++
T Consensus       232 s~N~l~~~~p~~-~~~~~~~~~L~~L~Ls~N~l~~--------------lp~~~~--~~L~~L~Ls~N~l~~~~~~~~l~  294 (310)
T 4glp_A          232 SHNSLRATVNPS-APRCMWSSALNSLNLSFAGLEQ--------------VPKGLP--AKLRVLDLSSNRLNRAPQPDELP  294 (310)
T ss_dssp             TTSCCCCCCCSC-CSSCCCCTTCCCEECCSSCCCS--------------CCSCCC--SCCSCEECCSCCCCSCCCTTSCC
T ss_pred             CCCCCCccchhh-HHhccCcCcCCEEECCCCCCCc--------------hhhhhc--CCCCEEECCCCcCCCCchhhhCC
Confidence            999887766776 5666   699999999999873              223332  79999999999999886644889


Q ss_pred             CCCeEEEEeCC
Q 003090          452 NLTSFSIAIGD  462 (848)
Q Consensus       452 ~L~~L~l~~~~  462 (848)
                      +|+.|++..+.
T Consensus       295 ~L~~L~L~~N~  305 (310)
T 4glp_A          295 EVDNLTLDGNP  305 (310)
T ss_dssp             CCSCEECSSTT
T ss_pred             CccEEECcCCC
Confidence            99999987544

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=99.57  E-value=1.2e-15  Score=166.07  Aligned_cols=198  Identities=17%  Similarity=0.120  Sum_probs=117.7

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcc-----cCCcc-cccccceeecccCcCcc----cChHH------HccCCceeEE
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHE-----VPDEL-ECPKLQALFLQENSPLA----IPDRF------FQGMKDLQVL  284 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~-----lp~~~-~~~~L~~L~l~~~~~~~----~~~~~------~~~~~~Lr~L  284 (848)
                      ++..+...+.....++.|++++|.+..     ++..+ .+++|++|++++|.+..    +|..+      +..+++|++|
T Consensus        20 ~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~~~~~~l~~~~~~~~~~l~~~l~~~~~L~~L   99 (386)
T 2ca6_A           20 DEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTV   99 (386)
T ss_dssp             HHHTTSHHHHHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEE
T ss_pred             HHHHHHHHHhcCCCccEEECCCCCCCHHHHHHHHHHHHhCCCccEEeCcccccCccccchhHHHHHHHHHHhhCCcccEE
Confidence            344555555556667777777777663     22223 56777777777764432    23332      3567777777


Q ss_pred             EccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-----hhhccc---------cCCCEEE
Q 003090          285 DLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-----SLIGEL---------SGLEILD  350 (848)
Q Consensus       285 ~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-----~~i~~l---------~~L~~L~  350 (848)
                      ++++              +.+.......+|..+..+++|++|++++|.+....     ..+..+         ++|++|+
T Consensus       100 ~Ls~--------------n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~  165 (386)
T 2ca6_A          100 RLSD--------------NAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSII  165 (386)
T ss_dssp             ECCS--------------CCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEE
T ss_pred             ECCC--------------CcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEE
Confidence            7777              55555211125566677777777777777654321     223333         6777777


Q ss_pred             ccCCCCc--ccC---hhhccCCcccEEeccCCcccc-----ccChhhhhccccccEEeccccccccccccccccccCccc
Q 003090          351 LSESDVS--EIP---VSFGRLSHLRLLDLTGCYILE-----LIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA  420 (848)
Q Consensus       351 l~~~~l~--~lp---~~i~~L~~L~~L~l~~~~~~~-----~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~  420 (848)
                      +++|.+.  .+|   ..+..+++|++|++++|....     ..|.. +.++++|+.|++++|.+...         ....
T Consensus       166 L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~-l~~~~~L~~L~Ls~n~l~~~---------g~~~  235 (386)
T 2ca6_A          166 CGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEG-LAYCQELKVLDLQDNTFTHL---------GSSA  235 (386)
T ss_dssp             CCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTT-GGGCTTCCEEECCSSCCHHH---------HHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHH-hhcCCCccEEECcCCCCCcH---------HHHH
Confidence            7777765  344   356667777777777765431     12213 56777777777777766421         0112


Q ss_pred             chhhhcccCCCcEEEeeccCCC
Q 003090          421 KFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       421 ~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      .+..+..+++|+.|++++|.+.
T Consensus       236 l~~~l~~~~~L~~L~L~~n~i~  257 (386)
T 2ca6_A          236 LAIALKSWPNLRELGLNDCLLS  257 (386)
T ss_dssp             HHHHGGGCTTCCEEECTTCCCC
T ss_pred             HHHHHccCCCcCEEECCCCCCc
Confidence            4456667777777777777654

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=99.57  E-value=2e-14  Score=153.87  Aligned_cols=250  Identities=15%  Similarity=0.122  Sum_probs=157.1

Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      |..++.+.. ++++.+++++...|..+  ..++++|++++|+|+.+|. .+.++++|++|++++|...+.+|.+.+.+++
T Consensus         3 p~~~C~C~~-~~v~C~~~~Lt~iP~~l--~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~   79 (350)
T 4ay9_X            3 HHRICHCSN-RVFLCQESKVTEIPSDL--PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLP   79 (350)
T ss_dssp             CCSSSEEET-TEEEEESTTCCSCCTTC--CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCT
T ss_pred             CCCccEeeC-CEEEecCCCCCccCcCc--CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcch
Confidence            444444543 56777777777777655  3678999999999998886 4788999999999998877778877678888


Q ss_pred             cccEE-eccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcc
Q 003090          393 KLEEL-YMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDF  471 (848)
Q Consensus       393 ~L~~L-~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l  471 (848)
                      +|+++ .+.+|.+...             .+..++.+++|+.|++++|.+..++.......                   
T Consensus        80 ~l~~~l~~~~N~l~~l-------------~~~~f~~l~~L~~L~l~~n~l~~~~~~~~~~~-------------------  127 (350)
T 4ay9_X           80 KLHEIRIEKANNLLYI-------------NPEAFQNLPNLQYLLISNTGIKHLPDVHKIHS-------------------  127 (350)
T ss_dssp             TCCEEEEEEETTCCEE-------------CTTSBCCCTTCCEEEEEEECCSSCCCCTTCCB-------------------
T ss_pred             hhhhhhcccCCccccc-------------CchhhhhccccccccccccccccCCchhhccc-------------------
Confidence            87764 4455666544             34567888888888888888776654321111                   


Q ss_pred             cceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeecc
Q 003090          472 IGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLN  551 (848)
Q Consensus       472 ~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~  551 (848)
                                                                                   .++..|.+.++..++.++.
T Consensus       128 -------------------------------------------------------------~~l~~l~l~~~~~i~~l~~  146 (350)
T 4ay9_X          128 -------------------------------------------------------------LQKVLLDIQDNINIHTIER  146 (350)
T ss_dssp             -------------------------------------------------------------SSCEEEEEESCTTCCEECT
T ss_pred             -------------------------------------------------------------chhhhhhhccccccccccc
Confidence                                                                         2223333333333332210


Q ss_pred             ccccccccc-CCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCcee
Q 003090          552 SLERTLRVT-LHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVS  630 (848)
Q Consensus       552 ~~~~~~~~~-~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~  630 (848)
                      .    .... ...|+.|+++++ +++.+..+.   ...++|++|.+.++..+ +.+|...+..+++|++|+++++ .++.
T Consensus       147 ~----~f~~~~~~l~~L~L~~N-~i~~i~~~~---f~~~~L~~l~l~~~n~l-~~i~~~~f~~l~~L~~LdLs~N-~l~~  216 (350)
T 4ay9_X          147 N----SFVGLSFESVILWLNKN-GIQEIHNSA---FNGTQLDELNLSDNNNL-EELPNDVFHGASGPVILDISRT-RIHS  216 (350)
T ss_dssp             T----SSTTSBSSCEEEECCSS-CCCEECTTS---STTEEEEEEECTTCTTC-CCCCTTTTTTEECCSEEECTTS-CCCC
T ss_pred             c----chhhcchhhhhhccccc-cccCCChhh---ccccchhHHhhccCCcc-cCCCHHHhccCcccchhhcCCC-CcCc
Confidence            0    0111 134555555555 344331111   12356677777776777 7777655567777888888776 4666


Q ss_pred             eeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeec
Q 003090          631 VFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEE  684 (848)
Q Consensus       631 ~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~  684 (848)
                      +|.           ..|.+|+.|.+.++.+++.+|.    +..+++|+.+++.+
T Consensus       217 lp~-----------~~~~~L~~L~~l~~~~l~~lP~----l~~l~~L~~l~l~~  255 (350)
T 4ay9_X          217 LPS-----------YGLENLKKLRARSTYNLKKLPT----LEKLVALMEASLTY  255 (350)
T ss_dssp             CCS-----------SSCTTCCEEECTTCTTCCCCCC----TTTCCSCCEEECSC
T ss_pred             cCh-----------hhhccchHhhhccCCCcCcCCC----chhCcChhhCcCCC
Confidence            642           2467777777777777777763    45677888877753

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.56  E-value=2.6e-14  Score=145.18  Aligned_cols=173  Identities=22%  Similarity=0.293  Sum_probs=147.6

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      ...++++++++.+..+|..+   .++++.|++++              +.+...    .+..+..+++|++|++++|.+.
T Consensus        14 ~~~~~l~~~~~~l~~~p~~~---~~~l~~L~L~~--------------n~l~~~----~~~~~~~l~~L~~L~L~~n~l~   72 (251)
T 3m19_A           14 EGKKEVDCQGKSLDSVPSGI---PADTEKLDLQS--------------TGLATL----SDATFRGLTKLTWLNLDYNQLQ   72 (251)
T ss_dssp             GGGTEEECTTCCCSSCCSCC---CTTCCEEECTT--------------SCCCCC----CTTTTTTCTTCCEEECTTSCCC
T ss_pred             CCCeEEecCCCCccccCCCC---CCCCCEEEccC--------------CCcCcc----CHhHhcCcccCCEEECCCCcCC
Confidence            56788999999999999764   36899999999              888884    5567999999999999999888


Q ss_pred             CCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccc
Q 003090          335 GDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESES  412 (848)
Q Consensus       335 ~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~  412 (848)
                      ..+ ..+..+++|++|++++|.++.+|. .+..+++|++|++++|.+. .+|...+..+++|++|++++|.+...     
T Consensus        73 ~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~l~~L~~L~Ls~N~l~~~-----  146 (251)
T 3m19_A           73 TLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDKLYLGGNQLK-SLPSGVFDRLTKLKELRLNTNQLQSI-----  146 (251)
T ss_dssp             CCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCTTCCEEECCSSCCCCC-----
T ss_pred             ccCHhHhccCCcCCEEECCCCcccccChhHhcccCCCCEEEcCCCcCC-CcChhHhccCCcccEEECcCCcCCcc-----
Confidence            876 568999999999999999998875 4689999999999998664 57766578999999999999988754     


Q ss_pred             ccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCC
Q 003090          413 EEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGD  462 (848)
Q Consensus       413 ~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~  462 (848)
                              .+..++.+++|+.|++++|.+..++...  .+++|+.|++..+.
T Consensus       147 --------~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~  190 (251)
T 3m19_A          147 --------PAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQ  190 (251)
T ss_dssp             --------CTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCC
T ss_pred             --------CHHHcCcCcCCCEEECCCCcCCccCHHHHhCCCCCCEEEeeCCc
Confidence                    3346889999999999999999888754  78999999987554

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.56  E-value=1.3e-14  Score=154.84  Aligned_cols=130  Identities=23%  Similarity=0.156  Sum_probs=101.4

Q ss_pred             CceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhc--ccCcEEEccCccccCCchhhccccCCCEEEccCCCC
Q 003090          279 KDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFL--INLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDV  356 (848)
Q Consensus       279 ~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l--~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l  356 (848)
                      ..++.+++++              +.+.       |..+..+  .++++|+++++.+...++.+..+++|++|++++|.+
T Consensus        47 ~~~~~l~l~~--------------~~~~-------~~~~~~~~~~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~~l  105 (336)
T 2ast_B           47 SLWQTLDLTG--------------KNLH-------PDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVI  105 (336)
T ss_dssp             TTSSEEECTT--------------CBCC-------HHHHHHHHHTTCSEEECTTCEECSCCCSCCCCBCCCEEECTTCEE
T ss_pred             hhheeecccc--------------ccCC-------HHHHHhhhhccceEEEcCCccccccchhhccCCCCCEEEccCCCc
Confidence            3478888888              5543       3557777  889999999998887777788899999999999988


Q ss_pred             c-c-cChhhccCCcccEEeccCCccccccChhhhhccccccEEecccc-ccccccccccccccCcccchhhhcccCCCcE
Q 003090          357 S-E-IPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS-FRHWQFESESEEDSSSNAKFIELGALSRLTS  433 (848)
Q Consensus       357 ~-~-lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~-~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~  433 (848)
                      . . +|..+.++++|++|++++|......+.. ++++++|++|++++| .+...            ..+..+..+++|++
T Consensus       106 ~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~-l~~~~~L~~L~L~~~~~l~~~------------~l~~~~~~~~~L~~  172 (336)
T 2ast_B          106 EVSTLHGILSQCSKLQNLSLEGLRLSDPIVNT-LAKNSNLVRLNLSGCSGFSEF------------ALQTLLSSCSRLDE  172 (336)
T ss_dssp             CHHHHHHHHTTBCCCSEEECTTCBCCHHHHHH-HTTCTTCSEEECTTCBSCCHH------------HHHHHHHHCTTCCE
T ss_pred             CHHHHHHHHhhCCCCCEEeCcCcccCHHHHHH-HhcCCCCCEEECCCCCCCCHH------------HHHHHHhcCCCCCE
Confidence            7 2 7888889999999999998766666666 788999999999988 44431            13455778888888


Q ss_pred             EEeecc-CCC
Q 003090          434 LHIHIP-EGK  442 (848)
Q Consensus       434 L~l~~~-~~~  442 (848)
                      |++++| .++
T Consensus       173 L~l~~~~~l~  182 (336)
T 2ast_B          173 LNLSWCFDFT  182 (336)
T ss_dssp             EECCCCTTCC
T ss_pred             EcCCCCCCcC
Confidence            888877 543

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=99.56  E-value=1.1e-14  Score=155.79  Aligned_cols=179  Identities=16%  Similarity=0.124  Sum_probs=113.7

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC-
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP-  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp-  314 (848)
                      +.++.+++.++++|..+ .+++++|++++|.+..+|...|.++++|++|+|++              |.+.+.    +| 
T Consensus        12 ~~v~C~~~~Lt~iP~~l-~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~--------------N~i~~~----i~~   72 (350)
T 4ay9_X           12 RVFLCQESKVTEIPSDL-PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQ--------------NDVLEV----IEA   72 (350)
T ss_dssp             TEEEEESTTCCSCCTTC-CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEEC--------------CTTCCE----ECT
T ss_pred             CEEEecCCCCCccCcCc-CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcC--------------CCCCCc----cCh
Confidence            45667777888888766 35788888888888888877778888888888888              665442    43 


Q ss_pred             chhhhcccCcE-EEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhcc
Q 003090          315 SSLSFLINLRT-LRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRL  391 (848)
Q Consensus       315 ~~~~~l~~L~~-L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l  391 (848)
                      ..|.++++|+. +.+.+|++...+ ..+..+++|++|++++|.+..+|. .+....++..|++.++.....+|...+..+
T Consensus        73 ~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~  152 (350)
T 4ay9_X           73 DVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGL  152 (350)
T ss_dssp             TSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTS
T ss_pred             hHhhcchhhhhhhcccCCcccccCchhhhhccccccccccccccccCCchhhcccchhhhhhhccccccccccccchhhc
Confidence            34567776654 445555555554 556777788888888777776654 344555677777766555666665444444


Q ss_pred             c-cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeec-cCCCCCCCC
Q 003090          392 R-KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHI-PEGKIMPSD  447 (848)
Q Consensus       392 ~-~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~-~~~~~~~~~  447 (848)
                      . .++.|++++|.+...              +.......+|+.|++.+ |.++.+|..
T Consensus       153 ~~~l~~L~L~~N~i~~i--------------~~~~f~~~~L~~l~l~~~n~l~~i~~~  196 (350)
T 4ay9_X          153 SFESVILWLNKNGIQEI--------------HNSAFNGTQLDELNLSDNNNLEELPND  196 (350)
T ss_dssp             BSSCEEEECCSSCCCEE--------------CTTSSTTEEEEEEECTTCTTCCCCCTT
T ss_pred             chhhhhhccccccccCC--------------ChhhccccchhHHhhccCCcccCCCHH
Confidence            3 466677777666532              22223334566666653 445555543

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=99.55  E-value=5.8e-16  Score=168.65  Aligned_cols=171  Identities=18%  Similarity=0.170  Sum_probs=107.0

Q ss_pred             ccCCcc-cccccceeecccCcCcccChH----HHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchh----
Q 003090          247 EVPDEL-ECPKLQALFLQENSPLAIPDR----FFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL----  317 (848)
Q Consensus       247 ~lp~~~-~~~~L~~L~l~~~~~~~~~~~----~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~----  317 (848)
                      .++..+ .+++|++|++++|.++.....    .+..+++|++|++++|...           .+.+.    +|..+    
T Consensus        23 ~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~~~~~-----------~l~~~----~~~~~~~l~   87 (386)
T 2ca6_A           23 SVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTG-----------RVKDE----IPEALRLLL   87 (386)
T ss_dssp             TTSHHHHHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTT-----------SCGGG----SHHHHHHHH
T ss_pred             HHHHHHhcCCCccEEECCCCCCCHHHHHHHHHHHHhCCCccEEeCcccccC-----------ccccc----hhHHHHHHH
Confidence            455555 678888888888866543221    2457888888888884221           12211    33333    


Q ss_pred             ---hhcccCcEEEccCccccCC-----chhhccccCCCEEEccCCCCc-----ccChhhccC---------CcccEEecc
Q 003090          318 ---SFLINLRTLRLHDRRIQGD-----LSLIGELSGLEILDLSESDVS-----EIPVSFGRL---------SHLRLLDLT  375 (848)
Q Consensus       318 ---~~l~~L~~L~L~~~~~~~~-----~~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L---------~~L~~L~l~  375 (848)
                         ..+++|++|++++|.+...     +..+.++++|++|++++|.+.     .++..+..+         ++|++|+++
T Consensus        88 ~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~  167 (386)
T 2ca6_A           88 QALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICG  167 (386)
T ss_dssp             HHHTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECC
T ss_pred             HHHhhCCcccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECC
Confidence               5778888888888876652     256777888888888888776     233334444         778888888


Q ss_pred             CCccc-cccCh--hhhhccccccEEeccccccccccccccccccCcccchh-hhcccCCCcEEEeeccCC
Q 003090          376 GCYIL-ELIPR--GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFI-ELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       376 ~~~~~-~~~p~--~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~-~L~~l~~L~~L~l~~~~~  441 (848)
                      +|... ..+|.  ..+..+++|++|++++|.+...         ...+... .+..+++|+.|++++|.+
T Consensus       168 ~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~---------g~~~l~~~~l~~~~~L~~L~Ls~n~l  228 (386)
T 2ca6_A          168 RNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPE---------GIEHLLLEGLAYCQELKVLDLQDNTF  228 (386)
T ss_dssp             SSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHH---------HHHHHHHTTGGGCTTCCEEECCSSCC
T ss_pred             CCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHh---------HHHHHHHHHhhcCCCccEEECcCCCC
Confidence            77654 33441  1256777888888887766521         0001222 567777788888777765

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.54  E-value=5.5e-15  Score=157.73  Aligned_cols=194  Identities=21%  Similarity=0.209  Sum_probs=142.7

Q ss_pred             cCCCceeeecCCCcccCCcc-cccccceeecccCcCccc-ChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAI-PDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~-~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      ..++.+++++|.+...+... .+++|++|++++|.+... ....+..+++|++|++++              +.+...  
T Consensus        70 ~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~--------------~~l~~~--  133 (336)
T 2ast_B           70 QGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEG--------------LRLSDP--  133 (336)
T ss_dssp             TTCSEEECTTCEECSCCCSCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTT--------------CBCCHH--
T ss_pred             ccceEEEcCCccccccchhhccCCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcC--------------cccCHH--
Confidence            46788889998888666555 889999999999876542 333468899999999998              666654  


Q ss_pred             CCCCchhhhcccCcEEEccCcc-ccC--CchhhccccCCCEEEccCC-CCcc--cChhhccCC-cccEEeccCCc--cc-
Q 003090          311 FLLPSSLSFLINLRTLRLHDRR-IQG--DLSLIGELSGLEILDLSES-DVSE--IPVSFGRLS-HLRLLDLTGCY--IL-  380 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~-~~~--~~~~i~~l~~L~~L~l~~~-~l~~--lp~~i~~L~-~L~~L~l~~~~--~~-  380 (848)
                        .|..++.+++|++|++++|. +..  .+..+.++++|++|++++| .++.  +|..+..++ +|++|++++|.  .. 
T Consensus       134 --~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~  211 (336)
T 2ast_B          134 --IVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQK  211 (336)
T ss_dssp             --HHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCH
T ss_pred             --HHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCH
Confidence              67778889999999999984 443  2355788999999999999 8883  677788899 99999999884  33 


Q ss_pred             cccChhhhhccccccEEeccccc-cccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC---CC-ccCCCCe
Q 003090          381 ELIPRGVLSRLRKLEELYMSHSF-RHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS---DM-SFQNLTS  455 (848)
Q Consensus       381 ~~~p~~~l~~l~~L~~L~l~~~~-~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~---~~-~~~~L~~  455 (848)
                      ..+|.. +.++++|++|++++|. ++..             .+..+..+++|+.|++++|. ...+.   .+ .+++|+.
T Consensus       212 ~~l~~~-~~~~~~L~~L~l~~~~~l~~~-------------~~~~l~~l~~L~~L~l~~~~-~~~~~~~~~l~~~~~L~~  276 (336)
T 2ast_B          212 SDLSTL-VRRCPNLVHLDLSDSVMLKND-------------CFQEFFQLNYLQHLSLSRCY-DIIPETLLELGEIPTLKT  276 (336)
T ss_dssp             HHHHHH-HHHCTTCSEEECTTCTTCCGG-------------GGGGGGGCTTCCEEECTTCT-TCCGGGGGGGGGCTTCCE
T ss_pred             HHHHHH-HhhCCCCCEEeCCCCCcCCHH-------------HHHHHhCCCCCCEeeCCCCC-CCCHHHHHHHhcCCCCCE
Confidence            345554 6889999999999887 4433             45677888999999998885 11111   12 4555555


Q ss_pred             EEEE
Q 003090          456 FSIA  459 (848)
Q Consensus       456 L~l~  459 (848)
                      |++.
T Consensus       277 L~l~  280 (336)
T 2ast_B          277 LQVF  280 (336)
T ss_dssp             EECT
T ss_pred             Eecc
Confidence            5554

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.54  E-value=4.5e-14  Score=141.00  Aligned_cols=151  Identities=25%  Similarity=0.338  Sum_probs=123.4

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      .++++.+++.+..+|..+. ++|++|++++|.+..++...|.++++|++|++++              +.+..     +|
T Consensus        21 ~~~v~c~~~~l~~ip~~~~-~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~--------------N~l~~-----i~   80 (229)
T 3e6j_A           21 GTTVDCRSKRHASVPAGIP-TNAQILYLHDNQITKLEPGVFDSLINLKELYLGS--------------NQLGA-----LP   80 (229)
T ss_dssp             TTEEECTTSCCSSCCSCCC-TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCS--------------SCCCC-----CC
T ss_pred             CCEeEccCCCcCccCCCCC-CCCCEEEcCCCccCccCHHHhhCccCCcEEECCC--------------CCCCC-----cC
Confidence            3568888888998887665 7899999999988888776778899999999999              77876     55


Q ss_pred             -chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          315 -SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       315 -~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                       ..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|..+..+++|++|++++|.+. .+|...+..++
T Consensus        81 ~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~l~  159 (229)
T 3e6j_A           81 VGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQNQLK-SIPHGAFDRLS  159 (229)
T ss_dssp             TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCSCCTTGGGCTTCSEEECCSSCCC-CCCTTTTTTCT
T ss_pred             hhhcccCCCcCEEECCCCcCCccChhHhCcchhhCeEeccCCcccccCcccccCCCCCEEECCCCcCC-ccCHHHHhCCC
Confidence             44688899999999999887776 4568899999999999999989888888999999999987654 56655578888


Q ss_pred             cccEEecccccccc
Q 003090          393 KLEELYMSHSFRHW  406 (848)
Q Consensus       393 ~L~~L~l~~~~~~~  406 (848)
                      +|+.|++.+|.+..
T Consensus       160 ~L~~L~l~~N~~~c  173 (229)
T 3e6j_A          160 SLTHAYLFGNPWDC  173 (229)
T ss_dssp             TCCEEECTTSCBCT
T ss_pred             CCCEEEeeCCCccC
Confidence            88888888887653

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.54  E-value=2.9e-14  Score=162.53  Aligned_cols=168  Identities=28%  Similarity=0.335  Sum_probs=96.3

Q ss_pred             CCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       235 l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      ++.|++++|.+..+|....+++|+.|+|++|.+..+++  +..+++|+.|+|++              +.+..     +|
T Consensus        45 L~~L~l~~n~i~~l~~l~~l~~L~~L~Ls~N~l~~~~~--l~~l~~L~~L~Ls~--------------N~l~~-----l~  103 (605)
T 1m9s_A           45 IDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKP--LTNLKNLGWLFLDE--------------NKIKD-----LS  103 (605)
T ss_dssp             CCCCBCTTCCCCCCTTGGGCTTCCEEECTTSCCCCCGG--GGGCTTCCEEECCS--------------SCCCC-----CT
T ss_pred             CCEEECcCCCCCCChHHccCCCCCEEEeeCCCCCCChh--hccCCCCCEEECcC--------------CCCCC-----Ch
Confidence            45566666666665543356666666666666555554  45666666666666              55554     43


Q ss_pred             chhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                       .+..+++|++|+|++|.+.. ++.+..+++|+.|+|++|.++.+ ..+..+++|++|++++|.+.. +++  +..+++|
T Consensus       104 -~l~~l~~L~~L~Ls~N~l~~-l~~l~~l~~L~~L~Ls~N~l~~l-~~l~~l~~L~~L~Ls~N~l~~-~~~--l~~l~~L  177 (605)
T 1m9s_A          104 -SLKDLKKLKSLSLEHNGISD-INGLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDNQISD-IVP--LAGLTKL  177 (605)
T ss_dssp             -TSTTCTTCCEEECTTSCCCC-CGGGGGCTTCSEEECCSSCCCCC-GGGGSCTTCSEEECCSSCCCC-CGG--GTTCTTC
T ss_pred             -hhccCCCCCEEEecCCCCCC-CccccCCCccCEEECCCCccCCc-hhhcccCCCCEEECcCCcCCC-chh--hccCCCC
Confidence             45566666666666664443 34456666666666666666655 355666666666666654433 332  4566666


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCC
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIM  444 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~  444 (848)
                      +.|++++|.+..               +..+..+++|+.|++++|.+...
T Consensus       178 ~~L~Ls~N~i~~---------------l~~l~~l~~L~~L~L~~N~l~~~  212 (605)
T 1m9s_A          178 QNLYLSKNHISD---------------LRALAGLKNLDVLELFSQECLNK  212 (605)
T ss_dssp             CEEECCSSCCCB---------------CGGGTTCTTCSEEECCSEEEECC
T ss_pred             CEEECcCCCCCC---------------ChHHccCCCCCEEEccCCcCcCC
Confidence            666666665542               13455566666666666655443

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.54  E-value=4.9e-14  Score=160.60  Aligned_cols=184  Identities=22%  Similarity=0.261  Sum_probs=155.3

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchh
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL  317 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~  317 (848)
                      +.+..+.+..+.....+++|+.|++++|.+..++.  +..+++|+.|+|++              +.+..     +|. +
T Consensus        26 l~l~~~~i~~~~~~~~L~~L~~L~l~~n~i~~l~~--l~~l~~L~~L~Ls~--------------N~l~~-----~~~-l   83 (605)
T 1m9s_A           26 DNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQG--IQYLPNVTKLFLNG--------------NKLTD-----IKP-L   83 (605)
T ss_dssp             HHTTCSCTTSEECHHHHTTCCCCBCTTCCCCCCTT--GGGCTTCCEEECTT--------------SCCCC-----CGG-G
T ss_pred             HhccCCCcccccchhcCCCCCEEECcCCCCCCChH--HccCCCCCEEEeeC--------------CCCCC-----Chh-h
Confidence            34455666666655588999999999999988875  68999999999999              88888     665 9


Q ss_pred             hhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEE
Q 003090          318 SFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEEL  397 (848)
Q Consensus       318 ~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L  397 (848)
                      ..+++|++|+|++|.+.. ++.+..+++|++|++++|.+..+| .+..+++|+.|++++|.... ++ . +..+++|+.|
T Consensus        84 ~~l~~L~~L~Ls~N~l~~-l~~l~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~Ls~N~l~~-l~-~-l~~l~~L~~L  158 (605)
T 1m9s_A           84 TNLKNLGWLFLDENKIKD-LSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKITD-IT-V-LSRLTKLDTL  158 (605)
T ss_dssp             GGCTTCCEEECCSSCCCC-CTTSTTCTTCCEEECTTSCCCCCG-GGGGCTTCSEEECCSSCCCC-CG-G-GGSCTTCSEE
T ss_pred             ccCCCCCEEECcCCCCCC-ChhhccCCCCCEEEecCCCCCCCc-cccCCCccCEEECCCCccCC-ch-h-hcccCCCCEE
Confidence            999999999999997655 558999999999999999999875 68999999999999987654 53 3 8999999999


Q ss_pred             eccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCC
Q 003090          398 YMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL  463 (848)
Q Consensus       398 ~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~  463 (848)
                      ++++|.+...              +. +..+++|+.|+|++|.+..++....+++|+.|++..+..
T Consensus       159 ~Ls~N~l~~~--------------~~-l~~l~~L~~L~Ls~N~i~~l~~l~~l~~L~~L~L~~N~l  209 (605)
T 1m9s_A          159 SLEDNQISDI--------------VP-LAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQEC  209 (605)
T ss_dssp             ECCSSCCCCC--------------GG-GTTCTTCCEEECCSSCCCBCGGGTTCTTCSEEECCSEEE
T ss_pred             ECcCCcCCCc--------------hh-hccCCCCCEEECcCCCCCCChHHccCCCCCEEEccCCcC
Confidence            9999988653              22 889999999999999999886433889999999986554

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.54  E-value=2.8e-14  Score=140.44  Aligned_cols=172  Identities=24%  Similarity=0.362  Sum_probs=139.1

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ++++.+++.+..+|..+ .+++++|++++|.+..++...|..+++|++|++++              +.+..     +|.
T Consensus        10 ~~v~c~~~~l~~~p~~~-~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~--------------n~l~~-----~~~   69 (208)
T 2o6s_A           10 TTVECYSQGRTSVPTGI-PAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGG--------------NKLQS-----LPN   69 (208)
T ss_dssp             TEEECCSSCCSSCCSCC-CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCS--------------SCCCC-----CCT
T ss_pred             CEEEecCCCccCCCCCC-CCCCcEEEcCCCccCcCChhhhcccccCcEEECCC--------------CccCc-----cCh
Confidence            46777888888888766 36899999999999889888888999999999999              78877     544


Q ss_pred             -hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccc
Q 003090          316 -SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       316 -~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                       .+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|.. +.++++|++|++++|... .+|...+..++
T Consensus        70 ~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~-~~~~~~~~~l~  148 (208)
T 2o6s_A           70 GVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLK-SVPDGVFDRLT  148 (208)
T ss_dssp             TTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCS-CCCTTTTTTCT
T ss_pred             hhcCCCCCcCEEECCCCcCCccCHhHhcCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCCCccc-eeCHHHhccCC
Confidence             4688999999999999888776 4578999999999999999988765 688999999999998665 46665578899


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC-CCCCCC
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK-IMPSDM  448 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~-~~~~~~  448 (848)
                      +|+.|++++|.+..                    .+++|+.|+++.|.+. .+|.++
T Consensus       149 ~L~~L~l~~N~~~~--------------------~~~~l~~L~~~~n~~~g~ip~~~  185 (208)
T 2o6s_A          149 SLQYIWLHDNPWDC--------------------TCPGIRYLSEWINKHSGVVRNSA  185 (208)
T ss_dssp             TCCEEECCSCCBCC--------------------CTTTTHHHHHHHHHCTTTBBCTT
T ss_pred             CccEEEecCCCeec--------------------CCCCHHHHHHHHHhCCceeeccC
Confidence            99999999986542                    3457788888777655 455443

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.53  E-value=3.2e-14  Score=138.56  Aligned_cols=151  Identities=18%  Similarity=0.203  Sum_probs=106.6

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+++|++|++++|.+..+|.  +..+++|++|++++              +.+..     + ..+..+++|++|++++|.
T Consensus        42 ~l~~L~~L~l~~n~i~~l~~--l~~l~~L~~L~l~~--------------n~~~~-----~-~~l~~l~~L~~L~l~~n~   99 (197)
T 4ezg_A           42 QMNSLTYITLANINVTDLTG--IEYAHNIKDLTINN--------------IHATN-----Y-NPISGLSNLERLRIMGKD   99 (197)
T ss_dssp             HHHTCCEEEEESSCCSCCTT--GGGCTTCSEEEEES--------------CCCSC-----C-GGGTTCTTCCEEEEECTT
T ss_pred             hcCCccEEeccCCCccChHH--HhcCCCCCEEEccC--------------CCCCc-----c-hhhhcCCCCCEEEeECCc
Confidence            56677777777777777762  56777888888877              55543     3 357777788888888876


Q ss_pred             ccC-CchhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccc
Q 003090          333 IQG-DLSLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFES  410 (848)
Q Consensus       333 ~~~-~~~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~  410 (848)
                      +.. .+..++.+++|++|++++|.++ ..|..++.+++|++|++++|...+.+|.  +..+++|++|++++|.+...   
T Consensus       100 l~~~~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~~--l~~l~~L~~L~l~~n~i~~~---  174 (197)
T 4ezg_A          100 VTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIMP--LKTLPELKSLNIQFDGVHDY---  174 (197)
T ss_dssp             CBGGGSCCCTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCGG--GGGCSSCCEEECTTBCCCCC---
T ss_pred             cCcccChhhcCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccHh--hcCCCCCCEEECCCCCCcCh---
Confidence            665 3466777888888888888777 3566777788888888888765566663  67788888888887776532   


Q ss_pred             ccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          411 ESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       411 ~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                                  ..+..+++|+.|++++|.+.
T Consensus       175 ------------~~l~~l~~L~~L~l~~N~i~  194 (197)
T 4ezg_A          175 ------------RGIEDFPKLNQLYAFSQTIG  194 (197)
T ss_dssp             ------------TTGGGCSSCCEEEECBC---
T ss_pred             ------------HHhccCCCCCEEEeeCcccC
Confidence                        25677778888888877654

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.53  E-value=4.1e-14  Score=140.21  Aligned_cols=150  Identities=23%  Similarity=0.324  Sum_probs=119.4

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.++++++.++.+|..+. ++++.|++++|.+..++...|..+++|++|++++              +.+...    .|.
T Consensus        14 ~~v~c~~~~l~~iP~~l~-~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~--------------N~i~~~----~~~   74 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNLP-ETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSN--------------NQISEL----APD   74 (220)
T ss_dssp             TEEECTTSCCSSCCSSCC-TTCCEEECCSSCCCEECTTSSTTCTTCCEEECCS--------------SCCCEE----CTT
T ss_pred             CEEEcCCCCcCcCCCccC-cCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCC--------------CcCCCc----CHH
Confidence            457788888888887665 6889999999988888877778888999999998              777774    477


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      .+..+++|++|+|++|.+...+ ..+..+++|++|++++|.++.+ |..+..+++|++|++++|.+.. ++.+.+..+++
T Consensus        75 ~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~-~~~~~~~~l~~  153 (220)
T 2v9t_B           75 AFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQT-IAKGTFSPLRA  153 (220)
T ss_dssp             TTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSC-CCTTTTTTCTT
T ss_pred             HhhCCcCCCEEECCCCcCCccCHhHccCCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCCCcCCE-ECHHHHhCCCC
Confidence            8888888999999988887776 4467888888888888888866 4567888888888888876544 55444778888


Q ss_pred             ccEEeccccccc
Q 003090          394 LEELYMSHSFRH  405 (848)
Q Consensus       394 L~~L~l~~~~~~  405 (848)
                      |+.|++++|.+.
T Consensus       154 L~~L~L~~N~~~  165 (220)
T 2v9t_B          154 IQTMHLAQNPFI  165 (220)
T ss_dssp             CCEEECCSSCEE
T ss_pred             CCEEEeCCCCcC
Confidence            888888887654

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.53  E-value=1e-14  Score=157.02  Aligned_cols=177  Identities=16%  Similarity=0.132  Sum_probs=103.2

Q ss_pred             eeeecCCCcccC-Ccccc-cccceeecccCcCcccCh----HHHccCC-ceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          238 ISLMFNDIHEVP-DELEC-PKLQALFLQENSPLAIPD----RFFQGMK-DLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       238 l~l~~n~l~~lp-~~~~~-~~L~~L~l~~~~~~~~~~----~~~~~~~-~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      +.++.|.+.... ..... ++|++|++++|.++..+.    ..+.+++ +|++|++++              +.+...  
T Consensus         3 ~~ls~n~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~--------------N~l~~~--   66 (362)
T 3goz_A            3 YKLTLHPGSNPVEEFTSIPHGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSG--------------NSLGFK--   66 (362)
T ss_dssp             EECCCCTTCCHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCS--------------SCGGGS--
T ss_pred             cccccccchHHHHHHHhCCCCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcC--------------CCCCHH--
Confidence            345666666333 33333 347777777777776665    4556676 777777777              666553  


Q ss_pred             CCCCchhhhc-----ccCcEEEccCccccCCc-hh----hccc-cCCCEEEccCCCCcccCh-h----hcc-CCcccEEe
Q 003090          311 FLLPSSLSFL-----INLRTLRLHDRRIQGDL-SL----IGEL-SGLEILDLSESDVSEIPV-S----FGR-LSHLRLLD  373 (848)
Q Consensus       311 ~~lp~~~~~l-----~~L~~L~L~~~~~~~~~-~~----i~~l-~~L~~L~l~~~~l~~lp~-~----i~~-L~~L~~L~  373 (848)
                        .+..+..+     ++|++|++++|.+.... ..    +..+ ++|++|++++|.++..+. .    +.. ..+|++|+
T Consensus        67 --~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~  144 (362)
T 3goz_A           67 --NSDELVQILAAIPANVTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLN  144 (362)
T ss_dssp             --CHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEE
T ss_pred             --HHHHHHHHHhccCCCccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEE
Confidence              34555554     77777777777666544 32    3333 677777777777765443 2    233 24777777


Q ss_pred             ccCCcccc----ccChhhhhccc-cccEEeccccccccccccccccccCcccchhhhccc-CCCcEEEeeccCCC
Q 003090          374 LTGCYILE----LIPRGVLSRLR-KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGAL-SRLTSLHIHIPEGK  442 (848)
Q Consensus       374 l~~~~~~~----~~p~~~l~~l~-~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l-~~L~~L~l~~~~~~  442 (848)
                      +++|....    .++.. +..++ +|++|++++|.+....+         .+....+... ++|+.|++++|.+.
T Consensus       145 Ls~N~l~~~~~~~l~~~-l~~~~~~L~~L~Ls~n~l~~~~~---------~~l~~~l~~~~~~L~~L~Ls~N~i~  209 (362)
T 3goz_A          145 LRGNDLGIKSSDELIQI-LAAIPANVNSLNLRGNNLASKNC---------AELAKFLASIPASVTSLDLSANLLG  209 (362)
T ss_dssp             CTTSCGGGSCHHHHHHH-HHTSCTTCCEEECTTSCGGGSCH---------HHHHHHHHTSCTTCCEEECTTSCGG
T ss_pred             ccCCcCCHHHHHHHHHH-HhcCCccccEeeecCCCCchhhH---------HHHHHHHHhCCCCCCEEECCCCCCC
Confidence            77765543    22232 34444 77777777776654310         1122234444 47777777776544

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.52  E-value=5.5e-14  Score=139.32  Aligned_cols=151  Identities=17%  Similarity=0.245  Sum_probs=113.3

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCccc-ChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAI-PDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~-~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      +.+++++|.++.+|..+ .+.+++|++++|.+..+ +..+|..+++|++|++++              +.+...    .+
T Consensus        14 ~~l~~s~n~l~~iP~~~-~~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~--------------N~i~~i----~~   74 (220)
T 2v70_A           14 TTVDCSNQKLNKIPEHI-PQYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSN--------------NKITDI----EE   74 (220)
T ss_dssp             TEEECCSSCCSSCCSCC-CTTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCS--------------SCCCEE----CT
T ss_pred             CEeEeCCCCcccCccCC-CCCCCEEEcCCCcCCccCchhhhccCCCCCEEECCC--------------CcCCEE----CH
Confidence            46788888888888765 24567888888887777 345567888888888888              777763    33


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      ..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+ |..+..+++|++|++++|.+.+..|.. +..++
T Consensus        75 ~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~-~~~l~  153 (220)
T 2v70_A           75 GAFEGASGVNEILLTSNRLENVQHKMFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQITTVAPGA-FDTLH  153 (220)
T ss_dssp             TTTTTCTTCCEEECCSSCCCCCCGGGGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSCCCCBCTTT-TTTCT
T ss_pred             HHhCCCCCCCEEECCCCccCccCHhHhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCcCCEECHHH-hcCCC
Confidence            46888888888888888777766 4578888888888888888866 566778888888888887665544554 77888


Q ss_pred             cccEEecccccccc
Q 003090          393 KLEELYMSHSFRHW  406 (848)
Q Consensus       393 ~L~~L~l~~~~~~~  406 (848)
                      +|+.|++++|.+..
T Consensus       154 ~L~~L~L~~N~l~c  167 (220)
T 2v70_A          154 SLSTLNLLANPFNC  167 (220)
T ss_dssp             TCCEEECCSCCEEC
T ss_pred             CCCEEEecCcCCcC
Confidence            88888888877653

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.50  E-value=1.1e-13  Score=155.70  Aligned_cols=177  Identities=18%  Similarity=0.257  Sum_probs=147.9

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.|++++|.+..+|..+. ++|++|++++|.+..+|    ..+++|++|++++              |.+..     +
T Consensus        60 ~L~~L~Ls~n~L~~lp~~l~-~~L~~L~Ls~N~l~~ip----~~l~~L~~L~Ls~--------------N~l~~-----i  115 (571)
T 3cvr_A           60 QFSELQLNRLNLSSLPDNLP-PQITVLEITQNALISLP----ELPASLEYLDACD--------------NRLST-----L  115 (571)
T ss_dssp             TCSEEECCSSCCSCCCSCCC-TTCSEEECCSSCCSCCC----CCCTTCCEEECCS--------------SCCSC-----C
T ss_pred             CccEEEeCCCCCCccCHhHc-CCCCEEECcCCCCcccc----cccCCCCEEEccC--------------CCCCC-----c
Confidence            68899999999999998774 88999999999999998    3578999999999              88888     7


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      |. +..  +|++|++++|.+...+.   .+++|++|++++|.++.+|.   .+++|++|++++|.+.. +|.  +.  ++
T Consensus       116 p~-l~~--~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N~L~~-lp~--l~--~~  181 (571)
T 3cvr_A          116 PE-LPA--SLKHLDVDNNQLTMLPE---LPALLEYINADNNQLTMLPE---LPTSLEVLSVRNNQLTF-LPE--LP--ES  181 (571)
T ss_dssp             CC-CCT--TCCEEECCSSCCSCCCC---CCTTCCEEECCSSCCSCCCC---CCTTCCEEECCSSCCSC-CCC--CC--TT
T ss_pred             ch-hhc--CCCEEECCCCcCCCCCC---cCccccEEeCCCCccCcCCC---cCCCcCEEECCCCCCCC-cch--hh--CC
Confidence            77 655  99999999998887555   78999999999999999997   68899999999987654 887  45  89


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcc-----cCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeCCC
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGA-----LSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIGDL  463 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~-----l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~~  463 (848)
                      |+.|++++|.+...              +. +..     ...|+.|++++|.++.+|..+ .+++|+.|++..+..
T Consensus       182 L~~L~Ls~N~L~~l--------------p~-~~~~L~~~~~~L~~L~Ls~N~l~~lp~~l~~l~~L~~L~L~~N~l  242 (571)
T 3cvr_A          182 LEALDVSTNLLESL--------------PA-VPVRNHHSEETEIFFRCRENRITHIPENILSLDPTCTIILEDNPL  242 (571)
T ss_dssp             CCEEECCSSCCSSC--------------CC-CC--------CCEEEECCSSCCCCCCGGGGGSCTTEEEECCSSSC
T ss_pred             CCEEECcCCCCCch--------------hh-HHHhhhcccccceEEecCCCcceecCHHHhcCCCCCEEEeeCCcC
Confidence            99999999988732              22 332     223399999999999999887 899999999875543

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.50  E-value=1.2e-13  Score=134.53  Aligned_cols=149  Identities=20%  Similarity=0.237  Sum_probs=127.8

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.+++++|.+..+|....+++|++|++++|.+..++.  +..+++|++|++++              +.+...    
T Consensus        44 ~~L~~L~l~~n~i~~l~~l~~l~~L~~L~l~~n~~~~~~~--l~~l~~L~~L~l~~--------------n~l~~~----  103 (197)
T 4ezg_A           44 NSLTYITLANINVTDLTGIEYAHNIKDLTINNIHATNYNP--ISGLSNLERLRIMG--------------KDVTSD----  103 (197)
T ss_dssp             HTCCEEEEESSCCSCCTTGGGCTTCSEEEEESCCCSCCGG--GTTCTTCCEEEEEC--------------TTCBGG----
T ss_pred             CCccEEeccCCCccChHHHhcCCCCCEEEccCCCCCcchh--hhcCCCCCEEEeEC--------------CccCcc----
Confidence            4578899999999999954489999999999997766653  68999999999999              777764    


Q ss_pred             CCchhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCC-CcccChhhccCCcccEEeccCCccccccChhhhhc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESD-VSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~-l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      .|..++.+++|++|++++|.+... +..++.+++|++|++++|. +..+| .+..+++|++|++++|... .++ . +..
T Consensus       104 ~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~i~-~~~-~-l~~  179 (197)
T 4ezg_A          104 KIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDGVH-DYR-G-IED  179 (197)
T ss_dssp             GSCCCTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBCCC-CCT-T-GGG
T ss_pred             cChhhcCCCCCCEEEecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCCCc-ChH-H-hcc
Confidence            678899999999999999988764 4889999999999999998 88887 7999999999999998764 466 3 899


Q ss_pred             cccccEEeccccccc
Q 003090          391 LRKLEELYMSHSFRH  405 (848)
Q Consensus       391 l~~L~~L~l~~~~~~  405 (848)
                      +++|++|++++|.+.
T Consensus       180 l~~L~~L~l~~N~i~  194 (197)
T 4ezg_A          180 FPKLNQLYAFSQTIG  194 (197)
T ss_dssp             CSSCCEEEECBC---
T ss_pred             CCCCCEEEeeCcccC
Confidence            999999999999864

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.49  E-value=8.8e-14  Score=141.96  Aligned_cols=167  Identities=19%  Similarity=0.174  Sum_probs=121.4

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ..++++.+.+.+++....+++|++|++++|.+..++.  +..+++|++|++++              +.+.+     +|.
T Consensus        22 ~~l~l~~~~i~~~~~~~~l~~L~~L~l~~n~i~~l~~--l~~l~~L~~L~L~~--------------N~i~~-----~~~   80 (263)
T 1xeu_A           22 VKQNLGKQSVTDLVSQKELSGVQNFNGDNSNIQSLAG--MQFFTNLKELHLSH--------------NQISD-----LSP   80 (263)
T ss_dssp             HHHHHTCSCTTSEECHHHHTTCSEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG
T ss_pred             HHHHhcCCCcccccchhhcCcCcEEECcCCCcccchH--HhhCCCCCEEECCC--------------CccCC-----Chh
Confidence            3456677777777744477888888888887777773  56788888888888              77777     555


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLE  395 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~  395 (848)
                       +..+++|++|++++|.+...+. +.. .+|++|++++|.++.+| .+..+++|++|++++|... .++.  ++.+++|+
T Consensus        81 -l~~l~~L~~L~L~~N~l~~l~~-~~~-~~L~~L~L~~N~l~~~~-~l~~l~~L~~L~Ls~N~i~-~~~~--l~~l~~L~  153 (263)
T 1xeu_A           81 -LKDLTKLEELSVNRNRLKNLNG-IPS-ACLSRLFLDNNELRDTD-SLIHLKNLEILSIRNNKLK-SIVM--LGFLSKLE  153 (263)
T ss_dssp             -GTTCSSCCEEECCSSCCSCCTT-CCC-SSCCEEECCSSCCSBSG-GGTTCTTCCEEECTTSCCC-BCGG--GGGCTTCC
T ss_pred             -hccCCCCCEEECCCCccCCcCc-ccc-CcccEEEccCCccCCCh-hhcCcccccEEECCCCcCC-CChH--HccCCCCC
Confidence             7788888888888886665443 333 78888888888888775 5778888888888887653 3553  67888888


Q ss_pred             EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCC
Q 003090          396 ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMP  445 (848)
Q Consensus       396 ~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~  445 (848)
                      +|++++|.+...               ..+..+++|+.|++++|.+...+
T Consensus       154 ~L~L~~N~i~~~---------------~~l~~l~~L~~L~l~~N~~~~~~  188 (263)
T 1xeu_A          154 VLDLHGNEITNT---------------GGLTRLKKVNWIDLTGQKCVNEP  188 (263)
T ss_dssp             EEECTTSCCCBC---------------TTSTTCCCCCEEEEEEEEEECCC
T ss_pred             EEECCCCcCcch---------------HHhccCCCCCEEeCCCCcccCCc
Confidence            888888876532               45677788888888887765444

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.49  E-value=7.3e-14  Score=142.59  Aligned_cols=170  Identities=18%  Similarity=0.171  Sum_probs=144.3

Q ss_pred             cccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccC
Q 003090          251 ELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD  330 (848)
Q Consensus       251 ~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~  330 (848)
                      ...+.++..++++.+.+..++.  +..+++|++|++++              +.+..     +| .+..+++|++|++++
T Consensus        15 d~~l~~l~~l~l~~~~i~~~~~--~~~l~~L~~L~l~~--------------n~i~~-----l~-~l~~l~~L~~L~L~~   72 (263)
T 1xeu_A           15 DPGLANAVKQNLGKQSVTDLVS--QKELSGVQNFNGDN--------------SNIQS-----LA-GMQFFTNLKELHLSH   72 (263)
T ss_dssp             SHHHHHHHHHHHTCSCTTSEEC--HHHHTTCSEEECTT--------------SCCCC-----CT-TGGGCTTCCEEECCS
T ss_pred             CHHHHHHHHHHhcCCCcccccc--hhhcCcCcEEECcC--------------CCccc-----ch-HHhhCCCCCEEECCC
Confidence            3367788889999998888873  57899999999999              88887     77 689999999999999


Q ss_pred             ccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccc
Q 003090          331 RRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFES  410 (848)
Q Consensus       331 ~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~  410 (848)
                      |.+...++ +.++++|++|++++|.++.+|....  ++|++|++++|... .++.  +.++++|+.|++++|.+...   
T Consensus        73 N~i~~~~~-l~~l~~L~~L~L~~N~l~~l~~~~~--~~L~~L~L~~N~l~-~~~~--l~~l~~L~~L~Ls~N~i~~~---  143 (263)
T 1xeu_A           73 NQISDLSP-LKDLTKLEELSVNRNRLKNLNGIPS--ACLSRLFLDNNELR-DTDS--LIHLKNLEILSIRNNKLKSI---  143 (263)
T ss_dssp             SCCCCCGG-GTTCSSCCEEECCSSCCSCCTTCCC--SSCCEEECCSSCCS-BSGG--GTTCTTCCEEECTTSCCCBC---
T ss_pred             CccCCChh-hccCCCCCEEECCCCccCCcCcccc--CcccEEEccCCccC-CChh--hcCcccccEEECCCCcCCCC---
Confidence            98877666 9999999999999999999886444  99999999998664 4554  89999999999999988642   


Q ss_pred             ccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCC
Q 003090          411 ESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDL  463 (848)
Q Consensus       411 ~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~  463 (848)
                                  ..+..+++|+.|++++|.+..++....+++|+.|++..+..
T Consensus       144 ------------~~l~~l~~L~~L~L~~N~i~~~~~l~~l~~L~~L~l~~N~~  184 (263)
T 1xeu_A          144 ------------VMLGFLSKLEVLDLHGNEITNTGGLTRLKKVNWIDLTGQKC  184 (263)
T ss_dssp             ------------GGGGGCTTCCEEECTTSCCCBCTTSTTCCCCCEEEEEEEEE
T ss_pred             ------------hHHccCCCCCEEECCCCcCcchHHhccCCCCCEEeCCCCcc
Confidence                        36889999999999999998883323889999999986553

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=99.49  E-value=1.5e-15  Score=172.12  Aligned_cols=189  Identities=21%  Similarity=0.242  Sum_probs=141.8

Q ss_pred             cCCCceeeecCCCcccCCcc-cccccceeecccCc-------------CcccChHHHccCCceeEEE-ccCccccccccc
Q 003090          233 LDLTGISLMFNDIHEVPDEL-ECPKLQALFLQENS-------------PLAIPDRFFQGMKDLQVLD-LGGIRRFSFSVR  297 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~-------------~~~~~~~~~~~~~~Lr~L~-l~~~~~~~~~~~  297 (848)
                      ..++.|++++|.+..+|..+ .+++|+.|++++|.             ....++..++.+++|+.|+ ++.         
T Consensus       349 ~~L~~L~Ls~n~L~~Lp~~i~~l~~L~~L~l~~n~~l~~l~~ll~~~~~~~~~~~~l~~l~~L~~L~~l~~---------  419 (567)
T 1dce_A          349 EQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRA---------  419 (567)
T ss_dssp             TTSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGH---------
T ss_pred             ccceeccCChhhHHhhHHHHHHHHHHHHhccccchhhhhHHHHHHhcccccCCHHHHHHHHhcccCcchhh---------
Confidence            34567888888888888877 78888888876653             2233334456777777777 444         


Q ss_pred             CCCCCCCCCCCCCCCCCc------hhhh--cccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcc
Q 003090          298 FPFLFPPLPSSPLFLLPS------SLSF--LINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHL  369 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~------~~~~--l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L  369 (848)
                           +.+..     ++.      .+..  ...|++|++++|.+...+. ++.+++|++|++++|.++.+|..++++++|
T Consensus       420 -----n~~~~-----L~~l~l~~n~i~~l~~~~L~~L~Ls~n~l~~lp~-~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L  488 (567)
T 1dce_A          420 -----AYLDD-----LRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCL  488 (567)
T ss_dssp             -----HHHHH-----HHHHHHHHHHHHHHHHTTCSEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTC
T ss_pred             -----cccch-----hhhhhhhcccccccCccCceEEEecCCCCCCCcC-ccccccCcEeecCcccccccchhhhcCCCC
Confidence                 22211     111      1111  1258899999998877655 999999999999999999999999999999


Q ss_pred             cEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccc-hhhhcccCCCcEEEeeccCCCCCCCCC
Q 003090          370 RLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAK-FIELGALSRLTSLHIHIPEGKIMPSDM  448 (848)
Q Consensus       370 ~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~-~~~L~~l~~L~~L~l~~~~~~~~~~~~  448 (848)
                      ++|++++|.+.+ +| . ++++++|+.|++++|.+...             . +..++.+++|+.|++++|.+...|...
T Consensus       489 ~~L~Ls~N~l~~-lp-~-l~~l~~L~~L~Ls~N~l~~~-------------~~p~~l~~l~~L~~L~L~~N~l~~~~~~~  552 (567)
T 1dce_A          489 EVLQASDNALEN-VD-G-VANLPRLQELLLCNNRLQQS-------------AAIQPLVSCPRLVLLNLQGNSLCQEEGIQ  552 (567)
T ss_dssp             CEEECCSSCCCC-CG-G-GTTCSSCCEEECCSSCCCSS-------------STTGGGGGCTTCCEEECTTSGGGGSSSCT
T ss_pred             CEEECCCCCCCC-Cc-c-cCCCCCCcEEECCCCCCCCC-------------CCcHHHhcCCCCCEEEecCCcCCCCccHH
Confidence            999999987654 77 4 89999999999999988754             2 678899999999999999988777654


Q ss_pred             -----ccCCCCeEE
Q 003090          449 -----SFQNLTSFS  457 (848)
Q Consensus       449 -----~~~~L~~L~  457 (848)
                           .+++|+.|+
T Consensus       553 ~~l~~~lp~L~~L~  566 (567)
T 1dce_A          553 ERLAEMLPSVSSIL  566 (567)
T ss_dssp             THHHHHCTTCSEEE
T ss_pred             HHHHHHCcccCccC
Confidence                 377888774

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.49  E-value=7.1e-14  Score=150.21  Aligned_cols=173  Identities=21%  Similarity=0.209  Sum_probs=127.1

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHc-cCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQ-GMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      +.++++++.+..+|..+. +.++.|++++|.+..++...|. ++++|++|++++              |.+...    .|
T Consensus        21 ~~l~c~~~~l~~iP~~~~-~~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~--------------N~i~~i----~~   81 (361)
T 2xot_A           21 NILSCSKQQLPNVPQSLP-SYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSH--------------NHLNFI----SS   81 (361)
T ss_dssp             TEEECCSSCCSSCCSSCC-TTCSEEECCSSCCCEECTTSSSSCCTTCCEEECCS--------------SCCCEE----CT
T ss_pred             CEEEeCCCCcCccCccCC-CCCCEEECCCCCCCccChhhhhhcccccCEEECCC--------------CcCCcc----Ch
Confidence            457888888888887663 4578888888888888877776 888888888888              777773    33


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCccccccChhhh---h
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILELIPRGVL---S  389 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~~~p~~~l---~  389 (848)
                      ..+..+++|++|+|++|.+...+ ..+..+.+|++|++++|.+..+ |..+..+++|++|++++|.+ ..+|...+   .
T Consensus        82 ~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l-~~l~~~~~~~~~  160 (361)
T 2xot_A           82 EAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQI-SRFPVELIKDGN  160 (361)
T ss_dssp             TTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCC-CSCCGGGTC---
T ss_pred             hhccCCCCCCEEECCCCcCCcCCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCcC-CeeCHHHhcCcc
Confidence            56888888888888888776655 4678888888888888888865 55678888888888888654 44776644   5


Q ss_pred             ccccccEEeccccccccccccccccccCcccchhhhcccCC--CcEEEeeccCC
Q 003090          390 RLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSR--LTSLHIHIPEG  441 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~--L~~L~l~~~~~  441 (848)
                      .+++|+.|++++|.+...             ....+..++.  |+.|++++|.+
T Consensus       161 ~l~~L~~L~L~~N~l~~l-------------~~~~~~~l~~~~l~~l~l~~N~~  201 (361)
T 2xot_A          161 KLPKLMLLDLSSNKLKKL-------------PLTDLQKLPAWVKNGLYLHNNPL  201 (361)
T ss_dssp             -CTTCCEEECCSSCCCCC-------------CHHHHHHSCHHHHTTEECCSSCE
T ss_pred             cCCcCCEEECCCCCCCcc-------------CHHHhhhccHhhcceEEecCCCc
Confidence            678888888888877643             3345555555  36677776643

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.48  E-value=5e-14  Score=151.63  Aligned_cols=198  Identities=15%  Similarity=0.165  Sum_probs=146.3

Q ss_pred             chhHHHHHHHhccC-CCceeeecCCCcccCC-----cc-ccc-ccceeecccCcCcccChHHHccC-----CceeEEEcc
Q 003090          221 SITKIQYEIAGWLD-LTGISLMFNDIHEVPD-----EL-ECP-KLQALFLQENSPLAIPDRFFQGM-----KDLQVLDLG  287 (848)
Q Consensus       221 ~~~~l~~~i~~~~~-l~~l~l~~n~l~~lp~-----~~-~~~-~L~~L~l~~~~~~~~~~~~~~~~-----~~Lr~L~l~  287 (848)
                      ++.....++..... ++.|++++|.+...+.     .+ .++ +|++|++++|.++......+..+     ++|++|+++
T Consensus         9 ~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls   88 (362)
T 3goz_A            9 PGSNPVEEFTSIPHGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLS   88 (362)
T ss_dssp             TTCCHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECC
T ss_pred             cchHHHHHHHhCCCCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECc
Confidence            44545555555555 9999999999998774     33 677 89999999998887765545554     999999999


Q ss_pred             CcccccccccCCCCCCCCCCCCCCCCCchhh----hc-ccCcEEEccCccccCCc-hhh----cc-ccCCCEEEccCCCC
Q 003090          288 GIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS----FL-INLRTLRLHDRRIQGDL-SLI----GE-LSGLEILDLSESDV  356 (848)
Q Consensus       288 ~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~----~l-~~L~~L~L~~~~~~~~~-~~i----~~-l~~L~~L~l~~~~l  356 (848)
                      +              +.+...    .+..+.    .+ ++|++|++++|.+.... ..+    .. ..+|++|++++|.+
T Consensus        89 ~--------------n~l~~~----~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l  150 (362)
T 3goz_A           89 G--------------NFLSYK----SSDELVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRGNDL  150 (362)
T ss_dssp             S--------------SCGGGS----CHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCG
T ss_pred             C--------------CcCChH----HHHHHHHHHHhCCCCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccCCcC
Confidence            9              777763    444444    44 89999999999887665 333    34 36999999999998


Q ss_pred             c-----ccChhhccCC-cccEEeccCCccccccChh---hhhcc-ccccEEeccccccccccccccccccCcccchhhhc
Q 003090          357 S-----EIPVSFGRLS-HLRLLDLTGCYILELIPRG---VLSRL-RKLEELYMSHSFRHWQFESESEEDSSSNAKFIELG  426 (848)
Q Consensus       357 ~-----~lp~~i~~L~-~L~~L~l~~~~~~~~~p~~---~l~~l-~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~  426 (848)
                      .     .++..+..++ +|++|++++|......+..   .+... ++|++|++++|.+...         ...+.+..+.
T Consensus       151 ~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~---------~~~~l~~~l~  221 (362)
T 3goz_A          151 GIKSSDELIQILAAIPANVNSLNLRGNNLASKNCAELAKFLASIPASVTSLDLSANLLGLK---------SYAELAYIFS  221 (362)
T ss_dssp             GGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGS---------CHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCccccEeeecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCCCChh---------HHHHHHHHHh
Confidence            8     5556667776 9999999998776544433   13444 6999999999988653         1122455666


Q ss_pred             cc-CCCcEEEeeccCCCCCC
Q 003090          427 AL-SRLTSLHIHIPEGKIMP  445 (848)
Q Consensus       427 ~l-~~L~~L~l~~~~~~~~~  445 (848)
                      .. ++|+.|++++|.+...+
T Consensus       222 ~~~~~L~~L~Ls~N~l~~~~  241 (362)
T 3goz_A          222 SIPNHVVSLNLCLNCLHGPS  241 (362)
T ss_dssp             HSCTTCCEEECCSSCCCCCC
T ss_pred             cCCCCceEEECcCCCCCcHH
Confidence            64 59999999999877544

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.47  E-value=1.2e-13  Score=135.92  Aligned_cols=149  Identities=23%  Similarity=0.310  Sum_probs=129.7

Q ss_pred             CCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLF  311 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~  311 (848)
                      .++.|++++|.+..++...  .+++|++|++++|.+..++...|..+++|++|++++              +.+..    
T Consensus        29 ~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~--------------n~l~~----   90 (208)
T 2o6s_A           29 QTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLST--------------NQLQS----   90 (208)
T ss_dssp             TCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCS--------------SCCCC----
T ss_pred             CCcEEEcCCCccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCC--------------CcCCc----
Confidence            5789999999999988764  899999999999999999988889999999999999              88887    


Q ss_pred             CCC-chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhh
Q 003090          312 LLP-SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVL  388 (848)
Q Consensus       312 ~lp-~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l  388 (848)
                       +| ..+..+++|++|++++|.+...+ ..+.++++|++|++++|.++.+|.. +.++++|++|++++|...        
T Consensus        91 -~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~--------  161 (208)
T 2o6s_A           91 -LPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWD--------  161 (208)
T ss_dssp             -CCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCCBC--------
T ss_pred             -cCHhHhcCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCCCccceeCHHHhccCCCccEEEecCCCee--------
Confidence             55 44789999999999999888777 4579999999999999999988875 788999999999998543        


Q ss_pred             hccccccEEeccccccccccc
Q 003090          389 SRLRKLEELYMSHSFRHWQFE  409 (848)
Q Consensus       389 ~~l~~L~~L~l~~~~~~~~~~  409 (848)
                      +.+++|+.|+++.|.+.+.+|
T Consensus       162 ~~~~~l~~L~~~~n~~~g~ip  182 (208)
T 2o6s_A          162 CTCPGIRYLSEWINKHSGVVR  182 (208)
T ss_dssp             CCTTTTHHHHHHHHHCTTTBB
T ss_pred             cCCCCHHHHHHHHHhCCceee
Confidence            456678889998888887643

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.45  E-value=4.5e-13  Score=133.69  Aligned_cols=150  Identities=23%  Similarity=0.296  Sum_probs=116.8

Q ss_pred             cceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC
Q 003090          257 LQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD  336 (848)
Q Consensus       257 L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~  336 (848)
                      -..++.+++.+..+|..+   .++|++|++++              +.+...    .|..+..+++|++|++++|.+...
T Consensus        21 ~~~v~c~~~~l~~ip~~~---~~~L~~L~Ls~--------------n~i~~~----~~~~~~~l~~L~~L~L~~N~l~~i   79 (229)
T 3e6j_A           21 GTTVDCRSKRHASVPAGI---PTNAQILYLHD--------------NQITKL----EPGVFDSLINLKELYLGSNQLGAL   79 (229)
T ss_dssp             TTEEECTTSCCSSCCSCC---CTTCSEEECCS--------------SCCCCC----CTTTTTTCTTCCEEECCSSCCCCC
T ss_pred             CCEeEccCCCcCccCCCC---CCCCCEEEcCC--------------CccCcc----CHHHhhCccCCcEEECCCCCCCCc
Confidence            456777788888888753   37888999998              778774    577788888999999999887766


Q ss_pred             c-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccccc
Q 003090          337 L-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE  414 (848)
Q Consensus       337 ~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  414 (848)
                      + ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.+. .+|.. +..+++|++|++++|.+...       
T Consensus        80 ~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~~L~Ls~N~l~-~lp~~-~~~l~~L~~L~L~~N~l~~~-------  150 (229)
T 3e6j_A           80 PVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMCCNKLT-ELPRG-IERLTHLTHLALDQNQLKSI-------  150 (229)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-SCCTT-GGGCTTCSEEECCSSCCCCC-------
T ss_pred             ChhhcccCCCcCEEECCCCcCCccChhHhCcchhhCeEeccCCccc-ccCcc-cccCCCCCEEECCCCcCCcc-------
Confidence            6 4568888899999998888877765 578888888888887654 68877 68888888888888877653       


Q ss_pred             ccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          415 DSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       415 ~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                            ....+..+++|+.|++++|.+.
T Consensus       151 ------~~~~~~~l~~L~~L~l~~N~~~  172 (229)
T 3e6j_A          151 ------PHGAFDRLSSLTHAYLFGNPWD  172 (229)
T ss_dssp             ------CTTTTTTCTTCCEEECTTSCBC
T ss_pred             ------CHHHHhCCCCCCEEEeeCCCcc
Confidence                  2245777888888888887654

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.44  E-value=3.8e-13  Score=115.70  Aligned_cols=63  Identities=13%  Similarity=0.189  Sum_probs=56.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 003090           37 HYIEALRTEAKKLTDRRNDLQAEIDAATRNR-EVIKDEVKSWIAEVNDIIPKAEKFLEDEVKVN   99 (848)
Q Consensus        37 ~~~~~~~~~l~~L~~~l~~i~~~l~~a~~~~-~~~~~~v~~wl~~lk~~~~d~eD~lde~~~~~   99 (848)
                      ....+++++++.|+++|++|+++|.+|+.+. +..++.++.|++++|++||||||+||+|.+..
T Consensus        19 ~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~~~~   82 (115)
T 3qfl_A           19 KLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFLVQV   82 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3456999999999999999999999999874 46899999999999999999999999996654

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.43  E-value=6.7e-13  Score=131.43  Aligned_cols=149  Identities=15%  Similarity=0.131  Sum_probs=110.3

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC-C-chhhhcccCcEEEccCccccC
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL-P-SSLSFLINLRTLRLHDRRIQG  335 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l-p-~~~~~l~~L~~L~L~~~~~~~  335 (848)
                      +++++++|.+..+|..+   ...+++|++++              +.+..     + | ..+..+++|++|++++|.+..
T Consensus        14 ~~l~~s~n~l~~iP~~~---~~~~~~L~L~~--------------N~l~~-----~~~~~~~~~l~~L~~L~L~~N~i~~   71 (220)
T 2v70_A           14 TTVDCSNQKLNKIPEHI---PQYTAELRLNN--------------NEFTV-----LEATGIFKKLPQLRKINFSNNKITD   71 (220)
T ss_dssp             TEEECCSSCCSSCCSCC---CTTCSEEECCS--------------SCCCE-----ECCCCCGGGCTTCCEEECCSSCCCE
T ss_pred             CEeEeCCCCcccCccCC---CCCCCEEEcCC--------------CcCCc-----cCchhhhccCCCCCEEECCCCcCCE
Confidence            57788888888888653   34567888888              77776     4 2 347788888888888887766


Q ss_pred             Cc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccc
Q 003090          336 DL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       336 ~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                      .+ ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.+....|.. +..+++|++|++++|.+...      
T Consensus        72 i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~-~~~l~~L~~L~L~~N~l~~~------  144 (220)
T 2v70_A           72 IEEGAFEGASGVNEILLTSNRLENVQHKMFKGLESLKTLMLRSNRITCVGNDS-FIGLSSVRLLSLYDNQITTV------  144 (220)
T ss_dssp             ECTTTTTTCTTCCEEECCSSCCCCCCGGGGTTCSSCCEEECTTSCCCCBCTTS-STTCTTCSEEECTTSCCCCB------
T ss_pred             ECHHHhCCCCCCCEEECCCCccCccCHhHhcCCcCCCEEECCCCcCCeECHhH-cCCCccCCEEECCCCcCCEE------
Confidence            65 4678888888888888888876654 777888888888887665544554 77888888888888877654      


Q ss_pred             cccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          414 EDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       414 ~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                             .+..+..+++|+.|++++|.+.
T Consensus       145 -------~~~~~~~l~~L~~L~L~~N~l~  166 (220)
T 2v70_A          145 -------APGAFDTLHSLSTLNLLANPFN  166 (220)
T ss_dssp             -------CTTTTTTCTTCCEEECCSCCEE
T ss_pred             -------CHHHhcCCCCCCEEEecCcCCc
Confidence                   3456777788888888777543

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.42  E-value=4.5e-13  Score=132.72  Aligned_cols=149  Identities=19%  Similarity=0.193  Sum_probs=92.3

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      +.++.+++.+..+|..+   .++++.|++++              +.+...    .+..+..+++|++|++++|.+....
T Consensus        14 ~~v~c~~~~l~~iP~~l---~~~l~~L~l~~--------------n~i~~i----~~~~~~~l~~L~~L~Ls~N~i~~~~   72 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNL---PETITEIRLEQ--------------NTIKVI----PPGAFSPYKKLRRIDLSNNQISELA   72 (220)
T ss_dssp             TEEECTTSCCSSCCSSC---CTTCCEEECCS--------------SCCCEE----CTTSSTTCTTCCEEECCSSCCCEEC
T ss_pred             CEEEcCCCCcCcCCCcc---CcCCCEEECCC--------------CcCCCc----CHhHhhCCCCCCEEECCCCcCCCcC
Confidence            45666666666666543   25677777777              666652    2335666777777777777665543


Q ss_pred             -hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccc
Q 003090          338 -SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEED  415 (848)
Q Consensus       338 -~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~  415 (848)
                       ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.+....|.. +..+++|++|++++|.+...        
T Consensus        73 ~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~-~~~l~~L~~L~L~~N~l~~~--------  143 (220)
T 2v9t_B           73 PDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDA-FQDLHNLNLLSLYDNKLQTI--------  143 (220)
T ss_dssp             TTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTT-TTTCTTCCEEECCSSCCSCC--------
T ss_pred             HHHhhCCcCCCEEECCCCcCCccCHhHccCCCCCCEEECCCCCCCEeCHHH-cCCCCCCCEEECCCCcCCEE--------
Confidence             5666777777777777777766654 456777777777776554433333 66667777777776666543        


Q ss_pred             cCcccchhhhcccCCCcEEEeeccCC
Q 003090          416 SSSNAKFIELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       416 ~~~~~~~~~L~~l~~L~~L~l~~~~~  441 (848)
                           ....+..+++|+.|++++|.+
T Consensus       144 -----~~~~~~~l~~L~~L~L~~N~~  164 (220)
T 2v9t_B          144 -----AKGTFSPLRAIQTMHLAQNPF  164 (220)
T ss_dssp             -----CTTTTTTCTTCCEEECCSSCE
T ss_pred             -----CHHHHhCCCCCCEEEeCCCCc
Confidence                 223455566666666666643

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=99.39  E-value=1.6e-13  Score=155.37  Aligned_cols=184  Identities=18%  Similarity=0.144  Sum_probs=143.4

Q ss_pred             chhHHHHHHHhccCCCceeeecCC-------------Cc-ccCCcc-cccccceee-cccCcCcccChHHH-----c--c
Q 003090          221 SITKIQYEIAGWLDLTGISLMFND-------------IH-EVPDEL-ECPKLQALF-LQENSPLAIPDRFF-----Q--G  277 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~-------------l~-~lp~~~-~~~~L~~L~-l~~~~~~~~~~~~~-----~--~  277 (848)
                      .+..++.+|.....++.|++++|.             +. ..|..+ .+++|+.|+ ++.|.+..++...+     .  .
T Consensus       360 ~L~~Lp~~i~~l~~L~~L~l~~n~~l~~l~~ll~~~~~~~~~~~~l~~l~~L~~L~~l~~n~~~~L~~l~l~~n~i~~l~  439 (567)
T 1dce_A          360 KSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKME  439 (567)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHhhHHHHHHHHHHHHhccccchhhhhHHHHHHhcccccCCHHHHHHHHhcccCcchhhcccchhhhhhhhcccccccC
Confidence            356788888888888888886653             22 334444 678888887 56554433332111     1  1


Q ss_pred             CCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCc
Q 003090          278 MKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS  357 (848)
Q Consensus       278 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~  357 (848)
                      ...|++|++++              +.+++     +|. ++.+++|++|++++|.+...|..++++++|++|++++|.++
T Consensus       440 ~~~L~~L~Ls~--------------n~l~~-----lp~-~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~  499 (567)
T 1dce_A          440 YADVRVLHLAH--------------KDLTV-----LCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALE  499 (567)
T ss_dssp             HTTCSEEECTT--------------SCCSS-----CCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCC
T ss_pred             ccCceEEEecC--------------CCCCC-----CcC-ccccccCcEeecCcccccccchhhhcCCCCCEEECCCCCCC
Confidence            23589999999              88988     887 99999999999999999988899999999999999999999


Q ss_pred             ccChhhccCCcccEEeccCCcccccc-ChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEe
Q 003090          358 EIPVSFGRLSHLRLLDLTGCYILELI-PRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHI  436 (848)
Q Consensus       358 ~lp~~i~~L~~L~~L~l~~~~~~~~~-p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l  436 (848)
                      .+| .++++++|++|++++|.+.+.. |.. ++.+++|+.|++++|.+....+.          ....+..+++|+.|++
T Consensus       500 ~lp-~l~~l~~L~~L~Ls~N~l~~~~~p~~-l~~l~~L~~L~L~~N~l~~~~~~----------~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          500 NVD-GVANLPRLQELLLCNNRLQQSAAIQP-LVSCPRLVLLNLQGNSLCQEEGI----------QERLAEMLPSVSSILT  567 (567)
T ss_dssp             CCG-GGTTCSSCCEEECCSSCCCSSSTTGG-GGGCTTCCEEECTTSGGGGSSSC----------TTHHHHHCTTCSEEEC
T ss_pred             CCc-ccCCCCCCcEEECCCCCCCCCCCcHH-HhcCCCCCEEEecCCcCCCCccH----------HHHHHHHCcccCccCC
Confidence            999 8999999999999998776654 777 89999999999999998765322          3344556889998864

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.38  E-value=1.8e-12  Score=122.59  Aligned_cols=140  Identities=21%  Similarity=0.159  Sum_probs=116.6

Q ss_pred             cCCceeEEEccCcccccccccCCCCCCCCC-CCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCC
Q 003090          277 GMKDLQVLDLGGIRRFSFSVRFPFLFPPLP-SSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESD  355 (848)
Q Consensus       277 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~-~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~  355 (848)
                      ..++|+.|++++              +.+. +.    +|..+..+++|++|++++|.+... ..++.+++|++|++++|.
T Consensus        22 ~~~~L~~L~l~~--------------n~l~~~~----i~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~N~   82 (168)
T 2ell_A           22 TPAAVRELVLDN--------------CKSNDGK----IEGLTAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSENR   82 (168)
T ss_dssp             CTTSCSEEECCS--------------CBCBTTB----CSSCCGGGGGCCEEEEESSCCCCC-SSCCCCSSCCEEEEESCC
T ss_pred             CcccCCEEECCC--------------CCCChhh----HHHHHHhCCCCCEEeCcCCCCCCh-hhhccCCCCCEEECcCCc
Confidence            457899999999              7776 22    888889999999999999987766 889999999999999999


Q ss_pred             Ccc-cChhhccCCcccEEeccCCccccccC--hhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCc
Q 003090          356 VSE-IPVSFGRLSHLRLLDLTGCYILELIP--RGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLT  432 (848)
Q Consensus       356 l~~-lp~~i~~L~~L~~L~l~~~~~~~~~p--~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~  432 (848)
                      ++. +|..+.++++|++|++++|... .+|  .. +..+++|++|++++|.+....+          .....+..+++|+
T Consensus        83 l~~~~~~~~~~l~~L~~L~Ls~N~l~-~~~~~~~-l~~l~~L~~L~l~~N~l~~~~~----------~~~~~~~~l~~L~  150 (168)
T 2ell_A           83 IFGGLDMLAEKLPNLTHLNLSGNKLK-DISTLEP-LKKLECLKSLDLFNCEVTNLND----------YRESVFKLLPQLT  150 (168)
T ss_dssp             CCSCCCHHHHHCTTCCEEECBSSSCC-SSGGGGG-GSSCSCCCEEECCSSGGGTSTT----------HHHHHHTTCSSCC
T ss_pred             CchHHHHHHhhCCCCCEEeccCCccC-cchhHHH-HhcCCCCCEEEeeCCcCcchHH----------HHHHHHHhCccCc
Confidence            997 8888888999999999998664 444  44 8999999999999998875311          0124788999999


Q ss_pred             EEEeeccCCCCCCCC
Q 003090          433 SLHIHIPEGKIMPSD  447 (848)
Q Consensus       433 ~L~l~~~~~~~~~~~  447 (848)
                      .|++++|....+|..
T Consensus       151 ~L~l~~n~~~~~~~~  165 (168)
T 2ell_A          151 YLDGYDREDQEAPDS  165 (168)
T ss_dssp             EETTEETTSCBCCSS
T ss_pred             EecCCCCChhhcccc
Confidence            999999998877764

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.37  E-value=2.8e-12  Score=144.34  Aligned_cols=167  Identities=14%  Similarity=0.161  Sum_probs=135.4

Q ss_pred             hhHHHHHHHhccCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCC
Q 003090          222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFL  301 (848)
Q Consensus       222 ~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~  301 (848)
                      +..++..+.  ..++.|++++|.+..+|  ..+++|++|++++|.+..+|.  +.+  +|++|++++             
T Consensus        71 L~~lp~~l~--~~L~~L~Ls~N~l~~ip--~~l~~L~~L~Ls~N~l~~ip~--l~~--~L~~L~Ls~-------------  129 (571)
T 3cvr_A           71 LSSLPDNLP--PQITVLEITQNALISLP--ELPASLEYLDACDNRLSTLPE--LPA--SLKHLDVDN-------------  129 (571)
T ss_dssp             CSCCCSCCC--TTCSEEECCSSCCSCCC--CCCTTCCEEECCSSCCSCCCC--CCT--TCCEEECCS-------------
T ss_pred             CCccCHhHc--CCCCEEECcCCCCcccc--cccCCCCEEEccCCCCCCcch--hhc--CCCEEECCC-------------
Confidence            334444333  35899999999999999  457899999999999988887  333  999999999             


Q ss_pred             CCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcccc
Q 003090          302 FPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE  381 (848)
Q Consensus       302 ~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~  381 (848)
                       |.+.+     +|.   .+++|++|++++|.+...+.   .+++|++|++++|.++.+|. +.  ++|++|++++|.+. 
T Consensus       130 -N~l~~-----lp~---~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N~L~~lp~-l~--~~L~~L~Ls~N~L~-  193 (571)
T 3cvr_A          130 -NQLTM-----LPE---LPALLEYINADNNQLTMLPE---LPTSLEVLSVRNNQLTFLPE-LP--ESLEALDVSTNLLE-  193 (571)
T ss_dssp             -SCCSC-----CCC---CCTTCCEEECCSSCCSCCCC---CCTTCCEEECCSSCCSCCCC-CC--TTCCEEECCSSCCS-
T ss_pred             -CcCCC-----CCC---cCccccEEeCCCCccCcCCC---cCCCcCEEECCCCCCCCcch-hh--CCCCEEECcCCCCC-
Confidence             88888     777   68899999999998877555   67899999999999999998 66  89999999998654 


Q ss_pred             ccChhhhhccccc-------cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCC
Q 003090          382 LIPRGVLSRLRKL-------EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKI  443 (848)
Q Consensus       382 ~~p~~~l~~l~~L-------~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~  443 (848)
                      .+|.  +..  +|       +.|++++|.+..              .+..+..+++|+.|++++|.+..
T Consensus       194 ~lp~--~~~--~L~~~~~~L~~L~Ls~N~l~~--------------lp~~l~~l~~L~~L~L~~N~l~~  244 (571)
T 3cvr_A          194 SLPA--VPV--RNHHSEETEIFFRCRENRITH--------------IPENILSLDPTCTIILEDNPLSS  244 (571)
T ss_dssp             SCCC--CC----------CCEEEECCSSCCCC--------------CCGGGGGSCTTEEEECCSSSCCH
T ss_pred             chhh--HHH--hhhcccccceEEecCCCccee--------------cCHHHhcCCCCCEEEeeCCcCCC
Confidence            6777  343  66       999999998864              45677889999999999998763

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.37  E-value=1.1e-12  Score=140.74  Aligned_cols=164  Identities=23%  Similarity=0.297  Sum_probs=136.8

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCcc---cccccceeecccCcCcccChHHHccCCceeEEEccCccccccccc
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL---ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~---~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      .+..++..+..  .++.|++++|.+..++...   .+++|++|++++|.+..++...|.++++|++|+|++         
T Consensus        29 ~l~~iP~~~~~--~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~---------   97 (361)
T 2xot_A           29 QLPNVPQSLPS--YTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSS---------   97 (361)
T ss_dssp             CCSSCCSSCCT--TCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS---------
T ss_pred             CcCccCccCCC--CCCEEECCCCCCCccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECCC---------
Confidence            34444444433  3678999999999988764   789999999999999999988789999999999999         


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChhh----ccCCcccEE
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVSF----GRLSHLRLL  372 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i----~~L~~L~~L  372 (848)
                           |.+...    .+..+..+.+|++|+|++|.+.... ..+..+++|++|++++|.++.+|..+    ..+++|++|
T Consensus        98 -----N~l~~~----~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~~l~~L~~L  168 (361)
T 2xot_A           98 -----NHLHTL----DEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQISRFPVELIKDGNKLPKLMLL  168 (361)
T ss_dssp             -----SCCCEE----CTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCSCCGGGTC----CTTCCEE
T ss_pred             -----CcCCcC----CHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCcCCeeCHHHhcCcccCCcCCEE
Confidence                 888873    3456899999999999999888764 78999999999999999999999875    679999999


Q ss_pred             eccCCccccccChhhhhcccc--ccEEeccccccc
Q 003090          373 DLTGCYILELIPRGVLSRLRK--LEELYMSHSFRH  405 (848)
Q Consensus       373 ~l~~~~~~~~~p~~~l~~l~~--L~~L~l~~~~~~  405 (848)
                      ++++|.+ ..+|...+..++.  |+.|++.+|.+.
T Consensus       169 ~L~~N~l-~~l~~~~~~~l~~~~l~~l~l~~N~~~  202 (361)
T 2xot_A          169 DLSSNKL-KKLPLTDLQKLPAWVKNGLYLHNNPLE  202 (361)
T ss_dssp             ECCSSCC-CCCCHHHHHHSCHHHHTTEECCSSCEE
T ss_pred             ECCCCCC-CccCHHHhhhccHhhcceEEecCCCcc
Confidence            9999865 4677666888887  488999998764

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.33  E-value=6.1e-13  Score=155.66  Aligned_cols=150  Identities=22%  Similarity=0.237  Sum_probs=103.1

Q ss_pred             ceeeecCCCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          237 GISLMFNDIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       237 ~l~l~~n~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      .++++.|.+...+..+ .++.|+.|+|++|.+..+|..++ ++++|++|+|++              |.+..     +|.
T Consensus       205 ~~~~~~n~~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~-~l~~L~~L~Ls~--------------N~l~~-----lp~  264 (727)
T 4b8c_D          205 EDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIF-KYDFLTRLYLNG--------------NSLTE-----LPA  264 (727)
T ss_dssp             -----------------CCCCCCEEECTTSCCSCCCGGGG-GCCSCSCCBCTT--------------SCCSC-----CCG
T ss_pred             CccccccceecChhhhccCCCCcEEECCCCCCCCCChhhc-CCCCCCEEEeeC--------------CcCcc-----cCh
Confidence            3444455555444444 77888888888888888887765 788888888888              77775     888


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc-c
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK-L  394 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~-L  394 (848)
                      .++.+++|++|+|++|.+...+..++++++|++|+|++|.++.+|..+++|++|++|++++|.+.+.+|.. +..+.. +
T Consensus       265 ~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~~lp~~~~~l~~L~~L~L~~N~l~~~~p~~-~~~~~~~~  343 (727)
T 4b8c_D          265 EIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKI-LTEKSVTG  343 (727)
T ss_dssp             GGGGGTTCCEEECTTSCCSSCCSSGGGGTTCSEEECCSSCCCCCCSSTTSCTTCCCEECTTSCCCSHHHHH-HHHHHHHH
T ss_pred             hhhCCCCCCEEeCcCCcCCccChhhcCCCCCCEEECCCCCCCccChhhhcCCCccEEeCCCCccCCCChHH-Hhhcchhh
Confidence            88888888888888888776677788888888888888888888888888888888888888777666655 444322 2


Q ss_pred             cEEeccccccccc
Q 003090          395 EELYMSHSFRHWQ  407 (848)
Q Consensus       395 ~~L~l~~~~~~~~  407 (848)
                      ..|++.+|.+.+.
T Consensus       344 ~~l~l~~N~l~~~  356 (727)
T 4b8c_D          344 LIFYLRDNRPEIP  356 (727)
T ss_dssp             HHHHHHHCCCCCC
T ss_pred             hHHhhccCcccCc
Confidence            2356677766554

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.31  E-value=5.1e-12  Score=119.39  Aligned_cols=130  Identities=26%  Similarity=0.301  Sum_probs=81.1

Q ss_pred             cccceeecccCcCc--ccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          255 PKLQALFLQENSPL--AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       255 ~~L~~L~l~~~~~~--~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      ++|++|++++|.+.  .+|.. +..+++|++|++++              +.+..     + ..+..+++|++|++++|.
T Consensus        24 ~~L~~L~l~~n~l~~~~i~~~-~~~l~~L~~L~l~~--------------n~l~~-----~-~~~~~l~~L~~L~Ls~N~   82 (168)
T 2ell_A           24 AAVRELVLDNCKSNDGKIEGL-TAEFVNLEFLSLIN--------------VGLIS-----V-SNLPKLPKLKKLELSENR   82 (168)
T ss_dssp             TSCSEEECCSCBCBTTBCSSC-CGGGGGCCEEEEES--------------SCCCC-----C-SSCCCCSSCCEEEEESCC
T ss_pred             ccCCEEECCCCCCChhhHHHH-HHhCCCCCEEeCcC--------------CCCCC-----h-hhhccCCCCCEEECcCCc
Confidence            55666666666555  55544 45666667777766              55555     4 456666667777777766


Q ss_pred             ccCC-chhhccccCCCEEEccCCCCcccC--hhhccCCcccEEeccCCccccccCh---hhhhccccccEEecccccccc
Q 003090          333 IQGD-LSLIGELSGLEILDLSESDVSEIP--VSFGRLSHLRLLDLTGCYILELIPR---GVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       333 ~~~~-~~~i~~l~~L~~L~l~~~~l~~lp--~~i~~L~~L~~L~l~~~~~~~~~p~---~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      +... +..+.++++|++|++++|.++.+|  ..+..+++|++|++++|.... +|.   ..+..+++|++|++++|....
T Consensus        83 l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~l~~l~~L~~L~l~~N~l~~-~~~~~~~~~~~l~~L~~L~l~~n~~~~  161 (168)
T 2ell_A           83 IFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTN-LNDYRESVFKLLPQLTYLDGYDREDQE  161 (168)
T ss_dssp             CCSCCCHHHHHCTTCCEEECBSSSCCSSGGGGGGSSCSCCCEEECCSSGGGT-STTHHHHHHTTCSSCCEETTEETTSCB
T ss_pred             CchHHHHHHhhCCCCCEEeccCCccCcchhHHHHhcCCCCCEEEeeCCcCcc-hHHHHHHHHHhCccCcEecCCCCChhh
Confidence            6653 344555777777777777776655  566677777777777765443 443   236677777777777766543

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.29  E-value=5.8e-12  Score=116.32  Aligned_cols=63  Identities=30%  Similarity=0.495  Sum_probs=29.2

Q ss_pred             hhhhcccCcEEEccCccccCC-chhhccccCCCEEEccCCCCcccC--hhhccCCcccEEeccCCc
Q 003090          316 SLSFLINLRTLRLHDRRIQGD-LSLIGELSGLEILDLSESDVSEIP--VSFGRLSHLRLLDLTGCY  378 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~-~~~i~~l~~L~~L~l~~~~l~~lp--~~i~~L~~L~~L~l~~~~  378 (848)
                      .++.+++|++|++++|.+... +..++.+++|++|++++|.++.+|  ..++.+++|++|++++|.
T Consensus        59 ~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~ls~N~i~~~~~~~~~~~l~~L~~L~l~~N~  124 (149)
T 2je0_A           59 NLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCE  124 (149)
T ss_dssp             TCCCCTTCCEEECCSSCCCSCTHHHHHHCTTCCEEECTTSCCCSHHHHGGGGGCTTCCEEECTTCG
T ss_pred             hhhcCCCCCEEECCCCcccchHHHHhhhCCCCCEEECCCCcCCChHHHHHHhhCCCCCEEeCcCCc
Confidence            344444555555555544442 233334455555555555444432  344445555555555443

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=99.29  E-value=8.4e-12  Score=120.62  Aligned_cols=127  Identities=22%  Similarity=0.308  Sum_probs=70.5

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChH-HHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDR-FFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      +.+++++|.++.+|..+. .++++|++++|.+..++.. +|..+++|++|++++              +.+.+.    .|
T Consensus        11 ~~l~~s~~~l~~ip~~~~-~~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~--------------N~l~~~----~~   71 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIP-LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKR--------------NQLTGI----EP   71 (192)
T ss_dssp             TEEECTTSCCSSCCSCCC-TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCS--------------SCCCCB----CT
T ss_pred             CEEEcCCCCcCcCccCCC-CCCCEEECCCCcCCccCCccccccCCCCCEEECCC--------------CCCCCc----CH
Confidence            445666666666665442 2566666666655555542 345666666666666              555552    35


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCccc-ChhhccCCcccEEeccCCcccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEI-PVSFGRLSHLRLLDLTGCYILE  381 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~l-p~~i~~L~~L~~L~l~~~~~~~  381 (848)
                      ..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+ |..+..+++|++|++++|.+..
T Consensus        72 ~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~c  140 (192)
T 1w8a_A           72 NAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNC  140 (192)
T ss_dssp             TTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBCC
T ss_pred             hHcCCcccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCccC
Confidence            55556666666666666555444 3355555566666655555533 4445555555555555554443

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.27  E-value=3.1e-12  Score=121.85  Aligned_cols=131  Identities=16%  Similarity=0.140  Sum_probs=72.9

Q ss_pred             ccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCc
Q 003090          252 LECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDR  331 (848)
Q Consensus       252 ~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~  331 (848)
                      ..+.+|++|++++|.+..++. +....++|++|++++              +.+.+     + ..+..+++|++|++++|
T Consensus        16 ~~~~~L~~L~l~~n~l~~i~~-~~~~~~~L~~L~Ls~--------------N~l~~-----~-~~l~~l~~L~~L~Ls~N   74 (176)
T 1a9n_A           16 TNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSD--------------NEIRK-----L-DGFPLLRRLKTLLVNNN   74 (176)
T ss_dssp             ECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCS--------------SCCCE-----E-CCCCCCSSCCEEECCSS
T ss_pred             CCcCCceEEEeeCCCCchhHH-hhhcCCCCCEEECCC--------------CCCCc-----c-cccccCCCCCEEECCCC
Confidence            355566666666665555543 222233666666666              55554     4 34555666666666666


Q ss_pred             cccCCchh-hccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCccccccChh---hhhccccccEEecccccc
Q 003090          332 RIQGDLSL-IGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCYILELIPRG---VLSRLRKLEELYMSHSFR  404 (848)
Q Consensus       332 ~~~~~~~~-i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~~---~l~~l~~L~~L~l~~~~~  404 (848)
                      .+...++. ++.+++|++|++++|.+..+|.  .+..+++|++|++++|... .+|..   .+..+++|+.|++++|..
T Consensus        75 ~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~l~~N~i~-~~~~~~~~~~~~l~~L~~Ld~~~n~~  152 (176)
T 1a9n_A           75 RICRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNPVT-NKKHYRLYVIYKVPQVRVLDFQKVKL  152 (176)
T ss_dssp             CCCEECSCHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGG-GSTTHHHHHHHHCTTCSEETTEECCH
T ss_pred             cccccCcchhhcCCCCCEEECCCCcCCcchhhHhhhcCCCCCEEEecCCCCC-CcHhHHHHHHHHCCccceeCCCcCCH
Confidence            55544432 3566666666666666665554  5556666666666665443 34432   245666666666655543

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.27  E-value=7.3e-12  Score=115.65  Aligned_cols=123  Identities=21%  Similarity=0.215  Sum_probs=108.7

Q ss_pred             CCCceeeecCCCc--ccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIH--EVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPL  310 (848)
Q Consensus       234 ~l~~l~l~~n~l~--~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~  310 (848)
                      .++.+++++|.+.  .+|..+ .+++|++|++++|.+..+  ..+..+++|++|++++              +.+.+.  
T Consensus        18 ~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~--~~~~~l~~L~~L~Ls~--------------n~i~~~--   79 (149)
T 2je0_A           18 DVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSI--ANLPKLNKLKKLELSD--------------NRVSGG--   79 (149)
T ss_dssp             GCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCCCC--TTCCCCTTCCEEECCS--------------SCCCSC--
T ss_pred             cCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCCCc--hhhhcCCCCCEEECCC--------------Ccccch--
Confidence            4789999999998  888876 899999999999988888  3468999999999999              888875  


Q ss_pred             CCCCchhhhcccCcEEEccCccccCCc--hhhccccCCCEEEccCCCCcccCh----hhccCCcccEEeccC
Q 003090          311 FLLPSSLSFLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESDVSEIPV----SFGRLSHLRLLDLTG  376 (848)
Q Consensus       311 ~~lp~~~~~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~~l~~lp~----~i~~L~~L~~L~l~~  376 (848)
                        +|..+..+++|++|++++|.+...+  ..++.+++|++|++++|.++.+|.    .++.+++|++|++++
T Consensus        80 --~~~~~~~l~~L~~L~ls~N~i~~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l~d  149 (149)
T 2je0_A           80 --LEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYD  149 (149)
T ss_dssp             --THHHHHHCTTCCEEECTTSCCCSHHHHGGGGGCTTCCEEECTTCGGGGSTTHHHHHHHHCTTCCEETTBC
T ss_pred             --HHHHhhhCCCCCEEECCCCcCCChHHHHHHhhCCCCCEEeCcCCcccchHHHHHHHHHHCCCcccccCCC
Confidence              7777888999999999999887754  789999999999999999998876    688899999998763

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.27  E-value=2.3e-11  Score=117.40  Aligned_cols=91  Identities=30%  Similarity=0.394  Sum_probs=45.2

Q ss_pred             CCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      +|..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|. .+..+++|++|++++|.+. .+|.+.+..
T Consensus        46 ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~L~~N~l~-~~~~~~~~~  124 (193)
T 2wfh_A           46 VPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLHGNDIS-VVPEGAFND  124 (193)
T ss_dssp             CCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCCC-BCCTTTTTT
T ss_pred             hHHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCccCEeCHHHhCCCCCCCEEECCCCCCC-eeChhhhhc
Confidence            4444555555555555555444443 334555555555555555554433 3455555555555554332 344433455


Q ss_pred             cccccEEecccccc
Q 003090          391 LRKLEELYMSHSFR  404 (848)
Q Consensus       391 l~~L~~L~l~~~~~  404 (848)
                      +++|+.|++++|.+
T Consensus       125 l~~L~~L~L~~N~~  138 (193)
T 2wfh_A          125 LSALSHLAIGANPL  138 (193)
T ss_dssp             CTTCCEEECCSSCE
T ss_pred             CccccEEEeCCCCe
Confidence            55555555555544

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=99.26  E-value=1.3e-11  Score=119.21  Aligned_cols=126  Identities=21%  Similarity=0.223  Sum_probs=95.2

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc--hhhhcccCcEEEccCccccC
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS--SLSFLINLRTLRLHDRRIQG  335 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~--~~~~l~~L~~L~L~~~~~~~  335 (848)
                      +++++++|.++.+|..++   .++++|++++              +.+..     ++.  .++.+++|++|++++|.+..
T Consensus        11 ~~l~~s~~~l~~ip~~~~---~~l~~L~l~~--------------n~i~~-----~~~~~~~~~l~~L~~L~Ls~N~l~~   68 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIP---LHTTELLLND--------------NELGR-----ISSDGLFGRLPHLVKLELKRNQLTG   68 (192)
T ss_dssp             TEEECTTSCCSSCCSCCC---TTCSEEECCS--------------CCCCS-----BCCSCSGGGCTTCCEEECCSSCCCC
T ss_pred             CEEEcCCCCcCcCccCCC---CCCCEEECCC--------------CcCCc-----cCCccccccCCCCCEEECCCCCCCC
Confidence            677888888888887543   3788888888              77776     554  37888888888888887777


Q ss_pred             Cc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEecccccccc
Q 003090          336 DL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       336 ~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      .. ..+..+++|++|++++|.++.++.. +..+++|++|++++|.+.+..|.. +..+++|++|++++|.+..
T Consensus        69 ~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~-~~~l~~L~~L~L~~N~l~c  140 (192)
T 1w8a_A           69 IEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGS-FEHLNSLTSLNLASNPFNC  140 (192)
T ss_dssp             BCTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEECTTS-STTCTTCCEEECTTCCBCC
T ss_pred             cCHhHcCCcccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCeeCHHH-hhcCCCCCEEEeCCCCccC
Confidence            64 6778888888888888888866543 777888888888887766655555 7788888888888877654

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.26  E-value=2.6e-11  Score=115.56  Aligned_cols=127  Identities=24%  Similarity=0.335  Sum_probs=80.4

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC-
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP-  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp-  314 (848)
                      ++++++++.+..+|..+. ++|++|++++|.+..++...|..+++|++|++++              +.+..     +| 
T Consensus        10 ~~l~~~~~~l~~~p~~~~-~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~--------------n~l~~-----~~~   69 (177)
T 2o6r_A           10 TEIRCNSKGLTSVPTGIP-SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQ--------------NQIQS-----LPD   69 (177)
T ss_dssp             TEEECCSSCCSSCCTTCC-TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCS--------------SCCCC-----CCT
T ss_pred             CEEEecCCCCccCCCCCC-CCCcEEEeCCCcccEeCHHHhcCcccccEEECCC--------------CcceE-----eCh
Confidence            456667777777765443 5677777777766666666566677777777777              66665     33 


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILEL  382 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~  382 (848)
                      ..+..+++|++|++++|.+...+ ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.....
T Consensus        70 ~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~~~  139 (177)
T 2o6r_A           70 GVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCS  139 (177)
T ss_dssp             TTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCBCCC
T ss_pred             hHccCCCccCEEECCCCCccccCHHHhhCCcccCEEECcCCcceEeCHHHhcCCcccCEEEecCCCeecc
Confidence            33566666777777766666555 3356666666666666666666654 35566666666666655443

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.22  E-value=4.6e-11  Score=115.34  Aligned_cols=125  Identities=23%  Similarity=0.334  Sum_probs=101.4

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.+++++|.+..+|..+. +++++|++++|.+..+|.. |.++++|++|++++              +.+...    .+.
T Consensus        13 ~~l~~~~~~l~~ip~~~~-~~l~~L~L~~n~i~~ip~~-~~~l~~L~~L~Ls~--------------N~i~~i----~~~   72 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGIP-RDVTELYLDGNQFTLVPKE-LSNYKHLTLIDLSN--------------NRISTL----SNQ   72 (193)
T ss_dssp             TEEECTTSCCSSCCSCCC-TTCCEEECCSSCCCSCCGG-GGGCTTCCEEECCS--------------SCCCCC----CTT
T ss_pred             CEEEcCCCCCCcCCCCCC-CCCCEEECCCCcCchhHHH-hhcccCCCEEECCC--------------CcCCEe----CHh
Confidence            467888888888887663 6788899998888888854 67888999999988              778773    446


Q ss_pred             hhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYIL  380 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~  380 (848)
                      .|..+++|++|+|++|.+...+ ..+..+++|++|++++|.++.+|.. +..+++|++|++++|...
T Consensus        73 ~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~~~  139 (193)
T 2wfh_A           73 SFSNMTQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGANPLY  139 (193)
T ss_dssp             TTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             HccCCCCCCEEECCCCccCEeCHHHhCCCCCCCEEECCCCCCCeeChhhhhcCccccEEEeCCCCee
Confidence            6888889999999998887776 5688888999999999988888764 778888999998887654

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.22  E-value=3e-11  Score=115.01  Aligned_cols=136  Identities=17%  Similarity=0.184  Sum_probs=105.0

Q ss_pred             HccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcc-cCcEEEccCccccCCchhhccccCCCEEEccC
Q 003090          275 FQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLI-NLRTLRLHDRRIQGDLSLIGELSGLEILDLSE  353 (848)
Q Consensus       275 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~-~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~  353 (848)
                      +..+.+|+.|++++              +.+..     +|. +..+. +|++|++++|.+... +.++.+++|++|++++
T Consensus        15 ~~~~~~L~~L~l~~--------------n~l~~-----i~~-~~~~~~~L~~L~Ls~N~l~~~-~~l~~l~~L~~L~Ls~   73 (176)
T 1a9n_A           15 YTNAVRDRELDLRG--------------YKIPV-----IEN-LGATLDQFDAIDFSDNEIRKL-DGFPLLRRLKTLLVNN   73 (176)
T ss_dssp             EECTTSCEEEECTT--------------SCCCS-----CCC-GGGGTTCCSEEECCSSCCCEE-CCCCCCSSCCEEECCS
T ss_pred             cCCcCCceEEEeeC--------------CCCch-----hHH-hhhcCCCCCEEECCCCCCCcc-cccccCCCCCEEECCC
Confidence            45788899999999              77776     655 55555 899999999976654 7888899999999999


Q ss_pred             CCCcccChhh-ccCCcccEEeccCCccccccCh-hhhhccccccEEeccccccccccccccccccCcccchhhhcccCCC
Q 003090          354 SDVSEIPVSF-GRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRL  431 (848)
Q Consensus       354 ~~l~~lp~~i-~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L  431 (848)
                      |.++.+|..+ +.+++|++|++++|.. +.+|. ..+..+++|+.|++++|.+... +.         .....+..+++|
T Consensus        74 N~l~~~~~~~~~~l~~L~~L~L~~N~i-~~~~~~~~l~~l~~L~~L~l~~N~i~~~-~~---------~~~~~~~~l~~L  142 (176)
T 1a9n_A           74 NRICRIGEGLDQALPDLTELILTNNSL-VELGDLDPLASLKSLTYLCILRNPVTNK-KH---------YRLYVIYKVPQV  142 (176)
T ss_dssp             SCCCEECSCHHHHCTTCCEEECCSCCC-CCGGGGGGGGGCTTCCEEECCSSGGGGS-TT---------HHHHHHHHCTTC
T ss_pred             CcccccCcchhhcCCCCCEEECCCCcC-CcchhhHhhhcCCCCCEEEecCCCCCCc-Hh---------HHHHHHHHCCcc
Confidence            9999888665 8899999999999765 55665 2278899999999999887632 10         012247888899


Q ss_pred             cEEEeeccCCC
Q 003090          432 TSLHIHIPEGK  442 (848)
Q Consensus       432 ~~L~l~~~~~~  442 (848)
                      +.|+++.|...
T Consensus       143 ~~Ld~~~n~~~  153 (176)
T 1a9n_A          143 RVLDFQKVKLK  153 (176)
T ss_dssp             SEETTEECCHH
T ss_pred             ceeCCCcCCHH
Confidence            99988887643

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.22  E-value=1.4e-11  Score=144.29  Aligned_cols=152  Identities=22%  Similarity=0.224  Sum_probs=104.0

Q ss_pred             CceeeecCCCcccCCcc-ccccccee-----ecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDEL-ECPKLQAL-----FLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSP  309 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~-~~~~L~~L-----~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~  309 (848)
                      +.+++..|.+...+... ...+|+.+     ++.+|.+. ++...|..++.|++|+|++              +.+..  
T Consensus       176 ~~l~L~~n~~~~~~~~~l~~l~Ls~~~i~~~~~~~n~~~-~~~~~~~~l~~L~~L~Ls~--------------n~l~~--  238 (727)
T 4b8c_D          176 PKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMV-MPKDSKYDDQLWHALDLSN--------------LQIFN--  238 (727)
T ss_dssp             -----------------------------------------------CCCCCCEEECTT--------------SCCSC--
T ss_pred             ceEEeeCCCCCcchhhHhhcCccCcccccCcccccccee-cChhhhccCCCCcEEECCC--------------CCCCC--
Confidence            45566666666554433 33333332     33444444 4455678999999999999              88887  


Q ss_pred             CCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhh
Q 003090          310 LFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       310 ~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                         +|..+..+++|++|+|++|.+...+..++++++|++|+|++|.++.+|..+++|++|++|++++|.+ +.+|.. ++
T Consensus       239 ---l~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l-~~lp~~-~~  313 (727)
T 4b8c_D          239 ---ISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMV-TTLPWE-FG  313 (727)
T ss_dssp             ---CCGGGGGCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCSSCCSSGGGGTTCSEEECCSSCC-CCCCSS-TT
T ss_pred             ---CChhhcCCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCCccChhhcCCCCCCEEECCCCCC-CccChh-hh
Confidence               9999999999999999999998777889999999999999999999999999999999999999865 589998 89


Q ss_pred             ccccccEEeccccccccccc
Q 003090          390 RLRKLEELYMSHSFRHWQFE  409 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~~~~~  409 (848)
                      ++++|++|++++|.+.+.++
T Consensus       314 ~l~~L~~L~L~~N~l~~~~p  333 (727)
T 4b8c_D          314 NLCNLQFLGVEGNPLEKQFL  333 (727)
T ss_dssp             SCTTCCCEECTTSCCCSHHH
T ss_pred             cCCCccEEeCCCCccCCCCh
Confidence            99999999999999987633

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=99.20  E-value=1.2e-12  Score=127.33  Aligned_cols=137  Identities=20%  Similarity=0.236  Sum_probs=63.0

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCc-------ccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccc
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIH-------EVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRF  292 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~-------~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~  292 (848)
                      ......+.+.....++.++++.+.+.       .+|..+ .+++|++|++++|.+..+|  .+.++++|++|++++    
T Consensus         6 ~~~~~~~~~~~~~~l~~l~l~~~~l~~~~~~l~~l~~~~~~l~~L~~L~ls~n~l~~l~--~~~~l~~L~~L~l~~----   79 (198)
T 1ds9_A            6 TIKDAIRIFEERKSVVATEAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKIS--SLSGMENLRILSLGR----   79 (198)
T ss_dssp             CHHHHHHHHHHTTCCCCTTCSEEECCBCCTTCCCCHHHHHHTTTCSEEECSEEEESCCC--CHHHHTTCCEEEEEE----
T ss_pred             HHHHHHHHHHhcccccCcchheeEeccccCcHhhhhHHHhcCCCCCEEECCCCCCcccc--ccccCCCCCEEECCC----
Confidence            34444444444444544444444443       222223 4445555555555444444  134455555555555    


Q ss_pred             cccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh--hhccCCccc
Q 003090          293 SFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV--SFGRLSHLR  370 (848)
Q Consensus       293 ~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~  370 (848)
                                +.+..     +|..+..+++|++|++++|.+.. ++.++.+++|++|++++|.++.+|.  .+..+++|+
T Consensus        80 ----------n~l~~-----l~~~~~~~~~L~~L~L~~N~l~~-l~~~~~l~~L~~L~l~~N~i~~~~~~~~l~~l~~L~  143 (198)
T 1ds9_A           80 ----------NLIKK-----IENLDAVADTLEELWISYNQIAS-LSGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLE  143 (198)
T ss_dssp             ----------EEECS-----CSSHHHHHHHCSEEEEEEEECCC-HHHHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCS
T ss_pred             ----------CCccc-----ccchhhcCCcCCEEECcCCcCCc-CCccccCCCCCEEECCCCcCCchhHHHHHhcCCCCC
Confidence                      44443     44444444555555555554333 2244445555555555554444332  344445555


Q ss_pred             EEeccCCcc
Q 003090          371 LLDLTGCYI  379 (848)
Q Consensus       371 ~L~l~~~~~  379 (848)
                      +|++++|..
T Consensus       144 ~L~l~~N~l  152 (198)
T 1ds9_A          144 DLLLAGNPL  152 (198)
T ss_dssp             EEEECSCHH
T ss_pred             EEEecCCcc
Confidence            555544433

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.14  E-value=2.2e-10  Score=109.09  Aligned_cols=129  Identities=22%  Similarity=0.332  Sum_probs=95.8

Q ss_pred             cceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC
Q 003090          257 LQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD  336 (848)
Q Consensus       257 L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~  336 (848)
                      .+.++++++.+..+|..+   .++|+.|++++              +.+...    .+..+..+++|++|++++|.+...
T Consensus         9 ~~~l~~~~~~l~~~p~~~---~~~l~~L~l~~--------------n~l~~~----~~~~~~~l~~L~~L~l~~n~l~~~   67 (177)
T 2o6r_A            9 GTEIRCNSKGLTSVPTGI---PSSATRLELES--------------NKLQSL----PHGVFDKLTQLTKLSLSQNQIQSL   67 (177)
T ss_dssp             TTEEECCSSCCSSCCTTC---CTTCSEEECCS--------------SCCCCC----CTTTTTTCTTCSEEECCSSCCCCC
T ss_pred             CCEEEecCCCCccCCCCC---CCCCcEEEeCC--------------CcccEe----CHHHhcCcccccEEECCCCcceEe
Confidence            466777888888887643   46788888888              777762    334467888888888888877766


Q ss_pred             c-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEeccccccccc
Q 003090          337 L-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQ  407 (848)
Q Consensus       337 ~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~  407 (848)
                      + ..++.+++|++|++++|.++.+|.. +..+++|++|++++|.+. .+|...+..+++|++|++++|.+...
T Consensus        68 ~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~-~~~~~~~~~l~~L~~L~l~~N~~~~~  139 (177)
T 2o6r_A           68 PDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELALDTNQLK-SVPDGIFDRLTSLQKIWLHTNPWDCS  139 (177)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCS-CCCTTTTTTCTTCCEEECCSSCBCCC
T ss_pred             ChhHccCCCccCEEECCCCCccccCHHHhhCCcccCEEECcCCcce-EeCHHHhcCCcccCEEEecCCCeecc
Confidence            6 4467888888888888888877764 577888888888887554 56666567788888888888876543

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=99.13  E-value=9.1e-11  Score=132.93  Aligned_cols=76  Identities=16%  Similarity=0.147  Sum_probs=68.8

Q ss_pred             cchhHHHHHHHHHHhcC---CccEEEEEeCCCCchhHHHHHHHH--HHhhccccCcEEEEEeccCC--chhHHHHHHHhc
Q 003090          160 KSRESTMKDIMEAMKDE---NVSITGICGMGGVGKTTLVKEIQK--QAKEMKMFDDVAMAVVSQTP--SITKIQYEIAGW  232 (848)
Q Consensus       160 vG~~~~~~~i~~~L~~~---~~~vi~i~G~gG~GKTtla~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~  232 (848)
                      |||++++++|.++|...   +.++|+|+||||+||||||+++|+  +.++..+|+.++|+++++.+  +...+.+.|+..
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            69999999999999843   679999999999999999999999  67889999999999999985  888999999987


Q ss_pred             cCC
Q 003090          233 LDL  235 (848)
Q Consensus       233 ~~l  235 (848)
                      +..
T Consensus       211 l~~  213 (549)
T 2a5y_B          211 LKS  213 (549)
T ss_dssp             HTT
T ss_pred             Hhc
Confidence            754

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=99.13  E-value=4.2e-12  Score=123.55  Aligned_cols=142  Identities=23%  Similarity=0.244  Sum_probs=95.6

Q ss_pred             cccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCC
Q 003090          268 LAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE  347 (848)
Q Consensus       268 ~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~  347 (848)
                      ..+|.. +..+++|++|++++              +.+..     +| .+..+++|++|++++|.+...+..+..+++|+
T Consensus        38 ~~l~~~-~~~l~~L~~L~ls~--------------n~l~~-----l~-~~~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~   96 (198)
T 1ds9_A           38 EKMDAT-LSTLKACKHLALST--------------NNIEK-----IS-SLSGMENLRILSLGRNLIKKIENLDAVADTLE   96 (198)
T ss_dssp             CCCHHH-HHHTTTCSEEECSE--------------EEESC-----CC-CHHHHTTCCEEEEEEEEECSCSSHHHHHHHCS
T ss_pred             hhhhHH-HhcCCCCCEEECCC--------------CCCcc-----cc-ccccCCCCCEEECCCCCcccccchhhcCCcCC
Confidence            334443 56788888888888              66766     66 77888888888888887776666677778888


Q ss_pred             EEEccCCCCcccChhhccCCcccEEeccCCccccccCh-hhhhccccccEEeccccccccccccccccccCcccchhhhc
Q 003090          348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELG  426 (848)
Q Consensus       348 ~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~  426 (848)
                      +|++++|.++.+| .+..+++|++|++++|... .++. ..+..+++|++|++++|.+....+..   ..........+.
T Consensus        97 ~L~L~~N~l~~l~-~~~~l~~L~~L~l~~N~i~-~~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~---~~~~~~~~~~~~  171 (198)
T 1ds9_A           97 ELWISYNQIASLS-GIEKLVNLRVLYMSNNKIT-NWGEIDKLAALDKLEDLLLAGNPLYNDYKEN---NATSEYRIEVVK  171 (198)
T ss_dssp             EEEEEEEECCCHH-HHHHHHHSSEEEESEEECC-CHHHHHHHTTTTTCSEEEECSCHHHHHHHTT---TTHHHHHHHHHH
T ss_pred             EEECcCCcCCcCC-ccccCCCCCEEECCCCcCC-chhHHHHHhcCCCCCEEEecCCccccccccc---cchHHHHHHHHH
Confidence            8888888888776 5777888888888886553 3333 22677888888888888765432110   000011123367


Q ss_pred             ccCCCcEEE
Q 003090          427 ALSRLTSLH  435 (848)
Q Consensus       427 ~l~~L~~L~  435 (848)
                      .+++|+.|+
T Consensus       172 ~l~~L~~Ld  180 (198)
T 1ds9_A          172 RLPNLKKLD  180 (198)
T ss_dssp             HCSSCSEEC
T ss_pred             hCCCcEEEC
Confidence            777777776

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=99.12  E-value=2.3e-10  Score=121.10  Aligned_cols=191  Identities=19%  Similarity=0.213  Sum_probs=138.1

Q ss_pred             ccCCCceeeecCCCc--------------------ccCCcc--c--------ccccceeecccCcCcccChHHHccCCce
Q 003090          232 WLDLTGISLMFNDIH--------------------EVPDEL--E--------CPKLQALFLQENSPLAIPDRFFQGMKDL  281 (848)
Q Consensus       232 ~~~l~~l~l~~n~l~--------------------~lp~~~--~--------~~~L~~L~l~~~~~~~~~~~~~~~~~~L  281 (848)
                      ...++.|+|++|++.                    .+|...  +        |++|+.+.+.. .+..+++..|.++++|
T Consensus        48 l~~L~~LdLs~n~i~~~~~~~~~~~~~~~~~~~~~~I~~~aF~~~~~~~~~g~~~L~~l~L~~-~i~~I~~~aF~~~~~L  126 (329)
T 3sb4_A           48 FPSLKVLDISNAEIKMYSGKAGTYPNGKFYIYMANFVPAYAFSNVVNGVTKGKQTLEKVILSE-KIKNIEDAAFKGCDNL  126 (329)
T ss_dssp             CTTCCEEEEEEEEECCEEESSSSSGGGCCEEECTTEECTTTTEEEETTEEEECTTCCC-CBCT-TCCEECTTTTTTCTTC
T ss_pred             hccCeEEecCcceeEEecCccccccccccccccccccCHHHhcccccccccccCCCcEEECCc-cccchhHHHhhcCccc
Confidence            456889999999887                    445444  6        89999999998 7888999889999999


Q ss_pred             eEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccC-------------------------------
Q 003090          282 QVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHD-------------------------------  330 (848)
Q Consensus       282 r~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~-------------------------------  330 (848)
                      +.+++.++              .+...    -+..|..+.++.++.+..                               
T Consensus       127 ~~l~l~~n--------------~i~~i----~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~~L~~~i~~~~~~  188 (329)
T 3sb4_A          127 KICQIRKK--------------TAPNL----LPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGEPLETTIQVGAMG  188 (329)
T ss_dssp             CEEEBCCS--------------SCCEE----CTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESCCCEEEEEECTTC
T ss_pred             ceEEcCCC--------------Ccccc----chhhhcCCCceEEecCcchhhhhccccccccccccccccceeEEecCCC
Confidence            99999983              33321    222333333333333332                               


Q ss_pred             -----------------------ccccCCchhh-ccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccCh
Q 003090          331 -----------------------RRIQGDLSLI-GELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPR  385 (848)
Q Consensus       331 -----------------------~~~~~~~~~i-~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~  385 (848)
                                             .-.......+ ..+.+|+.|++++|.++.+|.. +.++.+|+.+++.++  ...++.
T Consensus       189 ~l~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n~i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~  266 (329)
T 3sb4_A          189 KLEDEIMKAGLQPRDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKTNATTIPDFTFAQKKYLLKIKLPHN--LKTIGQ  266 (329)
T ss_dssp             CHHHHHHHTTCCGGGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTBCCCEECTTTTTTCTTCCEEECCTT--CCEECT
T ss_pred             cHHHHHhhcccCccccceEEEeeeecHHHHHHHHHhcCCCeEEECCCCCcceecHhhhhCCCCCCEEECCcc--cceehH
Confidence                                   1000000111 1378999999999999988864 888999999999986  677888


Q ss_pred             hhhhcccccc-EEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEE
Q 003090          386 GVLSRLRKLE-ELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFS  457 (848)
Q Consensus       386 ~~l~~l~~L~-~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~  457 (848)
                      ..|.++++|+ .+.+.. .+...             ....+.++++|+.+++..+.+..++...  .+++|+.++
T Consensus       267 ~aF~~~~~L~~~l~l~~-~l~~I-------------~~~aF~~c~~L~~l~l~~n~i~~I~~~aF~~~~~L~~ly  327 (329)
T 3sb4_A          267 RVFSNCGRLAGTLELPA-SVTAI-------------EFGAFMGCDNLRYVLATGDKITTLGDELFGNGVPSKLIY  327 (329)
T ss_dssp             TTTTTCTTCCEEEEECT-TCCEE-------------CTTTTTTCTTEEEEEECSSCCCEECTTTTCTTCCCCEEE
T ss_pred             HHhhCChhccEEEEEcc-cceEE-------------chhhhhCCccCCEEEeCCCccCccchhhhcCCcchhhhc
Confidence            8899999999 999877 44332             3467889999999999999998888765  778888765

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=99.03  E-value=8e-10  Score=116.91  Aligned_cols=293  Identities=11%  Similarity=0.068  Sum_probs=172.7

Q ss_pred             hcccCcEEEccCccccCCchhhcc-ccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhc-------
Q 003090          319 FLINLRTLRLHDRRIQGDLSLIGE-LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSR-------  390 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~~~i~~-l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~-------  390 (848)
                      .+.+++.|.++++-.......+.. +++|++|||++|.+......-+.++.++.+.+..+    .+|...+.+       
T Consensus        23 ~~~~l~~L~l~g~i~~~~~~~l~~~l~~L~~LdLs~n~i~~~~~~~~~~~~~~~~~~~~~----~I~~~aF~~~~~~~~~   98 (329)
T 3sb4_A           23 EANSITHLTLTGKLNAEDFRHLRDEFPSLKVLDISNAEIKMYSGKAGTYPNGKFYIYMAN----FVPAYAFSNVVNGVTK   98 (329)
T ss_dssp             HHHHCSEEEEEEEECHHHHHHHHHSCTTCCEEEEEEEEECCEEESSSSSGGGCCEEECTT----EECTTTTEEEETTEEE
T ss_pred             hhCceeEEEEeccccHHHHHHHHHhhccCeEEecCcceeEEecCcccccccccccccccc----ccCHHHhccccccccc
Confidence            477899999998622223355555 88999999999988822211223333455555543    567766778       


Q ss_pred             -cccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCCCeEEEEeCCCCCCC
Q 003090          391 -LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNLTSFSIAIGDLEERP  467 (848)
Q Consensus       391 -l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L~~L~l~~~~~~~~~  467 (848)
                       +++|+.+.+.. .+...             ....+.++++|+.|++..|.+..++...  .+.++.  .+.        
T Consensus        99 g~~~L~~l~L~~-~i~~I-------------~~~aF~~~~~L~~l~l~~n~i~~i~~~aF~~~~~l~--~l~--------  154 (329)
T 3sb4_A           99 GKQTLEKVILSE-KIKNI-------------EDAAFKGCDNLKICQIRKKTAPNLLPEALADSVTAI--FIP--------  154 (329)
T ss_dssp             ECTTCCC-CBCT-TCCEE-------------CTTTTTTCTTCCEEEBCCSSCCEECTTSSCTTTCEE--EEC--------
T ss_pred             ccCCCcEEECCc-cccch-------------hHHHhhcCcccceEEcCCCCccccchhhhcCCCceE--Eec--------
Confidence             99999999987 55443             3356888999999999988777665543  111111  111        


Q ss_pred             CCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCce
Q 003090          468 LSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMK  547 (848)
Q Consensus       468 ~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~  547 (848)
                                                                    +......         .....+......+|..++
T Consensus       155 ----------------------------------------------~~~~~~~---------~~~~~i~~~~f~~~~~L~  179 (329)
T 3sb4_A          155 ----------------------------------------------LGSSDAY---------RFKNRWEHFAFIEGEPLE  179 (329)
T ss_dssp             ----------------------------------------------TTCTHHH---------HTSTTTTTSCEEESCCCE
T ss_pred             ----------------------------------------------Ccchhhh---------hccccccccccccccccc
Confidence                                                          0000000         000111111122222222


Q ss_pred             eecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCC
Q 003090          548 YLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGL  627 (848)
Q Consensus       548 ~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~  627 (848)
                      .                 .+.+.....+......  ..-...++..+.+.+.-.- ... ..+...+++|++|++.++. 
T Consensus       180 ~-----------------~i~~~~~~~l~~~~~~--~~~~~~~~~~l~~~~~l~~-~~~-~~l~~~~~~L~~l~L~~n~-  237 (329)
T 3sb4_A          180 T-----------------TIQVGAMGKLEDEIMK--AGLQPRDINFLTIEGKLDN-ADF-KLIRDYMPNLVSLDISKTN-  237 (329)
T ss_dssp             E-----------------EEEECTTCCHHHHHHH--TTCCGGGCSEEEEEECCCH-HHH-HHHHHHCTTCCEEECTTBC-
T ss_pred             e-----------------eEEecCCCcHHHHHhh--cccCccccceEEEeeeecH-HHH-HHHHHhcCCCeEEECCCCC-
Confidence            1                 1112111111111000  0012455667777664322 222 2233458899999998754 


Q ss_pred             ceeeeeccccccccccccccCCcCEEecCCCccccccccCCCccccccCcc-EEEeecCccccccccCccccccccceee
Q 003090          628 LVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLK-KVRVEECDELRQVFPANFGKKAAAEEMV  706 (848)
Q Consensus       628 l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~-~L~i~~C~~L~~~~p~~~~~~~~~~~l~  706 (848)
                      ++.++.        ..+..+++|++|++.+  +++.++...  |.++++|+ .+.+.+  +++.+-              
T Consensus       238 i~~I~~--------~aF~~~~~L~~l~l~~--ni~~I~~~a--F~~~~~L~~~l~l~~--~l~~I~--------------  289 (329)
T 3sb4_A          238 ATTIPD--------FTFAQKKYLLKIKLPH--NLKTIGQRV--FSNCGRLAGTLELPA--SVTAIE--------------  289 (329)
T ss_dssp             CCEECT--------TTTTTCTTCCEEECCT--TCCEECTTT--TTTCTTCCEEEEECT--TCCEEC--------------
T ss_pred             cceecH--------hhhhCCCCCCEEECCc--ccceehHHH--hhCChhccEEEEEcc--cceEEc--------------
Confidence            677764        5678889999999987  488887764  78888998 888876  455431              


Q ss_pred             eccccccceeeeecCCCCCCCCCCCCccEEEEecCCCCceecccchhhccccccEEE
Q 003090          707 LYRKRRDQIHIHATTSTSSPTPSLGNLVSITIRGCGKLRNLFTTSMVKSLVRLESLE  763 (848)
Q Consensus       707 l~~l~~~~l~i~~c~~~~~~~~~l~~L~~L~i~~C~~L~~l~~~~~~~~l~~L~~L~  763 (848)
                                       ...+..+++|++|++.+ ++++.++. ..+.++++|++++
T Consensus       290 -----------------~~aF~~c~~L~~l~l~~-n~i~~I~~-~aF~~~~~L~~ly  327 (329)
T 3sb4_A          290 -----------------FGAFMGCDNLRYVLATG-DKITTLGD-ELFGNGVPSKLIY  327 (329)
T ss_dssp             -----------------TTTTTTCTTEEEEEECS-SCCCEECT-TTTCTTCCCCEEE
T ss_pred             -----------------hhhhhCCccCCEEEeCC-CccCccch-hhhcCCcchhhhc
Confidence                             23456788999999876 67888854 5677888888876

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=99.00  E-value=7.2e-10  Score=104.83  Aligned_cols=102  Identities=22%  Similarity=0.279  Sum_probs=65.1

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      +.+++++|.+..+|..+   .++|++|++++              +.+...    .|..+..+++|++|+|++|.+...+
T Consensus        15 ~~l~~~~n~l~~iP~~~---~~~L~~L~Ls~--------------N~l~~~----~~~~~~~l~~L~~L~Ls~N~l~~i~   73 (174)
T 2r9u_A           15 TLVNCQNIRLASVPAGI---PTDKQRLWLNN--------------NQITKL----EPGVFDHLVNLQQLYFNSNKLTAIP   73 (174)
T ss_dssp             SEEECCSSCCSSCCSCC---CTTCSEEECCS--------------SCCCCC----CTTTTTTCTTCCEEECCSSCCCCCC
T ss_pred             cEEEeCCCCCCccCCCc---CCCCcEEEeCC--------------CCcccc----CHHHhcCCcCCCEEECCCCCCCccC
Confidence            45566666666666543   25666666666              666653    3555666667777777777666655


Q ss_pred             h-hhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccc
Q 003090          338 S-LIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYIL  380 (848)
Q Consensus       338 ~-~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~  380 (848)
                      . .+.++++|++|++++|.++.+|.. +..+++|++|++++|.+.
T Consensus        74 ~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~~~  118 (174)
T 2r9u_A           74 TGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYLYNNPWD  118 (174)
T ss_dssp             TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCBC
T ss_pred             hhHhCCcchhhEEECCCCccceeCHHHhccccCCCEEEeCCCCcc
Confidence            3 346677777777777777766654 667777777777776543

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.96  E-value=1.5e-09  Score=102.20  Aligned_cols=102  Identities=21%  Similarity=0.222  Sum_probs=62.0

Q ss_pred             ceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc
Q 003090          258 QALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL  337 (848)
Q Consensus       258 ~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~  337 (848)
                      +++++++|.+..+|..+   .++|++|++++              |.+...    .|..+..+++|++|++++|.+...+
T Consensus        12 ~~l~~s~n~l~~ip~~~---~~~l~~L~L~~--------------N~i~~~----~~~~~~~l~~L~~L~Ls~N~l~~l~   70 (170)
T 3g39_A           12 TTVDCSGKSLASVPTGI---PTTTQVLYLYD--------------NQITKL----EPGVFDRLTQLTRLDLDNNQLTVLP   70 (170)
T ss_dssp             TEEECTTSCCSSCCSCC---CTTCSEEECCS--------------SCCCCC----CTTTTTTCTTCSEEECCSSCCCCCC
T ss_pred             CEEEeCCCCcCccCccC---CCCCcEEEcCC--------------CcCCcc----ChhhhcCcccCCEEECCCCCcCccC
Confidence            45555555555555432   25566666666              556552    3455666666666666666665555


Q ss_pred             -hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccc
Q 003090          338 -SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYIL  380 (848)
Q Consensus       338 -~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~  380 (848)
                       ..+..+++|++|++++|.++.+|.. +.++++|++|++++|.+.
T Consensus        71 ~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~~~  115 (170)
T 3g39_A           71 AGVFDKLTQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWLLNNPWD  115 (170)
T ss_dssp             TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCBC
T ss_pred             hhhccCCCCCCEEECCCCccCEeCHHHhcCCCCCCEEEeCCCCCC
Confidence             3346667777777777777766653 666777777777776544

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.95  E-value=1.8e-09  Score=102.00  Aligned_cols=84  Identities=25%  Similarity=0.447  Sum_probs=40.5

Q ss_pred             ccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEe
Q 003090          321 INLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY  398 (848)
Q Consensus       321 ~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~  398 (848)
                      .+|++|++++|.+...+ ..++++++|++|++++|+++.+|.. +.++++|++|++++|.+. .+|.+.+..+++|++|+
T Consensus        33 ~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~-~l~~~~~~~l~~L~~L~  111 (174)
T 2r9u_A           33 TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLK-SIPRGAFDNLKSLTHIY  111 (174)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCTTCSEEE
T ss_pred             CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccc-eeCHHHhccccCCCEEE
Confidence            44555555555444443 3445555555555555555544443 244555555555554332 33433344555555555


Q ss_pred             ccccccc
Q 003090          399 MSHSFRH  405 (848)
Q Consensus       399 l~~~~~~  405 (848)
                      +++|.+.
T Consensus       112 L~~N~~~  118 (174)
T 2r9u_A          112 LYNNPWD  118 (174)
T ss_dssp             CCSSCBC
T ss_pred             eCCCCcc
Confidence            5555443

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.91  E-value=2.9e-09  Score=100.29  Aligned_cols=84  Identities=25%  Similarity=0.434  Sum_probs=42.1

Q ss_pred             ccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccccEEe
Q 003090          321 INLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY  398 (848)
Q Consensus       321 ~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~  398 (848)
                      .+|++|++++|.+...+ ..+.++++|++|++++|+++.+|.. +..+++|++|++++|.+. .+|.+.+.++++|++|+
T Consensus        30 ~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~-~~~~~~~~~l~~L~~L~  108 (170)
T 3g39_A           30 TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLK-SIPRGAFDNLKSLTHIW  108 (170)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCC-CCCTTTTTTCTTCCEEE
T ss_pred             CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccC-EeCHHHhcCCCCCCEEE
Confidence            44555555555554443 3455555555555555555554443 345555555555554332 23333345555555555


Q ss_pred             ccccccc
Q 003090          399 MSHSFRH  405 (848)
Q Consensus       399 l~~~~~~  405 (848)
                      +++|.+.
T Consensus       109 L~~N~~~  115 (170)
T 3g39_A          109 LLNNPWD  115 (170)
T ss_dssp             CCSSCBC
T ss_pred             eCCCCCC
Confidence            5555443

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.79  E-value=1.7e-09  Score=115.61  Aligned_cols=114  Identities=17%  Similarity=0.132  Sum_probs=57.7

Q ss_pred             hcccCcEEEccCccccCCc-hhh-----ccccCCCEEEccCCCCcc-----cChhhccCCcccEEeccCCccccc----c
Q 003090          319 FLINLRTLRLHDRRIQGDL-SLI-----GELSGLEILDLSESDVSE-----IPVSFGRLSHLRLLDLTGCYILEL----I  383 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~-~~i-----~~l~~L~~L~l~~~~l~~-----lp~~i~~L~~L~~L~l~~~~~~~~----~  383 (848)
                      .+.+|++|+|++|.+.... ..+     ....+|++|++++|.++.     ++..+..+++|++|++++|.+...    +
T Consensus       124 ~L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~l~~~g~~~L  203 (372)
T 3un9_A          124 VFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELL  203 (372)
T ss_dssp             HHHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSSCHHHHHHHH
T ss_pred             HHHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCCCCcHHHHHH
Confidence            3445566666665443221 222     234556666666665542     344445566666666666543221    1


Q ss_pred             ChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          384 PRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       384 p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      +.. +...++|++|++++|.+...         ...+....+...++|++|++++|.++
T Consensus       204 ~~~-L~~~~~L~~L~Ls~N~i~~~---------g~~~l~~~L~~~~~L~~L~Ls~N~i~  252 (372)
T 3un9_A          204 AAQ-LDRNRQLQELNVAYNGAGDT---------AALALARAAREHPSLELLHLYFNELS  252 (372)
T ss_dssp             HHH-GGGCSCCCEEECCSSCCCHH---------HHHHHHHHHHHCSSCCEEECTTSSCC
T ss_pred             HHH-HhcCCCcCeEECCCCCCCHH---------HHHHHHHHHHhCCCCCEEeccCCCCC
Confidence            222 44555666666666655432         11123344555566666666666554

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=98.75  E-value=7.3e-09  Score=119.74  Aligned_cols=74  Identities=16%  Similarity=0.046  Sum_probs=66.4

Q ss_pred             ccchhHHHHHHHHHHhc-CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCc-EEEEEeccCCchhHHHHHHHhc
Q 003090          159 FKSRESTMKDIMEAMKD-ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDD-VAMAVVSQTPSITKIQYEIAGW  232 (848)
Q Consensus       159 ~vG~~~~~~~i~~~L~~-~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~l~~~i~~~  232 (848)
                      .|||+++++++.++|.. ++.++|+|+||||+||||||+.+|++.++..+|+. ++|+++++.++...+...+.+.
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~l  205 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL  205 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            49999999999999985 56889999999999999999999999888899997 9999999999887777776653

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.60  E-value=1.2e-08  Score=109.11  Aligned_cols=163  Identities=15%  Similarity=0.083  Sum_probs=116.7

Q ss_pred             HHHHHHHhccCCCceeeecCCCcccC-----Ccc--cccccceeecccCcCcccC-hHHHccCCceeEEEccCccccccc
Q 003090          224 KIQYEIAGWLDLTGISLMFNDIHEVP-----DEL--ECPKLQALFLQENSPLAIP-DRFFQGMKDLQVLDLGGIRRFSFS  295 (848)
Q Consensus       224 ~l~~~i~~~~~l~~l~l~~n~l~~lp-----~~~--~~~~L~~L~l~~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~  295 (848)
                      .+.+++..  .++.+++++|.+....     ..+  ..++|++|++++|.++... ..+...+++|+.|+|++       
T Consensus        65 ~l~~~~~~--~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~-------  135 (372)
T 3un9_A           65 RFSAEVLS--SLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQL-------  135 (372)
T ss_dssp             HHHHHHHT--TCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCS-------
T ss_pred             HHHHHHHh--hCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCC-------
Confidence            34444443  4678999999988432     222  2368999999999775432 23344567899999999       


Q ss_pred             ccCCCCCCCCCCCCCCCCCchh-----hhcccCcEEEccCccccCCc-----hhhccccCCCEEEccCCCCc-----ccC
Q 003090          296 VRFPFLFPPLPSSPLFLLPSSL-----SFLINLRTLRLHDRRIQGDL-----SLIGELSGLEILDLSESDVS-----EIP  360 (848)
Q Consensus       296 ~~~~~~~~~l~~~~~~~lp~~~-----~~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L~l~~~~l~-----~lp  360 (848)
                             |.+...    -...+     ....+|++|+|++|.+....     ..+..+++|++|++++|.+.     .++
T Consensus       136 -------n~l~~~----~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~l~~~g~~~L~  204 (372)
T 3un9_A          136 -------NSLGPE----ACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLA  204 (372)
T ss_dssp             -------SCCCHH----HHHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSSCHHHHHHHHH
T ss_pred             -------CCCCHH----HHHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCCCCcHHHHHHH
Confidence                   776552    12222     23578999999999765422     44578899999999999987     345


Q ss_pred             hhhccCCcccEEeccCCccccc----cChhhhhccccccEEeccccccccc
Q 003090          361 VSFGRLSHLRLLDLTGCYILEL----IPRGVLSRLRKLEELYMSHSFRHWQ  407 (848)
Q Consensus       361 ~~i~~L~~L~~L~l~~~~~~~~----~p~~~l~~l~~L~~L~l~~~~~~~~  407 (848)
                      ..+...++|++|++++|.+...    ++.. +...++|++|++++|.+...
T Consensus       205 ~~L~~~~~L~~L~Ls~N~i~~~g~~~l~~~-L~~~~~L~~L~Ls~N~i~~~  254 (372)
T 3un9_A          205 AQLDRNRQLQELNVAYNGAGDTAALALARA-AREHPSLELLHLYFNELSSE  254 (372)
T ss_dssp             HHGGGCSCCCEEECCSSCCCHHHHHHHHHH-HHHCSSCCEEECTTSSCCHH
T ss_pred             HHHhcCCCcCeEECCCCCCCHHHHHHHHHH-HHhCCCCCEEeccCCCCCHH
Confidence            6678889999999999876532    3333 55679999999999988654

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.55  E-value=1.3e-07  Score=100.83  Aligned_cols=102  Identities=18%  Similarity=0.204  Sum_probs=53.8

Q ss_pred             ceeeecC-CCcccCCcc-cccccceeeccc-CcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          237 GISLMFN-DIHEVPDEL-ECPKLQALFLQE-NSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       237 ~l~l~~n-~l~~lp~~~-~~~~L~~L~l~~-~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++++++ .+..+|. + .+++|++|+|++ |.+..++...|.++++|++|+|++              |.+.+.    .
T Consensus        12 ~v~~~~~n~l~~ip~-l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~--------------N~l~~~----~   72 (347)
T 2ifg_A           12 GLRCTRDGALDSLHH-LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVK--------------SGLRFV----A   72 (347)
T ss_dssp             CEECCSSCCCTTTTT-SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCS--------------SCCCEE----C
T ss_pred             EEEcCCCCCCCccCC-CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCC--------------Ccccee----C
Confidence            3555555 6666666 4 555666666664 666666655556666666666666              555552    3


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS  357 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~  357 (848)
                      |..|.++++|++|+|++|.+...++.+.....|++|++.+|.+.
T Consensus        73 ~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~~L~~l~l~~N~~~  116 (347)
T 2ifg_A           73 PDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPLH  116 (347)
T ss_dssp             TTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCCEEECCSSCCC
T ss_pred             HHHhcCCcCCCEEeCCCCccceeCHHHcccCCceEEEeeCCCcc
Confidence            33455555555555555544444422221112444444444443

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.53  E-value=6.8e-07  Score=96.42  Aligned_cols=176  Identities=14%  Similarity=0.165  Sum_probs=115.5

Q ss_pred             CCcccCCcc-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhccc
Q 003090          244 DIHEVPDEL-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLIN  322 (848)
Q Consensus       244 ~l~~lp~~~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~  322 (848)
                      .++.++... .-.+|+.+.+..+ +..++...|.++ +|+.+.+..               .+...    -+.+|..|.+
T Consensus       123 ~i~~I~~~aF~~~~L~~i~l~~~-i~~I~~~aF~~~-~L~~i~lp~---------------~l~~I----~~~aF~~c~~  181 (401)
T 4fdw_A          123 SVKSIPKDAFRNSQIAKVVLNEG-LKSIGDMAFFNS-TVQEIVFPS---------------TLEQL----KEDIFYYCYN  181 (401)
T ss_dssp             TCCEECTTTTTTCCCSEEECCTT-CCEECTTTTTTC-CCCEEECCT---------------TCCEE----CSSTTTTCTT
T ss_pred             ccCEehHhhcccCCccEEEeCCC-ccEECHHhcCCC-CceEEEeCC---------------CccEe----hHHHhhCccc
Confidence            455555544 2236888888766 667777777774 688888764               23331    2356888888


Q ss_pred             CcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEeccc
Q 003090          323 LRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH  401 (848)
Q Consensus       323 L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~  401 (848)
                      |+.+++..+.+...+.......+|+.+.+..+ ++.++. .+.++.+|+.+++..+  ...++...+.+ .+|+.+.+..
T Consensus       182 L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp~~-l~~I~~~aF~~~~~L~~l~l~~~--l~~I~~~aF~~-~~L~~i~lp~  257 (401)
T 4fdw_A          182 LKKADLSKTKITKLPASTFVYAGIEEVLLPVT-LKEIGSQAFLKTSQLKTIEIPEN--VSTIGQEAFRE-SGITTVKLPN  257 (401)
T ss_dssp             CCEEECTTSCCSEECTTTTTTCCCSEEECCTT-CCEECTTTTTTCTTCCCEECCTT--CCEECTTTTTT-CCCSEEEEET
T ss_pred             CCeeecCCCcceEechhhEeecccCEEEeCCc-hheehhhHhhCCCCCCEEecCCC--ccCcccccccc-CCccEEEeCC
Confidence            99999988766666533333688888888744 666654 4778888999988863  46677765666 7888888844


Q ss_pred             cccccccccccccccCcccchhhhcccCCCcEEEeeccCCC-----CCCCCC--ccCCCCeEEE
Q 003090          402 SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK-----IMPSDM--SFQNLTSFSI  458 (848)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~-----~~~~~~--~~~~L~~L~l  458 (848)
                      + +...             ....+.++++|+.+.+.++...     .++...  .+++|+.+.+
T Consensus       258 ~-i~~I-------------~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l  307 (401)
T 4fdw_A          258 G-VTNI-------------ASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEI  307 (401)
T ss_dssp             T-CCEE-------------CTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECC
T ss_pred             C-ccEE-------------ChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEe
Confidence            3 3222             3356788888999988876554     233332  4555555443

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=98.49  E-value=4.1e-08  Score=123.94  Aligned_cols=68  Identities=18%  Similarity=0.239  Sum_probs=56.6

Q ss_pred             cccccccchhHHHHHHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHHhh-ccc-cCcEEEEEeccCCc
Q 003090          154 EGVYAFKSRESTMKDIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQAKE-MKM-FDDVAMAVVSQTPS  221 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~~~-~~~-F~~~~wv~vs~~~~  221 (848)
                      .....+|||+++++++.++|.  +.+.++|+|+||||+||||||+.+|++.++ ..+ |+.+.|+++++..+
T Consensus       121 ~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~  192 (1249)
T 3sfz_A          121 QRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDK  192 (1249)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCH
T ss_pred             CCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCc
Confidence            345679999999999999996  467889999999999999999999987654 444 46677999998554

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.46  E-value=1.1e-06  Score=100.88  Aligned_cols=74  Identities=19%  Similarity=0.287  Sum_probs=60.3

Q ss_pred             ccccccchhHHHHHHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHHhh-cccc-CcEEEEEeccCCchhHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQAKE-MKMF-DDVAMAVVSQTPSITKIQYEI  229 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~~~-~~~F-~~~~wv~vs~~~~~~~l~~~i  229 (848)
                      ....+|||+.+++.+.++|.  ..+.++|.|+||||+||||||+.+|++..+ ..+| +.+.|++++.. +...+...+
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l  199 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKL  199 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHH
T ss_pred             CCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHH
Confidence            34679999999999999997  456789999999999999999999988766 7788 57999999875 333444443

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.44  E-value=2.5e-07  Score=98.50  Aligned_cols=90  Identities=22%  Similarity=0.188  Sum_probs=46.4

Q ss_pred             CCchhhhcccCcEEEccC-ccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhh
Q 003090          313 LPSSLSFLINLRTLRLHD-RRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLS  389 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~-~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~  389 (848)
                      +|. +..+.+|++|+|++ |.+...+ ..|+.+.+|++|+|++|.++.+|. .+.+|++|++|+|++|.+. .+|...+.
T Consensus        24 ip~-l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~-~~~~~~~~  101 (347)
T 2ifg_A           24 LHH-LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALE-SLSWKTVQ  101 (347)
T ss_dssp             TTT-SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCS-CCCSTTTC
T ss_pred             cCC-CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCccc-eeCHHHcc
Confidence            555 55555555555553 5444444 345555555555555555554433 3455555555555554432 34444333


Q ss_pred             ccccccEEeccccccc
Q 003090          390 RLRKLEELYMSHSFRH  405 (848)
Q Consensus       390 ~l~~L~~L~l~~~~~~  405 (848)
                      .+. |+.|++.+|.+.
T Consensus       102 ~~~-L~~l~l~~N~~~  116 (347)
T 2ifg_A          102 GLS-LQELVLSGNPLH  116 (347)
T ss_dssp             SCC-CCEEECCSSCCC
T ss_pred             cCC-ceEEEeeCCCcc
Confidence            333 555555555543

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=98.40  E-value=5e-06  Score=90.00  Aligned_cols=80  Identities=20%  Similarity=0.204  Sum_probs=48.7

Q ss_pred             cCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcccccccc
Q 003090          587 CLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMTDIWK  666 (848)
Q Consensus       587 ~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~  666 (848)
                      .+.+|+.+.+.+  .+ +.++...+..+.+|+.+.|.+  .++.+..        ..+..+++|+.+.+..  +++.+..
T Consensus       295 ~~~~L~~i~l~~--~i-~~I~~~aF~~c~~L~~i~lp~--~v~~I~~--------~aF~~c~~L~~i~lp~--~l~~I~~  359 (394)
T 4fs7_A          295 GCSSLTEVKLLD--SV-KFIGEEAFESCTSLVSIDLPY--LVEEIGK--------RSFRGCTSLSNINFPL--SLRKIGA  359 (394)
T ss_dssp             TCTTCCEEEECT--TC-CEECTTTTTTCTTCCEECCCT--TCCEECT--------TTTTTCTTCCEECCCT--TCCEECT
T ss_pred             cccccccccccc--cc-ceechhhhcCCCCCCEEEeCC--cccEEhH--------HhccCCCCCCEEEECc--cccEehH
Confidence            456666666643  34 555544445667777777642  3555532        4566777788777753  3666655


Q ss_pred             CCCccccccCccEEEee
Q 003090          667 GDTQFVSLHNLKKVRVE  683 (848)
Q Consensus       667 ~~~~l~~l~~L~~L~i~  683 (848)
                      ..  +.+|++|+++.+.
T Consensus       360 ~a--F~~C~~L~~i~lp  374 (394)
T 4fs7_A          360 NA--FQGCINLKKVELP  374 (394)
T ss_dssp             TT--BTTCTTCCEEEEE
T ss_pred             HH--hhCCCCCCEEEEC
Confidence            43  6777778877775

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.38  E-value=2.7e-06  Score=91.74  Aligned_cols=200  Identities=15%  Similarity=0.120  Sum_probs=125.3

Q ss_pred             hhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCC
Q 003090          222 ITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFP  299 (848)
Q Consensus       222 ~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~  299 (848)
                      +..|....+....++.+.+.. .+..++...  +|++|+.+++..|.+..++...|. ..+|+.+.+..           
T Consensus       146 i~~I~~~aF~~~~L~~i~lp~-~l~~I~~~aF~~c~~L~~l~l~~n~l~~I~~~aF~-~~~L~~l~lp~-----------  212 (401)
T 4fdw_A          146 LKSIGDMAFFNSTVQEIVFPS-TLEQLKEDIFYYCYNLKKADLSKTKITKLPASTFV-YAGIEEVLLPV-----------  212 (401)
T ss_dssp             CCEECTTTTTTCCCCEEECCT-TCCEECSSTTTTCTTCCEEECTTSCCSEECTTTTT-TCCCSEEECCT-----------
T ss_pred             ccEECHHhcCCCCceEEEeCC-CccEehHHHhhCcccCCeeecCCCcceEechhhEe-ecccCEEEeCC-----------
Confidence            445555455555677788775 677777655  789999999998888888888876 57888888875           


Q ss_pred             CCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccC-hhhccCCcccEEeccCC
Q 003090          300 FLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIP-VSFGRLSHLRLLDLTGC  377 (848)
Q Consensus       300 ~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp-~~i~~L~~L~~L~l~~~  377 (848)
                         + +...    -..+|.++.+|+.+.+..+ +.... ..+.+ .+|+.+.+. +.++.++ ..+.++.+|+.+++.++
T Consensus       213 ---~-l~~I----~~~aF~~~~~L~~l~l~~~-l~~I~~~aF~~-~~L~~i~lp-~~i~~I~~~aF~~c~~L~~l~l~~~  281 (401)
T 4fdw_A          213 ---T-LKEI----GSQAFLKTSQLKTIEIPEN-VSTIGQEAFRE-SGITTVKLP-NGVTNIASRAFYYCPELAEVTTYGS  281 (401)
T ss_dssp             ---T-CCEE----CTTTTTTCTTCCCEECCTT-CCEECTTTTTT-CCCSEEEEE-TTCCEECTTTTTTCTTCCEEEEESS
T ss_pred             ---c-hhee----hhhHhhCCCCCCEEecCCC-ccCcccccccc-CCccEEEeC-CCccEEChhHhhCCCCCCEEEeCCc
Confidence               2 3331    2345677777888877764 33222 34444 567777773 3455554 34667777777777664


Q ss_pred             ccc----cccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccC
Q 003090          378 YIL----ELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQ  451 (848)
Q Consensus       378 ~~~----~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~  451 (848)
                      ...    ..++...+.++++|+.+.+..+ +...             ....+.++.+|+.+.|..+ +..+....  .+ 
T Consensus       282 ~~~~~~~~~I~~~aF~~c~~L~~l~l~~~-i~~I-------------~~~aF~~c~~L~~l~lp~~-l~~I~~~aF~~~-  345 (401)
T 4fdw_A          282 TFNDDPEAMIHPYCLEGCPKLARFEIPES-IRIL-------------GQGLLGGNRKVTQLTIPAN-VTQINFSAFNNT-  345 (401)
T ss_dssp             CCCCCTTCEECTTTTTTCTTCCEECCCTT-CCEE-------------CTTTTTTCCSCCEEEECTT-CCEECTTSSSSS-
T ss_pred             cccCCcccEECHHHhhCCccCCeEEeCCc-eEEE-------------hhhhhcCCCCccEEEECcc-ccEEcHHhCCCC-
Confidence            321    2355555777777777777632 3222             2345666677777777433 44444443  45 


Q ss_pred             CCCeEEEEeC
Q 003090          452 NLTSFSIAIG  461 (848)
Q Consensus       452 ~L~~L~l~~~  461 (848)
                      +|+.+.+..+
T Consensus       346 ~L~~l~l~~n  355 (401)
T 4fdw_A          346 GIKEVKVEGT  355 (401)
T ss_dssp             CCCEEEECCS
T ss_pred             CCCEEEEcCC
Confidence            6777776644

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.29  E-value=7.5e-07  Score=94.20  Aligned_cols=140  Identities=19%  Similarity=0.197  Sum_probs=79.2

Q ss_pred             HHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhc--cccCCCEE
Q 003090          273 RFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIG--ELSGLEIL  349 (848)
Q Consensus       273 ~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~--~l~~L~~L  349 (848)
                      .++..+++|+.|++++|             ..+ .     ++. + .+++|+.|++..|.+.... ..+.  .+++|++|
T Consensus       166 ~ll~~~P~L~~L~L~g~-------------~~l-~-----l~~-~-~~~~L~~L~L~~~~l~~~~l~~l~~~~lp~L~~L  224 (362)
T 2ra8_A          166 PVLDAMPLLNNLKIKGT-------------NNL-S-----IGK-K-PRPNLKSLEIISGGLPDSVVEDILGSDLPNLEKL  224 (362)
T ss_dssp             HHHHTCTTCCEEEEECC-------------BTC-B-----CCS-C-BCTTCSEEEEECSBCCHHHHHHHHHSBCTTCCEE
T ss_pred             HHHhcCCCCcEEEEeCC-------------CCc-e-----ecc-c-cCCCCcEEEEecCCCChHHHHHHHHccCCCCcEE
Confidence            34566777888887762             112 1     333 2 2667788887776543332 3333  67778888


Q ss_pred             EccCC--C------CcccChhh--ccCCcccEEeccCCccccccChhhh--hccccccEEeccccccccccccccccccC
Q 003090          350 DLSES--D------VSEIPVSF--GRLSHLRLLDLTGCYILELIPRGVL--SRLRKLEELYMSHSFRHWQFESESEEDSS  417 (848)
Q Consensus       350 ~l~~~--~------l~~lp~~i--~~L~~L~~L~l~~~~~~~~~p~~~l--~~l~~L~~L~l~~~~~~~~~~~~~~~~~~  417 (848)
                      +|+.+  .      +..+...+  ..+++|++|++++|......+..+.  ..+++|++|+++.|.+...         .
T Consensus       225 ~L~~~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~L~d~---------G  295 (362)
T 2ra8_A          225 VLYVGVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGVLTDE---------G  295 (362)
T ss_dssp             EEECBCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSCCBHH---------H
T ss_pred             EEeccccccccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCCCChH---------H
Confidence            77531  1      21222222  3467888888877665433333311  2467788888877766532         1


Q ss_pred             cccchhhhcccCCCcEEEeeccCCC
Q 003090          418 SNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       418 ~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      ..+....+.++++|+.|+++.|.++
T Consensus       296 ~~~L~~~L~~l~~L~~L~L~~n~i~  320 (362)
T 2ra8_A          296 ARLLLDHVDKIKHLKFINMKYNYLS  320 (362)
T ss_dssp             HHHHHTTHHHHTTCSEEECCSBBCC
T ss_pred             HHHHHhhcccCCcceEEECCCCcCC
Confidence            1123444566778888888777544

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=98.24  E-value=8.5e-06  Score=88.15  Aligned_cols=100  Identities=12%  Similarity=0.062  Sum_probs=53.1

Q ss_pred             ccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeeccccc
Q 003090          559 VTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEIERVN  638 (848)
Q Consensus       559 ~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~~~~~  638 (848)
                      ..+.+|+.+.+.+.  ++.+  +......+.+|+.+.+.+  .+ +.+....+..+.+|+.+.+..  +++.+..     
T Consensus       294 ~~~~~L~~i~l~~~--i~~I--~~~aF~~c~~L~~i~lp~--~v-~~I~~~aF~~c~~L~~i~lp~--~l~~I~~-----  359 (394)
T 4fs7_A          294 YGCSSLTEVKLLDS--VKFI--GEEAFESCTSLVSIDLPY--LV-EEIGKRSFRGCTSLSNINFPL--SLRKIGA-----  359 (394)
T ss_dssp             TTCTTCCEEEECTT--CCEE--CTTTTTTCTTCCEECCCT--TC-CEECTTTTTTCTTCCEECCCT--TCCEECT-----
T ss_pred             cccccccccccccc--ccee--chhhhcCCCCCCEEEeCC--cc-cEEhHHhccCCCCCCEEEECc--cccEehH-----
Confidence            34456666665432  3332  111222456667666643  34 555544445667777777753  2555532     


Q ss_pred             cccccccccCCcCEEecCCCccccccccCCCccccccCccEE
Q 003090          639 IAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKV  680 (848)
Q Consensus       639 ~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L  680 (848)
                         ..+..+++|+.+++..  +++.+..   .+.++++|+.+
T Consensus       360 ---~aF~~C~~L~~i~lp~--~~~~~~~---~F~~c~~L~~I  393 (394)
T 4fs7_A          360 ---NAFQGCINLKKVELPK--RLEQYRY---DFEDTTKFKWI  393 (394)
T ss_dssp             ---TTBTTCTTCCEEEEEG--GGGGGGG---GBCTTCEEEEE
T ss_pred             ---HHhhCCCCCCEEEECC--CCEEhhh---eecCCCCCcEE
Confidence               5667778888887753  3443321   24555555543

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=98.13  E-value=1.3e-06  Score=80.74  Aligned_cols=68  Identities=21%  Similarity=0.270  Sum_probs=36.4

Q ss_pred             cCCCcceEEEecCchhhHhhhHHHHHh----hccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCCCcccc
Q 003090          587 CLSNVKRSDVVDCGSILKILLSHLVQS----FQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWDLPRMT  662 (848)
Q Consensus       587 ~l~~L~~L~l~~c~~l~~~l~~~~~~~----l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~c~~L~  662 (848)
                      .+++|++|++++|..+ ++-.-..+..    .++|++|+|++|+.+++---        ..+..+++|++|+|++|+.++
T Consensus        83 ~~~~L~~L~L~~C~~I-tD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl--------~~L~~~~~L~~L~L~~c~~It  153 (176)
T 3e4g_A           83 GLQYVEKIRLCKCHYI-EDGCLERLSQLENLQKSMLEMEIISCGNVTDKGI--------IALHHFRNLKYLFLSDLPGVK  153 (176)
T ss_dssp             TCSCCCEEEEESCTTC-CHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHH--------HHGGGCTTCCEEEEESCTTCC
T ss_pred             CCCCCCEEEeCCCCcc-CHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHH--------HHHhcCCCCCEEECCCCCCCC
Confidence            4566666666666555 2221111122    24566777776666654311        234456677777777776666


Q ss_pred             c
Q 003090          663 D  663 (848)
Q Consensus       663 ~  663 (848)
                      .
T Consensus       154 d  154 (176)
T 3e4g_A          154 E  154 (176)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=98.10  E-value=2.7e-06  Score=78.56  Aligned_cols=91  Identities=11%  Similarity=0.090  Sum_probs=44.4

Q ss_pred             CCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccc--cCCCcceEEEecCchhhHhhhHHHH
Q 003090          534 ELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAG--CLSNVKRSDVVDCGSILKILLSHLV  611 (848)
Q Consensus       534 ~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~--~l~~L~~L~l~~c~~l~~~l~~~~~  611 (848)
                      +|+.|++++|. ++.    .++.....+++|++|+|++|..+++.....+...  ..++|++|+|++|+.+ ++-.-..+
T Consensus        62 ~L~~LDLs~~~-Itd----~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~I-TD~Gl~~L  135 (176)
T 3e4g_A           62 KIQAIDATDSC-IMS----IGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNV-TDKGIIAL  135 (176)
T ss_dssp             CEEEEEEESCC-CCG----GGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTC-CHHHHHHG
T ss_pred             eEeEEeCcCCC-ccH----HHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcC-CHHHHHHH
Confidence            45666666664 322    1223334556666666666655554322222211  1235666666666655 33221122


Q ss_pred             HhhccCcEEEEeccCCcee
Q 003090          612 QSFQNLQRLRVYSCGLLVS  630 (848)
Q Consensus       612 ~~l~~L~~L~l~~c~~l~~  630 (848)
                      ..+++|++|+|++|+.++.
T Consensus       136 ~~~~~L~~L~L~~c~~Itd  154 (176)
T 3e4g_A          136 HHFRNLKYLFLSDLPGVKE  154 (176)
T ss_dssp             GGCTTCCEEEEESCTTCCC
T ss_pred             hcCCCCCEEECCCCCCCCc
Confidence            4456666666666665554

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.06  E-value=3.9e-06  Score=88.69  Aligned_cols=132  Identities=19%  Similarity=0.256  Sum_probs=75.3

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhh--hcccCcEEEccC
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS--FLINLRTLRLHD  330 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~--~l~~L~~L~L~~  330 (848)
                      .+++|+.|.+++|....++.  + .+++|+.|++..              +.+...    ....+.  .+++|++|+|+.
T Consensus       170 ~~P~L~~L~L~g~~~l~l~~--~-~~~~L~~L~L~~--------------~~l~~~----~l~~l~~~~lp~L~~L~L~~  228 (362)
T 2ra8_A          170 AMPLLNNLKIKGTNNLSIGK--K-PRPNLKSLEIIS--------------GGLPDS----VVEDILGSDLPNLEKLVLYV  228 (362)
T ss_dssp             TCTTCCEEEEECCBTCBCCS--C-BCTTCSEEEEEC--------------SBCCHH----HHHHHHHSBCTTCCEEEEEC
T ss_pred             cCCCCcEEEEeCCCCceecc--c-cCCCCcEEEEec--------------CCCChH----HHHHHHHccCCCCcEEEEec
Confidence            55777777777663223433  2 367777777776              443321    112233  567777777753


Q ss_pred             c--cccCC--c----hhh--ccccCCCEEEccCCCCc-ccChhh---ccCCcccEEeccCCccccc----cChhhhhccc
Q 003090          331 R--RIQGD--L----SLI--GELSGLEILDLSESDVS-EIPVSF---GRLSHLRLLDLTGCYILEL----IPRGVLSRLR  392 (848)
Q Consensus       331 ~--~~~~~--~----~~i--~~l~~L~~L~l~~~~l~-~lp~~i---~~L~~L~~L~l~~~~~~~~----~p~~~l~~l~  392 (848)
                      +  .....  .    ..+  ..+++|++|++++|.+. ..+..+   ..+++|++|+++.|.....    ++.+ +.+++
T Consensus       229 ~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~L~d~G~~~L~~~-L~~l~  307 (362)
T 2ra8_A          229 GVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGVLTDEGARLLLDH-VDKIK  307 (362)
T ss_dssp             BCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSCCBHHHHHHHHTT-HHHHT
T ss_pred             cccccccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCCCChHHHHHHHhh-cccCC
Confidence            1  11111  1    112  34678888888887765 222222   2467888888887654432    3333 45678


Q ss_pred             cccEEecccccccc
Q 003090          393 KLEELYMSHSFRHW  406 (848)
Q Consensus       393 ~L~~L~l~~~~~~~  406 (848)
                      +|+.|++++|.+..
T Consensus       308 ~L~~L~L~~n~i~d  321 (362)
T 2ra8_A          308 HLKFINMKYNYLSD  321 (362)
T ss_dssp             TCSEEECCSBBCCH
T ss_pred             cceEEECCCCcCCH
Confidence            88888888887654

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.83  E-value=1e-05  Score=76.88  Aligned_cols=118  Identities=11%  Similarity=0.039  Sum_probs=84.1

Q ss_pred             chhhhcccCcEEEccCc-cccCC-----chhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCccccc-
Q 003090          315 SSLSFLINLRTLRLHDR-RIQGD-----LSLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILEL-  382 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~-~~~~~-----~~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~-  382 (848)
                      ..+...++|++|+|++| .+...     ...+...++|++|++++|.+.     .+...+...++|++|++++|.+... 
T Consensus        30 ~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~i~~~g  109 (185)
T 1io0_A           30 RIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSG  109 (185)
T ss_dssp             HHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHH
T ss_pred             HHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCcCCHHH
Confidence            34566788999999998 65442     145667789999999999887     3455667778899999999865432 


Q ss_pred             ---cChhhhhccccccEEec--cccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          383 ---IPRGVLSRLRKLEELYM--SHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       383 ---~p~~~l~~l~~L~~L~l--~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                         +... +...++|++|++  ++|.+...         ...+....+...++|++|++++|.+.
T Consensus       110 ~~~l~~~-L~~n~~L~~L~L~~~~N~i~~~---------g~~~l~~~L~~n~~L~~L~L~~n~i~  164 (185)
T 1io0_A          110 ILALVEA-LQSNTSLIELRIDNQSQPLGNN---------VEMEIANMLEKNTTLLKFGYHFTQQG  164 (185)
T ss_dssp             HHHHHHG-GGGCSSCCEEECCCCSSCCCHH---------HHHHHHHHHHHCSSCCEEECCCSSHH
T ss_pred             HHHHHHH-HHhCCCceEEEecCCCCCCCHH---------HHHHHHHHHHhCCCcCEEeccCCCCC
Confidence               3333 566778999999  77877543         12234456677788999999887653

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.77  E-value=8.9e-06  Score=77.29  Aligned_cols=117  Identities=13%  Similarity=0.116  Sum_probs=79.6

Q ss_pred             HHccCCceeEEEccCcccccccccCCCCCC-CCCCCCCCCCCchhhhcccCcEEEccCccccCCc-----hhhccccCCC
Q 003090          274 FFQGMKDLQVLDLGGIRRFSFSVRFPFLFP-PLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-----SLIGELSGLE  347 (848)
Q Consensus       274 ~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~-~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~  347 (848)
                      ++...+.|+.|+|++              + .+.......+...+...++|++|+|++|.+...-     ..+...++|+
T Consensus        31 ~l~~~~~L~~L~L~~--------------n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~   96 (185)
T 1io0_A           31 IQNNDPDLEEVNLNN--------------IMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLK   96 (185)
T ss_dssp             HHTTCTTCCEEECTT--------------CTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCC
T ss_pred             HHhcCCCCCEEEecC--------------CCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcC
Confidence            356677888888888              5 5543211113344556678888888888654421     4455667899


Q ss_pred             EEEccCCCCcc-----cChhhccCCcccEEec--cCCccccc----cChhhhhccccccEEeccccccc
Q 003090          348 ILDLSESDVSE-----IPVSFGRLSHLRLLDL--TGCYILEL----IPRGVLSRLRKLEELYMSHSFRH  405 (848)
Q Consensus       348 ~L~l~~~~l~~-----lp~~i~~L~~L~~L~l--~~~~~~~~----~p~~~l~~l~~L~~L~l~~~~~~  405 (848)
                      +|++++|.+..     +...+...++|++|++  ++|.+...    +... +...++|++|++++|.+.
T Consensus        97 ~L~L~~N~i~~~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~g~~~l~~~-L~~n~~L~~L~L~~n~i~  164 (185)
T 1io0_A           97 SLNVESNFISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANM-LEKNTTLLKFGYHFTQQG  164 (185)
T ss_dssp             EEECCSSCCCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHH-HHHCSSCCEEECCCSSHH
T ss_pred             EEECcCCcCCHHHHHHHHHHHHhCCCceEEEecCCCCCCCHHHHHHHHHH-HHhCCCcCEEeccCCCCC
Confidence            99999998873     5667777888999999  66655432    2233 556688999999888764

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=97.64  E-value=0.0011  Score=71.41  Aligned_cols=31  Identities=13%  Similarity=0.222  Sum_probs=16.1

Q ss_pred             cceeecccCcCcccChHHHccCCceeEEEccC
Q 003090          257 LQALFLQENSPLAIPDRFFQGMKDLQVLDLGG  288 (848)
Q Consensus       257 L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~  288 (848)
                      |+.+.+..+ +..+.+..|.++.+|+.+.+..
T Consensus        66 L~sI~iP~s-vt~Ig~~AF~~C~~L~~i~~~~   96 (394)
T 4gt6_A           66 LTSVQIPDT-VTEIGSNAFYNCTSLKRVTIQD   96 (394)
T ss_dssp             CCEEEECTT-CCEECTTTTTTCTTCCEEEEGG
T ss_pred             CEEEEECCC-eeEEhHHHhhCCccCceEeecC
Confidence            444444432 4445555555666666665554

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.57  E-value=0.00011  Score=73.46  Aligned_cols=37  Identities=19%  Similarity=0.037  Sum_probs=22.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEE
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMA  214 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv  214 (848)
                      .+.--|.|-++....|+.+.+.|-+..  ...|..+.|-
T Consensus        22 ~~w~kv~I~~g~ky~k~~ll~~i~~~~--~~~f~p~~~~   58 (267)
T 3rw6_A           22 KNWFKITIPYGRKYDKAWLLSMIQSKC--SVPFTPIEFH   58 (267)
T ss_dssp             -CCEEEEETTGGGSCHHHHHHHHHHTC--SSCCCCEEEE
T ss_pred             CCeEEEEecCccccCHHHHHHHHHHhC--CCCcEeEEEE
Confidence            344556677777777888777775543  3446555554

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=97.52  E-value=0.0033  Score=67.65  Aligned_cols=114  Identities=18%  Similarity=0.222  Sum_probs=75.3

Q ss_pred             CcccChHHHccCC-ceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc--CCc--hhhc
Q 003090          267 PLAIPDRFFQGMK-DLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ--GDL--SLIG  341 (848)
Q Consensus       267 ~~~~~~~~~~~~~-~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~--~~~--~~i~  341 (848)
                      ...+.+..|.+++ .|+.+.+..               .++..    -..+|.++.+|+.+.+..+...  ..+  ..+.
T Consensus        51 Vt~Ig~~aF~~~~~~L~sI~iP~---------------svt~I----g~~AF~~C~~L~~i~~~~n~p~~l~~Ig~~aF~  111 (394)
T 4gt6_A           51 VSKIGDRVFCNYKYVLTSVQIPD---------------TVTEI----GSNAFYNCTSLKRVTIQDNKPSCVKKIGRQAFM  111 (394)
T ss_dssp             EEEECTTTTTTCCSCCCEEEECT---------------TCCEE----CTTTTTTCTTCCEEEEGGGCCCCCCEECTTTTT
T ss_pred             eeEcCHhhccCCCCcCEEEEECC---------------CeeEE----hHHHhhCCccCceEeecCCCCCeeeEechhhch
Confidence            4566777777775 588888765               23332    2356888999999998776321  112  5667


Q ss_pred             cccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEecccc
Q 003090          342 ELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHS  402 (848)
Q Consensus       342 ~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~  402 (848)
                      .+.+|+.+.+..+ ++.++. .+..+.+|+.+.+...  ...++...+..+.+|+.+.+..+
T Consensus       112 ~c~~L~~i~~~~~-~~~I~~~aF~~c~~L~~i~lp~~--~~~I~~~~F~~c~~L~~i~~~~~  170 (394)
T 4gt6_A          112 FCSELTDIPILDS-VTEIDSEAFHHCEELDTVTIPEG--VTSVADGMFSYCYSLHTVTLPDS  170 (394)
T ss_dssp             TCTTCCBCGGGTT-CSEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCEEECCTT
T ss_pred             hcccceeeccCCc-cceehhhhhhhhcccccccccce--eeeecccceecccccccccccce
Confidence            7788887776553 555543 4677888888888652  34566665778888888877654

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.52  E-value=5.8e-05  Score=75.38  Aligned_cols=65  Identities=20%  Similarity=0.236  Sum_probs=39.2

Q ss_pred             ccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhcccc--CCCEEEccC
Q 003090          276 QGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELS--GLEILDLSE  353 (848)
Q Consensus       276 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~--~L~~L~l~~  353 (848)
                      .++++|+.|+|++              |.+.+.  ..+|..+..+++|++|+|++|.+... ..+..+.  +|++|++++
T Consensus       167 ~~l~~L~~L~Ls~--------------N~l~~l--~~l~~~~~~l~~L~~L~Ls~N~i~~~-~~l~~l~~l~L~~L~L~~  229 (267)
T 3rw6_A          167 ENIPELLSLNLSN--------------NRLYRL--DDMSSIVQKAPNLKILNLSGNELKSE-RELDKIKGLKLEELWLDG  229 (267)
T ss_dssp             HHCTTCCEEECTT--------------SCCCCC--GGGTTHHHHSTTCCEEECTTSCCCSG-GGGGGGTTSCCSEEECTT
T ss_pred             hhCCCCCEEECCC--------------CCCCCC--ccchhHHhhCCCCCEEECCCCccCCc-hhhhhcccCCcceEEccC
Confidence            5677888888888              666651  00445566777777777777755443 2233333  666666666


Q ss_pred             CCCc
Q 003090          354 SDVS  357 (848)
Q Consensus       354 ~~l~  357 (848)
                      |.+.
T Consensus       230 Npl~  233 (267)
T 3rw6_A          230 NSLC  233 (267)
T ss_dssp             STTG
T ss_pred             CcCc
Confidence            6554

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=96.70  E-value=0.0015  Score=70.88  Aligned_cols=77  Identities=19%  Similarity=0.134  Sum_probs=55.2

Q ss_pred             ccccchhHHHHHHHHHH-h----c--CCccEEEE--EeCCCCchhHHHHHHHHHHhhcc---ccC-cEEEEEeccCCchh
Q 003090          157 YAFKSRESTMKDIMEAM-K----D--ENVSITGI--CGMGGVGKTTLVKEIQKQAKEMK---MFD-DVAMAVVSQTPSIT  223 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L-~----~--~~~~vi~i--~G~gG~GKTtla~~v~~~~~~~~---~F~-~~~wv~vs~~~~~~  223 (848)
                      ..++||+++++.+.+++ .    .  .....+-|  +|++|+||||+++.+++......   .|+ ..+|+......+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            67999999999999998 4    2  23445666  99999999999999998754321   122 24555554666677


Q ss_pred             HHHHHHHhcc
Q 003090          224 KIQYEIAGWL  233 (848)
Q Consensus       224 ~l~~~i~~~~  233 (848)
                      .+...+...+
T Consensus       102 ~~~~~l~~~l  111 (412)
T 1w5s_A          102 TILSLIVRQT  111 (412)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            7777777655

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=96.63  E-value=0.0024  Score=67.35  Aligned_cols=55  Identities=16%  Similarity=0.262  Sum_probs=44.6

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ  218 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~  218 (848)
                      ....++||+++.+.+.+++...  .++.|+|..|+|||||++.+.+..      + .+|+....
T Consensus        10 ~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~------~-~~~~~~~~   64 (350)
T 2qen_A           10 RREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER------P-GILIDCRE   64 (350)
T ss_dssp             SGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS------S-EEEEEHHH
T ss_pred             ChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc------C-cEEEEeec
Confidence            3467999999999999998754  789999999999999999998753      2 55665543

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.53  E-value=0.0032  Score=67.50  Aligned_cols=77  Identities=18%  Similarity=0.197  Sum_probs=55.2

Q ss_pred             ccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhccc-cCcEEEEEeccCCchhHHHHHHHh
Q 003090          157 YAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMKM-FDDVAMAVVSQTPSITKIQYEIAG  231 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~-F~~~~wv~vs~~~~~~~l~~~i~~  231 (848)
                      ..++||+++++.+.+++.    ......+.|+|..|+||||+++.+.+....... -...+|+......+...+...+..
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~   99 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLLE   99 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHTT
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            679999999999999987    344568999999999999999999986532210 123455554454555566666655


Q ss_pred             cc
Q 003090          232 WL  233 (848)
Q Consensus       232 ~~  233 (848)
                      .+
T Consensus       100 ~l  101 (386)
T 2qby_A          100 SL  101 (386)
T ss_dssp             TT
T ss_pred             Hh
Confidence            44

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=96.45  E-value=0.0098  Score=57.81  Aligned_cols=48  Identities=13%  Similarity=0.218  Sum_probs=41.7

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|+++.++.+.+++.......+-++|..|+|||++|+.+.+..
T Consensus        15 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~   62 (226)
T 2chg_A           15 TLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDL   62 (226)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            346789999999999999987665568999999999999999998764

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.44  E-value=0.0039  Score=59.09  Aligned_cols=47  Identities=17%  Similarity=0.362  Sum_probs=41.3

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|+++.++.+.+++.......+-++|..|+|||++|+.+.+..
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~   67 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999999987666678899999999999999998765

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.43  E-value=0.0043  Score=66.46  Aligned_cols=77  Identities=23%  Similarity=0.216  Sum_probs=54.1

Q ss_pred             ccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhcc----c--cCcEEEEEeccCC-chhHH
Q 003090          157 YAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMK----M--FDDVAMAVVSQTP-SITKI  225 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~----~--F~~~~wv~vs~~~-~~~~l  225 (848)
                      ..++||+++++.+.+++.    ......+-|+|.+|+||||+|+.+.+......    .  ....+|+..+... +...+
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            679999999999998876    33456899999999999999999998653221    1  2235566554444 55556


Q ss_pred             HHHHHhcc
Q 003090          226 QYEIAGWL  233 (848)
Q Consensus       226 ~~~i~~~~  233 (848)
                      ...+...+
T Consensus       100 ~~~l~~~l  107 (384)
T 2qby_B          100 LSSLAGKL  107 (384)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            56655443

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=96.40  E-value=0.26  Score=52.23  Aligned_cols=79  Identities=10%  Similarity=0.079  Sum_probs=39.3

Q ss_pred             hhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccccChhhhhccccc
Q 003090          317 LSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      +....+|+.+.+... +.... ..+.++.+|+.+++..+ ++.++.. +.++ +|..+.+..  .+..++...+.. .+|
T Consensus        42 ~~~~~~i~~v~ip~~-vt~Ig~~aF~~C~~L~~I~lp~~-v~~Ig~~aF~~c-~l~~i~~~~--~l~~I~~~aF~~-~~L  115 (379)
T 4h09_A           42 YKDRDRISEVRVNSG-ITSIGEANFNSCYNMTKVTVAST-VTSIGDGAFADT-KLQSYTGME--RVKKFGDYVFQG-TDL  115 (379)
T ss_dssp             GGGGGGCSEEEECTT-EEEECTTTTTTCTTCCEEEECTT-CCEECTTTTTTC-CCCEEEECT--TCCEECTTTTTT-CCC
T ss_pred             cccccCCEEEEeCCC-ccChHHHHhhCCCCCCEEEeCCc-ceEechhhhcCC-CCceEECCc--eeeEeccceecc-CCc
Confidence            445556666666544 33332 45666677777776543 4444432 3333 455555543  233444443333 356


Q ss_pred             cEEeccc
Q 003090          395 EELYMSH  401 (848)
Q Consensus       395 ~~L~l~~  401 (848)
                      +.+.+..
T Consensus       116 ~~i~lp~  122 (379)
T 4h09_A          116 DDFEFPG  122 (379)
T ss_dssp             SEEECCT
T ss_pred             ccccCCC
Confidence            6555543

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=96.35  E-value=0.0074  Score=63.76  Aligned_cols=55  Identities=16%  Similarity=0.227  Sum_probs=44.4

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEecc
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQ  218 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~  218 (848)
                      ....++||+++.+.+.+ +..   .++.|+|..|+|||||++.+.+...     ...+|+....
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~-----~~~~~~~~~~   65 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELN-----LPYIYLDLRK   65 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHT-----CCEEEEEGGG
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcC-----CCEEEEEchh
Confidence            34679999999999999 755   6999999999999999999987652     1256776654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.10  E-value=0.0058  Score=57.55  Aligned_cols=47  Identities=17%  Similarity=0.310  Sum_probs=41.2

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|+++.++.+.+++.......+-++|..|+||||+|+.+.+..
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~   67 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKI   67 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999999987666677899999999999999998765

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.82  E-value=0.014  Score=62.50  Aligned_cols=77  Identities=16%  Similarity=0.245  Sum_probs=55.1

Q ss_pred             ccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhcc----ccCcEEEEEeccCCchhHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMK----MFDDVAMAVVSQTPSITKIQYE  228 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~  228 (848)
                      ..++||+++++.+..++.    ......+-|+|..|+||||+|+.+.+......    .--..+|+......+...+...
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   98 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASA   98 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHHH
Confidence            679999999999999985    24556889999999999999999997653210    0112455555555565666666


Q ss_pred             HHhcc
Q 003090          229 IAGWL  233 (848)
Q Consensus       229 i~~~~  233 (848)
                      +...+
T Consensus        99 l~~~l  103 (387)
T 2v1u_A           99 IAEAV  103 (387)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            66555

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=95.81  E-value=0.021  Score=61.10  Aligned_cols=76  Identities=18%  Similarity=0.149  Sum_probs=54.7

Q ss_pred             ccccchhHHHHHHHHHHhc----CCcc--EEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD----ENVS--ITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIA  230 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~----~~~~--vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  230 (848)
                      ..++||+++++.+..++..    ....  .+.|+|..|+||||+++.+.+....... -..+++..+...+...+...+.
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            5799999999999999873    3334  8999999999999999999977532211 1244555455555566667666


Q ss_pred             hcc
Q 003090          231 GWL  233 (848)
Q Consensus       231 ~~~  233 (848)
                      ..+
T Consensus        96 ~~l   98 (389)
T 1fnn_A           96 RSL   98 (389)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            554

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=95.71  E-value=0.014  Score=57.59  Aligned_cols=49  Identities=16%  Similarity=0.223  Sum_probs=41.2

Q ss_pred             ccccccchhHHHHHHHHHHhcCC-ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMKDEN-VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~-~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ....++|++..++.+..++.... ...+-|+|..|+||||+|+.+.+...
T Consensus        21 ~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~   70 (250)
T 1njg_A           21 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLN   70 (250)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             cHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhc
Confidence            34679999999999999998544 35788999999999999999987654

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.39  E-value=0.023  Score=58.93  Aligned_cols=50  Identities=26%  Similarity=0.355  Sum_probs=42.7

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.....++|++..++.+.+++.......+-++|..|+||||+|+.+.+..
T Consensus        17 p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l   66 (323)
T 1sxj_B           17 PQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHEL   66 (323)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            33446799999999999999987666668899999999999999998764

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.83  E-value=0.034  Score=57.79  Aligned_cols=48  Identities=21%  Similarity=0.254  Sum_probs=41.9

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|+++.++.+..++.......+-++|..|+||||+|+.+.+..
T Consensus        23 ~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l   70 (327)
T 1iqp_A           23 RLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALAREL   70 (327)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            346799999999999999987766668999999999999999999764

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.63  E-value=0.033  Score=48.66  Aligned_cols=52  Identities=19%  Similarity=0.306  Sum_probs=46.3

Q ss_pred             CceeeecCCCc--ccCCcccccccceeecccCcCcccChHHHccCCceeEEEccC
Q 003090          236 TGISLMFNDIH--EVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGG  288 (848)
Q Consensus       236 ~~l~l~~n~l~--~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~  288 (848)
                      +.++.+++.++  .+|..+. ++|++|+|++|.+..++..+|..+++|++|+|.+
T Consensus        11 ~~v~Cs~~~L~~~~vP~~lp-~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~   64 (130)
T 3rfe_A           11 TLVDCGRRGLTWASLPTAFP-VDTTELVLTGNNLTALPPGLLDALPALRTAHLGA   64 (130)
T ss_dssp             TEEECCSSCCCTTTSCSCCC-TTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCS
T ss_pred             CEEEeCCCCCccccCCCCCC-cCCCEEECCCCcCCccChhhhhhccccCEEEecC
Confidence            45788889998  8997653 4699999999999999999999999999999999

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=94.58  E-value=0.064  Score=54.74  Aligned_cols=78  Identities=10%  Similarity=0.053  Sum_probs=54.3

Q ss_pred             ccccchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHhhccc---cCcEEEEEec--cCCchhHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAKEMKM---FDDVAMAVVS--QTPSITKIQY  227 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~---F~~~~wv~vs--~~~~~~~l~~  227 (848)
                      ..+.|||++++.+...|.    ......+-|+|..|.|||++++.|.+.......   .....++.+.  ...+...+..
T Consensus        20 ~~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~   99 (318)
T 3te6_A           20 ELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYE   99 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHH
T ss_pred             cccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHH
Confidence            458999999999998876    456678899999999999999999987743221   1123344444  3345556677


Q ss_pred             HHHhccC
Q 003090          228 EIAGWLD  234 (848)
Q Consensus       228 ~i~~~~~  234 (848)
                      .|.+++.
T Consensus       100 ~I~~~L~  106 (318)
T 3te6_A          100 KIWFAIS  106 (318)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhc
Confidence            7776663

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.26  E-value=0.044  Score=49.01  Aligned_cols=44  Identities=11%  Similarity=0.262  Sum_probs=35.0

Q ss_pred             cccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          158 AFKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++|....++++.+.+.   ..+. -|-|+|-.|+|||++|+.+++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~-~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDI-AVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCS-CEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCC-CEEEECCCCCCHHHHHHHHHHhC
Confidence            57899999999998886   3333 45699999999999999998754

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=93.96  E-value=0.11  Score=55.15  Aligned_cols=81  Identities=15%  Similarity=0.188  Sum_probs=35.8

Q ss_pred             hhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          317 LSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      +..+.+|+.+.+..+ +.... ..+.++.+|+.+.+..+ +..++. .+..+.+|+.+.+.++ ....++...+.++.+|
T Consensus       236 f~~~~~L~~i~lp~~-v~~I~~~aF~~~~~l~~i~l~~~-i~~i~~~aF~~c~~L~~i~l~~~-~i~~I~~~aF~~c~~L  312 (379)
T 4h09_A          236 FYGMKALDEIAIPKN-VTSIGSFLLQNCTALKTLNFYAK-VKTVPYLLCSGCSNLTKVVMDNS-AIETLEPRVFMDCVKL  312 (379)
T ss_dssp             TTTCSSCCEEEECTT-CCEECTTTTTTCTTCCEEEECCC-CSEECTTTTTTCTTCCEEEECCT-TCCEECTTTTTTCTTC
T ss_pred             ccCCccceEEEcCCC-ccEeCccccceeehhcccccccc-ceecccccccccccccccccccc-ccceehhhhhcCCCCC
Confidence            444455555555443 22111 33444555555555332 333332 2444555555555442 2233444445555555


Q ss_pred             cEEecc
Q 003090          395 EELYMS  400 (848)
Q Consensus       395 ~~L~l~  400 (848)
                      +.+.+.
T Consensus       313 ~~i~lp  318 (379)
T 4h09_A          313 SSVTLP  318 (379)
T ss_dssp             CEEECC
T ss_pred             CEEEcC
Confidence            555553

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=93.82  E-value=0.075  Score=53.90  Aligned_cols=48  Identities=25%  Similarity=0.256  Sum_probs=39.5

Q ss_pred             ccccccchhHHHHHHHHHHhc-------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKD-------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~-------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++.+.+.+..             .....+-++|..|+|||++|+.+.+..
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~   75 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET   75 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            346799999999999888752             344568899999999999999998764

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=93.68  E-value=0.067  Score=58.53  Aligned_cols=47  Identities=19%  Similarity=0.350  Sum_probs=40.1

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++|++++++.+++.+......-+-++|..|+|||++|+.+....
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            34699999999999999976555566799999999999999998764

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=93.55  E-value=0.082  Score=49.57  Aligned_cols=113  Identities=12%  Similarity=0.157  Sum_probs=62.2

Q ss_pred             hcccCcEEEccCc-cccCC----c-hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCccccc----c
Q 003090          319 FLINLRTLRLHDR-RIQGD----L-SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILEL----I  383 (848)
Q Consensus       319 ~l~~L~~L~L~~~-~~~~~----~-~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~----~  383 (848)
                      +-+.|+.|+|+++ .+...    + ..+..-..|+.|+|++|.+.     .+...+..-+.|++|+|++|.+...    +
T Consensus        39 ~n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga~al  118 (197)
T 1pgv_A           39 DDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARL  118 (197)
T ss_dssp             TCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHH
T ss_pred             cCCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHHHHH
Confidence            3456888888775 33221    1 44556677888888888776     3444455566777777777654321    1


Q ss_pred             ChhhhhccccccEEecccccc--ccccccccccccCcccchhhhcccCCCcEEEeeccC
Q 003090          384 PRGVLSRLRKLEELYMSHSFR--HWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE  440 (848)
Q Consensus       384 p~~~l~~l~~L~~L~l~~~~~--~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~  440 (848)
                      -.. +..=+.|++|+++++..  .+.        ....+....|..-+.|+.|+++++.
T Consensus       119 a~a-L~~N~tL~~L~L~n~~~~~ig~--------~g~~~ia~aL~~N~tL~~L~l~~~~  168 (197)
T 1pgv_A          119 LRS-TLVTQSIVEFKADNQRQSVLGN--------QVEMDMMMAIEENESLLRVGISFAS  168 (197)
T ss_dssp             HHH-TTTTCCCSEEECCCCSSCCCCH--------HHHHHHHHHHHHCSSCCEEECCCCC
T ss_pred             HHH-HhhCCceeEEECCCCcCcCcCH--------HHHHHHHHHHHhCCCcCeEeccCCC
Confidence            112 33334577777765422  010        1111234455566667777766543

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.48  E-value=0.058  Score=56.72  Aligned_cols=50  Identities=16%  Similarity=0.294  Sum_probs=42.1

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-..++|.++.++.+..++.......+-++|..|+||||+|+.+.+..
T Consensus        33 p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l   82 (353)
T 1sxj_D           33 PKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKEL   82 (353)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            33456799999999999999987655558899999999999999998764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=93.47  E-value=0.12  Score=53.18  Aligned_cols=47  Identities=17%  Similarity=0.188  Sum_probs=37.0

Q ss_pred             cccchhHHHHHHHHHHh---------------cCCccEEEEEeCCCCchhHHHHHHHHHHhh
Q 003090          158 AFKSRESTMKDIMEAMK---------------DENVSITGICGMGGVGKTTLVKEIQKQAKE  204 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~---------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~~  204 (848)
                      .++|.+..++.+.+++.               ......+-++|..|+|||++|+.+.+....
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~   93 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR   93 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            58999999988887654               223346889999999999999988876543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=93.20  E-value=0.087  Score=54.35  Aligned_cols=49  Identities=12%  Similarity=0.217  Sum_probs=41.5

Q ss_pred             cccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          154 EGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       154 ~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++|++..++.+.+++.......+-++|..|+|||++|+.+.+..
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l   62 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDL   62 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHh
Confidence            3346799999999999999887665568899999999999999998764

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.12  E-value=0.11  Score=57.62  Aligned_cols=52  Identities=12%  Similarity=0.166  Sum_probs=42.7

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcC-----------------CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDE-----------------NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~-----------------~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|....+++|+++.++.+.+|+..+                 ....+-++|..|+||||+|+.+.+..
T Consensus        33 yrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l  101 (516)
T 1sxj_A           33 YAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL  101 (516)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34445578999999999999999742                 23678899999999999999998765

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=92.89  E-value=0.091  Score=48.96  Aligned_cols=41  Identities=24%  Similarity=0.212  Sum_probs=29.5

Q ss_pred             hHHHHHHHHHHhc---CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          163 ESTMKDIMEAMKD---ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       163 ~~~~~~i~~~L~~---~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +..++.+.+++.+   ..-..+.++|..|+|||||++.+.+...
T Consensus        20 ~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           20 NRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             HHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3344444444443   2236899999999999999999998764

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=92.78  E-value=0.11  Score=53.91  Aligned_cols=47  Identities=21%  Similarity=0.282  Sum_probs=38.6

Q ss_pred             cccccchhHHHHHHHHHHhc-----CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKD-----ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~-----~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|++..++.+..++..     .....+-|+|..|+|||++|+.+.+..
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~   62 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL   62 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh
Confidence            46799999999988888762     233567899999999999999998765

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=92.67  E-value=0.14  Score=53.44  Aligned_cols=48  Identities=25%  Similarity=0.291  Sum_probs=39.6

Q ss_pred             ccccccchhHHHHHHHHHHhc-----CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKD-----ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~-----~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|++..++.+..++..     .....+-++|..|+|||++|+.+.+..
T Consensus        27 ~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~   79 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM   79 (338)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            356799999999999888862     344567899999999999999997653

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=92.55  E-value=0.084  Score=55.48  Aligned_cols=49  Identities=14%  Similarity=0.184  Sum_probs=40.0

Q ss_pred             CcccccccchhHHHHHHHHHH-hcCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAM-KDENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L-~~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      |..-.+++|.++.++.+.+++ .......+-++|..|+||||+|+.+...
T Consensus        10 P~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~   59 (354)
T 1sxj_E           10 PKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLES   59 (354)
T ss_dssp             CCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHH
T ss_pred             CCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            334467899999999998888 6555555899999999999999998874

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=92.45  E-value=0.17  Score=53.61  Aligned_cols=47  Identities=17%  Similarity=0.270  Sum_probs=39.7

Q ss_pred             cccccchhHHHHHHHHHHhcCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|+++.++.+..++..... ..+-++|..|+||||+|+.+.+..
T Consensus        15 ~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l   62 (373)
T 1jr3_A           15 FADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGL   62 (373)
T ss_dssp             TTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             hhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45699999999999999876543 467899999999999999998765

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=92.43  E-value=0.18  Score=51.44  Aligned_cols=48  Identities=15%  Similarity=0.143  Sum_probs=38.8

Q ss_pred             ccccccchhHHHHHHHHHHhc------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKD------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++.+.+++..            .....+-++|..|+||||+|+.+.+..
T Consensus        19 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~   78 (297)
T 3b9p_A           19 EWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATEC   78 (297)
T ss_dssp             CGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             CHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHh
Confidence            346799999999998887741            234578899999999999999998754

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=92.33  E-value=0.17  Score=51.58  Aligned_cols=48  Identities=21%  Similarity=0.196  Sum_probs=38.7

Q ss_pred             ccccccchhHHHHHHHHHHhc-------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKD-------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~-------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++.+.+++..             .....+-++|..|.|||++|+.+.+..
T Consensus        13 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~   73 (301)
T 3cf0_A           13 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC   73 (301)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh
Confidence            346799999999888877641             334568899999999999999999764

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=92.16  E-value=0.055  Score=50.73  Aligned_cols=87  Identities=13%  Similarity=0.083  Sum_probs=49.7

Q ss_pred             hhhhcccCcEEEccCccccCC----c-hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCcc--ccc-
Q 003090          316 SLSFLINLRTLRLHDRRIQGD----L-SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYI--LEL-  382 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~----~-~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~--~~~-  382 (848)
                      .+..-.+|+.|+|++|.+...    + ..+..-+.|++|+|++|.|.     .+-..+..-..|++|++++|..  .+. 
T Consensus        65 aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga~ala~aL~~N~tL~~L~L~n~~~~~ig~~  144 (197)
T 1pgv_A           65 AACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQ  144 (197)
T ss_dssp             HHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHH
T ss_pred             HHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHHHHHHHHHhhCCceeEEECCCCcCcCcCHH
Confidence            344445677777777754322    1 34445567777777777776     3334455556688888875421  121 


Q ss_pred             ----cChhhhhccccccEEeccccc
Q 003090          383 ----IPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       383 ----~p~~~l~~l~~L~~L~l~~~~  403 (848)
                          +... +..=+.|..|++..+.
T Consensus       145 g~~~ia~a-L~~N~tL~~L~l~~~~  168 (197)
T 1pgv_A          145 VEMDMMMA-IEENESLLRVGISFAS  168 (197)
T ss_dssp             HHHHHHHH-HHHCSSCCEEECCCCC
T ss_pred             HHHHHHHH-HHhCCCcCeEeccCCC
Confidence                2222 4455677888776554

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=91.91  E-value=0.19  Score=47.77  Aligned_cols=41  Identities=20%  Similarity=0.317  Sum_probs=32.0

Q ss_pred             hhHHHHHHHHHHhc---CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          162 RESTMKDIMEAMKD---ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       162 ~~~~~~~i~~~L~~---~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +++-++.+.+.+..   ....+++|+|..|.||||+++.+....
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45566777777763   344689999999999999999988654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=91.85  E-value=0.17  Score=54.81  Aligned_cols=48  Identities=23%  Similarity=0.337  Sum_probs=40.7

Q ss_pred             ccccccchhHHH---HHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTM---KDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~---~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-.+++|.+..+   ..+...+.......+-++|..|+||||+|+.+.+..
T Consensus        24 ~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~   74 (447)
T 3pvs_A           24 NLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA   74 (447)
T ss_dssp             STTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh
Confidence            346799999888   677777777777789999999999999999999765

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=91.82  E-value=0.2  Score=52.23  Aligned_cols=51  Identities=12%  Similarity=0.227  Sum_probs=41.6

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|.+..++.+..++.......+-++|..|+||||+|+.+.+..
T Consensus        20 rp~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l   70 (340)
T 1sxj_C           20 RPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREI   70 (340)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            344456788999888888888877666568999999999999999998764

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=91.80  E-value=0.19  Score=49.98  Aligned_cols=47  Identities=19%  Similarity=0.191  Sum_probs=36.0

Q ss_pred             cccccchhHHHHHHHHHHh---c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|.++.++.+.+++.   .         ....-+-++|..|+|||++|+.+.+..
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~   63 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA   63 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3578999988887766553   1         222456799999999999999998764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=91.76  E-value=0.26  Score=46.81  Aligned_cols=50  Identities=18%  Similarity=0.131  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhcCC----ccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEe
Q 003090          165 TMKDIMEAMKDEN----VSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVV  216 (848)
Q Consensus       165 ~~~~i~~~L~~~~----~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~v  216 (848)
                      .++.+.+++....    ...+-++|..|+||||+|+.+++.....  .....++..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~~~   90 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR--NVSSLIVYV   90 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEEEH
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEh
Confidence            3444555555331    1578899999999999999999876432  234455543

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=91.70  E-value=0.25  Score=42.96  Aligned_cols=54  Identities=22%  Similarity=0.370  Sum_probs=34.7

Q ss_pred             EEEccCCCCc--ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccc
Q 003090          348 ILDLSESDVS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFR  404 (848)
Q Consensus       348 ~L~l~~~~l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~  404 (848)
                      .++.+++.++  .+|..+-  .+|++|+|++|.+ ..+|.+.+..+++|+.|++.+|..
T Consensus        12 ~v~Cs~~~L~~~~vP~~lp--~~l~~L~Ls~N~l-~~l~~~~f~~l~~L~~L~L~~NP~   67 (130)
T 3rfe_A           12 LVDCGRRGLTWASLPTAFP--VDTTELVLTGNNL-TALPPGLLDALPALRTAHLGANPW   67 (130)
T ss_dssp             EEECCSSCCCTTTSCSCCC--TTCSEEECTTSCC-SSCCTTTGGGCTTCCEEECCSSCC
T ss_pred             EEEeCCCCCccccCCCCCC--cCCCEEECCCCcC-CccChhhhhhccccCEEEecCCCe
Confidence            5666666666  6664432  3577777777544 456666667777777777777654

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=91.65  E-value=0.38  Score=46.96  Aligned_cols=59  Identities=14%  Similarity=0.162  Sum_probs=38.1

Q ss_pred             ccccch---hHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEec
Q 003090          157 YAFKSR---ESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVS  217 (848)
Q Consensus       157 ~~~vG~---~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs  217 (848)
                      ..++|.   +..++.+..+........+-|+|..|+||||+|+.+.+.....  .....++..+
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~--~~~~~~~~~~   89 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL--ERRSFYIPLG   89 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEEGG
T ss_pred             hhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHH
Confidence            445653   3444555555544456788899999999999999998766433  2234555443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=91.64  E-value=0.24  Score=51.97  Aligned_cols=47  Identities=23%  Similarity=0.106  Sum_probs=38.4

Q ss_pred             cccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|.++.++.+.+++.            ......+-++|..|+|||++|+.+.+..
T Consensus        83 ~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~  141 (357)
T 3d8b_A           83 WEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS  141 (357)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT
T ss_pred             HHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            4679999999999888774            1234578899999999999999998754

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=91.56  E-value=0.089  Score=46.84  Aligned_cols=44  Identities=9%  Similarity=0.179  Sum_probs=32.6

Q ss_pred             ccccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++|.+..++++.+.+.   ..+. -|-|+|-.|.|||++|+.+.+.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~-~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTS-PVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSS-CEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCC-cEEEECCCCccHHHHHHHHHHh
Confidence            468899999988888876   3333 4669999999999999998754

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=91.19  E-value=0.2  Score=58.70  Aligned_cols=47  Identities=19%  Similarity=0.350  Sum_probs=40.4

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|+++.++.+++.+......-+=++|..|+|||++|+.+.+..
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l  225 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQI  225 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            35699999999999999986555567799999999999999998764

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=91.11  E-value=0.16  Score=60.24  Aligned_cols=47  Identities=17%  Similarity=0.357  Sum_probs=40.6

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++|+++++..+++.+.......+-++|..|+||||+|+.+.+..
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            35689999999999999986655567899999999999999998765

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=91.06  E-value=0.27  Score=48.74  Aligned_cols=48  Identities=21%  Similarity=0.247  Sum_probs=36.1

Q ss_pred             ccccccchhHHHHHHHHHHh---c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK---D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~---~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-..++|.+..++.+.+.+.   .         ....-+-++|..|.||||+|+.+.+..
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   69 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc
Confidence            34679999988887766543   1         112347799999999999999998765

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=90.87  E-value=1.1  Score=45.83  Aligned_cols=28  Identities=29%  Similarity=0.418  Sum_probs=23.8

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..-.+++++|..|+||||+++.+....+
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~  154 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLK  154 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4457999999999999999998886654

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=90.78  E-value=0.31  Score=50.13  Aligned_cols=44  Identities=18%  Similarity=0.313  Sum_probs=33.5

Q ss_pred             cchhHHHHHHHHHHh----cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          160 KSRESTMKDIMEAMK----DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       160 vG~~~~~~~i~~~L~----~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      |+.+.-.+.+++.+.    ......+.++|+.|+||||+++.+.....
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~   49 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIIN   49 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhC
Confidence            455666777777764    34456699999999999999999887653

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=90.77  E-value=0.22  Score=50.93  Aligned_cols=46  Identities=20%  Similarity=0.281  Sum_probs=37.2

Q ss_pred             ccccchhHHHHHHHHHHhc--------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD--------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~--------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+...+..              .....+-++|..|+|||++|+.+.+..
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l   74 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999988887753              223457799999999999999998765

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=90.66  E-value=0.24  Score=49.61  Aligned_cols=47  Identities=19%  Similarity=0.222  Sum_probs=33.8

Q ss_pred             cccccchhHHHHHHHHHHh----------cCCc---cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK----------DENV---SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----------~~~~---~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++.|.++.++.+.+.+.          .-++   .=+.++|..|.||||||+.+....
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~   68 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANES   68 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHT
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHc
Confidence            4678899988888777543          1111   228999999999999999998754

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=90.61  E-value=0.18  Score=45.23  Aligned_cols=44  Identities=16%  Similarity=0.258  Sum_probs=31.5

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..++|.+...   +..+....-..+.++|..|.|||||++.+.+...
T Consensus        18 ~f~~g~n~~~---~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~   61 (149)
T 2kjq_A           18 KFLGTENAEL---VYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQAL   61 (149)
T ss_dssp             CCCSCCTHHH---HHHCCCCCCSEEEEESSSTTTTCHHHHHHHHHHH
T ss_pred             hcCcCccHHH---HHHHHhcCCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3445655443   3444433556899999999999999999998764

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=90.57  E-value=0.3  Score=50.65  Aligned_cols=47  Identities=28%  Similarity=0.358  Sum_probs=36.2

Q ss_pred             cccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++|.+..++.+--.+.     .+....+.++|..|+||||||+.+.+..
T Consensus        24 l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           24 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            4567888777766655554     2344679999999999999999999865

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=90.42  E-value=0.26  Score=57.72  Aligned_cols=47  Identities=17%  Similarity=0.304  Sum_probs=40.8

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|++++++.+++.|......-+-++|..|+||||+|+.+.+..
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l  231 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHH
Confidence            35689999999999999986666667899999999999999998764

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=90.34  E-value=0.38  Score=49.52  Aligned_cols=48  Identities=21%  Similarity=0.171  Sum_probs=38.2

Q ss_pred             ccccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...+++|.++.++.+.+.+.            ....+-+-++|..|+|||++|+.+.+..
T Consensus        10 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A           10 KWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc
Confidence            45789999999988887763            1123567899999999999999999764

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=90.31  E-value=0.27  Score=47.01  Aligned_cols=39  Identities=18%  Similarity=0.370  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhc--CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          165 TMKDIMEAMKD--ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       165 ~~~~i~~~L~~--~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -.+++.+.+..  ..-.+++|+|..|.|||||++.+.....
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34455555542  3457999999999999999999987654

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=90.05  E-value=0.4  Score=49.40  Aligned_cols=48  Identities=23%  Similarity=0.212  Sum_probs=38.8

Q ss_pred             ccccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-..++|.++.++.+.+++.            .....-+=++|..|.|||++|+++.+..
T Consensus        16 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~   75 (322)
T 3eie_A           16 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA   75 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            45789999999999988873            1123457899999999999999998764

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=90.04  E-value=0.34  Score=46.89  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          164 STMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       164 ~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +..+.+.+.+......+|.++|.+|+||||++..+....
T Consensus        24 ~~a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           24 RLADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            334555555556677899999999999999998887654

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=90.03  E-value=0.33  Score=51.21  Aligned_cols=48  Identities=15%  Similarity=0.304  Sum_probs=36.8

Q ss_pred             cccccchhHHHHH---HHHHHhcCCc--cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          156 VYAFKSRESTMKD---IMEAMKDENV--SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       156 ~~~~vG~~~~~~~---i~~~L~~~~~--~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...++|.+..++.   +.+.+.....  ..+-++|..|+|||++|+.+.+...
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4579999988776   4444444333  4788999999999999999998763

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=89.98  E-value=0.24  Score=47.73  Aligned_cols=46  Identities=20%  Similarity=0.269  Sum_probs=34.1

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+-+.++..+.+.+.+......++.++|.+|+||||++..+....
T Consensus         9 ~~l~~~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A            9 DLLAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             --CHHHHHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHhhcHHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3344555666666666666677899999999999999998887654

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=89.89  E-value=0.37  Score=47.64  Aligned_cols=47  Identities=21%  Similarity=0.294  Sum_probs=33.8

Q ss_pred             cccccchhHHHHHHHHHHh---c------CC---ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---D------EN---VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~------~~---~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+++|.++.+.++.+...   .      -+   ..-+.++|..|+||||+++.+....
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4578898877766655433   1      11   1228899999999999999999765

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=89.88  E-value=1  Score=47.99  Aligned_cols=27  Identities=30%  Similarity=0.255  Sum_probs=22.6

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...++.++|.+|+||||++..+.....
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~  122 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYK  122 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999888776554

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=89.84  E-value=0.16  Score=46.88  Aligned_cols=20  Identities=35%  Similarity=0.552  Sum_probs=18.6

Q ss_pred             cEEEEEeCCCCchhHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEI  198 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v  198 (848)
                      .+|.++|+.|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            37899999999999999999

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=89.76  E-value=0.27  Score=49.01  Aligned_cols=45  Identities=13%  Similarity=0.234  Sum_probs=33.4

Q ss_pred             ccccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.+..+..+.+.+.   ..+ ..+-|+|-.|+|||++|+.+.+..
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~-~~vll~G~~GtGKt~la~~i~~~~   53 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLD-KPVLIIGERGTGKELIASRLHYLS   53 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSC-SCEEEECCTTSCHHHHHHHHHHTS
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCC-CCEEEECCCCCcHHHHHHHHHHhc
Confidence            457899999988887765   233 456699999999999999998754

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=89.36  E-value=0.19  Score=47.24  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=20.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      -.++.++|+.|.||||+++.+..
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~   31 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALAN   31 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHh
Confidence            36899999999999999999875

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=89.32  E-value=0.49  Score=50.28  Aligned_cols=48  Identities=17%  Similarity=0.178  Sum_probs=38.8

Q ss_pred             ccccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.+..++.+.+++.            .....-+-++|..|+|||++|+.+.+..
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~  172 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES  172 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence            45689999999999998874            1223568899999999999999997653

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=89.28  E-value=0.43  Score=47.94  Aligned_cols=48  Identities=21%  Similarity=0.293  Sum_probs=34.9

Q ss_pred             ccccccchhHHHHHHHHHHh---c------CCc---cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK---D------ENV---SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~---~------~~~---~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++++.+...   .      -+.   .-+.++|..|+||||+++.+....
T Consensus        38 ~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           38 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             CGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc
Confidence            34678999887776655543   1      111   128899999999999999998765

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=88.94  E-value=0.23  Score=46.11  Aligned_cols=23  Identities=17%  Similarity=0.346  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .++.|+|..|+||||+++.+...
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            58999999999999999998864

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=88.89  E-value=0.45  Score=48.68  Aligned_cols=46  Identities=20%  Similarity=0.332  Sum_probs=37.6

Q ss_pred             ccccchhHHHHHHHHHHhcC---------CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDE---------NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~---------~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.+..++.+...+...         ....+-++|..|+||||+|+.+.+..
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~   71 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   71 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHH
Confidence            45789999998888887631         23578999999999999999999765

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=88.86  E-value=0.25  Score=46.85  Aligned_cols=25  Identities=32%  Similarity=0.359  Sum_probs=21.9

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+|.++|+.|+||||+|+.+....
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3589999999999999999998654

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=88.79  E-value=0.46  Score=47.52  Aligned_cols=46  Identities=15%  Similarity=0.201  Sum_probs=34.5

Q ss_pred             ccccchhHHHHHHHHH-------Hh---cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEA-------MK---DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~-------L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|....++.+++.       +.   ......+-++|..|+|||++|+.+.+..
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~   88 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES   88 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHh
Confidence            4577887777766663       32   3344567899999999999999998864

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=88.78  E-value=0.51  Score=48.63  Aligned_cols=50  Identities=14%  Similarity=0.093  Sum_probs=40.1

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|.++.++.+.+++..... .++=+.|..|+|||++|+.+.+..
T Consensus        22 P~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l   72 (324)
T 3u61_B           22 PSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV   72 (324)
T ss_dssp             CCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT
T ss_pred             CCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            33457899999999999999986554 455667779999999999998754

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=88.77  E-value=0.25  Score=45.32  Aligned_cols=24  Identities=17%  Similarity=0.178  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|.|+.|+||||+|+.+....
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999987653

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=88.60  E-value=0.35  Score=44.07  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=22.8

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...++.|+|..|.||||++..+.....
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~   29 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAV   29 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhH
Confidence            457899999999999999999887653

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=88.44  E-value=0.41  Score=48.79  Aligned_cols=46  Identities=13%  Similarity=0.235  Sum_probs=36.4

Q ss_pred             ccccchhHHHHHHHHHHhc--CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD--ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~--~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|....+..+.+.+..  .....|-|+|-.|+|||++|+.+.+..
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            4589999999998888762  222346699999999999999998754

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=88.32  E-value=0.29  Score=45.31  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=20.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|-++|+.|+||||+|+.+.+.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~   26 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47889999999999999998764

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=88.29  E-value=1.7  Score=46.52  Aligned_cols=27  Identities=30%  Similarity=0.437  Sum_probs=22.4

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.++|.+|+||||++..+-....
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~  125 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLR  125 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            457999999999999999887775554

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=88.13  E-value=0.53  Score=49.20  Aligned_cols=48  Identities=23%  Similarity=0.212  Sum_probs=37.9

Q ss_pred             ccccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++.+.+.+.            .....-+-++|..|+|||++|+.+.+..
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~  108 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA  108 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            34679999999999888763            0112347789999999999999999865

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.10  E-value=0.32  Score=46.10  Aligned_cols=27  Identities=26%  Similarity=0.453  Sum_probs=22.7

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.++.++|+.|.||||+++.+....
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            445789999999999999999998654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=88.10  E-value=0.25  Score=45.48  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|+|+.|.||||+++.+....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999987653

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=87.68  E-value=3.9  Score=41.21  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=22.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..++.++|.+|+||||++..+.....
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~  123 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYK  123 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999988876543

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=87.66  E-value=0.81  Score=49.47  Aligned_cols=48  Identities=21%  Similarity=0.171  Sum_probs=38.6

Q ss_pred             ccccccchhHHHHHHHHHHh------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMK------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....++|.++.++.+.+.+.            ....+-+-++|..|+|||++|+.+.+..
T Consensus       132 ~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          132 KWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             CGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc
Confidence            35679999999998888763            1233568899999999999999999764

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=87.65  E-value=0.31  Score=48.65  Aligned_cols=47  Identities=21%  Similarity=0.266  Sum_probs=34.8

Q ss_pred             cccccchhHHHHHHHHHHh---c---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---D---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|.++.++.+.+.+.   .         ....-+-++|..|+|||++|+.+.+..
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            3568999888877776554   0         112235689999999999999998764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=87.64  E-value=0.28  Score=46.51  Aligned_cols=25  Identities=20%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.|+|..|+||||+|+.+....
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999988654

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=87.63  E-value=0.31  Score=46.16  Aligned_cols=29  Identities=24%  Similarity=0.418  Sum_probs=24.4

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...-.+|.|+|+.|.||||+++.+.....
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34457999999999999999999987653

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=87.55  E-value=0.6  Score=47.05  Aligned_cols=28  Identities=18%  Similarity=0.106  Sum_probs=23.6

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ....+|+|+|..|+||||+|+.+.....
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3456899999999999999998886654

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=87.45  E-value=0.35  Score=44.60  Aligned_cols=23  Identities=30%  Similarity=0.557  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .++.++|+.|.||||+++.+...
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHh
Confidence            58999999999999999998764

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=87.40  E-value=0.3  Score=45.79  Aligned_cols=22  Identities=36%  Similarity=0.501  Sum_probs=19.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .++.++|..|.||||+++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999964

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=87.36  E-value=0.3  Score=49.88  Aligned_cols=25  Identities=24%  Similarity=0.549  Sum_probs=20.6

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+.+||+|.|=|||||||.+-.+--
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~   70 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSA   70 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCceEEEEECCCccCHHHHHHHHHH
Confidence            5678999999999999998765543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=87.29  E-value=0.26  Score=45.38  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=18.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~  199 (848)
                      .+++++|..|.||||+++.++
T Consensus        10 ei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             EEEEEECCTTSCHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHc
Confidence            589999999999999999744

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=87.29  E-value=0.33  Score=46.09  Aligned_cols=23  Identities=35%  Similarity=0.501  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++++|..|+||||+++.+...
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHhh
Confidence            58999999999999999998764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=87.07  E-value=4.5  Score=43.08  Aligned_cols=27  Identities=30%  Similarity=0.439  Sum_probs=22.6

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.++|.+|+||||++..+.....
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~  125 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQ  125 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHH
Confidence            457999999999999999887776553

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=86.97  E-value=0.36  Score=44.66  Aligned_cols=22  Identities=32%  Similarity=0.385  Sum_probs=20.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+|.++|+.|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            4789999999999999999876

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=86.97  E-value=0.35  Score=47.56  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=22.5

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++.|+|..|+||||+++.+.+..
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998554

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=86.95  E-value=0.37  Score=44.61  Aligned_cols=24  Identities=50%  Similarity=0.540  Sum_probs=21.5

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .++|+|..|+|||||++.+.....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999997764

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=86.88  E-value=0.37  Score=45.76  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=19.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999875

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=86.83  E-value=0.39  Score=44.68  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=21.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...|.++|+.|+||||+|+.+....
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3578899999999999999987643

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=86.63  E-value=0.42  Score=45.64  Aligned_cols=26  Identities=31%  Similarity=0.460  Sum_probs=22.5

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-.+++|+|..|.||||+++.+....
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998754

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=86.51  E-value=0.4  Score=45.42  Aligned_cols=23  Identities=39%  Similarity=0.536  Sum_probs=20.6

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.|.|+.|+||||+++.+.+..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            58999999999999999998654

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=86.34  E-value=0.43  Score=44.67  Aligned_cols=25  Identities=28%  Similarity=0.534  Sum_probs=21.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|.|.|+.|+||||+|+.+.+...
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3688999999999999999987653

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=86.32  E-value=0.4  Score=45.53  Aligned_cols=23  Identities=35%  Similarity=0.471  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++++|..|+||||+++.+...
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            58999999999999999998754

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=86.28  E-value=0.38  Score=44.55  Aligned_cols=24  Identities=42%  Similarity=0.513  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.++|+.|+||||+++.+....
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHh
Confidence            568899999999999999988653

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=86.17  E-value=0.42  Score=43.15  Aligned_cols=27  Identities=30%  Similarity=0.364  Sum_probs=22.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++++|..|.|||||.+.+....
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            344689999999999999999998654

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.08  E-value=0.37  Score=45.53  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=21.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+++|+|..|+|||||++.+....
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            578999999999999999988654

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=86.04  E-value=0.39  Score=45.63  Aligned_cols=25  Identities=36%  Similarity=0.656  Sum_probs=21.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+|.++|+.|+||||+++.+....
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhC
Confidence            3578999999999999999987643

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=85.75  E-value=0.41  Score=45.64  Aligned_cols=25  Identities=24%  Similarity=0.436  Sum_probs=21.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|+|..|+|||||++.+....
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3689999999999999999988654

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=85.68  E-value=0.47  Score=44.33  Aligned_cols=24  Identities=25%  Similarity=0.343  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|.|+.|+||||+++.+.+..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l   27 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNL   27 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999998754

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=85.60  E-value=0.46  Score=45.29  Aligned_cols=25  Identities=28%  Similarity=0.376  Sum_probs=21.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-.++.++|..|+||||+++.+...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhh
Confidence            3468999999999999999998764

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=85.56  E-value=0.64  Score=48.46  Aligned_cols=47  Identities=19%  Similarity=0.224  Sum_probs=34.0

Q ss_pred             cccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -..++|.+..++.+..........-+=++|..|+|||++|+.+.+..
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             chhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhC
Confidence            45689998866654444333223347799999999999999998754

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=85.47  E-value=0.48  Score=45.83  Aligned_cols=24  Identities=33%  Similarity=0.479  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|+|+|..|.||||+++.+....
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999987643

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=85.46  E-value=0.42  Score=45.45  Aligned_cols=22  Identities=36%  Similarity=0.492  Sum_probs=19.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+|+|+|+.|.||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3799999999999999998864

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=85.39  E-value=0.44  Score=45.37  Aligned_cols=23  Identities=52%  Similarity=0.718  Sum_probs=20.4

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      ..+|+|+|..|.||||+|+.+..
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999998864

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=85.37  E-value=0.56  Score=44.37  Aligned_cols=26  Identities=31%  Similarity=0.412  Sum_probs=22.2

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ....+|+|+|+.|.||||+++.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            34568999999999999999998763

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=85.31  E-value=0.52  Score=43.95  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=22.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -.+|.++|+.|.||||+++.+.....
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~   38 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQ   38 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            35799999999999999999987654

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=85.29  E-value=0.43  Score=48.69  Aligned_cols=27  Identities=30%  Similarity=0.346  Sum_probs=23.4

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .-.+++|+|..|.|||||++.+.....
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            446999999999999999999987654

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=85.29  E-value=0.53  Score=44.06  Aligned_cols=24  Identities=25%  Similarity=0.354  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.++|+.|+||||+|+.+....
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            578999999999999999987643

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=85.18  E-value=0.96  Score=45.55  Aligned_cols=24  Identities=29%  Similarity=0.320  Sum_probs=21.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..+|-++|+.|+||||+|+.+...
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~   56 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEE   56 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            467889999999999999998754

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=85.13  E-value=0.47  Score=43.71  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=20.4

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|.|+|+.|.||||+|+.+....
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58899999999999999997654

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=85.02  E-value=0.87  Score=47.76  Aligned_cols=46  Identities=22%  Similarity=0.164  Sum_probs=36.7

Q ss_pred             ccccchhHHHHHHHHHHh---------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.+..++.+...+.               ......+-++|..|+|||++|+.+.+..
T Consensus        15 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           15 DYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             HHCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hhccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            357999999998888773               0133568899999999999999998764

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=84.90  E-value=0.9  Score=47.94  Aligned_cols=46  Identities=22%  Similarity=0.177  Sum_probs=35.4

Q ss_pred             ccccchhHHHHHHHHHHh------------------------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK------------------------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~------------------------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+...+.                              ......+-++|..|+|||++|+.+.+..
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l   96 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL   96 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHh
Confidence            458899988888877762                              0122457799999999999999998754

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=84.87  E-value=0.88  Score=46.42  Aligned_cols=26  Identities=31%  Similarity=0.358  Sum_probs=22.2

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...+++|.|..|+||||+++.+....
T Consensus        91 ~p~iigI~GpsGSGKSTl~~~L~~ll  116 (321)
T 3tqc_A           91 VPYIIGIAGSVAVGKSTTSRVLKALL  116 (321)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34589999999999999999987654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=84.79  E-value=0.57  Score=42.75  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=21.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.+.|+.|+||||+|+.+.+..
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999987653

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=84.70  E-value=0.56  Score=46.28  Aligned_cols=26  Identities=19%  Similarity=0.345  Sum_probs=21.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ....+|+|.|..|.||||+|+.+...
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~   45 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQL   45 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            34468999999999999999988764

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=84.69  E-value=0.47  Score=45.61  Aligned_cols=23  Identities=43%  Similarity=0.687  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|+|||||++.+...
T Consensus        24 ~~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            58999999999999999998764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.62  E-value=1.1  Score=47.54  Aligned_cols=49  Identities=24%  Similarity=0.249  Sum_probs=38.2

Q ss_pred             ccccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.|.++.++++.+.+.             -...+=+=.+|..|.|||++|++|.+...
T Consensus       170 ~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~  231 (428)
T 4b4t_K          170 TYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTK  231 (428)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHT
T ss_pred             CHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            45679999999988887664             12234467899999999999999998763

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=84.56  E-value=0.6  Score=43.44  Aligned_cols=24  Identities=29%  Similarity=0.315  Sum_probs=21.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..+|.++|+.|+||||+++.+.+.
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHh
Confidence            357999999999999999988764

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=84.56  E-value=1  Score=48.87  Aligned_cols=47  Identities=17%  Similarity=0.191  Sum_probs=35.9

Q ss_pred             cccccchhHHHHHHHHHHh---cC--CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---DE--NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~~--~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|.++.++.+..++.   ..  ..+-+=++|..|.|||++|+.+.+..
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHh
Confidence            3679999998886555443   22  22457799999999999999999875

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=84.45  E-value=0.57  Score=46.25  Aligned_cols=24  Identities=25%  Similarity=0.307  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++.|+|+.|+||||+|+.+....
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcC
Confidence            368899999999999999997654

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=84.33  E-value=1.1  Score=48.44  Aligned_cols=47  Identities=21%  Similarity=0.297  Sum_probs=35.6

Q ss_pred             cccccchhHHHHHHHHHHh---cC---------CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---DE---------NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~~---------~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|.++.++++.+...   ..         -..-+-++|..|.||||+|+.+.+..
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~   73 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA   73 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            4679999988877766543   11         11336799999999999999999865

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=84.32  E-value=0.69  Score=47.82  Aligned_cols=44  Identities=14%  Similarity=0.171  Sum_probs=36.4

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+...+....  -+-++|..|+|||++|+.+.+..
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHT
T ss_pred             cceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHh
Confidence            468899999988888877543  57789999999999999998754

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.26  E-value=1.2  Score=47.41  Aligned_cols=49  Identities=16%  Similarity=0.190  Sum_probs=38.2

Q ss_pred             ccccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.|.++.++++.+.+.             -...+=|=++|..|.|||++|++|.+...
T Consensus       179 ~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~  240 (437)
T 4b4t_L          179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIG  240 (437)
T ss_dssp             CSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhC
Confidence            45678999999988877664             12234567899999999999999998763

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.18  E-value=1.2  Score=47.53  Aligned_cols=49  Identities=18%  Similarity=0.212  Sum_probs=38.4

Q ss_pred             ccccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.|.++.++++.+.+.             -...+=|=++|..|.|||.+|++|.+...
T Consensus       179 t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~  240 (434)
T 4b4t_M          179 TYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTN  240 (434)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhC
Confidence            45679999999998887653             12234567899999999999999998763

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=84.14  E-value=0.51  Score=46.59  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=21.9

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-.+|+|+|+.|.||||+++.+...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~   50 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAES   50 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999999854

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=84.10  E-value=0.6  Score=45.55  Aligned_cols=25  Identities=20%  Similarity=0.280  Sum_probs=22.0

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .. .+++|+|..|.|||||.+.+.--
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCC
Confidence            45 79999999999999999998753

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=83.99  E-value=0.54  Score=43.69  Aligned_cols=24  Identities=25%  Similarity=0.454  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|+|+.|+||||+|+.+....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            368999999999999999987653

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=83.91  E-value=0.67  Score=43.43  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=21.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-.++.|+|..|+|||||++.+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhh
Confidence            3468999999999999999998864

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=83.87  E-value=0.63  Score=43.49  Aligned_cols=25  Identities=36%  Similarity=0.429  Sum_probs=21.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+++|+|..|+||||+++.+....+
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhcc
Confidence            3689999999999999999987654

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=83.81  E-value=0.68  Score=43.46  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=21.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.++|+.|+||||+|+.+.+..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999987643

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=83.69  E-value=0.6  Score=44.40  Aligned_cols=23  Identities=35%  Similarity=0.239  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+.-.
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999865

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=83.62  E-value=0.76  Score=43.47  Aligned_cols=25  Identities=32%  Similarity=0.412  Sum_probs=21.6

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ...+|.+.|+.|+||||+++.+.+.
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4468999999999999999998754

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=83.61  E-value=1.2  Score=48.52  Aligned_cols=47  Identities=15%  Similarity=0.186  Sum_probs=37.6

Q ss_pred             cccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|.+..++.+.+++.             .....-+=++|..|.|||++|+.+.+..
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~  262 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET  262 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh
Confidence            3569999999999888765             1333457899999999999999997653

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=83.61  E-value=0.62  Score=45.74  Aligned_cols=26  Identities=23%  Similarity=0.368  Sum_probs=22.2

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-.+|+|.|..|.||||+++.+....
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999987643

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=83.60  E-value=43  Score=34.46  Aligned_cols=24  Identities=33%  Similarity=0.491  Sum_probs=20.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~  199 (848)
                      .....+.++|..|+|||||...+.
T Consensus       165 ~~~~~v~lvG~~gvGKSTLin~L~  188 (357)
T 2e87_A          165 LEIPTVVIAGHPNVGKSTLLKALT  188 (357)
T ss_dssp             SSSCEEEEECSTTSSHHHHHHHHC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHh
Confidence            345689999999999999987765

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=83.59  E-value=0.67  Score=43.42  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.+.|+.|+||||+|+.+.+..
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999887643

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=83.58  E-value=6.6  Score=46.36  Aligned_cols=46  Identities=20%  Similarity=0.335  Sum_probs=37.1

Q ss_pred             ccccchhHHHHHHHHHHhc---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.+..++.+...+..         .....+-++|..|+|||++|+.+.+..
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~  612 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL  612 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999888887752         123578899999999999999998765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=83.58  E-value=0.7  Score=43.49  Aligned_cols=24  Identities=29%  Similarity=0.309  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.+.|+.|+||||+|+.+....
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999997654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=83.51  E-value=0.68  Score=43.02  Aligned_cols=24  Identities=21%  Similarity=0.259  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|.++|+.|+||||+++.+.+..
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999987643

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=83.48  E-value=0.71  Score=43.24  Aligned_cols=25  Identities=24%  Similarity=0.501  Sum_probs=21.6

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ...+|++.|+.|.||||+++.+-+.
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999988764

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=83.44  E-value=0.66  Score=42.26  Aligned_cols=23  Identities=17%  Similarity=0.157  Sum_probs=20.3

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|.+.|+.|+||||+|+.+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999988653

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=83.43  E-value=0.61  Score=45.03  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999988743

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=83.31  E-value=0.77  Score=42.16  Aligned_cols=25  Identities=28%  Similarity=0.500  Sum_probs=22.1

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++.|+|..|+||||+++.+....
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            5689999999999999999988754

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=83.29  E-value=0.42  Score=43.82  Aligned_cols=26  Identities=35%  Similarity=0.475  Sum_probs=22.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKE  204 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~  204 (848)
                      .+++|+|..|.|||||++.+......
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            57999999999999999999876543

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=83.28  E-value=0.94  Score=44.67  Aligned_cols=25  Identities=32%  Similarity=0.307  Sum_probs=21.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+|.++|..|.||||+|+.+....
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            4678999999999999999987643

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=83.21  E-value=0.61  Score=45.40  Aligned_cols=22  Identities=32%  Similarity=0.480  Sum_probs=20.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+++|+|..|.|||||.+.+.-
T Consensus        32 e~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhc
Confidence            6899999999999999998874

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=83.18  E-value=1.3  Score=48.28  Aligned_cols=47  Identities=21%  Similarity=0.304  Sum_probs=35.2

Q ss_pred             cccccchhHHHHHHHHHHh---cC------C---ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---DE------N---VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~~------~---~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+++|.++.++++.+...   ..      +   ..-+.++|..|.||||||+.+....
T Consensus        30 f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~   88 (499)
T 2dhr_A           30 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   88 (499)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             HHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4679999988877666543   11      1   1238899999999999999999765

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=83.17  E-value=0.63  Score=42.62  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=20.8

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.+.|+.|+||||+|+.+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            368999999999999999987653

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=83.16  E-value=0.69  Score=44.42  Aligned_cols=25  Identities=20%  Similarity=0.383  Sum_probs=21.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+++|+|..|+|||||.+.+....
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhccC
Confidence            3689999999999999999988653

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=83.12  E-value=0.62  Score=43.18  Aligned_cols=23  Identities=35%  Similarity=0.421  Sum_probs=16.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|.+.|+.|+||||+|+.+.+.
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~   28 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHER   28 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999998754

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=83.06  E-value=0.9  Score=46.08  Aligned_cols=27  Identities=26%  Similarity=0.460  Sum_probs=23.4

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .-.+++|+|.+|+||||+++.+.....
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            457999999999999999999887654

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=83.03  E-value=0.73  Score=43.13  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=20.7

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|.+.|+.|+||||+++.+.+..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999998754

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.00  E-value=1.2  Score=46.61  Aligned_cols=49  Identities=18%  Similarity=0.214  Sum_probs=37.7

Q ss_pred             ccccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.|.++.++++.+.+.             -...+=+=.+|..|.|||.+|++|.+...
T Consensus       146 ~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~  207 (405)
T 4b4t_J          146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTD  207 (405)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHT
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhC
Confidence            45678999999988877654             12224466899999999999999998763

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=82.91  E-value=0.73  Score=43.87  Aligned_cols=25  Identities=16%  Similarity=0.343  Sum_probs=22.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|.|.|+.|+||||+|+.+.+...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~   29 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIE   29 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            4789999999999999999987653

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=82.88  E-value=0.78  Score=42.87  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.+.|+.|+||||+|+.+....
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999987643

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=82.85  E-value=0.68  Score=45.91  Aligned_cols=23  Identities=35%  Similarity=0.569  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|.++|+.|+||||+|+.+...
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHH
Confidence            57899999999999999999875

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=82.62  E-value=0.66  Score=46.93  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=22.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .-.++.++|.+|+||||++..+.....
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            346999999999999999988876554

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=82.61  E-value=1.4  Score=42.04  Aligned_cols=43  Identities=23%  Similarity=0.112  Sum_probs=30.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQ  226 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~  226 (848)
                      .++.|+|.+|+||||++..+.. .    .-..++|+.....++..++.
T Consensus        21 ~~~~i~G~~GsGKTtl~~~l~~-~----~~~~v~~i~~~~~~~~~~~~   63 (220)
T 2cvh_A           21 VLTQVYGPYASGKTTLALQTGL-L----SGKKVAYVDTEGGFSPERLV   63 (220)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH-H----HCSEEEEEESSCCCCHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-H----cCCcEEEEECCCCCCHHHHH
Confidence            6899999999999999998876 2    11356676655544554444

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=82.58  E-value=0.65  Score=45.60  Aligned_cols=24  Identities=33%  Similarity=0.376  Sum_probs=21.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|+|+.|.||||+++.+....
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhc
Confidence            579999999999999999998643

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=82.58  E-value=1.3  Score=45.43  Aligned_cols=37  Identities=30%  Similarity=0.320  Sum_probs=26.9

Q ss_pred             HHHHHHHhcC--CccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          167 KDIMEAMKDE--NVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       167 ~~i~~~L~~~--~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..+..+....  ....+-|+|..|+||||+|+.+.+...
T Consensus        24 ~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~   62 (324)
T 1l8q_A           24 EVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAK   62 (324)
T ss_dssp             HHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHH
Confidence            3444444332  245788999999999999999998664

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=82.35  E-value=1.3  Score=49.29  Aligned_cols=46  Identities=30%  Similarity=0.359  Sum_probs=36.7

Q ss_pred             ccccchhHHHHHHHHHHh------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++-++.+.+.+.      ...-.++.++|..|+||||+|+.+....
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l  132 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSL  132 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            458899888887766554      2234689999999999999999998765

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=82.32  E-value=0.44  Score=45.58  Aligned_cols=24  Identities=33%  Similarity=0.594  Sum_probs=21.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHHh
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|.|+|..|+||||+++.+.....
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999987653

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=82.24  E-value=0.81  Score=43.21  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=21.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.++|+.|+||||+|+.+....
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            479999999999999999987654

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=82.18  E-value=1.4  Score=47.53  Aligned_cols=45  Identities=22%  Similarity=0.228  Sum_probs=30.3

Q ss_pred             ccchhHH--HHHHHHHHhcCC-ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          159 FKSREST--MKDIMEAMKDEN-VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       159 ~vG~~~~--~~~i~~~L~~~~-~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++|....  ...+..+..... ...+-++|..|+||||||+.+.+...
T Consensus       108 v~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~  155 (440)
T 2z4s_A          108 VVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVV  155 (440)
T ss_dssp             CCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            4465433  233333333322 56788999999999999999998653

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=82.17  E-value=0.7  Score=45.01  Aligned_cols=23  Identities=22%  Similarity=0.546  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        32 e~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999988743

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=82.11  E-value=0.81  Score=42.26  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=21.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.++|+.|.||||+++.+....
T Consensus         6 ~~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            6 CTVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999998754

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=81.98  E-value=0.71  Score=45.78  Aligned_cols=23  Identities=30%  Similarity=0.502  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+.--
T Consensus        33 e~~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            68999999999999999988743

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=81.90  E-value=0.71  Score=46.04  Aligned_cols=22  Identities=41%  Similarity=0.655  Sum_probs=20.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+++|+|..|.|||||.+.+.-
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            5899999999999999998874

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=81.75  E-value=0.9  Score=43.25  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=22.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|.+.|+.|+||||+++.+.+...
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            5799999999999999999987653

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=81.64  E-value=1.4  Score=45.91  Aligned_cols=37  Identities=24%  Similarity=0.448  Sum_probs=27.8

Q ss_pred             HHHHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          166 MKDIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       166 ~~~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...+.+.+.  ..+..+|+|+|.+|+||||++..+....
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            344555554  4567799999999999999998876554

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=81.62  E-value=1.2  Score=48.66  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=36.1

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|.++.++.+...+....  -+-++|..|+|||++|+.+.+..
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHH
Confidence            468999999988887776543  56789999999999999998644

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=81.60  E-value=0.79  Score=45.07  Aligned_cols=23  Identities=30%  Similarity=0.495  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998853

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=81.56  E-value=0.91  Score=43.31  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=22.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -.+|.|.|+.|+||||+++.+.+...
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35899999999999999999987653

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=81.49  E-value=0.98  Score=45.77  Aligned_cols=26  Identities=31%  Similarity=0.456  Sum_probs=22.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -.+++++|..|+||||+++.+.....
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            36999999999999999999887654

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=81.45  E-value=0.86  Score=43.45  Aligned_cols=28  Identities=25%  Similarity=0.331  Sum_probs=23.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..-.+|.++|+.|.||||+++.+.....
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3446899999999999999999987543

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=81.43  E-value=0.76  Score=45.64  Aligned_cols=23  Identities=30%  Similarity=0.535  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||++.+..-
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl   60 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGY   60 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            68999999999999999988743

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.39  E-value=1.6  Score=46.63  Aligned_cols=48  Identities=13%  Similarity=0.171  Sum_probs=37.4

Q ss_pred             cccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          156 VYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..+|.|.++.++++.+.+.             -...+=|=++|..|.|||++|++|.+...
T Consensus       208 ~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~  268 (467)
T 4b4t_H          208 YSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTD  268 (467)
T ss_dssp             CSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHT
T ss_pred             HHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccC
Confidence            3578999999988877653             12334566899999999999999998763

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=81.35  E-value=0.6  Score=45.36  Aligned_cols=23  Identities=35%  Similarity=0.466  Sum_probs=15.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHH-HH
Q 003090          179 SITGICGMGGVGKTTLVKEIQ-KQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~-~~  201 (848)
                      .+++++|..|+||||+++.+. ..
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             CEEEEECSCC----CHHHHHHC--
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcC
Confidence            589999999999999999887 54

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=81.33  E-value=0.78  Score=44.78  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+.--
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999988743

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=81.31  E-value=0.78  Score=45.44  Aligned_cols=24  Identities=21%  Similarity=0.362  Sum_probs=20.9

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcC
Confidence            368999999999999999988743

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=81.23  E-value=0.79  Score=44.37  Aligned_cols=23  Identities=30%  Similarity=0.528  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+...
T Consensus        35 e~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998754

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=81.19  E-value=0.71  Score=44.10  Aligned_cols=23  Identities=39%  Similarity=0.648  Sum_probs=20.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+...
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            57999999999999999998743

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=81.13  E-value=0.87  Score=46.46  Aligned_cols=27  Identities=30%  Similarity=0.294  Sum_probs=22.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-.+++|+|..|.||||+++.+....
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l  104 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            344699999999999999999988654

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=81.12  E-value=0.83  Score=45.41  Aligned_cols=23  Identities=30%  Similarity=0.524  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        47 e~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            68999999999999999998853

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=81.08  E-value=0.8  Score=45.26  Aligned_cols=23  Identities=39%  Similarity=0.507  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999988743

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=81.00  E-value=2  Score=41.93  Aligned_cols=27  Identities=22%  Similarity=0.159  Sum_probs=22.5

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+|.+.|..|+||||+|+.+.+..
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            345689999999999999999987543

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=80.98  E-value=0.9  Score=43.57  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=19.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+|+|.|+.|.||||+++.+..
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999864

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=80.94  E-value=1.7  Score=46.80  Aligned_cols=26  Identities=31%  Similarity=0.491  Sum_probs=22.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      -.+++|+|..|+||||+++.+.....
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll~  318 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQFE  318 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHhh
Confidence            36899999999999999999886654

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=80.86  E-value=1.3  Score=47.37  Aligned_cols=46  Identities=20%  Similarity=0.281  Sum_probs=36.0

Q ss_pred             ccccchhHHHHHHHHHHhc--------------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD--------------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~--------------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|+|.++.++.+...+..              ...+-+-++|..|+||||+|+.+....
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l   74 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHc
Confidence            4689999988888766631              123457899999999999999998765

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.85  E-value=2  Score=45.24  Aligned_cols=49  Identities=24%  Similarity=0.289  Sum_probs=38.1

Q ss_pred             ccccccchhHHHHHHHHHHh-------------cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          155 GVYAFKSRESTMKDIMEAMK-------------DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~-------------~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ...+|.|.++.++++.+.+.             -...+=|=.+|..|.|||.+|++|.+...
T Consensus       180 ~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~  241 (437)
T 4b4t_I          180 SYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTS  241 (437)
T ss_dssp             CGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHT
T ss_pred             cceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhC
Confidence            45678899999988877654             12234577899999999999999998763

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=80.83  E-value=0.98  Score=43.62  Aligned_cols=23  Identities=30%  Similarity=0.343  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..|.++|+.|+||||+|+.+.+.
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~   30 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTH   30 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999998754

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=80.81  E-value=0.89  Score=43.91  Aligned_cols=23  Identities=35%  Similarity=0.449  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|+|||||++.+...
T Consensus        26 ~~~~l~G~nGsGKSTll~~l~g~   48 (231)
T 4a74_A           26 AITEVFGEFGSGKTQLAHTLAVM   48 (231)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999864

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=80.55  E-value=0.86  Score=44.68  Aligned_cols=23  Identities=48%  Similarity=0.713  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        36 e~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999988743

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=80.52  E-value=1.1  Score=43.03  Aligned_cols=24  Identities=25%  Similarity=0.263  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|.++|+.|+||||+|+.+.+..
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            478999999999999999997653

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=80.38  E-value=2.2  Score=41.47  Aligned_cols=47  Identities=17%  Similarity=0.062  Sum_probs=31.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhhcc----ccCcEEEEEeccCCchhHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKEMK----MFDDVAMAVVSQTPSITKI  225 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l  225 (848)
                      .++.|+|..|+||||++..+........    .-..++|+.....++..++
T Consensus        25 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~   75 (243)
T 1n0w_A           25 SITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL   75 (243)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH
Confidence            6899999999999999998876432211    1235677765554444433

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=80.33  E-value=0.88  Score=44.86  Aligned_cols=23  Identities=39%  Similarity=0.574  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+.--
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            68999999999999999988743

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=80.32  E-value=0.87  Score=45.70  Aligned_cols=22  Identities=23%  Similarity=0.706  Sum_probs=20.2

Q ss_pred             ccEEEEEeCCCCchhHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~  199 (848)
                      ..+|+|.|+.|+||||+|+.+-
T Consensus        75 ~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           75 LYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4689999999999999999887

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=80.28  E-value=0.88  Score=44.53  Aligned_cols=23  Identities=30%  Similarity=0.495  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        29 e~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           29 SIIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            68999999999999999988743

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=80.25  E-value=1  Score=42.58  Aligned_cols=23  Identities=26%  Similarity=0.328  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|.+.|+.|+||||+++.+.+.
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            57999999999999999998754

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=80.17  E-value=0.9  Score=44.57  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999988743

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=80.05  E-value=0.91  Score=44.92  Aligned_cols=23  Identities=26%  Similarity=0.462  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+..-
T Consensus        47 e~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            58999999999999999998753

---

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	848
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	1e-14
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	4e-06
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	3e-07
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	5e-07
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	4e-05
d2astb2	284	c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p1	8e-06
d2astb2	284	c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p1	1e-05
d1dcea3	124	c.10.2.2 (A:444-567) Rab geranylgeranyltransferase	3e-05
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	3e-04
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	5e-04
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	0.003
d1ogqa_	313	c.10.2.8 (A:) Polygalacturonase inhibiting protein	7e-04
d1ogqa_	313	c.10.2.8 (A:) Polygalacturonase inhibiting protein	0.002
d1h6ua2	227	c.10.2.1 (A:36-262) Internalin H {Listeria monocyt	0.001
d1a9na_	162	c.10.2.4 (A:) Splicesomal U2A' protein {Human (Hom	0.002
d1ozna_	284	c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 recept	0.003
d1z7xw1	460	c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (	0.004

>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 = 74.7 bits (182), Expect = 1e-14
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 9/172 (5%)

Query: 232 WLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRR 291
             +L  +SL  N + ++        L  L L  N    +      G+  L  L LG  + 
Sbjct: 218 LTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAP--LSGLTKLTELKLGANQI 275

Query: 292 FSFSVRFPFLFPPLPSSPL--FLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEIL 349
            + S                     S +S L NL  L L+   I   +S +  L+ L+ L
Sbjct: 276 SNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISD-ISPVSSLTKLQRL 334

Query: 350 DLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
             + + VS++  S   L+++  L      I +L P   L+ L ++ +L ++ 
Sbjct: 335 FFANNKVSDVS-SLANLTNINWLSAGHNQISDLTP---LANLTRITQLGLND 382

>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 = 47.3 bits (111), Expect = 4e-06
 Identities = 16/106 (15%), Positives = 37/106 (34%), Gaps = 9/106 (8%)

Query: 303 PPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS 362
              P + +F   +    L       L    +   +S   +L  +  L      +  I   
Sbjct: 8   QDTPINQIFTDTA----LAEKMKTVLGKTNVTDTVSQ-TDLDQVTTLQADRLGIKSID-G 61

Query: 363 FGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
              L++L  ++ +   + ++ P   L  L KL ++ M+++      
Sbjct: 62  VEYLNNLTQINFSNNQLTDITP---LKNLTKLVDILMNNNQIADIT 104

>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 = 50.6 bits (120), Expect = 3e-07
 Identities = 17/118 (14%), Positives = 40/118 (33%), Gaps = 7/118 (5%)

Query: 162 RESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQAKEM--KMFDDVAMAVV 216
           RE  +  +++ +    D +     + G  G GK+ +  +   ++ ++    +D +     
Sbjct: 25  REYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKD 84

Query: 217 SQTPSITKIQYEIAGWLDLTG--ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPD 272
           S T   +         L L      L F  +  V   +    +    +   + L + D
Sbjct: 85  SGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFD 142

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]} Length = 305

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 50.0 bits (118), Expect = 5e-07
 Identities = 26/164 (15%), Positives = 50/164 (30%), Gaps = 13/164 (7%)

Query: 221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKD 280
           S         G   L+ I +   +I  +P  L  P L  L L  N    +     +G+ +
Sbjct: 138 SSGIENGAFQGMKKLSYIRIADTNITTIPQGL-PPSLTELHLDGNKITKVDAASLKGLNN 196

Query: 281 LQVLDLGGIRRFSFSVRFPFLFPPLP-----SSPLFLLPSSLSFLINLRTLRLHDRRIQG 335
           L  L L      +         P L      ++ L  +P  L+    ++ + LH+  I  
Sbjct: 197 LAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISA 256

Query: 336 -------DLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLL 372
                        + +    + L  + V    +       + + 
Sbjct: 257 IGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVR 300

>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 = 44.3 bits (103), Expect = 4e-05
 Identities = 41/171 (23%), Positives = 67/171 (39%), Gaps = 15/171 (8%)

Query: 234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFS 293
            L  +      + +VP +L  P    L LQ N    I D  F+ +K+L  L L   +   
Sbjct: 11  HLRVVQCSDLGLEKVPKDLP-PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISK 69

Query: 294 FSVRFPFLFPPLPS-SPLFLLPSSLSFL-----INLRTLRLHDRRIQG-DLSLIGELSGL 346
            S   P  F PL     L+L  + L  L       L+ LR+H+  I     S+   L+ +
Sbjct: 70  IS---PGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQM 126

Query: 347 EILDL---SESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL 394
            +++L             +F  +  L  + +    I   IP+G+   L +L
Sbjct: 127 IVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITT-IPQGLPPSLTEL 176

>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 = 46.3 bits (108), Expect = 8e-06
 Identities = 21/129 (16%), Positives = 43/129 (33%), Gaps = 13/129 (10%)

Query: 324 RTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELI 383
           +TL L  + +  D++      G+       S + +          ++ +DL+   I    
Sbjct: 3   QTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVST 62

Query: 384 PRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKI 443
             G+LS+  KL+ L +                  S+     L   S L  L++    G  
Sbjct: 63  LHGILSQCSKLQNLSLEGL-------------RLSDPIVNTLAKNSNLVRLNLSGCSGFS 109

Query: 444 MPSDMSFQN 452
             +  +  +
Sbjct: 110 EFALQTLLS 118

>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 = 45.5 bits (106), Expect = 1e-05
 Identities = 20/101 (19%), Positives = 37/101 (36%), Gaps = 5/101 (4%)

Query: 312 LLPSSLSFLI--NLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSE--IPVSFGRLS 367
           L P     L+   +   R     +   L+       ++ +DLS S +    +     + S
Sbjct: 12  LHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCS 71

Query: 368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQF 408
            L+ L L G  + + I    L++   L  L +S      +F
Sbjct: 72  KLQNLSLEGLRLSDPIVN-TLAKNSNLVRLNLSGCSGFSEF 111

>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 = 42.4 bits (99), Expect = 3e-05
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 1/88 (1%)

Query: 314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLD 373
              L  L+ +  L L   R++     +  L  LE+L  S++ +  +      L  L+ L 
Sbjct: 13  LCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELL 71

Query: 374 LTGCYILELIPRGVLSRLRKLEELYMSH 401
           L    + +      L    +L  L +  
Sbjct: 72  LCNNRLQQSAAIQPLVSCPRLVLLNLQG 99

>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 = 41.7 bits (96), Expect = 3e-04
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 6/59 (10%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRL 371
           LP+       L  L      +     +      L+ L +  + + E P     +  LR+
Sbjct: 299 LPALPP---RLERLIASFNHLA---EVPELPQNLKQLHVEYNPLREFPDIPESVEDLRM 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 = 41.0 bits (94), Expect = 5e-04
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 11/82 (13%)

Query: 319 FLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCY 378
              +L  L + + ++     L      LE L  S + ++E+P       +L+ L +    
Sbjct: 282 LPPSLEELNVSNNKLI---ELPALPPRLERLIASFNHLAEVPEL---PQNLKQLHVEYNP 335

Query: 379 ILELIPRGVLSRLRKLEELYMS 400
           + E            +E+L M+
Sbjct: 336 LREF-----PDIPESVEDLRMN 352

>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 = 38.3 bits (87), Expect = 0.003
 Identities = 14/89 (15%), Positives = 29/89 (32%), Gaps = 3/89 (3%)

Query: 322 NLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILE 381
               L L++  +    SL      LE L  S + ++E+P     L  L + +     + +
Sbjct: 39  QAHELELNNLGLS---SLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSD 95

Query: 382 LIPRGVLSRLRKLEELYMSHSFRHWQFES 410
           L P      +   +   +         + 
Sbjct: 96  LPPLLEYLGVSNNQLEKLPELQNSSFLKI 124

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]} Length = 313

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]

 Score = 40.1 bits (92), Expect = 7e-04
 Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 2/44 (4%)

Query: 358 EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSH 401
            +P    +L  L  L+++   +   IP+     L++ +    ++
Sbjct: 259 TLPQGLTQLKFLHSLNVSFNNLCGEIPQ--GGNLQRFDVSAYAN 300

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]} Length = 313

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]

 Score = 39.0 bits (89), Expect = 0.002
 Identities = 9/40 (22%), Positives = 18/40 (45%)

Query: 313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLS 352
           LP  L+ L  L +L +    + G++   G L   ++   +
Sbjct: 260 LPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYA 299

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]} Length = 227

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]

 Score = 38.9 bits (89), Expect = 0.001
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 340 IGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM 399
           +  LS L  L   ++ +S+I      L +L  + L    I ++ P   L+    L  + +
Sbjct: 169 LANLSKLTTLKADDNKISDIS-PLASLPNLIEVHLKNNQISDVSP---LANTSNLFIVTL 224

Query: 400 SH 401
           ++
Sbjct: 225 TN 226

>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 = 37.6 bits (86), Expect = 0.002
 Identities = 11/49 (22%), Positives = 16/49 (32%)

Query: 343 LSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRL 391
                 LDL    +  I      L     +D +   I +L    +L RL
Sbjct: 17  AVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRL 65

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {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: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (87), Expect = 0.003
 Identities = 25/133 (18%), Positives = 43/133 (32%), Gaps = 9/133 (6%)

Query: 232 WLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGI 289
             +LT + L  N I  VP+        L  L L +N    +    F+ +  L  L L   
Sbjct: 152 LGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFAN 211

Query: 290 RRFSFSVRFPFLFPPLPS-----SPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELS 344
              +           L       +P      +      L+  R     +    SL   L+
Sbjct: 212 NLSALPTEALAPLRALQYLRLNDNPWVCDCRARPLWAWLQKFRGSSSEVPC--SLPQRLA 269

Query: 345 GLEILDLSESDVS 357
           G ++  L+ +D+ 
Sbjct: 270 GRDLKRLAANDLQ 282

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]} Length = 460

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]

 Score = 38.0 bits (86), Expect = 0.004
 Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 7/62 (11%)

Query: 346 LEILDLSESDVSEIPVS--FGRLSHLRLLDLTGCYI----LELIPRGVLSRLRKLEELYM 399
           ++ LD+   ++S+   +     L   +++ L  C +     + I    L     L EL +
Sbjct: 4   IQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISS-ALRVNPALAELNL 62

Query: 400 SH 401
             
Sbjct: 63  RS 64

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	848
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.78
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.76
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.68
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.65
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.64
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.63
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.61
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.58
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.58
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.57
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.54
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.54
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.51
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.51
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.5
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.49
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.48
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.47
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.43
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.43
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.33
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.3
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.3
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.28
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.27
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.26
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.25
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.18
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.1
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.08
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.05
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.99
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.84
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	98.75
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.64
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.64
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.64
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.7
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.39
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.79
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.59
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.53
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	96.3
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.21
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.19
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.05
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.03
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	96.03
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	95.98
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.79
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	95.76
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	95.34
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	95.29
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.29
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.17
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.14
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.91
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.36
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	93.44
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	93.05
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	93.03
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.98
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.88
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.73
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.54
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.96
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.95
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.75
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	91.4
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.8
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	90.8
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	90.65
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	90.58
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.56
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	90.52
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	90.5
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	90.41
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	89.99
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	89.98
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	89.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	89.76
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	89.71
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	89.6
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	89.57
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	88.92
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	88.89
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	88.72
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	88.3
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	88.14
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	88.09
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	87.94
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	87.71
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	87.42
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	87.16
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	87.13
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	86.48
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	85.71
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.46
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	85.42
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	84.97
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	84.79
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	84.77
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	84.71
d1g2912	240	Maltose transport protein MalK, N-terminal domain	84.67
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	84.39
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	84.04
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	84.02
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	83.78
d2awna2	232	Maltose transport protein MalK, N-terminal domain	83.76
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	83.65
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	83.52
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	83.38
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	83.23
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	83.07
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	83.06
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.02
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	82.96
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	82.94
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	82.85
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	82.76
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	82.66
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	82.64
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	82.54
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	82.53
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	82.38
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	82.22
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	82.15
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	82.12
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	82.05
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	81.48
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	81.33
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	81.12
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	80.84
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	80.77
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	80.52
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	80.52
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	80.49
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	80.48
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	80.42
d1ls1a2	207	GTPase domain of the signal sequence recognition p	80.28
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	80.22
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	80.21
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	80.02

>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=99.78  E-value=5.5e-18  Score=182.31  Aligned_cols=323  Identities=19%  Similarity=0.208  Sum_probs=188.3

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+.+|++|+++++.+..+..  ++.+++|++|++++              +.+++     +|. ++++++|++|++++|.
T Consensus        42 ~l~~l~~L~l~~~~I~~l~g--l~~L~nL~~L~Ls~--------------N~l~~-----l~~-l~~L~~L~~L~L~~n~   99 (384)
T d2omza2          42 DLDQVTTLQADRLGIKSIDG--VEYLNNLTQINFSN--------------NQLTD-----ITP-LKNLTKLVDILMNNNQ   99 (384)
T ss_dssp             HHTTCCEEECCSSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GTTCTTCCEEECCSSC
T ss_pred             HhCCCCEEECCCCCCCCccc--cccCCCCCEEeCcC--------------CcCCC-----Ccc-ccCCcccccccccccc
Confidence            45667777777777666642  46677777777777              66766     553 7777777777777775


Q ss_pred             ccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChh------------------hhhccccc
Q 003090          333 IQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRG------------------VLSRLRKL  394 (848)
Q Consensus       333 ~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~------------------~l~~l~~L  394 (848)
                      +... ..++.+++|+.|+++++.++.++. ......+..+....+......+..                  .+......
T Consensus       100 i~~i-~~l~~l~~L~~L~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (384)
T d2omza2         100 IADI-TPLANLTNLTGLTLFNNQITDIDP-LKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTL  177 (384)
T ss_dssp             CCCC-GGGTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTC
T ss_pred             cccc-cccccccccccccccccccccccc-ccccccccccccccccccccccccccccccccccccccchhhhhcccccc
Confidence            5443 346777777777777776665543 233344444444332211110000                  01111111


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEEeCCCCCCCCCcccce
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGL  474 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l  474 (848)
                      .......+               ..........+++++.++++.+.+..++.....++|+.|.+..+..           
T Consensus       178 ~~~~~~~~---------------~~~~~~~~~~l~~~~~l~l~~n~i~~~~~~~~~~~L~~L~l~~n~l-----------  231 (384)
T d2omza2         178 ERLDISSN---------------KVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQL-----------  231 (384)
T ss_dssp             CEEECCSS---------------CCCCCGGGGGCTTCSEEECCSSCCCCCGGGGGCTTCCEEECCSSCC-----------
T ss_pred             cccccccc---------------ccccccccccccccceeeccCCccCCCCcccccCCCCEEECCCCCC-----------
Confidence            11111111               1123345667778888888888777665544667777777763332           


Q ss_pred             EEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCCCCcEEEEecCCCceeeccccc
Q 003090          475 FLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFNELMFLVIFRCNEMKYLLNSLE  554 (848)
Q Consensus       475 ~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~  554 (848)
                                           +.++. + ..+++|+.|.+.++... ....   ...+++|+.|++.++.. +.      
T Consensus       232 ---------------------~~~~~-l-~~l~~L~~L~l~~n~l~-~~~~---~~~~~~L~~L~l~~~~l-~~------  277 (384)
T d2omza2         232 ---------------------KDIGT-L-ASLTNLTDLDLANNQIS-NLAP---LSGLTKLTELKLGANQI-SN------  277 (384)
T ss_dssp             ---------------------CCCGG-G-GGCTTCSEEECCSSCCC-CCGG---GTTCTTCSEEECCSSCC-CC------
T ss_pred             ---------------------CCcch-h-hcccccchhccccCccC-CCCc---ccccccCCEeeccCccc-CC------
Confidence                                 00000 0 01356777777666432 2221   24567888888877642 22      


Q ss_pred             ccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCcEEEEeccCCceeeeec
Q 003090          555 RTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQRLRVYSCGLLVSVFEI  634 (848)
Q Consensus       555 ~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~~L~l~~c~~l~~~~~~  634 (848)
                      ......++.++.+.+.++. ++.+    .....+++++.|+++++ ++ ..+++.  ..+++|++|++++| .++.++  
T Consensus       278 ~~~~~~~~~l~~l~~~~n~-l~~~----~~~~~~~~l~~L~ls~n-~l-~~l~~l--~~l~~L~~L~L~~n-~l~~l~--  345 (384)
T d2omza2         278 ISPLAGLTALTNLELNENQ-LEDI----SPISNLKNLTYLTLYFN-NI-SDISPV--SSLTKLQRLFFANN-KVSDVS--  345 (384)
T ss_dssp             CGGGTTCTTCSEEECCSSC-CSCC----GGGGGCTTCSEEECCSS-CC-SCCGGG--GGCTTCCEEECCSS-CCCCCG--
T ss_pred             CCccccccccccccccccc-cccc----cccchhcccCeEECCCC-CC-CCCccc--ccCCCCCEEECCCC-CCCCCh--
Confidence            2234556777788777663 3322    22345778888888876 45 555543  67788888888887 555552  


Q ss_pred             cccccccccccccCCcCEEecCCCccccccccCCCccccccCccEEEeec
Q 003090          635 ERVNIAKEETELFSSLEKLTLWDLPRMTDIWKGDTQFVSLHNLKKVRVEE  684 (848)
Q Consensus       635 ~~~~~~~~~~~~l~~L~~L~l~~c~~L~~l~~~~~~l~~l~~L~~L~i~~  684 (848)
                              .+..+++|++|+++++ .++.++    ++.++++|+.|+|++
T Consensus       346 --------~l~~l~~L~~L~l~~N-~l~~l~----~l~~l~~L~~L~L~~  382 (384)
T d2omza2         346 --------SLANLTNINWLSAGHN-QISDLT----PLANLTRITQLGLND  382 (384)
T ss_dssp             --------GGGGCTTCCEEECCSS-CCCBCG----GGTTCTTCSEEECCC
T ss_pred             --------hHcCCCCCCEEECCCC-cCCCCh----hhccCCCCCEeeCCC
Confidence                    3567788888888776 466553    366778888888764

>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=99.76  E-value=2.1e-17  Score=177.71  Aligned_cols=318  Identities=20%  Similarity=0.216  Sum_probs=207.8

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.|+++++.++.+...-.+++|++|++++|.+..+++  ++++++|++|++++              +.+..     +
T Consensus        45 ~l~~L~l~~~~I~~l~gl~~L~nL~~L~Ls~N~l~~l~~--l~~L~~L~~L~L~~--------------n~i~~-----i  103 (384)
T d2omza2          45 QVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITP--LKNLTKLVDILMNN--------------NQIAD-----I  103 (384)
T ss_dssp             TCCEEECCSSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----C
T ss_pred             CCCEEECCCCCCCCccccccCCCCCEEeCcCCcCCCCcc--ccCCcccccccccc--------------ccccc-----c
Confidence            478899999999988543389999999999999999876  68999999999999              78877     5


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccC--------------------hhhccCCcccEEe
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIP--------------------VSFGRLSHLRLLD  373 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp--------------------~~i~~L~~L~~L~  373 (848)
                      + .++.+++|++|++.++...... .......+..+....+.+..+.                    ..+..........
T Consensus       104 ~-~l~~l~~L~~L~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (384)
T d2omza2         104 T-PLANLTNLTGLTLFNNQITDID-PLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLD  181 (384)
T ss_dssp             G-GGTTCTTCCEEECCSSCCCCCG-GGTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEE
T ss_pred             c-cccccccccccccccccccccc-cccccccccccccccccccccccccccccccccccccccchhhhhcccccccccc
Confidence            4 3889999999999988655443 3334445555555444332111                    1122222233333


Q ss_pred             ccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCC
Q 003090          374 LTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNL  453 (848)
Q Consensus       374 l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L  453 (848)
                      ...+..  ..... ...+++++.+++++|.+...               ......++|+.|++++|.++.++....+++|
T Consensus       182 ~~~~~~--~~~~~-~~~l~~~~~l~l~~n~i~~~---------------~~~~~~~~L~~L~l~~n~l~~~~~l~~l~~L  243 (384)
T d2omza2         182 ISSNKV--SDISV-LAKLTNLESLIATNNQISDI---------------TPLGILTNLDELSLNGNQLKDIGTLASLTNL  243 (384)
T ss_dssp             CCSSCC--CCCGG-GGGCTTCSEEECCSSCCCCC---------------GGGGGCTTCCEEECCSSCCCCCGGGGGCTTC
T ss_pred             cccccc--ccccc-cccccccceeeccCCccCCC---------------CcccccCCCCEEECCCCCCCCcchhhccccc
Confidence            333221  12222 56777777777777765532               2345566777777777777666533366777


Q ss_pred             CeEEEEeCCCCCCCCCcccceEEecccccccccccCccccchhhHHHHHHHHHhhcceeeeccccccccccccccccCCC
Q 003090          454 TSFSIAIGDLEERPLSDFIGLFLQKFKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVNYFENIVSDLANDGFN  533 (848)
Q Consensus       454 ~~L~l~~~~~~~~~~~~l~~l~l~~~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~  533 (848)
                      +.|.+..+..-  ...                  .+              ...++|+.|+++++.... ...   ...++
T Consensus       244 ~~L~l~~n~l~--~~~------------------~~--------------~~~~~L~~L~l~~~~l~~-~~~---~~~~~  285 (384)
T d2omza2         244 TDLDLANNQIS--NLA------------------PL--------------SGLTKLTELKLGANQISN-ISP---LAGLT  285 (384)
T ss_dssp             SEEECCSSCCC--CCG------------------GG--------------TTCTTCSEEECCSSCCCC-CGG---GTTCT
T ss_pred             chhccccCccC--CCC------------------cc--------------cccccCCEeeccCcccCC-CCc---ccccc
Confidence            77766533220  000                  00              013567777776554322 111   24668


Q ss_pred             CCcEEEEecCCCceeecccccccccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHh
Q 003090          534 ELMFLVIFRCNEMKYLLNSLERTLRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQS  613 (848)
Q Consensus       534 ~L~~L~l~~~~~l~~l~~~~~~~~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~  613 (848)
                      .++.+.+.++.. +.      ......+++++.|+++++ +++.+    .+...+|+|++|++++| .+ +.++..  ..
T Consensus       286 ~l~~l~~~~n~l-~~------~~~~~~~~~l~~L~ls~n-~l~~l----~~l~~l~~L~~L~L~~n-~l-~~l~~l--~~  349 (384)
T d2omza2         286 ALTNLELNENQL-ED------ISPISNLKNLTYLTLYFN-NISDI----SPVSSLTKLQRLFFANN-KV-SDVSSL--AN  349 (384)
T ss_dssp             TCSEEECCSSCC-SC------CGGGGGCTTCSEEECCSS-CCSCC----GGGGGCTTCCEEECCSS-CC-CCCGGG--GG
T ss_pred             cccccccccccc-cc------ccccchhcccCeEECCCC-CCCCC----cccccCCCCCEEECCCC-CC-CCChhH--cC
Confidence            888888877642 22      234566899999999988 56554    23557999999999998 56 667643  78


Q ss_pred             hccCcEEEEeccCCceeeeeccccccccccccccCCcCEEecCC
Q 003090          614 FQNLQRLRVYSCGLLVSVFEIERVNIAKEETELFSSLEKLTLWD  657 (848)
Q Consensus       614 l~~L~~L~l~~c~~l~~~~~~~~~~~~~~~~~~l~~L~~L~l~~  657 (848)
                      +++|++|++++| .++.++          .+..+++|++|+|++
T Consensus       350 l~~L~~L~l~~N-~l~~l~----------~l~~l~~L~~L~L~~  382 (384)
T d2omza2         350 LTNINWLSAGHN-QISDLT----------PLANLTRITQLGLND  382 (384)
T ss_dssp             CTTCCEEECCSS-CCCBCG----------GGTTCTTCSEEECCC
T ss_pred             CCCCCEEECCCC-cCCCCh----------hhccCCCCCEeeCCC
Confidence            999999999876 566663          367889999999876

>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=99.68  E-value=1.4e-16  Score=160.85  Aligned_cols=192  Identities=22%  Similarity=0.221  Sum_probs=166.2

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      ..++.+++.++.+|+.+. +++++|+|++|.+..++...|.++++|++|++++              +.++.     +|.
T Consensus        13 ~~v~C~~~~L~~iP~~lp-~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~--------------N~l~~-----l~~   72 (266)
T d1p9ag_          13 LEVNCDKRNLTALPPDLP-KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDR--------------AELTK-----LQV   72 (266)
T ss_dssp             CEEECTTSCCSSCCSCCC-TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTT--------------SCCCE-----EEC
T ss_pred             eEEEccCCCCCeeCcCcC-cCCCEEECcCCcCCCcCHHHhhcccccccccccc--------------ccccc-----ccc
Confidence            346778889999998774 6899999999999999988889999999999999              88876     654


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                       ++.+++|++|++++|++...+..+..+++|++|+++++.+..++. .+..+.++++|++++|.. ..+|...+..+++|
T Consensus        73 -~~~l~~L~~L~Ls~N~l~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~l-~~l~~~~~~~l~~l  150 (266)
T d1p9ag_          73 -DGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNEL-KTLPPGLLTPTPKL  150 (266)
T ss_dssp             -CSCCTTCCEEECCSSCCSSCCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCC-CCCCTTTTTTCTTC
T ss_pred             -ccccccccccccccccccccccccccccccccccccccccceeecccccccccccccccccccc-ceeccccccccccc
Confidence             678999999999999888888889999999999999999886654 567899999999999755 56777768899999


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeCC
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIGD  462 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~~  462 (848)
                      +.|++++|.+...             .+..++.+++|++|++++|.++.+|..+ .+++|+.|.+.++.
T Consensus       151 ~~l~l~~N~l~~~-------------~~~~~~~l~~L~~L~Ls~N~L~~lp~~~~~~~~L~~L~L~~Np  206 (266)
T d1p9ag_         151 EKLSLANNNLTEL-------------PAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNP  206 (266)
T ss_dssp             CEEECTTSCCSCC-------------CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCCCSEEECCSCC
T ss_pred             hhccccccccccc-------------CccccccccccceeecccCCCcccChhHCCCCCCCEEEecCCC
Confidence            9999999998765             3456889999999999999999999888 88999999988443

>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=99.65  E-value=1.5e-15  Score=156.99  Aligned_cols=147  Identities=20%  Similarity=0.267  Sum_probs=79.7

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCc
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPS  315 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~  315 (848)
                      +.++-+++.++.+|..+. +++++|++++|.+..+|+..|.++++|++|++++              +.+...    .|.
T Consensus        13 ~~~~C~~~~L~~lP~~l~-~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~--------------n~~~~i----~~~   73 (305)
T d1xkua_          13 RVVQCSDLGLEKVPKDLP-PDTALLDLQNNKITEIKDGDFKNLKNLHTLILIN--------------NKISKI----SPG   73 (305)
T ss_dssp             TEEECTTSCCCSCCCSCC-TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS--------------SCCCCB----CTT
T ss_pred             CEEEecCCCCCccCCCCC-CCCCEEECcCCcCCCcChhHhhcccccccccccc--------------cccccc----chh
Confidence            345555556666666553 4566666666666666665556666666666666              555552    345


Q ss_pred             hhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccc--cccChhhhhccc
Q 003090          316 SLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYIL--ELIPRGVLSRLR  392 (848)
Q Consensus       316 ~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~--~~~p~~~l~~l~  392 (848)
                      .|.++++|++|++++|++...+..  ....++.|++.+|.+..++.. +.....++.++...+...  ...+.. +..++
T Consensus        74 ~f~~l~~L~~L~l~~n~l~~l~~~--~~~~l~~L~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~-~~~l~  150 (305)
T d1xkua_          74 AFAPLVKLERLYLSKNQLKELPEK--MPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGA-FQGMK  150 (305)
T ss_dssp             TTTTCTTCCEEECCSSCCSBCCSS--CCTTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTG-GGGCT
T ss_pred             hhhCCCccCEecccCCccCcCccc--hhhhhhhhhccccchhhhhhhhhhccccccccccccccccccCCCccc-ccccc
Confidence            566666666666666655544432  223556666666655555433 334445555555443211  111222 45555


Q ss_pred             cccEEecccccc
Q 003090          393 KLEELYMSHSFR  404 (848)
Q Consensus       393 ~L~~L~l~~~~~  404 (848)
                      +|+.+++.+|.+
T Consensus       151 ~L~~l~l~~n~l  162 (305)
T d1xkua_         151 KLSYIRIADTNI  162 (305)
T ss_dssp             TCCEEECCSSCC
T ss_pred             ccCccccccCCc
Confidence            555555555544

>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=99.64  E-value=5.4e-16  Score=161.05  Aligned_cols=173  Identities=20%  Similarity=0.300  Sum_probs=86.8

Q ss_pred             CCceeeecCCCc---ccCCcc-cccccceeeccc-Cc-CcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCC
Q 003090          235 LTGISLMFNDIH---EVPDEL-ECPKLQALFLQE-NS-PLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSS  308 (848)
Q Consensus       235 l~~l~l~~n~l~---~lp~~~-~~~~L~~L~l~~-~~-~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~  308 (848)
                      ++.|+++++.+.   .+|..+ .+++|++|++++ |. .+.+|+. +.++++|++|++++              +.+.+.
T Consensus        52 v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~-i~~L~~L~~L~Ls~--------------N~l~~~  116 (313)
T d1ogqa_          52 VNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPA-IAKLTQLHYLYITH--------------TNVSGA  116 (313)
T ss_dssp             EEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGG-GGGCTTCSEEEEEE--------------ECCEEE
T ss_pred             EEEEECCCCCCCCCCCCChHHhcCccccccccccccccccccccc-cccccccchhhhcc--------------cccccc
Confidence            345666666555   345554 555555555553 32 2345554 34555555555555              444442


Q ss_pred             CCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCc-ccChhhccCCcc-cEEeccCCccccccCh
Q 003090          309 PLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVS-EIPVSFGRLSHL-RLLDLTGCYILELIPR  385 (848)
Q Consensus       309 ~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L-~~L~l~~~~~~~~~p~  385 (848)
                          .|..+..+.+|+++++++|...... ..++++++|+++++++|.+. .+|..+..+.++ +.+++++|...+..|.
T Consensus       117 ----~~~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~  192 (313)
T d1ogqa_         117 ----IPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPP  192 (313)
T ss_dssp             ----CCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCG
T ss_pred             ----ccccccchhhhcccccccccccccCchhhccCcccceeeccccccccccccccccccccccccccccccccccccc
Confidence                3444555555555555555444433 45555555555555555555 455555555443 5555555544444444


Q ss_pred             hhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCC
Q 003090          386 GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEG  441 (848)
Q Consensus       386 ~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~  441 (848)
                      . +.++..+ .+++..+...+.             .+..+..+++|+.+++.++.+
T Consensus       193 ~-~~~l~~~-~l~l~~~~~~~~-------------~~~~~~~~~~l~~l~~~~~~l  233 (313)
T d1ogqa_         193 T-FANLNLA-FVDLSRNMLEGD-------------ASVLFGSDKNTQKIHLAKNSL  233 (313)
T ss_dssp             G-GGGCCCS-EEECCSSEEEEC-------------CGGGCCTTSCCSEEECCSSEE
T ss_pred             c-ccccccc-cccccccccccc-------------ccccccccccccccccccccc
Confidence            3 3444332 345444443332             333444555555555554443

>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=99.63  E-value=4e-16  Score=162.06  Aligned_cols=132  Identities=23%  Similarity=0.369  Sum_probs=63.8

Q ss_pred             ccceeecccCcCc---ccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          256 KLQALFLQENSPL---AIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       256 ~L~~L~l~~~~~~---~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      +++.|+++++.+.   .+|+.+ .++++|++|+|++|             +.+.+.    +|..++++++|++|++++|+
T Consensus        51 ~v~~L~L~~~~l~g~~~lp~~l-~~L~~L~~L~Ls~~-------------N~l~g~----iP~~i~~L~~L~~L~Ls~N~  112 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYPIPSSL-ANLPYLNFLYIGGI-------------NNLVGP----IPPAIAKLTQLHYLYITHTN  112 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGG-GGCTTCSEEEEEEE-------------TTEESC----CCGGGGGCTTCSEEEEEEEC
T ss_pred             EEEEEECCCCCCCCCCCCChHH-hcCccccccccccc-------------cccccc----cccccccccccchhhhcccc
Confidence            3445555554332   344442 45555555555542             344433    55555555555555555554


Q ss_pred             ccCCc-hhhccccCCCEEEccCCCCc-ccChhhccCCcccEEeccCCccccccChhhhhccccc-cEEecccccccc
Q 003090          333 IQGDL-SLIGELSGLEILDLSESDVS-EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL-EELYMSHSFRHW  406 (848)
Q Consensus       333 ~~~~~-~~i~~l~~L~~L~l~~~~l~-~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L-~~L~l~~~~~~~  406 (848)
                      +.+.+ ..+..+.+|+++++++|.+. .+|..++++++|+++++++|...+.+|.. +..+.++ +.+.+++|.+.+
T Consensus       113 l~~~~~~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~-~~~l~~l~~~l~~~~n~l~~  188 (313)
T d1ogqa_         113 VSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDS-YGSFSKLFTSMTISRNRLTG  188 (313)
T ss_dssp             CEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGG-GGCCCTTCCEEECCSSEEEE
T ss_pred             ccccccccccchhhhcccccccccccccCchhhccCcccceeeccccccccccccc-cccccccccccccccccccc
Confidence            44433 33455555555555555433 44555555555555555555444445544 3444443 444455444443

>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=99.61  E-value=2.6e-15  Score=153.23  Aligned_cols=210  Identities=24%  Similarity=0.311  Sum_probs=168.4

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCccccccccc
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      .+++.++..|..  .++.|++++|.|+.+|...  ++++|++|++++|.+..++...+..+..++.++...+        
T Consensus        21 ~~L~~iP~~ip~--~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~--------   90 (284)
T d1ozna_          21 QGLQAVPVGIPA--ASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDN--------   90 (284)
T ss_dssp             SCCSSCCTTCCT--TCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSC--------
T ss_pred             CCCCccCCCCCC--CCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccc--------
Confidence            345555555542  3577888888888888653  7888888888888888887777777888888876652        


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEecc
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLT  375 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~  375 (848)
                           +.+...    -|..+.++++|++|++++|...... ..+....+|+.+++++|.++.+|. .+..+++|++|+++
T Consensus        91 -----~~~~~l----~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~  161 (284)
T d1ozna_          91 -----AQLRSV----DPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLH  161 (284)
T ss_dssp             -----TTCCCC----CTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECC
T ss_pred             -----cccccc----cchhhcccccCCEEecCCcccccccccccchhcccchhhhccccccccChhHhccccchhhcccc
Confidence                 555553    4677899999999999999876655 678889999999999999998875 57789999999999


Q ss_pred             CCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--ccCCC
Q 003090          376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SFQNL  453 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~~~L  453 (848)
                      +|.. ..++...+.++++|+.+++.+|.+...             .+..+..+++|+.|+++.|.+..++...  .+++|
T Consensus       162 ~N~l-~~l~~~~f~~l~~L~~l~l~~N~l~~i-------------~~~~f~~l~~L~~L~l~~N~i~~~~~~~~~~~~~L  227 (284)
T d1ozna_         162 GNRI-SSVPERAFRGLHSLDRLLLHQNRVAHV-------------HPHAFRDLGRLMTLYLFANNLSALPTEALAPLRAL  227 (284)
T ss_dssp             SSCC-CEECTTTTTTCTTCCEEECCSSCCCEE-------------CTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTC
T ss_pred             cCcc-cccchhhhccccccchhhhhhcccccc-------------ChhHhhhhhhccccccccccccccccccccccccc
Confidence            9865 556666689999999999999998765             4567899999999999999999887654  78899


Q ss_pred             CeEEEEeCC
Q 003090          454 TSFSIAIGD  462 (848)
Q Consensus       454 ~~L~l~~~~  462 (848)
                      +.|++..+.
T Consensus       228 ~~L~l~~N~  236 (284)
T d1ozna_         228 QYLRLNDNP  236 (284)
T ss_dssp             CEEECCSSC
T ss_pred             CEEEecCCC
Confidence            999887443

>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=99.58  E-value=3.9e-14  Score=146.18  Aligned_cols=216  Identities=17%  Similarity=0.218  Sum_probs=136.6

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCc-c-cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccC
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDE-L-ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRF  298 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~-~-~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~  298 (848)
                      .++.++..+.  ..++.|++++|.++.+|+. + ++++|++|++++|.+..+++..|.++++|++|++++|+...+....
T Consensus        21 ~L~~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_          21 GLEKVPKDLP--PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKM   98 (305)
T ss_dssp             CCCSCCCSCC--TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSC
T ss_pred             CCCccCCCCC--CCCCEEECcCCcCCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccCCccCcCccch
Confidence            3555555554  3578999999999999975 4 8999999999999999998777899999999999995322221111


Q ss_pred             CCC-------CCCCCCCCCCCCCc-hhhhcccCcEEEccCccccCC---chhhccccCCCEEEccCCCCcccChhhccCC
Q 003090          299 PFL-------FPPLPSSPLFLLPS-SLSFLINLRTLRLHDRRIQGD---LSLIGELSGLEILDLSESDVSEIPVSFGRLS  367 (848)
Q Consensus       299 ~~~-------~~~l~~~~~~~lp~-~~~~l~~L~~L~L~~~~~~~~---~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~  367 (848)
                      ...       .+.+..     ++. .+.....++.+....+.....   ...+..+++|+++++++|.+..+|..+  ++
T Consensus        99 ~~~l~~L~~~~n~l~~-----l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~--~~  171 (305)
T d1xkua_          99 PKTLQELRVHENEITK-----VRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGL--PP  171 (305)
T ss_dssp             CTTCCEEECCSSCCCB-----BCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSC--CT
T ss_pred             hhhhhhhhccccchhh-----hhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCccc--CC
Confidence            111       011222     221 123344455555544432221   134556666777777777666666443  56


Q ss_pred             cccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC
Q 003090          368 HLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD  447 (848)
Q Consensus       368 ~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~  447 (848)
                      +|++|++++|......+.. +.+++.++.|++++|.+...             .+..+.++++|++|++++|.++.+|.+
T Consensus       172 ~L~~L~l~~n~~~~~~~~~-~~~~~~l~~L~~s~n~l~~~-------------~~~~~~~l~~L~~L~L~~N~L~~lp~~  237 (305)
T d1xkua_         172 SLTELHLDGNKITKVDAAS-LKGLNNLAKLGLSFNSISAV-------------DNGSLANTPHLRELHLNNNKLVKVPGG  237 (305)
T ss_dssp             TCSEEECTTSCCCEECTGG-GTTCTTCCEEECCSSCCCEE-------------CTTTGGGSTTCCEEECCSSCCSSCCTT
T ss_pred             ccCEEECCCCcCCCCChhH-hhcccccccccccccccccc-------------ccccccccccceeeecccccccccccc
Confidence            6777777776655554444 66677777777777666544             334556667777777777777766665


Q ss_pred             C-ccCCCCeEEEE
Q 003090          448 M-SFQNLTSFSIA  459 (848)
Q Consensus       448 ~-~~~~L~~L~l~  459 (848)
                      + .+++|+.|++.
T Consensus       238 l~~l~~L~~L~Ls  250 (305)
T d1xkua_         238 LADHKYIQVVYLH  250 (305)
T ss_dssp             TTTCSSCCEEECC
T ss_pred             cccccCCCEEECC
Confidence            5 56666666665

>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=99.58  E-value=6.3e-15  Score=148.57  Aligned_cols=185  Identities=19%  Similarity=0.145  Sum_probs=156.1

Q ss_pred             CchhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCcccChHHHccCCceeEEEccCccccccccc
Q 003090          220 PSITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       220 ~~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      .++..|+..+.  ..++.|+|++|.|+.+|...  .+++|++|++++|.+..++.  +..+++|++|++++         
T Consensus        20 ~~L~~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~~--~~~l~~L~~L~Ls~---------   86 (266)
T d1p9ag_          20 RNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQV--DGTLPVLGTLDLSH---------   86 (266)
T ss_dssp             SCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEEC--CSCCTTCCEEECCS---------
T ss_pred             CCCCeeCcCcC--cCCCEEECcCCcCCCcCHHHhhcccccccccccccccccccc--cccccccccccccc---------
Confidence            34555554443  25789999999999998653  89999999999999998875  47899999999999         


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEecc
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLT  375 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~  375 (848)
                           |.+..     .+..+..+++|++|+++++.+.... ..+..+.++++|++++|.+..+|.. +..+++|+.|+++
T Consensus        87 -----N~l~~-----~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~l~~l~~~~~~~l~~l~~l~l~  156 (266)
T d1p9ag_          87 -----NQLQS-----LPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLA  156 (266)
T ss_dssp             -----SCCSS-----CCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECT
T ss_pred             -----ccccc-----cccccccccccccccccccccceeeccccccccccccccccccccceeccccccccccchhcccc
Confidence                 88887     7888999999999999999887766 7778999999999999999988765 5679999999999


Q ss_pred             CCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCC
Q 003090          376 GCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       376 ~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      +|... .+|.+.+..+++|++|++++|.++.              .+..+..+++|+.|+|++|...
T Consensus       157 ~N~l~-~~~~~~~~~l~~L~~L~Ls~N~L~~--------------lp~~~~~~~~L~~L~L~~Np~~  208 (266)
T d1p9ag_         157 NNNLT-ELPAGLLNGLENLDTLLLQENSLYT--------------IPKGFFGSHLLPFAFLHGNPWL  208 (266)
T ss_dssp             TSCCS-CCCTTTTTTCTTCCEEECCSSCCCC--------------CCTTTTTTCCCSEEECCSCCBC
T ss_pred             ccccc-ccCccccccccccceeecccCCCcc--------------cChhHCCCCCCCEEEecCCCCC
Confidence            98765 4665558999999999999999874              4556778899999999998643

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=99.57  E-value=4.9e-14  Score=148.89  Aligned_cols=137  Identities=18%  Similarity=0.214  Sum_probs=98.5

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.|+++++.++.+|+.  .++|++|++++|.+..+|..    +.+|+.|++++              +.+..     +
T Consensus        39 ~l~~LdLs~~~L~~lp~~--~~~L~~L~Ls~N~l~~lp~~----~~~L~~L~l~~--------------n~l~~-----l   93 (353)
T d1jl5a_          39 QAHELELNNLGLSSLPEL--PPHLESLVASCNSLTELPEL----PQSLKSLLVDN--------------NNLKA-----L   93 (353)
T ss_dssp             TCSEEECTTSCCSCCCSC--CTTCSEEECCSSCCSSCCCC----CTTCCEEECCS--------------SCCSC-----C
T ss_pred             CCCEEEeCCCCCCCCCCC--CCCCCEEECCCCCCcccccc----hhhhhhhhhhh--------------cccch-----h
Confidence            578899999999999864  46899999999998888853    56888999988              65555     4


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      +.-   .+.|++|++++|.+...+ .++.+++|++|+++++.+...|..+   ..+..+.+.++....  +.. +..++.
T Consensus        94 ~~l---p~~L~~L~L~~n~l~~lp-~~~~l~~L~~L~l~~~~~~~~~~~~---~~l~~l~~~~~~~~~--~~~-l~~l~~  163 (353)
T d1jl5a_          94 SDL---PPLLEYLGVSNNQLEKLP-ELQNSSFLKIIDVDNNSLKKLPDLP---PSLEFIAAGNNQLEE--LPE-LQNLPF  163 (353)
T ss_dssp             CSC---CTTCCEEECCSSCCSSCC-CCTTCTTCCEEECCSSCCSCCCCCC---TTCCEEECCSSCCSS--CCC-CTTCTT
T ss_pred             hhh---cccccccccccccccccc-chhhhccceeecccccccccccccc---ccccchhhccccccc--ccc-cccccc
Confidence            321   135889999988766544 4678888999999888887766543   445566666543322  222 677888


Q ss_pred             ccEEeccccccc
Q 003090          394 LEELYMSHSFRH  405 (848)
Q Consensus       394 L~~L~l~~~~~~  405 (848)
                      ++.|.+.++...
T Consensus       164 l~~L~l~~n~~~  175 (353)
T d1jl5a_         164 LTAIYADNNSLK  175 (353)
T ss_dssp             CCEEECCSSCCS
T ss_pred             ceeccccccccc
Confidence            888888777654

>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=99.54  E-value=2.6e-14  Score=145.72  Aligned_cols=192  Identities=19%  Similarity=0.220  Sum_probs=154.2

Q ss_pred             eeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchh
Q 003090          238 ISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSL  317 (848)
Q Consensus       238 l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~  317 (848)
                      ++.++..++.+|..+. +.+++|++++|.+..+|...|.++++|++|++++              +.+...    .+..+
T Consensus        16 v~c~~~~L~~iP~~ip-~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~--------------n~l~~i----~~~~~   76 (284)
T d1ozna_          16 TSCPQQGLQAVPVGIP-AASQRIFLHGNRISHVPAASFRACRNLTILWLHS--------------NVLARI----DAAAF   76 (284)
T ss_dssp             EECCSSCCSSCCTTCC-TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCS--------------SCCCEE----CTTTT
T ss_pred             EEcCCCCCCccCCCCC-CCCCEEECcCCcCCCCCHHHhhcccccccccccc--------------cccccc----ccccc
Confidence            5566778889998764 5789999999999999988889999999999999              777764    45566


Q ss_pred             hhcccCcEEEccCccccC-Cc-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccc
Q 003090          318 SFLINLRTLRLHDRRIQG-DL-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKL  394 (848)
Q Consensus       318 ~~l~~L~~L~L~~~~~~~-~~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L  394 (848)
                      ..+..++.+....+.... .. ..+.++++|++|++++|.+..++. .+....+|+.+++++|.. +.+|.+.+..+++|
T Consensus        77 ~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~~~L~~l~l~~N~l-~~i~~~~f~~~~~L  155 (284)
T d1ozna_          77 TGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNAL-QALPDDTFRDLGNL  155 (284)
T ss_dssp             TTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCC-CCCCTTTTTTCTTC
T ss_pred             cccccccccccccccccccccchhhcccccCCEEecCCcccccccccccchhcccchhhhccccc-cccChhHhccccch
Confidence            778889998876554443 33 678999999999999999886654 567789999999999766 45776668899999


Q ss_pred             cEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCC-CC-ccCCCCeEEEEeCC
Q 003090          395 EELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPS-DM-SFQNLTSFSIAIGD  462 (848)
Q Consensus       395 ~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~-~~-~~~~L~~L~l~~~~  462 (848)
                      ++|++++|.+...             .+..+.++++|+.+++++|.+..+.. .+ .+++|+.|++..+.
T Consensus       156 ~~L~l~~N~l~~l-------------~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~  212 (284)
T d1ozna_         156 THLFLHGNRISSV-------------PERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANN  212 (284)
T ss_dssp             CEEECCSSCCCEE-------------CTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             hhcccccCccccc-------------chhhhccccccchhhhhhccccccChhHhhhhhhcccccccccc
Confidence            9999999988764             34577899999999999999876643 34 67778887776443

>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=99.54  E-value=3.8e-14  Score=135.69  Aligned_cols=175  Identities=19%  Similarity=0.258  Sum_probs=129.5

Q ss_pred             eecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhh
Q 003090          240 LMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSF  319 (848)
Q Consensus       240 l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~  319 (848)
                      ++.+.+.+.+....++++++|++++|.+..++.  ++.+++|++|++++              +.+++     ++. +++
T Consensus        25 l~~~~~~~~~~~~~l~~l~~L~l~~~~i~~l~~--l~~l~nL~~L~Ls~--------------N~l~~-----~~~-l~~   82 (199)
T d2omxa2          25 LGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDG--VEYLNNLTQINFSN--------------NQLTD-----ITP-LKN   82 (199)
T ss_dssp             TTCSSTTSEECHHHHTTCCEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CGG-GTT
T ss_pred             hCCCCCCCccCHHHhcCCCEEECCCCCCCCccc--cccCCCcCcCcccc--------------ccccC-----ccc-ccC
Confidence            344555555444467788888888888877754  57788888888888              77776     543 888


Q ss_pred             cccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEec
Q 003090          320 LINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYM  399 (848)
Q Consensus       320 l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l  399 (848)
                      +++|++|++++|.... .+.++++++|++|+++++.+..++ .+..+++|+.|++++|.. ..++.  +..+++|+.|++
T Consensus        83 l~~L~~L~l~~n~~~~-~~~l~~l~~L~~L~l~~~~~~~~~-~~~~l~~L~~L~l~~n~l-~~~~~--l~~~~~L~~L~l  157 (199)
T d2omxa2          83 LTKLVDILMNNNQIAD-ITPLANLTNLTGLTLFNNQITDID-PLKNLTNLNRLELSSNTI-SDISA--LSGLTSLQQLNF  157 (199)
T ss_dssp             CTTCCEEECCSSCCCC-CGGGTTCTTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSSCC-CCCGG--GTTCTTCSEEEC
T ss_pred             Cccccccccccccccc-cccccccccccccccccccccccc-ccchhhhhHHhhhhhhhh-ccccc--cccccccccccc
Confidence            8888888888885544 345788888888888888777654 477888888888888754 44553  788888888888


Q ss_pred             cccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeE
Q 003090          400 SHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSF  456 (848)
Q Consensus       400 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L  456 (848)
                      .+|.+...               ..++++++|+.|++++|.++.++.-..+++|++|
T Consensus       158 ~~n~l~~l---------------~~l~~l~~L~~L~ls~N~i~~i~~l~~L~~L~~L  199 (199)
T d2omxa2         158 SSNQVTDL---------------KPLANLTTLERLDISSNKVSDISVLAKLTNLESL  199 (199)
T ss_dssp             CSSCCCCC---------------GGGTTCTTCCEEECCSSCCCCCGGGGGCTTCSEE
T ss_pred             ccccccCC---------------ccccCCCCCCEEECCCCCCCCCccccCCCCCCcC
Confidence            88876532               3478888888999988888776532267777764

>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=99.51  E-value=1.2e-13  Score=133.22  Aligned_cols=164  Identities=23%  Similarity=0.290  Sum_probs=75.3

Q ss_pred             ccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      +.+|+.|++++|.+..++.  ++.+++|++|++++              +.+++     ++ .++.+++|++|++++|++
T Consensus        45 L~~L~~L~l~~~~i~~l~~--l~~l~~L~~L~L~~--------------n~i~~-----l~-~~~~l~~L~~L~l~~n~i  102 (210)
T d1h6ta2          45 LNSIDQIIANNSDIKSVQG--IQYLPNVTKLFLNG--------------NKLTD-----IK-PLANLKNLGWLFLDENKV  102 (210)
T ss_dssp             HHTCCEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CG-GGTTCTTCCEEECCSSCC
T ss_pred             hcCccEEECcCCCCCCchh--HhhCCCCCEEeCCC--------------ccccC-----cc-ccccCccccccccccccc
Confidence            3444455555554444432  34455555555555              44444     33 244455555555555533


Q ss_pred             cCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccc
Q 003090          334 QGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESE  413 (848)
Q Consensus       334 ~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~  413 (848)
                      .. ++.+..+++|+.|++++|.+..++ .+..+++|+.+++++|... ..+.  +.++++|+++++++|.+..       
T Consensus       103 ~~-l~~l~~l~~L~~L~l~~~~~~~~~-~l~~l~~l~~l~~~~n~l~-~~~~--~~~l~~L~~l~l~~n~l~~-------  170 (210)
T d1h6ta2         103 KD-LSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNNKIT-DITV--LSRLTKLDTLSLEDNQISD-------  170 (210)
T ss_dssp             CC-GGGGTTCTTCCEEECTTSCCCCCG-GGGGCTTCCEEECCSSCCC-CCGG--GGGCTTCSEEECCSSCCCC-------
T ss_pred             cc-cccccccccccccccccccccccc-ccccccccccccccccccc-cccc--ccccccccccccccccccc-------
Confidence            22 233444555555555555444433 3444555555555544332 2222  3445555555555554432       


Q ss_pred             cccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          414 EDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       414 ~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                              +..+.++++|++|++++|.++.++.-..+++|+.|+++
T Consensus       171 --------i~~l~~l~~L~~L~Ls~N~i~~l~~l~~l~~L~~L~Ls  208 (210)
T d1h6ta2         171 --------IVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELF  208 (210)
T ss_dssp             --------CGGGTTCTTCCEEECCSSCCCBCGGGTTCTTCSEEEEE
T ss_pred             --------cccccCCCCCCEEECCCCCCCCChhhcCCCCCCEEEcc
Confidence                    12244455555555555555444421144555555543

>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=99.51  E-value=1.1e-13  Score=133.46  Aligned_cols=163  Identities=29%  Similarity=0.349  Sum_probs=140.4

Q ss_pred             CCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC
Q 003090          234 DLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL  313 (848)
Q Consensus       234 ~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l  313 (848)
                      .++.+++++|.+..++..-.+++|++|++++|.+..++.  +..+++|++|++++              +.++.     +
T Consensus        47 ~L~~L~l~~~~i~~l~~l~~l~~L~~L~L~~n~i~~l~~--~~~l~~L~~L~l~~--------------n~i~~-----l  105 (210)
T d1h6ta2          47 SIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKP--LANLKNLGWLFLDE--------------NKVKD-----L  105 (210)
T ss_dssp             TCCEEECTTSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----G
T ss_pred             CccEEECcCCCCCCchhHhhCCCCCEEeCCCccccCccc--cccCcccccccccc--------------ccccc-----c
Confidence            578899999999988764489999999999999988875  57899999999999              88887     7


Q ss_pred             CchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhcccc
Q 003090          314 PSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRK  393 (848)
Q Consensus       314 p~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~  393 (848)
                      | .+..+++|+.|++++|... .++.+..+++|+.+++++|.++..+ .+.++++|+++++++|... .++.  ++++++
T Consensus       106 ~-~l~~l~~L~~L~l~~~~~~-~~~~l~~l~~l~~l~~~~n~l~~~~-~~~~l~~L~~l~l~~n~l~-~i~~--l~~l~~  179 (210)
T d1h6ta2         106 S-SLKDLKKLKSLSLEHNGIS-DINGLVHLPQLESLYLGNNKITDIT-VLSRLTKLDTLSLEDNQIS-DIVP--LAGLTK  179 (210)
T ss_dssp             G-GGTTCTTCCEEECTTSCCC-CCGGGGGCTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSSCCC-CCGG--GTTCTT
T ss_pred             c-ccccccccccccccccccc-ccccccccccccccccccccccccc-ccccccccccccccccccc-cccc--ccCCCC
Confidence            6 5899999999999999654 4567899999999999999998765 5788999999999998664 4654  799999


Q ss_pred             ccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeec
Q 003090          394 LEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHI  438 (848)
Q Consensus       394 L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~  438 (848)
                      |++|++++|.++.               +..+.++++|+.|+|++
T Consensus       180 L~~L~Ls~N~i~~---------------l~~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         180 LQNLYLSKNHISD---------------LRALAGLKNLDVLELFS  209 (210)
T ss_dssp             CCEEECCSSCCCB---------------CGGGTTCTTCSEEEEEE
T ss_pred             CCEEECCCCCCCC---------------ChhhcCCCCCCEEEccC
Confidence            9999999998763               24689999999999975

>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=99.50  E-value=1.3e-12  Score=137.65  Aligned_cols=141  Identities=20%  Similarity=0.241  Sum_probs=92.8

Q ss_pred             cccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          255 PKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       255 ~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      .++++|+++++.++.+|+    ..++|++|++++              +.++.     +|..+   .+|+.|++.+|++.
T Consensus        38 ~~l~~LdLs~~~L~~lp~----~~~~L~~L~Ls~--------------N~l~~-----lp~~~---~~L~~L~l~~n~l~   91 (353)
T d1jl5a_          38 RQAHELELNNLGLSSLPE----LPPHLESLVASC--------------NSLTE-----LPELP---QSLKSLLVDNNNLK   91 (353)
T ss_dssp             HTCSEEECTTSCCSCCCS----CCTTCSEEECCS--------------SCCSS-----CCCCC---TTCCEEECCSSCCS
T ss_pred             cCCCEEEeCCCCCCCCCC----CCCCCCEEECCC--------------CCCcc-----cccch---hhhhhhhhhhcccc
Confidence            467788888888888875    356788888888              77776     77653   46778888887655


Q ss_pred             CCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEecccccccccccccccc
Q 003090          335 GDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEE  414 (848)
Q Consensus       335 ~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~  414 (848)
                      .... +  .+.|++|++++|.+..+|. ++++++|++|++++|... ..+.    ....+..+.+..+...         
T Consensus        92 ~l~~-l--p~~L~~L~L~~n~l~~lp~-~~~l~~L~~L~l~~~~~~-~~~~----~~~~l~~l~~~~~~~~---------  153 (353)
T d1jl5a_          92 ALSD-L--PPLLEYLGVSNNQLEKLPE-LQNSSFLKIIDVDNNSLK-KLPD----LPPSLEFIAAGNNQLE---------  153 (353)
T ss_dssp             CCCS-C--CTTCCEEECCSSCCSSCCC-CTTCTTCCEEECCSSCCS-CCCC----CCTTCCEEECCSSCCS---------
T ss_pred             hhhh-h--ccccccccccccccccccc-hhhhccceeecccccccc-cccc----ccccccchhhcccccc---------
Confidence            4321 1  1358888888888888874 577888888888876543 2332    2344555555444332         


Q ss_pred             ccCcccchhhhcccCCCcEEEeeccCCCCCC
Q 003090          415 DSSSNAKFIELGALSRLTSLHIHIPEGKIMP  445 (848)
Q Consensus       415 ~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~  445 (848)
                            ....++.++.++.|.+.++.....+
T Consensus       154 ------~~~~l~~l~~l~~L~l~~n~~~~~~  178 (353)
T d1jl5a_         154 ------ELPELQNLPFLTAIYADNNSLKKLP  178 (353)
T ss_dssp             ------SCCCCTTCTTCCEEECCSSCCSSCC
T ss_pred             ------ccccccccccceecccccccccccc
Confidence                  2234566777777777777655443

>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=99.49  E-value=2.4e-13  Score=130.00  Aligned_cols=160  Identities=21%  Similarity=0.276  Sum_probs=135.6

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      -.++.|+++++.+..++..-.+++|++|++++|.+..+++  ++++++|++|++++              +.+..     
T Consensus        40 ~~l~~L~l~~~~i~~l~~l~~l~nL~~L~Ls~N~l~~~~~--l~~l~~L~~L~l~~--------------n~~~~-----   98 (199)
T d2omxa2          40 DQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITP--LKNLTKLVDILMNN--------------NQIAD-----   98 (199)
T ss_dssp             TTCCEEECTTSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCS--------------SCCCC-----
T ss_pred             cCCCEEECCCCCCCCccccccCCCcCcCccccccccCccc--ccCCcccccccccc--------------ccccc-----
Confidence            3567899999999988754489999999999999988876  68999999999999              77776     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      ++ .+..+++|++|+++++.... ...+..+++|+.|++++|.+..+| .+..+++|+.|++.+|.. ..++.  +++++
T Consensus        99 ~~-~l~~l~~L~~L~l~~~~~~~-~~~~~~l~~L~~L~l~~n~l~~~~-~l~~~~~L~~L~l~~n~l-~~l~~--l~~l~  172 (199)
T d2omxa2          99 IT-PLANLTNLTGLTLFNNQITD-IDPLKNLTNLNRLELSSNTISDIS-ALSGLTSLQQLNFSSNQV-TDLKP--LANLT  172 (199)
T ss_dssp             CG-GGTTCTTCSEEECCSSCCCC-CGGGTTCTTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSSCC-CCCGG--GTTCT
T ss_pred             cc-cccccccccccccccccccc-ccccchhhhhHHhhhhhhhhcccc-cccccccccccccccccc-cCCcc--ccCCC
Confidence            55 48899999999999985544 466889999999999999998876 588999999999999865 44664  79999


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEE
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSL  434 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L  434 (848)
                      +|++|++++|.++.               +..+..+++|+.|
T Consensus       173 ~L~~L~ls~N~i~~---------------i~~l~~L~~L~~L  199 (199)
T d2omxa2         173 TLERLDISSNKVSD---------------ISVLAKLTNLESL  199 (199)
T ss_dssp             TCCEEECCSSCCCC---------------CGGGGGCTTCSEE
T ss_pred             CCCEEECCCCCCCC---------------CccccCCCCCCcC
Confidence            99999999998763               2457888888876

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.48  E-value=5.9e-13  Score=130.42  Aligned_cols=185  Identities=20%  Similarity=0.287  Sum_probs=150.7

Q ss_pred             cCCCceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFL  312 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~  312 (848)
                      ..++.+++.+|.+++++....+++|++|++++|.+..+++  +.++++|+++++++              +.++.     
T Consensus        41 ~~L~~L~l~~~~i~~l~~l~~l~~L~~L~ls~n~i~~~~~--l~~l~~l~~l~~~~--------------n~~~~-----   99 (227)
T d1h6ua2          41 DGITTLSAFGTGVTTIEGVQYLNNLIGLELKDNQITDLAP--LKNLTKITELELSG--------------NPLKN-----   99 (227)
T ss_dssp             HTCCEEECTTSCCCCCTTGGGCTTCCEEECCSSCCCCCGG--GTTCCSCCEEECCS--------------CCCSC-----
T ss_pred             CCcCEEECCCCCCCcchhHhcCCCCcEeecCCceeecccc--cccccccccccccc--------------ccccc-----
Confidence            4578899999999998654489999999999998888765  68999999999998              77766     


Q ss_pred             CCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccc
Q 003090          313 LPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLR  392 (848)
Q Consensus       313 lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~  392 (848)
                      ++ .+..+++|+++.++++... ....+...+.++.+.++++.+...+ .+...++|++|++++|... ..+.  +++++
T Consensus       100 i~-~l~~l~~L~~l~l~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~L~~L~l~~n~~~-~~~~--l~~l~  173 (227)
T d1h6ua2         100 VS-AIAGLQSIKTLDLTSTQIT-DVTPLAGLSNLQVLYLDLNQITNIS-PLAGLTNLQYLSIGNAQVS-DLTP--LANLS  173 (227)
T ss_dssp             CG-GGTTCTTCCEEECTTSCCC-CCGGGTTCTTCCEEECCSSCCCCCG-GGGGCTTCCEEECCSSCCC-CCGG--GTTCT
T ss_pred             cc-ccccccccccccccccccc-ccchhccccchhhhhchhhhhchhh-hhccccccccccccccccc-cchh--hcccc
Confidence            54 5888999999999988543 4456778889999999998887554 4778899999999997654 3333  78999


Q ss_pred             cccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEEE
Q 003090          393 KLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSIA  459 (848)
Q Consensus       393 ~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l~  459 (848)
                      +|+.|++++|.+..               +..++++++|++|++++|+++.++.-..+++|+.|++.
T Consensus       174 ~L~~L~Ls~n~l~~---------------l~~l~~l~~L~~L~Ls~N~lt~i~~l~~l~~L~~L~ls  225 (227)
T d1h6ua2         174 KLTTLKADDNKISD---------------ISPLASLPNLIEVHLKNNQISDVSPLANTSNLFIVTLT  225 (227)
T ss_dssp             TCCEEECCSSCCCC---------------CGGGGGCTTCCEEECTTSCCCBCGGGTTCTTCCEEEEE
T ss_pred             cceecccCCCccCC---------------ChhhcCCCCCCEEECcCCcCCCCcccccCCCCCEEEee
Confidence            99999999998753               24588899999999999999888753388999999886

>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=99.47  E-value=1.2e-14  Score=147.59  Aligned_cols=80  Identities=18%  Similarity=0.072  Sum_probs=42.8

Q ss_pred             CCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhhh
Q 003090          346 LEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIEL  425 (848)
Q Consensus       346 L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L  425 (848)
                      ...+.++.+.+...........+|++|++++|.........++.++++|++|++.+|.+...             .+..+
T Consensus        25 ~~~lrl~~~~~~~~~~~~~~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~-------------~~~~l   91 (284)
T d2astb2          25 VIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDP-------------IVNTL   91 (284)
T ss_dssp             CSEEECTTCEECSCCCSCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHH-------------HHHHH
T ss_pred             ceEeeccccccccchhhhccCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcH-------------HHHHH
Confidence            34444444433322223344556777777766544433333356667777777766654432             44555


Q ss_pred             cccCCCcEEEeec
Q 003090          426 GALSRLTSLHIHI  438 (848)
Q Consensus       426 ~~l~~L~~L~l~~  438 (848)
                      ..+++|++|++++
T Consensus        92 ~~~~~L~~L~Ls~  104 (284)
T d2astb2          92 AKNSNLVRLNLSG  104 (284)
T ss_dssp             TTCTTCSEEECTT
T ss_pred             hcCCCCcCccccc
Confidence            5666666666654

>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=99.43  E-value=8.4e-13  Score=129.30  Aligned_cols=178  Identities=21%  Similarity=0.262  Sum_probs=126.4

Q ss_pred             eeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhh
Q 003090          239 SLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLS  318 (848)
Q Consensus       239 ~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~  318 (848)
                      +++.+.+.++.....+.+|+.|++.+|.+..++.  +..+++|++|++++              +.+..     ++ .+.
T Consensus        25 ~l~~~~~~d~~~~~~l~~L~~L~l~~~~i~~l~~--l~~l~~L~~L~ls~--------------n~i~~-----~~-~l~   82 (227)
T d1h6ua2          25 AAGKSNVTDTVTQADLDGITTLSAFGTGVTTIEG--VQYLNNLIGLELKD--------------NQITD-----LA-PLK   82 (227)
T ss_dssp             HTTCSSTTSEECHHHHHTCCEEECTTSCCCCCTT--GGGCTTCCEEECCS--------------SCCCC-----CG-GGT
T ss_pred             HhCCCCcCCcCCHHHcCCcCEEECCCCCCCcchh--HhcCCCCcEeecCC--------------ceeec-----cc-ccc
Confidence            3445555555433467888999999888888753  57899999999998              77776     43 378


Q ss_pred             hcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEe
Q 003090          319 FLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELY  398 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~  398 (848)
                      .+.+|+++++++|.+. .++.+.++++|++++++++....++ .+...+.++.+.++++.... .+.  +.+.++|++|+
T Consensus        83 ~l~~l~~l~~~~n~~~-~i~~l~~l~~L~~l~l~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~-~~~--~~~~~~L~~L~  157 (227)
T d1h6ua2          83 NLTKITELELSGNPLK-NVSAIAGLQSIKTLDLTSTQITDVT-PLAGLSNLQVLYLDLNQITN-ISP--LAGLTNLQYLS  157 (227)
T ss_dssp             TCCSCCEEECCSCCCS-CCGGGTTCTTCCEEECTTSCCCCCG-GGTTCTTCCEEECCSSCCCC-CGG--GGGCTTCCEEE
T ss_pred             cccccccccccccccc-ccccccccccccccccccccccccc-hhccccchhhhhchhhhhch-hhh--hcccccccccc
Confidence            8889999999888544 4567888889999999888776554 46677888888888765543 322  67788888888


Q ss_pred             ccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCCccCCCCeEEE
Q 003090          399 MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDMSFQNLTSFSI  458 (848)
Q Consensus       399 l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~~~~~L~~L~l  458 (848)
                      +++|.+...               ..++++++|+.|++++|.++.++.-..+++|+.|++
T Consensus       158 l~~n~~~~~---------------~~l~~l~~L~~L~Ls~n~l~~l~~l~~l~~L~~L~L  202 (227)
T d1h6ua2         158 IGNAQVSDL---------------TPLANLSKLTTLKADDNKISDISPLASLPNLIEVHL  202 (227)
T ss_dssp             CCSSCCCCC---------------GGGTTCTTCCEEECCSSCCCCCGGGGGCTTCCEEEC
T ss_pred             ccccccccc---------------hhhcccccceecccCCCccCCChhhcCCCCCCEEEC
Confidence            888876532               347788888888888887765543113344444433

>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=99.43  E-value=2.6e-13  Score=137.70  Aligned_cols=222  Identities=18%  Similarity=0.091  Sum_probs=129.9

Q ss_pred             CcEEEccCccccCCchhhccccCCCEEEccCCCCc--ccChhhccCCcccEEeccCCccccccChhhhhccccccEEecc
Q 003090          323 LRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVS--EIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMS  400 (848)
Q Consensus       323 L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~--~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~  400 (848)
                      ...+.+................+|++||+++|.+.  .++..+.++++|++|++++|......+.. ++++++|++|+++
T Consensus        25 ~~~lrl~~~~~~~~~~~~~~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~-l~~~~~L~~L~Ls  103 (284)
T d2astb2          25 VIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNT-LAKNSNLVRLNLS  103 (284)
T ss_dssp             CSEEECTTCEECSCCCSCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHH-HTTCTTCSEEECT
T ss_pred             ceEeeccccccccchhhhccCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcHHHHH-HhcCCCCcCcccc
Confidence            56666766644443455556778999999998776  46666788999999999998766666666 7889999999999


Q ss_pred             ccc-cccccccccccccCcccchhhhcccCCCcEEEeeccC-CCCCCCCCccCCCCeEEEEeCCCCCCCCCcccceEEec
Q 003090          401 HSF-RHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE-GKIMPSDMSFQNLTSFSIAIGDLEERPLSDFIGLFLQK  478 (848)
Q Consensus       401 ~~~-~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~-~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~l~l~~  478 (848)
                      +|. ++..            ....-...+++|++|+++++. ++.                                   
T Consensus       104 ~c~~itd~------------~l~~l~~~~~~L~~L~ls~c~~~~~-----------------------------------  136 (284)
T d2astb2         104 GCSGFSEF------------ALQTLLSSCSRLDELNLSWCFDFTE-----------------------------------  136 (284)
T ss_dssp             TCBSCCHH------------HHHHHHHHCTTCCEEECCCCTTCCH-----------------------------------
T ss_pred             cccccccc------------ccchhhHHHHhcccccccccccccc-----------------------------------
Confidence            864 3221            122334567888888887753 110                                   


Q ss_pred             ccccccccccCccccchhhHHHHHHHHHhhcceeeecccc-ccccc-cccccccCCCCCcEEEEecCCCceeeccccccc
Q 003090          479 FKKRCSRAMGLSQDMRISALHSWIKNLLLRSEILALAEVN-YFENI-VSDLANDGFNELMFLVIFRCNEMKYLLNSLERT  556 (848)
Q Consensus       479 ~~~~c~~~~~l~~~~~l~~l~~~~~~~~~~L~~L~l~~~~-~~~~~-~~~l~~~~l~~L~~L~l~~~~~l~~l~~~~~~~  556 (848)
                                       ..+...+....++|+.|.+.++. .+++. ...+ ...+|+|++|++++|..++.    ....
T Consensus       137 -----------------~~~~~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l-~~~~~~L~~L~L~~~~~itd----~~~~  194 (284)
T d2astb2         137 -----------------KHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTL-VRRCPNLVHLDLSDSVMLKN----DCFQ  194 (284)
T ss_dssp             -----------------HHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHH-HHHCTTCSEEECTTCTTCCG----GGGG
T ss_pred             -----------------ccchhhhcccccccchhhhccccccccccccccc-ccccccccccccccccCCCc----hhhh
Confidence                             01111111222445555555442 11111 1111 12457777777777766543    1223


Q ss_pred             ccccCCCccEEecccccccccccccccccccCCCcceEEEecCchhhHhhhHHHHHhhccCc
Q 003090          557 LRVTLHKLEWLFIRENQNFVEICHGQLPAGCLSNVKRSDVVDCGSILKILLSHLVQSFQNLQ  618 (848)
Q Consensus       557 ~~~~~p~L~~L~l~~~~~L~~~~~~~~~~~~l~~L~~L~l~~c~~l~~~l~~~~~~~l~~L~  618 (848)
                      ....+|+|++|++++|.++++-..  ...+.+|+|+.|++.+|-.- ..+.. +...+|+|+
T Consensus       195 ~l~~~~~L~~L~L~~C~~i~~~~l--~~L~~~~~L~~L~l~~~~~d-~~l~~-l~~~lp~L~  252 (284)
T d2astb2         195 EFFQLNYLQHLSLSRCYDIIPETL--LELGEIPTLKTLQVFGIVPD-GTLQL-LKEALPHLQ  252 (284)
T ss_dssp             GGGGCTTCCEEECTTCTTCCGGGG--GGGGGCTTCCEEECTTSSCT-TCHHH-HHHHSTTSE
T ss_pred             hhcccCcCCEEECCCCCCCChHHH--HHHhcCCCCCEEeeeCCCCH-HHHHH-HHHhCcccc
Confidence            344567777777777766654311  12235677777777777332 23322 224455554

>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=99.33  E-value=8.1e-13  Score=125.41  Aligned_cols=128  Identities=20%  Similarity=0.265  Sum_probs=101.3

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcc-cChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCC
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLA-IPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLP  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~-~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp  314 (848)
                      +.++.+++.++.+|..+. +++++|+|++|.+.. ++...|.++++|+.|++++              +.+...    .+
T Consensus        11 ~~v~Cs~~~L~~iP~~lp-~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~--------------N~i~~~----~~   71 (192)
T d1w8aa_          11 TTVDCTGRGLKEIPRDIP-LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKR--------------NQLTGI----EP   71 (192)
T ss_dssp             TEEECTTSCCSSCCSCCC-TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCS--------------SCCCCB----CT
T ss_pred             CEEEEeCCCcCccCCCCC-CCCCEEEeCCCCCcccccccccCCCceEeeeeccc--------------cccccc----cc
Confidence            457788888888888764 678889999998864 6666678888999999988              777764    56


Q ss_pred             chhhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChh-hccCCcccEEeccCCccccc
Q 003090          315 SSLSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVS-FGRLSHLRLLDLTGCYILEL  382 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~-i~~L~~L~~L~l~~~~~~~~  382 (848)
                      ..+..+++|++|++++|++...+ ..|.++++|++|+|++|.|+.+|.. +..+++|++|++++|.....
T Consensus        72 ~~~~~~~~L~~L~Ls~N~l~~l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~~~~~  141 (192)
T d1w8aa_          72 NAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFNCN  141 (192)
T ss_dssp             TTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBCCS
T ss_pred             cccccccccceeeeccccccccCHHHHhCCCcccccccCCccccccCHHHhcCCcccccccccccccccc
Confidence            67788888888888888777765 5678888888888888888877654 67788888888888766543

>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=99.30  E-value=8e-12  Score=108.24  Aligned_cols=86  Identities=20%  Similarity=0.224  Sum_probs=37.6

Q ss_pred             hhhcccCcEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccCh-hhhhcccccc
Q 003090          317 LSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPR-GVLSRLRKLE  395 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~  395 (848)
                      +..+.+|++|++++|.+...++.++.+++|++|++++|.++.+| .++++++|++|++++|.... +|. ..+..+++|+
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 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCNNRLQQ-SAAIQPLVSCPRLV   93 (124)
T ss_dssp             GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCSSCCCS-SSTTGGGGGCTTCC
T ss_pred             cccCCCCCEEECCCCccCcchhhhhhhhcccccccccccccccC-ccccccccCeEECCCCccCC-CCCchhhcCCCCCC
Confidence            44444444444444444433334444444444444444444443 24444444444444443321 221 1134444455


Q ss_pred             EEecccccc
Q 003090          396 ELYMSHSFR  404 (848)
Q Consensus       396 ~L~l~~~~~  404 (848)
                      .|++++|.+
T Consensus        94 ~L~l~~N~i  102 (124)
T d1dcea3          94 LLNLQGNSL  102 (124)
T ss_dssp             EEECTTSGG
T ss_pred             EEECCCCcC
Confidence            555544444

>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=99.30  E-value=1.1e-11  Score=107.23  Aligned_cols=117  Identities=20%  Similarity=0.234  Sum_probs=97.5

Q ss_pred             cEEEccCccccCCchhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccc
Q 003090          324 RTLRLHDRRIQGDLSLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       324 ~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~  403 (848)
                      |+|++++|.+... +.++++.+|++|++++|.++.+|..++.+++|++|++++|.+ ..+|.  +.++++|++|++++|.
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 RVLHLAHKDLTVL-CHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNAL-ENVDG--VANLPRLQELLLCNNR   76 (124)
T ss_dssp             SEEECTTSCCSSC-CCGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCC-CCCGG--GTTCSSCCEEECCSSC
T ss_pred             CEEEcCCCCCCCC-cccccCCCCCEEECCCCccCcchhhhhhhhcccccccccccc-cccCc--cccccccCeEECCCCc
Confidence            6899999977644 568999999999999999999999999999999999999865 45764  8999999999999998


Q ss_pred             cccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCC---C--ccCCCCeE
Q 003090          404 RHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSD---M--SFQNLTSF  456 (848)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~---~--~~~~L~~L  456 (848)
                      +...            ..+..+..+++|+.|++++|.+...+..   +  .+++|+.+
T Consensus        77 i~~~------------~~~~~l~~~~~L~~L~l~~N~i~~~~~~~~~l~~~lp~L~~L  122 (124)
T d1dcea3          77 LQQS------------AAIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSI  122 (124)
T ss_dssp             CCSS------------STTGGGGGCTTCCEEECTTSGGGGSSSCTTHHHHHCTTCSEE
T ss_pred             cCCC------------CCchhhcCCCCCCEEECCCCcCCcCccHHHHHHHHCcCcceE
Confidence            8643            1345688999999999999988755433   2  56777765

>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=99.28  E-value=9.9e-12  Score=122.98  Aligned_cols=150  Identities=16%  Similarity=0.189  Sum_probs=90.6

Q ss_pred             CceeeecCCCcccCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCC-C
Q 003090          236 TGISLMFNDIHEVPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLL-P  314 (848)
Q Consensus       236 ~~l~l~~n~l~~lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~l-p  314 (848)
                      +.++.++..++.+|..+. +++++|++++|.+..+|...|.++++|++|++++              +.+...    + +
T Consensus        11 ~~i~c~~~~l~~iP~~l~-~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~--------------n~~~~~----i~~   71 (242)
T d1xwdc1          11 RVFLCQESKVTEIPSDLP-RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQ--------------NDVLEV----IEA   71 (242)
T ss_dssp             SEEEEESCSCSSCCSCSC-SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEES--------------CTTCCE----ECS
T ss_pred             CEEEEeCCCCCCcCCCCC-CCCCEEECcCCcCCccChhHhhccchhhhhhhcc--------------ccccce----eec
Confidence            456677777888887653 4678888888888888877777888888888888              555442    2 3


Q ss_pred             chhhhcccCcEEEccCc-cccCCc-hhhccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCccccccChhhhhc
Q 003090          315 SSLSFLINLRTLRLHDR-RIQGDL-SLIGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCYILELIPRGVLSR  390 (848)
Q Consensus       315 ~~~~~l~~L~~L~L~~~-~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~~~l~~  390 (848)
                      ..+..+.+++++.+..+ .+.... ..+..+++|++|+++++.+...|.  .+..+..+..+...++ ....++...+..
T Consensus        72 ~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~-~l~~i~~~~~~~  150 (242)
T d1xwdc1          72 DVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNI-NIHTIERNSFVG  150 (242)
T ss_dssp             SSEESCTTCCEEEEECCTTCCEECTTSEECCTTCCEEEEESCCCCSCCCCTTTCBSSCEEEEEESCT-TCCEECTTSSTT
T ss_pred             cccccccccccccccccccccccccccccccccccccccchhhhccccccccccccccccccccccc-cccccccccccc
Confidence            34667777777776543 233322 456777777777777777665442  2233444444444332 233344332333


Q ss_pred             cc-cccEEeccccccc
Q 003090          391 LR-KLEELYMSHSFRH  405 (848)
Q Consensus       391 l~-~L~~L~l~~~~~~  405 (848)
                      ++ .++.|++.+|.+.
T Consensus       151 ~~~~l~~L~l~~n~l~  166 (242)
T d1xwdc1         151 LSFESVILWLNKNGIQ  166 (242)
T ss_dssp             SBSSCEEEECCSSCCC
T ss_pred             ccccceeeeccccccc
Confidence            33 5555666555544

>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=99.27  E-value=2.9e-12  Score=128.56  Aligned_cols=77  Identities=13%  Similarity=0.123  Sum_probs=67.1

Q ss_pred             cccccchhHHHHHHHHHHh---cCCccEEEEEeCCCCchhHHHHHHHHHHh--hccccCcEEEEEeccCCchhHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK---DENVSITGICGMGGVGKTTLVKEIQKQAK--EMKMFDDVAMAVVSQTPSITKIQYEIA  230 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~---~~~~~vi~i~G~gG~GKTtla~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~l~~~i~  230 (848)
                      +..+|||+.++++|+++|.   +.+..+|+|+||||+||||||+++|++..  +..+|+.++|+++++.++...+...+.
T Consensus        19 ~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~   98 (277)
T d2a5yb3          19 QMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTD   98 (277)
T ss_dssp             CCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHH
Confidence            4668999999999999996   46678999999999999999999999854  677899999999999998888777665


Q ss_pred             hc
Q 003090          231 GW  232 (848)
Q Consensus       231 ~~  232 (848)
                      ..
T Consensus        99 ~~  100 (277)
T d2a5yb3          99 IL  100 (277)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.26  E-value=2.1e-12  Score=118.03  Aligned_cols=129  Identities=17%  Similarity=0.167  Sum_probs=67.4

Q ss_pred             cCCcccccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEE
Q 003090          248 VPDELECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLR  327 (848)
Q Consensus       248 lp~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~  327 (848)
                      .|...++.++++|++++|.+..++. ++..+++|++|++++              |.+..     ++ .+..+++|++|+
T Consensus        11 ~~~~~n~~~lr~L~L~~n~I~~i~~-~~~~l~~L~~L~Ls~--------------N~i~~-----l~-~~~~l~~L~~L~   69 (162)
T d1a9na_          11 AAQYTNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSD--------------NEIRK-----LD-GFPLLRRLKTLL   69 (162)
T ss_dssp             SCEEECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCS--------------SCCCE-----EC-CCCCCSSCCEEE
T ss_pred             hHhccCcCcCcEEECCCCCCCccCc-cccccccCCEEECCC--------------CCCCc-----cC-CcccCcchhhhh
Confidence            3333344556666666666655543 234556666666666              55554     42 355555666666


Q ss_pred             ccCccccCCch-hhccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCccccccCh---hhhhccccccEEe
Q 003090          328 LHDRRIQGDLS-LIGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCYILELIPR---GVLSRLRKLEELY  398 (848)
Q Consensus       328 L~~~~~~~~~~-~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~~~~~~p~---~~l~~l~~L~~L~  398 (848)
                      +++|.+...++ .+..+++|++|++++|.++.++.  .+..+++|++|++++|... ..|.   .++..+++|+.|+
T Consensus        70 ls~N~i~~l~~~~~~~l~~L~~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~~N~i~-~~~~~r~~~i~~lp~L~~LD  145 (162)
T d1a9na_          70 VNNNRICRIGEGLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCILRNPVT-NKKHYRLYVIYKVPQVRVLD  145 (162)
T ss_dssp             CCSSCCCEECSCHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGG-GSTTHHHHHHHHCTTCSEET
T ss_pred             cccccccCCCccccccccccccceeccccccccccccccccccccchhhcCCCccc-cccchHHHHHHHCCCcCeeC
Confidence            66665544442 23455566666666665554442  3455555666666555432 2231   2245555555554

>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=99.25  E-value=5.6e-12  Score=115.13  Aligned_cols=130  Identities=18%  Similarity=0.200  Sum_probs=88.1

Q ss_pred             HccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCCEEEccCC
Q 003090          275 FQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLEILDLSES  354 (848)
Q Consensus       275 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~~L~l~~~  354 (848)
                      |.+..++|.|+|++              +.++.     +|..+..+.+|++|++++|.+.. ++.+..+++|++|++++|
T Consensus        14 ~~n~~~lr~L~L~~--------------n~I~~-----i~~~~~~l~~L~~L~Ls~N~i~~-l~~~~~l~~L~~L~ls~N   73 (162)
T d1a9na_          14 YTNAVRDRELDLRG--------------YKIPV-----IENLGATLDQFDAIDFSDNEIRK-LDGFPLLRRLKTLLVNNN   73 (162)
T ss_dssp             EECTTSCEEEECTT--------------SCCCS-----CCCGGGGTTCCSEEECCSSCCCE-ECCCCCCSSCCEEECCSS
T ss_pred             ccCcCcCcEEECCC--------------CCCCc-----cCccccccccCCEEECCCCCCCc-cCCcccCcchhhhhcccc
Confidence            45667788888888              77777     66666777888888888886553 356777888888888888


Q ss_pred             CCcccChhh-ccCCcccEEeccCCccccccCh-hhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCc
Q 003090          355 DVSEIPVSF-GRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLT  432 (848)
Q Consensus       355 ~l~~lp~~i-~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~  432 (848)
                      .++.+|..+ ..+++|++|++++|... .++. ..+..+++|++|++++|.+...          .......+..+++|+
T Consensus        74 ~i~~l~~~~~~~l~~L~~L~L~~N~i~-~~~~l~~l~~l~~L~~L~l~~N~i~~~----------~~~r~~~i~~lp~L~  142 (162)
T d1a9na_          74 RICRIGEGLDQALPDLTELILTNNSLV-ELGDLDPLASLKSLTYLCILRNPVTNK----------KHYRLYVIYKVPQVR  142 (162)
T ss_dssp             CCCEECSCHHHHCTTCCEEECCSCCCC-CGGGGGGGGGCTTCCEEECCSSGGGGS----------TTHHHHHHHHCTTCS
T ss_pred             cccCCCccccccccccccceecccccc-ccccccccccccccchhhcCCCccccc----------cchHHHHHHHCCCcC
Confidence            888776653 56788888888876543 3332 2267777888888887766432          001123456677777


Q ss_pred             EEE
Q 003090          433 SLH  435 (848)
Q Consensus       433 ~L~  435 (848)
                      .|+
T Consensus       143 ~LD  145 (162)
T d1a9na_         143 VLD  145 (162)
T ss_dssp             EET
T ss_pred             eeC
Confidence            665

>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=99.18  E-value=4.9e-11  Score=117.85  Aligned_cols=204  Identities=17%  Similarity=0.127  Sum_probs=147.4

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCcccCCcc--cccccceeecccCcCc-ccChHHHccCCceeEEEccCccccccccc
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIHEVPDEL--ECPKLQALFLQENSPL-AIPDRFFQGMKDLQVLDLGGIRRFSFSVR  297 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~~lp~~~--~~~~L~~L~l~~~~~~-~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~  297 (848)
                      ++..++..+.  ..++.|++++|.+..+|...  ++++|++|++++|.+. .++...|.+++.++.+.+..+        
T Consensus        19 ~l~~iP~~l~--~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~--------   88 (242)
T d1xwdc1          19 KVTEIPSDLP--RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKA--------   88 (242)
T ss_dssp             SCSSCCSCSC--SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECC--------
T ss_pred             CCCCcCCCCC--CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeecccccccccccccccccc--------
Confidence            3445554444  35789999999999999854  8999999999999665 466666889999999998764        


Q ss_pred             CCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc--hhhccccCCCEEEccCCCCcccCh-hhccC-CcccEEe
Q 003090          298 FPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL--SLIGELSGLEILDLSESDVSEIPV-SFGRL-SHLRLLD  373 (848)
Q Consensus       298 ~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~--~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L-~~L~~L~  373 (848)
                           +.+...    .+..+..+++|++|+++++.+...+  ..+..+..+..+...++.+..++. .+..+ ..++.|+
T Consensus        89 -----n~l~~~----~~~~~~~l~~L~~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~~~~~~l~~L~  159 (242)
T d1xwdc1          89 -----NNLLYI----NPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILW  159 (242)
T ss_dssp             -----TTCCEE----CTTSEECCTTCCEEEEESCCCCSCCCCTTTCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEE
T ss_pred             -----cccccc----ccccccccccccccccchhhhcccccccccccccccccccccccccccccccccccccccceeee
Confidence                 566553    5566889999999999999776544  345566667677777778887754 34444 4799999


Q ss_pred             ccCCccccccChhhhhccccccEEe-ccccccccccccccccccCcccchhhhcccCCCcEEEeeccCCCCCCCCC--cc
Q 003090          374 LTGCYILELIPRGVLSRLRKLEELY-MSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPEGKIMPSDM--SF  450 (848)
Q Consensus       374 l~~~~~~~~~p~~~l~~l~~L~~L~-l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~~~~~~~~~--~~  450 (848)
                      +++|.. ..++.. ..+..+++.+. +.+|.++..             ....+.++++|+.|++++|.++.+|...  .+
T Consensus       160 l~~n~l-~~i~~~-~~~~~~l~~~~~l~~n~l~~l-------------~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~l  224 (242)
T d1xwdc1         160 LNKNGI-QEIHNC-AFNGTQLDELNLSDNNNLEEL-------------PNDVFHGASGPVILDISRTRIHSLPSYGLENL  224 (242)
T ss_dssp             CCSSCC-CEECTT-TTTTCCEEEEECTTCTTCCCC-------------CTTTTTTSCCCSEEECTTSCCCCCCSSSCTTC
T ss_pred             cccccc-cccccc-cccchhhhccccccccccccc-------------cHHHhcCCCCCCEEECCCCcCCccCHHHHcCC
Confidence            998655 467776 45666666654 566666542             2235788999999999999999888763  44


Q ss_pred             CCCCeEEE
Q 003090          451 QNLTSFSI  458 (848)
Q Consensus       451 ~~L~~L~l  458 (848)
                      ++|+.+++
T Consensus       225 ~~L~~l~~  232 (242)
T d1xwdc1         225 KKLRARST  232 (242)
T ss_dssp             CEEESSSE
T ss_pred             cccccCcC
Confidence            44444443

>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=99.10  E-value=1.2e-10  Score=110.10  Aligned_cols=128  Identities=20%  Similarity=0.181  Sum_probs=92.6

Q ss_pred             cceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC
Q 003090          257 LQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD  336 (848)
Q Consensus       257 L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~  336 (848)
                      .++++.+++.+..+|..+   ..++++|+|++              |.+....   -+..|..+++|+.|++++|.+...
T Consensus        10 ~~~v~Cs~~~L~~iP~~l---p~~l~~L~Ls~--------------N~i~~~~---~~~~f~~l~~L~~L~L~~N~i~~~   69 (192)
T d1w8aa_          10 GTTVDCTGRGLKEIPRDI---PLHTTELLLND--------------NELGRIS---SDGLFGRLPHLVKLELKRNQLTGI   69 (192)
T ss_dssp             TTEEECTTSCCSSCCSCC---CTTCSEEECCS--------------CCCCSBC---CSCSGGGCTTCCEEECCSSCCCCB
T ss_pred             CCEEEEeCCCcCccCCCC---CCCCCEEEeCC--------------CCCcccc---cccccCCCceEeeeeccccccccc
Confidence            356677777777888654   25778888888              7775420   345567888888888888877766


Q ss_pred             c-hhhccccCCCEEEccCCCCcccCh-hhccCCcccEEeccCCccccccChhhhhccccccEEeccccccc
Q 003090          337 L-SLIGELSGLEILDLSESDVSEIPV-SFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRH  405 (848)
Q Consensus       337 ~-~~i~~l~~L~~L~l~~~~l~~lp~-~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~  405 (848)
                      + ..+..+++|++|++++|+++.+|. .+.++++|++|++++|.+ ..+|++.+..+++|++|++++|.+.
T Consensus        70 ~~~~~~~~~~L~~L~Ls~N~l~~l~~~~F~~l~~L~~L~L~~N~l-~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          70 EPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNLYDNQI-SCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             CTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEECCSSCC-CEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cccccccccccceeeeccccccccCHHHHhCCCcccccccCCccc-cccCHHHhcCCcccccccccccccc
Confidence            5 677778888888888888887765 467788888888888654 4466655777888888888877654

>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=99.08  E-value=1.2e-11  Score=117.15  Aligned_cols=104  Identities=24%  Similarity=0.292  Sum_probs=53.3

Q ss_pred             cccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcc
Q 003090          253 ECPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRR  332 (848)
Q Consensus       253 ~~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~  332 (848)
                      .+++|++|++++|.+..++.  +.++++|++|++++              |.+..     +|.....+++|++|++++|.
T Consensus        46 ~L~~L~~L~Ls~n~I~~i~~--l~~l~~L~~L~Ls~--------------N~i~~-----i~~~~~~~~~L~~L~l~~N~  104 (198)
T d1m9la_          46 TLKACKHLALSTNNIEKISS--LSGMENLRILSLGR--------------NLIKK-----IENLDAVADTLEELWISYNQ  104 (198)
T ss_dssp             HTTTCCEEECSEEEESCCCC--HHHHTTCCEEECCE--------------EEECS-----CSSHHHHHHHCCEEECSEEE
T ss_pred             cccccceeECcccCCCCccc--ccCCccccChhhcc--------------ccccc-----cccccccccccccccccccc
Confidence            45555555555555555542  34555555555555              44444     44444444455555555553


Q ss_pred             ccCCchhhccccCCCEEEccCCCCcccCh--hhccCCcccEEeccCCc
Q 003090          333 IQGDLSLIGELSGLEILDLSESDVSEIPV--SFGRLSHLRLLDLTGCY  378 (848)
Q Consensus       333 ~~~~~~~i~~l~~L~~L~l~~~~l~~lp~--~i~~L~~L~~L~l~~~~  378 (848)
                      +. .++.+..+++|++|++++|.++.++.  .+..+++|++|++++|.
T Consensus       105 i~-~l~~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~L~~N~  151 (198)
T d1m9la_         105 IA-SLSGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLLAGNP  151 (198)
T ss_dssp             CC-CHHHHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEEECSSH
T ss_pred             cc-ccccccccccccccccccchhccccccccccCCCccceeecCCCc
Confidence            33 23445555555555555555554432  34555555555555543

>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=99.05  E-value=1.6e-12  Score=142.36  Aligned_cols=109  Identities=17%  Similarity=0.144  Sum_probs=51.1

Q ss_pred             ccceeecccCcCcccC-hHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCcccc
Q 003090          256 KLQALFLQENSPLAIP-DRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQ  334 (848)
Q Consensus       256 ~L~~L~l~~~~~~~~~-~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~  334 (848)
                      +|+.|+++++.++... ..++..++++++|+|++              +.++......++..+..+++|++|+|++|.+.
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~--------------~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~   68 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDD--------------CGLTEARCKDISSALRVNPALAELNLRSNELG   68 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEES--------------SCCCHHHHHHHHHHHHTCTTCCEEECTTCCCH
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCC--------------CCCCHHHHHHHHHHHhcCCCCCEEECcCCcCC
Confidence            4555666555544321 22344556666666666              33332110113334455556666666655432


Q ss_pred             CCc-hhhc-----cccCCCEEEccCCCCcc-----cChhhccCCcccEEeccCCc
Q 003090          335 GDL-SLIG-----ELSGLEILDLSESDVSE-----IPVSFGRLSHLRLLDLTGCY  378 (848)
Q Consensus       335 ~~~-~~i~-----~l~~L~~L~l~~~~l~~-----lp~~i~~L~~L~~L~l~~~~  378 (848)
                      ... ..+.     ...+|++|++++|.++.     ++..+..+++|++|++++|.
T Consensus        69 ~~~~~~l~~~l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~  123 (460)
T d1z7xw1          69 DVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNL  123 (460)
T ss_dssp             HHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSB
T ss_pred             hHHHHHHHHHHhcCCCCCCEEECCCCCccccccccccchhhcccccccccccccc
Confidence            111 1111     12346666666665542     33344555566666665553

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.99  E-value=2e-11  Score=115.57  Aligned_cols=116  Identities=24%  Similarity=0.222  Sum_probs=77.7

Q ss_pred             cccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCchhhccccCCC
Q 003090          268 LAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDLSLIGELSGLE  347 (848)
Q Consensus       268 ~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~~~i~~l~~L~  347 (848)
                      ..++.+ +..+++|++|++++              +.++.     ++ .+..+++|++|++++|.+...+.....+++|+
T Consensus        38 ~~l~~s-l~~L~~L~~L~Ls~--------------n~I~~-----i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~   96 (198)
T d1m9la_          38 EKMDAT-LSTLKACKHLALST--------------NNIEK-----IS-SLSGMENLRILSLGRNLIKKIENLDAVADTLE   96 (198)
T ss_dssp             CCCHHH-HHHTTTCCEEECSE--------------EEESC-----CC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCC
T ss_pred             hhhhhH-HhcccccceeECcc--------------cCCCC-----cc-cccCCccccChhhccccccccccccccccccc
Confidence            334444 46777888888877              66665     54 47777788888888776655544455566777


Q ss_pred             EEEccCCCCcccChhhccCCcccEEeccCCccccccCh-hhhhccccccEEecccccccc
Q 003090          348 ILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPR-GVLSRLRKLEELYMSHSFRHW  406 (848)
Q Consensus       348 ~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~-~~l~~l~~L~~L~l~~~~~~~  406 (848)
                      +|++++|.++.++ .+.++++|++|++++|... .++. ..+..+++|+.|++++|.+..
T Consensus        97 ~L~l~~N~i~~l~-~~~~l~~L~~L~L~~N~i~-~~~~~~~l~~l~~L~~L~L~~N~l~~  154 (198)
T d1m9la_          97 ELWISYNQIASLS-GIEKLVNLRVLYMSNNKIT-NWGEIDKLAALDKLEDLLLAGNPLYN  154 (198)
T ss_dssp             EEECSEEECCCHH-HHHHHHHSSEEEESEEECC-CHHHHHHHTTTTTCSEEEECSSHHHH
T ss_pred             ccccccccccccc-cccccccccccccccchhc-cccccccccCCCccceeecCCCcccc
Confidence            8888777777664 4677777888887776543 3332 226777777888777776544

>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=98.84  E-value=1.1e-09  Score=114.28  Aligned_cols=198  Identities=15%  Similarity=0.051  Sum_probs=123.9

Q ss_pred             chhHHHHHHHhccCCCceeeecCCCc-----ccCCcc-cccccceeecccCcCcccC----------hHHHccCCceeEE
Q 003090          221 SITKIQYEIAGWLDLTGISLMFNDIH-----EVPDEL-ECPKLQALFLQENSPLAIP----------DRFFQGMKDLQVL  284 (848)
Q Consensus       221 ~~~~l~~~i~~~~~l~~l~l~~n~l~-----~lp~~~-~~~~L~~L~l~~~~~~~~~----------~~~~~~~~~Lr~L  284 (848)
                      +...+.+.+.....++.+++++|.+.     .+...+ ..++|+.++++++......          ...+...++|+.|
T Consensus        19 ~~~~l~~~L~~~~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L   98 (344)
T d2ca6a1          19 DEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTV   98 (344)
T ss_dssp             HHHTTSHHHHHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEE
T ss_pred             HHHHHHHHHhhCCCCCEEECcCCcCCHHHHHHHHHHHHhCCCCCEEECCCCcccccccccchHHHHHHHHHhhCCCcccc
Confidence            45556666666777888888888775     233333 5678888888766433221          1123567788888


Q ss_pred             EccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc--------------hhhccccCCCEEE
Q 003090          285 DLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL--------------SLIGELSGLEILD  350 (848)
Q Consensus       285 ~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~--------------~~i~~l~~L~~L~  350 (848)
                      ++++              +.+.......+...+...++|++|++++|.+...-              ......+.|+.++
T Consensus        99 ~L~~--------------n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~  164 (344)
T d2ca6a1          99 RLSD--------------NAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSII  164 (344)
T ss_dssp             ECCS--------------CCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEE
T ss_pred             cccc--------------cccccccccchhhhhcccccchheecccccccccccccccccccccccccccccCcccceee
Confidence            8888              65555322224445567788888888887542210              0123456788888


Q ss_pred             ccCCCCc-----ccChhhccCCcccEEeccCCccccc-----cChhhhhccccccEEeccccccccccccccccccCccc
Q 003090          351 LSESDVS-----EIPVSFGRLSHLRLLDLTGCYILEL-----IPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNA  420 (848)
Q Consensus       351 l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~-----~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~  420 (848)
                      ++++.+.     .+...+....+|+.|++++|.....     +... +..+++|+.|++++|.+...         ...+
T Consensus       165 l~~n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~-l~~~~~L~~L~Ls~N~i~~~---------g~~~  234 (344)
T d2ca6a1         165 CGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEG-LAYCQELKVLDLQDNTFTHL---------GSSA  234 (344)
T ss_dssp             CCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTT-GGGCTTCCEEECCSSCCHHH---------HHHH
T ss_pred             cccccccccccccccchhhhhhhhcccccccccccccccccchhhh-hcchhhhccccccccccccc---------cccc
Confidence            8887665     3444566777888888888765321     1122 56677888888888776432         1122


Q ss_pred             chhhhcccCCCcEEEeeccCCC
Q 003090          421 KFIELGALSRLTSLHIHIPEGK  442 (848)
Q Consensus       421 ~~~~L~~l~~L~~L~l~~~~~~  442 (848)
                      ....+...++|++|++++|.+.
T Consensus       235 L~~~l~~~~~L~~L~Ls~n~i~  256 (344)
T d2ca6a1         235 LAIALKSWPNLRELGLNDCLLS  256 (344)
T ss_dssp             HHHHGGGCTTCCEEECTTCCCC
T ss_pred             ccccccccccchhhhhhcCccC
Confidence            4456677788888888877654

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.75  E-value=6e-10  Score=121.38  Aligned_cols=112  Identities=17%  Similarity=0.213  Sum_probs=76.9

Q ss_pred             cCCCceeeecCCCccc--CCcc-cccccceeecccCcCcccC----hHHHccCCceeEEEccCcccccccccCCCCCCCC
Q 003090          233 LDLTGISLMFNDIHEV--PDEL-ECPKLQALFLQENSPLAIP----DRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPL  305 (848)
Q Consensus       233 ~~l~~l~l~~n~l~~l--p~~~-~~~~L~~L~l~~~~~~~~~----~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l  305 (848)
                      ..++.|++++|+++..  .+.+ .++++++|+|++|.+....    ...+..+++|+.|+|++              +.+
T Consensus         2 ~~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~--------------N~i   67 (460)
T d1z7xw1           2 LDIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRS--------------NEL   67 (460)
T ss_dssp             EEEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTT--------------CCC
T ss_pred             CCCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcC--------------CcC
Confidence            3467899999999842  3333 6789999999999765321    12357899999999999              666


Q ss_pred             CCCCCCCCCchhh-hcccCcEEEccCccccCCc-----hhhccccCCCEEEccCCCCcc
Q 003090          306 PSSPLFLLPSSLS-FLINLRTLRLHDRRIQGDL-----SLIGELSGLEILDLSESDVSE  358 (848)
Q Consensus       306 ~~~~~~~lp~~~~-~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L~l~~~~l~~  358 (848)
                      .......+...+. ...+|++|++++|.+....     ..+..+++|++|++++|.+..
T Consensus        68 ~~~~~~~l~~~l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~i~~  126 (460)
T d1z7xw1          68 GDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGD  126 (460)
T ss_dssp             HHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHH
T ss_pred             ChHHHHHHHHHHhcCCCCCCEEECCCCCccccccccccchhhccccccccccccccchh
Confidence            4310000111121 2347999999999765432     456789999999999998873

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=5.3e-08  Score=87.49  Aligned_cols=104  Identities=13%  Similarity=0.045  Sum_probs=65.6

Q ss_pred             CCCEEEccCCCCcccChhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccCcccchhh
Q 003090          345 GLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIE  424 (848)
Q Consensus       345 ~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~  424 (848)
                      ....++.+++.+...|..+..+++|++|++.++..+..++.+.|.++++|+.|++++|.+...             .+..
T Consensus         9 ~~~~l~c~~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i-------------~~~~   75 (156)
T d2ifga3           9 GSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFV-------------APDA   75 (156)
T ss_dssp             SSSCEECCSSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEE-------------CTTG
T ss_pred             CCCeEEecCCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCc-------------cccc
Confidence            344566666666666666666667777777665555556655566677777777777766543             3345


Q ss_pred             hcccCCCcEEEeeccCCCCCCCCC-ccCCCCeEEEEeC
Q 003090          425 LGALSRLTSLHIHIPEGKIMPSDM-SFQNLTSFSIAIG  461 (848)
Q Consensus       425 L~~l~~L~~L~l~~~~~~~~~~~~-~~~~L~~L~l~~~  461 (848)
                      +..+++|+.|+|++|.++.++... ...+|+.|++..+
T Consensus        76 f~~l~~L~~L~Ls~N~l~~l~~~~~~~~~l~~L~L~~N  113 (156)
T d2ifga3          76 FHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGN  113 (156)
T ss_dssp             GGSCSCCCEEECCSSCCSCCCSTTTCSCCCCEEECCSS
T ss_pred             ccccccccceeccCCCCcccChhhhccccccccccCCC
Confidence            666677777777777777666665 4445666666533

>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=98.64  E-value=7.8e-09  Score=107.52  Aligned_cols=197  Identities=16%  Similarity=0.160  Sum_probs=129.4

Q ss_pred             HHHHHHHhccCCCceeeecCCCcc-----cCCcc-cccccceeecccCcCcccC-----h--------HHHccCCceeEE
Q 003090          224 KIQYEIAGWLDLTGISLMFNDIHE-----VPDEL-ECPKLQALFLQENSPLAIP-----D--------RFFQGMKDLQVL  284 (848)
Q Consensus       224 ~l~~~i~~~~~l~~l~l~~n~l~~-----lp~~~-~~~~L~~L~l~~~~~~~~~-----~--------~~~~~~~~Lr~L  284 (848)
                      .+...+.....++.+++++|.+..     +...+ .+++|++|++++|.++...     .        ......+.|+.+
T Consensus        84 ~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l  163 (344)
T d2ca6a1          84 LLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSI  163 (344)
T ss_dssp             HHHHHHTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEE
T ss_pred             HHHHHHhhCCCcccccccccccccccccchhhhhcccccchheecccccccccccccccccccccccccccccCccccee
Confidence            344555555668889999888763     33333 5688999999888654211     0        112456788899


Q ss_pred             EccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCC-----c-hhhccccCCCEEEccCCCCc-
Q 003090          285 DLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGD-----L-SLIGELSGLEILDLSESDVS-  357 (848)
Q Consensus       285 ~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~-----~-~~i~~l~~L~~L~l~~~~l~-  357 (848)
                      ++++              +.+.......+...+....+|++|++++|.+...     + ..+..+++|++|++++|.+. 
T Consensus       164 ~l~~--------------n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~  229 (344)
T d2ca6a1         164 ICGR--------------NRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTH  229 (344)
T ss_dssp             ECCS--------------SCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHH
T ss_pred             eccc--------------ccccccccccccchhhhhhhhcccccccccccccccccchhhhhcchhhhcccccccccccc
Confidence            9888              6555432222444566788899999999876542     1 34677889999999998875 


Q ss_pred             ----ccChhhccCCcccEEeccCCccccccChhh---hhc--cccccEEeccccccccccccccccccCcccchhhhc-c
Q 003090          358 ----EIPVSFGRLSHLRLLDLTGCYILELIPRGV---LSR--LRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELG-A  427 (848)
Q Consensus       358 ----~lp~~i~~L~~L~~L~l~~~~~~~~~p~~~---l~~--l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~-~  427 (848)
                          .+...+..+++|++|++++|.....-...+   +..  .+.|++|++++|.+...         ........+. +
T Consensus       230 ~g~~~L~~~l~~~~~L~~L~Ls~n~i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~i~~~---------~~~~l~~~l~~~  300 (344)
T d2ca6a1         230 LGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELD---------AVRTLKTVIDEK  300 (344)
T ss_dssp             HHHHHHHHHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHH---------HHHHHHHHHHHH
T ss_pred             cccccccccccccccchhhhhhcCccCchhhHHHHHHhhhccCCCCCEEECCCCcCChH---------HHHHHHHHHHcc
Confidence                355667888899999999986543211111   222  35689999999886543         1112334443 5


Q ss_pred             cCCCcEEEeeccCCCC
Q 003090          428 LSRLTSLHIHIPEGKI  443 (848)
Q Consensus       428 l~~L~~L~l~~~~~~~  443 (848)
                      .++|+.|++++|.+..
T Consensus       301 ~~~L~~L~l~~N~~~~  316 (344)
T d2ca6a1         301 MPDLLFLELNGNRFSE  316 (344)
T ss_dssp             CTTCCEEECTTSBSCT
T ss_pred             CCCCCEEECCCCcCCC
Confidence            7789999998887653

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=4.2e-08  Score=88.18  Aligned_cols=63  Identities=21%  Similarity=0.093  Sum_probs=33.8

Q ss_pred             hhhcccCcEEEccCccccCCc-hhhccccCCCEEEccCCCCcccChhhccCCcccEEeccCCcc
Q 003090          317 LSFLINLRTLRLHDRRIQGDL-SLIGELSGLEILDLSESDVSEIPVSFGRLSHLRLLDLTGCYI  379 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~-~~i~~l~~L~~L~l~~~~l~~lp~~i~~L~~L~~L~l~~~~~  379 (848)
                      |..+++|+.|++++|++.... ..+..+++|++|+|++|+++.+|..+....+|++|++++|.+
T Consensus        52 f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~~~l~~L~L~~Np~  115 (156)
T d2ifga3          52 LRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPL  115 (156)
T ss_dssp             SCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCCEEECCSSCC
T ss_pred             hccccccCcceeeccccCCcccccccccccccceeccCCCCcccChhhhccccccccccCCCcc
Confidence            444555555555555444432 345555555666666666666665544444566666666543

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.70  E-value=9.3e-06  Score=72.92  Aligned_cols=87  Identities=17%  Similarity=0.048  Sum_probs=45.6

Q ss_pred             ccccceeecccCcCcccChHHHccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccc
Q 003090          254 CPKLQALFLQENSPLAIPDRFFQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRI  333 (848)
Q Consensus       254 ~~~L~~L~l~~~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~  333 (848)
                      +..+..++...+....+ ..++.++++|++|++++              |.++..  ..++..+..+++|++|++++|.+
T Consensus        41 ~~~~~~l~~~~~~~~~l-~~~~~~~~~L~~L~Ls~--------------N~i~~l--~~~~~~~~~l~~L~~L~Ls~N~i  103 (162)
T d1koha1          41 QNIDVVLNRRSSMAATL-RIIEENIPELLSLNLSN--------------NRLYRL--DDMSSIVQKAPNLKILNLSGNEL  103 (162)
T ss_dssp             TTCCCCTTSHHHHHHHH-HHHHHHCTTCCCCCCCS--------------SCCCCC--SGGGTHHHHSTTCCCCCCTTSCC
T ss_pred             ccchhhcchhhhHhhhh-HHHHHhCCCCCEeeCCC--------------ccccCC--chhHHHHhhCCcccccccccCcc
Confidence            33444444444433333 33456777888888888              666551  00234455666666666666654


Q ss_pred             cCCch-hhccccCCCEEEccCCCCc
Q 003090          334 QGDLS-LIGELSGLEILDLSESDVS  357 (848)
Q Consensus       334 ~~~~~-~i~~l~~L~~L~l~~~~l~  357 (848)
                      ....+ ......+|+.|++++|.+.
T Consensus       104 ~~l~~l~~l~~~~L~~L~L~~Npl~  128 (162)
T d1koha1         104 KSERELDKIKGLKLEELWLDGNSLS  128 (162)
T ss_dssp             CCGGGHHHHTTCCCSSCCCTTSTTS
T ss_pred             ccchhhhhhhccccceeecCCCCcC
Confidence            44331 1122234566666666554

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=5.8e-06  Score=74.31  Aligned_cols=88  Identities=19%  Similarity=0.171  Sum_probs=50.6

Q ss_pred             ccccCCCEEEccCCCCcccC---hhhccCCcccEEeccCCccccccChhhhhccccccEEeccccccccccccccccccC
Q 003090          341 GELSGLEILDLSESDVSEIP---VSFGRLSHLRLLDLTGCYILELIPRGVLSRLRKLEELYMSHSFRHWQFESESEEDSS  417 (848)
Q Consensus       341 ~~l~~L~~L~l~~~~l~~lp---~~i~~L~~L~~L~l~~~~~~~~~p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~  417 (848)
                      .++++|++|++++|+++.++   ..+..+++|++|++++|... .++.-...+..+|+.|++.+|.+......      .
T Consensus        62 ~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~-~l~~l~~l~~~~L~~L~L~~Npl~~~~~~------~  134 (162)
T d1koha1          62 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELK-SERELDKIKGLKLEELWLDGNSLSDTFRD------Q  134 (162)
T ss_dssp             HHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCC-CGGGHHHHTTCCCSSCCCTTSTTSSSSSS------H
T ss_pred             HhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccc-cchhhhhhhccccceeecCCCCcCcCccc------c
Confidence            46777777777777777543   34566777777777776543 34432123344677777777766543110      1


Q ss_pred             cccchhhhcccCCCcEEE
Q 003090          418 SNAKFIELGALSRLTSLH  435 (848)
Q Consensus       418 ~~~~~~~L~~l~~L~~L~  435 (848)
                      .......+..+++|+.||
T Consensus       135 ~~y~~~i~~~~P~L~~LD  152 (162)
T d1koha1         135 STYISAIRERFPKLLRLD  152 (162)
T ss_dssp             HHHHHHHHTTSTTCCEET
T ss_pred             hhHHHHHHHHCCCCCEEC
Confidence            111223455667777664

>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=96.79  E-value=0.0006  Score=60.97  Aligned_cols=113  Identities=10%  Similarity=0.113  Sum_probs=58.8

Q ss_pred             hcccCcEEEccCccccCCc------hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCcccccc----
Q 003090          319 FLINLRTLRLHDRRIQGDL------SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILELI----  383 (848)
Q Consensus       319 ~l~~L~~L~L~~~~~~~~~------~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~~----  383 (848)
                      +.++|+.|+|+++......      ..+...++|++|++++|.+.     .+...+...+.|++|++++|.+...-    
T Consensus        13 n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l   92 (167)
T d1pgva_          13 DDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARL   92 (167)
T ss_dssp             TCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHH
T ss_pred             CCCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHH
Confidence            3466788888764322221      34556677777777777665     23334455566777777776443221    


Q ss_pred             ChhhhhccccccEEeccccccccccccccccccCcccchhhhcccCCCcEEEeec
Q 003090          384 PRGVLSRLRKLEELYMSHSFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHI  438 (848)
Q Consensus       384 p~~~l~~l~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~  438 (848)
                      -.. +..-++|++|+++++.....      ......+....+..-+.|+.|+++.
T Consensus        93 ~~a-L~~n~sL~~L~l~~n~~~~~------g~~~~~~l~~~L~~n~sL~~l~l~~  140 (167)
T d1pgva_          93 LRS-TLVTQSIVEFKADNQRQSVL------GNQVEMDMMMAIEENESLLRVGISF  140 (167)
T ss_dssp             HHH-TTTTCCCSEEECCCCSSCCC------CHHHHHHHHHHHHHCSSCCEEECCC
T ss_pred             HHH-HHhCCcCCEEECCCCcCCCc------cHHHHHHHHHHHHhCCCccEeeCcC
Confidence            112 34445566666665543211      0011122344455555666666544

>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=96.59  E-value=0.00051  Score=61.43  Aligned_cols=85  Identities=12%  Similarity=0.060  Sum_probs=46.1

Q ss_pred             hhhcccCcEEEccCccccCC----c-hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCcccc-----
Q 003090          317 LSFLINLRTLRLHDRRIQGD----L-SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILE-----  381 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~----~-~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~-----  381 (848)
                      +...++|++|++++|.+...    + ..+...+.|++|++++|.+.     .+-..+..-++|++|++++|....     
T Consensus        40 L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~~aL~~n~sL~~L~l~~n~~~~~g~~~  119 (167)
T d1pgva_          40 ACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQV  119 (167)
T ss_dssp             HTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHHH
T ss_pred             HhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHHHHHHHhCCcCCEEECCCCcCCCccHHH
Confidence            34445566666666644321    1 34445566777777776665     233345556667777776653211     


Q ss_pred             --ccChhhhhccccccEEecccc
Q 003090          382 --LIPRGVLSRLRKLEELYMSHS  402 (848)
Q Consensus       382 --~~p~~~l~~l~~L~~L~l~~~  402 (848)
                        .+... +..-++|+.|+++.+
T Consensus       120 ~~~l~~~-L~~n~sL~~l~l~~~  141 (167)
T d1pgva_         120 EMDMMMA-IEENESLLRVGISFA  141 (167)
T ss_dssp             HHHHHHH-HHHCSSCCEEECCCC
T ss_pred             HHHHHHH-HHhCCCccEeeCcCC
Confidence              12222 455567777776554

>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=96.53  E-value=0.0028  Score=61.66  Aligned_cols=75  Identities=17%  Similarity=0.139  Sum_probs=51.8

Q ss_pred             ccccchhHHHHHHHHHHhc------CCccEEEEEeCCCCchhHHHHHHHHHHhhccccCcEEEEEeccCCchhHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKD------ENVSITGICGMGGVGKTTLVKEIQKQAKEMKMFDDVAMAVVSQTPSITKIQYEIA  230 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~------~~~~vi~i~G~gG~GKTtla~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  230 (848)
                      ..++|||.+++.+.++|..      .....+-|+|..|+||||+|+.+.+.......+. .+|+..........+...+.
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTAR-FVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCE-EEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCc-EEEecchhhhhhhhhhhhhH
Confidence            4689999999999999862      3346788999999999999999998764333322 33444444444445555444


Q ss_pred             hc
Q 003090          231 GW  232 (848)
Q Consensus       231 ~~  232 (848)
                      ..
T Consensus        95 ~~   96 (276)
T d1fnna2          95 RS   96 (276)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>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=96.30  E-value=0.0024  Score=57.35  Aligned_cols=58  Identities=16%  Similarity=0.258  Sum_probs=43.5

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh---h-ccccCcEEEE
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK---E-MKMFDDVAMA  214 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~---~-~~~F~~~~wv  214 (848)
                      +.++|||+++++++..|....-+.+-+||-.|+|||++++.+.....   + ...-+..+|.
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~   83 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA   83 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             CCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            35789999999999999966666778999999999999876665432   1 2233455654

>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=96.21  E-value=0.0038  Score=58.64  Aligned_cols=53  Identities=25%  Similarity=0.309  Sum_probs=45.0

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +.|..-.+++|-++.++.+.+|+.+++...+=++|..|+||||+|+.+.+...
T Consensus         9 yrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~   61 (224)
T d1sxjb2           9 YRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELL   61 (224)
T ss_dssp             TCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHh
Confidence            34445678999999999999999988887777999999999999998887653

>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=96.19  E-value=0.0036  Score=58.96  Aligned_cols=52  Identities=12%  Similarity=0.210  Sum_probs=43.9

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .|..-.+++|.++.++.+.+|+.++....+=++|..|+||||+|+.+.+...
T Consensus         9 rP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~   60 (227)
T d1sxjc2           9 RPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIY   60 (227)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhh
Confidence            3344577999999999999999988776667999999999999999987654

>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=96.05  E-value=0.0038  Score=59.02  Aligned_cols=52  Identities=19%  Similarity=0.234  Sum_probs=44.8

Q ss_pred             cCCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          151 SSSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       151 ~~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|....+++|-++.++.+..|+..+....+=++|..|+||||+|+.+-+..
T Consensus        18 y~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l   69 (231)
T d1iqpa2          18 YRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALAREL   69 (231)
T ss_dssp             TCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHH
Confidence            3344457899999999999999998888888899999999999999988754

>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=96.03  E-value=0.0035  Score=59.80  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=37.7

Q ss_pred             ccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++|||+++++++..|....-+.+-+||..|+|||+++..+...
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~r   62 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWR   62 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHH
Confidence            358999999999999998555566679999999999988776654

>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=96.03  E-value=0.0032  Score=61.48  Aligned_cols=44  Identities=20%  Similarity=0.290  Sum_probs=36.7

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+.+|||+++++.+.+.    .-+.+.|+|.+|+|||+|++++.+..
T Consensus        10 ~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~   53 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINEL   53 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHC
Confidence            357899999999988764    34688899999999999999887654

>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=95.98  E-value=0.0028  Score=56.33  Aligned_cols=114  Identities=11%  Similarity=0.022  Sum_probs=74.1

Q ss_pred             hhhcccCcEEEccCccccCCc------hhhccccCCCEEEccCCCCc-----ccChhhccCCcccEEeccCCccccc---
Q 003090          317 LSFLINLRTLRLHDRRIQGDL------SLIGELSGLEILDLSESDVS-----EIPVSFGRLSHLRLLDLTGCYILEL---  382 (848)
Q Consensus       317 ~~~l~~L~~L~L~~~~~~~~~------~~i~~l~~L~~L~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~~~~~~---  382 (848)
                      ..+.++|++|+++++...+..      ..+...++|++|++++|.+.     .+...+...++++.+++++|.....   
T Consensus        13 ~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~~g~~   92 (166)
T d1io0a_          13 QNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGIL   92 (166)
T ss_dssp             HTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHH
T ss_pred             HhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccchhHH
Confidence            345678999999875333221      44567888999999999876     3444566778899999988765432   


Q ss_pred             -cChhhhhccccccEEeccc--cccccccccccccccCcccchhhhcccCCCcEEEeeccC
Q 003090          383 -IPRGVLSRLRKLEELYMSH--SFRHWQFESESEEDSSSNAKFIELGALSRLTSLHIHIPE  440 (848)
Q Consensus       383 -~p~~~l~~l~~L~~L~l~~--~~~~~~~~~~~~~~~~~~~~~~~L~~l~~L~~L~l~~~~  440 (848)
                       +... +...++|+.+++..  +.+..         ....+....+...++|++|+++++.
T Consensus        93 ~l~~~-l~~~~~L~~l~L~l~~n~i~~---------~~~~~La~~L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          93 ALVEA-LQSNTSLIELRIDNQSQPLGN---------NVEMEIANMLEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             HHHHG-GGGCSSCCEEECCCCSSCCCH---------HHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             HHHHH-HHhCccccEEeeccCCCcCcH---------HHHHHHHHHHHhCCCcCEEeCcCCC
Confidence             2223 56667788766653  33322         1223455667778888888887653

>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=95.79  E-value=0.0034  Score=59.58  Aligned_cols=51  Identities=16%  Similarity=0.287  Sum_probs=43.4

Q ss_pred             CCcccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|.++.++.+..|+..+....+-++|..|+||||+|+.+.+..
T Consensus         7 ~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l   57 (237)
T d1sxjd2           7 RPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKEL   57 (237)
T ss_dssp             CCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHH
Confidence            344456799999999999999998887778899999999999999998764

>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=95.76  E-value=0.0026  Score=56.55  Aligned_cols=115  Identities=14%  Similarity=0.130  Sum_probs=67.1

Q ss_pred             HccCCceeEEEccCcccccccccCCCCCCCCCCCCCCCCCchhhhcccCcEEEccCccccCCc-----hhhccccCCCEE
Q 003090          275 FQGMKDLQVLDLGGIRRFSFSVRFPFLFPPLPSSPLFLLPSSLSFLINLRTLRLHDRRIQGDL-----SLIGELSGLEIL  349 (848)
Q Consensus       275 ~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~l~~~~~~~lp~~~~~l~~L~~L~L~~~~~~~~~-----~~i~~l~~L~~L  349 (848)
                      ..+.+.|+.|+++++             +.++......+-..+...++|+.|++++|.+....     ..+...+.++.+
T Consensus        13 ~~~~~~L~~L~L~~~-------------~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l   79 (166)
T d1io0a_          13 QNNDPDLEEVNLNNI-------------MNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSL   79 (166)
T ss_dssp             HTTCTTCCEEECTTC-------------TTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEE
T ss_pred             HhcCCCCcEEEcCCC-------------CCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhh
Confidence            445677777777762             23332111112233446677888888877544321     345667788888


Q ss_pred             EccCCCCc-----ccChhhccCCcccEEeccCC--cccc----ccChhhhhccccccEEeccccc
Q 003090          350 DLSESDVS-----EIPVSFGRLSHLRLLDLTGC--YILE----LIPRGVLSRLRKLEELYMSHSF  403 (848)
Q Consensus       350 ~l~~~~l~-----~lp~~i~~L~~L~~L~l~~~--~~~~----~~p~~~l~~l~~L~~L~l~~~~  403 (848)
                      ++++|.+.     .+...+...++|+.+++..+  ....    .+... +...++|++|++..+.
T Consensus        80 ~l~~~~~~~~g~~~l~~~l~~~~~L~~l~L~l~~n~i~~~~~~~La~~-L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          80 NVESNFISGSGILALVEALQSNTSLIELRIDNQSQPLGNNVEMEIANM-LEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             ECCSSCCCHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHH-HHHCSSCCEEECCCSS
T ss_pred             hhccccccchhHHHHHHHHHhCccccEEeeccCCCcCcHHHHHHHHHH-HHhCCCcCEEeCcCCC
Confidence            88887765     34456677778887666533  2211    12233 5677888888886654

>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=95.34  E-value=0.0072  Score=61.17  Aligned_cols=57  Identities=16%  Similarity=0.268  Sum_probs=40.9

Q ss_pred             cccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHH----HHHhhccccCcEEEE
Q 003090          158 AFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQ----KQAKEMKMFDDVAMA  214 (848)
Q Consensus       158 ~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~----~~~~~~~~F~~~~wv  214 (848)
                      .++|||++++++++.|....-..+-+||..|||||+++..+.    +..-.....+.++|.
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~   83 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS   83 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             CCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEE
Confidence            478999999999999985554556789999999999775444    332223334556665

>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=95.29  E-value=0.0098  Score=56.32  Aligned_cols=47  Identities=21%  Similarity=0.288  Sum_probs=38.0

Q ss_pred             cccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -+++||-++.++.+..++.     ....+-+=++|..|+||||+|+.+.+..
T Consensus         8 ~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~   59 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL   59 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4678999999988877775     2334556699999999999999998765

>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=95.29  E-value=0.0045  Score=60.56  Aligned_cols=47  Identities=28%  Similarity=0.301  Sum_probs=36.7

Q ss_pred             cccccchhHHHHHHHHHHh--------cCCc-cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK--------DENV-SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~--------~~~~-~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++||+++++.+.+++.        ..+. .++-++|..|+||||+++.+.+..
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l   70 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRV   70 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHH
Confidence            3678999999999999874        1111 235567999999999999999764

>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=95.17  E-value=0.011  Score=55.80  Aligned_cols=47  Identities=28%  Similarity=0.358  Sum_probs=38.8

Q ss_pred             cccccchhHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -++++|-++.++.+..|+.     .....-+=++|..|+||||+|+.+.+..
T Consensus         8 ~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~   59 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL   59 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc
Confidence            4679999999999988886     2334456699999999999999998765

>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=95.14  E-value=0.0073  Score=57.81  Aligned_cols=51  Identities=14%  Similarity=0.169  Sum_probs=39.7

Q ss_pred             CCcccccccchhHHHHHHHHHHhcC-CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDE-NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~-~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-++++|.++.++.+.+++... ....+-++|..|+||||+|+++.+..
T Consensus         6 ~P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l   57 (252)
T d1sxje2           6 RPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI   57 (252)
T ss_dssp             CCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHH
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhh
Confidence            3445678999998888888777633 34446699999999999999998764

>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=94.91  E-value=0.017  Score=55.14  Aligned_cols=51  Identities=12%  Similarity=0.182  Sum_probs=41.3

Q ss_pred             CCcccccccchhHHHHHHHHHHhcC-----------------CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          152 SSEGVYAFKSRESTMKDIMEAMKDE-----------------NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       152 ~~~~~~~~vG~~~~~~~i~~~L~~~-----------------~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|..-.+++|.++.++++.+|+..+                 ..+.+=++|..|+||||+|+.+.+..
T Consensus         9 ~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~   76 (253)
T d1sxja2           9 APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL   76 (253)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3444678999999999999998631                 23568899999999999999998764

>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=94.36  E-value=0.013  Score=51.74  Aligned_cols=26  Identities=27%  Similarity=0.445  Sum_probs=22.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +.|+.|+|..|+|||||++.+-+...
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~   27 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALC   27 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999987643

>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=93.44  E-value=0.025  Score=49.72  Aligned_cols=25  Identities=28%  Similarity=0.336  Sum_probs=22.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +|++|+|+.|+|||||+.++-...+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~   26 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAV   26 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            5899999999999999999887654

>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=93.05  E-value=0.057  Score=50.70  Aligned_cols=50  Identities=16%  Similarity=0.261  Sum_probs=41.6

Q ss_pred             CcccccccchhHHHHHHHHHHhcCCcc-EEEEEeCCCCchhHHHHHHHHHH
Q 003090          153 SEGVYAFKSRESTMKDIMEAMKDENVS-ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       153 ~~~~~~~vG~~~~~~~i~~~L~~~~~~-vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |..-.+++|.++.++.+.+++..++.. .+=++|..|+||||+|+.+.+..
T Consensus         8 P~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l   58 (239)
T d1njfa_           8 PQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGL   58 (239)
T ss_dssp             CSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHh
Confidence            334578999999999999999877654 46689999999999999887654

>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=93.03  E-value=0.052  Score=49.06  Aligned_cols=29  Identities=28%  Similarity=0.469  Sum_probs=24.5

Q ss_pred             cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          175 DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       175 ~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ..+.-+|+|.|..|.||||+|+.+.+...
T Consensus        19 ~~~~~iIgI~G~~GSGKSTla~~L~~~l~   47 (198)
T d1rz3a_          19 TAGRLVLGIDGLSRSGKTTLANQLSQTLR   47 (198)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            45556899999999999999999987654

>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=92.98  E-value=0.027  Score=48.57  Aligned_cols=23  Identities=30%  Similarity=0.390  Sum_probs=19.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|-++|+.|+||||+|+.+...
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            46789999999999999987643

>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=92.88  E-value=0.024  Score=49.61  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|-+.|+.|+||||+|+.+.+..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            467888999999999999998653

>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=92.73  E-value=0.027  Score=50.60  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.4

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+.|.|.|..|+||||+|+.+.+.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            467999999999999999998864

>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=92.54  E-value=0.033  Score=49.61  Aligned_cols=25  Identities=16%  Similarity=0.199  Sum_probs=21.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|-++|+.|+||||+|+.+.....
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4788999999999999999987654

>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=91.96  E-value=0.039  Score=48.67  Aligned_cols=24  Identities=42%  Similarity=0.513  Sum_probs=20.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|.|.|+.|+||||+|+.+....
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            457799999999999999997653

>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=91.95  E-value=0.043  Score=48.39  Aligned_cols=23  Identities=39%  Similarity=0.518  Sum_probs=20.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ++|.|+|+.|+||||+|+.+...
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~   25 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQ   25 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            47889999999999999988753

>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=91.75  E-value=0.044  Score=47.82  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=19.7

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.++||.|+||||+|+.+....
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
Confidence            6788999999999999998765

>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=91.40  E-value=0.051  Score=47.64  Aligned_cols=22  Identities=27%  Similarity=0.521  Sum_probs=19.1

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-++||.|+||||+++.+.+..
T Consensus         4 IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4567999999999999998765

>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=90.80  E-value=0.076  Score=46.59  Aligned_cols=27  Identities=26%  Similarity=0.468  Sum_probs=23.4

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+.+++-++|..|+||||+|+.+....
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
Confidence            456789999999999999999998654

>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=90.80  E-value=0.075  Score=47.43  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=22.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++|.|.|+.|+||||+++.+.+...
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~   26 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLR   26 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Confidence            6899999999999999999987653

>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=90.65  E-value=0.11  Score=50.64  Aligned_cols=46  Identities=20%  Similarity=0.285  Sum_probs=35.9

Q ss_pred             ccccchhHHHHHHHHHHh--------------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK--------------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~--------------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..|+|-++.++.+...+.              ....+.+-.+|..|+|||.+|+++.+..
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~   73 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   73 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcc
Confidence            458899999988876551              1244667799999999999999998754

>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=90.58  E-value=0.084  Score=48.29  Aligned_cols=25  Identities=20%  Similarity=0.391  Sum_probs=22.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      .+|.++|..|+||||+|+++.....
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5789999999999999999987553

>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=90.56  E-value=0.072  Score=46.91  Aligned_cols=23  Identities=30%  Similarity=0.377  Sum_probs=20.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..|.|.|+.|+||||+|+.+.+.
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHH
Confidence            46889999999999999999865

>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=90.52  E-value=0.08  Score=47.81  Aligned_cols=26  Identities=31%  Similarity=0.431  Sum_probs=23.2

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+.+||-|+|..|+||||+|+.+.+.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            46789999999999999999999764

>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=90.50  E-value=0.078  Score=47.82  Aligned_cols=27  Identities=22%  Similarity=0.256  Sum_probs=23.3

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ....+|.|+|+.|.||||+|+.+.+..
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            455799999999999999999998654

>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=90.41  E-value=0.07  Score=47.53  Aligned_cols=25  Identities=36%  Similarity=0.429  Sum_probs=22.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      +.|.|.|.+|+|||||++.+.....
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH
Confidence            4688999999999999999987764

>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=89.99  E-value=0.25  Score=46.19  Aligned_cols=47  Identities=23%  Similarity=0.302  Sum_probs=35.1

Q ss_pred             cccccchhHHHHHHHHHH---hc---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAM---KD---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L---~~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+|+|.|+.++.+.+.+   ..         ...+-+=++|..|.|||++|+.+.+..
T Consensus         8 ~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~   66 (247)
T d1ixza_           8 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   66 (247)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc
Confidence            467999998887765543   21         112457799999999999999999754

>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=89.98  E-value=0.17  Score=47.42  Aligned_cols=47  Identities=13%  Similarity=0.191  Sum_probs=35.2

Q ss_pred             cccccchhHHHHHHHHHHh-------c---CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK-------D---ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~-------~---~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...++|..++++.+++...       .   ....-|=++|..|+|||++|++|.+..
T Consensus         8 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~   64 (246)
T d1d2na_           8 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES   64 (246)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcc
Confidence            3458888888877777654       1   123446689999999999999998765

>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=89.93  E-value=0.076  Score=46.70  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=19.8

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|-++|+.|+||||+|+.+.+..
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            35588999999999999998765

>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=89.76  E-value=0.092  Score=46.26  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ++|.|.|..|+||||+|+.+.+.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~   26 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSV   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999864

>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=89.71  E-value=0.17  Score=47.55  Aligned_cols=47  Identities=21%  Similarity=0.270  Sum_probs=35.8

Q ss_pred             cccccchhHHHHHHHHHH---hc---------CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAM---KD---------ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L---~~---------~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..+++|.|+.++++.+.+   ..         ...+-+=++|..|.|||++|+.+.+..
T Consensus        11 ~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~   69 (256)
T d1lv7a_          11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (256)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc
Confidence            468999999988776543   21         113446699999999999999998765

>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=89.60  E-value=0.084  Score=46.53  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=20.1

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      -++|.+.|+.|+||||+|+.+-+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999988853

>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=89.57  E-value=0.17  Score=49.31  Aligned_cols=46  Identities=24%  Similarity=0.346  Sum_probs=37.2

Q ss_pred             ccccchhHHHHHHHHHHh---------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|-++.++.+...+.         +....++-.+|..|+|||.||+.+-...
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l   76 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL   76 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc
Confidence            568999999998887664         2334578899999999999999988653

>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=88.92  E-value=0.065  Score=48.31  Aligned_cols=24  Identities=25%  Similarity=0.436  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|-++|+.|+||||+|+.+....
T Consensus        20 ~vI~L~G~pGSGKTTiAk~La~~l   43 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSMALEEYL   43 (195)
T ss_dssp             EEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            477899999999999999997654

>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=88.89  E-value=0.11  Score=47.53  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -+|+|.|..|.||||+|+.+.+..
T Consensus         3 ~iIgI~G~~gSGKSTla~~L~~~l   26 (213)
T d1uj2a_           3 FLIGVSGGTASGKSSVCAKIVQLL   26 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            489999999999999999988654

>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=88.72  E-value=0.26  Score=46.44  Aligned_cols=47  Identities=15%  Similarity=0.198  Sum_probs=36.4

Q ss_pred             cccccchhHHHHHHHHHHh----------c---CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          156 VYAFKSRESTMKDIMEAMK----------D---ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       156 ~~~~vG~~~~~~~i~~~L~----------~---~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.+|+|.|+.++++.+.+.          .   ...+-+=++|..|.|||++|+++.+..
T Consensus         3 ~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~   62 (258)
T d1e32a2           3 YDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET   62 (258)
T ss_dssp             GGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             hhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh
Confidence            3579999999988888643          1   123456689999999999999998754

>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=88.30  E-value=0.14  Score=45.04  Aligned_cols=23  Identities=52%  Similarity=0.593  Sum_probs=20.7

Q ss_pred             EEEEeCCCCchhHHHHHHHHHHh
Q 003090          181 TGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      |.|+|..|+|||||++.+.....
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCC
Confidence            78999999999999999987654

>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=88.14  E-value=0.14  Score=45.05  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=21.2

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .+..+|-++|+.|+||||+|+.+..
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567899999999999999987753

>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=88.09  E-value=0.13  Score=45.84  Aligned_cols=25  Identities=28%  Similarity=0.534  Sum_probs=21.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++|-|.|+.|+||||+++.+.....
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~   26 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5788999999999999999976653

>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=87.94  E-value=0.22  Score=47.33  Aligned_cols=40  Identities=28%  Similarity=0.351  Sum_probs=28.5

Q ss_pred             hHHHHHHHHHHh-----cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          163 ESTMKDIMEAMK-----DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       163 ~~~~~~i~~~L~-----~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+...+.++.+.     ....+.|-++|..|+||||+|+.+.+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          12 ENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            444455555554     2334557799999999999999998764

>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=87.71  E-value=0.42  Score=46.54  Aligned_cols=36  Identities=22%  Similarity=0.367  Sum_probs=27.3

Q ss_pred             HHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHHh
Q 003090          168 DIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQAK  203 (848)
Q Consensus       168 ~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~~  203 (848)
                      ++++.+.  ..+..+|+|.|.+|+|||||...+-....
T Consensus        42 ~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~   79 (327)
T d2p67a1          42 QLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLI   79 (327)
T ss_dssp             HHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHH
Confidence            4444443  45678999999999999999988776553

>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=87.42  E-value=0.14  Score=45.87  Aligned_cols=22  Identities=36%  Similarity=0.489  Sum_probs=19.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQ  199 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~  199 (848)
                      .-+|||.|..|.||||+|+.+-
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4589999999999999998764

>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=87.16  E-value=0.49  Score=45.98  Aligned_cols=37  Identities=27%  Similarity=0.507  Sum_probs=27.8

Q ss_pred             HHHHHHHHh--cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          166 MKDIMEAMK--DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       166 ~~~i~~~L~--~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++++.+.  ..+..+|+|.|.+|+|||||...+-...
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~   75 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   75 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHH
Confidence            344455543  4567899999999999999988877554

>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=87.13  E-value=0.14  Score=48.82  Aligned_cols=24  Identities=29%  Similarity=0.542  Sum_probs=20.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +.|+|+|=||+||||+|-.+-...
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~L   25 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGL   25 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHH
Confidence            578999999999999987766544

>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=86.48  E-value=0.22  Score=47.65  Aligned_cols=37  Identities=24%  Similarity=0.483  Sum_probs=28.8

Q ss_pred             HHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          166 MKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       166 ~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ...+++.+.....+||-+.|-||+||||+|-.+-...
T Consensus         8 ~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~l   44 (279)
T d1ihua2           8 LSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRL   44 (279)
T ss_dssp             HHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4556677777888899999999999999876665433

>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=85.71  E-value=0.22  Score=45.75  Aligned_cols=25  Identities=32%  Similarity=0.461  Sum_probs=22.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..||.|-|+.|+||+|.|+.+-++.
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999998765

>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=85.46  E-value=0.23  Score=44.42  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=21.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+|.|.|..|.||||.|+.+.+..
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999998754

>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=85.42  E-value=0.32  Score=47.22  Aligned_cols=46  Identities=20%  Similarity=0.353  Sum_probs=36.3

Q ss_pred             ccccchhHHHHHHHHHHh---------cCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          157 YAFKSRESTMKDIMEAMK---------DENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       157 ~~~vG~~~~~~~i~~~L~---------~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..++|-++.++.+...+.         +....++-.+|..|+|||.+|+.+-+..
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l   77 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATL   77 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHh
Confidence            468899999998877664         1234478899999999999999887654

>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=84.97  E-value=0.24  Score=47.69  Aligned_cols=26  Identities=31%  Similarity=0.300  Sum_probs=22.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ..-+|+|.|-.|+||||+|+.+....
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL  104 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHH
Confidence            34699999999999999999998654

>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=84.79  E-value=0.27  Score=43.73  Aligned_cols=24  Identities=25%  Similarity=0.184  Sum_probs=20.4

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      -.|.|.|+.|.||||+|+.+.+..
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            357799999999999999987654

>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=84.77  E-value=0.2  Score=45.08  Aligned_cols=23  Identities=39%  Similarity=0.648  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|+|||||.+.+...
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
Confidence            58999999999999999998753

>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=84.71  E-value=0.21  Score=47.42  Aligned_cols=27  Identities=19%  Similarity=0.367  Sum_probs=19.8

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+..||+|.|-.|.||||+++.+.+..
T Consensus         2 ~k~pIIgIaG~SGSGKTTva~~l~~i~   28 (288)
T d1a7ja_           2 KKHPIISVTGSSGAGTSTVKHTFDQIF   28 (288)
T ss_dssp             TTSCEEEEESCC---CCTHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHHHH
Confidence            355799999999999999999876644

>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=84.67  E-value=0.24  Score=45.63  Aligned_cols=23  Identities=30%  Similarity=0.374  Sum_probs=20.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++++|..|.||||+++.++--
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl   52 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGL   52 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcC
Confidence            58999999999999999999854

>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=84.39  E-value=0.47  Score=42.85  Aligned_cols=30  Identities=23%  Similarity=0.413  Sum_probs=24.6

Q ss_pred             HhcCCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          173 MKDENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       173 L~~~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +..+.-.+|=+.|+.|.||||+|+.+....
T Consensus        19 ~~~~kg~vIwltGlsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          19 LRNQRGLTIWLTGLSASGKSTLAVELEHQL   48 (208)
T ss_dssp             HHTSSCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HhCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            344555799999999999999999998654

>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=84.04  E-value=0.18  Score=45.34  Aligned_cols=23  Identities=35%  Similarity=0.300  Sum_probs=20.0

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .-+|+|-|.-|+||||+++.+.+
T Consensus         9 p~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           9 PFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CEEEEEECSTTSCHHHHHHTTGG
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            34899999999999999988764

>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=84.02  E-value=0.31  Score=43.08  Aligned_cols=23  Identities=26%  Similarity=0.533  Sum_probs=20.1

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+|.|+|..|+||||+++.+.+.
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            46889999999999999988754

>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=83.78  E-value=0.31  Score=47.99  Aligned_cols=46  Identities=20%  Similarity=0.237  Sum_probs=34.3

Q ss_pred             ccccccchhHHHHHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHH
Q 003090          155 GVYAFKSRESTMKDIMEAMKDENVSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       155 ~~~~~vG~~~~~~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      +-..|+|.+..+..+.-........-+=++|..|+||||+|+.+-.
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHH
Confidence            3468999998777655444333334577999999999999998864

>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=83.76  E-value=0.28  Score=44.89  Aligned_cols=23  Identities=30%  Similarity=0.458  Sum_probs=20.6

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+.--
T Consensus        27 ei~~liGpsGsGKSTLl~~i~Gl   49 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAGL   49 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHhcC
Confidence            68999999999999999988743

>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=83.65  E-value=0.26  Score=47.46  Aligned_cols=22  Identities=32%  Similarity=0.587  Sum_probs=18.3

Q ss_pred             cEEEEEeCCCCchhHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      +.|+|.|=||+||||+|-.+-.
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~   24 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4678999999999998876654

>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=83.52  E-value=0.28  Score=45.84  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=20.5

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      -.+++|+|..|.|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            36899999999999999998864

>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=83.38  E-value=0.3  Score=44.96  Aligned_cols=23  Identities=30%  Similarity=0.381  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++|+|..|.|||||.+.+.--
T Consensus        33 e~~~liGpsGaGKSTLl~~i~Gl   55 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAGL   55 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCChHHHHHHHHHcC
Confidence            58999999999999999988754

>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=83.23  E-value=0.27  Score=45.32  Aligned_cols=24  Identities=33%  Similarity=0.620  Sum_probs=21.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+++|+|..|.|||||++.+.--.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCc
Confidence            689999999999999999987543

>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=83.07  E-value=0.33  Score=44.43  Aligned_cols=23  Identities=35%  Similarity=0.359  Sum_probs=20.6

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      +|+|-|..|+||||.|+.+-...
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68899999999999999998654

>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=83.06  E-value=0.3  Score=44.69  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=20.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      -.+++|+|..|.|||||.+.+.--
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl   54 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCL   54 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCcchhhHhccCC
Confidence            368999999999999999988753

>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=83.02  E-value=0.36  Score=42.89  Aligned_cols=24  Identities=29%  Similarity=0.383  Sum_probs=19.6

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .++| ++|+.|+||||.|+.+.+..
T Consensus         4 ~rii-l~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           4 VRAV-LLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             cEEE-EECCCCCCHHHHHHHHHHHh
Confidence            4455 89999999999999987643

>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=82.96  E-value=0.32  Score=46.26  Aligned_cols=24  Identities=33%  Similarity=0.421  Sum_probs=21.1

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      -.+++|+|..|.|||||++.+.-.
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            368999999999999999998743

>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=82.94  E-value=0.29  Score=45.81  Aligned_cols=23  Identities=30%  Similarity=0.478  Sum_probs=20.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      -.+++|+|..|.|||||++.+.-
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            36899999999999999999874

>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=82.85  E-value=0.33  Score=42.73  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=19.2

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-|.|+.|.||||+|+.+.+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6699999999999999987654

>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=82.76  E-value=0.5  Score=41.21  Aligned_cols=33  Identities=21%  Similarity=0.321  Sum_probs=24.8

Q ss_pred             HHHHHHHhcCCccEEEEEeCCCCchhHHHHHHHH
Q 003090          167 KDIMEAMKDENVSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       167 ~~i~~~L~~~~~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      ..++.++...+. .|.++|-.|+|||||...+-.
T Consensus         5 ~~~~~~~~~k~~-kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1           5 TRIWRLFNHQEH-KVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             HHHHHHHTTSCE-EEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHHhCCCeE-EEEEECCCCCCHHHHHHHHhc
Confidence            456666655555 567999999999999877653

>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=82.66  E-value=0.34  Score=43.10  Aligned_cols=22  Identities=36%  Similarity=0.495  Sum_probs=19.1

Q ss_pred             EEEEEeCCCCchhHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .|.|.|+.|+||||+|+.+...
T Consensus         8 rIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4668999999999999998764

>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=82.64  E-value=0.37  Score=42.49  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=20.0

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .|-|.|+.|.||||+|+.+.+..
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
Confidence            36789999999999999998764

>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=82.54  E-value=0.32  Score=45.40  Aligned_cols=25  Identities=28%  Similarity=0.432  Sum_probs=21.5

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .-.+++|+|..|.|||||++.+..-
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl   63 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNL   63 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcc
Confidence            3368999999999999999998753

>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=82.53  E-value=0.32  Score=45.00  Aligned_cols=23  Identities=48%  Similarity=0.713  Sum_probs=20.5

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      ..++|+|..|.|||||++.+..-
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc
Confidence            57999999999999999988743

>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=82.38  E-value=0.34  Score=44.47  Aligned_cols=24  Identities=21%  Similarity=0.300  Sum_probs=21.0

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+++|+|..|.|||||.+.+..-.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC
Confidence            478999999999999999998543

>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=82.22  E-value=0.33  Score=45.01  Aligned_cols=23  Identities=30%  Similarity=0.501  Sum_probs=20.3

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999988864

>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=82.15  E-value=0.36  Score=42.48  Aligned_cols=22  Identities=23%  Similarity=0.297  Sum_probs=19.6

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-|.|+.|+||||+|+.+.+..
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6788999999999999998765

>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=82.12  E-value=0.32  Score=45.23  Aligned_cols=23  Identities=39%  Similarity=0.507  Sum_probs=20.2

Q ss_pred             EEEEEeCCCCchhHHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ||.|.|+.|.|||||.+.+-...
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Confidence            78999999999999998887543

>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=82.05  E-value=0.37  Score=42.89  Aligned_cols=22  Identities=32%  Similarity=0.569  Sum_probs=19.1

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |.|+|..|+||||+++.+.+..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            5599999999999999987653

>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=81.48  E-value=0.4  Score=42.48  Aligned_cols=21  Identities=38%  Similarity=0.586  Sum_probs=18.8

Q ss_pred             EEEEeCCCCchhHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~  201 (848)
                      |.++|..|+||||+++.+.+.
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~~   24 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFAE   24 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            669999999999999998765

>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=81.33  E-value=0.37  Score=44.45  Aligned_cols=25  Identities=36%  Similarity=0.497  Sum_probs=21.4

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +-.+++++|..|.|||||.+.+...
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~   51 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTL   51 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3368999999999999999888754

>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=81.12  E-value=1.1  Score=40.30  Aligned_cols=48  Identities=23%  Similarity=0.270  Sum_probs=31.1

Q ss_pred             ccccchhHHH--HHHHHHHhc--CCccEEEEEeCCCCchhHHHHHHHHHHhh
Q 003090          157 YAFKSRESTM--KDIMEAMKD--ENVSITGICGMGGVGKTTLVKEIQKQAKE  204 (848)
Q Consensus       157 ~~~vG~~~~~--~~i~~~L~~--~~~~vi~i~G~gG~GKTtla~~v~~~~~~  204 (848)
                      .-++|-....  ..+.++...  .....+-|+|..|+|||.|++++.+....
T Consensus        11 nF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~   62 (213)
T d1l8qa2          11 NFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKK   62 (213)
T ss_dssp             SCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHH
T ss_pred             hccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhcc
Confidence            4466754333  333333332  22234779999999999999999988753

>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=80.84  E-value=0.66  Score=43.86  Aligned_cols=25  Identities=20%  Similarity=0.145  Sum_probs=21.7

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .-+|||-|..|+||||+|..+....
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHH
Confidence            4589999999999999999887654

>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=80.77  E-value=0.59  Score=42.24  Aligned_cols=26  Identities=15%  Similarity=0.266  Sum_probs=22.2

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHHHhh
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQAKE  204 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~~~~  204 (848)
                      ..|.|.|+-|+||||+++.+.+....
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~   29 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCA   29 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46889999999999999999886543

>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=80.52  E-value=0.51  Score=43.73  Aligned_cols=25  Identities=36%  Similarity=0.307  Sum_probs=21.8

Q ss_pred             ccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          178 VSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       178 ~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      .+.|.|-|+-|+||||+++.+.+..
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4689999999999999999998653

>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=80.52  E-value=0.46  Score=40.49  Aligned_cols=21  Identities=24%  Similarity=0.434  Sum_probs=18.2

Q ss_pred             EEEEeCCCCchhHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~  201 (848)
                      |.++|..|+|||||.+.+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            569999999999999887654

>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=80.49  E-value=0.51  Score=41.41  Aligned_cols=23  Identities=17%  Similarity=0.346  Sum_probs=19.9

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +.|-++|..|+|||||++.+...
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
Confidence            46889999999999999888754

>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=80.48  E-value=0.47  Score=41.60  Aligned_cols=22  Identities=23%  Similarity=0.125  Sum_probs=19.2

Q ss_pred             EEEEeCCCCchhHHHHHHHHHH
Q 003090          181 TGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       181 i~i~G~gG~GKTtla~~v~~~~  202 (848)
                      |-+.|+.|.||||.|+.+.+..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999999999998654

>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=80.42  E-value=0.55  Score=41.83  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=21.7

Q ss_pred             CccEEEEEeCCCCchhHHHHHHHHH
Q 003090          177 NVSITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       177 ~~~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      +.++|-+.|+.|.||||+|+.+.+.
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
Confidence            3478999999999999999998764

>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=80.28  E-value=0.67  Score=41.55  Aligned_cols=27  Identities=22%  Similarity=0.300  Sum_probs=19.8

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQKQA  202 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~~~  202 (848)
                      ++.+|+.++|..|+||||.+-.+-...
T Consensus         8 ~~~~vi~lvGp~GvGKTTTiaKLA~~~   34 (207)
T d1ls1a2           8 KDRNLWFLVGLQGSGKTTTAAKLALYY   34 (207)
T ss_dssp             CSSEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            345789999999999998654444333

>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=80.22  E-value=0.46  Score=42.36  Aligned_cols=25  Identities=16%  Similarity=0.428  Sum_probs=21.9

Q ss_pred             CCccEEEEEeCCCCchhHHHHHHHH
Q 003090          176 ENVSITGICGMGGVGKTTLVKEIQK  200 (848)
Q Consensus       176 ~~~~vi~i~G~gG~GKTtla~~v~~  200 (848)
                      .++..|+++|..|+|||||...+.+
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcC
Confidence            4566899999999999999988874

>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=80.21  E-value=0.41  Score=41.27  Aligned_cols=22  Identities=36%  Similarity=0.483  Sum_probs=18.9

Q ss_pred             EEEEEeCCCCchhHHHHHHHHH
Q 003090          180 ITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       180 vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      -|.|+|..|+|||||.+.+.++
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3779999999999999887654

>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=80.02  E-value=0.44  Score=44.02  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=20.7

Q ss_pred             cEEEEEeCCCCchhHHHHHHHHH
Q 003090          179 SITGICGMGGVGKTTLVKEIQKQ  201 (848)
Q Consensus       179 ~vi~i~G~gG~GKTtla~~v~~~  201 (848)
                      .+++++|..|.|||||.+.+.-.
T Consensus        33 ei~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCC
Confidence            58999999999999999998754