Citrus Sinensis ID: 004021

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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-------78
Protein Sequence
MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Secondary Structure (PSIPRED)
cHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEccccccccccccHHHHHHHHHHHHHHHHHHccccccEEEEccccccccccccccccccHHcHHHHHHHHHHcccccccEEEEEEcccccHHHHHHHHHcccccccccccEEEEEEEcccHHHHHHHHccccccccccccHHHHHHHHHHHHcccEEEEEcccccccccccccccEEEEEEccHHHHHHcccccEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccHHHHHcccccccccHHHHHHHHHccccccccccHHHHHHHHHHccccccHHHHHHHHHHHHHcccccccccccEEEcccHHHHHHHHHHHHccccccEEEEcccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccEEEccccccccccHHHHccccccccccccccccccccHHHHcccccccEEEcccccccccccccccccccccHHHHHHHccccccccEEEEEccccccccccccccccHHHHHHccccccccccccccccccccccccccccccHHHHcccccccccccEEEEEcccccccccccccccccccEEEEEccccccccccccccccccEEEEcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHccccccEEEccccccccccccccccEEccHHHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccccccccccEEEEEEEEccHHHHHHHHHccccccccccccHHHHHHHHHHHHccccEEEEEEcccccccccccccEEEEEEccHHHHHHcccccEEEccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHccccHHHHHHHHHHHHHcHHccccccccccHHEEEcHcccccHHHHHHHHHHEccccccEEcHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccEEEEHHHHHHHHHHHHHHccccccEEEEEccccccccccccccccEEEEEEcccccccccccccEEEHcccccHHHcccHccccccccEEEcccccccccccHHcccccccEEEEcccccHccccccHccccccccEEEEEccccccccccccccccccccccHHHHHccHHccEccccccccccHHccccccccccccccccccccEEEEcccHcHcccccccccccHHHHcHcccccccccccccEEEEcccccHHcccccccccccccEEEEcccccHcccccccccHHHHEEEEcccHHHHHHcccHHHHHHHHcccccccccc
Coil and Loop (DISEMBL)
mgnlistslppdlfsrtlhrvgeQANYVWGLKKNLEGLKTEMRKLTRTRDDLVnkveveeqprrtrrtnrvAGWLEDVQKLGTEFTELQQVRAQEMDRLClgglcsknlvssynygreVVELTDRVINLNKDGEKIAVVVEkapdgaaielpleqtivgqeklLPRVWRCItdqqknrgiiglygiggvgkTTLLKQVnnnfchqqhNFDVVIWAAVQTFQDdigkrigfsedkKWKEKslqdkavdissilspkkfridltelgvplqMLNAGFKIVLKTrsagvcdqmdsknleVYSLAHDEAWKLFQEMIERstldshtsiPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTsastfsgmeENVFLRLKFSYDSLSMDKLRSCLLYCclypedykipkrsLIDYWIsegfmadfdRGCEFINDLLHACLleeegddhvKMHDMIREMSLWIAWTIEKEKKNFLVRAGvklteapkvkewegAKRISLMANEIESLSeiptllslrrndsltelpSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLecgsegvtkeegnvlcddAEPLMRELLGLKRLNVLSWSFRSSLAVqkffkypkldlTWLVFVQNLKELEIIVCTEMEEIIcvdklrdvsdiseiigsehnfFTQLESlgilygpdlksiypnplhfpklkkigvygcpklkklpinsssaKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Flexible Loop (DISEMBL)
mgnlistslppdlFSRTLHRVGEQANYVWGLKKNLEGLKTEmrkltrtrddlvnkveveeqprrtrrtnrvagwledVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITdqqknrgiigLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKrigfsedkkwkekslqdkavdissilspkkfRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALktvgramksqkkvgdreraIEKMrtsastfsgmeenVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVragvklteapkvkewegakRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECgsegvtkeegnvlcdDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPklkklpinsssakerRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Low Complexity Region (SEG)
MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRgiiglygiggvgKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRIsslvslhhldlslthIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Disordered region (IsUnstruct)
************LFSRTLHRVGEQANYVWGLKKNLEGLK******************************RVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWK***LQDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV*******************************ENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRR***LTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINS**AKERRVVIEGLKEWWEELQWEDQATQNAF*********
Disordered Region (DISOPRED)
MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE******RRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKD*************************VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIG***************AVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTS*****GM*ENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNV***********LLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Disordered Region (DISEMBL)
MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSED********QDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG***************IEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
Disordered Region (DISPRO)
*GNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKA****AIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVI****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNLISTSLPPDLFSRTLHRVGEQANYxxxxxxxxxxxxxxxxxxxxxxxxxxxxVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSSGVILGGD
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	779	2.2.26 [Sep-21-2011]
O64973	889	Disease resistance protei	yes	no	0.979	0.858	0.361	1e-128
Q8RXS5	888	Probable disease resistan	no	no	0.753	0.661	0.383	1e-115
P60839	884	Probable disease resistan	no	no	0.960	0.846	0.343	1e-114
O22727	967	Probable disease resistan	no	no	0.965	0.777	0.347	1e-114
O82484	892	Putative disease resistan	no	no	0.975	0.852	0.328	1e-113
P60838	894	Probable disease resistan	no	no	0.698	0.608	0.402	1e-113
Q940K0	889	Probable disease resistan	no	no	0.964	0.844	0.346	1e-112
O64789	925	Probable disease resistan	no	no	0.935	0.788	0.349	1e-112
Q8L3R3	885	Disease resistance protei	no	no	0.799	0.703	0.373	1e-108
Q9SI85	893	Probable disease resistan	no	no	0.966	0.843	0.331	1e-103

>sp|O64973|RPS5_ARATH Disease resistance protein RPS5 OS=Arabidopsis thaliana GN=RPS5 PE=1 SV=2

 Score =  459 bits (1180), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 320/885 (36%), Positives = 455/885 (51%), Gaps = 122/885 (13%)

Query: 1   MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MG   S SLP D + S+    +  + +Y+  L KNL  L+  MR L   + D++ ++E E
Sbjct: 1   MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSKNLASLQKAMRMLKARQYDVIRRLETE 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E   R +R ++V  WL  V  +  +F +L +    E+ RLCL G CSK+L  SY YG+ V
Sbjct: 61  EFTGRQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRV 120

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
           + +   V +L+  G    VV E  P     E+P + TIVGQE +L + W  + +     G
Sbjct: 121 IMMLKEVESLSSQG-FFDVVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMED--GSG 177

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGFSED 233
           I+GLYG+GGVGKTTLL ++NN F      FDVVIW      + V+  Q DI +++G    
Sbjct: 178 ILGLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLG-G 236

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
            +W EK+    AVDI ++L  +KF         +++L  +GVP    + G K+   TRS 
Sbjct: 237 MEWSEKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSR 296

Query: 285 GVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            VC +M   + +EV  L  +E+W LFQ  + ++TL SH  IP LA  +AR+C  LPLAL 
Sbjct: 297 DVCGRMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALN 356

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
            +G AM  ++ V +   AI+ + +SA  FSGME+ +   LK+SYD+L+ + ++SC LYC 
Sbjct: 357 VIGEAMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCS 416

Query: 404 LYPEDYKIPKRSLIDYWISEGFMA-------DFDRGCEFINDLLHACLL--EEEGDDHVK 454
           L+PEDY I K  L+DYWISEGF+        + ++G E I  L+ ACLL  EE    +VK
Sbjct: 417 LFPEDYLIDKEGLVDYWISEGFINEKEGRERNINQGYEIIGTLVRACLLLEEERNKSNVK 476

Query: 455 MHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSE-- 512
           MHD++REM+LWI+  + K+K+  +VRAGV L E PKVK+W   ++ISLM NEIE + +  
Sbjct: 477 MHDVVREMALWISSDLGKQKEKCIVRAGVGLREVPKVKDWNTVRKISLMNNEIEEIFDSH 536

Query: 513 -------------------------IPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSL 545
                                    +P L  L L  N SL ELP  IS L SL + +LS 
Sbjct: 537 ECAALTTLFLQKNDVVKISAEFFRCMPHLVVLDLSENQSLNELPEEISELASLRYFNLSY 596

Query: 546 THIRGLPQELKALEKLRYLNLEYT------------------------------------ 569
           T I  LP  L  L+KL +LNLE+                                     
Sbjct: 597 TCIHQLPVGLWTLKKLIHLNLEHMSSLGSILGISNLWNLRTLGLRDSRLLLDMSLVKELQ 656

Query: 570 --HYLSIIPHQLISGFLKLEVL---RLLECGSE----GVTKEEGNVLCDDAEPLMREL-- 618
              +L +I   + S  +   +L   RL+EC  E     + +E   VL     P M  L  
Sbjct: 657 LLEHLEVITLDISSSLVAEPLLCSQRLVECIKEVDFKYLKEESVRVL---TLPTMGNLRK 713

Query: 619 LGLKRLNVLSWSFRSSLAVQKFFKYP------KLDLTWLVFVQNLKELEIIVCTEMEEII 672
           LG+KR  +       + +     K P       L   ++     LK+L  ++       +
Sbjct: 714 LGIKRCGMREIKIERTTSSSSRNKSPTTPCFSNLSRVFIAKCHGLKDLTWLLFAPNLTFL 773

Query: 673 CVDKLRDVSD-ISEIIGSEHNF----FTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVY 727
            V   ++V D ISE    EH+     F +LE+L +     LK IY   LHFP LK I V 
Sbjct: 774 EVGFSKEVEDIISEEKAEEHSATIVPFRKLETLHLFELRGLKRIYAKALHFPCLKVIHVE 833

Query: 728 GCPKLKKLPINSSS--AKERRVVIEGLKEWWEELQWEDQATQNAF 770
            C KL+KLP++S S  A E  V+  G +EW E ++WEDQATQ  F
Sbjct: 834 KCEKLRKLPLDSKSGIAGEELVIYYGEREWIERVEWEDQATQLRF 878

Disease resistance (R) protein that specifically recognizes the avrPphB type III effector avirulence protein from Pseudomonas syringae. Also confers resistance against Hyaloperonospora parasitica (downy mildew). 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. Requires PBS1 to trigger the defense reaction against avrPphB. Probably triggers the defense mechanism when PBS1 is cleaved by avrPphB, suggesting that it detects indirectly the protease activity of avrPphB, and possibly binds to the cleaved RPS5.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  416 bits (1070), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 248/646 (38%), Positives = 371/646 (57%), Gaps = 59/646 (9%)

Query: 1   MGNLISTSLPPDLFSRTLHR-VGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MG  +S S+  D  ++ +   +    +Y+ GL++NL  L+  + ++ + R+DL+ K+  E
Sbjct: 1   MGGCVSVSISCDQLTKNVCSCLNRNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSE 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E+ R  +R + V GW+  V+ +     EL ++R+ ++ RLCL G CSKNLVSSY YG+ V
Sbjct: 61  ER-RGLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
           +++ + V  L   G+  AVV E+  D A +E    + +V  + +L   W  + + +   G
Sbjct: 120 MKMIEEVEVLRYQGD-FAVVAERV-DAARVEERPTRPMVAMDPMLESAWNRLMEDEI--G 175

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
           I+GL+G+GGVGKTTLL  +NN F      FD+VIW  V      Q  QD+I +++  S++
Sbjct: 176 ILGLHGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLR-SDN 234

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
           +KWK+K+   KA +I ++L  K+F         ++DLTE+GVP      G KIV  TR  
Sbjct: 235 EKWKQKTEDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLK 294

Query: 285 GVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            +C +M    ++EV  LA D+AW LF + +   TL SH  IP +A T+A++C  LPLAL 
Sbjct: 295 EICGRMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALN 354

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
            +G  M  ++ V +   AI+ + +SA+ FSGME+ +   LK+SYD+L  ++L+ C  YC 
Sbjct: 355 VIGETMAYKRTVQEWRSAIDVLTSSAAEFSGMEDEILPILKYSYDNLKSEQLKLCFQYCA 414

Query: 404 LYPEDYKIPKRSLIDYWISEGFM-----ADFDRGCEFINDLLHACLLEEEGDDHVKMHDM 458
           L+PED+ I K  L+DYWI EGF+        ++G E I  L+ +CLL EE  + VKMHD+
Sbjct: 415 LFPEDHNIEKNDLVDYWIGEGFIDRNKGKAENQGYEIIGILVRSCLLMEENQETVKMHDV 474

Query: 459 IREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP---- 514
           +REM+LWIA    K+K+NF+V+AG++    P++++W+ A+R+SLM N IES+ + P    
Sbjct: 475 VREMALWIASDFGKQKENFIVQAGLQSRNIPEIEKWKVARRVSLMFNNIESIRDAPESPQ 534

Query: 515 -------------------------TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIR 549
                                     +L L  N  L  LP+ IS  VSL +L LS T IR
Sbjct: 535 LITLLLRKNFLGHISSSFFRLMPMLVVLDLSMNRDLRHLPNEISECVSLQYLSLSRTRIR 594

Query: 550 GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG 595
             P  L  L KL YLNLEYT  +  I    ISG   L+VLRL   G
Sbjct: 595 IWPAGLVELRKLLYLNLEYTRMVESICG--ISGLTSLKVLRLFVSG 638

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P60839|DRL2_ARATH Probable disease resistance protein At1g12290 OS=Arabidopsis thaliana GN=At1g12290 PE=2 SV=1

 Score =  414 bits (1063), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 307/895 (34%), Positives = 440/895 (49%), Gaps = 147/895 (16%)

Query: 1   MGNLISTSLPPDLFSRTLHRV-GEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MG  +S  +  D     L R    +  Y+  +K+NL  L+  M  L   RDDL+ KV+  
Sbjct: 1   MGGCVSVQVSCDQLLNHLGRCFCRKLYYIQNIKENLTSLEEAMEDLKALRDDLLRKVQTA 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E+    +R +++  WL+ V+ + ++F +L   R  E+ RLC  G+ S+NL  SY+YGR V
Sbjct: 61  EEGG-LQRLHQIKVWLKRVKTIESQFNDLDSSRTVELQRLCCCGVGSRNLRLSYDYGRRV 119

Query: 120 VELTDRVINLNKDG--EKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKN 177
             + + V +L   G  E++A     A      E PL+ TIVGQE +L + W  + D    
Sbjct: 120 FLMLNIVEDLKSKGIFEEVA---HPATRAVGEERPLQPTIVGQETILEKAWDHLMDDGTK 176

Query: 178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFS 231
             I+GLYG+GGVGKTTLL Q+NN FC      ++VIW  V         Q +IG++IGF 
Sbjct: 177 --IMGLYGMGGVGKTTLLTQINNRFCDTDDGVEIVIWVVVSGDLQIHKIQKEIGEKIGFI 234

Query: 232 EDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTR 282
              +W +KS   KAVDI + LS K+F         R++LTE+G+P      G KI   TR
Sbjct: 235 -GVEWNQKSENQKAVDILNFLSKKRFVLLLDDIWKRVELTEIGIPNPTSENGCKIAFTTR 293

Query: 283 SAGVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA 341
              VC  M   + +EV  L  D+AW LF++ +   TL SH  IPE+A  +A+ C  LPLA
Sbjct: 294 CQSVCASMGVHDPMEVRCLGADDAWDLFKKKVGDITLSSHPDIPEIARKVAQACCGLPLA 353

Query: 342 LKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLY 401
           L  +G  M  +K   + +RA++   T A+ F  ++E +   LK+SYD+L  + +++C LY
Sbjct: 354 LNVIGETMACKKTTQEWDRAVDVSTTYAANFGAVKERILPILKYSYDNLESESVKTCFLY 413

Query: 402 CCLYPEDYKIPKRSLIDYWISEGFM-------ADFDRGCEFINDLLHACLLEEEGD---- 450
           C L+PED  I K  LIDYWI EGF+            G E +  L+ A LL E G     
Sbjct: 414 CSLFPEDDLIEKERLIDYWICEGFIDGDENKKGAVGEGYEILGTLVCASLLVEGGKFNNK 473

Query: 451 DHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMAN---EI 507
            +VKMHD++REM+LWIA  + K K N +VRAG +L E PKVK+W+   R+SL+ N   EI
Sbjct: 474 SYVKMHDVVREMALWIASDLRKHKDNCIVRAGFRLNEIPKVKDWKVVSRMSLVNNRIKEI 533

Query: 508 ESLSEIPTL---------------------------LSLRRNDSLTELPSRISSLVSLHH 540
               E P L                           L L  N +L+ LP +IS LVSL +
Sbjct: 534 HGSPECPKLTTLFLQDNRHLVNISGEFFRSMPRLVVLDLSWNVNLSGLPDQISELVSLRY 593

Query: 541 LD---------------------------LSLTHIRGLPQELKALEKLRYLNLEYTHYLS 573
           LD                           L L  + G+   L  L+ +R LNL     +S
Sbjct: 594 LDLSYSSIGRLPVGLLKLKKLMHLNLESMLCLESVSGI-DHLSNLKTVRLLNLRMWLTIS 652

Query: 574 ---------------------------IIPHQLISGFLKLEV-------LRLLECGSEGV 599
                                      +  H+L+    K+ V       +R+L   S G 
Sbjct: 653 LLEELERLENLEVLTIEIISSSALEQLLCSHRLVRCLQKVSVKYLDEESVRILTLPSIGD 712

Query: 600 TKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKE 659
            +E     C      MR+++  +  ++ S  F +   V         DLTWL+F  NL  
Sbjct: 713 LREVFIGGCG-----MRDIIIERNTSLTSPCFPNLSKVLITGCNGLKDLTWLLFAPNLTH 767

Query: 660 LEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFP 719
           L +    ++EEII  +K    +  ++I+      F +LE L +   P+LKSIY NPL FP
Sbjct: 768 LNVWNSRQIEEIISQEK----ASTADIVP-----FRKLEYLHLWDLPELKSIYWNPLPFP 818

Query: 720 KLKKIGVYG-CPKLKKLPINSSS---AKERRVVIEGLKEWWEELQWEDQATQNAF 770
            L +I V   C KL KLP++S S   A E  V+  G +EW E ++WED+AT+  F
Sbjct: 819 CLNQINVQNKCRKLTKLPLDSQSCIVAGEELVIQYGDEEWKERVEWEDKATRLRF 873

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 =  412 bits (1060), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 313/901 (34%), Positives = 443/901 (49%), Gaps = 149/901 (16%)

Query: 1   MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEE 60
           MGN +   +  D     + R      Y+  L+KNL  L+ EM  L  T+ ++ NKV  EE
Sbjct: 1   MGNFVCIEISGDQMLDRIIRCLCGKGYIRNLEKNLRALQREMEDLRATQHEVQNKVAREE 60

Query: 61  QPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVV 120
             R  +R   V  WL+ V  +  E  +L  V   E+ +LCL GLCSK + SSY YG+ V 
Sbjct: 61  S-RHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVF 119

Query: 121 ELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGI 180
            L + V  L  +G     V +  P     E P + TI GQE++L + W  + +     GI
Sbjct: 120 LLLEEVTKLKSEG-NFDEVSQPPPRSEVEERPTQPTI-GQEEMLKKAWNRLMED--GVGI 175

Query: 181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGFSEDK 234
           +GL+G+GGVGKTTL K+++N F      FD+VIW      A +   Q+DI +++   +D 
Sbjct: 176 MGLHGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDL 235

Query: 235 KWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAG 285
            WK K+  DKA DI  +L  K+F         ++DL  +G+P        K+   TR   
Sbjct: 236 -WKNKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQK 294

Query: 286 VCDQM-DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT 344
           VC QM D K ++V  L  ++AW+LF+  +  +TL S   I  LA  +A++C  LPLAL  
Sbjct: 295 VCGQMGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSC 354

Query: 345 VGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCL 404
           +G  M S+  V + E AI+ +  SA+ FS M+  +   LK+SYDSL  + ++SC LYC L
Sbjct: 355 IGETMASKTMVQEWEHAIDVLTRSAAEFSDMQNKILPILKYSYDSLEDEHIKSCFLYCAL 414

Query: 405 YPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDD---HVK 454
           +PED KI  ++LI+ WI EGF+ +        ++G E +  L+ A LL  +      HV 
Sbjct: 415 FPEDDKIDTKTLINKWICEGFIGEDQVIKRARNKGYEMLGTLIRANLLTNDRGFVKWHVV 474

Query: 455 MHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL---- 510
           MHD++REM+LWIA    K+K+N++VRA V L E PKVK+W   +R+SLM NEIE +    
Sbjct: 475 MHDVVREMALWIASDFGKQKENYVVRARVGLHEIPKVKDWGAVRRMSLMMNEIEEITCES 534

Query: 511 --SEIPTL-----------------------LSLRRNDSLTELPSRISSLVSLHHLDLSL 545
             SE+ TL                       L L  N    ELP +IS LVSL +LDLS 
Sbjct: 535 KCSELTTLFLQSNQLKNLSGEFIRYMQKLVVLDLSHNPDFNELPEQISGLVSLQYLDLSW 594

Query: 546 THIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN 605
           T I  LP  LK L+KL +LNL +T  L       ISG  +L            ++  E N
Sbjct: 595 TRIEQLPVGLKELKKLIFLNLCFTERLCS-----ISGISRLLS-------LRWLSLRESN 642

Query: 606 VLCDDAEPLMRELLGLKRLNVLSWS--------------FRSSLAVQKFFKYPKLDLTWL 651
           V  D +  +++EL  L+ L  L  +                S L ++ F + P  DL++L
Sbjct: 643 VHGDAS--VLKELQQLENLQDLRITESAELISLDQRLAKLISVLRIEGFLQKP-FDLSFL 699

Query: 652 VFVQNLKELEI---------IVCTEME----------EIICVDKL--------------- 677
             ++NL  L +         I C E E          +I C   L               
Sbjct: 700 ASMENLYGLLVENSYFSEINIKCRESETESSYLHINPKIPCFTNLTGLIIMKCHSMKDLT 759

Query: 678 -------------RDVSDISEIIGSEHNF--------FTQLESLGILYG-PDLKSIYPNP 715
                        RD  ++ EII  E           F +LE L  LYG P L+SIY +P
Sbjct: 760 WILFAPNLVNLDIRDSREVGEIINKEKAINLTSIITPFQKLERL-FLYGLPKLESIYWSP 818

Query: 716 LHFPKLKKIGVYGCPKLKKLPINSSSAK--ERRVVIEGLKEWWEELQWEDQATQNAFSSG 773
           L FP L  I V  CPKL+KLP+N++S    E   +     E   EL+WED+ T+N F   
Sbjct: 819 LPFPLLSNIVVKYCPKLRKLPLNATSVPLVEEFEIRMDPPEQENELEWEDEDTKNRFLPS 878

Query: 774 V 774
           +
Sbjct: 879 I 879

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|O82484|DRL23_ARATH Putative disease resistance protein At4g10780 OS=Arabidopsis thaliana GN=At4g10780 PE=2 SV=1

 Score =  411 bits (1056), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 293/891 (32%), Positives = 446/891 (50%), Gaps = 131/891 (14%)

Query: 1   MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MG+ IS  +  D + +R         NY+  LK N+  L+  +  LT TRDD++ +V++E
Sbjct: 1   MGSCISLQISCDQVLTRAYSCFFSLGNYIHKLKDNIVALEKAIEDLTATRDDVLRRVQME 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E  +   R  +V  WL+ V+ +  +F +L   R  E+ RLC    CS NL SSY YG+ V
Sbjct: 61  E-GKGLERLQQVQVWLKRVEIIRNQFYDLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIEL-PLEQTIVGQEKLLPRVWRCITDQQKNR 178
             +   V NLN +G    +V   AP    +E+ P++ TI+G+E +  R W  + D     
Sbjct: 120 FLMIKEVENLNSNG-FFEIVAAPAP---KLEMRPIQPTIMGRETIFQRAWNRLMDD--GV 173

Query: 179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT------FQDDIGKRIGFSE 232
           G +GLYG+GGVGKTTLL Q++N     ++  D+VIW  V +       Q+DIG+++GF  
Sbjct: 174 GTMGLYGMGGVGKTTLLTQIHNTLHDTKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFI- 232

Query: 233 DKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRS 283
            K+W +K    KAVDI + LS K+F         ++DLT++G+P Q      K+V  TRS
Sbjct: 233 GKEWNKKQESQKAVDILNCLSKKRFVLLLDDIWKKVDLTKIGIPSQTRENKCKVVFTTRS 292

Query: 284 AGVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL 342
             VC +M   + +EV  L+ ++AW+LFQE + + +L SH  I ELA+ +A +C  LPLAL
Sbjct: 293 LDVCARMGVHDPMEVQCLSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLAL 352

Query: 343 KTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYC 402
             +G  M  ++ V +   A++ + + A+ FSGM++++ L LK+SYD+L+   +RSC  YC
Sbjct: 353 NVIGETMAGKRAVQEWHHAVDVLTSYAAEFSGMDDHILLILKYSYDNLNDKHVRSCFQYC 412

Query: 403 CLYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDD--HV 453
            LYPEDY I K  LIDYWI EGF+          ++G E +  L+ ACLL EEG +   V
Sbjct: 413 ALYPEDYSIKKYRLIDYWICEGFIDGNIGKERAVNQGYEILGTLVRACLLSEEGKNKLEV 472

Query: 454 KMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEI 513
           KMHD++REM+LW    + K K+  +V+AG  L + PKV++W   +R+SLM N IE +S  
Sbjct: 473 KMHDVVREMALWTLSDLGKNKERCIVQAGSGLRKVPKVEDWGAVRRLSLMNNGIEEISGS 532

Query: 514 P------------------------------TLLSLRRNDSLTELPSRISSLVSLH---- 539
           P                               +L L  N  L  LP +IS LV+L     
Sbjct: 533 PECPELTTLFLQENKSLVHISGEFFRHMRKLVVLDLSENHQLDGLPEQISELVALRYLDL 592

Query: 540 -------------------HLDLSLTHIRGLPQELKALEKLRYLNLEYTHYL-------- 572
                              HL+L      G    +  L  LR L L  ++ +        
Sbjct: 593 SHTNIEGLPACLQDLKTLIHLNLECMRRLGSIAGISKLSSLRTLGLRNSNIMLDVMSVKE 652

Query: 573 ----SIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLC--DDAE-------PLMRELL 619
                 +    I     + + ++++ G+     +E ++ C   D E       P M  L 
Sbjct: 653 LHLLEHLEILTIDIVSTMVLEQMIDAGTLMNCMQEVSIRCLIYDQEQDTKLRLPTMDSLR 712

Query: 620 GLKRLNV---------LSWSFRSSLAVQKFFKYPKL---------DLTWLVFVQNLKELE 661
            L   N          L+W+   +     FF   ++         DLTWL+F  N+  L 
Sbjct: 713 SLTMWNCEISEIEIERLTWNTNPTSPC--FFNLSQVIIHVCSSLKDLTWLLFAPNITYLM 770

Query: 662 IIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKL 721
           I    +++E+I   K   V++  +    +   F +L+ L +   P+LKSIY   L FP L
Sbjct: 771 IEQLEQLQELISHAKATGVTEEEQQQLHKIIPFQKLQILHLSSLPELKSIYWISLSFPCL 830

Query: 722 KKIGVYGCPKLKKLPINSSSAKERRVVIEGLK--EWWEELQWEDQATQNAF 770
             I V  CPKL+KLP++S +    +  +   K  EW E ++W+D+AT+  F
Sbjct: 831 SGIYVERCPKLRKLPLDSKTGTVGKKFVLQYKETEWIESVEWKDEATKLHF 881

Potential 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 =  411 bits (1056), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 243/604 (40%), Positives = 344/604 (56%), Gaps = 60/604 (9%)

Query: 24  QANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGT 83
              Y+  L KN+  +K +M  L + RDD+  +V++EE  RR  R ++V GWL +V  +  
Sbjct: 25  NVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLSQVQGWLTNVSTVEN 84

Query: 84  EFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKA 143
           +F EL      E+ RLCL G CSKN+  SY YG+ VV +   + +L+  G+    V    
Sbjct: 85  KFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESLSSQGD-FDTVTLAT 143

Query: 144 PDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFC 203
           P     E+P++ TIVGQE +L RVW  +T+      I+GLYG+GGVGKTTLL ++NN F 
Sbjct: 144 PIARIEEMPIQPTIVGQETMLERVWTRLTEDGDE--IVGLYGMGGVGKTTLLTRINNKFS 201

Query: 204 HQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF 257
            +   F VVIW  V         Q DIGKR+     ++W   +   +A+DI ++L  +KF
Sbjct: 202 EKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLG-GEEWDNVNENQRALDIYNVLGKQKF 260

Query: 258 ---------RIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKN-LEVYSLAHDEAWK 307
                    +++L  LGVP      G K+V  TRS  VC +M   + +EV  L  +EAW+
Sbjct: 261 VLLLDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGRMRVDDPMEVSCLEPNEAWE 320

Query: 308 LFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRT 367
           LFQ  +  +TL  H  IPELA  +A +C  LPLAL  +G  M  ++ V +   AI+ + +
Sbjct: 321 LFQMKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMACKRMVQEWRNAIDVLSS 380

Query: 368 SASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMA 427
            A+ F GME+ +   LK+SYD+L+ ++++ C LYC L+PEDY++ K  LIDYWI EGF+ 
Sbjct: 381 YAAEFPGMEQ-ILPILKYSYDNLNKEQVKPCFLYCSLFPEDYRMEKERLIDYWICEGFID 439

Query: 428 D-------FDRGCEFINDLLHACLLEEEG--DDHVKMHDMIREMSLWIAWTIEKEKKNFL 478
           +         +G E I  L+ ACLL EE    + VKMHD++REM+LWIA  + + K+  +
Sbjct: 440 ENESRERALSQGYEIIGILVRACLLLEEAINKEQVKMHDVVREMALWIASDLGEHKERCI 499

Query: 479 VRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP-----TLLSLRRNDSLT------- 526
           V+ GV L E PKVK W   +R+SLM NEIE LS  P     T L L++NDSL        
Sbjct: 500 VQVGVGLREVPKVKNWSSVRRMSLMENEIEILSGSPECLELTTLFLQKNDSLLHISDEFF 559

Query: 527 ------------------ELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEY 568
                             +LP++IS LVSL +LDLS T+I+ LP  L+ L+KLRYL L+Y
Sbjct: 560 RCIPMLVVLDLSGNSSLRKLPNQISKLVSLRYLDLSWTYIKRLPVGLQELKKLRYLRLDY 619

Query: 569 THYL 572
              L
Sbjct: 620 MKRL 623

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 =  408 bits (1048), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 308/888 (34%), Positives = 447/888 (50%), Gaps = 137/888 (15%)

Query: 1   MGNLISTSLPPDLFSRTLH-RVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MG+  S  +     +R  +  +G+  +Y+  L+KNL  L+ EM  L   + ++ NKV   
Sbjct: 1   MGSCFSLQVSDQTLNRIFNCLIGK--SYIRTLEKNLRALQREMEDLRAIQHEVQNKV-AR 57

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           ++ R  RR   V  WL+ V  +  E  +L  V   E+ +LCL GLCSK + SSY YG++V
Sbjct: 58  DEARHQRRLEAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKV 117

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
             L + V  LN +G     V +  P     E P + TI GQE +L + W  +   +   G
Sbjct: 118 FLLLEEVKKLNSEG-NFDEVSQPPPRSEVEERPTQPTI-GQEDMLEKAWNRL--MEDGVG 173

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT------FQDDIGKRIGFSED 233
           I+GL+G+GGVGKTTL K+++N F      FD+VIW  V         Q+DI +++   +D
Sbjct: 174 IMGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDD 233

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
             WK K+  DKA DI  +L  K+F         ++DL  +G+P        K+   TRS 
Sbjct: 234 L-WKNKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSR 292

Query: 285 GVCDQM-DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            VC +M D K ++V  L  ++AW+LF+  +  +TL S   I ELA  +A++C  LPLAL 
Sbjct: 293 EVCGEMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKCRGLPLALN 352

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
            +G  M S+  V + E AI    TSA+ FS M+  +   LK+SYDSL  + ++SC LYC 
Sbjct: 353 VIGETMSSKTMVQEWEHAIHVFNTSAAEFSDMQNKILPILKYSYDSLGDEHIKSCFLYCA 412

Query: 404 LYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDDHVKMH 456
           L+PED +I    LIDYWI EGF+ +        ++G   +  L  A LL + G  +  MH
Sbjct: 413 LFPEDGEIYNEKLIDYWICEGFIGEDQVIKRARNKGYAMLGTLTRANLLTKVGTYYCVMH 472

Query: 457 DMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL------ 510
           D++REM+LWIA    K+K+NF+V+AGV L E PKVK+W   +++SLM N+IE +      
Sbjct: 473 DVVREMALWIASDFGKQKENFVVQAGVGLHEIPKVKDWGAVRKMSLMDNDIEEITCESKC 532

Query: 511 SEIPTL-----------------------LSLRRNDSLTELPSRISSLVSLHHLDLSLTH 547
           SE+ TL                       L L  N    +LP +IS LVSL  LDLS T 
Sbjct: 533 SELTTLFLQSNKLKNLPGAFIRYMQKLVVLDLSYNRDFNKLPEQISGLVSLQFLDLSNTS 592

Query: 548 IRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL 607
           I  +P  LK L+KL +L+L YT  L       ISG  +L  LRLL      V   + +VL
Sbjct: 593 IEHMPIGLKELKKLTFLDLTYTDRLCS-----ISGISRLLSLRLLRLLGSKV-HGDASVL 646

Query: 608 ---------CDDAEPLMRELLGL-KRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNL 657
                     + A  +  EL+ L +RL  L     S+L ++ F + P  DL++L  ++NL
Sbjct: 647 KELQQLQNLQELAITVSAELISLDQRLAKLI----SNLCIEGFLQKP-FDLSFLASMENL 701

Query: 658 KE-------------------------------------LEIIVCTEMEEI--------I 672
                                                  LEI+ C  M+++        +
Sbjct: 702 SSLRVENSYFSEIKCRESETESSYLRINPKIPCFTNLSRLEIMKCHSMKDLTWILFAPNL 761

Query: 673 CVDKLRDVSDISEIIGSEH-------NFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIG 725
            V  + D  ++ EII  E          F +LE L +   P L+SIY +PL FP L  + 
Sbjct: 762 VVLLIEDSREVGEIINKEKATNLTSITPFLKLEWLILYNLPKLESIYWSPLPFPVLLTMD 821

Query: 726 VYGCPKLKKLPINSSS---AKERRVVIEGLKEWWEELQWEDQATQNAF 770
           V  CPKL+KLP+N++S    +E  + +    E   EL+WED  T+N F
Sbjct: 822 VSNCPKLRKLPLNATSVSKVEEFEIHMYPPPEQENELEWEDDDTKNRF 869

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 =  408 bits (1048), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 303/867 (34%), Positives = 439/867 (50%), Gaps = 138/867 (15%)

Query: 26  NYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEF 85
           +Y+  L+KNL  L+ EM  L  T+ ++ NKV  EE  R  +R   V  WL+ V  +  E 
Sbjct: 27  SYIRTLEKNLRALQREMEDLRATQHEVQNKVAREES-RHQQRLEAVQVWLDRVNSIDIEC 85

Query: 86  TELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPD 145
            +L  V   E+ +LCL GLC+K + SSY YG++V  L + V  L  +G     V +  P 
Sbjct: 86  KDLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFLLLEEVKILKSEG-NFDEVSQPPPR 144

Query: 146 GAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ 205
               E P + TI GQE++L + W  +   +   GI+GL+G+GGVGKTTL K+++N F   
Sbjct: 145 SEVEERPTQPTI-GQEEMLEKAWNRL--MEDGVGIMGLHGMGGVGKTTLFKKIHNKFAEI 201

Query: 206 QHNFDVVIW------AAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF-- 257
              FD+VIW      A +   Q+DI +++   +D  WK K+  DKA DI  +L  K+F  
Sbjct: 202 GGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDL-WKNKNESDKATDIHRVLKGKRFVL 260

Query: 258 -------RIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQM-DSKNLEVYSLAHDEAWKLF 309
                  ++DL  +G+P        K+   TRS  VC +M D K ++V  L  ++AW+LF
Sbjct: 261 MLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRSREVCGEMGDHKPMQVNCLEPEDAWELF 320

Query: 310 QEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSA 369
           +  +  +TL S   I  LA  +A++C  LPLAL  +G  M S+  V + E AI+ +  SA
Sbjct: 321 KNKVGDNTLSSDPVIVGLAREVAQKCRGLPLALNVIGETMASKTMVQEWEYAIDVLTRSA 380

Query: 370 STFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMAD- 428
           + FSGME  +   LK+SYDSL  + ++SC LYC L+PED +I   +LID  I EGF+ + 
Sbjct: 381 AEFSGMENKILPILKYSYDSLGDEHIKSCFLYCALFPEDGQIYTETLIDKLICEGFIGED 440

Query: 429 ------FDRGCEFINDLLHACLLEEEGDD-----------HVKMHDMIREMSLWIAWTIE 471
                  ++G   +  L  A LL + G +           H  MHD++REM+LWIA    
Sbjct: 441 QVIKRARNKGYAMLGTLTRANLLTKVGTELANLLTKVSIYHCVMHDVVREMALWIASDFG 500

Query: 472 KEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL------SEIPTL--------- 516
           K+K+NF+V+A   L E P+VK+W   +R+SLM NEIE +      SE+ TL         
Sbjct: 501 KQKENFVVQASAGLHEIPEVKDWGAVRRMSLMRNEIEEITCESKCSELTTLFLQSNQLKN 560

Query: 517 --------------LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLR 562
                         L L  N    ELP +IS LVSL +LDLS T I  LP  LK L+KL 
Sbjct: 561 LSGEFIRYMQKLVVLDLSDNRDFNELPEQISGLVSLQYLDLSFTRIEQLPVGLKELKKLT 620

Query: 563 YLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC-GSEGVTKEEGNV--LCDDAEPLMRELL 619
           +L+L YT  L  I        L++  L   +  G   V KE   +  L D A  L  EL+
Sbjct: 621 FLDLAYTARLCSISGISRLLSLRVLSLLGSKVHGDASVLKELQQLENLQDLAITLSAELI 680

Query: 620 GL-KRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKE------------------- 659
            L +RL        S L ++ F + P  DL++L  ++NL                     
Sbjct: 681 SLDQRLA----KVISILGIEGFLQKP-FDLSFLASMENLSSLWVKNSYFSEIKCRESETD 735

Query: 660 ------------------LEIIVCTEMEEI--------ICVDKLRDVSDISEIIGSEH-- 691
                             L+I+ C  M+++        + V  + D  ++ EII  E   
Sbjct: 736 SSYLHINPKIPCFTNLSRLDIVKCHSMKDLTWILFAPNLVVLFIEDSREVGEIINKEKAT 795

Query: 692 -----NFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA---K 743
                  F +LE L + Y P L+SIY +PL FP L  I V  CPKL+KLP+N++SA   +
Sbjct: 796 NLTSITPFLKLERLILCYLPKLESIYWSPLPFPLLLNIDVEECPKLRKLPLNATSAPKVE 855

Query: 744 ERRVVIEGLKEWWEELQWEDQATQNAF 770
           E R+++     +  EL+WED+ T+N F
Sbjct: 856 EFRILM-----YPPELEWEDEDTKNRF 877

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L3R3|RFL1_ARATH Disease resistance protein RFL1 OS=Arabidopsis thaliana GN=RFL1 PE=3 SV=2

 Score =  394 bits (1011), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 263/705 (37%), Positives = 369/705 (52%), Gaps = 82/705 (11%)

Query: 1   MGNLISTSLPPD----LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKV 56
           MG  +S SL  D     FS+ L   G   +Y+  L +NL  L+  M  L   RDD+  ++
Sbjct: 1   MGGCVSVSLSCDREVNQFSQWLCVSG---SYIQNLSENLASLQKAMGVLNAKRDDVQGRI 57

Query: 57  EVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYG 116
             EE     RR  +V  WL  +Q +  +F +L      E+ RLCL G CSKN+  SY YG
Sbjct: 58  NREEFTGHRRRLAQVQVWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYG 117

Query: 117 REVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQK 176
           + V+ L   V  L+  G    +V E AP     ELP++ TIVGQ+ +L +VW C+ + + 
Sbjct: 118 KRVIVLLREVEGLSSQG-VFDIVTEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKV 176

Query: 177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGF 230
              I+GLYG+GGVGKTTLL Q+NN F      FDVVIW      A V   Q  IG+++G 
Sbjct: 177 --WIVGLYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGL 234

Query: 231 SEDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKT 281
              K W EK+   +A+DI ++L  KKF         +++L  +GVP      G K+   T
Sbjct: 235 V-GKNWDEKNKNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTT 293

Query: 282 RSAGVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL 340
            S  VC +M   N +E+  L    AW L ++ +  +TL SH  IP+LA  ++ +C  LPL
Sbjct: 294 HSKEVCGRMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPL 353

Query: 341 ALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLL 400
           AL  +G  M  ++ + +   A E + TSA+ FSGME+ +   LK+SYDSL+ +  +SC L
Sbjct: 354 ALNVIGETMSFKRTIQEWRHATEVL-TSATDFSGMEDEILPILKYSYDSLNGEDAKSCFL 412

Query: 401 YCCLYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDDH- 452
           YC L+PED++I K  LI+YWI EGF+ +       F++G + +  L+ + LL E   D  
Sbjct: 413 YCSLFPEDFEIRKEMLIEYWICEGFIKEKQGREKAFNQGYDILGTLVRSSLLLEGAKDKD 472

Query: 453 -VKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLS 511
            V MHDM+REM+LWI   + K K+  +V+AG+ L E P+V+ W   KR+SLM N  E + 
Sbjct: 473 VVSMHDMVREMALWIFSDLGKHKERCIVQAGIGLDELPEVENWRAVKRMSLMNNNFEKIL 532

Query: 512 EIP------------------------------TLLSLRRNDSLTELPSRISSLVSLHHL 541
             P                               +L L  N SL+ELP  IS LVSL +L
Sbjct: 533 GSPECVELITLFLQNNYKLVDISMEFFRCMPSLAVLDLSENHSLSELPEEISELVSLQYL 592

Query: 542 DLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTK 601
           DLS T+I  LP  L  L KL +L LE T  L     + ISG   L  LR L       T 
Sbjct: 593 DLSGTYIERLPHGLHELRKLVHLKLERTRRL-----ESISGISYLSSLRTLRLRDSKTTL 647

Query: 602 EEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL 646
           + G         LM+EL  L+ L +++    S L V + F YP++
Sbjct: 648 DTG---------LMKELQLLEHLELITTDISSGL-VGELFCYPRV 682

Disease resistance (R) protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SI85|DRL14_ARATH Probable disease resistance protein At1g62630 OS=Arabidopsis thaliana GN=At1g62630 PE=3 SV=2

 Score =  377 bits (967), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 294/887 (33%), Positives = 433/887 (48%), Gaps = 134/887 (15%)

Query: 5   ISTSLPPDLFSRTLHRVGE----QANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEE 60
           IS S+P   F   +++V +    + +Y   L+KNL  L+T M +L   RDDL+ +++ EE
Sbjct: 3   ISFSIP---FDPCVNKVSQWLDMKGSYTHNLEKNLVALETTMEELKAKRDDLLRRLKREE 59

Query: 61  QPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVV 120
             R  +R +    WL  V  +      L + R  E+ RLCL   CSKNL +SY YG+ V 
Sbjct: 60  D-RGLQRLSEFQVWLNRVATVEDIIITLLRDRDVEIQRLCLCRFCSKNLTTSYRYGKSVF 118

Query: 121 ELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGI 180
                V  L   GE   V+ E+A   A  E PL+ TIVGQ+K+L + W+ + +       
Sbjct: 119 LRLREVEKLK--GEVFGVITEQASTSAFEERPLQPTIVGQKKMLDKAWKHLMEDGTGIMG 176

Query: 181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDK 234
           +   G   VGKTTLL Q+ N F   +  FD+ IW  V      +  QD+I +++G     
Sbjct: 177 MYGMGG--VGKTTLLTQLFNMFNKDKCGFDIGIWVVVSQEVNVEKIQDEIAQKLGLG-GH 233

Query: 235 KWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAG 285
           +W ++ +  K V + + L  KKF         +++L  +GVP      G K+   +RS  
Sbjct: 234 EWTQRDISQKGVHLFNFLKNKKFVLFLDDLWDKVELANIGVPDPRTQKGCKLAFTSRSLN 293

Query: 286 VCDQM-DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT 344
           VC  M D + +EV  L  + A+ LFQ+ + + TL S   IP+LA  +A++C  LPLAL  
Sbjct: 294 VCTSMGDEEPMEVQCLEENVAFDLFQKKVGQKTLGSDPGIPQLARIVAKKCCGLPLALNV 353

Query: 345 VGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCL 404
           +G  M  ++ + +   AI  + + A+ F GME+ +   LK+SYD+L  + ++S LLYC L
Sbjct: 354 IGETMSCKRTIQEWRNAIHVLNSYAAEFIGMEDKILPLLKYSYDNLKGEHVKSSLLYCAL 413

Query: 405 YPEDYKIPKRSLIDYWI-------SEGFMADFDRGCEFINDLLHACLLEE----EGDDHV 453
           YPED KI K  LI++WI       SEG     D+G + I  L+ A LL E    +G   V
Sbjct: 414 YPEDAKIRKEDLIEHWICEEIIDGSEGIEKAEDKGYDIIGSLVRASLLMECVDLKGKSSV 473

Query: 454 KMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL--- 510
            MHD++REM+LWIA  +  +K+ F+VRAGV + E PKVK W   +R+SLM N+I  L   
Sbjct: 474 IMHDVVREMALWIASELGIQKEAFIVRAGVGVREIPKVKNWNVVRRMSLMGNKIHHLVGS 533

Query: 511 ----------------------SEIPTL-------------LSLRRNDSLTELPSRISSL 535
                                 SEI T+             L L  N SL ELP  IS+L
Sbjct: 534 YECMELTTLLLGEGEYGSIWRWSEIKTISSEFFNCMPKLAVLDLSHNQSLFELPEEISNL 593

Query: 536 VSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL---- 591
           VSL +L+LS T IR L + ++ L+K+ +LNLE+T  L  I    IS    L+VL+L    
Sbjct: 594 VSLKYLNLSHTGIRHLSKGIQELKKIIHLNLEHTSKLESIDG--ISSLHNLKVLKLYGSR 651

Query: 592 ----LECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD 647
               L    E  T E   +L    +P  ++ L   RL  +S S    +     F   +  
Sbjct: 652 LPWDLNTVKELETLEHLEILTTTIDPRAKQFLSSHRL--MSRSRLLQIFGSNIFSPDRQL 709

Query: 648 LTWLVFVQNLKELEIIVCT---------------------------EMEEIICVDKLR-- 678
            +  V    L+E EI+ C+                           E+  +I   KLR  
Sbjct: 710 ESLSVSTDKLREFEIMCCSISEIKMGGICNFLSLVDVTIYNCEGLRELTFLIFAPKLRSL 769

Query: 679 ---DVSDISEIIGSEHNF---------FTQLESLGILYGPDLKSIYPNPLHFPKLKKIGV 726
              D  D+ +II  E            F +L+ L +   P LK+IY  PL F  L+KI +
Sbjct: 770 SVVDAKDLEDIINEEKACEGEDSGIVPFPELKYLNLDDLPKLKNIYRRPLPFLCLEKITI 829

Query: 727 YGCPKLKKLPINSSSAKERR---VVIEGLKEWWEELQWEDQATQNAF 770
             CP L+KLP++S S K+     ++      W + ++W D+AT+  F
Sbjct: 830 GECPNLRKLPLDSRSGKQGENGCIIHYKDSRWLKGVKWADEATKKRF 876

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	779
24461866	890	NBS-LRR type disease resistance protein	0.975	0.853	0.414	1e-170
24461864	899	NBS-LRR type disease resistance protein	0.976	0.846	0.403	1e-158
24461861	890	NBS-LRR type disease resistance protein	0.982	0.859	0.405	1e-152
24461865	892	NBS-LRR type disease resistance protein	0.982	0.857	0.398	1e-150
24461863	889	NBS-LRR type disease resistance protein	0.965	0.845	0.395	1e-147
224055915	880	cc-nbs-lrr resistance protein [Populus t	0.879	0.778	0.405	1e-142
225443158	903	PREDICTED: probable disease resistance p	0.966	0.833	0.376	1e-141
255553103	910	Disease resistance protein RPS5, putativ	0.970	0.830	0.374	1e-139
224122896	820	cc-nbs-lrr resistance protein [Populus t	0.894	0.85	0.383	1e-134
147852651	882	hypothetical protein VITISV_017542 [Viti	0.964	0.851	0.385	1e-133

>gi|24461866|gb|AAN62353.1|AF506028_20 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  604 bits (1557), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 371/894 (41%), Positives = 508/894 (56%), Gaps = 134/894 (14%)

Query: 1   MGNLISTSLP-PDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MGN+    +P  ++F R L  +  +A Y+  L+ NL+ L+T++ +L   +DD++N+VE+ 
Sbjct: 1   MGNVFGVQIPWSNIFPRCLDWILNEAKYISQLEDNLDDLQTKLEQLIEAKDDVMNRVEIA 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E+ ++  R N+V GW+  V+ +  E  +L +V +QE++RLCL G CSKN  SSY++G++V
Sbjct: 61  ER-QQMSRLNQVQGWVSRVEAVKAEADQLIRVGSQEIERLCLWGYCSKNCKSSYDFGKKV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
            +    V  L  +G    VV EK P  AA E P E T++G +  L +VWRC+ ++    G
Sbjct: 120 TKKLQLVETLMGEG-IFEVVAEKVPGAAATERPTEPTVIGLQSQLEQVWRCLVEEPA--G 176

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
           I+GLYG+GGVGKTTLL  +NN F     NF+ VIW  V      +  Q+ IG++IG   D
Sbjct: 177 IVGLYGMGGVGKTTLLTHINNKFLESTTNFNYVIWVVVSKDLRLENIQETIGEKIGLLND 236

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGF-KIVLKTRS 283
             WK + ++ KA+DI  IL  KKF         R+DL E+GVPL    +   K+V  +RS
Sbjct: 237 T-WKNRRIEQKALDIFKILKEKKFVLLLDDLWQRVDLVEVGVPLPGPQSSTSKVVFTSRS 295

Query: 284 AGVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL 342
             VC  M++ K  +V  L+  +AW+LFQ+ +   TL S   I +LA+T A+ECG LPLAL
Sbjct: 296 EEVCGLMEAHKKFKVACLSDIDAWELFQQKVGEETLKS-PDIRQLAQTAAKECGGLPLAL 354

Query: 343 KTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYC 402
            T+GRAM  +K   +   AIE +RTS+S F G+   V+  LKFSYDSL  D +RSCLLYC
Sbjct: 355 ITIGRAMACKKTPEEWTYAIEVLRTSSSQFPGLGNEVYPLLKFSYDSLPSDTIRSCLLYC 414

Query: 403 CLYPEDYKIPKRSLIDYWISEGFMADFDR------GCEFINDLLHACLLEEEGDDHVKMH 456
           CLYPEDY I K  LID WI EGF+ + DR      G   +  LLHACLLEE GD  VKMH
Sbjct: 415 CLYPEDYCISKEILIDCWIGEGFLTERDRFGEQNQGYHILGILLHACLLEEGGDGEVKMH 474

Query: 457 DMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEI--- 513
           D++R+M+LWIA  IEKEK NFLV AGV L EAP V  WE A+R+SLM N+I +LSE+   
Sbjct: 475 DVVRDMALWIACAIEKEKDNFLVYAGVGLIEAPDVSGWEKARRLSLMHNQITNLSEVATC 534

Query: 514 PTLLSLRRND-------------------------SLTELPSRISSLVSLHHLDLSLTHI 548
           P LL+L  N+                         SLT LP  IS LVSL HLDLS + I
Sbjct: 535 PHLLTLFLNENELQMIHNDFFRFMPSLKVLNLADSSLTNLPEGISKLVSLQHLDLSKSSI 594

Query: 549 RGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTK-EEGNVL 607
             LP ELKAL  L+ LNLEYT  L+ IP QLIS   +L VLR+         +  E ++L
Sbjct: 595 EELPLELKALVNLKCLNLEYTWSLTTIPRQLISNLSRLHVLRMFAASHSAFDRASEDSIL 654

Query: 608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL--------------------- 646
               E ++ ELLGLK L V+S++ RSS  +Q F    KL                     
Sbjct: 655 FGGGELIVEELLGLKYLEVISFTLRSSHGLQSFLSSHKLRSCTRALLLQCFNDSTSLEVS 714

Query: 647 ---DLT-----WLV------------------FV-QNLKELEIIVCTE------------ 667
              DL      W+                   FV  +LK++EI+ C++            
Sbjct: 715 ALADLKQLNRLWITECKKLEELKMDYTREVQQFVFHSLKKVEILACSKLKDLTFLVFAPN 774

Query: 668 -----------MEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPL 716
                      MEE++ + K  +V ++     +  N F +L++L +    +LKSIY  PL
Sbjct: 775 LESIELMGCPAMEEMVSMGKFAEVPEVV----ANLNPFAKLQNLKLFGATNLKSIYWKPL 830

Query: 717 HFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAF 770
            FP LK +    C KLKKLP++S+SA+ER +VI G + WWE+L+W D+AT+NAF
Sbjct: 831 PFPHLKSMSFSHCYKLKKLPLDSNSARERNIVISGTRRWWEQLEWVDEATRNAF 884

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461864|gb|AAN62351.1|AF506028_18 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  564 bits (1453), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 363/900 (40%), Positives = 494/900 (54%), Gaps = 139/900 (15%)

Query: 1   MGNLISTSLPPD--LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEV 58
           MGN++  S+  D   F+R L     +A YV  L+KN+E LK E+ KL   +DD++ +V  
Sbjct: 1   MGNILQISISCDGTCFNRCLDCFLGKAAYVRNLQKNVEALKNELPKLIAKKDDVMARVVN 60

Query: 59  EEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGRE 118
            E+ +   R N V  WL  V  +     EL ++ +QE+++LCLGG CSKN  SS  +G++
Sbjct: 61  AERQQMMTRLNEVQLWLSRVDAVTAGADELIRIGSQEIEKLCLGGYCSKNCKSSKKFGKQ 120

Query: 119 VVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNR 178
           V +    V  L  +G   AVV ++AP+  A E P+E   VG +  L +VWRC+ ++    
Sbjct: 121 VDKKLSDVKILLAEG-SFAVVAQRAPESVADERPIEPA-VGIQSQLEQVWRCLVEEPV-- 176

Query: 179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAV------QTFQDDIGKRIGFS 231
           GI+GLYG+GGVGKTTLL  +NN F  Q+  +FD +IW  V      +  Q+ IGK++G  
Sbjct: 177 GIVGLYGMGGVGKTTLLTHLNNKFLGQRDFHFDFLIWVVVSKDLQIEKIQEIIGKKVGLF 236

Query: 232 EDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLN-AGFKIVLKT 281
            D  W +K+L ++AVDI ++L  KKF         R+D   +GVP+   + +  K+V  T
Sbjct: 237 NDS-WMKKNLAERAVDIYNVLKEKKFVLLLDDVWQRVDFATVGVPIPPRDKSASKVVFTT 295

Query: 282 RSAGVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL 340
           RS  VC +M + K +EV  L+ ++AW+LF++ +   TL+    I ELAE +A+ECG LPL
Sbjct: 296 RSTEVCGRMGAHKKIEVECLSANDAWELFRQNVGEETLNGQPKILELAERVAKECGCLPL 355

Query: 341 ALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLL 400
           AL   GRAM  +K   +   AI+ ++TSAS F G+E NV   LKFSYDSL  D  RSCLL
Sbjct: 356 ALIVTGRAMACKKTPAEWRDAIKVLQTSASEFPGLENNVLRVLKFSYDSLPDDTTRSCLL 415

Query: 401 YCCLYPEDYKIPKRSLIDYWISEGFMADF------DRGCEFINDLLHACLLEEEGDDHVK 454
           YCCL+PEDY+I K +LID WI EGF+         DRG   + +++HACLLEEEGDD VK
Sbjct: 416 YCCLFPEDYRIYKENLIDCWIGEGFLKVTGKYELQDRGHTILGNIVHACLLEEEGDDVVK 475

Query: 455 MHDMIREMSLWIAW------TIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIE 508
           MHD+IR+M+LWIA         EK+K+N+LV  G  LTEAP V+EWE AKR+SLM  +I 
Sbjct: 476 MHDVIRDMTLWIACDTEKTEDTEKKKENYLVYEGAGLTEAPNVREWENAKRLSLMETQIR 535

Query: 509 SLSEIPT------------------------------LLSLRRNDSLTELPSRISSLVSL 538
           +LSE+PT                              +L+L     ++  P  +S LVSL
Sbjct: 536 NLSEVPTCLHLLTLFLVFNEELEMITGDFFKSMPCLKVLNLSGARRMSSFPLGVSVLVSL 595

Query: 539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG 598
            HLDLS T I+ LP+EL ALE L+ LNL+ THYL  IP QLIS F  L VLR+   G   
Sbjct: 596 QHLDLSGTAIQELPKELNALENLKSLNLDQTHYLITIPRQLISRFSCLVVLRMFGVGDWS 655

Query: 599 VT-KEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS------------------LAVQK 639
              K   + L    + L+  L GLK L VLS +  +S                  L +  
Sbjct: 656 PNGKRNDSDLFSGGDLLVEALRGLKHLEVLSLTLNNSQDLQCVLNSEKLRSCTQALYLHS 715

Query: 640 FFKYPKLDLTWLVFVQNLKELEIIVCTE-------------------------------- 667
           F +   LD++ L  +++L  L I  C E                                
Sbjct: 716 FKRSEPLDVSALAGLEHLNRLWIHECEELEELKMARQPFVFQSLEKIQIYGCHRLKNLTF 775

Query: 668 -----------------MEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS 710
                            MEEII   K  D  ++  II      F QL SL +     LKS
Sbjct: 776 LLFAPNLKSIEVSSCFAMEEIISEVKFADFPEVMPIIKP----FAQLYSLRLGGLTVLKS 831

Query: 711 IYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAF 770
           IY  PL FP L+ + V  C +L+KLP++S+SAKER++VI G  +WWE+LQWEDQ TQNAF
Sbjct: 832 IYKRPLPFPCLRDLTVNSCDELRKLPLDSNSAKERKIVIRGYTKWWEQLQWEDQDTQNAF 891

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461861|gb|AAN62348.1|AF506028_15 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  544 bits (1402), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 361/891 (40%), Positives = 494/891 (55%), Gaps = 126/891 (14%)

Query: 1   MGNLISTSLPPD--LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEV 58
           MGN+   S+  D   F+R L     +A Y+  L+ NL  L TE+RKL   ++DL+ +V  
Sbjct: 1   MGNICQISISCDGAFFNRCLDCFLGKAAYISNLQDNLVALDTELRKLIAAKNDLMRRVND 60

Query: 59  EEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGRE 118
            E+ ++ RR ++V  W+  V+ + TE         QE+++LCLGG CSKN  SSY +G++
Sbjct: 61  AER-QQMRRLDQVQVWVSRVETVETEADAFIGDGTQEIEKLCLGGYCSKNCKSSYKFGKQ 119

Query: 119 VVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNR 178
           V      +  L  +G    VV +K P+ A  E P E T+VG +  L  VWRC+ ++    
Sbjct: 120 VARKLRDIKTLMGEG-VFEVVADKVPEPAVDERPTEPTVVGLQSQLEEVWRCLVEEPV-- 176

Query: 179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSE 232
           GI+GLYG+GGVGKTTLL  +NN F     NFD+VI   V      ++ Q+ IG++IG   
Sbjct: 177 GIVGLYGMGGVGKTTLLTHINNKFLGSPTNFDLVILVVVSKDLRLESIQEVIGEKIGLLN 236

Query: 233 DKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPL-QMLNAGFKIVLKTR 282
           D  WK + ++ KA+DI  IL  K F         R+DL ++G+PL     +  K+V  TR
Sbjct: 237 DA-WKSRRIEQKALDIFRILRGKNFVVLLDDIWQRVDLAKVGIPLPNSQTSASKVVFTTR 295

Query: 283 SAGVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA 341
           S  VC  M++ K  +V  L+ ++AW+LF++ +   TL+ H  I ELA+T+ +ECG LPLA
Sbjct: 296 SEEVCGLMEAHKKFKVECLSGNDAWELFRQKVGEETLNCHHDILELAQTVTKECGGLPLA 355

Query: 342 LKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLY 401
           L T+GRAM  +K   +   AI+ +RTS+S F G+   V+  LKFSYD+L  D +RSCLLY
Sbjct: 356 LITIGRAMACKKTPEEWSYAIQVLRTSSSQFPGLGNEVYPLLKFSYDNLPNDTIRSCLLY 415

Query: 402 CCLYPEDYKIPKRSLIDYWISEGF------MADFDRGCEFINDLLHACLLEEEGDDHVKM 455
           CCLYPED  I K +L+D WI EG       +   ++G   +  L+H+CLLEE  +D VKM
Sbjct: 416 CCLYPEDCCISKENLVDCWIGEGLLNGSVTLGSHEQGYHVVGILVHSCLLEEVDEDEVKM 475

Query: 456 HDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT 515
           HD+IR+M+LW+A   EKEK+N+LV AG  L EAP V EWE  +R+SLM N+IE+LSE+PT
Sbjct: 476 HDVIRDMALWLACDAEKEKENYLVYAGAGLREAPDVIEWEKLRRLSLMENQIENLSEVPT 535

Query: 516 ------------------------------LLSLRRNDSLTELPSRISSLVSLHHLDLSL 545
                                         +L+L R   L  LP  IS LVSL +LDLS 
Sbjct: 536 CPHLLTLFLNSDDILWRINSDFLQSMLRLKVLNLSRYMGLLVLPLGISKLVSLEYLDLST 595

Query: 546 THIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG--SEGVTKEE 603
           + I  +P+ELKAL  L+ LNLEYT  L  IP QLIS F +L VLR+      S G    E
Sbjct: 596 SLISEIPEELKALVNLKCLNLEYTGRLLKIPLQLISNFSRLHVLRMFGNAYFSYGNYPIE 655

Query: 604 GNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL----------------- 646
            +VL    E L+ ELLGLK L VLS +  SS A+Q F     L                 
Sbjct: 656 -SVLFGGGELLVEELLGLKHLEVLSLTLGSSRALQSFLTSHMLRSCTRAMLLQDFQGSTS 714

Query: 647 -DLTWLVFVQNLKELEIIVCTEMEEI----------------------ICVDKLRDVS-- 681
            D++ L  ++ LK L I  C E+ E+                       C  KL+D++  
Sbjct: 715 VDVSGLADLKRLKRLRISDCYELVELKIDYAGEVQRYGFHSLQSFEVNYC-SKLKDLTLL 773

Query: 682 ---------------DISEII-----GSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKL 721
                           + EII         N F +L+ LGI   P+LKSIY  PL FP L
Sbjct: 774 VLIPNLKSIEVTDCEAMEEIISVGEFAGNPNAFAKLQYLGIGNLPNLKSIYWKPLPFPCL 833

Query: 722 KKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFSS 772
           +++ V  C +LKKLP++S+SAKE ++VI G   WW  LQWED+ATQNAF S
Sbjct: 834 EELTVSDCYELKKLPLDSNSAKEHKIVIRGAANWWRNLQWEDEATQNAFLS 884

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461865|gb|AAN62352.1|AF506028_19 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  540 bits (1390), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 355/890 (39%), Positives = 484/890 (54%), Gaps = 125/890 (14%)

Query: 1   MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEE 60
           MGN+   +    LF+R L     +A Y+  LK+NL  L+TE+ KL   ++D++ +V   E
Sbjct: 1   MGNIFQITCDGALFNRCLDCFLGKAAYIKNLKQNLADLETELGKLIDAKEDVMRRVNTAE 60

Query: 61  QPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVV 120
           +    +R N+V GWL  V+   ++  +L    +QE+ +LCLGG CSKN  SSY +G++V 
Sbjct: 61  RHPMMKRLNKVQGWLSRVEAAKSDGDKLITCGSQEIKKLCLGGYCSKNCKSSYEFGKQVA 120

Query: 121 ELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGI 180
                V  L    E    V E+ P  A  E P E T+VG +    +V  C+  ++++  I
Sbjct: 121 RKLGDVKTL-MAEEAFEAVAEEVPQPAVDERPTEPTVVGLQSQFEQVCNCL--EEESARI 177

Query: 181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA------VQTFQDDIGKRIGFSEDK 234
           +GLYG+GGVGKTTLL  ++N F     NF+ VIW        ++  Q+ IG++IG   D 
Sbjct: 178 VGLYGMGGVGKTTLLTHIHNKFIQSPTNFNYVIWVVASKDLRLENIQETIGEQIGLLNDT 237

Query: 235 KWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQ-MLNAGFKIVLKTRSA 284
            WK K ++ KA DI  IL  KKF         R+DLT++GVPL    N   K+V  TRS 
Sbjct: 238 -WKNKRIEQKAQDIFRILKQKKFLLLLDDLWQRVDLTKVGVPLPGPQNNASKVVFTTRSE 296

Query: 285 GVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            VC  M +    +V  L++ +AW+LF++ +   T++SH  I +LA+T ARECG LPLAL 
Sbjct: 297 EVCGLMGAHTRFKVACLSNIDAWELFRQNVGEETMNSHPDILQLAQTAARECGGLPLALI 356

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
           T+GRAM  +K   +   AIE +RTS+S F G+   V+  LKFSYDSL  D +RSC LYC 
Sbjct: 357 TIGRAMACKKTPEEWSYAIEVLRTSSSQFPGLGNEVYPLLKFSYDSLPSDTIRSCHLYCS 416

Query: 404 LYPEDYKIPKRSLIDYWISEGFMADFDR------GCEFINDLLHACLLEEEGDDHVKMHD 457
           LYPEDY I K  LID WI E  + + DR      G   +  LLHACLLEE GD  VKMHD
Sbjct: 417 LYPEDYCISKEKLIDCWIGERLLTERDRTGEQKEGYHILGILLHACLLEEGGDGEVKMHD 476

Query: 458 MIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-- 515
           +IR+M+LWIA  IE+EK+NF V AGV L EAP V+ WE A+R+SLM N+I +LSEIPT  
Sbjct: 477 VIRDMALWIACDIEREKENFFVYAGVGLVEAPDVRGWEKARRLSLMQNQIRNLSEIPTCP 536

Query: 516 ---------------------------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHI 548
                                      +L+L   + LT+LP  IS LVSL HLDLS + I
Sbjct: 537 HLLTLLLNENNLRKIQNYFFQFMPSLKVLNLSHCE-LTKLPVGISELVSLQHLDLSESDI 595

Query: 549 RGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTK-EEGNVL 607
              P ELKAL  L+ L+LEYT  L  IP QLIS   +L VLR+         +  E ++L
Sbjct: 596 EEFPGELKALVNLKCLDLEYTRNLITIPRQLISNLSRLRVLRMFGASHNAFDEASENSIL 655

Query: 608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK------------------LDLT 649
               E ++ ELLGLK L V++ + RSS  +Q F    K                  L+++
Sbjct: 656 FGGGELIVEELLGLKHLEVITLTLRSSYGLQSFLNSHKLRSCTQALLLQHFKDSTSLEVS 715

Query: 650 WLVFVQNLKELEIIVCTEMEEI--------------------IC-VDKLRD--------- 679
            L  ++ L  L+I     +EE+                    IC   +L+D         
Sbjct: 716 ALADLKQLNRLQIANSVILEELKMDYAEEVQQFAFRSLNMVEICNCIQLKDLTFLVFAPN 775

Query: 680 -------VSDISEIIGSEHNF------------FTQLESLGILYGPDLKSIYPNPLHFPK 720
                  +    E I SE  F            F +L++L +    +LKSIY   L FP 
Sbjct: 776 LKSIKVGICHAMEEIASEGKFAEVPEVMANLNPFEKLQNLEVAGARNLKSIYWKSLPFPH 835

Query: 721 LKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAF 770
           LK +    C KLKKLP++S+SAKER++VI G + W E+LQWED+AT+NAF
Sbjct: 836 LKAMSFLHCKKLKKLPLDSNSAKERKIVISGERNWREQLQWEDEATRNAF 885

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|24461863|gb|AAN62350.1|AF506028_17 NBS-LRR type disease resistance protein [Citrus trifoliata]

 Score =  530 bits (1365), Expect = e-147,   Method: Compositional matrix adjust.
 Identities = 357/903 (39%), Positives = 486/903 (53%), Gaps = 151/903 (16%)

Query: 1   MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKV-EVE 59
           MGN++  ++   +F+R +     +A Y+  L++N+  L+TE+ KL   ++D++ +V   E
Sbjct: 1   MGNILQIAIDGAVFNRCMDCFLGKAAYIRNLQENVVALETELGKLIEAKNDVMARVVNTE 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
            QP  TR  N+V GWL  V  +  E  EL +  +QE+++LCLGG CSKN  SSY +G++V
Sbjct: 61  RQPMMTR-LNKVQGWLSGVDAVKAEADELIRHGSQEIEKLCLGGYCSKNWKSSYKFGKQV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
            +       L  +G    VV E+AP+ AA         VG +  L  VWRC+ ++    G
Sbjct: 120 AKKLRDAGTLMAEG-VFEVVAERAPESAA---------VGMQSRLEPVWRCLVEEPV--G 167

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAV------QTFQDDIGKRIGFSE 232
           I+GLYG+GGVGKTTLL  +NN F  Q+  +FD +IW  V      +  Q+ IGK++GF  
Sbjct: 168 IVGLYGMGGVGKTTLLTHLNNKFLGQRDFHFDFLIWVVVSKDLQIEKIQEIIGKKVGFFN 227

Query: 233 DKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLN-AGFKIVLKTR 282
           D  W +K+L ++AVDI ++L  KKF         R+D   +GVP+   + +  K+V  TR
Sbjct: 228 DS-WMKKNLAERAVDIYNVLKEKKFVLLLDDVWQRVDFATVGVPIPPRDKSASKVVFTTR 286

Query: 283 SAGVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA 341
           SA VC  M + K   V  L+ ++AW+LF++ +   TL S   I ELA+ +A ECG LPLA
Sbjct: 287 SAEVCVWMGAHKKFGVGCLSANDAWELFRQNVGEETLTSDHDIAELAQIVAEECGGLPLA 346

Query: 342 LKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLY 401
           L T+G+AM  +K V +   AIE +R SAS F G + NV    KFSYDSL  D  RSC LY
Sbjct: 347 LITIGQAMAYKKTVEEWRHAIEVLRRSASEFPGFD-NVLRVFKFSYDSLPDDTTRSCFLY 405

Query: 402 CCLYPEDYKIPKRSLIDYWISEGFMADFDR------GCEFINDLLHACLLEEEGDDHVKM 455
           CCLYP+DY I K  LID WI EGF+ +  R      G   +  L+ ACLLEE  DD VKM
Sbjct: 406 CCLYPKDYGILKWDLIDCWIGEGFLEESARFVAENQGYCIVGTLVDACLLEEIEDDKVKM 465

Query: 456 HDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT 515
           HD++R M+LWI   IE+EK+NFLVRAG  L +AP VKEWE  +R+SLM N+I+ LSE+PT
Sbjct: 466 HDVVRYMALWIVCEIEEEKRNFLVRAGAGLEQAPAVKEWENVRRLSLMQNDIKILSEVPT 525

Query: 516 L-----LSLRRNDSLT---------------------------ELPSRISSLVSLHHLDL 543
                 L L  N++L                            +LP  +S L SL  LD+
Sbjct: 526 CPDLHTLFLASNNNLQRITDGFFKFMPSLKVLKMSHCGDLKVLKLPLGMSMLGSLELLDI 585

Query: 544 SLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEE 603
           S T I  LP+ELK L  L+ LNL +  +LS IP QLIS   +L VLR+   G       E
Sbjct: 586 SQTSIGELPEELKLLVNLKCLNLRWATWLSKIPRQLISNSSRLHVLRMFATGCSHSEASE 645

Query: 604 GNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL----------------- 646
            +VL    E L++ELLGLK L VL  + RSS A+Q FF   KL                 
Sbjct: 646 DSVLFGGGEVLIQELLGLKYLEVLELTLRSSHALQLFFSSNKLKSCIRSLLLDEVRGTKS 705

Query: 647 --DLTWLVFVQNLKELEIIVCTEMEEI--------------------------ICVDKLR 678
             D T    + +L EL I    E+EE+                           C+ KL+
Sbjct: 706 IIDATAFADLNHLNELRIDSVAEVEELKIDYTEIVRKRREPFVFGSLHRVTLGQCL-KLK 764

Query: 679 DVS-----------------------------DISEIIGSEHNFFTQLESLGILYGPDLK 709
           D++                             ++ E++G   + F  L+ L +   P LK
Sbjct: 765 DLTFLVFAPNLKSLQLLNCRAMEEIISVGKFAEVPEVMG-HISPFENLQRLHLFDLPRLK 823

Query: 710 SIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNA 769
           SIY  PL F  LK++ V+GC +LKKLP++S+SAK    VI G  E W  LQWED ATQ A
Sbjct: 824 SIYWKPLPFTHLKEMRVHGCNQLKKLPLDSNSAK---FVIRGEAEGWNRLQWEDDATQIA 880

Query: 770 FSS 772
           F S
Sbjct: 881 FRS 883

Source: Citrus trifoliata

Species: Citrus trifoliata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224055915|ref|XP_002298700.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222845958|gb|EEE83505.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  511 bits (1315), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 312/769 (40%), Positives = 447/769 (58%), Gaps = 84/769 (10%)

Query: 1   MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MGN  S S+  D L S  L     +A Y+  LK+N++GLK  + +LT   +D+  +V+V+
Sbjct: 1   MGNFCSISISCDKLLSGCLDFTFRKAVYISKLKENVDGLKIAVEELTDLHNDVTRRVKVD 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E+ ++ ++ ++V  W+   +    +  EL +  +QE++RLCL G CSKN  SSY + +EV
Sbjct: 61  EE-QQLKQLDQVQRWISRAKAAIDKANELLREDSQEIERLCLRGYCSKNYKSSYRFAKEV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
            +    V +L  +G+   VV EK P  + +  P E T VG E    +VW C+  ++K  G
Sbjct: 120 DKRLRDVADLKANGD-FKVVAEKVPAASGVPRPSEPT-VGLESTFNQVWTCLR-EEKQVG 176

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
           I+GLYG+GGVGKTTLL Q+NN       +FD+VIW  V       T Q+ IG+ IG S+D
Sbjct: 177 IVGLYGMGGVGKTTLLTQINNESLKTPDDFDIVIWVVVSKDLKLNTVQESIGRNIGCSDD 236

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
             WK KSL +KAVDI + L  K+F         R+DL +LGVPL  +N G K+V  TRS 
Sbjct: 237 L-WKNKSLDEKAVDIFNALRHKRFVMLLDDIWERVDLKKLGVPLPDMNNGSKVVFTTRSE 295

Query: 285 GVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            +C  MD+ K ++V  LA D+AW LFQ+ +   TL  HT IP+LA  +A+ECG LPLAL 
Sbjct: 296 EICGLMDAHKTMKVDCLAWDDAWDLFQKKVGDQTLCVHTDIPKLARNVAKECGGLPLALI 355

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
           T+GRAM  +K   +   AIE +R SAS FSGM + VF  LKFSYD+LS  K+R+C LYC 
Sbjct: 356 TIGRAMACKKTPQEWRHAIEVLRKSASEFSGMGDEVFPLLKFSYDNLSKQKIRTCFLYCS 415

Query: 404 LYPEDYKIPKRSLIDYWISEGFMADFDR-------GCEFINDLLHACLLEEEGDDHVKMH 456
           L+PED+ I K  LIDYWI EG     D        G   I  LLHACLLE++ DD V+MH
Sbjct: 416 LFPEDFLINKNDLIDYWIGEGIFDGSDGREVVENWGYHVIGCLLHACLLEDK-DDCVRMH 474

Query: 457 DMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP-- 514
           D+IR+M+LWIA  IE++++NF V+ G + ++A +V +WEG +++SLMAN I  LS  P  
Sbjct: 475 DVIRDMALWIASDIERDQQNFFVQTGAQSSKALEVGKWEGVRKVSLMANHIVHLSGTPNC 534

Query: 515 ---------------------------TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTH 547
                                      T+L L  N+SL  LP  +  LVSL +L+LS T 
Sbjct: 535 SNLRTLFLGSIHLNKISRGFFQFMPNLTVLDLSNNNSLLGLPRDVWKLVSLQYLNLSRTG 594

Query: 548 IRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL 607
           I+ LP EL  L KLRYLNLEYTH L ++PH +ISGF  + +LR+  CGS     E+  +L
Sbjct: 595 IKELPTELNELVKLRYLNLEYTHSLYLLPHGVISGFPMMRILRMFRCGSSEQAAEDC-IL 653

Query: 608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL------------------DLT 649
             D E L+ EL  L+ LN+L+ + RS+ A+++   +  +                  + +
Sbjct: 654 SRD-ESLVEELQCLEELNMLTVTIRSAAALERLSSFQGMQSSTRVLYLELFHDSKLVNFS 712

Query: 650 WLVFVQNLKELEIIVCTEMEEIIC-----VDKLRDVSDISEIIGSEHNF 693
            L  ++NL  L I  C  +EE+       + K++ +++++++  +E  F
Sbjct: 713 SLANMKNLDTLHICHCGSLEELQIDWEGELQKMQAINNLAQVATTERPF 761

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443158|ref|XP_002263674.1| PREDICTED: probable disease resistance protein At5g63020-like [Vitis vinifera]

 Score =  508 bits (1308), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 344/913 (37%), Positives = 476/913 (52%), Gaps = 160/913 (17%)

Query: 1   MGNLISTSLP-PDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MGNL S S+   D           +A Y+   ++N++ LK  +  L   R+D+  KVE+ 
Sbjct: 1   MGNLFSVSISMQDSLPGCKGGTALRAKYICEFEENIKALKEALEDLKDFRNDMKRKVEMG 60

Query: 60  E-QPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGRE 118
           E QP    + ++V  W    + +  E  +L +   +E  + CLGG CSKN +SSY  GR+
Sbjct: 61  EGQP--MEQLDQVQRWFSRAEAMELEVDQLIRDGTRETQKFCLGGCCSKNCLSSYKLGRK 118

Query: 119 VVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNR 178
           +V+  D V  L +       + ++ P  A  E P E T VG E  +  VW C+ ++Q   
Sbjct: 119 LVKKADDVATL-RSTRLFDGLADRLPPPAVDERPSEPT-VGFESTIDEVWSCLREEQVQ- 175

Query: 179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSE 232
            IIGLYG+GGVGKTTL+ QVNN F    H FD+VIW  V      +  QD+I K++GF +
Sbjct: 176 -IIGLYGMGGVGKTTLMTQVNNEFLKTIHQFDIVIWVVVSRDPNPEKVQDEIWKKVGFCD 234

Query: 233 DKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRS 283
           DK WK KS  +KA+ I  IL  KKF         R DL ++G+PL       K+V  TRS
Sbjct: 235 DK-WKSKSQDEKAISIFRILGKKKFVLFLDDVWERFDLLKVGIPLPNQQNNSKLVFTTRS 293

Query: 284 AGVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL 342
             VC +M + + ++V  LA  +AW LFQ M+   TL+SH  IP+LAET+ +EC  LPLAL
Sbjct: 294 EEVCGRMGAHRRIKVECLAWKQAWDLFQNMVGEDTLNSHPEIPQLAETIVKECLGLPLAL 353

Query: 343 KTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYC 402
            T GR M  +K   + + AI+ +++S+S+F GM + VF  LKFSYD+L  D  RSC LYC
Sbjct: 354 VTTGRTMACKKAPQEWKFAIKMLQSSSSSFPGMRDEVFSLLKFSYDNLPSDTARSCFLYC 413

Query: 403 CLYPEDYKIPKRSLIDYWISEGFMADFD-------RGCEFINDLLHACLLEEEGDDHVKM 455
            LYPED  I K  LID WI EGF+ +FD       +G + I  L+ ACLLEE  +  VKM
Sbjct: 414 SLYPEDNDIFKEDLIDCWICEGFLDEFDDRDGARNQGFDIIGSLIRACLLEESREYFVKM 473

Query: 456 HDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT 515
           HD+IR+M+LWIA    + K  FLV+AG  LTE P++ +W+G +R+SLM+N IE L+++PT
Sbjct: 474 HDVIRDMALWIACECGRVKDKFLVQAGAGLTELPEIGKWKGVERMSLMSNHIEKLTQVPT 533

Query: 516 L-------------------------------LSLRRNDSLTELPSRISSLVSLHHLDLS 544
                                           LS  R   ++ELP+ I  LVSL +LDLS
Sbjct: 534 CPNLLTLFLNNNSLEVITDGFFQLMPRLQVLNLSWSR---VSELPTEIFRLVSLRYLDLS 590

Query: 545 LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEG 604
            T I  LP E K L  L+YLNL+YT  L IIP  ++S   +L+VL++  CG  GV   E 
Sbjct: 591 WTCISHLPNEFKNLVNLKYLNLDYTQQLGIIPRHVVSSMSRLQVLKMFHCGFYGVG--ED 648

Query: 605 NVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK-----------------FFK-YPKL 646
           NVL D  E L+ EL  L  L  L+ + RS+ A+Q+                 FF     L
Sbjct: 649 NVLSDGNEALVNELECLNNLCDLNITIRSASALQRCLCSEKIEGCTQDLFLQFFNGLNSL 708

Query: 647 DLTWLVFVQNLKELEIIVCT-----------EMEEIICVDKLRDVSDISEIIGSEHNFFT 695
           D+++L  ++ L  L I  C            E +EI+  D   D S I+ +       F 
Sbjct: 709 DISFLENMKRLDTLHISDCATLADLNINGTDEGQEILTSDNYLDNSKITSLKN-----FH 763

Query: 696 QLESLGI------------LYGPDLKSIY------------------------PNP---- 715
            L S+ I            ++ P+L +++                         +P    
Sbjct: 764 SLRSVRIERCLMLKDLTWLVFAPNLVNLWIVFCRNIEQVIDSGKWVEAAEGRNMSPFAKL 823

Query: 716 -----LHFPKLKKI-------------GVYGCPKLKKLPINSSSAKERRVVIEGLKEWWE 757
                +  PKLK I              V+ CPKLKKLP+NS+SAK R +VI G K+W  
Sbjct: 824 EDLILIDLPKLKSIYRNTLAFPCLKEVRVHCCPKLKKLPLNSNSAKGRGMVIYGEKDWRN 883

Query: 758 ELQWEDQATQNAF 770
           EL+WED+A  NAF
Sbjct: 884 ELEWEDEAAHNAF 896

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553103|ref|XP_002517594.1| Disease resistance protein RPS5, putative [Ricinus communis] gi|223543226|gb|EEF44758.1| Disease resistance protein RPS5, putative [Ricinus communis]

 Score =  501 bits (1291), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 335/894 (37%), Positives = 474/894 (53%), Gaps = 138/894 (15%)

Query: 5   ISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRR 64
           I  SL P L  R L  +  +A Y+  L+ NL  L+ E  +L     D    +   E+   
Sbjct: 7   IQPSLDPCL-ERCLDCLIPKALYICQLEDNLIALEAERDRLKAVHTDWTQMIMTAEEGPG 65

Query: 65  TRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTD 124
             R+  + GWL  V+ L  E   L     +E  RLCLGG CS N+ +SY +G+ V    D
Sbjct: 66  MSRSKLIDGWLLRVEALTKEVELLIARGPREKARLCLGGCCSMNISASYKFGKRV----D 121

Query: 125 RVINLNKD--GEK-IAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGII 181
           +V+N  K+  G++ I  V  K P    +E P E T+ G + +L  VW  + D+++   II
Sbjct: 122 KVLNEVKELTGQRDIQEVAYKRPVEPVVERPSELTL-GFKTMLDNVWSYL-DEEEPVCII 179

Query: 182 GLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDKK 235
           G+YG+GGVGKTTLL  +NN F       DVVIW  V      +  Q+DIGKR+GF  +++
Sbjct: 180 GVYGMGGVGKTTLLTHINNKFLDSSKKVDVVIWITVSKDFTLERVQEDIGKRMGFF-NEQ 238

Query: 236 WKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAGV 286
           WKEKS Q+KAVDI + +  KKF         R+DL ++GVPL     G K+V  TRS  V
Sbjct: 239 WKEKSFQEKAVDILNGMRKKKFVLLLDDMWERVDLVKMGVPLPSRQKGSKVVFTTRSKEV 298

Query: 287 CDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV 345
           C QMD+ K + +  LA + AW+LFQE I   TL  H  IP LA  +A++C  LPLAL T+
Sbjct: 299 CGQMDAEKIIYLKPLAWEIAWELFQEKIGEETLHIHPEIPRLAHDIAKKCQGLPLALITI 358

Query: 346 GRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLY 405
            RAM S++ + +   A+E +    S F GM +NVF  LK+SYDSL  DK++SC LYC L+
Sbjct: 359 ARAMASRRTLQEWNHAVEVLSNPTSDFHGMWDNVFTILKYSYDSLPNDKIKSCFLYCTLF 418

Query: 406 PEDYKIPKRSLIDYWISEGFMADF-------DRGCEFINDLLHACLLEEEGDDHVKMHDM 458
           P ++KI K  LI YW+ E F  ++       D+G   +  L+ ACLLE+EG D+VKMHD+
Sbjct: 419 PRNFKIFKSDLIAYWMCEEFWDEYDNGSSANDKGHHIMGVLVRACLLEDEG-DYVKMHDV 477

Query: 459 IREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTL-- 516
           IR+M L IA    + K+  LV+AG  L EAP+ ++WE  KR+SLM N I  L+E+PT   
Sbjct: 478 IRDMGLRIACNCARTKETNLVQAGALLIEAPEARKWEHIKRMSLMENSIRVLTEVPTCPE 537

Query: 517 -----------LSLRRND----------------SLTELPSRISSLVSLHHLDLSLTHIR 549
                      L + R D                 + ELPS IS +VSL +L++S T I 
Sbjct: 538 LFTLFLCHNPNLVMIRGDFFRSMKALTVLDLSKTGIQELPSGISDMVSLQYLNISYTVIN 597

Query: 550 GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCD 609
            LP  L  LEKL+YLNLE+   L +IP QL+    +L+ LR+L CG     + + N+L D
Sbjct: 598 QLPAGLMRLEKLKYLNLEHNENLYMIPKQLVRSLSRLQALRMLGCGPVHYPQAKDNLLSD 657

Query: 610 DAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK------------------LDLTWL 651
                ++EL  L+ LN LS + R + A+Q FF   K                  L+++WL
Sbjct: 658 GV--CVKELQCLENLNRLSITVRCASALQSFFSTHKLRSCVEAISLENFSSSVSLNISWL 715

Query: 652 VFVQ--------------------------------------NLKELEIIVCTEMEEI-- 671
             +Q                                      NL+E+ +  C ++ ++  
Sbjct: 716 ANMQHLLTCPNSLNINSNMARTERQAVGNLHNSTILRTRCFNNLQEVRVRKCFQLRDLTW 775

Query: 672 ------ICVDKLRDVSDISEIIGSEH--------NFFTQLESLGILYGPDLKSIYPNPLH 717
                 + V ++    ++ EII  E         N F +L+ L +   P +K IYP+ L 
Sbjct: 776 LILVPNLTVLEVTMCRNLEEIISVEQLGFVGKILNPFARLQVLELHDLPQMKRIYPSILP 835

Query: 718 FPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAFS 771
           FP LKKI V+ CP LKK+P+ S+SAK R+VVIE    WW  ++WE++ T+ AFS
Sbjct: 836 FPFLKKIEVFNCPMLKKVPLGSNSAKGRKVVIEADDHWWNGVEWENRETKAAFS 889

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122896|ref|XP_002318943.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222857319|gb|EEE94866.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  485 bits (1248), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 323/843 (38%), Positives = 444/843 (52%), Gaps = 146/843 (17%)

Query: 42  MRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCL 101
           M +L   ++DL  KV++ E       T+RV GW+  V+++ TE  EL    AQEM + C 
Sbjct: 1   MDELLHLKNDLTGKVQMAEV---RSMTSRVTGWVSRVERMITEVNELTNQAAQEMQKNCF 57

Query: 102 GGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQE 161
           G  C KN  S Y  G+++              EK+  V +    G       E+ +    
Sbjct: 58  GSCCPKNCWSRYKIGKKI-------------DEKLRAVSDHIEKG-------EKYLSSVS 97

Query: 162 KLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---- 217
             +  V  C+ +  K+   IG+YG GGVGKT LL QV+NN    Q  FD VIW       
Sbjct: 98  SPVESVMGCLCEVGKS--TIGIYGPGGVGKTALLTQVSNNLLSSQLPFDFVIWVVASQDP 155

Query: 218 --QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGV 266
             +  Q DIGK IGF ED+ WK KS Q+KA ++SS+LS KKF          +DL E+GV
Sbjct: 156 DSERIQGDIGKEIGFLEDR-WKGKSFQEKAREVSSVLSQKKFVLLVDDLWKPVDLAEVGV 214

Query: 267 PLQMLNAGFKIVLKTRSAGVCDQMDSK-NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIP 325
           P +    G K+V  T S  +C+ M ++  + V  LA ++AWKLFQE +   TL  H  IP
Sbjct: 215 PSR--ENGSKLVFTTSSEELCNSMGAEEKIRVGGLAWEKAWKLFQEKVGEDTLKIHPDIP 272

Query: 326 ELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKF 385
           ELAET+A+ C  LPLAL TVGRAM  +K + +   +IE +  + + FS      F+ LKF
Sbjct: 273 ELAETIAKMCNGLPLALITVGRAMAFRKTLLEWRHSIEALSRATAEFSRTPCRDFVLLKF 332

Query: 386 SYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFD-------RGCEFIND 438
            YDSL  DK+RSC LYC L+PE + I K  LIDYWI EGF+  +         G   I+ 
Sbjct: 333 GYDSLRNDKVRSCFLYCALFPEGFFINKSYLIDYWIGEGFLGAYSDAYEARTEGHNIIDI 392

Query: 439 LLHACLLEEEGDDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAK 498
           L  ACLLE+EG D VKMH +IR+M+LW+     KE   +LV AG +L +AP+V +WE  +
Sbjct: 393 LTQACLLEDEGRD-VKMHQVIRDMALWM--DSRKENPVYLVEAGTQLADAPEVGKWEVVR 449

Query: 499 RISLMANEIESLSEIP-----------------------------TLLSLRRNDSLTELP 529
           R+SLMAN I++LS+ P                              +L L  N  +TE P
Sbjct: 450 RVSLMANNIQNLSKAPRCNDLVTLFLKKNNLKMISDTFFQFMLSLKVLDLSENREITEFP 509

Query: 530 SRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVL 589
           S I  LVSL +L+LS T IR LP +LK L KL+ LNLE+T+ L  IP Q+IS F  L VL
Sbjct: 510 SGILKLVSLQYLNLSRTGIRQLPVQLKNLVKLKCLNLEHTYELRTIPMQVISNFSSLTVL 569

Query: 590 RLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRS---------------- 633
           R+  C S      +G V       L R+L  L+ LN+L+ + RS                
Sbjct: 570 RMFHCASSDSVVGDG-VQTGGPGSLARDLQCLEHLNLLTITIRSQYSLQTFASFNKFLTA 628

Query: 634 --SLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEE--------------------- 670
             +L++QKF     LD++ L  + +L +LE+I C+ +++                     
Sbjct: 629 TQALSLQKFHHARSLDISLLEGMNSLDDLELIDCSNLKDLSINNSSITRETSFNSLRRVS 688

Query: 671 IICVDKLRDV-----------------SDISEIIGSEHN------FFTQLESLGILYGPD 707
           I+   KL D+                 S + EII  E +       F +LE L ++  P 
Sbjct: 689 IVNCTKLEDLAWLTLAPNIKFLTISRCSKMEEIIRQEKSGQRNLKVFEELEFLRLVSLPK 748

Query: 708 LKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQ 767
           LK IYP+ L FP LK+I V  CP L+KLP+NS+SAKE R+VI+G ++WW  L+WED+A Q
Sbjct: 749 LKVIYPDALPFPSLKEIFVDDCPNLRKLPLNSNSAKEHRIVIQGWEDWWRRLEWEDEAAQ 808

Query: 768 NAF 770
           + F
Sbjct: 809 HTF 811

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147852651|emb|CAN80649.1| hypothetical protein VITISV_017542 [Vitis vinifera]

 Score =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 340/883 (38%), Positives = 479/883 (54%), Gaps = 132/883 (14%)

Query: 1   MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
           MGN+ S  +  +   S   +R  E ANY+  L +NL  L T   +L   R+D++ +V++ 
Sbjct: 1   MGNIFSVEISVNHAISSCWNRTTEHANYLCKLPENLVALGTACERLREFRNDVMRRVDIA 60

Query: 60  EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
           E+  + +R ++V GWL  V+ L T+ ++L +   +E+++ CLGG C +   + Y  G+ V
Sbjct: 61  ER-EQMQRLDQVQGWLSRVENLETQVSQLIEDGTEEIEKKCLGGCCPRRCSTGYKLGKRV 119

Query: 120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRG 179
                 V  L        VV E+ P     E P + T VG +  L +V R   D+++  G
Sbjct: 120 ARKLKEVDTLISQRPS-DVVAERLPSPRLGERPSKAT-VGMDSRLDKV-RSSMDEER-VG 175

Query: 180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
           IIGLYG+GGVGKTTLL Q+NN F  + H+FD VIW+ V      +  Q+DI K IGF +D
Sbjct: 176 IIGLYGLGGVGKTTLLTQINNAFTRRTHDFDFVIWSTVSKNVNLENIQNDIWKTIGFCDD 235

Query: 234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
           K WK KS  +KA  I  +LS K+F          +DL+++GVP Q  N   K+V  TRS 
Sbjct: 236 K-WKSKSRDEKATSIWRVLSEKRFVLLLDDLWEWLDLSDVGVPFQ--NKKNKVVFTTRSE 292

Query: 285 GVCDQMDS-KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
            VC QM++ K ++V  L   E+W+LF+  +   TLD H  IPELA+ +A+EC  LPL L 
Sbjct: 293 EVCAQMEADKKIKVECLTWTESWELFRMKLGEDTLDFHPEIPELAQAVAQECCGLPLVLT 352

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
            +GRAM  +K   + + AI+  ++SAS   G+ + VF  LK+SYDSL  +  RSC LYC 
Sbjct: 353 IMGRAMACKKTPEEWKYAIKVFQSSASKLPGIGDRVFPLLKYSYDSLPTEVARSCFLYCS 412

Query: 404 LYPEDYKIPKRSLIDYWISEGFMADFD-------RGCEFINDLLHACLLEE-EGDDHVKM 455
           LYPED ++ K SLI+ WI EGF+ +FD       +G   I  L+HACLLEE + D  VK+
Sbjct: 413 LYPEDDEMSKSSLINRWICEGFLDEFDDWEGAENQGYNIIGTLIHACLLEECDVDYQVKL 472

Query: 456 HDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP- 514
           HD+IR+M+LWIA    KE+  FLV+AG  LTEAP+V EW G KRISLM N+IE L+  P 
Sbjct: 473 HDVIRDMALWIARETGKEQDKFLVKAGSTLTEAPEVAEWMGPKRISLMNNQIEKLTGSPI 532

Query: 515 ----TLLSLRRN-----------------------DSLTELPSRISSLVSLHHLDLSLTH 547
               + L LR N                       +S+TELP  IS+LVSL +LDLS T 
Sbjct: 533 CPNLSTLFLRENSLKMITDSFFQFMPNLRVLDLSDNSITELPREISNLVSLRYLDLSFTE 592

Query: 548 IRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL 607
           I+ LP ELK L  L+ L L +   LS +P QLIS  L L+V+ + +CG           +
Sbjct: 593 IKELPIELKNLGNLKCLLLSFMPQLSSVPEQLISSLLMLQVIDMFDCG-----------I 641

Query: 608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK---------------------- 645
           CD  E L+ EL  LK L+ LS +  S+ A ++     K                      
Sbjct: 642 CDGDEALVEELESLKYLHDLSVTITSTSAFKRLLSSDKLRSCISRRLRNLFISNCGSLED 701

Query: 646 LDLTWL---------------VFVQN----LKELEIIVCTEMEE--------------II 672
           L++ W+               V   N    L+ L ++ C+ +++              II
Sbjct: 702 LEIDWVGEGKKTVESNYLNSKVSSHNSFHSLEALTVVSCSRLKDLTWVAFAPNLKVLTII 761

Query: 673 CVDKLRDV-----SDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVY 727
             D++++V     SD S   G     F +L+ L ++  P LKSI+   L    L +I V 
Sbjct: 762 DCDQMQEVIGTRKSDESAENGENLGPFAKLQVLHLVGLPQLKSIFWKALPLIYLNRIHVR 821

Query: 728 GCPKLKKLPINSSSAKERRVVIEGLKEWWEELQWEDQATQNAF 770
            CP LKKLP+N++SAK  R+VI G  EWW E++WED+AT NAF
Sbjct: 822 NCPLLKKLPLNANSAKGHRIVISGQTEWWNEVEWEDEATHNAF 864

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	779
TAIR|locus:2201996	889	RPS5 "AT1G12220" [Arabidopsis	0.743	0.651	0.371	1.6e-117
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.759	0.666	0.359	6.8e-117
TAIR|locus:2132741	892	AT4G10780 [Arabidopsis thalian	0.748	0.653	0.363	2.1e-109
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.731	0.644	0.356	5.6e-109
TAIR|locus:2036214	851	AT1G15890 [Arabidopsis thalian	0.717	0.656	0.354	1.2e-104
TAIR|locus:2153474	874	AT5G05400 [Arabidopsis thalian	0.718	0.640	0.323	1e-103
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.866	0.698	0.335	5.8e-103
TAIR|locus:2031366	898	AT1G63350 "AT1G63350" [Arabido	0.734	0.636	0.336	8.8e-96
TAIR|locus:2203881	893	AT1G62630 [Arabidopsis thalian	0.641	0.559	0.363	2.6e-94
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.507	0.441	0.377	4.4e-90

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

 Score = 951 (339.8 bits), Expect = 1.6e-117, Sum P(2) = 1.6e-117
 Identities = 231/622 (37%), Positives = 337/622 (54%)

Query:     1 MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
             MG   S SLP D + S+    +  + +Y+  L KNL  L+  MR L   + D++ ++E E
Sbjct:     1 MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSKNLASLQKAMRMLKARQYDVIRRLETE 60

Query:    60 EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
             E   R +R ++V  WL  V  +  +F +L +    E+ RLCL G CSK+L  SY YG+ V
Sbjct:    61 EFTGRQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRV 120

Query:   120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRX 179
             + +   V +L+  G    VV E  P     E+P + TIVGQE +L + W  + +      
Sbjct:   121 IMMLKEVESLSSQGF-FDVVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMEDGSG-- 177

Query:   180 XXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGFSED 233
                        KTTLL ++NN F      FDVVIW      + V+  Q DI +++G    
Sbjct:   178 ILGLYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLG-G 236

Query:   234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
              +W EK+    AVDI ++L  +KF         +++L  +GVP    + G K+   TRS 
Sbjct:   237 MEWSEKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSR 296

Query:   285 GVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
              VC +M   + +EV  L  +E+W LFQ  + ++TL SH  IP LA  +AR+C  LPLAL 
Sbjct:   297 DVCGRMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALN 356

Query:   344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
              +G AM  ++ V +   AI+ + +SA  FSGME+ +   LK+SYD+L+ + ++SC LYC 
Sbjct:   357 VIGEAMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCS 416

Query:   404 LYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLL--EEEGDDHVK 454
             L+PEDY I K  L+DYWISEGF+ +        ++G E I  L+ ACLL  EE    +VK
Sbjct:   417 LFPEDYLIDKEGLVDYWISEGFINEKEGRERNINQGYEIIGTLVRACLLLEEERNKSNVK 476

Query:   455 MHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP 514
             MHD++REM+LWI+  + K+K+  +VRAGV L E PKVK+W   ++ISLM NEIE + +  
Sbjct:   477 MHDVVREMALWISSDLGKQKEKCIVRAGVGLREVPKVKDWNTVRKISLMNNEIEEIFDSH 536

Query:   515 -----TLLSLRRNDSLTELPSRIXXXX--XXXXXXXXXXXIRGLPQELKALEKLRYLNLE 567
                  T L L++ND + ++ +                   +  LP+E+  L  LRY NL 
Sbjct:   537 ECAALTTLFLQKND-VVKISAEFFRCMPHLVVLDLSENQSLNELPEEISELASLRYFNLS 595

Query:   568 YTHYLSIIPHQLISGFLKLEVL 589
             YT       HQL  G   L+ L
Sbjct:   596 YTCI-----HQLPVGLWTLKKL 612

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:2166320 AT5G63020 [Arabidopsis thaliana (taxid:3702)]

 Score = 966 (345.1 bits), Expect = 6.8e-117, Sum P(2) = 6.8e-117
 Identities = 228/635 (35%), Positives = 357/635 (56%)

Query:     1 MGNLISTSLPPDLFSRTLHR-VGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
             MG  +S S+  D  ++ +   +    +Y+ GL++NL  L+  + ++ + R+DL+ K+  E
Sbjct:     1 MGGCVSVSISCDQLTKNVCSCLNRNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSE 60

Query:    60 EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
             E+ R  +R + V GW+  V+ +     EL ++R+ ++ RLCL G CSKNLVSSY YG+ V
Sbjct:    61 ER-RGLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRV 119

Query:   120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRX 179
             +++ + V  L   G+  AVV E+  D A +E    + +V  + +L   W  + + +    
Sbjct:   120 MKMIEEVEVLRYQGD-FAVVAERV-DAARVEERPTRPMVAMDPMLESAWNRLMEDEIG-- 175

Query:   180 XXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
                        KTTLL  +NN F      FD+VIW  V      Q  QD+I +++  S++
Sbjct:   176 ILGLHGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLR-SDN 234

Query:   234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
             +KWK+K+   KA +I ++L  K+F         ++DLTE+GVP      G KIV  TR  
Sbjct:   235 EKWKQKTEDIKASNIYNVLKHKRFVLLLDDIWSKVDLTEVGVPFPSRENGCKIVFTTRLK 294

Query:   285 GVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
              +C +M    ++EV  LA D+AW LF + +   TL SH  IP +A T+A++C  LPLAL 
Sbjct:   295 EICGRMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALN 354

Query:   344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
              +G  M  ++ V +   AI+ + +SA+ FSGME+ +   LK+SYD+L  ++L+ C  YC 
Sbjct:   355 VIGETMAYKRTVQEWRSAIDVLTSSAAEFSGMEDEILPILKYSYDNLKSEQLKLCFQYCA 414

Query:   404 LYPEDYKIPKRSLIDYWISEGFM------ADFDRGCEFINDLLHACLLEEEGDDHVKMHD 457
             L+PED+ I K  L+DYWI EGF+      A+ ++G E I  L+ +CLL EE  + VKMHD
Sbjct:   415 LFPEDHNIEKNDLVDYWIGEGFIDRNKGKAE-NQGYEIIGILVRSCLLMEENQETVKMHD 473

Query:   458 MIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLS---EIP 514
             ++REM+LWIA    K+K+NF+V+AG++    P++++W+ A+R+SLM N IES+    E P
Sbjct:   474 VVREMALWIASDFGKQKENFIVQAGLQSRNIPEIEKWKVARRVSLMFNNIESIRDAPESP 533

Query:   515 TLLSLR-RNDSLTELPSRIXXXX--XXXXXXXXXXXIRGLPQELKALEKLRYLNLEYTHY 571
              L++L  R + L  + S                   +R LP E+     L+YL+L  T  
Sbjct:   534 QLITLLLRKNFLGHISSSFFRLMPMLVVLDLSMNRDLRHLPNEISECVSLQYLSLSRTR- 592

Query:   572 LSIIPHQLISG----FLKLEVLRLLE--CGSEGVT 600
             + I P  L+      +L LE  R++E  CG  G+T
Sbjct:   593 IRIWPAGLVELRKLLYLNLEYTRMVESICGISGLT 627

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2132741 AT4G10780 [Arabidopsis thaliana (taxid:3702)]

 Score = 925 (330.7 bits), Expect = 2.1e-109, Sum P(2) = 2.1e-109
 Identities = 228/628 (36%), Positives = 342/628 (54%)

Query:     1 MGNLISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
             MG+ IS  +  D + +R         NY+  LK N+  L+  +  LT TRDD++ +V++E
Sbjct:     1 MGSCISLQISCDQVLTRAYSCFFSLGNYIHKLKDNIVALEKAIEDLTATRDDVLRRVQME 60

Query:    60 EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
             E  +   R  +V  WL+ V+ +  +F +L   R  E+ RLC    CS NL SSY YG+ V
Sbjct:    61 EG-KGLERLQQVQVWLKRVEIIRNQFYDLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRV 119

Query:   120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIEL-PLEQTIVGQEKLLPRVWRCITDQQKNR 178
               +   V NLN +G    +V   AP    +E+ P++ TI+G+E +  R W  + D     
Sbjct:   120 FLMIKEVENLNSNGF-FEIVAAPAPK---LEMRPIQPTIMGRETIFQRAWNRLMDDGVG- 174

Query:   179 XXXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAVQT------FQDDIGKRIGFSE 232
                         KTTLL Q++N     ++  D+VIW  V +       Q+DIG+++GF  
Sbjct:   175 -TMGLYGMGGVGKTTLLTQIHNTLHDTKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFI- 232

Query:   233 DKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRS 283
              K+W +K    KAVDI + LS K+F         ++DLT++G+P Q      K+V  TRS
Sbjct:   233 GKEWNKKQESQKAVDILNCLSKKRFVLLLDDIWKKVDLTKIGIPSQTRENKCKVVFTTRS 292

Query:   284 AGVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL 342
               VC +M   + +EV  L+ ++AW+LFQE + + +L SH  I ELA+ +A +C  LPLAL
Sbjct:   293 LDVCARMGVHDPMEVQCLSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLAL 352

Query:   343 KTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYC 402
               +G  M  ++ V +   A++ + + A+ FSGM++++ L LK+SYD+L+   +RSC  YC
Sbjct:   353 NVIGETMAGKRAVQEWHHAVDVLTSYAAEFSGMDDHILLILKYSYDNLNDKHVRSCFQYC 412

Query:   403 CLYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDD--HV 453
              LYPEDY I K  LIDYWI EGF+          ++G E +  L+ ACLL EEG +   V
Sbjct:   413 ALYPEDYSIKKYRLIDYWICEGFIDGNIGKERAVNQGYEILGTLVRACLLSEEGKNKLEV 472

Query:   454 KMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLS-- 511
             KMHD++REM+LW    + K K+  +V+AG  L + PKV++W   +R+SLM N IE +S  
Sbjct:   473 KMHDVVREMALWTLSDLGKNKERCIVQAGSGLRKVPKVEDWGAVRRLSLMNNGIEEISGS 532

Query:   512 -EIP--TLLSLRRNDSLTELPSRIXXXXXXXXXXXXXXX--IRGLPQELKALEKLRYLNL 566
              E P  T L L+ N SL  +                     + GLP+++  L  LRYL+L
Sbjct:   533 PECPELTTLFLQENKSLVHISGEFFRHMRKLVVLDLSENHQLDGLPEQISELVALRYLDL 592

Query:   567 EYTHYLSIIPHQLISGFLKLEVLRLLEC 594
              +T+ +  +P  L    LK  +   LEC
Sbjct:   593 SHTN-IEGLPACLQD--LKTLIHLNLEC 617

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 888 (317.7 bits), Expect = 5.6e-109, Sum P(2) = 5.6e-109
 Identities = 219/615 (35%), Positives = 318/615 (51%)

Query:     1 MGNLISTSLPPDL----FSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKV 56
             MG  +S SL  D     FS+ L   G   +Y+  L +NL  L+  M  L   RDD+  ++
Sbjct:     1 MGGCVSVSLSCDREVNQFSQWLCVSG---SYIQNLSENLASLQKAMGVLNAKRDDVQGRI 57

Query:    57 EVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYG 116
               EE     RR  +V  WL  +Q +  +F +L      E+ RLCL G CSKN+  SY YG
Sbjct:    58 NREEFTGHRRRLAQVQVWLTRIQTIENQFNDLLSTCNAEIQRLCLCGFCSKNVKMSYLYG 117

Query:   117 REVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQK 176
             + V+ L   V  L+  G    +V E AP     ELP++ TIVGQ+ +L +VW C+ + + 
Sbjct:   118 KRVIVLLREVEGLSSQGV-FDIVTEAAPIAEVEELPIQSTIVGQDSMLDKVWNCLMEDKV 176

Query:   177 NRXXXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGF 230
                           KTTLL Q+NN F      FDVVIW      A V   Q  IG+++G 
Sbjct:   177 --WIVGLYGMGGVGKTTLLTQINNKFSKLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGL 234

Query:   231 SEDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKT 281
                K W EK+   +A+DI ++L  KKF         +++L  +GVP      G K+   T
Sbjct:   235 V-GKNWDEKNKNQRALDIHNVLRRKKFVLLLDDIWEKVELKVIGVPYPSGENGCKVAFTT 293

Query:   282 RSAGVCDQMDSKN-LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL 340
              S  VC +M   N +E+  L    AW L ++ +  +TL SH  IP+LA  ++ +C  LPL
Sbjct:   294 HSKEVCGRMGVDNPMEISCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPL 353

Query:   341 ALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLL 400
             AL  +G  M  ++ + +   A E + TSA+ FSGME+ +   LK+SYDSL+ +  +SC L
Sbjct:   354 ALNVIGETMSFKRTIQEWRHATEVL-TSATDFSGMEDEILPILKYSYDSLNGEDAKSCFL 412

Query:   401 YCCLYPEDYKIPKRSLIDYWISEGFMAD-------FDRGCEFINDLLHACLLEEEGDDH- 452
             YC L+PED++I K  LI+YWI EGF+ +       F++G + +  L+ + LL E   D  
Sbjct:   413 YCSLFPEDFEIRKEMLIEYWICEGFIKEKQGREKAFNQGYDILGTLVRSSLLLEGAKDKD 472

Query:   453 -VKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLS 511
              V MHDM+REM+LWI   + K K+  +V+AG+ L E P+V+ W   KR+SLM N  E + 
Sbjct:   473 VVSMHDMVREMALWIFSDLGKHKERCIVQAGIGLDELPEVENWRAVKRMSLMNNNFEKIL 532

Query:   512 EIPTL-----LSLRRNDSLTELPSRIXXX--XXXXXXXXXXXXIRGLPQELKALEKLRYL 564
               P       L L+ N  L ++                     +  LP+E+  L  L+YL
Sbjct:   533 GSPECVELITLFLQNNYKLVDISMEFFRCMPSLAVLDLSENHSLSELPEEISELVSLQYL 592

Query:   565 NLEYTHYLSIIPHQL 579
             +L  T Y+  +PH L
Sbjct:   593 DLSGT-YIERLPHGL 606

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:2036214 AT1G15890 [Arabidopsis thaliana (taxid:3702)]

 Score = 839 (300.4 bits), Expect = 1.2e-104, Sum P(3) = 1.2e-104
 Identities = 214/603 (35%), Positives = 316/603 (52%)

Query:     1 MGNLISTSLPPDLFSRTL-HRVG---EQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKV 56
             MGN ++  +  D   +TL H  G      NY+  ++ NLE L+  M++L   RDDL+ +V
Sbjct:     1 MGNCVALEISCD---QTLNHACGCLFGDRNYILKMEANLEALQNTMQELEERRDDLLRRV 57

Query:    57 EVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYG 116
              +EE  +  +R  +V GWL  V+ + ++  +L + ++ + +RLCL G CSKN +S  NYG
Sbjct:    58 VIEED-KGLQRLAQVQGWLSRVKDVCSQVNDLLKAKSIQTERLCLCGYCSKNFISGRNYG 116

Query:   117 REVVELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQK 176
               V++    V  L   G    VV EK P    +E    QT VG + ++ R W  +   + 
Sbjct:   117 INVLKKLKHVEGLLAKGV-FEVVAEKIP-APKVEKKHIQTTVGLDAMVGRAWNSLMKDE- 173

Query:   177 NRXXXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGF 230
              R            KTTLL  +NN F    + FD+VIW  V      +  Q+ I  R+G 
Sbjct:   174 -RRTLGLYGMGGVGKTTLLASINNKFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGL 232

Query:   231 SEDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKT 281
                + WK+ + ++KA  I +IL+ KKF          +DL ++GVP      G KIV  T
Sbjct:   233 H--RGWKQVTEKEKASYICNILNVKKFVLLLDDLWSEVDLEKIGVPPLTRENGSKIVFTT 290

Query:   282 RSAGVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL 340
             RS  VC  M+    ++V  L  DEAW+LFQ+ +    L SH  IP LA  +A +C  LPL
Sbjct:   291 RSKDVCRDMEVDGEMKVDCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPL 350

Query:   341 ALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLL 400
             AL  +G+AM S++ V + +  I  + +S+  F  MEE +   LKFSYD L  +K++ C L
Sbjct:   351 ALSVIGKAMASRETVQEWQHVIHVLNSSSHEFPSMEEKILPVLKFSYDDLKDEKVKLCFL 410

Query:   401 YCCLYPEDYKIPKRSLIDYWISEGFM---ADFD----RGCEFINDLLHACLLEE-EGDDH 452
             YC L+PEDY++ K  LI+YW+ EGF+    D D    +G + I  L+ A LL + E    
Sbjct:   411 YCSLFPEDYEVRKEELIEYWMCEGFIDGNEDEDGANNKGHDIIGSLVRAHLLMDGELTTK 470

Query:   453 VKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSE 512
             VKMHD+IREM+LWIA    K+K+   V+ GV+L   PK   WE  +R+SLM N+I ++S 
Sbjct:   471 VKMHDVIREMALWIASNFGKQKETLCVKPGVQLCHIPKDINWESLRRMSLMCNQIANISS 530

Query:   513 I---PTLLSLR-RNDSLTELPSRIXXX--XXXXXXXXXXXXIRGLPQELKALEKLRYLNL 566
                 P L +L  +N+ L  +                     +  LP+ +  L  L+Y+NL
Sbjct:   531 SSNSPNLSTLLLQNNKLVHISCDFFRFMPALVVLDLSRNSSLSSLPEAISKLGSLQYINL 590

Query:   567 EYT 569
               T
Sbjct:   591 STT 593

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 721 (258.9 bits), Expect = 1.0e-103, Sum P(3) = 1.0e-103
 Identities = 195/603 (32%), Positives = 295/603 (48%)

Query:     1 MGNLISTSLPPDLFSRTLHR-VGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVE 59
             MG   S ++  D     L   +    N    L  ++  LK  +R+L   RDDL+ +++V+
Sbjct:     1 MGACFSVAISCDQAVNNLTSCLSRNQNRFRNLVDHVAALKKTVRQLEARRDDLLKRIKVQ 60

Query:    60 EQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREV 119
             E  R     + V  WL +V+    E  ++     +E+D LC G  CSK    SY+Y + V
Sbjct:    61 ED-RGLNLLDEVQQWLSEVESRVCEAHDILSQSDEEIDNLCCGQYCSKRCKYSYDYSKSV 119

Query:   120 VELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRX 179
             +     V NL   G     V +K P     E    Q IVGQE ++   W  +   +    
Sbjct:   120 INKLQDVENLLSKGV-FDEVAQKGPIPKVEERLFHQEIVGQEAIVESTWNSM--MEVGVG 176

Query:   180 XXXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED 233
                        KTTLL Q+NN F    ++FD+ IW  V      +  Q+DIGKR+    +
Sbjct:   177 LLGIYGMGGVGKTTLLSQINNKFRTVSNDFDIAIWVVVSKNPTVKRIQEDIGKRLDLYNE 236

Query:   234 KKWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSA 284
               W++K+  + A  I   L  KK+         ++DL  +G+P+   N G KI   +RS 
Sbjct:   237 G-WEQKTENEIASTIKRSLENKKYMLLLDDMWTKVDLANIGIPVPKRN-GSKIAFTSRSN 294

Query:   285 GVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
              VC +M   K +EV  L  D+AW LF   + + TL+SH  IPE+A+++AR+C  LPLAL 
Sbjct:   295 EVCGKMGVDKEIEVTCLMWDDAWDLFTRNM-KETLESHPKIPEVAKSIARKCNGLPLALN 353

Query:   344 TVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC 403
              +G  M        R+++IE+   +   FSG+E ++   LKFSYD L  +K +SC L+  
Sbjct:   354 VIGETMA-------RKKSIEEWHDAVGVFSGIEADILSILKFSYDDLKCEKTKSCFLFSA 406

Query:   404 LYPEDYKIPKRSLIDYWISEGFMADFD----RGCEFINDLLHACLLEE-EGDDHVKMHDM 458
             L+PEDY+I K  LI+YW+ +G +        +G   I  L  A LL+E E  + VKMHD+
Sbjct:   407 LFPEDYEIGKDDLIEYWVGQGIILGSKGINYKGYTIIGTLTRAYLLKESETKEKVKMHDV 466

Query:   459 IREMSLWIAWTI--EKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSE---I 513
             +REM+LWI+     +K+K   +V A  +L + PK+++ +  +R+SL+ N+IE   E    
Sbjct:   467 VREMALWISSGCGDQKQKNVLVVEANAQLRDIPKIEDQKAVRRMSLIYNQIEEACESLHC 526

Query:   514 PTLLSLRRNDSLTELPSRIXXXXXXXXXXXXXXXIRGLPQ--ELKALEKLRYLNLEYTHY 571
             P L +L   D+     SR                   L +      L  LR+LNL  T  
Sbjct:   527 PKLETLLLRDNRLRKISREFLSHVPILMVLDLSLNPNLIELPSFSPLYSLRFLNLSCTGI 586

Query:   572 LSI 574
              S+
Sbjct:   587 TSL 589

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

 Score = 846 (302.9 bits), Expect = 5.8e-103, Sum P(2) = 5.8e-103
 Identities = 252/751 (33%), Positives = 369/751 (49%)

Query:     1 MGNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEE 60
             MGN +   +  D     + R      Y+  L+KNL  L+ EM  L  T+ ++ NKV  EE
Sbjct:     1 MGNFVCIEISGDQMLDRIIRCLCGKGYIRNLEKNLRALQREMEDLRATQHEVQNKVAREE 60

Query:    61 QPRRTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVV 120
               R  +R   V  WL+ V  +  E  +L  V   E+ +LCL GLCSK + SSY YG+ V 
Sbjct:    61 S-RHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVF 119

Query:   121 ELTDRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRXX 180
              L + V  L  +G     V +  P     E P + TI GQE++L + W  + +       
Sbjct:   120 LLLEEVTKLKSEGN-FDEVSQPPPRSEVEERPTQPTI-GQEEMLKKAWNRLMEDGVG--I 175

Query:   181 XXXXXXXXXXKTTLLKQVNNNFCHQQHNFDVVIW------AAVQTFQDDIGKRIGFSEDK 234
                       KTTL K+++N F      FD+VIW      A +   Q+DI +++   +D 
Sbjct:   176 MGLHGMGGVGKTTLFKKIHNKFAETGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDL 235

Query:   235 KWKEKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAG 285
              WK K+  DKA DI  +L  K+F         ++DL  +G+P        K+   TR   
Sbjct:   236 -WKNKNESDKATDIHRVLKGKRFVLMLDDIWEKVDLEAIGIPYPSEVNKCKVAFTTRDQK 294

Query:   286 VCDQM-DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT 344
             VC QM D K ++V  L  ++AW+LF+  +  +TL S   I  LA  +A++C  LPLAL  
Sbjct:   295 VCGQMGDHKPMQVKCLEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSC 354

Query:   345 VGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCL 404
             +G  M S+  V + E AI+ +  SA+ FS M+  +   LK+SYDSL  + ++SC LYC L
Sbjct:   355 IGETMASKTMVQEWEHAIDVLTRSAAEFSDMQNKILPILKYSYDSLEDEHIKSCFLYCAL 414

Query:   405 YPEDYKIPKRSLIDYWISEGFMADF-------DRGCEFINDLLHACLL-EEEG--DDHVK 454
             +PED KI  ++LI+ WI EGF+ +        ++G E +  L+ A LL  + G    HV 
Sbjct:   415 FPEDDKIDTKTLINKWICEGFIGEDQVIKRARNKGYEMLGTLIRANLLTNDRGFVKWHVV 474

Query:   455 MHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL---- 510
             MHD++REM+LWIA    K+K+N++VRA V L E PKVK+W   +R+SLM NEIE +    
Sbjct:   475 MHDVVREMALWIASDFGKQKENYVVRARVGLHEIPKVKDWGAVRRMSLMMNEIEEITCES 534

Query:   511 --SEIPTLLSLRRNDSLTELPSRIXXXXXXXXXXXXXXX--IRGLPQELKALEKLRYLNL 566
               SE+ TL  L+ N  L  L                        LP+++  L  L+YL+L
Sbjct:   535 KCSELTTLF-LQSNQ-LKNLSGEFIRYMQKLVVLDLSHNPDFNELPEQISGLVSLQYLDL 592

Query:   567 EYTHYLSIIPHQLISGFLKLEVLRLLE-CGSEGVTKEEGNVLCDDAEPLMRELLGLKRLN 625
              +T        QL  G  +L+ L  L  C +E         LC         + G+ RL 
Sbjct:   593 SWTRI-----EQLPVGLKELKKLIFLNLCFTER--------LCS--------ISGISRLL 631

Query:   626 VLSW-SFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD-KLRDVSDI 683
              L W S R S  V         D + L  +Q L+ L+ +  TE  E+I +D +L  +  +
Sbjct:   632 SLRWLSLRES-NVHG-------DASVLKELQQLENLQDLRITESAELISLDQRLAKLISV 683

Query:   684 SEIIGSEHNFF--TQLESLGILYGPDLKSIY 712
               I G     F  + L S+  LYG  +++ Y
Sbjct:   684 LRIEGFLQKPFDLSFLASMENLYGLLVENSY 714

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2031366 AT1G63350 "AT1G63350" [Arabidopsis thaliana (taxid:3702)]

 Score = 762 (273.3 bits), Expect = 8.8e-96, Sum P(2) = 8.8e-96
 Identities = 210/625 (33%), Positives = 311/625 (49%)

Query:     5 ISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPR 63
             IS S+P D   ++    +  + +Y   L+KNL  L+T M +L   RDDL+ K++ EE  R
Sbjct:     3 ISFSIPFDPCVNKVSQWLDMKVSYTHNLEKNLVALETTMEELKAKRDDLLRKLKREED-R 61

Query:    64 RTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELT 123
               +    +  WL  V+ + +   +L   R  E+ RLCL G CSK+L +SY YG+ V    
Sbjct:    62 GLQTLGEIKVWLNRVETIESRVNDLLNARNAELQRLCLCGFCSKSLTTSYRYGKSVFLKL 121

Query:   124 DRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRXXXXX 183
               V  L +      V+ ++A      E  L+ TIVGQE +L   W  + +          
Sbjct:   122 REVEKLER--RVFEVISDQASTSEVEEQQLQPTIVGQETMLDNAWNHLMEDGVG--IMGL 177

Query:   184 XXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDKKWK 237
                    KTTLL Q+NN F      FD VIW  V      +   D+I +++  S +K W 
Sbjct:   178 YGMGGVGKTTLLTQINNKFSKYMCGFDSVIWVVVSKEVNVENILDEIAQKVHISGEK-WD 236

Query:   238 EKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAGVCD 288
              K    K V + + L   +F         +++L E+GVP   +    K+V  TRS  VC 
Sbjct:   237 TKYKYQKGVYLYNFLRKMRFVLFLDDIWEKVNLVEIGVPFPTIKNKCKVVFTTRSLDVCT 296

Query:   289 QMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGR 347
              M   K +EV  LA ++A+ LFQ+ + + TL S   I EL+  +A++C  LPLAL  V  
Sbjct:   297 SMGVEKPMEVQCLADNDAYDLFQKKVGQITLGSDPEIRELSRVVAKKCCGLPLALNVVSE 356

Query:   348 AMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPE 407
              M  ++ V +   AI  + + A+ FSGM++ +   LK+SYDSL  + ++ CLLYC L+PE
Sbjct:   357 TMSCKRTVQEWRHAIYVLNSYAAKFSGMDDKILPLLKYSYDSLKGEDVKMCLLYCALFPE 416

Query:   408 DYKIPKRSLIDYWI-------SEGFMADFDRGCEFINDLLHACLLEEE----GDDHVKMH 456
             D KI K +LI+YWI       SEG     ++G E I  L+ A LL EE    G + V +H
Sbjct:   417 DAKIRKENLIEYWICEEIIDGSEGIDKAENQGYEIIGSLVRASLLMEEVELDGANIVCLH 476

Query:   457 DMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTL 516
             D++REM+LWIA  + K+ + F+VRA V L E  KV+ W   +R+SLM N I  L      
Sbjct:   477 DVVREMALWIASDLGKQNEAFIVRASVGLREILKVENWNVVRRMSLMKNNIAHLDG---- 532

Query:   517 LSLRRNDSLTELPSRIXXXXXXXXXXXXXXXIRGLPQELKALEKLRYLNLEYTHYLSIIP 576
                 R D + EL + +                    +   ++ KL  L+L   +YLS +P
Sbjct:   533 ----RLDCM-ELTTLLLQSTHLEKISS---------EFFNSMPKLAVLDLSGNYYLSELP 578

Query:   577 HQLISGFLKLEVLRLLECGSEGVTK 601
             +  IS  + L+ L L   G   + K
Sbjct:   579 NG-ISELVSLQYLNLSSTGIRHLPK 602

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2203881 AT1G62630 [Arabidopsis thaliana (taxid:3702)]

 Score = 790 (283.2 bits), Expect = 2.6e-94, Sum P(2) = 2.6e-94
 Identities = 194/534 (36%), Positives = 287/534 (53%)

Query:     5 ISTSLPPD-LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPR 63
             IS S+P D   ++    +  + +Y   L+KNL  L+T M +L   RDDL+ +++ EE  R
Sbjct:     3 ISFSIPFDPCVNKVSQWLDMKGSYTHNLEKNLVALETTMEELKAKRDDLLRRLKREED-R 61

Query:    64 RTRRTNRVAGWLEDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELT 123
               +R +    WL  V  +      L + R  E+ RLCL   CSKNL +SY YG+ V  L 
Sbjct:    62 GLQRLSEFQVWLNRVATVEDIIITLLRDRDVEIQRLCLCRFCSKNLTTSYRYGKSVF-LR 120

Query:   124 DRVINLNKDGEKIAVVVEKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRXXXXX 183
              R +   K GE   V+ E+A   A  E PL+ TIVGQ+K+L + W+ + +          
Sbjct:   121 LREVEKLK-GEVFGVITEQASTSAFEERPLQPTIVGQKKMLDKAWKHLMED--GTGIMGM 177

Query:   184 XXXXXXXKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDKKWK 237
                    KTTLL Q+ N F   +  FD+ IW  V      +  QD+I +++G     +W 
Sbjct:   178 YGMGGVGKTTLLTQLFNMFNKDKCGFDIGIWVVVSQEVNVEKIQDEIAQKLGLG-GHEWT 236

Query:   238 EKSLQDKAVDISSILSPKKF---------RIDLTELGVPLQMLNAGFKIVLKTRSAGVCD 288
             ++ +  K V + + L  KKF         +++L  +GVP      G K+   +RS  VC 
Sbjct:   237 QRDISQKGVHLFNFLKNKKFVLFLDDLWDKVELANIGVPDPRTQKGCKLAFTSRSLNVCT 296

Query:   289 QM-DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGR 347
              M D + +EV  L  + A+ LFQ+ + + TL S   IP+LA  +A++C  LPLAL  +G 
Sbjct:   297 SMGDEEPMEVQCLEENVAFDLFQKKVGQKTLGSDPGIPQLARIVAKKCCGLPLALNVIGE 356

Query:   348 AMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPE 407
              M  ++ + +   AI  + + A+ F GME+ +   LK+SYD+L  + ++S LLYC LYPE
Sbjct:   357 TMSCKRTIQEWRNAIHVLNSYAAEFIGMEDKILPLLKYSYDNLKGEHVKSSLLYCALYPE 416

Query:   408 DYKIPKRSLIDYWI-------SEGFMADFDRGCEFINDLLHACLLEE----EGDDHVKMH 456
             D KI K  LI++WI       SEG     D+G + I  L+ A LL E    +G   V MH
Sbjct:   417 DAKIRKEDLIEHWICEEIIDGSEGIEKAEDKGYDIIGSLVRASLLMECVDLKGKSSVIMH 476

Query:   457 DMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESL 510
             D++REM+LWIA  +  +K+ F+VRAGV + E PKVK W   +R+SLM N+I  L
Sbjct:   477 DVVREMALWIASELGIQKEAFIVRAGVGVREIPKVKNWNVVRRMSLMGNKIHHL 530

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 706 (253.6 bits), Expect = 4.4e-90, Sum P(2) = 4.4e-90
 Identities = 157/416 (37%), Positives = 232/416 (55%)

Query:    27 YVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFT 86
             Y+  L KN+  +K +M  L + RDD+  +V++EE  RR  R ++V GWL +V  +  +F 
Sbjct:    28 YICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEFTRRRERLSQVQGWLTNVSTVENKFN 87

Query:    87 ELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVEKAPDG 146
             EL      E+ RLCL G CSKN+  SY YG+ VV +   + +L+  G+   V +   P  
Sbjct:    88 ELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVLMLKEIESLSSQGDFDTVTLA-TPIA 146

Query:   147 AAIELPLEQTIVGQEKLLPRVWRCITDQQKNRXXXXXXXXXXXXKTTLLKQVNNNFCHQQ 206
                E+P++ TIVGQE +L RVW  +T+                 KTTLL ++NN F  + 
Sbjct:   147 RIEEMPIQPTIVGQETMLERVWTRLTEDGDE--IVGLYGMGGVGKTTLLTRINNKFSEKC 204

Query:   207 HNFDVVIWAAVQT------FQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF--- 257
               F VVIW  V         Q DIGKR+    ++ W   +   +A+DI ++L  +KF   
Sbjct:   205 SGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGEE-WDNVNENQRALDIYNVLGKQKFVLL 263

Query:   258 ------RIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKN-LEVYSLAHDEAWKLFQ 310
                   +++L  LGVP      G K+V  TRS  VC +M   + +EV  L  +EAW+LFQ
Sbjct:   264 LDDIWEKVNLEVLGVPYPSRQNGCKVVFTTRSRDVCGRMRVDDPMEVSCLEPNEAWELFQ 323

Query:   311 EMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSAS 370
               +  +TL  H  IPELA  +A +C  LPLAL  +G  M  ++ V +   AI+ + + A+
Sbjct:   324 MKVGENTLKGHPDIPELARKVAGKCCGLPLALNVIGETMACKRMVQEWRNAIDVLSSYAA 383

Query:   371 TFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFM 426
              F GME+ +   LK+SYD+L+ ++++ C LYC L+PEDY++ K  LIDYWI EGF+
Sbjct:   384 EFPGMEQ-ILPILKYSYDNLNKEQVKPCFLYCSLFPEDYRMEKERLIDYWICEGFI 438

GO:0006952 "defense response" evidence=IGI;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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O64973	RPS5_ARATH	No assigned EC number	0.3615	0.9794	0.8582	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pm.C_LG_I001004 cc-nbs-lrr resistance protein (880 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	779
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-55
PLN03210	1153	PLN03210, PLN03210, Resistant to P	0.003
pfam13855	60	pfam13855, LRR_8, Leucine rich repeat	0.003

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

 Score =  191 bits (488), Expect = 2e-55
 Identities = 97/283 (34%), Positives = 148/283 (52%), Gaps = 21/283 (7%)

Query: 160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-Q 218
           +E ++  +   + +   N G++G+ G+GGVGKTTL KQ+ N+      +FD V W  V +
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDD-SVGGHFDSVAWVVVSK 59

Query: 219 TF-----QDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF---------RIDLTEL 264
           T+     Q DI + +G  +D  W EK+  + AV I   L  K+F         + D  ++
Sbjct: 60  TYTEFRLQKDILQELG-LDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDKI 118

Query: 265 GVPLQMLNAGFKIVLKTRSAGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHT 322
           GVP      G ++++ TRS  V  +M   SK  EV SL  +E+W+LF   +    L    
Sbjct: 119 GVPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCP 178

Query: 323 SIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLR 382
            + E+A+ +  +C  LPLALK +G  +  +  V + E  +E++    +   G+ E V   
Sbjct: 179 ELEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNE-VLSI 237

Query: 383 LKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGF 425
           L  SYD+L M  L+ C LY  L+PEDY I K  LI  WI+EGF
Sbjct: 238 LSLSYDNLPMH-LKRCFLYLALFPEDYNIRKEQLIKLWIAEGF 279

Length = 285

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

 Score = 41.0 bits (96), Expect = 0.003
 Identities = 70/279 (25%), Positives = 110/279 (39%), Gaps = 53/279 (18%)

Query: 491 VKEWEGAKRISLMANEIESLSEIPTL--------LSLRRNDSLTELPSRISSLVSLHHLD 542
           V    G + I L  ++  +L EIP L        L L    SL ELPS I  L  L  LD
Sbjct: 630 VHSLTGLRNIDLRGSK--NLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLD 687

Query: 543 LS-LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTK 601
           +S   ++  LP  +  L+ L  LNL     L   P   IS    +  L L E   E    
Sbjct: 688 MSRCENLEILPTGIN-LKSLYRLNLSGCSRLKSFPD--IST--NISWLDLDETAIEEFPS 742

Query: 602 EEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELE 661
                            L L+ L+ L      S   +K ++           VQ L  L 
Sbjct: 743 N----------------LRLENLDELILCEMKS---EKLWER----------VQPLTPLM 773

Query: 662 IIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKL 721
            ++   +  +     L D+  + E+  S  N   +LE L I    +L+++ P  ++   L
Sbjct: 774 TMLSPSLTRLF----LSDIPSLVELPSSIQNL-HKLEHLEIENCINLETL-PTGINLESL 827

Query: 722 KKIGVYGCPKLKKLPINSSSAKERRVVIEGLKE--WWEE 758
           + + + GC +L+  P  S++  +  +   G++E  WW E
Sbjct: 828 ESLDLSGCSRLRTFPDISTNISDLNLSRTGIEEVPWWIE 866

syringae 6; Provisional. Length = 1153

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

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTH 570
             L L  N  LT +P      L +L  LDLS  ++  +  E    L  LR L+L   +
Sbjct: 3   KSLDLSNN-RLTVIPDGAFKGLPNLKVLDLSGNNLTSISPEAFSGLPSLRSLDLSGNN 59

Length = 60

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	779
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.66
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.65
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.64
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.61
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.59
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.52
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.52
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.5
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.46
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.44
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.38
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.35
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.29
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.25
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.2
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.19
PRK04841	903	transcriptional regulator MalT; Provisional	99.18
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	99.15
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.14
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.09
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.02
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.01
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.97
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.88
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.85
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.84
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.79
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.78
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.71
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.7
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.68
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.63
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.61
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.61
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.59
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.57
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.51
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.47
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.47
PRK06893	229	DNA replication initiation factor; Validated	98.42
PF05729	166	NACHT: NACHT domain	98.39
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.36
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.33
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.31
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	98.31
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.3
PRK13342	413	recombination factor protein RarA; Reviewed	98.28
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.25
COG3903	414	Predicted ATPase [General function prediction only	98.24
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.23
PLN03150	623	hypothetical protein; Provisional	98.22
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.14
COG3899	849	Predicted ATPase [General function prediction only	98.12
PRK08727	233	hypothetical protein; Validated	98.12
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.1
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	98.1
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.07
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	98.01
PTZ00202	550	tuzin; Provisional	98.01
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.99
KOG2028	554	consensus ATPase related to the helicase subunit o	97.98
PRK12402	337	replication factor C small subunit 2; Reviewed	97.96
PRK15386	426	type III secretion protein GogB; Provisional	97.92
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.9
PLN03150	623	hypothetical protein; Provisional	97.89
PRK09087	226	hypothetical protein; Validated	97.89
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.87
PRK04195	482	replication factor C large subunit; Provisional	97.87
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.85
PRK08084	235	DNA replication initiation factor; Provisional	97.83
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.77
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.77
PRK15386	426	type III secretion protein GogB; Provisional	97.76
PRK13341	725	recombination factor protein RarA/unknown domain f	97.74
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.73
PRK05642	234	DNA replication initiation factor; Validated	97.72
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.72
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.71
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.7
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.67
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.67
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.65
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.63
PLN03025	319	replication factor C subunit; Provisional	97.62
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.62
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.62
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.61
cd01128	249	rho_factor Transcription termination factor rho is	97.58
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.57
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.56
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.56
PF13173	128	AAA_14: AAA domain	97.56
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.54
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.53
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.52
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.5
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.45
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.43
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.38
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	97.38
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.38
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.37
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.36
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.36
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.36
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.36
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.35
PRK09376	416	rho transcription termination factor Rho; Provisio	97.33
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	97.32
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.31
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.31
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.3
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.27
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.27
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.26
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.25
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.23
PF14516	331	AAA_35: AAA-like domain	97.22
PRK06620	214	hypothetical protein; Validated	97.22
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.21
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.21
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.2
PRK12422	445	chromosomal replication initiation protein; Provis	97.19
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.19
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.19
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.17
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.16
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.14
CHL00181	287	cbbX CbbX; Provisional	97.11
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.1
PRK08118	167	topology modulation protein; Reviewed	97.1
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.09
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.07
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.07
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.05
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.04
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.04
TIGR00767	415	rho transcription termination factor Rho. Members	97.0
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.97
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.96
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.95
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.92
PRK08116	268	hypothetical protein; Validated	96.91
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.88
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.86
PRK07261	171	topology modulation protein; Provisional	96.85
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.85
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.85
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	96.83
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.83
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.82
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.8
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.79
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.77
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.77
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	96.77
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.75
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.75
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.73
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.73
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.71
CHL00095	821	clpC Clp protease ATP binding subunit	96.69
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.69
PRK12377	248	putative replication protein; Provisional	96.67
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.66
PRK06696	223	uridine kinase; Validated	96.63
PRK07952	244	DNA replication protein DnaC; Validated	96.56
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.56
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.53
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.46
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.43
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.43
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.41
KOG4341	483	consensus F-box protein containing LRR [General fu	96.38
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.37
PRK07667	193	uridine kinase; Provisional	96.37
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.35
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	96.33
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.3
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.28
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.28
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.26
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.24
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	96.16
PRK15455	644	PrkA family serine protein kinase; Provisional	96.15
CHL00176	638	ftsH cell division protein; Validated	96.14
PHA00729	226	NTP-binding motif containing protein	96.13
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.13
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.1
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.08
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.08
PRK07399	314	DNA polymerase III subunit delta'; Validated	96.03
PRK13531	498	regulatory ATPase RavA; Provisional	96.01
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.0
PRK10536	262	hypothetical protein; Provisional	95.97
PRK06547	172	hypothetical protein; Provisional	95.94
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.94
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	95.93
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.93
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	95.89
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.83
PRK05541	176	adenylylsulfate kinase; Provisional	95.78
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.76
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.76
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.73
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	95.73
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.7
PRK10865	857	protein disaggregation chaperone; Provisional	95.65
PRK08233	182	hypothetical protein; Provisional	95.64
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.63
PRK04040	188	adenylate kinase; Provisional	95.62
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.61
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.59
KOG1947	482	consensus Leucine rich repeat proteins, some prote	95.58
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.57
KOG2123	388	consensus Uncharacterized conserved protein [Funct	95.56
PRK05480	209	uridine/cytidine kinase; Provisional	95.54
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	95.53
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.52
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.5
PRK10867	433	signal recognition particle protein; Provisional	95.46
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.46
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.43
PRK06762	166	hypothetical protein; Provisional	95.43
PHA02544	316	44 clamp loader, small subunit; Provisional	95.42
PTZ00301	210	uridine kinase; Provisional	95.41
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	95.39
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.38
PRK09354	349	recA recombinase A; Provisional	95.35
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.35
PRK03839	180	putative kinase; Provisional	95.31
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.24
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.24
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	95.24
PF00004	132	AAA: ATPase family associated with various cellula	95.22
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.19
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.16
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	95.15
smart00382	148	AAA ATPases associated with a variety of cellular	95.12
CHL00195	489	ycf46 Ycf46; Provisional	95.1
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.1
PRK00625	173	shikimate kinase; Provisional	95.05
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.02
PRK05439	311	pantothenate kinase; Provisional	95.01
KOG2123	388	consensus Uncharacterized conserved protein [Funct	94.97
PRK06217	183	hypothetical protein; Validated	94.96
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	94.87
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	94.87
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	94.85
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.8
PF07726	131	AAA_3: ATPase family associated with various cellu	94.79
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.78
PRK00131	175	aroK shikimate kinase; Reviewed	94.78
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	94.78
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.75
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.74
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.73
) 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	94.72
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	94.72
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	94.71
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	94.7
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	94.69
KOG1514	767	consensus Origin recognition complex, subunit 1, a	94.68
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.68
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	94.67
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.65
PRK12608	380	transcription termination factor Rho; Provisional	94.63
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.61
PRK10865	857	protein disaggregation chaperone; Provisional	94.61
PRK00889	175	adenylylsulfate kinase; Provisional	94.56
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.54
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	94.53
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	94.52
PRK13947	171	shikimate kinase; Provisional	94.49
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	94.49
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	94.48
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.47
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	94.45
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.44
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	94.41
cd01394	218	radB RadB. The archaeal protein radB shares simila	94.4
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.39
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	94.39
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	94.34
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	94.34
PRK13949	169	shikimate kinase; Provisional	94.32
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.31
TIGR00064	272	ftsY signal recognition particle-docking protein F	94.3
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.28
PRK13765	637	ATP-dependent protease Lon; Provisional	94.27
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	94.24
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	94.23
PRK04328	249	hypothetical protein; Provisional	94.23
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.22
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	94.21
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	94.19
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.18
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.17
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	94.17
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	94.11
PRK14530	215	adenylate kinase; Provisional	94.11
PRK08181	269	transposase; Validated	94.09
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	94.08
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	94.07
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	94.06
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.03
PRK13948	182	shikimate kinase; Provisional	94.03
PRK12339	197	2-phosphoglycerate kinase; Provisional	94.01
PRK06835	329	DNA replication protein DnaC; Validated	94.01
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.99
PRK14738	206	gmk guanylate kinase; Provisional	93.98
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	93.97
PLN02318	656	phosphoribulokinase/uridine kinase	93.95
PRK08939	306	primosomal protein DnaI; Reviewed	93.95
PRK03846	198	adenylylsulfate kinase; Provisional	93.92
PRK08058	329	DNA polymerase III subunit delta'; Validated	93.91
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	93.9
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	93.9
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.87
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	93.86
PRK14974	336	cell division protein FtsY; Provisional	93.84
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	93.84
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	93.84
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	93.82
PF13245	76	AAA_19: Part of AAA domain	93.8
KOG4341	483	consensus F-box protein containing LRR [General fu	93.79
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	93.79
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	93.79
COG2884	223	FtsE Predicted ATPase involved in cell division [C	93.79
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	93.78
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	93.78
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	93.75
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	93.74
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.73
cd03216	163	ABC_Carb_Monos_I This family represents the domain	93.71
PRK06067	234	flagellar accessory protein FlaH; Validated	93.7
PRK00409	782	recombination and DNA strand exchange inhibitor pr	93.7
PRK13975	196	thymidylate kinase; Provisional	93.69
PRK14527	191	adenylate kinase; Provisional	93.69
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	93.69
PRK00300	205	gmk guanylate kinase; Provisional	93.68
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	93.66
TIGR00959	428	ffh signal recognition particle protein. This mode	93.63
PRK06526	254	transposase; Provisional	93.63
PRK09435	332	membrane ATPase/protein kinase; Provisional	93.62
cd03115	173	SRP The signal recognition particle (SRP) mediates	93.6
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	93.59
PRK13946	184	shikimate kinase; Provisional	93.59
PRK05057	172	aroK shikimate kinase I; Reviewed	93.58
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	93.57
PLN02200	234	adenylate kinase family protein	93.54
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	93.49
PRK09183	259	transposase/IS protein; Provisional	93.48
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	93.48
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	93.46
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	93.46
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	93.45
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	93.45
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.43
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	93.4
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	93.39
TIGR01287	275	nifH nitrogenase iron protein. This model describe	93.35
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	93.35
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	93.32
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.32
PRK06871	325	DNA polymerase III subunit delta'; Validated	93.32
COG0714	329	MoxR-like ATPases [General function prediction onl	93.32
cd02117	212	NifH_like This family contains the NifH (iron prot	93.31
PRK06921	266	hypothetical protein; Provisional	93.3
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	93.27
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.26
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	93.24
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	93.22
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.2
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	93.19
PRK05973	237	replicative DNA helicase; Provisional	93.16
PRK04182	180	cytidylate kinase; Provisional	93.15
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	93.15
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	93.15
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	93.14
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	93.13
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	93.12
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	93.11
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	93.1
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	93.08
PRK04296	190	thymidine kinase; Provisional	93.07
PRK15453	290	phosphoribulokinase; Provisional	93.05
PRK13695	174	putative NTPase; Provisional	93.01
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	93.01
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	93.0
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	93.0
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	92.99
CHL00095	821	clpC Clp protease ATP binding subunit	92.97
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	92.95
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	92.94
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	92.93
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	92.92
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	92.92
PTZ00088	229	adenylate kinase 1; Provisional	92.91
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	92.91
PLN02348	395	phosphoribulokinase	92.9
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	92.89
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	92.88
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	92.88
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	92.87
PRK14737	186	gmk guanylate kinase; Provisional	92.85
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	92.85
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	92.85
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	92.82
PRK03731	171	aroL shikimate kinase II; Reviewed	92.82
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	92.81
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	92.78
PRK14532	188	adenylate kinase; Provisional	92.77
PRK06761	282	hypothetical protein; Provisional	92.76
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	92.71
KOG0736	953	consensus Peroxisome assembly factor 2 containing	92.7
KOG4252	246	consensus GTP-binding protein [Signal transduction	92.7
PRK07993	334	DNA polymerase III subunit delta'; Validated	92.7
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.68
KOG1969	877	consensus DNA replication checkpoint protein CHL12	92.65
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	92.65
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	92.65
PRK13230	279	nitrogenase reductase-like protein; Reviewed	92.64
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	92.63
PF06564	243	YhjQ: YhjQ protein; InterPro: IPR017746 The YhjQ p	92.61
PRK13236	296	nitrogenase reductase; Reviewed	92.61
PRK13768	253	GTPase; Provisional	92.61
KOG0473	326	consensus Leucine-rich repeat protein [Function un	92.61
PRK09825	176	idnK D-gluconate kinase; Provisional	92.56
PRK13232	273	nifH nitrogenase reductase; Reviewed	92.54
PTZ00494	664	tuzin-like protein; Provisional	92.53
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	92.51
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.49
PRK10416	318	signal recognition particle-docking protein FtsY;	92.43
cd02040	270	NifH NifH gene encodes component II (iron protein)	92.38
PRK14531	183	adenylate kinase; Provisional	92.37
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	92.36
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	92.35
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	92.35
PRK11823	446	DNA repair protein RadA; Provisional	92.33
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	92.3
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	92.29
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	92.27
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	92.26
PRK09519	790	recA DNA recombination protein RecA; Reviewed	92.25
PRK10646	153	ADP-binding protein; Provisional	92.24
PRK08840	464	replicative DNA helicase; Provisional	92.21
PRK08099	399	bifunctional DNA-binding transcriptional repressor	92.18
PRK12338	319	hypothetical protein; Provisional	92.18
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	92.17
PRK08533	230	flagellar accessory protein FlaH; Reviewed	92.17
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	92.17
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	92.14
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	92.12
PRK08506	472	replicative DNA helicase; Provisional	92.12
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	92.11
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	92.11
PRK01184	184	hypothetical protein; Provisional	92.1
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.1
PLN02165	334	adenylate isopentenyltransferase	92.09
PRK14528	186	adenylate kinase; Provisional	92.05
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	92.05
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	92.05
PF00005	137	ABC_tran: ABC transporter This structure is on hol	92.04
PRK13235	274	nifH nitrogenase reductase; Reviewed	91.98
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	91.98
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	91.96
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	91.95
COG1100	219	GTPase SAR1 and related small G proteins [General	91.94
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	91.94
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	91.94
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	91.93
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	91.91
PRK13233	275	nifH nitrogenase reductase; Reviewed	91.9
PRK08356	195	hypothetical protein; Provisional	91.88
cd03269	210	ABC_putative_ATPase This subfamily is involved in	91.85
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	91.84
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.84
PRK04301	317	radA DNA repair and recombination protein RadA; Va	91.84
PRK02496	184	adk adenylate kinase; Provisional	91.81
PHA02530	300	pseT polynucleotide kinase; Provisional	91.81
cd03116	159	MobB Molybdenum is an essential trace element in t	91.8
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	91.8
PRK00279	215	adk adenylate kinase; Reviewed	91.79
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	91.78
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	91.78
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	91.76
PHA02244	383	ATPase-like protein	91.74
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	91.74
cd03114	148	ArgK-like The function of this protein family is u	91.74
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	91.71
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	91.7
PLN02796	347	D-glycerate 3-kinase	91.69
PRK05748	448	replicative DNA helicase; Provisional	91.67
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	91.67
TIGR02016	296	BchX chlorophyllide reductase iron protein subunit	91.67

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=1.3e-85  Score=754.33  Aligned_cols=740  Identities=38%  Similarity=0.606  Sum_probs=591.6

Q ss_pred             hhhHHHHHHHHHhhhhcchhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCchhHHHHHHHHHHHHHHHHHHH
Q 004021           10 PPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQ   89 (779)
Q Consensus        10 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~~~~~~~~~~~Wl~~l~~~~~d~ed~l   89 (779)
                      ++-.++++.+.+.+++..+.+.++++..+++++..|+++++|       ++.++  .....+..|...+++++|+++|.+
T Consensus         5 ~s~~~~~~~~~l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d-------~~a~~--~~~~~~~~~~e~~~~~~~~~e~~~   75 (889)
T KOG4658|consen    5 VSFGVEKLDQLLNRESECLDGKDNYILELKENLKALQSALED-------LDAKR--DDLERRVNWEEDVGDLVYLAEDII   75 (889)
T ss_pred             EEEehhhHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHH-------HHhhc--chHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567888899999999999999999999999999999998       55555  456778999999999999999999


Q ss_pred             HHHHHHhhh----------------hhcCCCCccccccccchHHHHHHHHHHHHHHHhcCcccccccc-cCCCCcccccc
Q 004021           90 QVRAQEMDR----------------LCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVVE-KAPDGAAIELP  152 (779)
Q Consensus        90 d~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~i~~~~~~i~~~~~~~~~~~~~~~-~~~~~~~~~~~  152 (779)
                      +.|......                .|..+++.......+.+++++-.+.+.++.+..++. |..+.. ..+......+|
T Consensus        76 ~~~~v~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~-~~~~~~~~~~~~~~e~~~  154 (889)
T KOG4658|consen   76 WLFLVEEIERKANDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGV-FEVVGESLDPREKVETRP  154 (889)
T ss_pred             HHHHHHHHHHHHhHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccc-eecccccccchhhcccCC
Confidence            988655422                233355666667778888888888888888876654 555543 22222333344


Q ss_pred             ccccc-cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHH
Q 004021          153 LEQTI-VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       153 ~~~~~-vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~  225 (779)
                      ..+.. ||.+..++++.+.|.++  +..+++|+||||+||||||+.++|+...++.+||.++||+|      ..++.+|+
T Consensus       155 ~~~~~~VG~e~~~~kl~~~L~~d--~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il  232 (889)
T KOG4658|consen  155 IQSESDVGLETMLEKLWNRLMED--DVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTIL  232 (889)
T ss_pred             CCccccccHHHHHHHHHHHhccC--CCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHH
Confidence            43333 99999999999999988  44999999999999999999999999339999999999999      78999999


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhh---------ccccccccCCCcEEEEEeCchhhhhh-cC-Cce
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTE---------LGVPLQMLNAGFKIVLKTRSAGVCDQ-MD-SKN  294 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~---------l~~~~~~~~~gs~IivTTR~~~va~~-~~-~~~  294 (779)
                      +.++.. +..+.....++++..+.+.|+++||++++||         ++.++|...+||||++|||+..||.. ++ ...
T Consensus       233 ~~l~~~-~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~  311 (889)
T KOG4658|consen  233 ERLGLL-DEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYP  311 (889)
T ss_pred             HHhccC-CcccchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCcc
Confidence            998875 4444555558899999999999999665555         56678888899999999999999999 77 789


Q ss_pred             eEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcc-cCcCC
Q 004021          295 LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTS-ASTFS  373 (779)
Q Consensus       295 ~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~-~~~~~  373 (779)
                      ++++.|+++|||.||++.++.......+.++++|++|+++|+|+|||++++|+.|+.+.+..+|+++.+.+.+. ..+.+
T Consensus       312 ~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~  391 (889)
T KOG4658|consen  312 IEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFS  391 (889)
T ss_pred             ccccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCC
Confidence            99999999999999999999886566677999999999999999999999999999999999999999999887 55566


Q ss_pred             CchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcch-------hhHHHHHHHHHHccccc
Q 004021          374 GMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADF-------DRGCEFINDLLHACLLE  446 (779)
Q Consensus       374 ~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~-------~~~~~~l~~L~~~sll~  446 (779)
                      ++.+.++.++++||+.||+ ++|.||+|||+||+||.|+++.|+.+|+||||+.+.       +.|+.|+++|++++|++
T Consensus       392 ~~~~~i~~iLklSyd~L~~-~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~  470 (889)
T KOG4658|consen  392 GMEESILPILKLSYDNLPE-ELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLI  470 (889)
T ss_pred             chhhhhHHhhhccHhhhhH-HHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHh
Confidence            7778999999999999996 999999999999999999999999999999999773       79999999999999999


Q ss_pred             ccC----CCcEEechHHHHHHHHHHhhhhhccccEEEEcCcccccCccccccCCccEEEcccccccccccCcc-------
Q 004021          447 EEG----DDHVKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-------  515 (779)
Q Consensus       447 ~~~----~~~~~mHdlv~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-------  515 (779)
                      ...    ..+|+|||+||++|.+++++.+++++++++..+....+.|....|..+|++++++|.+..++..+.       
T Consensus       471 ~~~~~~~~~~~kmHDvvRe~al~ias~~~~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~~~~~~~~~~~~L~tL  550 (889)
T KOG4658|consen  471 EERDEGRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKIEHIAGSSENPKLRTL  550 (889)
T ss_pred             hcccccceeEEEeeHHHHHHHHHHhccccccccceEEECCcCccccccccchhheeEEEEeccchhhccCCCCCCccceE
Confidence            873    378999999999999999988887788888887777778888899999999999887644322110       


Q ss_pred             ------------------------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcC
Q 004021          516 ------------------------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       516 ------------------------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~  571 (779)
                                              +|||++|..+.++|.+|++|.|||||+++++.|+.+|.++++|++|.+|++..+..
T Consensus       551 ll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~  630 (889)
T KOG4658|consen  551 LLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGR  630 (889)
T ss_pred             EEeecchhhhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccc
Confidence                                    39999998999999999999999999999999999999999999999999999987


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcc---cccCC--------------------------------cc--CCCchhh
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVT---KEEGN--------------------------------VL--CDDAEPL  614 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~---~~~~~--------------------------------~~--~~~~~~~  614 (779)
                      +..+|. ++..|++|++|.+.......-.   .++.+                                ..  .......
T Consensus       631 l~~~~~-i~~~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s~~~~e~l~~~~~L~~~~~~l~~~~~~~~~~  709 (889)
T KOG4658|consen  631 LESIPG-ILLELQSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISSVLLLEDLLGMTRLRSLLQSLSIEGCSKRTL  709 (889)
T ss_pred             cccccc-hhhhcccccEEEeeccccccchhhHHhhhcccchhhheeecchhHhHhhhhhhHHHHHHhHhhhhccccccee
Confidence            777765 3777999999999866422100   00000                                00  0111223


Q ss_pred             HHhhcCCCCCCceeEEeeccccc----------cc-CCCCCcc---------cCcccccccCcceEEeccccccceeccc
Q 004021          615 MRELLGLKRLNVLSWSFRSSLAV----------QK-FFKYPKL---------DLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       615 ~~~l~~L~~L~~L~l~~~~~~~~----------~~-~~~L~~L---------~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      +..+..+.+|+.|.+..+.....          .. ++++..+         .+.|....|+|+.|.+.+|..++++++.
T Consensus       710 ~~~~~~l~~L~~L~i~~~~~~e~~~~~~~~~~~~~~f~~l~~~~~~~~~~~r~l~~~~f~~~L~~l~l~~~~~~e~~i~~  789 (889)
T KOG4658|consen  710 ISSLGSLGNLEELSILDCGISEIVIEWEESLIVLLCFPNLSKVSILNCHMLRDLTWLLFAPHLTSLSLVSCRLLEDIIPK  789 (889)
T ss_pred             ecccccccCcceEEEEcCCCchhhcccccccchhhhHHHHHHHHhhccccccccchhhccCcccEEEEecccccccCCCH
Confidence            33455666777777776554321          00 2233332         4566677899999999999998888763


Q ss_pred             ccccCcccchhhccCCCCCCCCccEE-EccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc---ccEEEe
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESL-GILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE---RRVVIE  750 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L-~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~---~~l~i~  750 (779)
                      ........      .....|+++..+ .+.+.+.+.++......+++|+.+.+..||+++.+|......-.   ..+...
T Consensus       790 ~k~~~~l~------~~i~~f~~~~~l~~~~~l~~l~~i~~~~l~~~~l~~~~ve~~p~l~~~P~~~~~~i~~~~~~~~~~  863 (889)
T KOG4658|consen  790 LKALLELK------ELILPFNKLEGLRMLCSLGGLPQLYWLPLSFLKLEELIVEECPKLGKLPLLSTLTIVGCEEKLKEY  863 (889)
T ss_pred             HHHhhhcc------cEEecccccccceeeecCCCCceeEecccCccchhheehhcCcccccCccccccceeccccceeec
Confidence            32211100      123456777777 57777778877777778888999999999999999987554322   223334


Q ss_pred             chHhhhhhCcccccchhhhc
Q 004021          751 GLKEWWEELQWEDQATQNAF  770 (779)
Q Consensus       751 ~~~~~~~~l~w~~~~~~~~~  770 (779)
                      .+.+|.+.++|+++.++..+
T Consensus       864 ~~~~~~~~v~~~~~~~~~~~  883 (889)
T KOG4658|consen  864 PDGEWLEGVYWEDELTKLRF  883 (889)
T ss_pred             CCccceeeEEehhhhhhhhc
Confidence            66788999999999888766

>PLN03210 Resistant to P

Probab=100.00  E-value=1.3e-55  Score=535.60  Aligned_cols=556  Identities=19%  Similarity=0.258  Sum_probs=388.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---c-------------
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---Q-------------  218 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~-------------  218 (779)
                      +.+|||++.++++..+|.-+..++++|+||||||+||||||+++|++.   ..+|++.+|+..   .             
T Consensus       184 ~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l---~~~F~g~vfv~~~~v~~~~~~~~~~~~~~  260 (1153)
T PLN03210        184 EDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRL---SRQFQSSVFIDRAFISKSMEIYSSANPDD  260 (1153)
T ss_pred             ccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHH---hhcCCeEEEeeccccccchhhcccccccc
Confidence            568999999999999987666689999999999999999999999987   678999888742   0             


Q ss_pred             -----hHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhcccc---------ccccCCCcEEEEEeCch
Q 004021          219 -----TFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP---------LQMLNAGFKIVLKTRSA  284 (779)
Q Consensus       219 -----~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~---------~~~~~~gs~IivTTR~~  284 (779)
                           .++..++..+.....     .... ....+++.++++|+++++|++...         ..+.++||+||||||+.
T Consensus       261 ~~~~~~l~~~~l~~il~~~~-----~~~~-~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTrd~  334 (1153)
T PLN03210        261 YNMKLHLQRAFLSEILDKKD-----IKIY-HLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITKDK  334 (1153)
T ss_pred             cchhHHHHHHHHHHHhCCCC-----cccC-CHHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeCcH
Confidence                 122223332211100     0011 124577889999999999987532         23457899999999999


Q ss_pred             hhhhhcC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHH
Q 004021          285 GVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIE  363 (779)
Q Consensus       285 ~va~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~  363 (779)
                      +++..++ .+.|+++.|++++||+||+++||... .++.++.+++++|+++|+|+|||++++|++|++ ++..+|+.+++
T Consensus       335 ~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~-~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~-k~~~~W~~~l~  412 (1153)
T PLN03210        335 HFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKN-SPPDGFMELASEVALRAGNLPLGLNVLGSYLRG-RDKEDWMDMLP  412 (1153)
T ss_pred             HHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcC-CCHHHHHHHHH
Confidence            9998877 78999999999999999999999765 344568899999999999999999999999998 57899999999


Q ss_pred             HHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHHHHHHcc
Q 004021          364 KMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHAC  443 (779)
Q Consensus       364 ~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~~L~~~s  443 (779)
                      .++...      +..+..+|++||+.|+++..|.||+++|+|+.++.++   .+..|++.+....    ...++.|+++|
T Consensus       413 ~L~~~~------~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~~----~~~l~~L~~ks  479 (1153)
T PLN03210        413 RLRNGL------DGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLDV----NIGLKNLVDKS  479 (1153)
T ss_pred             HHHhCc------cHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCCc----hhChHHHHhcC
Confidence            987643      3489999999999998645899999999999887553   4677888765432    23489999999


Q ss_pred             cccccCCCcEEechHHHHHHHHHHhhhh--hccccEEEEcCc---------c-------------ccc--C--ccccccC
Q 004021          444 LLEEEGDDHVKMHDMIREMSLWIAWTIE--KEKKNFLVRAGV---------K-------------LTE--A--PKVKEWE  495 (779)
Q Consensus       444 ll~~~~~~~~~mHdlv~~~a~~~~~~~~--~~~~~~~~~~~~---------~-------------~~~--~--~~~~~~~  495 (779)
                      |++.. .+++.|||++|+||+++++++.  +.++.+++...+         .             ..+  +  ..+..+.
T Consensus       480 Li~~~-~~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~  558 (1153)
T PLN03210        480 LIHVR-EDIVEMHSLLQEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMR  558 (1153)
T ss_pred             CEEEc-CCeEEhhhHHHHHHHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCc
Confidence            99886 5689999999999999998753  122344432210         0             000  0  0123456


Q ss_pred             CccEEEccccccc--------------ccccCcccccccccccccccchhhcccccCceeeecCCcccccchhhccCccC
Q 004021          496 GAKRISLMANEIE--------------SLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKL  561 (779)
Q Consensus       496 ~lr~l~l~~~~~~--------------~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L  561 (779)
                      +++.|.+.++...              .+|....+|.+.++ .+..+|..| .+.+|+.|++++|.+..+|.++..+++|
T Consensus       559 ~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~-~l~~lP~~f-~~~~L~~L~L~~s~l~~L~~~~~~l~~L  636 (1153)
T PLN03210        559 NLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKY-PLRCMPSNF-RPENLVKLQMQGSKLEKLWDGVHSLTGL  636 (1153)
T ss_pred             cccEEEEecccccccccceeecCcchhhcCcccEEEEecCC-CCCCCCCcC-CccCCcEEECcCccccccccccccCCCC
Confidence            6777766544211              12222235788888 788888777 5788888888888888888888888888


Q ss_pred             cEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc-cccc--
Q 004021          562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS-LAVQ--  638 (779)
Q Consensus       562 ~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~-~~~~--  638 (779)
                      +.|+|++|..++.+|.  ++.+++|++|++.+|....              ..+..++.|++|+.|+++.+.. ..++  
T Consensus       637 k~L~Ls~~~~l~~ip~--ls~l~~Le~L~L~~c~~L~--------------~lp~si~~L~~L~~L~L~~c~~L~~Lp~~  700 (1153)
T PLN03210        637 RNIDLRGSKNLKEIPD--LSMATNLETLKLSDCSSLV--------------ELPSSIQYLNKLEDLDMSRCENLEILPTG  700 (1153)
T ss_pred             CEEECCCCCCcCcCCc--cccCCcccEEEecCCCCcc--------------ccchhhhccCCCCEEeCCCCCCcCccCCc
Confidence            8888888877788885  7888888888888876442              3556677778888888775321 1111  


Q ss_pred             -cCCCCCcccCcc---c----ccccCcceEEeccccccceecccccccCcccchh--------------hccCCCCCCCC
Q 004021          639 -KFFKYPKLDLTW---L----VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISE--------------IIGSEHNFFTQ  696 (779)
Q Consensus       639 -~~~~L~~L~~~~---l----~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~  696 (779)
                       .+++|+.|.+..   +    ...++|+.|+|+++. ++.+|..........+..              ..+.....+++
T Consensus       701 i~l~sL~~L~Lsgc~~L~~~p~~~~nL~~L~L~~n~-i~~lP~~~~l~~L~~L~l~~~~~~~l~~~~~~l~~~~~~~~~s  779 (1153)
T PLN03210        701 INLKSLYRLNLSGCSRLKSFPDISTNISWLDLDETA-IEEFPSNLRLENLDELILCEMKSEKLWERVQPLTPLMTMLSPS  779 (1153)
T ss_pred             CCCCCCCEEeCCCCCCccccccccCCcCeeecCCCc-cccccccccccccccccccccchhhccccccccchhhhhcccc
Confidence             122333331110   0    012355556665543 333332110000000000              00001123467


Q ss_pred             ccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEechHh
Q 004021          697 LESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLKE  754 (779)
Q Consensus       697 L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~~~  754 (779)
                      |+.|+|++|+.+..+|..++.+++|+.|++++|++|+.+|......+++.+.+++|..
T Consensus       780 L~~L~Ls~n~~l~~lP~si~~L~~L~~L~Ls~C~~L~~LP~~~~L~sL~~L~Ls~c~~  837 (1153)
T PLN03210        780 LTRLFLSDIPSLVELPSSIQNLHKLEHLEIENCINLETLPTGINLESLESLDLSGCSR  837 (1153)
T ss_pred             chheeCCCCCCccccChhhhCCCCCCEEECCCCCCcCeeCCCCCccccCEEECCCCCc
Confidence            8888888877777788777788888888888888888888776555557777777643

syringae 6; Provisional

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

Probab=100.00  E-value=2.5e-41  Score=353.15  Aligned_cols=268  Identities=29%  Similarity=0.567  Sum_probs=221.7

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHHHHhCCCcc
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSED  233 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~~~l~~~~~  233 (779)
                      ||.++++|.+.|.+...+.++|+|+||||+||||||++++++. .++.+|+.++|+.+      ..++..|+.+++....
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~-~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~   79 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDL-RIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDS   79 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHH-HHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-S
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccc-cccccccccccccccccccccccccccccccccccc
Confidence            7899999999999865689999999999999999999999996 56899999999999      5678889999887622


Q ss_pred             hhhhhcchhhHHHHHHHhhCCCcceeehhhcccc---------ccccCCCcEEEEEeCchhhhhhcC--CceeEccCCCh
Q 004021          234 KKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP---------LQMLNAGFKIVLKTRSAGVCDQMD--SKNLEVYSLAH  302 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~---------~~~~~~gs~IivTTR~~~va~~~~--~~~~~l~~L~~  302 (779)
                      ......+.++....+.+.|+++++++++|++...         ++....||+||||||+..++..++  ...|++++|++
T Consensus        80 ~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~~  159 (287)
T PF00931_consen   80 SISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLSE  159 (287)
T ss_dssp             TSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--H
T ss_pred             ccccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            1114456777899999999999999998887543         344567999999999999988776  57899999999


Q ss_pred             HHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCCCchHHHHHH
Q 004021          303 DEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLR  382 (779)
Q Consensus       303 ~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~  382 (779)
                      +||++||.+.++......++.+++.+++|+++|+|+||||+++|++|+.+.+..+|..+++.+.....+..+....+..+
T Consensus       160 ~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~~  239 (287)
T PF00931_consen  160 EEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFSA  239 (287)
T ss_dssp             HHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999999876533445667899999999999999999999999776678999999998888765544455799999


Q ss_pred             HHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcch
Q 004021          383 LKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADF  429 (779)
Q Consensus       383 l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~  429 (779)
                      +.+||+.||+ ++|.||+|||+||+++.|+++.|+++|+++||+...
T Consensus       240 l~~s~~~L~~-~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~~  285 (287)
T PF00931_consen  240 LELSYDSLPD-ELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISSK  285 (287)
T ss_dssp             HHHHHHSSHT-CCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC--
T ss_pred             ceechhcCCc-cHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCccc
Confidence            9999999999 999999999999999999999999999999998763

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

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

Probab=99.66  E-value=3.9e-18  Score=178.36  Aligned_cols=240  Identities=17%  Similarity=0.168  Sum_probs=121.8

Q ss_pred             ccccCCccEEEcccccccccccCcc------cccccccccccccchhh-cccccCceeeecCCcccccchhhccCccCcE
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQELKALEKLRY  563 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i-~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~  563 (779)
                      +-.+..+..|++++|.++++|....      +|+||+| +|.++|.++ .+|+.|-+|||++|++..+|+.+..|.+|++
T Consensus        99 iF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N-~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~RRL~~Lqt  177 (1255)
T KOG0444|consen   99 IFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYN-NIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIRRLSMLQT  177 (1255)
T ss_pred             hcccccceeeecchhhhhhcchhhhhhcCcEEEEcccC-ccccCCchHHHhhHhHhhhccccchhhhcCHHHHHHhhhhh
Confidence            3344555566666666665554322      3566666 666665543 3556666666666666666666666666666


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCC--CcccccCC--------ccCCCchhhHHhhcCCCCCCceeEEeec
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE--GVTKEEGN--------VLCDDAEPLMRELLGLKRLNVLSWSFRS  633 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~--~~~~~~~~--------~~~~~~~~~~~~l~~L~~L~~L~l~~~~  633 (779)
                      |.|++|.. ....-.-+..|++|++|++++..-+  .+|..+..        ...++.+..|+.+-++.+|+.|++++|.
T Consensus       178 L~Ls~NPL-~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~N~Lp~vPecly~l~~LrrLNLS~N~  256 (1255)
T KOG0444|consen  178 LKLSNNPL-NHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSENNLPIVPECLYKLRNLRRLNLSGNK  256 (1255)
T ss_pred             hhcCCChh-hHHHHhcCccchhhhhhhcccccchhhcCCCchhhhhhhhhccccccCCCcchHHHhhhhhhheeccCcCc
Confidence            66665531 1000000223344444444443221  12221111        1112223456666677777777777766


Q ss_pred             cccc----ccCCCCCcc---------cCcccccccCcceEEecccccc-ceecccc-----------cccCcccchhhcc
Q 004021          634 SLAV----QKFFKYPKL---------DLTWLVFVQNLKELEIIVCTEM-EEIICVD-----------KLRDVSDISEIIG  688 (779)
Q Consensus       634 ~~~~----~~~~~L~~L---------~~~~l~~l~~L~~L~L~~~~~~-~~~~~~~-----------~~~~~~~~~~~~~  688 (779)
                      .+.+    ....+|++|         .|..+..|+.|+.|.+.+|... +.+|+..           .....+..|    
T Consensus       257 iteL~~~~~~W~~lEtLNlSrNQLt~LP~avcKL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN~LElVP----  332 (1255)
T KOG0444|consen  257 ITELNMTEGEWENLETLNLSRNQLTVLPDAVCKLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANNKLELVP----  332 (1255)
T ss_pred             eeeeeccHHHHhhhhhhccccchhccchHHHhhhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhccccccCc----
Confidence            6544    111222222         1344555566666655554321 1111100           001111222    


Q ss_pred             CCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCC
Q 004021          689 SEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPI  737 (779)
Q Consensus       689 ~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~  737 (779)
                      ..++.+++|+.|.|++ +.|-.+|..+.-+|-|+.|+++.+|+|-.-|.
T Consensus       333 EglcRC~kL~kL~L~~-NrLiTLPeaIHlL~~l~vLDlreNpnLVMPPK  380 (1255)
T KOG0444|consen  333 EGLCRCVKLQKLKLDH-NRLITLPEAIHLLPDLKVLDLRENPNLVMPPK  380 (1255)
T ss_pred             hhhhhhHHHHHhcccc-cceeechhhhhhcCCcceeeccCCcCccCCCC
Confidence            4666777777777774 66777777777777788888887777765554

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

Probab=99.65  E-value=5e-16  Score=189.95  Aligned_cols=242  Identities=20%  Similarity=0.224  Sum_probs=133.4

Q ss_pred             ccCCccEEEcccccccc-cccC--cc--ccccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcEee
Q 004021          493 EWEGAKRISLMANEIES-LSEI--PT--LLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRYLN  565 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~-l~~~--~~--lL~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~  565 (779)
                      .+.++|+|++++|.+.. +|..  +.  .|+|++| .+. .+|..|+++++|++|+|++|.+. .+|..++++++|++|+
T Consensus       116 ~l~~L~~L~Ls~n~l~~~~p~~~l~~L~~L~Ls~n-~~~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~  194 (968)
T PLN00113        116 TSSSLRYLNLSNNNFTGSIPRGSIPNLETLDLSNN-MLSGEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLT  194 (968)
T ss_pred             cCCCCCEEECcCCccccccCccccCCCCEEECcCC-cccccCChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeee
Confidence            45677777777776643 2221  11  3777777 554 56777778888888888777664 4677777788888888


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc-----ccccC
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL-----AVQKF  640 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~-----~~~~~  640 (779)
                      +++|.....+|.. ++++++|++|++++|.+.+              ..+..++.+++|+.|+++.|...     .+..+
T Consensus       195 L~~n~l~~~~p~~-l~~l~~L~~L~L~~n~l~~--------------~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l  259 (968)
T PLN00113        195 LASNQLVGQIPRE-LGQMKSLKWIYLGYNNLSG--------------EIPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNL  259 (968)
T ss_pred             ccCCCCcCcCChH-HcCcCCccEEECcCCccCC--------------cCChhHhcCCCCCEEECcCceeccccChhHhCC
Confidence            8777555566765 7777788888777776653              23444555555555555544332     12333


Q ss_pred             CCCCcc----------cCcccccccCcceEEeccccccceeccccc-ccCcc-------cchhhccCCCCCCCCccEEEc
Q 004021          641 FKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDK-LRDVS-------DISEIIGSEHNFFTQLESLGI  702 (779)
Q Consensus       641 ~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~-~~~~~-------~~~~~~~~~~~~~~~L~~L~l  702 (779)
                      ++|+.|          .+.++..+++|+.|+|++|.....++.... .....       .+....+..+..+++|+.|++
T Consensus       260 ~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L  339 (968)
T PLN00113        260 KNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNSLSGEIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQL  339 (968)
T ss_pred             CCCCEEECcCCeeeccCchhHhhccCcCEEECcCCeeccCCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEEC
Confidence            344433          123344555566666655543322221000 00000       000000023455666777777


Q ss_pred             cCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcc-cccEEEe
Q 004021          703 LYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAK-ERRVVIE  750 (779)
Q Consensus       703 ~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~-~~~l~i~  750 (779)
                      +++.....+|...+.+++|+.|++++|.-...+|..+...+ ++.+.+.
T Consensus       340 ~~n~l~~~~p~~l~~~~~L~~L~Ls~n~l~~~~p~~~~~~~~L~~L~l~  388 (968)
T PLN00113        340 WSNKFSGEIPKNLGKHNNLTVLDLSTNNLTGEIPEGLCSSGNLFKLILF  388 (968)
T ss_pred             cCCCCcCcCChHHhCCCCCcEEECCCCeeEeeCChhHhCcCCCCEEECc
Confidence            66544445555566666777777766654445555443322 2445444

>PLN03210 Resistant to P

Probab=99.64  E-value=1.6e-15  Score=185.74  Aligned_cols=266  Identities=22%  Similarity=0.252  Sum_probs=137.8

Q ss_pred             cccCccccccCCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCC-cccccchhhcc
Q 004021          485 LTEAPKVKEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLT-HIRGLPQELKA  557 (779)
Q Consensus       485 ~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~-~i~~lp~~~~~  557 (779)
                      +..+|......+++.|++.+|.+..++....      .|+|++|..+..+| .++.+++|++|+|++| .+..+|..+++
T Consensus       601 l~~lP~~f~~~~L~~L~L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~ip-~ls~l~~Le~L~L~~c~~L~~lp~si~~  679 (1153)
T PLN03210        601 LRCMPSNFRPENLVKLQMQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEIP-DLSMATNLETLKLSDCSSLVELPSSIQY  679 (1153)
T ss_pred             CCCCCCcCCccCCcEEECcCccccccccccccCCCCCEEECCCCCCcCcCC-ccccCCcccEEEecCCCCccccchhhhc
Confidence            3344443344566667776666666554322      36777664566666 3667777777777776 56677777777


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC-cccccCC----ccCCCc-hhhHHhhcCCCCCCceeEEe
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG-VTKEEGN----VLCDDA-EPLMRELLGLKRLNVLSWSF  631 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~-~~~~~~~----~~~~~~-~~~~~~l~~L~~L~~L~l~~  631 (779)
                      |++|+.|++++|..++.+|.+ + ++++|++|++++|.... +|....+    .+.++. ...+.. ..+++|+.|++..
T Consensus       680 L~~L~~L~L~~c~~L~~Lp~~-i-~l~sL~~L~Lsgc~~L~~~p~~~~nL~~L~L~~n~i~~lP~~-~~l~~L~~L~l~~  756 (1153)
T PLN03210        680 LNKLEDLDMSRCENLEILPTG-I-NLKSLYRLNLSGCSRLKSFPDISTNISWLDLDETAIEEFPSN-LRLENLDELILCE  756 (1153)
T ss_pred             cCCCCEEeCCCCCCcCccCCc-C-CCCCCCEEeCCCCCCccccccccCCcCeeecCCCcccccccc-ccccccccccccc
Confidence            777777777777777777775 3 67777777777764332 1111000    001100 011111 1234444444432


Q ss_pred             eccccc------------ccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccC
Q 004021          632 RSSLAV------------QKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGS  689 (779)
Q Consensus       632 ~~~~~~------------~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~  689 (779)
                      +....+            ..+++|+.|          .|.+++++++|+.|+|++|+.++.+|.......+..+.-..+.
T Consensus       757 ~~~~~l~~~~~~l~~~~~~~~~sL~~L~Ls~n~~l~~lP~si~~L~~L~~L~Ls~C~~L~~LP~~~~L~sL~~L~Ls~c~  836 (1153)
T PLN03210        757 MKSEKLWERVQPLTPLMTMLSPSLTRLFLSDIPSLVELPSSIQNLHKLEHLEIENCINLETLPTGINLESLESLDLSGCS  836 (1153)
T ss_pred             cchhhccccccccchhhhhccccchheeCCCCCCccccChhhhCCCCCCEEECCCCCCcCeeCCCCCccccCEEECCCCC
Confidence            110000            011233333          1344566777777777777776666542110000000000000


Q ss_pred             CC----CCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc-ccEEEechHhh
Q 004021          690 EH----NFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE-RRVVIEGLKEW  755 (779)
Q Consensus       690 ~~----~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~-~~l~i~~~~~~  755 (779)
                      .+    ...++|+.|+|++ +.++.+|..+..+++|+.|++++|++|+.+|......+. +.+.+.+|...
T Consensus       837 ~L~~~p~~~~nL~~L~Ls~-n~i~~iP~si~~l~~L~~L~L~~C~~L~~l~~~~~~L~~L~~L~l~~C~~L  906 (1153)
T PLN03210        837 RLRTFPDISTNISDLNLSR-TGIEEVPWWIEKFSNLSFLDMNGCNNLQRVSLNISKLKHLETVDFSDCGAL  906 (1153)
T ss_pred             ccccccccccccCEeECCC-CCCccChHHHhcCCCCCEEECCCCCCcCccCcccccccCCCeeecCCCccc
Confidence            00    0123444455444 344455555566777777777777777777765544333 66667777554

syringae 6; Provisional

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

Probab=99.61  E-value=2.2e-15  Score=184.28  Aligned_cols=242  Identities=21%  Similarity=0.272  Sum_probs=147.6

Q ss_pred             ccCCccEEEcccccccc-cccC----cc--ccccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcE
Q 004021          493 EWEGAKRISLMANEIES-LSEI----PT--LLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRY  563 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~-l~~~----~~--lL~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~  563 (779)
                      .+.++++|++++|.+.. +|..    ..  .|+|++| .+. .+|..|+++++|++|+|++|.+. .+|..++++++|++
T Consensus       138 ~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n-~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~  216 (968)
T PLN00113        138 SIPNLETLDLSNNMLSGEIPNDIGSFSSLKVLDLGGN-VLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKW  216 (968)
T ss_pred             ccCCCCEEECcCCcccccCChHHhcCCCCCEEECccC-cccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccE
Confidence            34567777777776642 3321    11  3777777 443 56777777777777777777655 36777777777777


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCCC-cccccCC-------ccCCC--chhhHHhhcCCCCCCceeEEeec
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG-VTKEEGN-------VLCDD--AEPLMRELLGLKRLNVLSWSFRS  633 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~-~~~~~~~-------~~~~~--~~~~~~~l~~L~~L~~L~l~~~~  633 (779)
                      |++++|.....+|.. ++++++|++|++++|.+.+ .|..+.+       .+..+  ....+..+..+++|+.|+++.|.
T Consensus       217 L~L~~n~l~~~~p~~-l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~  295 (968)
T PLN00113        217 IYLGYNNLSGEIPYE-IGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLSDNS  295 (968)
T ss_pred             EECcCCccCCcCChh-HhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECcCCe
Confidence            777777544466665 6777777777777776553 1111111       00000  01234445556666666665544


Q ss_pred             ccc-----cccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCcc
Q 004021          634 SLA-----VQKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLE  698 (779)
Q Consensus       634 ~~~-----~~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~  698 (779)
                      ...     +..+++|+.|          .+.++..+++|+.|+|++|.....++                ..++.+++|+
T Consensus       296 l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~p----------------~~l~~~~~L~  359 (968)
T PLN00113        296 LSGEIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQLWSNKFSGEIP----------------KNLGKHNNLT  359 (968)
T ss_pred             eccCCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEECcCCCCcCcCC----------------hHHhCCCCCc
Confidence            321     1234444444          22334556666666666654433332                3567889999


Q ss_pred             EEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCc-ccccEEEech
Q 004021          699 SLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA-KERRVVIEGL  752 (779)
Q Consensus       699 ~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~-~~~~l~i~~~  752 (779)
                      .|+++++.-...+|.....+++|+.|++.+|+....+|..+... .++.+.+.++
T Consensus       360 ~L~Ls~n~l~~~~p~~~~~~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n  414 (968)
T PLN00113        360 VLDLSTNNLTGEIPEGLCSSGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDN  414 (968)
T ss_pred             EEECCCCeeEeeCChhHhCcCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCC
Confidence            99999875555677777788999999999998777788765443 3477777655

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

Probab=99.59  E-value=8.6e-17  Score=168.46  Aligned_cols=215  Identities=21%  Similarity=0.226  Sum_probs=159.3

Q ss_pred             cccCCccEEEcccccccccccCcc-------cccccccccccccchhhcccccCceeeecCCccc---------------
Q 004021          492 KEWEGAKRISLMANEIESLSEIPT-------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIR---------------  549 (779)
Q Consensus       492 ~~~~~lr~l~l~~~~~~~l~~~~~-------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~---------------  549 (779)
                      ...++.-.|++++|+|..+|...+       .||||+| .+..+|+.+..|.+|++|.|++|.+.               
T Consensus       123 E~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS~N-rLe~LPPQ~RRL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~v  201 (1255)
T KOG0444|consen  123 EYAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLSNN-RLEMLPPQIRRLSMLQTLKLSNNPLNHFQLRQLPSMTSLSV  201 (1255)
T ss_pred             hhhcCcEEEEcccCccccCCchHHHhhHhHhhhccccc-hhhhcCHHHHHHhhhhhhhcCCChhhHHHHhcCccchhhhh
Confidence            344577789999999999998765       3899999 99999999999999999999888442               


Q ss_pred             -----------ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC--------ccCCC
Q 004021          550 -----------GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN--------VLCDD  610 (779)
Q Consensus       550 -----------~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~--------~~~~~  610 (779)
                                 .+|.++..|.+|+.+|++.| .+..+|.- +-++.+|+.|++++|.+.......+.        ...+.
T Consensus       202 Lhms~TqRTl~N~Ptsld~l~NL~dvDlS~N-~Lp~vPec-ly~l~~LrrLNLS~N~iteL~~~~~~W~~lEtLNlSrNQ  279 (1255)
T KOG0444|consen  202 LHMSNTQRTLDNIPTSLDDLHNLRDVDLSEN-NLPIVPEC-LYKLRNLRRLNLSGNKITELNMTEGEWENLETLNLSRNQ  279 (1255)
T ss_pred             hhcccccchhhcCCCchhhhhhhhhcccccc-CCCcchHH-HhhhhhhheeccCcCceeeeeccHHHHhhhhhhccccch
Confidence                       24667778889999999998 78889986 88999999999999988865332221        23333


Q ss_pred             chhhHHhhcCCCCCCceeEEeeccc------ccccCCCCCc---------ccCcccccccCcceEEeccccccceecccc
Q 004021          611 AEPLMRELLGLKRLNVLSWSFRSSL------AVQKFFKYPK---------LDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       611 ~~~~~~~l~~L~~L~~L~l~~~~~~------~~~~~~~L~~---------L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      ....|..+.+|++|+.|.+..|...      .++.+.+|+.         |.|..+..++.|+.|.|+.|..++ +|   
T Consensus       280 Lt~LP~avcKL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN~LElVPEglcRC~kL~kL~L~~NrLiT-LP---  355 (1255)
T KOG0444|consen  280 LTVLPDAVCKLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANNKLELVPEGLCRCVKLQKLKLDHNRLIT-LP---  355 (1255)
T ss_pred             hccchHHHhhhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhccccccCchhhhhhHHHHHhcccccceee-ch---
Confidence            4567777888888888887766541      2223333332         356778888899999998865543 33   


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEee
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGV  726 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l  726 (779)
                                   ..+.-++-|+.|++.++++|.-.|....+-++|+.-+|
T Consensus       356 -------------eaIHlL~~l~vLDlreNpnLVMPPKP~da~~~lefYNI  393 (1255)
T KOG0444|consen  356 -------------EAIHLLPDLKVLDLRENPNLVMPPKPNDARKKLEFYNI  393 (1255)
T ss_pred             -------------hhhhhcCCcceeeccCCcCccCCCCcchhhhcceeeec
Confidence                         36778999999999999999877764444455554443

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

Probab=99.52  E-value=1.1e-15  Score=152.76  Aligned_cols=106  Identities=27%  Similarity=0.372  Sum_probs=95.2

Q ss_pred             cccccCCccEEEcccccccccccCcc---c--ccccccccccccchhhc-ccccCceeeecCCcccccchhhccCccCcE
Q 004021          490 KVKEWEGAKRISLMANEIESLSEIPT---L--LSLRRNDSLTELPSRIS-SLVSLHHLDLSLTHIRGLPQELKALEKLRY  563 (779)
Q Consensus       490 ~~~~~~~lr~l~l~~~~~~~l~~~~~---l--L~L~~~~~l~~lp~~i~-~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~  563 (779)
                      .+..+.++..|+++.|++..+|..+.   |  |.+..| .++.+|..++ +|.+|.+|||+.|+++++|.+++.|.+|.+
T Consensus       201 ~lg~l~~L~~LyL~~Nki~~lPef~gcs~L~Elh~g~N-~i~~lpae~~~~L~~l~vLDLRdNklke~Pde~clLrsL~r  279 (565)
T KOG0472|consen  201 ELGGLESLELLYLRRNKIRFLPEFPGCSLLKELHVGEN-QIEMLPAEHLKHLNSLLVLDLRDNKLKEVPDEICLLRSLER  279 (565)
T ss_pred             hhcchhhhHHHHhhhcccccCCCCCccHHHHHHHhccc-HHHhhHHHHhcccccceeeeccccccccCchHHHHhhhhhh
Confidence            45677788888999999999998776   2  788889 9999999987 899999999999999999999999999999


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCCCc
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGV  599 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~  599 (779)
                      ||+++| .++.+|.+ +|+| .|+.|-+.||.+..+
T Consensus       280 LDlSNN-~is~Lp~s-Lgnl-hL~~L~leGNPlrTi  312 (565)
T KOG0472|consen  280 LDLSNN-DISSLPYS-LGNL-HLKFLALEGNPLRTI  312 (565)
T ss_pred             hcccCC-ccccCCcc-cccc-eeeehhhcCCchHHH
Confidence            999999 78999998 9999 999999999987754

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

Probab=99.52  E-value=2.1e-16  Score=139.78  Aligned_cols=155  Identities=28%  Similarity=0.301  Sum_probs=113.5

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |.||+| .++.+|+.|..|.+|+.|++.+|+|+++|.+++.|++|++|+++-| .+..+|.+ |+.++-|+.|++.+|++
T Consensus        38 LtLSHN-Kl~~vppnia~l~nlevln~~nnqie~lp~~issl~klr~lnvgmn-rl~~lprg-fgs~p~levldltynnl  114 (264)
T KOG0617|consen   38 LTLSHN-KLTVVPPNIAELKNLEVLNLSNNQIEELPTSISSLPKLRILNVGMN-RLNILPRG-FGSFPALEVLDLTYNNL  114 (264)
T ss_pred             hhcccC-ceeecCCcHHHhhhhhhhhcccchhhhcChhhhhchhhhheecchh-hhhcCccc-cCCCchhhhhhcccccc
Confidence            677788 8888999999999999999999999999999999999999999988 78899999 99999999999999887


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      .+             ...+..+-.++.|+.|.++.|+...          .|+.++++++|+.|.+..|..++ +|    
T Consensus       115 ~e-------------~~lpgnff~m~tlralyl~dndfe~----------lp~dvg~lt~lqil~lrdndll~-lp----  166 (264)
T KOG0617|consen  115 NE-------------NSLPGNFFYMTTLRALYLGDNDFEI----------LPPDVGKLTNLQILSLRDNDLLS-LP----  166 (264)
T ss_pred             cc-------------ccCCcchhHHHHHHHHHhcCCCccc----------CChhhhhhcceeEEeeccCchhh-Cc----
Confidence            75             4555566666666666666554321          13445566666666666644332 22    


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCC
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNP  715 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~  715 (779)
                                  ..++.+..|++|.+.+ +.+.-+|..+
T Consensus       167 ------------keig~lt~lrelhiqg-nrl~vlppel  192 (264)
T KOG0617|consen  167 ------------KEIGDLTRLRELHIQG-NRLTVLPPEL  192 (264)
T ss_pred             ------------HHHHHHHHHHHHhccc-ceeeecChhh
Confidence                        2445556666666665 4555555543

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

Probab=99.50  E-value=3.5e-16  Score=156.29  Aligned_cols=228  Identities=22%  Similarity=0.255  Sum_probs=118.9

Q ss_pred             ccCCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeec
Q 004021          493 EWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNL  566 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l  566 (779)
                      .+..+..+.+++|....+|....      -|+.+.| ++..+|+.++.+.+|+.|+.++|.+.++|++++.+..|..|+.
T Consensus        66 nL~~l~vl~~~~n~l~~lp~aig~l~~l~~l~vs~n-~ls~lp~~i~s~~~l~~l~~s~n~~~el~~~i~~~~~l~dl~~  144 (565)
T KOG0472|consen   66 NLACLTVLNVHDNKLSQLPAAIGELEALKSLNVSHN-KLSELPEQIGSLISLVKLDCSSNELKELPDSIGRLLDLEDLDA  144 (565)
T ss_pred             cccceeEEEeccchhhhCCHHHHHHHHHHHhhcccc-hHhhccHHHhhhhhhhhhhccccceeecCchHHHHhhhhhhhc
Confidence            33445555555555554444332      1444444 4444444444444444444444444444444444444444444


Q ss_pred             cCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC--------ccCCCchhhHHhhcCCCCCCceeEEeecccccc
Q 004021          567 EYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN--------VLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ  638 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~--------~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~  638 (779)
                      .+| .+..+|++ ++.+.+|..|++.+|.+...|....+        ...+.....|++++.|.+|..|++..|....  
T Consensus       145 ~~N-~i~slp~~-~~~~~~l~~l~~~~n~l~~l~~~~i~m~~L~~ld~~~N~L~tlP~~lg~l~~L~~LyL~~Nki~~--  220 (565)
T KOG0472|consen  145 TNN-QISSLPED-MVNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCNSNLLETLPPELGGLESLELLYLRRNKIRF--  220 (565)
T ss_pred             ccc-ccccCchH-HHHHHHHHHhhccccchhhCCHHHHHHHHHHhcccchhhhhcCChhhcchhhhHHHHhhhccccc--
Confidence            444 34444444 44444444444444443332211110        0001112355666666666666666444322  


Q ss_pred             cCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCC
Q 004021          639 KFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHF  718 (779)
Q Consensus       639 ~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l  718 (779)
                               +|.|..+..|+.|+++. +.++.++.               .....+++|..|++.+ +++++.|.++.-+
T Consensus       221 ---------lPef~gcs~L~Elh~g~-N~i~~lpa---------------e~~~~L~~l~vLDLRd-Nklke~Pde~clL  274 (565)
T KOG0472|consen  221 ---------LPEFPGCSLLKELHVGE-NQIEMLPA---------------EHLKHLNSLLVLDLRD-NKLKEVPDEICLL  274 (565)
T ss_pred             ---------CCCCCccHHHHHHHhcc-cHHHhhHH---------------HHhcccccceeeeccc-cccccCchHHHHh
Confidence                     12344455555555554 33444433               2334677778888877 6777777777777


Q ss_pred             CCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          719 PKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       719 ~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      .+|++|+++++ .+..+|..+....++.+.+.|.
T Consensus       275 rsL~rLDlSNN-~is~Lp~sLgnlhL~~L~leGN  307 (565)
T KOG0472|consen  275 RSLERLDLSNN-DISSLPYSLGNLHLKFLALEGN  307 (565)
T ss_pred             hhhhhhcccCC-ccccCCcccccceeeehhhcCC
Confidence            77888888764 5777777776665566666665

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

Probab=99.46  E-value=2e-14  Score=150.24  Aligned_cols=240  Identities=21%  Similarity=0.181  Sum_probs=144.1

Q ss_pred             CCccEEEcccccccccccCcc-------cccccccccccccch-hhcccccCceeeecCCccccc-chhhccCccCcEee
Q 004021          495 EGAKRISLMANEIESLSEIPT-------LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~-------lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~  565 (779)
                      .++++|+|.+|.|..+....+       .|.|+.| .++.+|. .|.+|++|+.|+|..|+|+.. .-.|..|.+|+.|.
T Consensus       173 ~ni~~L~La~N~It~l~~~~F~~lnsL~tlkLsrN-rittLp~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~nlk  251 (873)
T KOG4194|consen  173 VNIKKLNLASNRITTLETGHFDSLNSLLTLKLSRN-RITTLPQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQNLK  251 (873)
T ss_pred             CCceEEeeccccccccccccccccchheeeecccC-cccccCHHHhhhcchhhhhhccccceeeehhhhhcCchhhhhhh
Confidence            467778888877776654332       2778888 8888865 455688888888888877665 44567777777777


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccc-cCC-------ccCCCc--hhhHHhhcCCCCCCceeEEeeccc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKE-EGN-------VLCDDA--EPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~-~~~-------~~~~~~--~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      |..| .+..+.++.|..|.++++|++..|++..+..+ +++       .++.+.  ...+....-.++|++|+++.|...
T Consensus       252 lqrN-~I~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~lfgLt~L~~L~lS~NaI~rih~d~WsftqkL~~LdLs~N~i~  330 (873)
T KOG4194|consen  252 LQRN-DISKLDDGAFYGLEKMEHLNLETNRLQAVNEGWLFGLTSLEQLDLSYNAIQRIHIDSWSFTQKLKELDLSSNRIT  330 (873)
T ss_pred             hhhc-CcccccCcceeeecccceeecccchhhhhhcccccccchhhhhccchhhhheeecchhhhcccceeEeccccccc
Confidence            7777 56677777677777777777777766543211 111       000000  112233334455555555555443


Q ss_pred             cc-----ccCCCCCcccC----------cccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEE
Q 004021          636 AV-----QKFFKYPKLDL----------TWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESL  700 (779)
Q Consensus       636 ~~-----~~~~~L~~L~~----------~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L  700 (779)
                      .+     ..+..|+.|.+          ..+..+.+|+.|+|+.|..-..+-+    ..         ..+.++++|+.|
T Consensus       331 ~l~~~sf~~L~~Le~LnLs~Nsi~~l~e~af~~lssL~~LdLr~N~ls~~IED----aa---------~~f~gl~~LrkL  397 (873)
T KOG4194|consen  331 RLDEGSFRVLSQLEELNLSHNSIDHLAEGAFVGLSSLHKLDLRSNELSWCIED----AA---------VAFNGLPSLRKL  397 (873)
T ss_pred             cCChhHHHHHHHhhhhcccccchHHHHhhHHHHhhhhhhhcCcCCeEEEEEec----ch---------hhhccchhhhhe
Confidence            32     22333333311          1234567777777777543332211    00         356789999999


Q ss_pred             EccCCCCCccccC-CCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEe
Q 004021          701 GILYGPDLKSIYP-NPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIE  750 (779)
Q Consensus       701 ~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~  750 (779)
                      .+.+ ++++.++. .+..|++|++|++.+++--.--|..+....++++.+.
T Consensus       398 ~l~g-Nqlk~I~krAfsgl~~LE~LdL~~NaiaSIq~nAFe~m~Lk~Lv~n  447 (873)
T KOG4194|consen  398 RLTG-NQLKSIPKRAFSGLEALEHLDLGDNAIASIQPNAFEPMELKELVMN  447 (873)
T ss_pred             eecC-ceeeecchhhhccCcccceecCCCCcceeecccccccchhhhhhhc
Confidence            9998 78999987 4557999999999887643333444443344555543

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

Probab=99.44  E-value=3.8e-14  Score=148.13  Aligned_cols=197  Identities=20%  Similarity=0.282  Sum_probs=135.5

Q ss_pred             ccccCcccccc-CCccEEEcccccccccccCc-----c--cccccccccccccch-hhcccccCceeeecCCcccccch-
Q 004021          484 KLTEAPKVKEW-EGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQ-  553 (779)
Q Consensus       484 ~~~~~~~~~~~-~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~-  553 (779)
                      .+..+|..... .++..|+|.+|.|..+....     .  .||||.| .|.++|. +|..=.++++|+|++|.|+.+-. 
T Consensus       113 ~Lt~IP~f~~~sghl~~L~L~~N~I~sv~se~L~~l~alrslDLSrN-~is~i~~~sfp~~~ni~~L~La~N~It~l~~~  191 (873)
T KOG4194|consen  113 ELTRIPRFGHESGHLEKLDLRHNLISSVTSEELSALPALRSLDLSRN-LISEIPKPSFPAKVNIKKLNLASNRITTLETG  191 (873)
T ss_pred             hhhhcccccccccceeEEeeeccccccccHHHHHhHhhhhhhhhhhc-hhhcccCCCCCCCCCceEEeeccccccccccc
Confidence            44556655433 35888888888887764431     1  3899999 8888854 46666789999999999988753 


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeec
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRS  633 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~  633 (779)
                      .|.+|.+|-+|.|+.| .++.+|..+|.+|++|+.|++..|.+..              ...-.|++|++|+.|.+..|+
T Consensus       192 ~F~~lnsL~tlkLsrN-rittLp~r~Fk~L~~L~~LdLnrN~iri--------------ve~ltFqgL~Sl~nlklqrN~  256 (873)
T KOG4194|consen  192 HFDSLNSLLTLKLSRN-RITTLPQRSFKRLPKLESLDLNRNRIRI--------------VEGLTFQGLPSLQNLKLQRND  256 (873)
T ss_pred             cccccchheeeecccC-cccccCHHHhhhcchhhhhhccccceee--------------ehhhhhcCchhhhhhhhhhcC
Confidence            4888889999999998 6888988878889999999998887763              122335556666666666555


Q ss_pred             cccc-----ccCC----------CCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCcc
Q 004021          634 SLAV-----QKFF----------KYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLE  698 (779)
Q Consensus       634 ~~~~-----~~~~----------~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~  698 (779)
                      +..+     ..+.          +++.+.-.|+.+|+.|+.|+|+.| .+..+-.               ......++|+
T Consensus       257 I~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~lfgLt~L~~L~lS~N-aI~rih~---------------d~WsftqkL~  320 (873)
T KOG4194|consen  257 ISKLDDGAFYGLEKMEHLNLETNRLQAVNEGWLFGLTSLEQLDLSYN-AIQRIHI---------------DSWSFTQKLK  320 (873)
T ss_pred             cccccCcceeeecccceeecccchhhhhhcccccccchhhhhccchh-hhheeec---------------chhhhcccce
Confidence            5433     2233          334445578888899999999884 3444422               2445567777


Q ss_pred             EEEccCCCCCccccC
Q 004021          699 SLGILYGPDLKSIYP  713 (779)
Q Consensus       699 ~L~l~~~~~l~~l~~  713 (779)
                      .|+|++ +.+.+++.
T Consensus       321 ~LdLs~-N~i~~l~~  334 (873)
T KOG4194|consen  321 ELDLSS-NRITRLDE  334 (873)
T ss_pred             eEeccc-cccccCCh
Confidence            777776 55666654

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

Probab=99.38  E-value=6.1e-15  Score=130.58  Aligned_cols=172  Identities=22%  Similarity=0.284  Sum_probs=141.7

Q ss_pred             ccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCc
Q 004021          527 ELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNV  606 (779)
Q Consensus       527 ~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~  606 (779)
                      .+| .+.++.+...|.|++|+++.+|+.|..|.+|+.|++.+| .++.+|.. ++.|++|++|++.-|++.         
T Consensus        25 ~~~-gLf~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nn-qie~lp~~-issl~klr~lnvgmnrl~---------   92 (264)
T KOG0617|consen   25 ELP-GLFNMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNN-QIEELPTS-ISSLPKLRILNVGMNRLN---------   92 (264)
T ss_pred             hcc-cccchhhhhhhhcccCceeecCCcHHHhhhhhhhhcccc-hhhhcChh-hhhchhhhheecchhhhh---------
Confidence            344 345678888899999999999999999999999999999 78999998 999999999999988765         


Q ss_pred             cCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcc-cCcccccccCcceEEeccccccceecccccccCcccchh
Q 004021          607 LCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL-DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISE  685 (779)
Q Consensus       607 ~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L-~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~  685 (779)
                            ..+..+++++.|+.|+++.|..         .+= .|..+..+..|+.|+|+.|. .+.+|             
T Consensus        93 ------~lprgfgs~p~levldltynnl---------~e~~lpgnff~m~tlralyl~dnd-fe~lp-------------  143 (264)
T KOG0617|consen   93 ------ILPRGFGSFPALEVLDLTYNNL---------NENSLPGNFFYMTTLRALYLGDND-FEILP-------------  143 (264)
T ss_pred             ------cCccccCCCchhhhhhcccccc---------ccccCCcchhHHHHHHHHHhcCCC-cccCC-------------
Confidence                  3778899999999999995543         222 24456678889999998854 34444             


Q ss_pred             hccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc
Q 004021          686 IIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE  744 (779)
Q Consensus       686 ~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~  744 (779)
                         ...+.+++|+.|.+.. +.+-++|..++.+..|++|.|.++ .|.-+|..+....+
T Consensus       144 ---~dvg~lt~lqil~lrd-ndll~lpkeig~lt~lrelhiqgn-rl~vlppel~~l~l  197 (264)
T KOG0617|consen  144 ---PDVGKLTNLQILSLRD-NDLLSLPKEIGDLTRLRELHIQGN-RLTVLPPELANLDL  197 (264)
T ss_pred             ---hhhhhhcceeEEeecc-CchhhCcHHHHHHHHHHHHhcccc-eeeecChhhhhhhh
Confidence               3778999999999998 577889999999999999999885 69999987765433

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.35  E-value=4.7e-12  Score=144.19  Aligned_cols=189  Identities=20%  Similarity=0.120  Sum_probs=107.1

Q ss_pred             HHHHHHhhhhhccccEEEEcCcccccCccccccCCccEEEcccccccccccCcc---cccccccccccccchhhcccccC
Q 004021          462 MSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSL  538 (779)
Q Consensus       462 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L  538 (779)
                      .|....+++.+.+...+......+..+|... ..+++.|++.+|.+..+|..++   .|+|++| .++.+|..   .++|
T Consensus       190 ~a~~r~~~Cl~~~~~~LdLs~~~LtsLP~~l-~~~L~~L~L~~N~Lt~LP~lp~~Lk~LdLs~N-~LtsLP~l---p~sL  264 (788)
T PRK15387        190 AVVQKMRACLNNGNAVLNVGESGLTTLPDCL-PAHITTLVIPDNNLTSLPALPPELRTLEVSGN-QLTSLPVL---PPGL  264 (788)
T ss_pred             HHHHHHHHHhcCCCcEEEcCCCCCCcCCcch-hcCCCEEEccCCcCCCCCCCCCCCcEEEecCC-ccCcccCc---cccc
Confidence            4444444444444445544555566666421 2478888888888888776544   4888888 88888753   3577


Q ss_pred             ceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC----ccCCCchhh
Q 004021          539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPL  614 (779)
Q Consensus       539 ~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~  614 (779)
                      +.|++++|.++.+|...   .+|+.|++++| .++.+|..    +++|+.|++++|.+..+|....+    .+.++   .
T Consensus       265 ~~L~Ls~N~L~~Lp~lp---~~L~~L~Ls~N-~Lt~LP~~----p~~L~~LdLS~N~L~~Lp~lp~~L~~L~Ls~N---~  333 (788)
T PRK15387        265 LELSIFSNPLTHLPALP---SGLCKLWIFGN-QLTSLPVL----PPGLQELSVSDNQLASLPALPSELCKLWAYNN---Q  333 (788)
T ss_pred             ceeeccCCchhhhhhch---hhcCEEECcCC-cccccccc----ccccceeECCCCccccCCCCcccccccccccC---c
Confidence            78888888777777533   45667777777 56777652    35677777777776664321111    00010   0


Q ss_pred             HHhhcCC-CCCCceeEEeecccccccC-CCCCcccCc--ccc----cccCcceEEecccc
Q 004021          615 MRELLGL-KRLNVLSWSFRSSLAVQKF-FKYPKLDLT--WLV----FVQNLKELEIIVCT  666 (779)
Q Consensus       615 ~~~l~~L-~~L~~L~l~~~~~~~~~~~-~~L~~L~~~--~l~----~l~~L~~L~L~~~~  666 (779)
                      +..+..+ .+|+.|+++.|....++.. .+|+.|.+.  .+.    ..++|+.|+|++|.
T Consensus       334 L~~LP~lp~~Lq~LdLS~N~Ls~LP~lp~~L~~L~Ls~N~L~~LP~l~~~L~~LdLs~N~  393 (788)
T PRK15387        334 LTSLPTLPSGLQELSVSDNQLASLPTLPSELYKLWAYNNRLTSLPALPSGLKELIVSGNR  393 (788)
T ss_pred             cccccccccccceEecCCCccCCCCCCCcccceehhhccccccCcccccccceEEecCCc
Confidence            1111111 3677888887766554321 233333110  011    12367777777653

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.29  E-value=9.2e-12  Score=142.82  Aligned_cols=218  Identities=20%  Similarity=0.232  Sum_probs=132.0

Q ss_pred             cccccCccccccCCccEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCcccccchhhccC
Q 004021          483 VKLTEAPKVKEWEGAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKAL  558 (779)
Q Consensus       483 ~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L  558 (779)
                      ..+..+|.. -...++.|++++|.+..+|....    .|+|++| .++.+|..+.  .+|+.|+|++|.+..+|..+.  
T Consensus       188 ~~LtsLP~~-Ip~~L~~L~Ls~N~LtsLP~~l~~nL~~L~Ls~N-~LtsLP~~l~--~~L~~L~Ls~N~L~~LP~~l~--  261 (754)
T PRK15370        188 LGLTTIPAC-IPEQITTLILDNNELKSLPENLQGNIKTLYANSN-QLTSIPATLP--DTIQEMELSINRITELPERLP--  261 (754)
T ss_pred             CCcCcCCcc-cccCCcEEEecCCCCCcCChhhccCCCEEECCCC-ccccCChhhh--ccccEEECcCCccCcCChhHh--
Confidence            344445531 12468888888888887775422    4888888 7888887654  478888888888888887764  


Q ss_pred             ccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccc
Q 004021          559 EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ  638 (779)
Q Consensus       559 ~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~  638 (779)
                      .+|+.|++++| .+..+|.. +.  .+|++|++++|.+..+|..+.                 ++|+.|+++.|....++
T Consensus       262 s~L~~L~Ls~N-~L~~LP~~-l~--~sL~~L~Ls~N~Lt~LP~~lp-----------------~sL~~L~Ls~N~Lt~LP  320 (754)
T PRK15370        262 SALQSLDLFHN-KISCLPEN-LP--EELRYLSVYDNSIRTLPAHLP-----------------SGITHLNVQSNSLTALP  320 (754)
T ss_pred             CCCCEEECcCC-ccCccccc-cC--CCCcEEECCCCccccCcccch-----------------hhHHHHHhcCCccccCC
Confidence            47888888877 67788875 43  478888888887776442221                 12333444433322211


Q ss_pred             --cCCCCCccc---------CcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCC
Q 004021          639 --KFFKYPKLD---------LTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPD  707 (779)
Q Consensus       639 --~~~~L~~L~---------~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~  707 (779)
                        ..++|+.|.         +..+  .++|+.|+|++|+ +..++.                .+  .++|+.|+|++| .
T Consensus       321 ~~l~~sL~~L~Ls~N~Lt~LP~~l--~~sL~~L~Ls~N~-L~~LP~----------------~l--p~~L~~LdLs~N-~  378 (754)
T PRK15370        321 ETLPPGLKTLEAGENALTSLPASL--PPELQVLDVSKNQ-ITVLPE----------------TL--PPTITTLDVSRN-A  378 (754)
T ss_pred             ccccccceeccccCCccccCChhh--cCcccEEECCCCC-CCcCCh----------------hh--cCCcCEEECCCC-c
Confidence              011222220         1111  2578888888764 333332                12  367888888874 5


Q ss_pred             CccccCCCCCCCCccEEeeeCCCCCCCCCCCCCC-----cccccEEEech
Q 004021          708 LKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSS-----AKERRVVIEGL  752 (779)
Q Consensus       708 l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~-----~~~~~l~i~~~  752 (779)
                      +..+|..+.  ++|+.|++++| +|..+|..+..     ..+..+.+.+.
T Consensus       379 Lt~LP~~l~--~sL~~LdLs~N-~L~~LP~sl~~~~~~~~~l~~L~L~~N  425 (754)
T PRK15370        379 LTNLPENLP--AALQIMQASRN-NLVRLPESLPHFRGEGPQPTRIIVEYN  425 (754)
T ss_pred             CCCCCHhHH--HHHHHHhhccC-CcccCchhHHHHhhcCCCccEEEeeCC
Confidence            677766432  46888888875 57788765432     12245555543

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

Probab=99.25  E-value=7e-13  Score=146.28  Aligned_cols=218  Identities=19%  Similarity=0.250  Sum_probs=138.3

Q ss_pred             CCccEEEcccccccccccC-----cccccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCC
Q 004021          495 EGAKRISLMANEIESLSEI-----PTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT  569 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~-----~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~  569 (779)
                      .++++|....|.+..+...     ...++++.| .+..+|+.++.+.+|+.|++.+|.+..+|..+...++|+.|.+..|
T Consensus       219 ~~l~~L~a~~n~l~~~~~~p~p~nl~~~dis~n-~l~~lp~wi~~~~nle~l~~n~N~l~~lp~ri~~~~~L~~l~~~~n  297 (1081)
T KOG0618|consen  219 PSLTALYADHNPLTTLDVHPVPLNLQYLDISHN-NLSNLPEWIGACANLEALNANHNRLVALPLRISRITSLVSLSAAYN  297 (1081)
T ss_pred             cchheeeeccCcceeeccccccccceeeecchh-hhhcchHHHHhcccceEecccchhHHhhHHHHhhhhhHHHHHhhhh
Confidence            3667777777766543222     125899999 8999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCc--------------------cC---------------CCchhh
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNV--------------------LC---------------DDAEPL  614 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~--------------------~~---------------~~~~~~  614 (779)
                       .++.+|+. .+++++|++|++..|.+..+|..+...                    ..               ......
T Consensus       298 -el~yip~~-le~~~sL~tLdL~~N~L~~lp~~~l~v~~~~l~~ln~s~n~l~~lp~~~e~~~~~Lq~LylanN~Ltd~c  375 (1081)
T KOG0618|consen  298 -ELEYIPPF-LEGLKSLRTLDLQSNNLPSLPDNFLAVLNASLNTLNVSSNKLSTLPSYEENNHAALQELYLANNHLTDSC  375 (1081)
T ss_pred             -hhhhCCCc-ccccceeeeeeehhccccccchHHHhhhhHHHHHHhhhhccccccccccchhhHHHHHHHHhcCcccccc
Confidence             78999986 788999999999999888765432220                    00               001223


Q ss_pred             HHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc-c----------ccCcccc
Q 004021          615 MRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD-K----------LRDVSDI  683 (779)
Q Consensus       615 ~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~-~----------~~~~~~~  683 (779)
                      ..-|.++.+|+.|+++.|.         |.+++-..+.+++.|+.|+|++| .++.++... .          ...+..+
T Consensus       376 ~p~l~~~~hLKVLhLsyNr---------L~~fpas~~~kle~LeeL~LSGN-kL~~Lp~tva~~~~L~tL~ahsN~l~~f  445 (1081)
T KOG0618|consen  376 FPVLVNFKHLKVLHLSYNR---------LNSFPASKLRKLEELEELNLSGN-KLTTLPDTVANLGRLHTLRAHSNQLLSF  445 (1081)
T ss_pred             hhhhccccceeeeeecccc---------cccCCHHHHhchHHhHHHhcccc-hhhhhhHHHHhhhhhHHHhhcCCceeec
Confidence            3345566777777777443         33333344566677777777774 334443200 0          0001111


Q ss_pred             hhhccCCCCCCCCccEEEccCCCCCccccCCCCC-CCCccEEeeeCCCC
Q 004021          684 SEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLH-FPKLKKIGVYGCPK  731 (779)
Q Consensus       684 ~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~-l~~L~~L~l~~c~~  731 (779)
                           ..+..++.|+.++++. ++|+.+...... -|+|++|++++++.
T Consensus       446 -----Pe~~~l~qL~~lDlS~-N~L~~~~l~~~~p~p~LkyLdlSGN~~  488 (1081)
T KOG0618|consen  446 -----PELAQLPQLKVLDLSC-NNLSEVTLPEALPSPNLKYLDLSGNTR  488 (1081)
T ss_pred             -----hhhhhcCcceEEeccc-chhhhhhhhhhCCCcccceeeccCCcc
Confidence                 1344556666666653 455544332211 15666666666553

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.20  E-value=4.1e-11  Score=137.51  Aligned_cols=206  Identities=17%  Similarity=0.201  Sum_probs=143.5

Q ss_pred             CccEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~  571 (779)
                      +...|.+.++.+..+|...+    .|+|++| .++.+|..+.  .+|++|++++|.++.+|..+.  .+|+.|+|++| .
T Consensus       179 ~~~~L~L~~~~LtsLP~~Ip~~L~~L~Ls~N-~LtsLP~~l~--~nL~~L~Ls~N~LtsLP~~l~--~~L~~L~Ls~N-~  252 (754)
T PRK15370        179 NKTELRLKILGLTTIPACIPEQITTLILDNN-ELKSLPENLQ--GNIKTLYANSNQLTSIPATLP--DTIQEMELSIN-R  252 (754)
T ss_pred             CceEEEeCCCCcCcCCcccccCCcEEEecCC-CCCcCChhhc--cCCCEEECCCCccccCChhhh--ccccEEECcCC-c
Confidence            45678888888888876322    5999999 9999998775  599999999999999998765  47999999999 6


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccccc--CCCCCcccC-
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK--FFKYPKLDL-  648 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~--~~~L~~L~~-  648 (779)
                      +..+|.. +.  ++|+.|++++|.+..+|               ..+.  ++|+.|+++.|....++.  .++|+.|.+ 
T Consensus       253 L~~LP~~-l~--s~L~~L~Ls~N~L~~LP---------------~~l~--~sL~~L~Ls~N~Lt~LP~~lp~sL~~L~Ls  312 (754)
T PRK15370        253 ITELPER-LP--SALQSLDLFHNKISCLP---------------ENLP--EELRYLSVYDNSIRTLPAHLPSGITHLNVQ  312 (754)
T ss_pred             cCcCChh-Hh--CCCCEEECcCCccCccc---------------cccC--CCCcEEECCCCccccCcccchhhHHHHHhc
Confidence            7899987 54  58999999998877532               2222  478999998876654421  122333310 


Q ss_pred             ----ccc--ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCcc
Q 004021          649 ----TWL--VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLK  722 (779)
Q Consensus       649 ----~~l--~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~  722 (779)
                          ..+  ...++|+.|++++|.. ..++.                .+  +++|+.|+++++ ++..+|..+  .++|+
T Consensus       313 ~N~Lt~LP~~l~~sL~~L~Ls~N~L-t~LP~----------------~l--~~sL~~L~Ls~N-~L~~LP~~l--p~~L~  370 (754)
T PRK15370        313 SNSLTALPETLPPGLKTLEAGENAL-TSLPA----------------SL--PPELQVLDVSKN-QITVLPETL--PPTIT  370 (754)
T ss_pred             CCccccCCccccccceeccccCCcc-ccCCh----------------hh--cCcccEEECCCC-CCCcCChhh--cCCcC
Confidence                000  1125677777777543 33332                22  368999999985 677777644  37899


Q ss_pred             EEeeeCCCCCCCCCCCCCCcccccEEEec
Q 004021          723 KIGVYGCPKLKKLPINSSSAKERRVVIEG  751 (779)
Q Consensus       723 ~L~l~~c~~L~~lP~~~~~~~~~~l~i~~  751 (779)
                      .|+|++| +|..+|..+.. .++.+.+.+
T Consensus       371 ~LdLs~N-~Lt~LP~~l~~-sL~~LdLs~  397 (754)
T PRK15370        371 TLDVSRN-ALTNLPENLPA-ALQIMQASR  397 (754)
T ss_pred             EEECCCC-cCCCCCHhHHH-HHHHHhhcc
Confidence            9999987 58888875432 234455543

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

Probab=99.19  E-value=2.4e-12  Score=129.07  Aligned_cols=96  Identities=22%  Similarity=0.283  Sum_probs=68.7

Q ss_pred             cccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCC
Q 004021          502 LMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSII  575 (779)
Q Consensus       502 l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~l  575 (779)
                      .++..+.++|...+    .+.|..| .|+.+|+ .|+.+++||.|||++|.|+.+ |..|..|.+|..|-+-+++.++.+
T Consensus        53 Cr~~GL~eVP~~LP~~tveirLdqN-~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l  131 (498)
T KOG4237|consen   53 CRGKGLTEVPANLPPETVEIRLDQN-QISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDL  131 (498)
T ss_pred             ccCCCcccCcccCCCcceEEEeccC-CcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhh
Confidence            33444555544332    5777888 7887754 577888888888888888775 667888888777777775578888


Q ss_pred             chhhhcCCccCcEeeeccccCCC
Q 004021          576 PHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       576 p~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      |.+.|++|.+|+.|.+.-|.+..
T Consensus       132 ~k~~F~gL~slqrLllNan~i~C  154 (498)
T KOG4237|consen  132 PKGAFGGLSSLQRLLLNANHINC  154 (498)
T ss_pred             hhhHhhhHHHHHHHhcChhhhcc
Confidence            88878888888888777766654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.18  E-value=1.1e-09  Score=133.71  Aligned_cols=275  Identities=15%  Similarity=0.210  Sum_probs=169.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKR  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~  227 (779)
                      +.+|-|+.-.+.+    ... ...+++.|+|++|.||||++..+.+..    .   .++|+++       ..+...++..
T Consensus        14 ~~~~~R~rl~~~l----~~~-~~~~~~~v~apaG~GKTtl~~~~~~~~----~---~~~w~~l~~~d~~~~~f~~~l~~~   81 (903)
T PRK04841         14 HNTVVRERLLAKL----SGA-NNYRLVLVTSPAGYGKTTLISQWAAGK----N---NLGWYSLDESDNQPERFASYLIAA   81 (903)
T ss_pred             cccCcchHHHHHH----hcc-cCCCeEEEECCCCCCHHHHHHHHHHhC----C---CeEEEecCcccCCHHHHHHHHHHH
Confidence            5567777555544    322 267899999999999999999987543    2   5899999       2344555555


Q ss_pred             hCCCcc---hhh-------hhcchhhHHHHHHHhhC--CCcceeehhhccccc------------cccCCCcEEEEEeCc
Q 004021          228 IGFSED---KKW-------KEKSLQDKAVDISSILS--PKKFRIDLTELGVPL------------QMLNAGFKIVLKTRS  283 (779)
Q Consensus       228 l~~~~~---~~~-------~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~~------------~~~~~gs~IivTTR~  283 (779)
                      +.....   ...       ...+.......+...+.  +.++.+++||+-..-            .....+.++|||||.
T Consensus        82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~  161 (903)
T PRK04841         82 LQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRN  161 (903)
T ss_pred             HHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCC
Confidence            531100   000       00122233333433443  567788888863321            122456788899998


Q ss_pred             hhhhh--hc--CCceeEcc----CCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCCh
Q 004021          284 AGVCD--QM--DSKNLEVY----SLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKV  355 (779)
Q Consensus       284 ~~va~--~~--~~~~~~l~----~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~  355 (779)
                      ..-..  ..  ......+.    +|+.+|+.++|....+..-      -.+....|.+.|+|.|+++..++..+......
T Consensus       162 ~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~------~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~  235 (903)
T PRK04841        162 LPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPI------EAAESSRLCDDVEGWATALQLIALSARQNNSS  235 (903)
T ss_pred             CCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCC------CHHHHHHHHHHhCChHHHHHHHHHHHhhCCCc
Confidence            42111  11  13344555    8999999999987655421      14667899999999999999888776543210


Q ss_pred             hHHHHHHHHHhcccCcCCC-chHHHHHHHHH-HHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHH
Q 004021          356 GDRERAIEKMRTSASTFSG-MEENVFLRLKF-SYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGC  433 (779)
Q Consensus       356 ~~w~~~~~~l~~~~~~~~~-~~~~i~~~l~~-sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~  433 (779)
                      .  ......+       .+ ....+...+.- .++.||+ ..+..+...|+++   .++.+. ..     .+.. .+.+.
T Consensus       236 ~--~~~~~~~-------~~~~~~~~~~~l~~~v~~~l~~-~~~~~l~~~a~~~---~~~~~l-~~-----~l~~-~~~~~  295 (903)
T PRK04841        236 L--HDSARRL-------AGINASHLSDYLVEEVLDNVDL-ETRHFLLRCSVLR---SMNDAL-IV-----RVTG-EENGQ  295 (903)
T ss_pred             h--hhhhHhh-------cCCCchhHHHHHHHHHHhcCCH-HHHHHHHHhcccc---cCCHHH-HH-----HHcC-CCcHH
Confidence            0  0101111       11 01245554433 4789999 8999999999986   334332 22     1122 24567


Q ss_pred             HHHHHHHHcccccc-c--CCCcEEechHHHHHHHHHH
Q 004021          434 EFINDLLHACLLEE-E--GDDHVKMHDMIREMSLWIA  467 (779)
Q Consensus       434 ~~l~~L~~~sll~~-~--~~~~~~mHdlv~~~a~~~~  467 (779)
                      ..+++|.+.+++.. .  +...|+.|++++++.+...
T Consensus       296 ~~L~~l~~~~l~~~~~~~~~~~yr~H~L~r~~l~~~l  332 (903)
T PRK04841        296 MRLEELERQGLFIQRMDDSGEWFRYHPLFASFLRHRC  332 (903)
T ss_pred             HHHHHHHHCCCeeEeecCCCCEEehhHHHHHHHHHHH
Confidence            88999999999653 2  3347999999999998765

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

Probab=99.15  E-value=2.2e-12  Score=135.07  Aligned_cols=186  Identities=22%  Similarity=0.229  Sum_probs=118.1

Q ss_pred             CccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~  569 (779)
                      .....+++.|.+.++|....      .+.|+.| .+..+|..+++|..|.||||+.|++..+|..++.|+ |+.|-+++|
T Consensus        76 dt~~aDlsrNR~~elp~~~~~f~~Le~liLy~n-~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lp-Lkvli~sNN  153 (722)
T KOG0532|consen   76 DTVFADLSRNRFSELPEEACAFVSLESLILYHN-CIRTIPEAICNLEALTFLDLSSNQLSHLPDGLCDLP-LKVLIVSNN  153 (722)
T ss_pred             chhhhhccccccccCchHHHHHHHHHHHHHHhc-cceecchhhhhhhHHHHhhhccchhhcCChhhhcCc-ceeEEEecC
Confidence            34456666677766665543      2666777 777777777777777777777777777777777776 777777777


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLT  649 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~  649 (779)
                       +++.+|.+ ++.+..|.+|+.+.|.+..               .+..++.|.+|+.|.+..|.         |..| |.
T Consensus       154 -kl~~lp~~-ig~~~tl~~ld~s~nei~s---------------lpsql~~l~slr~l~vrRn~---------l~~l-p~  206 (722)
T KOG0532|consen  154 -KLTSLPEE-IGLLPTLAHLDVSKNEIQS---------------LPSQLGYLTSLRDLNVRRNH---------LEDL-PE  206 (722)
T ss_pred             -ccccCCcc-cccchhHHHhhhhhhhhhh---------------chHHhhhHHHHHHHHHhhhh---------hhhC-CH
Confidence             67777777 7777777777777776543               56667777777777666433         2222 22


Q ss_pred             ccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCC---CCCCCccEEee
Q 004021          650 WLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNP---LHFPKLKKIGV  726 (779)
Q Consensus       650 ~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~---~~l~~L~~L~l  726 (779)
                      .+..| .|..|++++ +.+..+|.                .+..+..|++|.|.+ +-|.+.|..+   |...--++|++
T Consensus       207 El~~L-pLi~lDfSc-Nkis~iPv----------------~fr~m~~Lq~l~Len-NPLqSPPAqIC~kGkVHIFKyL~~  267 (722)
T KOG0532|consen  207 ELCSL-PLIRLDFSC-NKISYLPV----------------DFRKMRHLQVLQLEN-NPLQSPPAQICEKGKVHIFKYLST  267 (722)
T ss_pred             HHhCC-ceeeeeccc-Cceeecch----------------hhhhhhhheeeeecc-CCCCCChHHHHhccceeeeeeecc
Confidence            23323 366666665 44444543                556677777777776 3456655432   23333466666


Q ss_pred             eCC
Q 004021          727 YGC  729 (779)
Q Consensus       727 ~~c  729 (779)
                      .-|
T Consensus       268 qA~  270 (722)
T KOG0532|consen  268 QAC  270 (722)
T ss_pred             hhc
Confidence            666

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.14  E-value=1.4e-10  Score=132.37  Aligned_cols=192  Identities=20%  Similarity=0.187  Sum_probs=104.0

Q ss_pred             CCccEEEcccccccccccCcc---cccccccccccccchhhc-----------------ccccCceeeecCCcccccchh
Q 004021          495 EGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRIS-----------------SLVSLHHLDLSLTHIRGLPQE  554 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~-----------------~L~~L~~L~L~~~~i~~lp~~  554 (779)
                      .+++.|++++|.++.+|..+.   -|+|++| .+..+|....                 .+++|++|++++|.++.+|..
T Consensus       242 ~~Lk~LdLs~N~LtsLP~lp~sL~~L~Ls~N-~L~~Lp~lp~~L~~L~Ls~N~Lt~LP~~p~~L~~LdLS~N~L~~Lp~l  320 (788)
T PRK15387        242 PELRTLEVSGNQLTSLPVLPPGLLELSIFSN-PLTHLPALPSGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQLASLPAL  320 (788)
T ss_pred             CCCcEEEecCCccCcccCcccccceeeccCC-chhhhhhchhhcCEEECcCCccccccccccccceeECCCCccccCCCC
Confidence            466677777776666654332   2455555 4444443211                 124455555555555555432


Q ss_pred             hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC----ccCCCchhhHHhhcCCCCCCceeEE
Q 004021          555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       555 ~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                      .   .+|+.|++++| .++.+|.  +  ..+|++|++++|.+..+|....+    .+.++....+..  ...+|+.|+++
T Consensus       321 p---~~L~~L~Ls~N-~L~~LP~--l--p~~Lq~LdLS~N~Ls~LP~lp~~L~~L~Ls~N~L~~LP~--l~~~L~~LdLs  390 (788)
T PRK15387        321 P---SELCKLWAYNN-QLTSLPT--L--PSGLQELSVSDNQLASLPTLPSELYKLWAYNNRLTSLPA--LPSGLKELIVS  390 (788)
T ss_pred             c---ccccccccccC-ccccccc--c--ccccceEecCCCccCCCCCCCcccceehhhccccccCcc--cccccceEEec
Confidence            2   23444455555 3444443  1  13677788877777664421111    000000000000  11345555555


Q ss_pred             eecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcc
Q 004021          631 FRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS  710 (779)
Q Consensus       631 ~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~  710 (779)
                      .|...         .+  +.  ..++|+.|++++|. +..+|.                   .+.+|+.|++++ +.++.
T Consensus       391 ~N~Lt---------~L--P~--l~s~L~~LdLS~N~-LssIP~-------------------l~~~L~~L~Ls~-NqLt~  436 (788)
T PRK15387        391 GNRLT---------SL--PV--LPSELKELMVSGNR-LTSLPM-------------------LPSGLLSLSVYR-NQLTR  436 (788)
T ss_pred             CCccc---------CC--CC--cccCCCEEEccCCc-CCCCCc-------------------chhhhhhhhhcc-Ccccc
Confidence            43322         11  11  13579999999965 444432                   135788899987 67889


Q ss_pred             ccCCCCCCCCccEEeeeCCCC
Q 004021          711 IYPNPLHFPKLKKIGVYGCPK  731 (779)
Q Consensus       711 l~~~~~~l~~L~~L~l~~c~~  731 (779)
                      +|..++.+++|+.|++++|+-
T Consensus       437 LP~sl~~L~~L~~LdLs~N~L  457 (788)
T PRK15387        437 LPESLIHLSSETTVNLEGNPL  457 (788)
T ss_pred             cChHHhhccCCCeEECCCCCC
Confidence            998888999999999998864

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

Probab=99.09  E-value=9.9e-12  Score=137.39  Aligned_cols=96  Identities=29%  Similarity=0.413  Sum_probs=75.3

Q ss_pred             CccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~  569 (779)
                      ++++|++++|.+..+|....      -|+++.| .+..+|.+++++.+|++|+|.+|.+..+|.++..+++|++|++++|
T Consensus        46 ~L~~l~lsnn~~~~fp~~it~l~~L~~ln~s~n-~i~~vp~s~~~~~~l~~lnL~~n~l~~lP~~~~~lknl~~LdlS~N  124 (1081)
T KOG0618|consen   46 KLKSLDLSNNQISSFPIQITLLSHLRQLNLSRN-YIRSVPSSCSNMRNLQYLNLKNNRLQSLPASISELKNLQYLDLSFN  124 (1081)
T ss_pred             eeEEeeccccccccCCchhhhHHHHhhcccchh-hHhhCchhhhhhhcchhheeccchhhcCchhHHhhhcccccccchh
Confidence            47788888888877776544      2788888 8888888888888888888888888888888888888888888888


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                       ....+|.- +..++.+..+..++|
T Consensus       125 -~f~~~Pl~-i~~lt~~~~~~~s~N  147 (1081)
T KOG0618|consen  125 -HFGPIPLV-IEVLTAEEELAASNN  147 (1081)
T ss_pred             -ccCCCchh-HHhhhHHHHHhhhcc
Confidence             45677774 677777777777766

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.02  E-value=9.7e-09  Score=108.01  Aligned_cols=270  Identities=16%  Similarity=0.103  Sum_probs=147.2

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---chHHHHHHHHh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---QTFQDDIGKRI  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~~i~~~i~~~l  228 (779)
                      ..|+|+++.++++..++...   ......+.++|++|+|||+||+.+++..   ...+.. .....   ...+...+..+
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~---~~~~~~-~~~~~~~~~~~l~~~l~~~   79 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEM---GVNLKI-TSGPALEKPGDLAAILTNL   79 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh---CCCEEE-eccchhcCchhHHHHHHhc
Confidence            46899999999999888642   2245668899999999999999999887   222211 11111   11222223333


Q ss_pred             CCCcc---hhhhhcchhhHHHHHHHhhCCCcceeehhhccccc---cccCCCcEEEEEeCchhhhhhcC---CceeEccC
Q 004021          229 GFSED---KKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPL---QMLNAGFKIVLKTRSAGVCDQMD---SKNLEVYS  299 (779)
Q Consensus       229 ~~~~~---~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~---~~~~~gs~IivTTR~~~va~~~~---~~~~~l~~  299 (779)
                      +...-   +.....+ ......+...+.+.+..++++.-..+-   ....+.+-|..||+...+.....   ...+.+++
T Consensus        80 ~~~~vl~iDEi~~l~-~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~sR~~~~~~l~~  158 (305)
T TIGR00635        80 EEGDVLFIDEIHRLS-PAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEF  158 (305)
T ss_pred             ccCCEEEEehHhhhC-HHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHhhcceEEEeCC
Confidence            22100   0000011 122344566666655544443321110   01123556667777655543321   35679999


Q ss_pred             CChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCCCchHHH
Q 004021          300 LAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENV  379 (779)
Q Consensus       300 L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~i  379 (779)
                      ++.++..+++.+.+.......   -++....|++.|+|.|-.+..++..+        |... ......... ...-...
T Consensus       159 l~~~e~~~il~~~~~~~~~~~---~~~al~~ia~~~~G~pR~~~~ll~~~--------~~~a-~~~~~~~it-~~~v~~~  225 (305)
T TIGR00635       159 YTVEELAEIVSRSAGLLNVEI---EPEAALEIARRSRGTPRIANRLLRRV--------RDFA-QVRGQKIIN-RDIALKA  225 (305)
T ss_pred             CCHHHHHHHHHHHHHHhCCCc---CHHHHHHHHHHhCCCcchHHHHHHHH--------HHHH-HHcCCCCcC-HHHHHHH
Confidence            999999999998887544222   25677899999999997665554432        1100 000000000 0000122


Q ss_pred             HHHHHHHHhcCCccchhhhhh-hccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHH-HHHHcccccccC
Q 004021          380 FLRLKFSYDSLSMDKLRSCLL-YCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFIN-DLLHACLLEEEG  449 (779)
Q Consensus       380 ~~~l~~sy~~L~~~~~k~cf~-~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~-~L~~~sll~~~~  449 (779)
                      ...+...|..+++ +.+..+. ..+.++.+ .+....+..     -+=.+...++..++ .|++++|+....
T Consensus       226 l~~l~~~~~~l~~-~~~~~L~al~~~~~~~-~~~~~~ia~-----~lg~~~~~~~~~~e~~Li~~~li~~~~  290 (305)
T TIGR00635       226 LEMLMIDELGLDE-IDRKLLSVLIEQFQGG-PVGLKTLAA-----ALGEDADTIEDVYEPYLLQIGFLQRTP  290 (305)
T ss_pred             HHHhCCCCCCCCH-HHHHHHHHHHHHhCCC-cccHHHHHH-----HhCCCcchHHHhhhHHHHHcCCcccCC
Confidence            2234556777776 5555555 44555433 444433322     12122256777788 699999997653

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.01  E-value=4.7e-09  Score=111.09  Aligned_cols=270  Identities=15%  Similarity=0.072  Sum_probs=148.8

Q ss_pred             ccccchhhhHHHHHHHHhc---cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEE--EEEechHHHHHHHHhC
Q 004021          155 QTIVGQEKLLPRVWRCITD---QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVI--WAAVQTFQDDIGKRIG  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~--wv~v~~i~~~i~~~l~  229 (779)
                      .+|+|+++.++.+..++..   .......+.|+|++|+|||+||+.+++.. .  ..+....  ++.....+..++..+.
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l-~--~~~~~~~~~~~~~~~~l~~~l~~l~  101 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM-G--VNIRITSGPALEKPGDLAAILTNLE  101 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHh-C--CCeEEEecccccChHHHHHHHHhcc
Confidence            5689999999999888764   23345678899999999999999999987 2  2221100  0111222333444433


Q ss_pred             CCcc---hhhhhcchhhHHHHHHHhhCCCcceeehhhcccccc---ccCCCcEEEEEeCchhhhhhcC---CceeEccCC
Q 004021          230 FSED---KKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQ---MLNAGFKIVLKTRSAGVCDQMD---SKNLEVYSL  300 (779)
Q Consensus       230 ~~~~---~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~---~~~~gs~IivTTR~~~va~~~~---~~~~~l~~L  300 (779)
                      ...-   +..+..+ ......+...+.+.+....+++-..+-.   .-.+.+-|..|||...+.....   ...+.++++
T Consensus       102 ~~~vl~IDEi~~l~-~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~  180 (328)
T PRK00080        102 EGDVLFIDEIHRLS-PVVEEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFY  180 (328)
T ss_pred             cCCEEEEecHhhcc-hHHHHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHHHHHhcCeeeecCCC
Confidence            2100   0000000 1122334555555554444433211100   0112455666777655443322   356899999


Q ss_pred             ChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCCCchHHHH
Q 004021          301 AHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVF  380 (779)
Q Consensus       301 ~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~i~  380 (779)
                      +.++..+++.+.+.......+   ++....|++.|+|.|-.+..+...+.      .|....   ...... ...-....
T Consensus       181 ~~~e~~~il~~~~~~~~~~~~---~~~~~~ia~~~~G~pR~a~~~l~~~~------~~a~~~---~~~~I~-~~~v~~~l  247 (328)
T PRK00080        181 TVEELEKIVKRSARILGVEID---EEGALEIARRSRGTPRIANRLLRRVR------DFAQVK---GDGVIT-KEIADKAL  247 (328)
T ss_pred             CHHHHHHHHHHHHHHcCCCcC---HHHHHHHHHHcCCCchHHHHHHHHHH------HHHHHc---CCCCCC-HHHHHHHH
Confidence            999999999998876543322   56789999999999965554443221      121100   000000 00011333


Q ss_pred             HHHHHHHhcCCccchhhhhh-hccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHH-HHHHccccccc
Q 004021          381 LRLKFSYDSLSMDKLRSCLL-YCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFIN-DLLHACLLEEE  448 (779)
Q Consensus       381 ~~l~~sy~~L~~~~~k~cf~-~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~-~L~~~sll~~~  448 (779)
                      ..+...+..|++ ..+..+. ....|+.+ .+..+.+...     +-.+...+++.++ .|++.+|++..
T Consensus       248 ~~~~~~~~~l~~-~~~~~l~~~~~~~~~~-~~~~~~~a~~-----lg~~~~~~~~~~e~~Li~~~li~~~  310 (328)
T PRK00080        248 DMLGVDELGLDE-MDRKYLRTIIEKFGGG-PVGLDTLAAA-----LGEERDTIEDVYEPYLIQQGFIQRT  310 (328)
T ss_pred             HHhCCCcCCCCH-HHHHHHHHHHHHcCCC-ceeHHHHHHH-----HCCCcchHHHHhhHHHHHcCCcccC
Confidence            445556677776 5555554 55666655 4555544322     2122256666777 89999999865

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

Probab=98.97  E-value=6.4e-11  Score=124.31  Aligned_cols=187  Identities=23%  Similarity=0.278  Sum_probs=139.1

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      .||+.| .+.++|..++.+..|..|.|..|.+..+|..+++|..|.+|||+.| .+..+|.+ +..|+ |+.|.+++|++
T Consensus        80 aDlsrN-R~~elp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~N-qlS~lp~~-lC~lp-Lkvli~sNNkl  155 (722)
T KOG0532|consen   80 ADLSRN-RFSELPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSN-QLSHLPDG-LCDLP-LKVLIVSNNKL  155 (722)
T ss_pred             hhcccc-ccccCchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccc-hhhcCChh-hhcCc-ceeEEEecCcc
Confidence            788888 8888888888888888888888888888888889988999999888 67888887 66654 88888888877


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      ..               .+.+++.+..|..|+.+.|         ++++| ++.++.+.+|+.|.+..|+. ..+|.   
T Consensus       156 ~~---------------lp~~ig~~~tl~~ld~s~n---------ei~sl-psql~~l~slr~l~vrRn~l-~~lp~---  206 (722)
T KOG0532|consen  156 TS---------------LPEEIGLLPTLAHLDVSKN---------EIQSL-PSQLGYLTSLRDLNVRRNHL-EDLPE---  206 (722)
T ss_pred             cc---------------CCcccccchhHHHhhhhhh---------hhhhc-hHHhhhHHHHHHHHHhhhhh-hhCCH---
Confidence            64               5556666777788888744         34444 55677788888888888554 33433   


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc----ccEEEech
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE----RRVVIEGL  752 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~----~~l~i~~~  752 (779)
                                   .+..+ .|..|++++ +++..+|..+..|..|++|.+.++| |++=|..+...-.    +.|.++.|
T Consensus       207 -------------El~~L-pLi~lDfSc-Nkis~iPv~fr~m~~Lq~l~LenNP-LqSPPAqIC~kGkVHIFKyL~~qA~  270 (722)
T KOG0532|consen  207 -------------ELCSL-PLIRLDFSC-NKISYLPVDFRKMRHLQVLQLENNP-LQSPPAQICEKGKVHIFKYLSTQAC  270 (722)
T ss_pred             -------------HHhCC-ceeeeeccc-CceeecchhhhhhhhheeeeeccCC-CCCChHHHHhccceeeeeeecchhc
Confidence                         34444 378888884 7888888888888889998888776 7776655432211    55566555

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.88  E-value=4.5e-07  Score=99.19  Aligned_cols=279  Identities=15%  Similarity=0.172  Sum_probs=155.3

Q ss_pred             cccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~  225 (779)
                      ++.++||++++++|...+.+.  ......+.|+|.+|+|||++++.++++. ......-..++++.      ..++..|+
T Consensus        29 P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l-~~~~~~~~~v~in~~~~~~~~~~~~~i~  107 (394)
T PRK00411         29 PENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEEL-EEIAVKVVYVYINCQIDRTRYAIFSEIA  107 (394)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHH-HHhcCCcEEEEEECCcCCCHHHHHHHHH
Confidence            367899999999999998553  2344567899999999999999999987 22221223444444      35777888


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCC--Ccceeehhhccccc------------c--ccCCCcE--EEEEeCchhhh
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSP--KKFRIDLTELGVPL------------Q--MLNAGFK--IVLKTRSAGVC  287 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l~~~~------------~--~~~~gs~--IivTTR~~~va  287 (779)
                      .++..... .....+..+....+.+.++.  +...+.+|++....            .  ....+++  +|.+++...+.
T Consensus       108 ~~l~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~~~  186 (394)
T PRK00411        108 RQLFGHPP-PSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLTFL  186 (394)
T ss_pred             HHhcCCCC-CCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcchh
Confidence            88764211 01223445666677777753  33455555542211            0  1113334  66676654433


Q ss_pred             hh--------cCCceeEccCCChHHHHHHHHHHhhcc---CCCCCCChHHHHHHHHHHhCCChhHHHHHHHHh--c--CC
Q 004021          288 DQ--------MDSKNLEVYSLAHDEAWKLFQEMIERS---TLDSHTSIPELAETLARECGRLPLALKTVGRAM--K--SQ  352 (779)
Q Consensus       288 ~~--------~~~~~~~l~~L~~~~a~~Lf~~~a~~~---~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l--~--~~  352 (779)
                      ..        .+...+.+++++.++..+++..++...   ..-.+..++.+++......|..+.|+.++-...  +  ..
T Consensus       187 ~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~  266 (394)
T PRK00411        187 YILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREG  266 (394)
T ss_pred             hhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcC
Confidence            22        123567899999999999999887432   111111222233333333466777877654321  1  11


Q ss_pred             ---CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhcccc-CC-CcccChHHHHHH--HHH--c
Q 004021          353 ---KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLY-PE-DYKIPKRSLIDY--WIS--E  423 (779)
Q Consensus       353 ---~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~f-p~-~~~i~~~~Li~~--W~a--~  423 (779)
                         -+.+....+.+...             .....-.+..||. +.|..+..++.. .. ...+....+...  .++  .
T Consensus       267 ~~~I~~~~v~~a~~~~~-------------~~~~~~~~~~L~~-~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~  332 (394)
T PRK00411        267 SRKVTEEDVRKAYEKSE-------------IVHLSEVLRTLPL-HEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEEL  332 (394)
T ss_pred             CCCcCHHHHHHHHHHHH-------------HHHHHHHHhcCCH-HHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHc
Confidence               13444444443321             1223446788987 555544433322 11 133455554432  122  2


Q ss_pred             CCCc-chhhHHHHHHHHHHccccccc
Q 004021          424 GFMA-DFDRGCEFINDLLHACLLEEE  448 (779)
Q Consensus       424 g~~~-~~~~~~~~l~~L~~~sll~~~  448 (779)
                      |.-. ......+++..|...+++...
T Consensus       333 ~~~~~~~~~~~~~l~~L~~~glI~~~  358 (394)
T PRK00411        333 GYEPRTHTRFYEYINKLDMLGIINTR  358 (394)
T ss_pred             CCCcCcHHHHHHHHHHHHhcCCeEEE
Confidence            3221 114566788899999998753

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

Probab=98.85  E-value=4.7e-10  Score=112.92  Aligned_cols=101  Identities=25%  Similarity=0.317  Sum_probs=59.1

Q ss_pred             CccEEEcccccccccccCcc-------ccccccccccccc-chhhcccccCceeeecC-Ccccccchh-hccCccCcEee
Q 004021          496 GAKRISLMANEIESLSEIPT-------LLSLRRNDSLTEL-PSRISSLVSLHHLDLSL-THIRGLPQE-LKALEKLRYLN  565 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~-------lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~-~~i~~lp~~-~~~L~~L~~L~  565 (779)
                      ....|.|..|.|+.+|...+       -||||+| .|+.+ |..|.+|..|-.|-+.+ |+|+.+|+. |++|..|+.|.
T Consensus        68 ~tveirLdqN~I~~iP~~aF~~l~~LRrLdLS~N-~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLl  146 (498)
T KOG4237|consen   68 ETVEIRLDQNQISSIPPGAFKTLHRLRRLDLSKN-NISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQRLL  146 (498)
T ss_pred             cceEEEeccCCcccCChhhccchhhhceeccccc-chhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHHHh
Confidence            34455566666666665433       2666666 66655 66666666665555544 566666654 56666666666


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      +.-| .+.-++.+.+..|++|..|.++.|.+..
T Consensus       147 lNan-~i~Cir~~al~dL~~l~lLslyDn~~q~  178 (498)
T KOG4237|consen  147 LNAN-HINCIRQDALRDLPSLSLLSLYDNKIQS  178 (498)
T ss_pred             cChh-hhcchhHHHHHHhhhcchhcccchhhhh
Confidence            6555 4555555556666666666666655443

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.84  E-value=1.7e-09  Score=126.27  Aligned_cols=137  Identities=29%  Similarity=0.299  Sum_probs=95.9

Q ss_pred             hcccccCceeeecCC-cccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC-----
Q 004021          532 ISSLVSLHHLDLSLT-HIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN-----  605 (779)
Q Consensus       532 i~~L~~L~~L~L~~~-~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~-----  605 (779)
                      |..|++|++|||++| .+.++|..|++|-+||+|+++++ .+..+|.+ +++|.+|.+|++..+.....+.++..     
T Consensus       567 f~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t-~I~~LP~~-l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~L  644 (889)
T KOG4658|consen  567 FRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDT-GISHLPSG-LGNLKKLIYLNLEVTGRLESIPGILLELQSL  644 (889)
T ss_pred             HhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCC-CccccchH-HHHHHhhheeccccccccccccchhhhcccc
Confidence            677999999999988 78999999999999999999999 78999998 99999999999998765432211111     


Q ss_pred             -------ccCCCchhhHHhhcCCCCCCceeEEeecc---cccccCCCCCcc-------------cCcccccccCcceEEe
Q 004021          606 -------VLCDDAEPLMRELLGLKRLNVLSWSFRSS---LAVQKFFKYPKL-------------DLTWLVFVQNLKELEI  662 (779)
Q Consensus       606 -------~~~~~~~~~~~~l~~L~~L~~L~l~~~~~---~~~~~~~~L~~L-------------~~~~l~~l~~L~~L~L  662 (779)
                             ...........++..|++|+.|++.....   ..+..+..|.++             .++.+..+.+|+.|.+
T Consensus       645 r~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s~~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~~~l~~L~~L~i  724 (889)
T KOG4658|consen  645 RVLRLPRSALSNDKLLLKELENLEHLENLSITISSVLLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSLGSLGNLEELSI  724 (889)
T ss_pred             cEEEeeccccccchhhHHhhhcccchhhheeecchhHhHhhhhhhHHHHHHhHhhhhcccccceeecccccccCcceEEE
Confidence                   11122345566677777777777754443   111111111111             2345677889999999


Q ss_pred             ccccccce
Q 004021          663 IVCTEMEE  670 (779)
Q Consensus       663 ~~~~~~~~  670 (779)
                      .+|...+.
T Consensus       725 ~~~~~~e~  732 (889)
T KOG4658|consen  725 LDCGISEI  732 (889)
T ss_pred             EcCCCchh
Confidence            98877543

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

Probab=98.79  E-value=5.5e-07  Score=92.92  Aligned_cols=165  Identities=14%  Similarity=0.177  Sum_probs=100.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSI  251 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~  251 (779)
                      ...++.|+|.+|+|||||++.+++.. .. ..+ ..+|+..     .+++..|+..++.+..    ..+.......+...
T Consensus        42 ~~~~~~l~G~~G~GKTtl~~~l~~~l-~~-~~~-~~~~~~~~~~~~~~~l~~i~~~lG~~~~----~~~~~~~~~~l~~~  114 (269)
T TIGR03015        42 REGFILITGEVGAGKTTLIRNLLKRL-DQ-ERV-VAAKLVNTRVDAEDLLRMVAADFGLETE----GRDKAALLRELEDF  114 (269)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHhc-CC-CCe-EEeeeeCCCCCHHHHHHHHHHHcCCCCC----CCCHHHHHHHHHHH
Confidence            34689999999999999999999886 21 221 2233332     5677788888776522    11222222333322


Q ss_pred             -----hCCCcceeehhhcccc----------ccc----cCCCcEEEEEeCchhhhhh--------cC---CceeEccCCC
Q 004021          252 -----LSPKKFRIDLTELGVP----------LQM----LNAGFKIVLKTRSAGVCDQ--------MD---SKNLEVYSLA  301 (779)
Q Consensus       252 -----L~~kr~~~~ld~l~~~----------~~~----~~~gs~IivTTR~~~va~~--------~~---~~~~~l~~L~  301 (779)
                           ..+++..+.+|++...          +..    ......|++|.... ....        ..   ...+++++++
T Consensus       115 l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~~~l~~l~  193 (269)
T TIGR03015       115 LIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIASCHLGPLD  193 (269)
T ss_pred             HHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeeeeeCCCCC
Confidence                 2566766666664221          111    11223445555432 2111        11   3457899999


Q ss_pred             hHHHHHHHHHHhhccCCCCC-CChHHHHHHHHHHhCCChhHHHHHHHHh
Q 004021          302 HDEAWKLFQEMIERSTLDSH-TSIPELAETLARECGRLPLALKTVGRAM  349 (779)
Q Consensus       302 ~~~a~~Lf~~~a~~~~~~~~-~~l~~~~~~I~~~c~glPLai~~~g~~l  349 (779)
                      .+|..+++...+........ .--.+..+.|++.|+|.|..|..++..+
T Consensus       194 ~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       194 REETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            99999999887754432111 2235789999999999999999888765

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.

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

Probab=98.78  E-value=1.7e-09  Score=101.17  Aligned_cols=63  Identities=30%  Similarity=0.315  Sum_probs=21.9

Q ss_pred             ccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          534 SLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       534 ~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      .|.+|+.|+|++|.|+.++ .+..|++|++|++++| .++.++.++...+++|++|++++|.+..
T Consensus        40 ~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~N-~I~~i~~~l~~~lp~L~~L~L~~N~I~~  102 (175)
T PF14580_consen   40 TLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSNN-RISSISEGLDKNLPNLQELYLSNNKISD  102 (175)
T ss_dssp             T-TT--EEE-TTS--S--T-T----TT--EEE--SS----S-CHHHHHH-TT--EEE-TTS---S
T ss_pred             hhcCCCEEECCCCCCcccc-CccChhhhhhcccCCC-CCCccccchHHhCCcCCEEECcCCcCCC
Confidence            4566667777777666664 4666667777777766 5666655422356667777776666553

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

Probab=98.71  E-value=1e-08  Score=96.05  Aligned_cols=107  Identities=26%  Similarity=0.333  Sum_probs=41.1

Q ss_pred             ccccccCCccEEEcccccccccccCc----c--cccccccccccccchhhcccccCceeeecCCcccccchhh-ccCccC
Q 004021          489 PKVKEWEGAKRISLMANEIESLSEIP----T--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQEL-KALEKL  561 (779)
Q Consensus       489 ~~~~~~~~lr~l~l~~~~~~~l~~~~----~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~-~~L~~L  561 (779)
                      +......++|.|++.+|.|..+....    .  .|+|++| .|..++ .+..|++|++|++++|.|+.++..+ ..+++|
T Consensus        13 ~~~~n~~~~~~L~L~~n~I~~Ie~L~~~l~~L~~L~Ls~N-~I~~l~-~l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~L   90 (175)
T PF14580_consen   13 AQYNNPVKLRELNLRGNQISTIENLGATLDKLEVLDLSNN-QITKLE-GLPGLPRLKTLDLSNNRISSISEGLDKNLPNL   90 (175)
T ss_dssp             -----------------------S--TT-TT--EEE-TTS---S--T-T----TT--EEE--SS---S-CHHHHHH-TT-
T ss_pred             cccccccccccccccccccccccchhhhhcCCCEEECCCC-CCcccc-CccChhhhhhcccCCCCCCccccchHHhCCcC
Confidence            33334457899999999988765432    1  4999999 999886 6888999999999999999997766 479999


Q ss_pred             cEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCC
Q 004021          562 RYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       562 ~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ++|++++| .+..+.. ..+..+++|++|++.+|.+..
T Consensus        91 ~~L~L~~N-~I~~l~~l~~L~~l~~L~~L~L~~NPv~~  127 (175)
T PF14580_consen   91 QELYLSNN-KISDLNELEPLSSLPKLRVLSLEGNPVCE  127 (175)
T ss_dssp             -EEE-TTS----SCCCCGGGGG-TT--EEE-TT-GGGG
T ss_pred             CEEECcCC-cCCChHHhHHHHcCCCcceeeccCCcccc
Confidence            99999999 5554432 126789999999999998763

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

Probab=98.70  E-value=2e-07  Score=94.04  Aligned_cols=181  Identities=21%  Similarity=0.250  Sum_probs=94.3

Q ss_pred             ccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHH-------
Q 004021          157 IVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDI-------  224 (779)
Q Consensus       157 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i-------  224 (779)
                      |+||++++++|.+++..+  ..+.+.|+|..|+|||+|++.+.+.. . ...+ .++|+..     ......+       
T Consensus         1 F~gR~~el~~l~~~l~~~--~~~~~~l~G~rg~GKTsLl~~~~~~~-~-~~~~-~~~y~~~~~~~~~~~~~~~~~~~~~~   75 (234)
T PF01637_consen    1 FFGREKELEKLKELLESG--PSQHILLYGPRGSGKTSLLKEFINEL-K-EKGY-KVVYIDFLEESNESSLRSFIEETSLA   75 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHHC-T---EE-CCCHHCCTTBSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhh--cCcEEEEEcCCcCCHHHHHHHHHHHh-h-hcCC-cEEEEecccchhhhHHHHHHHHHHHH
Confidence            799999999999999876  56889999999999999999999876 2 1112 2333333     1111111       


Q ss_pred             -------HHHhCCCcch---hhhhcchhhHHHHHHHhhC--CCcceeehhhccccc-----------------cc--cCC
Q 004021          225 -------GKRIGFSEDK---KWKEKSLQDKAVDISSILS--PKKFRIDLTELGVPL-----------------QM--LNA  273 (779)
Q Consensus       225 -------~~~l~~~~~~---~~~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~~-----------------~~--~~~  273 (779)
                             ...+......   .............+.+.+.  +++..+++|++....                 ..  ...
T Consensus        76 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  155 (234)
T PF01637_consen   76 DELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQ  155 (234)
T ss_dssp             CHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----T
T ss_pred             HHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccC
Confidence                   1111110000   0001122233344444443  234666666653322                 00  123


Q ss_pred             CcEEEEEeCchhhhhh--------cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          274 GFKIVLKTRSAGVCDQ--------MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       274 gs~IivTTR~~~va~~--------~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      .-.+|+++-...+...        .+ ...+.+++|+.+++++++...+... ... +.-.+..++|...+||.|..|..
T Consensus       156 ~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~-~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  156 NVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-IKL-PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             TEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC--------HHHHHHHHHHHTT-HHHHHH
T ss_pred             CceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh-hcc-cCCHHHHHHHHHHhCCCHHHHhc
Confidence            3344555544444332        22 3458999999999999999976544 121 12256679999999999988754

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

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.68  E-value=7.4e-06  Score=88.65  Aligned_cols=278  Identities=14%  Similarity=0.118  Sum_probs=152.3

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC---CEEEEEEe------chHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF---DVVIWAAV------QTFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F---~~~~wv~v------~~i~~~  223 (779)
                      +.++||++++++|...|...  ......+.|+|++|+|||++++.+++.........   -..+|+..      ..++..
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            57899999999999998752  22456789999999999999999998762111111   13455554      457777


Q ss_pred             HHHHhC---CCcchhhhhcchhhHHHHHHHhhC--CCcceeehhhccccc-----------c----ccC--CCcEEEEEe
Q 004021          224 IGKRIG---FSEDKKWKEKSLQDKAVDISSILS--PKKFRIDLTELGVPL-----------Q----MLN--AGFKIVLKT  281 (779)
Q Consensus       224 i~~~l~---~~~~~~~~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~~-----------~----~~~--~gs~IivTT  281 (779)
                      |+.++.   .. . .....+..+....+.+.+.  ++++.+++|++....           .    ...  ....+|.+|
T Consensus        95 i~~~l~~~~~~-~-~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~  172 (365)
T TIGR02928        95 LANQLRGSGEE-V-PTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGIS  172 (365)
T ss_pred             HHHHHhhcCCC-C-CCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEE
Confidence            888773   21 1 0112233445555666653  344555555542210           0    011  223455566


Q ss_pred             Cchhhhhhc--------CCceeEccCCChHHHHHHHHHHhhcc--CCCCCCChHHHHHHHHHHhCCChhHH-HHHHHH--
Q 004021          282 RSAGVCDQM--------DSKNLEVYSLAHDEAWKLFQEMIERS--TLDSHTSIPELAETLARECGRLPLAL-KTVGRA--  348 (779)
Q Consensus       282 R~~~va~~~--------~~~~~~l~~L~~~~a~~Lf~~~a~~~--~~~~~~~l~~~~~~I~~~c~glPLai-~~~g~~--  348 (779)
                      +.......+        ....+.+++.+.++..+++..++...  ....+++..+....++..+.|-|-.+ .++-..  
T Consensus       173 n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~  252 (365)
T TIGR02928       173 NDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGE  252 (365)
T ss_pred             CCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            544332111        12468999999999999999887421  11122233344555677777877443 332111  


Q ss_pred             hc--CC---CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhcccc--CCCcccChHHHHHHHH
Q 004021          349 MK--SQ---KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLY--PEDYKIPKRSLIDYWI  421 (779)
Q Consensus       349 l~--~~---~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~f--p~~~~i~~~~Li~~W~  421 (779)
                      +.  .+   -+.+....+.+.+.             .....-++..||. +.+..+..+...  ..+..+...++...+.
T Consensus       253 ~a~~~~~~~it~~~v~~a~~~~~-------------~~~~~~~i~~l~~-~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~  318 (365)
T TIGR02928       253 IAEREGAERVTEDHVEKAQEKIE-------------KDRLLELIRGLPT-HSKLVLLAIANLAANDEDPFRTGEVYEVYK  318 (365)
T ss_pred             HHHHcCCCCCCHHHHHHHHHHHH-------------HHHHHHHHHcCCH-HHHHHHHHHHHHHhcCCCCccHHHHHHHHH
Confidence            11  11   22333333333221             1223446678887 666554444321  1334466666655331


Q ss_pred             --HcCC-Ccch--hhHHHHHHHHHHccccccc
Q 004021          422 --SEGF-MADF--DRGCEFINDLLHACLLEEE  448 (779)
Q Consensus       422 --a~g~-~~~~--~~~~~~l~~L~~~sll~~~  448 (779)
                        ++.+ +.+.  ....+++..|...|++...
T Consensus       319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~  350 (365)
T TIGR02928       319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAE  350 (365)
T ss_pred             HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEE
Confidence              2211 1111  5677788889999998764

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

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

Probab=98.63  E-value=7.3e-09  Score=100.53  Aligned_cols=123  Identities=21%  Similarity=0.190  Sum_probs=67.2

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      +|||+| .|+.+-+++.-++.++.|++++|+|..+-. +..|++|++|||++| .+..+... -.+|-|.++|.+.+|.+
T Consensus       289 lDLS~N-~I~~iDESvKL~Pkir~L~lS~N~i~~v~n-La~L~~L~~LDLS~N-~Ls~~~Gw-h~KLGNIKtL~La~N~i  364 (490)
T KOG1259|consen  289 LDLSGN-LITQIDESVKLAPKLRRLILSQNRIRTVQN-LAELPQLQLLDLSGN-LLAECVGW-HLKLGNIKTLKLAQNKI  364 (490)
T ss_pred             cccccc-chhhhhhhhhhccceeEEeccccceeeehh-hhhcccceEeecccc-hhHhhhhh-HhhhcCEeeeehhhhhH
Confidence            566666 666666565556666666666666655543 555666666666666 44444432 34555666666665543


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~  667 (779)
                      .                .+..|++|-+|..|+++.|.+..+.        ....++++|.|++|.|.+|+.
T Consensus       365 E----------------~LSGL~KLYSLvnLDl~~N~Ie~ld--------eV~~IG~LPCLE~l~L~~NPl  411 (490)
T KOG1259|consen  365 E----------------TLSGLRKLYSLVNLDLSSNQIEELD--------EVNHIGNLPCLETLRLTGNPL  411 (490)
T ss_pred             h----------------hhhhhHhhhhheeccccccchhhHH--------HhcccccccHHHHHhhcCCCc
Confidence            3                3444555556666666644432211        123455666666666666443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.61  E-value=2e-06  Score=95.99  Aligned_cols=278  Identities=17%  Similarity=0.186  Sum_probs=172.2

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRI  228 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l  228 (779)
                      ..|-|.    ++++.|... .+.+++.|..++|.|||||+.+.....    ..=..+.|.+.       ..+...++..+
T Consensus        20 ~~v~R~----rL~~~L~~~-~~~RL~li~APAGfGKttl~aq~~~~~----~~~~~v~Wlslde~dndp~rF~~yLi~al   90 (894)
T COG2909          20 NYVVRP----RLLDRLRRA-NDYRLILISAPAGFGKTTLLAQWRELA----ADGAAVAWLSLDESDNDPARFLSYLIAAL   90 (894)
T ss_pred             cccccH----HHHHHHhcC-CCceEEEEeCCCCCcHHHHHHHHHHhc----CcccceeEeecCCccCCHHHHHHHHHHHH
Confidence            345554    455555543 267999999999999999999997633    33456899999       34555555555


Q ss_pred             CCC--c-chh-------hhhcchhhHHHHHHHhhCC--Ccceeehhhc---ccc---------ccccCCCcEEEEEeCch
Q 004021          229 GFS--E-DKK-------WKEKSLQDKAVDISSILSP--KKFRIDLTEL---GVP---------LQMLNAGFKIVLKTRSA  284 (779)
Q Consensus       229 ~~~--~-~~~-------~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l---~~~---------~~~~~~gs~IivTTR~~  284 (779)
                      +..  . ++.       ....+.....+.+..-+..  ++..+++||.   ..+         +.....+-..|||||+.
T Consensus        91 ~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~r  170 (894)
T COG2909          91 QQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSR  170 (894)
T ss_pred             HHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccC
Confidence            421  0 100       0122233344444443332  3557777774   222         12335688999999985


Q ss_pred             hhhhhcC----CceeEcc----CCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChh
Q 004021          285 GVCDQMD----SKNLEVY----SLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVG  356 (779)
Q Consensus       285 ~va~~~~----~~~~~l~----~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~  356 (779)
                      --.....    ...++++    .++.+|+-++|....+..-      -..-.+.+.+...|-+-|+..++=.++.+.+..
T Consensus       171 P~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~L------d~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~  244 (894)
T COG2909         171 PQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPL------DAADLKALYDRTEGWAAALQLIALALRNNTSAE  244 (894)
T ss_pred             CCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCC------ChHHHHHHHhhcccHHHHHHHHHHHccCCCcHH
Confidence            4322111    3333443    3789999999987653321      145578999999999999999887777433332


Q ss_pred             HHHHHHHHHhcccCcCCCchHHHHHHH-HHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHH
Q 004021          357 DRERAIEKMRTSASTFSGMEENVFLRL-KFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEF  435 (779)
Q Consensus       357 ~w~~~~~~l~~~~~~~~~~~~~i~~~l-~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~  435 (779)
                      .-...          ..+..+.+..-| .=-++.||+ ++|..++.||+++.=    -..|+..-..+      +.+...
T Consensus       245 q~~~~----------LsG~~~~l~dYL~eeVld~Lp~-~l~~FLl~~svl~~f----~~eL~~~Ltg~------~ng~am  303 (894)
T COG2909         245 QSLRG----------LSGAASHLSDYLVEEVLDRLPP-ELRDFLLQTSVLSRF----NDELCNALTGE------ENGQAM  303 (894)
T ss_pred             HHhhh----------ccchHHHHHHHHHHHHHhcCCH-HHHHHHHHHHhHHHh----hHHHHHHHhcC------CcHHHH
Confidence            22211          111222332222 234788999 899999999998532    12333321111      567888


Q ss_pred             HHHHHHccccccc---CCCcEEechHHHHHHHHHHhh
Q 004021          436 INDLLHACLLEEE---GDDHVKMHDMIREMSLWIAWT  469 (779)
Q Consensus       436 l~~L~~~sll~~~---~~~~~~mHdlv~~~a~~~~~~  469 (779)
                      +++|.+++|+-..   ....|+.|.++.||.+.-...
T Consensus       304 Le~L~~~gLFl~~Ldd~~~WfryH~LFaeFL~~r~~~  340 (894)
T COG2909         304 LEELERRGLFLQRLDDEGQWFRYHHLFAEFLRQRLQR  340 (894)
T ss_pred             HHHHHhCCCceeeecCCCceeehhHHHHHHHHhhhcc
Confidence            9999999987654   677899999999999865543

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

Probab=98.61  E-value=1.8e-08  Score=106.91  Aligned_cols=13  Identities=15%  Similarity=0.084  Sum_probs=6.7

Q ss_pred             cccCcceEEeccc
Q 004021          653 FVQNLKELEIIVC  665 (779)
Q Consensus       653 ~l~~L~~L~L~~~  665 (779)
                      .+++|++|++++|
T Consensus       219 ~~~~L~~L~ls~n  231 (319)
T cd00116         219 SLKSLEVLNLGDN  231 (319)
T ss_pred             ccCCCCEEecCCC
Confidence            3445555555554

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

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

Probab=98.59  E-value=3.8e-08  Score=107.70  Aligned_cols=79  Identities=34%  Similarity=0.501  Sum_probs=52.4

Q ss_pred             ccccccccccccchhhcccc-cCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLV-SLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~-~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      |++.+| .+..+|..++.+. +|+.|++++|.+..+|..++.+++|+.|++++| .+..+|.. .+.+++|+.|++++|.
T Consensus       121 L~l~~n-~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N-~l~~l~~~-~~~~~~L~~L~ls~N~  197 (394)
T COG4886         121 LDLDNN-NITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFN-DLSDLPKL-LSNLSNLNNLDLSGNK  197 (394)
T ss_pred             EecCCc-ccccCccccccchhhcccccccccchhhhhhhhhccccccccccCCc-hhhhhhhh-hhhhhhhhheeccCCc
Confidence            566666 6666666666664 677777777777777666677777777777776 56666664 4466677777777666


Q ss_pred             CCC
Q 004021          596 SEG  598 (779)
Q Consensus       596 ~~~  598 (779)
                      +..
T Consensus       198 i~~  200 (394)
T COG4886         198 ISD  200 (394)
T ss_pred             ccc
Confidence            554

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

Probab=98.57  E-value=6.8e-09  Score=100.77  Aligned_cols=127  Identities=19%  Similarity=0.195  Sum_probs=107.7

Q ss_pred             ccccCCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEe
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYL  564 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L  564 (779)
                      ...|+.+..+++++|.|+.+.....      .|++|.| .+..+-. +..|.+|+.|||++|.++++-..=.+|.|.++|
T Consensus       280 ~dTWq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N-~i~~v~n-La~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKtL  357 (490)
T KOG1259|consen  280 ADTWQELTELDLSGNLITQIDESVKLAPKLRRLILSQN-RIRTVQN-LAELPQLQLLDLSGNLLAECVGWHLKLGNIKTL  357 (490)
T ss_pred             cchHhhhhhccccccchhhhhhhhhhccceeEEecccc-ceeeehh-hhhcccceEeecccchhHhhhhhHhhhcCEeee
Confidence            4579999999999999988776644      4999999 8887764 889999999999999888876656688899999


Q ss_pred             eccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc
Q 004021          565 NLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       565 ~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      .|++| .++.+..  +++|.+|..|++.+|++..             -.....+++|+.|+.+.+.+|...
T Consensus       358 ~La~N-~iE~LSG--L~KLYSLvnLDl~~N~Ie~-------------ldeV~~IG~LPCLE~l~L~~NPl~  412 (490)
T KOG1259|consen  358 KLAQN-KIETLSG--LRKLYSLVNLDLSSNQIEE-------------LDEVNHIGNLPCLETLRLTGNPLA  412 (490)
T ss_pred             ehhhh-hHhhhhh--hHhhhhheeccccccchhh-------------HHHhcccccccHHHHHhhcCCCcc
Confidence            99999 7888876  8999999999999998875             345667889999999999877654

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

Probab=98.51  E-value=2.6e-08  Score=105.72  Aligned_cols=205  Identities=20%  Similarity=0.133  Sum_probs=124.3

Q ss_pred             CCccEEEcccccccc-----ccc----Ccc--ccccccccccc-------ccchhhcccccCceeeecCCcccc-cchhh
Q 004021          495 EGAKRISLMANEIES-----LSE----IPT--LLSLRRNDSLT-------ELPSRISSLVSLHHLDLSLTHIRG-LPQEL  555 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~-----l~~----~~~--lL~L~~~~~l~-------~lp~~i~~L~~L~~L~L~~~~i~~-lp~~~  555 (779)
                      ..++.+.+.++.+..     ++.    .+.  .|+++++ .+.       .++..+.++.+|++|++++|.+.. .+..+
T Consensus        23 ~~L~~l~l~~~~l~~~~~~~i~~~l~~~~~l~~l~l~~~-~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~~~~~~~  101 (319)
T cd00116          23 LCLQVLRLEGNTLGEEAAKALASALRPQPSLKELCLSLN-ETGRIPRGLQSLLQGLTKGCGLQELDLSDNALGPDGCGVL  101 (319)
T ss_pred             hhccEEeecCCCCcHHHHHHHHHHHhhCCCceEEecccc-ccCCcchHHHHHHHHHHhcCceeEEEccCCCCChhHHHHH
Confidence            457888888877632     211    111  3667666 444       235567778899999998887763 45555


Q ss_pred             ccCcc---CcEeeccCCcCCC-----CCchhhhcCC-ccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCc
Q 004021          556 KALEK---LRYLNLEYTHYLS-----IIPHQLISGF-LKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNV  626 (779)
Q Consensus       556 ~~L~~---L~~L~l~~~~~l~-----~lp~~~i~~L-~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~  626 (779)
                      ..+.+   |++|++++|. +.     .+... +..+ ++|+.|++.+|.+..          .........+..+++|+.
T Consensus       102 ~~l~~~~~L~~L~ls~~~-~~~~~~~~l~~~-l~~~~~~L~~L~L~~n~l~~----------~~~~~~~~~~~~~~~L~~  169 (319)
T cd00116         102 ESLLRSSSLQELKLNNNG-LGDRGLRLLAKG-LKDLPPALEKLVLGRNRLEG----------ASCEALAKALRANRDLKE  169 (319)
T ss_pred             HHHhccCcccEEEeeCCc-cchHHHHHHHHH-HHhCCCCceEEEcCCCcCCc----------hHHHHHHHHHHhCCCcCE
Confidence            55555   9999998884 43     22233 5566 888999999888763          101234556677788888


Q ss_pred             eeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCC
Q 004021          627 LSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGP  706 (779)
Q Consensus       627 L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~  706 (779)
                      |+++.+....-    .+..+ +..+..+++|+.|++++|........        .+.    ..+..+++|+.|++++++
T Consensus       170 L~l~~n~l~~~----~~~~l-~~~l~~~~~L~~L~L~~n~i~~~~~~--------~l~----~~~~~~~~L~~L~ls~n~  232 (319)
T cd00116         170 LNLANNGIGDA----GIRAL-AEGLKANCNLEVLDLNNNGLTDEGAS--------ALA----ETLASLKSLEVLNLGDNN  232 (319)
T ss_pred             EECcCCCCchH----HHHHH-HHHHHhCCCCCEEeccCCccChHHHH--------HHH----HHhcccCCCCEEecCCCc
Confidence            88885543210    00011 12234557999999998754321110        011    245678899999999863


Q ss_pred             CCccccC-C-----CCCCCCccEEeeeCCC
Q 004021          707 DLKSIYP-N-----PLHFPKLKKIGVYGCP  730 (779)
Q Consensus       707 ~l~~l~~-~-----~~~l~~L~~L~l~~c~  730 (779)
                       +..... .     ....+.|++|++.+|.
T Consensus       233 -l~~~~~~~l~~~~~~~~~~L~~L~l~~n~  261 (319)
T cd00116         233 -LTDAGAAALASALLSPNISLLTLSLSCND  261 (319)
T ss_pred             -CchHHHHHHHHHHhccCCCceEEEccCCC
Confidence             443211 0     1124789999999884

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).

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.47  E-value=1.3e-07  Score=72.48  Aligned_cols=60  Identities=28%  Similarity=0.387  Sum_probs=51.1

Q ss_pred             ccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          536 VSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       536 ~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      ++|++|++++|.++.+|. .|.++++|++|++++| .++.+|++.+.++++|++|++++|.+
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N~l   61 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNN-NLTSIPPDAFSNLPNLRYLDLSNNNL   61 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETSS-SESEEETTTTTTSTTESEEEETSSSB
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccCC-ccCccCHHHHcCCCCCCEEeCcCCcC
Confidence            478899999999999885 5788999999999988 67888887788999999999988853

...

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

Probab=98.47  E-value=6.9e-08  Score=98.99  Aligned_cols=200  Identities=21%  Similarity=0.194  Sum_probs=99.5

Q ss_pred             ccCCccEEEccccccccccc------Cccc--ccccccccccc---cchhhcccccCceeeecCCcccccchh--hccCc
Q 004021          493 EWEGAKRISLMANEIESLSE------IPTL--LSLRRNDSLTE---LPSRISSLVSLHHLDLSLTHIRGLPQE--LKALE  559 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~------~~~l--L~L~~~~~l~~---lp~~i~~L~~L~~L~L~~~~i~~lp~~--~~~L~  559 (779)
                      .++++|.+++.+..+...+.      .+.+  ||||.| -+..   +-.-...|++|+.|+|+.|.+....++  -..++
T Consensus       119 n~kkL~~IsLdn~~V~~~~~~~~~k~~~~v~~LdLS~N-L~~nw~~v~~i~eqLp~Le~LNls~Nrl~~~~~s~~~~~l~  197 (505)
T KOG3207|consen  119 NLKKLREISLDNYRVEDAGIEEYSKILPNVRDLDLSRN-LFHNWFPVLKIAEQLPSLENLNLSSNRLSNFISSNTTLLLS  197 (505)
T ss_pred             hHHhhhheeecCccccccchhhhhhhCCcceeecchhh-hHHhHHHHHHHHHhcccchhcccccccccCCccccchhhhh
Confidence            34678888888766544332      1111  555555 3322   122234555666666665554433222  12345


Q ss_pred             cCcEeeccCCcCCC--CCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc
Q 004021          560 KLRYLNLEYTHYLS--IIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV  637 (779)
Q Consensus       560 ~L~~L~l~~~~~l~--~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~  637 (779)
                      +|+.|.|++|. +.  .+-. ++..+++|+.|++.+|....              ........++.|++|+|+.|..-.+
T Consensus       198 ~lK~L~l~~CG-ls~k~V~~-~~~~fPsl~~L~L~~N~~~~--------------~~~~~~~i~~~L~~LdLs~N~li~~  261 (505)
T KOG3207|consen  198 HLKQLVLNSCG-LSWKDVQW-ILLTFPSLEVLYLEANEIIL--------------IKATSTKILQTLQELDLSNNNLIDF  261 (505)
T ss_pred             hhheEEeccCC-CCHHHHHH-HHHhCCcHHHhhhhcccccc--------------eecchhhhhhHHhhccccCCccccc
Confidence            55556666552 22  1111 13345555556555553110              0111122344556666664433221


Q ss_pred             ccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC--CC
Q 004021          638 QKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP--NP  715 (779)
Q Consensus       638 ~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~--~~  715 (779)
                      .        ..+..+.+|.|..|+++.|.. .++-. .+++.   .     .....||+|+.|.+.. ++...|+.  .+
T Consensus       262 ~--------~~~~~~~l~~L~~Lnls~tgi-~si~~-~d~~s---~-----~kt~~f~kL~~L~i~~-N~I~~w~sl~~l  322 (505)
T KOG3207|consen  262 D--------QGYKVGTLPGLNQLNLSSTGI-ASIAE-PDVES---L-----DKTHTFPKLEYLNISE-NNIRDWRSLNHL  322 (505)
T ss_pred             c--------cccccccccchhhhhccccCc-chhcC-CCccc---h-----hhhcccccceeeeccc-Cccccccccchh
Confidence            1        123456788888888887543 22211 00000   0     1245689999999887 45556654  44


Q ss_pred             CCCCCccEEeeeC
Q 004021          716 LHFPKLKKIGVYG  728 (779)
Q Consensus       716 ~~l~~L~~L~l~~  728 (779)
                      ..+++|+.|.+..
T Consensus       323 ~~l~nlk~l~~~~  335 (505)
T KOG3207|consen  323 RTLENLKHLRITL  335 (505)
T ss_pred             hccchhhhhhccc
Confidence            5677888877653

>PRK06893 DNA replication initiation factor; Validated

Probab=98.42  E-value=7.4e-06  Score=81.74  Aligned_cols=138  Identities=17%  Similarity=0.244  Sum_probs=84.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech---HHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT---FQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~---i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~  253 (779)
                      ..+.+.|+|.+|+|||+||+++++...   .....+.|+++..   ....+...                        ++
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~~~---~~~~~~~y~~~~~~~~~~~~~~~~------------------------~~   90 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNHYL---LNQRTAIYIPLSKSQYFSPAVLEN------------------------LE   90 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCCeEEeeHHHhhhhhHHHHhh------------------------cc
Confidence            346789999999999999999999872   2233456666521   11111111                        11


Q ss_pred             CCcceeehhhcccc-------------ccc-cCCCcEEEEEeCc----------hhhhhhcC-CceeEccCCChHHHHHH
Q 004021          254 PKKFRIDLTELGVP-------------LQM-LNAGFKIVLKTRS----------AGVCDQMD-SKNLEVYSLAHDEAWKL  308 (779)
Q Consensus       254 ~kr~~~~ld~l~~~-------------~~~-~~~gs~IivTTR~----------~~va~~~~-~~~~~l~~L~~~~a~~L  308 (779)
                      +. -++.+|++...             +.. ...|..+||+|.+          ..+.+.+. ...++++++++++.+++
T Consensus        91 ~~-dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~i  169 (229)
T PRK06893         91 QQ-DLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIV  169 (229)
T ss_pred             cC-CEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHH
Confidence            11 12333333211             111 1235566555443          35555555 67889999999999999


Q ss_pred             HHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          309 FQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       309 f~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      +.+.+.......+   +++..-|++++.|-.-++..+
T Consensus       170 L~~~a~~~~l~l~---~~v~~~L~~~~~~d~r~l~~~  203 (229)
T PRK06893        170 LQRNAYQRGIELS---DEVANFLLKRLDRDMHTLFDA  203 (229)
T ss_pred             HHHHHHHcCCCCC---HHHHHHHHHhccCCHHHHHHH
Confidence            9999876543333   567788888888766555443

>PF05729 NACHT: NACHT domain

Probab=98.39  E-value=4.1e-06  Score=79.26  Aligned_cols=125  Identities=16%  Similarity=0.317  Sum_probs=76.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCC----CCEEEEEEec---------hHHHHHHHHhCCCcchhhhhcchhhHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHN----FDVVIWAAVQ---------TFQDDIGKRIGFSEDKKWKEKSLQDKA  245 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~----F~~~~wv~v~---------~i~~~i~~~l~~~~~~~~~~~~~~~~~  245 (779)
                      +++.|+|.+|+||||+++.++.+. .....    +...+|++..         .+...|..+....      ......  
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~~~~--   71 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQL-AEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPES------IAPIEE--   71 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHH-HhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccc------hhhhHH--
Confidence            588999999999999999999887 32222    4566677771         2333333333221      011111  


Q ss_pred             HHHHHh-hCCCcceeehhhc---ccc----------------ccc-cCCCcEEEEEeCchhh---hhhcC-CceeEccCC
Q 004021          246 VDISSI-LSPKKFRIDLTEL---GVP----------------LQM-LNAGFKIVLKTRSAGV---CDQMD-SKNLEVYSL  300 (779)
Q Consensus       246 ~~l~~~-L~~kr~~~~ld~l---~~~----------------~~~-~~~gs~IivTTR~~~v---a~~~~-~~~~~l~~L  300 (779)
                       .+... -+.+++++.+|.+   ...                +.. ..++++++||||....   ..... ...+.+.+|
T Consensus        72 -~~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~  150 (166)
T PF05729_consen   72 -LLQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPF  150 (166)
T ss_pred             -HHHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCC
Confidence             12222 2455665544443   221                111 2468999999998766   33333 457899999


Q ss_pred             ChHHHHHHHHHHh
Q 004021          301 AHDEAWKLFQEMI  313 (779)
Q Consensus       301 ~~~~a~~Lf~~~a  313 (779)
                      ++++..+++.++.
T Consensus       151 ~~~~~~~~~~~~f  163 (166)
T PF05729_consen  151 SEEDIKQYLRKYF  163 (166)
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998775

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

Probab=98.36  E-value=3.6e-07  Score=100.05  Aligned_cols=185  Identities=24%  Similarity=0.267  Sum_probs=130.1

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCc-cCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALE-KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~-~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++++++ .+..-+..+..+.++..|++.++.++.+|.....+. +|+.|++++| .+..+|.. ++.+++|+.|+++.|.
T Consensus        98 l~~~~~-~~~~~~~~~~~~~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N-~i~~l~~~-~~~l~~L~~L~l~~N~  174 (394)
T COG4886          98 LDLNLN-RLRSNISELLELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDN-KIESLPSP-LRNLPNLKNLDLSFND  174 (394)
T ss_pred             eecccc-ccccCchhhhcccceeEEecCCcccccCccccccchhhccccccccc-chhhhhhh-hhccccccccccCCch
Confidence            556666 554455567777899999999999999999999985 9999999999 78899865 8999999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccC----CCCCcc---------cCcccccccCcceEEe
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKF----FKYPKL---------DLTWLVFVQNLKELEI  662 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~----~~L~~L---------~~~~l~~l~~L~~L~L  662 (779)
                      +..               .+...+.+++|+.|+++.+....++..    .+|+.+         .+..+..+.++..|.+
T Consensus       175 l~~---------------l~~~~~~~~~L~~L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l  239 (394)
T COG4886         175 LSD---------------LPKLLSNLSNLNNLDLSGNKISDLPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLEL  239 (394)
T ss_pred             hhh---------------hhhhhhhhhhhhheeccCCccccCchhhhhhhhhhhhhhcCCcceecchhhhhccccccccc
Confidence            875               333333677888888887766554321    113333         1223344555555554


Q ss_pred             ccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCC
Q 004021          663 IVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPIN  738 (779)
Q Consensus       663 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~  738 (779)
                      .++. +..++                ..++.+++|+.|++++ +.+..++. ++.+.+|+.|++++......+|..
T Consensus       240 ~~n~-~~~~~----------------~~~~~l~~l~~L~~s~-n~i~~i~~-~~~~~~l~~L~~s~n~~~~~~~~~  296 (394)
T COG4886         240 SNNK-LEDLP----------------ESIGNLSNLETLDLSN-NQISSISS-LGSLTNLRELDLSGNSLSNALPLI  296 (394)
T ss_pred             CCce-eeecc----------------chhccccccceecccc-cccccccc-ccccCccCEEeccCccccccchhh
Confidence            4422 22211                3566778889999887 56777776 778888999998887655555543

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

Probab=98.33  E-value=8.5e-08  Score=98.34  Aligned_cols=179  Identities=18%  Similarity=0.109  Sum_probs=109.8

Q ss_pred             ccccCCccEEEccccccccccc-------Ccc--cccccccccccccchh--hcccccCceeeecCCcccc--cchhhcc
Q 004021          491 VKEWEGAKRISLMANEIESLSE-------IPT--LLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIRG--LPQELKA  557 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~-------~~~--lL~L~~~~~l~~lp~~--i~~L~~L~~L~L~~~~i~~--lp~~~~~  557 (779)
                      ...+..+|.|+++.|-+.+...       .+.  -|+|+.| .+...-.+  -..+.+|+.|.|+.|+++.  +-.....
T Consensus       142 ~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~N-rl~~~~~s~~~~~l~~lK~L~l~~CGls~k~V~~~~~~  220 (505)
T KOG3207|consen  142 SKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSN-RLSNFISSNTTLLLSHLKQLVLNSCGLSWKDVQWILLT  220 (505)
T ss_pred             hhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccc-cccCCccccchhhhhhhheEEeccCCCCHHHHHHHHHh
Confidence            4566788889998876654322       122  2888888 55543222  2367888999999998763  3334556


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV  637 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~  637 (779)
                      +++|+.|+|..|..+..-... ..-+..|+.|++++|.+..             .......+.|+.|+.|+++.++..++
T Consensus       221 fPsl~~L~L~~N~~~~~~~~~-~~i~~~L~~LdLs~N~li~-------------~~~~~~~~~l~~L~~Lnls~tgi~si  286 (505)
T KOG3207|consen  221 FPSLEVLYLEANEIILIKATS-TKILQTLQELDLSNNNLID-------------FDQGYKVGTLPGLNQLNLSSTGIASI  286 (505)
T ss_pred             CCcHHHhhhhcccccceecch-hhhhhHHhhccccCCcccc-------------cccccccccccchhhhhccccCcchh
Confidence            788899999888422211111 3456778889998887664             22334566778888888886665543


Q ss_pred             cc--CCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccC
Q 004021          638 QK--FFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILY  704 (779)
Q Consensus       638 ~~--~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~  704 (779)
                      ..  ...+.     -...+++|++|++..|+. .+...         +     ..+..+++|+.|.+..
T Consensus       287 ~~~d~~s~~-----kt~~f~kL~~L~i~~N~I-~~w~s---------l-----~~l~~l~nlk~l~~~~  335 (505)
T KOG3207|consen  287 AEPDVESLD-----KTHTFPKLEYLNISENNI-RDWRS---------L-----NHLRTLENLKHLRITL  335 (505)
T ss_pred             cCCCccchh-----hhcccccceeeecccCcc-ccccc---------c-----chhhccchhhhhhccc
Confidence            21  11111     135678899999988554 22211         0     2445567777777654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.31  E-value=2e-05  Score=78.86  Aligned_cols=154  Identities=17%  Similarity=0.221  Sum_probs=91.5

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHH---HHHHhCCCcchhh
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDD---IGKRIGFSEDKKW  236 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~---i~~~l~~~~~~~~  236 (779)
                      .+..++.+.+++...  ....|.|+|.+|+|||+||+.+++..   .......+++++..+...   +...+        
T Consensus        22 ~~~~~~~l~~~~~~~--~~~~lll~G~~G~GKT~la~~~~~~~---~~~~~~~~~i~~~~~~~~~~~~~~~~--------   88 (226)
T TIGR03420        22 NAELLAALRQLAAGK--GDRFLYLWGESGSGKSHLLQAACAAA---EERGKSAIYLPLAELAQADPEVLEGL--------   88 (226)
T ss_pred             cHHHHHHHHHHHhcC--CCCeEEEECCCCCCHHHHHHHHHHHH---HhcCCcEEEEeHHHHHHhHHHHHhhc--------
Confidence            344666676665443  56789999999999999999999876   223344566666333221   11111        


Q ss_pred             hhcchhhHHHHHHHhhCCCcceeehhhccc-------------cccc-cCCCcEEEEEeCchh---------hhhhcC-C
Q 004021          237 KEKSLQDKAVDISSILSPKKFRIDLTELGV-------------PLQM-LNAGFKIVLKTRSAG---------VCDQMD-S  292 (779)
Q Consensus       237 ~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~-------------~~~~-~~~gs~IivTTR~~~---------va~~~~-~  292 (779)
                                      ++.. .+.+|++..             .+.. ...+.++|+||+...         +...+. .
T Consensus        89 ----------------~~~~-lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~  151 (226)
T TIGR03420        89 ----------------EQAD-LVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWG  151 (226)
T ss_pred             ----------------ccCC-EEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcC
Confidence                            1111 111222110             0000 123457888887532         222232 4


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      ..+.++++++++-..++...+.......+   ++....|++.++|.|..+..+.
T Consensus       152 ~~i~l~~l~~~e~~~~l~~~~~~~~~~~~---~~~l~~L~~~~~gn~r~L~~~l  202 (226)
T TIGR03420       152 LVFQLPPLSDEEKIAALQSRAARRGLQLP---DEVADYLLRHGSRDMGSLMALL  202 (226)
T ss_pred             eeEecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhccCCHHHHHHHH
Confidence            57899999999999999876543332222   4667888888999888776554

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.

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

Probab=98.31  E-value=5.6e-08  Score=105.26  Aligned_cols=150  Identities=21%  Similarity=0.255  Sum_probs=109.0

Q ss_pred             cccccCCccEEEcccccccccccCcc--------------------------------------cccccccccccccchh
Q 004021          490 KVKEWEGAKRISLMANEIESLSEIPT--------------------------------------LLSLRRNDSLTELPSR  531 (779)
Q Consensus       490 ~~~~~~~lr~l~l~~~~~~~l~~~~~--------------------------------------lL~L~~~~~l~~lp~~  531 (779)
                      ++..++.+|+|.+.++++........                                      ..+.+.| .+..+-.+
T Consensus       104 ~ifpF~sLr~LElrg~~L~~~~GL~~lr~qLe~LIC~~Sl~Al~~v~ascggd~~ns~~Wn~L~~a~fsyN-~L~~mD~S  182 (1096)
T KOG1859|consen  104 SIFPFRSLRVLELRGCDLSTAKGLQELRHQLEKLICHNSLDALRHVFASCGGDISNSPVWNKLATASFSYN-RLVLMDES  182 (1096)
T ss_pred             eeccccceeeEEecCcchhhhhhhHHHHHhhhhhhhhccHHHHHHHHHHhccccccchhhhhHhhhhcchh-hHHhHHHH
Confidence            45567899999999887654322111                                      0567777 77777788


Q ss_pred             hcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCc
Q 004021          532 ISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDA  611 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~  611 (779)
                      +.-+++|+.|||++|++...- .+..|++|++|||++| .+..+|.-....+. |+.|.+.+|...              
T Consensus       183 Lqll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN-~L~~vp~l~~~gc~-L~~L~lrnN~l~--------------  245 (1096)
T KOG1859|consen  183 LQLLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYN-CLRHVPQLSMVGCK-LQLLNLRNNALT--------------  245 (1096)
T ss_pred             HHHHHHhhhhccchhhhhhhH-HHHhcccccccccccc-hhccccccchhhhh-heeeeecccHHH--------------
Confidence            888999999999999988875 7888999999999999 78888873223444 999999988655              


Q ss_pred             hhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccc
Q 004021          612 EPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       612 ~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~  667 (779)
                        .+..+.+|++|+.|+++.|-......        +..+..|..|..|.|.+|+.
T Consensus       246 --tL~gie~LksL~~LDlsyNll~~hse--------L~pLwsLs~L~~L~LeGNPl  291 (1096)
T KOG1859|consen  246 --TLRGIENLKSLYGLDLSYNLLSEHSE--------LEPLWSLSSLIVLWLEGNPL  291 (1096)
T ss_pred             --hhhhHHhhhhhhccchhHhhhhcchh--------hhHHHHHHHHHHHhhcCCcc
Confidence              46677788999999999776443221        12344566777777777653

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.30  E-value=7.6e-05  Score=76.81  Aligned_cols=143  Identities=17%  Similarity=0.200  Sum_probs=86.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHH-HhhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDIS-SILSPK  255 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~-~~L~~k  255 (779)
                      .+.-...||++|+||||||+.++...   ...|...-=+..                   ...+..+..+.-+ ....++
T Consensus        47 ~l~SmIl~GPPG~GKTTlA~liA~~~---~~~f~~~sAv~~-------------------gvkdlr~i~e~a~~~~~~gr  104 (436)
T COG2256          47 HLHSMILWGPPGTGKTTLARLIAGTT---NAAFEALSAVTS-------------------GVKDLREIIEEARKNRLLGR  104 (436)
T ss_pred             CCceeEEECCCCCCHHHHHHHHHHhh---CCceEEeccccc-------------------cHHHHHHHHHHHHHHHhcCC
Confidence            67778899999999999999999877   555632211100                   1111222222221 223366


Q ss_pred             cceeehhhcc--------ccccccCCCcEEEE--EeCchhhh---hhcC-CceeEccCCChHHHHHHHHHHhhccCCCC-
Q 004021          256 KFRIDLTELG--------VPLQMLNAGFKIVL--KTRSAGVC---DQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDS-  320 (779)
Q Consensus       256 r~~~~ld~l~--------~~~~~~~~gs~Iiv--TTR~~~va---~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~-  320 (779)
                      +..+-+|+|-        ..+|.-..|.-|+|  ||-+....   .... ..++.+++|+.+|-.+++.+.+......- 
T Consensus       105 ~tiLflDEIHRfnK~QQD~lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~  184 (436)
T COG2256         105 RTILFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLG  184 (436)
T ss_pred             ceEEEEehhhhcChhhhhhhhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCC
Confidence            7666666652        12445567877777  77775432   2223 68999999999999999998543322111 


Q ss_pred             --CCCh-HHHHHHHHHHhCCChhH
Q 004021          321 --HTSI-PELAETLARECGRLPLA  341 (779)
Q Consensus       321 --~~~l-~~~~~~I~~~c~glPLa  341 (779)
                        ...+ ++...-+++.++|=--+
T Consensus       185 ~~~~~i~~~a~~~l~~~s~GD~R~  208 (436)
T COG2256         185 GQIIVLDEEALDYLVRLSNGDARR  208 (436)
T ss_pred             cccccCCHHHHHHHHHhcCchHHH
Confidence              1112 44667788888885443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.28  E-value=7.1e-05  Score=81.84  Aligned_cols=168  Identities=20%  Similarity=0.216  Sum_probs=94.0

Q ss_pred             ccccchhhhHHH---HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLPR---VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      .++||++..+..   +.+++..+  ....+.++|.+|+||||||+.+++..   ...|..   ++....           
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~--~~~~ilL~GppGtGKTtLA~~ia~~~---~~~~~~---l~a~~~-----------   72 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAG--RLSSMILWGPPGTGKTTLARIIAGAT---DAPFEA---LSAVTS-----------   72 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcC--CCceEEEECCCCCCHHHHHHHHHHHh---CCCEEE---Eecccc-----------
Confidence            457898887665   77777655  56678899999999999999999876   333321   111000           


Q ss_pred             cchhhhhcchhhHHHHHHHhh-CCCcceeehhhcccc--------ccccCCCcEEEE--EeCchh--hhhh-cC-CceeE
Q 004021          232 EDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVP--------LQMLNAGFKIVL--KTRSAG--VCDQ-MD-SKNLE  296 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~--------~~~~~~gs~Iiv--TTR~~~--va~~-~~-~~~~~  296 (779)
                           ...+..+......... .+++..+.+|++...        ++.-..|..++|  ||.+..  +... .. ...+.
T Consensus        73 -----~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~iilI~att~n~~~~l~~aL~SR~~~~~  147 (413)
T PRK13342         73 -----GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRAQVFE  147 (413)
T ss_pred             -----cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhcCcEEEEEeCCCChhhhccHHHhccceeeE
Confidence                 0001111111111111 233344444443211        111123555555  344332  2111 12 46789


Q ss_pred             ccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      +.+++.++...++.+.+.........--.+....|++.|+|-|..+..+.
T Consensus       148 ~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        148 LKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             eCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            99999999999999876442111101225677889999999987665443

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.25  E-value=0.00011  Score=83.80  Aligned_cols=187  Identities=16%  Similarity=0.132  Sum_probs=106.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC---CEEEEEEe--ch-------HHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF---DVVIWAAV--QT-------FQD  222 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F---~~~~wv~v--~~-------i~~  222 (779)
                      +.++|++..+..+.+.+...  ....+.|+|.+|+||||||+.+++.. .....+   ...-|+.+  ..       +..
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~--~~~~vlL~Gp~GtGKTTLAr~i~~~~-~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~  230 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASP--FPQHIILYGPPGVGKTTAARLALEEA-KKLKHTPFAEDAPFVEVDGTTLRWDPREVTN  230 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcC--CCCeEEEECCCCCCHHHHHHHHHHhh-hhccCCcccCCCCeEEEechhccCCHHHHhH
Confidence            45899999999988887644  45679999999999999999998765 322322   12345555  11       111


Q ss_pred             HHH---------------HHhCCCcc---------------hhhhhcchhhHHHHHHHhhCCCccee-----------eh
Q 004021          223 DIG---------------KRIGFSED---------------KKWKEKSLQDKAVDISSILSPKKFRI-----------DL  261 (779)
Q Consensus       223 ~i~---------------~~l~~~~~---------------~~~~~~~~~~~~~~l~~~L~~kr~~~-----------~l  261 (779)
                      .++               ...+....               ...... ....+..+...++++++..           +|
T Consensus       231 ~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~L-d~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~  309 (615)
T TIGR02903       231 PLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGEL-DPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVP  309 (615)
T ss_pred             HhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccC-CHHHHHHHHHHHhhCeEEeecceeccCCcccc
Confidence            111               11110000               000000 1234667888888877633           23


Q ss_pred             hhccccccccCCCcEEEE--EeCchhh-hhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhC
Q 004021          262 TELGVPLQMLNAGFKIVL--KTRSAGV-CDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECG  336 (779)
Q Consensus       262 d~l~~~~~~~~~gs~Iiv--TTR~~~v-a~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~  336 (779)
                      +.+...+....+...|++  ||++... ...+.  ...+.+.+++.+|.+.++.+.+.......+   +++...|.+.+.
T Consensus       310 ~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~ls---~eal~~L~~ys~  386 (615)
T TIGR02903       310 KYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHLA---AGVEELIARYTI  386 (615)
T ss_pred             hhhhhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHCCC
Confidence            344444444444445555  6665432 22221  356789999999999999998764331111   345555666555


Q ss_pred             CChhHHHHHHHH
Q 004021          337 RLPLALKTVGRA  348 (779)
Q Consensus       337 glPLai~~~g~~  348 (779)
                      .-+-|+..++..
T Consensus       387 ~gRraln~L~~~  398 (615)
T TIGR02903       387 EGRKAVNILADV  398 (615)
T ss_pred             cHHHHHHHHHHH
Confidence            455666555443

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.

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.24  E-value=2.8e-06  Score=87.67  Aligned_cols=275  Identities=16%  Similarity=0.142  Sum_probs=171.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCC-CEEEEEEe------chHHHHHHHHhCCCcchhhhhcchhhHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF-DVVIWAAV------QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDIS  249 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F-~~~~wv~v------~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~  249 (779)
                      ..+.+.++|.|||||||++-++.+ .   ...| +.+.++..      ..+.-.....++.+.      .+-+.....+.
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~---~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~------~~g~~~~~~~~   82 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-A---ASEYADGVAFVDLAPITDPALVFPTLAGALGLHV------QPGDSAVDTLV   82 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-H---hhhcccceeeeeccccCchhHhHHHHHhhccccc------ccchHHHHHHH
Confidence            458999999999999999999988 4   3445 56666666      223333344455441      12223344555


Q ss_pred             HhhCCCcceeehhhcc----------ccccccCCCcEEEEEeCchhhhhhcCCceeEccCCChH-HHHHHHHHHhhccCC
Q 004021          250 SILSPKKFRIDLTELG----------VPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHD-EAWKLFQEMIERSTL  318 (779)
Q Consensus       250 ~~L~~kr~~~~ld~l~----------~~~~~~~~gs~IivTTR~~~va~~~~~~~~~l~~L~~~-~a~~Lf~~~a~~~~~  318 (779)
                      ....++|.+.++|+-.          ..+..+...-.|+.|+|......  +...+.+++|+.. ++.++|...+.....
T Consensus        83 ~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~--ge~~~~~~~L~~~d~a~~lf~~ra~~~~~  160 (414)
T COG3903          83 RRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVA--GEVHRRVPSLSLFDEAIELFVCRAVLVAL  160 (414)
T ss_pred             HHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhccc--ccccccCCccccCCchhHHHHHHHHHhcc
Confidence            6666667666665531          11223445557888888643321  2556778888765 799999887754321


Q ss_pred             --CCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHH----HHHHHhcccCcCCCchHHHHHHHHHHHhcCCc
Q 004021          319 --DSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRER----AIEKMRTSASTFSGMEENVFLRLKFSYDSLSM  392 (779)
Q Consensus       319 --~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~----~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~  392 (779)
                        .-...-.....+|.++..|.|++|..+++..+.- ...+-..    -...+........--+......+..||.-|..
T Consensus       161 ~f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl-~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtg  239 (414)
T COG3903         161 SFWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSL-SPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTG  239 (414)
T ss_pred             ceeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhc-CHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhh
Confidence              1122335778999999999999999998877652 2222222    12222222111111134677899999999998


Q ss_pred             cchhhhhhhccccCCCcccChHHHHHHHHHcCCCc--chhhHHHHHHHHHHccccccc---CCCcEEechHHHHHHHHHH
Q 004021          393 DKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMA--DFDRGCEFINDLLHACLLEEE---GDDHVKMHDMIREMSLWIA  467 (779)
Q Consensus       393 ~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~--~~~~~~~~l~~L~~~sll~~~---~~~~~~mHdlv~~~a~~~~  467 (779)
                       ..+..|..++.|...+...    ...|.+-|-..  +.......+..+++.++....   ....|+.-+-++.|+..+.
T Consensus       240 -we~~~~~rLa~~~g~f~~~----l~~~~a~g~~~~~~~y~~~~a~~ll~~kslv~a~~~~~~a~~Rl~eT~r~YalaeL  314 (414)
T COG3903         240 -WERALFGRLAVFVGGFDLG----LALAVAAGADVDVPRYLVLLALTLLVDKSLVVALDLLGRARYRLLETGRRYALAEL  314 (414)
T ss_pred             -HHHHHhcchhhhhhhhccc----HHHHHhcCCccccchHHHHHHHHHHhhccchhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence             8899999999998776554    23455555332  224455556778888886553   3445666667777777666


Q ss_pred             hh
Q 004021          468 WT  469 (779)
Q Consensus       468 ~~  469 (779)
                      .+
T Consensus       315 ~r  316 (414)
T COG3903         315 HR  316 (414)
T ss_pred             Hh
Confidence            55

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.23  E-value=0.00022  Score=80.86  Aligned_cols=194  Identities=17%  Similarity=0.136  Sum_probs=109.2

Q ss_pred             cccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccc--cCCCC--EEEEEEe------chH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ--QHNFD--VVIWAAV------QTF  220 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~--~~~F~--~~~wv~v------~~i  220 (779)
                      +..+.|||+++++|...|...   .+...++-|+|.+|.|||+.++.|.+.....  +....  .+++|..      ..+
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            456889999999999998752   3334678899999999999999998776211  12222  2344443      456


Q ss_pred             HHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCC-C-cc-eeehhhccccc-----------c-ccCCCcEEEE--EeCc
Q 004021          221 QDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSP-K-KF-RIDLTELGVPL-----------Q-MLNAGFKIVL--KTRS  283 (779)
Q Consensus       221 ~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~-k-r~-~~~ld~l~~~~-----------~-~~~~gs~Iiv--TTR~  283 (779)
                      ...|..++... . ........+....+...+.. . .. .+++|++-...           . ....+++|+|  +|..
T Consensus       834 YqvI~qqL~g~-~-P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNd  911 (1164)
T PTZ00112        834 YQVLYKQLFNK-K-PPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNT  911 (1164)
T ss_pred             HHHHHHHHcCC-C-CCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCc
Confidence            77777777432 1 11222233444555555422 2 22 55666652111           1 1224566655  3433


Q ss_pred             hh--------hhhhcCCceeEccCCChHHHHHHHHHHhhccC-CCCCCChHHHHHHHHHHhCCChhHHHHHHHHh
Q 004021          284 AG--------VCDQMDSKNLEVYSLAHDEAWKLFQEMIERST-LDSHTSIPELAETLARECGRLPLALKTVGRAM  349 (779)
Q Consensus       284 ~~--------va~~~~~~~~~l~~L~~~~a~~Lf~~~a~~~~-~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l  349 (779)
                      .+        +...++...+..+|.+.++-.+++..++.... .-.+..++-+|+.++..-|-.-.||.++-.+.
T Consensus       912 lDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAg  986 (1164)
T PTZ00112        912 MDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAF  986 (1164)
T ss_pred             hhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHH
Confidence            22        22222333467799999999999999886432 11112223334444444455666766654433

>PLN03150 hypothetical protein; Provisional

Probab=98.22  E-value=1.8e-06  Score=99.13  Aligned_cols=80  Identities=30%  Similarity=0.500  Sum_probs=63.9

Q ss_pred             cccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |+|++| .+. .+|..|++|++|++|+|++|.+. .+|..++++++|+.|+|++|.....+|.. +++|++|++|++++|
T Consensus       423 L~L~~n-~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~-l~~L~~L~~L~Ls~N  500 (623)
T PLN03150        423 LGLDNQ-GLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPES-LGQLTSLRILNLNGN  500 (623)
T ss_pred             EECCCC-CccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchH-HhcCCCCCEEECcCC
Confidence            677777 554 57888888888888888888886 57888888888888888888554577776 888888888888888


Q ss_pred             cCCC
Q 004021          595 GSEG  598 (779)
Q Consensus       595 ~~~~  598 (779)
                      .+.+
T Consensus       501 ~l~g  504 (623)
T PLN03150        501 SLSG  504 (623)
T ss_pred             cccc
Confidence            7764

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

Probab=98.14  E-value=2.1e-07  Score=90.72  Aligned_cols=180  Identities=21%  Similarity=0.179  Sum_probs=115.4

Q ss_pred             cccccccccccc--cchhhcccccCceeeecCCcccc-cchhhccCccCcEeeccCCcCCCCCchh-hhcCCccCcEeee
Q 004021          516 LLSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRYLNLEYTHYLSIIPHQ-LISGFLKLEVLRL  591 (779)
Q Consensus       516 lL~L~~~~~l~~--lp~~i~~L~~L~~L~L~~~~i~~-lp~~~~~L~~L~~L~l~~~~~l~~lp~~-~i~~L~~L~~L~l  591 (779)
                      +||||+. .|+.  +-.-+..+.+|+.|.|.++++.. +-..|.+=.+|+.|+|+.|..++...-. ++.+++.|..|++
T Consensus       189 ~lDLS~s-~it~stl~~iLs~C~kLk~lSlEg~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~ll~~scs~L~~LNl  267 (419)
T KOG2120|consen  189 HLDLSNS-VITVSTLHGILSQCSKLKNLSLEGLRLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQLLLSSCSRLDELNL  267 (419)
T ss_pred             Hhhcchh-heeHHHHHHHHHHHHhhhhccccccccCcHHHHHHhccccceeeccccccccchhHHHHHHHhhhhHhhcCc
Confidence            4788877 6652  33345667788888888887654 5556777788888888888665543322 3577888888888


Q ss_pred             ccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcc-cccccCcceEEeccccccce
Q 004021          592 LECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTW-LVFVQNLKELEIIVCTEMEE  670 (779)
Q Consensus       592 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~-l~~l~~L~~L~L~~~~~~~~  670 (779)
                      +.|....          +........+  -++|..|+++++.       .||..=.+.. ...+|+|.+|+|++|..++.
T Consensus       268 sWc~l~~----------~~Vtv~V~hi--se~l~~LNlsG~r-------rnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~  328 (419)
T KOG2120|consen  268 SWCFLFT----------EKVTVAVAHI--SETLTQLNLSGYR-------RNLQKSHLSTLVRRCPNLVHLDLSDSVMLKN  328 (419)
T ss_pred             hHhhccc----------hhhhHHHhhh--chhhhhhhhhhhH-------hhhhhhHHHHHHHhCCceeeeccccccccCc
Confidence            8886553          1001111111  2456666666432       1111111111 24679999999999887765


Q ss_pred             ecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEeeeCCC
Q 004021          671 IICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       671 ~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c~  730 (779)
                      -..               ..+..|+.|++|.++.|..+--- ......+|+|.+|++.+|-
T Consensus       329 ~~~---------------~~~~kf~~L~~lSlsRCY~i~p~~~~~l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  329 DCF---------------QEFFKFNYLQHLSLSRCYDIIPETLLELNSKPSLVYLDVFGCV  374 (419)
T ss_pred             hHH---------------HHHHhcchheeeehhhhcCCChHHeeeeccCcceEEEEecccc
Confidence            211               35668999999999998764211 1256689999999999873

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.12  E-value=6.8e-05  Score=88.62  Aligned_cols=159  Identities=12%  Similarity=0.112  Sum_probs=102.8

Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCC------CChhHHHHHHHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQ------KKVGDRERAIEKM  365 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~------~~~~~w~~~~~~l  365 (779)
                      ...+.|.||+..+...+.....+...    ....+..+.|+++..|+|+-+..+-..+...      .+...|..-...+
T Consensus       211 i~~I~L~PL~~~d~~~lV~~~l~~~~----~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i  286 (849)
T COG3899         211 ITTITLAPLSRADTNQLVAATLGCTK----LLPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASL  286 (849)
T ss_pred             eeEEecCcCchhhHHHHHHHHhCCcc----cccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhc
Confidence            46889999999999999988876533    2235778999999999999999888877663      3344454322111


Q ss_pred             hcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHHHHHHcccc
Q 004021          366 RTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLL  445 (779)
Q Consensus       366 ~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~~L~~~sll  445 (779)
                          ......+ .+...+..-.+.||. ..+..+...|++...  |+...|...+-...    ...+....+.|....++
T Consensus       287 ----~~~~~~~-~vv~~l~~rl~kL~~-~t~~Vl~~AA~iG~~--F~l~~La~l~~~~~----~~~a~~l~~al~e~lI~  354 (849)
T COG3899         287 ----GILATTD-AVVEFLAARLQKLPG-TTREVLKAAACIGNR--FDLDTLAALAEDSP----ALEAAALLDALQEGLIL  354 (849)
T ss_pred             ----CCchhhH-HHHHHHHHHHhcCCH-HHHHHHHHHHHhCcc--CCHHHHHHHHhhch----HHHHHHHHHHhHhhcee
Confidence                1112222 356668888999998 899999999998644  45555555443211    14555555555555544


Q ss_pred             ccc-------CCCc---EEechHHHHHHHHH
Q 004021          446 EEE-------GDDH---VKMHDMIREMSLWI  466 (779)
Q Consensus       446 ~~~-------~~~~---~~mHdlv~~~a~~~  466 (779)
                      ...       ....   --.||.|++.|-..
T Consensus       355 ~~~~~yr~~~~~~~~~Y~F~H~~vqqaaY~~  385 (849)
T COG3899         355 PLSETYRFGSNVDIATYKFLHDRVQQAAYNL  385 (849)
T ss_pred             ccccccccccccchhhHHhhHHHHHHHHhcc
Confidence            321       1111   25688888777543

>PRK08727 hypothetical protein; Validated

Probab=98.12  E-value=0.00013  Score=72.99  Aligned_cols=135  Identities=15%  Similarity=0.099  Sum_probs=81.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH---HHHhCCCcchhhhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI---GKRIGFSEDKKWKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i---~~~l~~~~~~~~~~~~~~~~~~~l~~~L~  253 (779)
                      ....+.|+|..|+|||.|++++++...   .....+.|+++.+....+   ++.+...                      
T Consensus        40 ~~~~l~l~G~~G~GKThL~~a~~~~~~---~~~~~~~y~~~~~~~~~~~~~~~~l~~~----------------------   94 (233)
T PRK08727         40 SSDWLYLSGPAGTGKTHLALALCAAAE---QAGRSSAYLPLQAAAGRLRDALEALEGR----------------------   94 (233)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEeHHHhhhhHHHHHHHHhcC----------------------
Confidence            345699999999999999999998872   223355677763322221   1111110                      


Q ss_pred             CCcceeehhhcccc-------------cc-ccCCCcEEEEEeCch---------hhhhhcC-CceeEccCCChHHHHHHH
Q 004021          254 PKKFRIDLTELGVP-------------LQ-MLNAGFKIVLKTRSA---------GVCDQMD-SKNLEVYSLAHDEAWKLF  309 (779)
Q Consensus       254 ~kr~~~~ld~l~~~-------------~~-~~~~gs~IivTTR~~---------~va~~~~-~~~~~l~~L~~~~a~~Lf  309 (779)
                         -.+.+|++...             +. ....|..||+||+..         .+.+.+. ...+++++++.++-..++
T Consensus        95 ---dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL  171 (233)
T PRK08727         95 ---SLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVL  171 (233)
T ss_pred             ---CEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHH
Confidence               02223332110             00 012466799999852         2233333 458899999999999999


Q ss_pred             HHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          310 QEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       310 ~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      .+++.......+   ++...-|++.++|-.-.+
T Consensus       172 ~~~a~~~~l~l~---~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        172 RERAQRRGLALD---EAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHHHHHcCCCCC---HHHHHHHHHhCCCCHHHH
Confidence            987765433222   567788888887655444

>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=98.10  E-value=4.7e-05  Score=73.05  Aligned_cols=180  Identities=18%  Similarity=0.167  Sum_probs=96.0

Q ss_pred             ccccchhhhHHHHHHHHhc---cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD---QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~  226 (779)
                      .+|||.++-++.+.-++..   ......-+-+||++|+||||||.-+++..   ...|.   +++.     ..-+..++.
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~---~~~~~---~~sg~~i~k~~dl~~il~   97 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL---GVNFK---ITSGPAIEKAGDLAAILT   97 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC---T--EE---EEECCC--SCHHHHHHHH
T ss_pred             HHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc---CCCeE---eccchhhhhHHHHHHHHH
Confidence            5689999888886655542   23467789999999999999999999987   44552   2332     122333444


Q ss_pred             HhCCCcchhhhhcch----hhHHHHHHHhhCCCcceeehhh------ccccccccCCCcEEEEEeCchhhhhhcC---Cc
Q 004021          227 RIGFSEDKKWKEKSL----QDKAVDISSILSPKKFRIDLTE------LGVPLQMLNAGFKIVLKTRSAGVCDQMD---SK  293 (779)
Q Consensus       227 ~l~~~~~~~~~~~~~----~~~~~~l~~~L~~kr~~~~ld~------l~~~~~~~~~gs~IivTTR~~~va~~~~---~~  293 (779)
                      .+... + ..-.+..    ...++.+...+++.+..+....      +...++   +=+-|=.|||...+...+.   ..
T Consensus        98 ~l~~~-~-ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~---~FTligATTr~g~ls~pLrdRFgi  172 (233)
T PF05496_consen   98 NLKEG-D-ILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLP---PFTLIGATTRAGLLSSPLRDRFGI  172 (233)
T ss_dssp             T--TT---EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE-------EEEEEESSGCCTSHCCCTTSSE
T ss_pred             hcCCC-c-EEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCC---CceEeeeeccccccchhHHhhcce
Confidence            44321 0 0000111    1223344555555443222211      001111   2234556898866654444   23


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRA  348 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~  348 (779)
                      ..+++..+.+|-.++..+.+..-...-   -++.+.+|+++|.|-|--+.-+-+.
T Consensus       173 ~~~l~~Y~~~el~~Iv~r~a~~l~i~i---~~~~~~~Ia~rsrGtPRiAnrll~r  224 (233)
T PF05496_consen  173 VLRLEFYSEEELAKIVKRSARILNIEI---DEDAAEEIARRSRGTPRIANRLLRR  224 (233)
T ss_dssp             EEE----THHHHHHHHHHCCHCTT-EE----HHHHHHHHHCTTTSHHHHHHHHHH
T ss_pred             ecchhcCCHHHHHHHHHHHHHHhCCCc---CHHHHHHHHHhcCCChHHHHHHHHH
Confidence            458999999999999988776544222   2678999999999999755544333

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.

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=98.10  E-value=3.8e-06  Score=58.87  Aligned_cols=41  Identities=41%  Similarity=0.485  Sum_probs=33.1

Q ss_pred             ccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCch
Q 004021          536 VSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPH  577 (779)
Q Consensus       536 ~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~  577 (779)
                      ++|++|++++|+|+.+|..+++|++|++|++++| .++.+|.
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N-~i~~i~~   41 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNN-PISDISP   41 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSS-CCSBEGG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCC-CCCCCcC
Confidence            4789999999999999888999999999999999 5676665

...

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.07  E-value=0.00017  Score=81.26  Aligned_cols=185  Identities=14%  Similarity=0.133  Sum_probs=99.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEE-echHHHHHHHHh-----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA-VQTFQDDIGKRI-----  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~-v~~i~~~i~~~l-----  228 (779)
                      .++||.+..++.|.+++..+. -...+.++|..|+||||+|+.+.+.. .-...++..  -| .-..+..|...-     
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaL-nCe~~~~~~--PCG~C~sCr~I~~G~h~Dvi   91 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKAL-NCETGVTSQ--PCGVCRACREIDEGRFVDYV   91 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHh-cCccCCCCC--CCcccHHHHHHhcCCCceEE
Confidence            568999999999999988762 23466799999999999999988876 211111100  00 001111221100     


Q ss_pred             CCCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhcc-----------ccccccCCCcEEEEEeCc-hhhhhhcC--Cc
Q 004021          229 GFSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELG-----------VPLQMLNAGFKIVLKTRS-AGVCDQMD--SK  293 (779)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~-----------~~~~~~~~gs~IivTTR~-~~va~~~~--~~  293 (779)
                      ..+........+..++...+...-.+.+| .+.+|++.           ..+.......++|+||++ ..+...+-  ..
T Consensus        92 EIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TIrSRCq  171 (830)
T PRK07003         92 EMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCL  171 (830)
T ss_pred             EecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchhhhheE
Confidence            00000000001111111111111112233 33334331           111122346677777766 44433322  57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LALKTVG  346 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai~~~g  346 (779)
                      .|.++.++.++..+.+.+.+.......+   .+..+.|++.++|.. -|+..+-
T Consensus       172 ~f~Fk~Ls~eeIv~~L~~Il~~EgI~id---~eAL~lIA~~A~GsmRdALsLLd  222 (830)
T PRK07003        172 QFNLKQMPAGHIVSHLERILGEERIAFE---PQALRLLARAAQGSMRDALSLTD  222 (830)
T ss_pred             EEecCCcCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHH
Confidence            8899999999999999988766543222   567889999998855 4555533

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

Probab=98.01  E-value=1.2e-06  Score=96.14  Aligned_cols=122  Identities=30%  Similarity=0.332  Sum_probs=87.9

Q ss_pred             CCccEEEcccccccc----cccCcc--cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccC
Q 004021          495 EGAKRISLMANEIES----LSEIPT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEY  568 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~----l~~~~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~  568 (779)
                      ..+..+++..|.+..    +.....  .|++.+| .|..+...+..+.+|++|++++|.|+.+. .+..++.|+.|++++
T Consensus        72 ~~l~~l~l~~n~i~~~~~~l~~~~~l~~l~l~~n-~i~~i~~~l~~~~~L~~L~ls~N~I~~i~-~l~~l~~L~~L~l~~  149 (414)
T KOG0531|consen   72 TSLKELNLRQNLIAKILNHLSKLKSLEALDLYDN-KIEKIENLLSSLVNLQVLDLSFNKITKLE-GLSTLTLLKELNLSG  149 (414)
T ss_pred             HhHHhhccchhhhhhhhcccccccceeeeecccc-chhhcccchhhhhcchheecccccccccc-chhhccchhhheecc
Confidence            345555566666655    222222  3888888 88887766888899999999999888885 477788899999999


Q ss_pred             CcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHh--hcCCCCCCceeEEeeccccc
Q 004021          569 THYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRE--LLGLKRLNVLSWSFRSSLAV  637 (779)
Q Consensus       569 ~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~--l~~L~~L~~L~l~~~~~~~~  637 (779)
                      | .+..++.  +..+++|+.+++.+|.+..                ++.  +..+.+|+.+.+..+....+
T Consensus       150 N-~i~~~~~--~~~l~~L~~l~l~~n~i~~----------------ie~~~~~~~~~l~~l~l~~n~i~~i  201 (414)
T KOG0531|consen  150 N-LISDISG--LESLKSLKLLDLSYNRIVD----------------IENDELSELISLEELDLGGNSIREI  201 (414)
T ss_pred             C-cchhccC--CccchhhhcccCCcchhhh----------------hhhhhhhhccchHHHhccCCchhcc
Confidence            8 6777776  6778889999988887764                122  46677777777776665443

>PTZ00202 tuzin; Provisional

Probab=98.01  E-value=6.4e-05  Score=78.75  Aligned_cols=152  Identities=13%  Similarity=0.079  Sum_probs=91.2

Q ss_pred             cccccchhhhHHHHHHHHhccC-CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---chHHHHHHHHhC
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQ-KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---QTFQDDIGKRIG  229 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~-~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~~i~~~i~~~l~  229 (779)
                      .+.|+||+.+...+...|.+.+ ...+++.|.|++|+|||||++.+.... .     ....+++.   .+++..|+.+|+
T Consensus       261 ~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l-~-----~~qL~vNprg~eElLr~LL~ALG  334 (550)
T PTZ00202        261 IRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE-G-----MPAVFVDVRGTEDTLRSVVKALG  334 (550)
T ss_pred             ccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC-C-----ceEEEECCCCHHHHHHHHHHHcC
Confidence            4789999999999999997532 245699999999999999999998766 2     12344444   789999999999


Q ss_pred             CCcchhhhhcchhhHHHHHHHhhC--CCcceeeh--------hhc---cccccccCCCcEEEEEeCchhhhhhc---C-C
Q 004021          230 FSEDKKWKEKSLQDKAVDISSILS--PKKFRIDL--------TEL---GVPLQMLNAGFKIVLKTRSAGVCDQM---D-S  292 (779)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~l~~~L~--~kr~~~~l--------d~l---~~~~~~~~~gs~IivTTR~~~va~~~---~-~  292 (779)
                      .+... ....-.....+.+.+.-.  +++..+++        ..+   ...+.....-|.|++---.+.+.-..   . -
T Consensus       335 V~p~~-~k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~v~la~drr~ch~v~evpleslt~~~~~lprl  413 (550)
T PTZ00202        335 VPNVE-ACGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEVVALACDRRLCHVVIEVPLESLTIANTLLPRL  413 (550)
T ss_pred             CCCcc-cHHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHHHHHHccchhheeeeeehHhhcchhcccCccc
Confidence            75221 111112233333333222  33332221        111   01122334556666644433332111   1 3


Q ss_pred             ceeEccCCChHHHHHHHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEM  312 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~  312 (779)
                      ..|.+++++.++|...-.+.
T Consensus       414 df~~vp~fsr~qaf~y~~h~  433 (550)
T PTZ00202        414 DFYLVPNFSRSQAFAYTQHA  433 (550)
T ss_pred             eeEecCCCCHHHHHHHHhhc
Confidence            56788999999988776554

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.99  E-value=0.00031  Score=69.34  Aligned_cols=173  Identities=17%  Similarity=0.308  Sum_probs=97.0

Q ss_pred             ccccch-hhhHHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCc
Q 004021          155 QTIVGQ-EKLLPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr-~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~  232 (779)
                      ..++|- .+..-...+.+.+. ......+-|+|..|+|||.|.+++++.. .....=..+++++..++...+...+... 
T Consensus         9 nfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~-~~~~~~~~v~y~~~~~f~~~~~~~~~~~-   86 (219)
T PF00308_consen    9 NFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEA-QKQHPGKRVVYLSAEEFIREFADALRDG-   86 (219)
T ss_dssp             CS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHH-HHHCTTS-EEEEEHHHHHHHHHHHHHTT-
T ss_pred             cCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHH-HhccccccceeecHHHHHHHHHHHHHcc-
Confidence            444674 33334444555443 3234568899999999999999999987 2222223577888777766666554321 


Q ss_pred             chhhhhcchhhHHHHHHHhhCCCcceeehhhcccc-------------cc-ccCCCcEEEEEeCch---------hhhhh
Q 004021          233 DKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP-------------LQ-MLNAGFKIVLKTRSA---------GVCDQ  289 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~-------------~~-~~~~gs~IivTTR~~---------~va~~  289 (779)
                                 ....+.+.+++-. .+.+|++...             +. ....|.+||+|++..         .+.+.
T Consensus        87 -----------~~~~~~~~~~~~D-lL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SR  154 (219)
T PF00308_consen   87 -----------EIEEFKDRLRSAD-LLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSR  154 (219)
T ss_dssp             -----------SHHHHHHHHCTSS-EEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHH
T ss_pred             -----------cchhhhhhhhcCC-EEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhh
Confidence                       1123344444333 2333333111             00 113577899999652         22333


Q ss_pred             cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          290 MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       290 ~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      +. .-.+++++++.++-..++.+.+......-+   +++..-|++.+.+..-.+..
T Consensus       155 l~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~---~~v~~~l~~~~~~~~r~L~~  207 (219)
T PF00308_consen  155 LSWGLVVELQPPDDEDRRRILQKKAKERGIELP---EEVIEYLARRFRRDVRELEG  207 (219)
T ss_dssp             HHCSEEEEE----HHHHHHHHHHHHHHTT--S----HHHHHHHHHHTTSSHHHHHH
T ss_pred             HhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCc---HHHHHHHHHhhcCCHHHHHH
Confidence            33 568899999999999999999877653322   56667777776665544443

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

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

Probab=97.98  E-value=0.00071  Score=68.42  Aligned_cols=114  Identities=16%  Similarity=0.186  Sum_probs=69.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHHHHhCCCcchhhhhcchhhHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISS  250 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~  250 (779)
                      .++-+.+||.+|+||||||+.+....   +.+-  ..||..      ..-.++|.++-                 +.. .
T Consensus       161 ~ipSmIlWGppG~GKTtlArlia~ts---k~~S--yrfvelSAt~a~t~dvR~ife~a-----------------q~~-~  217 (554)
T KOG2028|consen  161 RIPSMILWGPPGTGKTTLARLIASTS---KKHS--YRFVELSATNAKTNDVRDIFEQA-----------------QNE-K  217 (554)
T ss_pred             CCCceEEecCCCCchHHHHHHHHhhc---CCCc--eEEEEEeccccchHHHHHHHHHH-----------------HHH-H
Confidence            78889999999999999999999876   2221  344554      11122222211                 111 1


Q ss_pred             hhCCCcceeehhhc--------cccccccCCCcEEEE--EeCchhh---hhhcC-CceeEccCCChHHHHHHHHHHh
Q 004021          251 ILSPKKFRIDLTEL--------GVPLQMLNAGFKIVL--KTRSAGV---CDQMD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       251 ~L~~kr~~~~ld~l--------~~~~~~~~~gs~Iiv--TTR~~~v---a~~~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      .+..+|..+-+|+|        ...+|.-.+|.-++|  ||.+...   +..+. ..++-|++|+.++-..++.+..
T Consensus       218 ~l~krkTilFiDEiHRFNksQQD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~rai  294 (554)
T KOG2028|consen  218 SLTKRKTILFIDEIHRFNKSQQDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAI  294 (554)
T ss_pred             hhhcceeEEEeHHhhhhhhhhhhcccceeccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHH
Confidence            12233333334443        123455567776666  7777554   23333 6889999999999999988743

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.96  E-value=0.00024  Score=75.98  Aligned_cols=183  Identities=16%  Similarity=0.140  Sum_probs=101.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|++..++.+.+++..+  ..+.+.++|.+|+||||+|+.+++.. . ...++ ..+.+++.++.......+.....
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~GtGKT~la~~~~~~l-~-~~~~~~~~~~i~~~~~~~~~~~~~~~~~~   90 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP--NLPHLLVQGPPGSGKTAAVRALAREL-Y-GDPWENNFTEFNVADFFDQGKKYLVEDPR   90 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHHh-c-CcccccceEEechhhhhhcchhhhhcCcc
Confidence            56899999999999988766  45568899999999999999999876 2 12222 23344443332211111110000


Q ss_pred             -h-hh-----hhcchhhHHHHHHHhh------CCCcceeehhhccc-----------cccccCCCcEEEEEeCc-hhhhh
Q 004021          234 -K-KW-----KEKSLQDKAVDISSIL------SPKKFRIDLTELGV-----------PLQMLNAGFKIVLKTRS-AGVCD  288 (779)
Q Consensus       234 -~-~~-----~~~~~~~~~~~l~~~L------~~kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~-~~va~  288 (779)
                       . ..     ...........+.+..      .+.+-.+.+|++..           .+......+++|+||.. ..+..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~~~  170 (337)
T PRK12402         91 FAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIP  170 (337)
T ss_pred             hhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhCch
Confidence             0 00     0000111111111111      11122344444311           11122345678877754 33323


Q ss_pred             hcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          289 QMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       289 ~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ...  ...+.+.+++.++....+.+.+...+...+   .+....+++.++|.+-.+..
T Consensus       171 ~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~---~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        171 PIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYD---DDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             hhcCCceEEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence            222  457788999999999999887765442222   56788999999887655443

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.92  E-value=3.5e-05  Score=81.24  Aligned_cols=54  Identities=24%  Similarity=0.307  Sum_probs=28.6

Q ss_pred             cccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          535 LVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       535 L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      +.++++|++++|.++.+|.   --.+|++|.+++|..+..+|.. +  ..+|++|.+.+|
T Consensus        51 ~~~l~~L~Is~c~L~sLP~---LP~sLtsL~Lsnc~nLtsLP~~-L--P~nLe~L~Ls~C  104 (426)
T PRK15386         51 ARASGRLYIKDCDIESLPV---LPNELTEITIENCNNLTTLPGS-I--PEGLEKLTVCHC  104 (426)
T ss_pred             hcCCCEEEeCCCCCcccCC---CCCCCcEEEccCCCCcccCCch-h--hhhhhheEccCc
Confidence            4555566666665555551   1224566666655555555543 3  235556666555

>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=97.90  E-value=8.2e-06  Score=62.45  Aligned_cols=53  Identities=40%  Similarity=0.659  Sum_probs=45.8

Q ss_pred             ccccccccccccc-hhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCc
Q 004021          517 LSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTH  570 (779)
Q Consensus       517 L~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~  570 (779)
                      |++++| .+..+| ..|.++++|++|++++|.++.+|+ .|.++++|++|++++|.
T Consensus         6 L~l~~n-~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    6 LDLSNN-KLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             EEETSS-TESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSS
T ss_pred             EECCCC-CCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCc
Confidence            566677 777776 478899999999999999999875 68999999999999983

...

>PLN03150 hypothetical protein; Provisional

Probab=97.89  E-value=2.5e-05  Score=89.89  Aligned_cols=107  Identities=21%  Similarity=0.171  Sum_probs=80.9

Q ss_pred             cCceeeecCCccc-ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhH
Q 004021          537 SLHHLDLSLTHIR-GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLM  615 (779)
Q Consensus       537 ~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~  615 (779)
                      .++.|+|++|.+. .+|..+++|++|+.|+|++|.....+|.. ++.+++|+.|++++|.+.+              ..+
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  483 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPS-LGSITSLEVLDLSYNSFNG--------------SIP  483 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChH-HhCCCCCCEEECCCCCCCC--------------CCc
Confidence            3778899999887 48889999999999999999655588887 8999999999999998874              467


Q ss_pred             HhhcCCCCCCceeEEeecccccccCCCCCcccCccccc-ccCcceEEeccccc
Q 004021          616 RELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVF-VQNLKELEIIVCTE  667 (779)
Q Consensus       616 ~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~-l~~L~~L~L~~~~~  667 (779)
                      ..+++|++|+.|+++.|...         .-.|..++. +.++..+++.+|..
T Consensus       484 ~~l~~L~~L~~L~Ls~N~l~---------g~iP~~l~~~~~~~~~l~~~~N~~  527 (623)
T PLN03150        484 ESLGQLTSLRILNLNGNSLS---------GRVPAALGGRLLHRASFNFTDNAG  527 (623)
T ss_pred             hHHhcCCCCCEEECcCCccc---------ccCChHHhhccccCceEEecCCcc
Confidence            77888999999999865432         112333332 23566777777644

>PRK09087 hypothetical protein; Validated

Probab=97.89  E-value=0.00039  Score=68.95  Aligned_cols=137  Identities=15%  Similarity=0.123  Sum_probs=80.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC----cchhhhhcchhhHHHHHHHhhC
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS----EDKKWKEKSLQDKAVDISSILS  253 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~----~~~~~~~~~~~~~~~~l~~~L~  253 (779)
                      .+.+.|+|..|+|||+|++.++... ..       .+++...+..++...+...    ++-.....+.+++...+.    
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~-~~-------~~i~~~~~~~~~~~~~~~~~l~iDDi~~~~~~~~~lf~l~n----  111 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKS-DA-------LLIHPNEIGSDAANAAAEGPVLIEDIDAGGFDETGLFHLIN----  111 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhc-CC-------EEecHHHcchHHHHhhhcCeEEEECCCCCCCCHHHHHHHHH----
Confidence            4678999999999999999988765 21       1444322222222211100    000000001111111000    


Q ss_pred             CCcceeehhhccccccccCCCcEEEEEeCc---------hhhhhhcC-CceeEccCCChHHHHHHHHHHhhccCCCCCCC
Q 004021          254 PKKFRIDLTELGVPLQMLNAGFKIVLKTRS---------AGVCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTS  323 (779)
Q Consensus       254 ~kr~~~~ld~l~~~~~~~~~gs~IivTTR~---------~~va~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~  323 (779)
                                   .  ....|..||+|++.         ..+...+. ...+++++++.++-.+++.+.+.......+  
T Consensus       112 -------------~--~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~--  174 (226)
T PRK09087        112 -------------S--VRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQLYVD--  174 (226)
T ss_pred             -------------H--HHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCC--
Confidence                         0  11246779998873         33344444 678999999999999999998866443222  


Q ss_pred             hHHHHHHHHHHhCCChhHHHH
Q 004021          324 IPELAETLARECGRLPLALKT  344 (779)
Q Consensus       324 l~~~~~~I~~~c~glPLai~~  344 (779)
                       +++..-|++.+.|..-++..
T Consensus       175 -~ev~~~La~~~~r~~~~l~~  194 (226)
T PRK09087        175 -PHVVYYLVSRMERSLFAAQT  194 (226)
T ss_pred             -HHHHHHHHHHhhhhHHHHHH
Confidence             67788888888887766654

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.87  E-value=7.5e-06  Score=80.11  Aligned_cols=44  Identities=23%  Similarity=0.246  Sum_probs=24.0

Q ss_pred             CCCCCCccEEEccCCCCCccccC--CCCCCCCccEEeeeCCCCCCCC
Q 004021          691 HNFFTQLESLGILYGPDLKSIYP--NPLHFPKLKKIGVYGCPKLKKL  735 (779)
Q Consensus       691 ~~~~~~L~~L~l~~~~~l~~l~~--~~~~l~~L~~L~l~~c~~L~~l  735 (779)
                      ...||.+-.|.|.. +++.+|..  ....||.|..|.+.+.|-+..+
T Consensus       220 se~~p~~~~LnL~~-~~idswasvD~Ln~f~~l~dlRv~~~Pl~d~l  265 (418)
T KOG2982|consen  220 SEPFPSLSCLNLGA-NNIDSWASVDALNGFPQLVDLRVSENPLSDPL  265 (418)
T ss_pred             CCCCCcchhhhhcc-cccccHHHHHHHcCCchhheeeccCCcccccc
Confidence            34555555555554 44555543  3445666666666666654443

>PRK04195 replication factor C large subunit; Provisional

Probab=97.87  E-value=0.00099  Score=74.45  Aligned_cols=164  Identities=18%  Similarity=0.247  Sum_probs=97.0

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGKR  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~~  227 (779)
                      .+++|.++.++++.+|+..-  ....+.+.|+|++|+||||+|+++++..     .|+.+. ++.     ......++..
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el-----~~~~ie-lnasd~r~~~~i~~~i~~   87 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY-----GWEVIE-LNASDQRTADVIERVAGE   87 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc-----CCCEEE-EcccccccHHHHHHHHHH
Confidence            56899999999999998753  1236789999999999999999999976     133221 222     1112222211


Q ss_pred             hCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhcccccc-------------ccCCCcEEEEEeCchh-hhh-hcC-
Q 004021          228 IGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQ-------------MLNAGFKIVLKTRSAG-VCD-QMD-  291 (779)
Q Consensus       228 l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~-------------~~~~gs~IivTTR~~~-va~-~~~-  291 (779)
                      ....                 ......++.++.+|++.....             ....+..||+|+.+.. ... ... 
T Consensus        88 ~~~~-----------------~sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~~~~~iIli~n~~~~~~~k~Lrs  150 (482)
T PRK04195         88 AATS-----------------GSLFGARRKLILLDEVDGIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRN  150 (482)
T ss_pred             hhcc-----------------CcccCCCCeEEEEecCcccccccchhHHHHHHHHHHcCCCCEEEeccCccccchhhHhc
Confidence            1100                 000111222333443321110             0023455777775422 211 122 


Q ss_pred             -CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          292 -SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       292 -~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                       ...+.+.+++.++....+.+.+.......+   .+....|++.++|-.-.+..
T Consensus       151 r~~~I~f~~~~~~~i~~~L~~i~~~egi~i~---~eaL~~Ia~~s~GDlR~ain  201 (482)
T PRK04195        151 ACLMIEFKRLSTRSIVPVLKRICRKEGIECD---DEALKEIAERSGGDLRSAIN  201 (482)
T ss_pred             cceEEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence             567899999999999999888765543333   57789999999996655543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.85  E-value=0.00073  Score=67.60  Aligned_cols=168  Identities=11%  Similarity=0.137  Sum_probs=86.3

Q ss_pred             ccchhhhH-HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchh
Q 004021          157 IVGQEKLL-PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKK  235 (779)
Q Consensus       157 ~vGr~~~~-~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~  235 (779)
                      +.|..... ..+.++.. .....+.+.|+|..|+|||+||+++++...  .... ...+++.......+ ...... + .
T Consensus        21 ~~~~~~~~~~~l~~~~~-~~~~~~~~~l~G~~G~GKT~La~ai~~~~~--~~~~-~~~~i~~~~~~~~~-~~~~~~-~-~   93 (227)
T PRK08903         21 VAGENAELVARLRELAA-GPVADRFFYLWGEAGSGRSHLLQALVADAS--YGGR-NARYLDAASPLLAF-DFDPEA-E-L   93 (227)
T ss_pred             ccCCcHHHHHHHHHHHh-ccCCCCeEEEECCCCCCHHHHHHHHHHHHH--hCCC-cEEEEehHHhHHHH-hhcccC-C-E
Confidence            34554443 33333333 222456788999999999999999998762  1222 34455543322221 000000 0 0


Q ss_pred             hhhcchh----hHHHHHHHhhCCCcceeehhhccccccccCCCc-EEEEEeCchhh--------hhhcC-CceeEccCCC
Q 004021          236 WKEKSLQ----DKAVDISSILSPKKFRIDLTELGVPLQMLNAGF-KIVLKTRSAGV--------CDQMD-SKNLEVYSLA  301 (779)
Q Consensus       236 ~~~~~~~----~~~~~l~~~L~~kr~~~~ld~l~~~~~~~~~gs-~IivTTR~~~v--------a~~~~-~~~~~l~~L~  301 (779)
                      .-.++.+    .....+...+.         .      ....|. .||+|++....        ...+. ...+.+++++
T Consensus        94 liiDdi~~l~~~~~~~L~~~~~---------~------~~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~  158 (227)
T PRK08903         94 YAVDDVERLDDAQQIALFNLFN---------R------VRAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLS  158 (227)
T ss_pred             EEEeChhhcCchHHHHHHHHHH---------H------HHHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCC
Confidence            0000000    01111111110         0      011333 36666654321        11222 3688999999


Q ss_pred             hHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHh
Q 004021          302 HDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAM  349 (779)
Q Consensus       302 ~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l  349 (779)
                      +++-..++.+.+.......+   ++....+++.+.|.+..+..+-..+
T Consensus       159 ~~~~~~~l~~~~~~~~v~l~---~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        159 DADKIAALKAAAAERGLQLA---DEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhccCCHHHHHHHHHHH
Confidence            98877777765543332222   5678888889999998887665544

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.83  E-value=0.00066  Score=68.03  Aligned_cols=160  Identities=13%  Similarity=0.195  Sum_probs=89.3

Q ss_pred             ccccchhh-hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEK-LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~-~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|-.. .+..+.++....  ..+.+.|+|+.|+|||+|++++++.. .  ..-..+.++++........        
T Consensus        23 ~f~~~~n~~a~~~l~~~~~~~--~~~~l~l~Gp~G~GKThLl~a~~~~~-~--~~~~~v~y~~~~~~~~~~~--------   89 (235)
T PRK08084         23 SFYPGDNDSLLAALQNALRQE--HSGYIYLWSREGAGRSHLLHAACAEL-S--QRGRAVGYVPLDKRAWFVP--------   89 (235)
T ss_pred             ccccCccHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHH-H--hCCCeEEEEEHHHHhhhhH--------
Confidence            44457333 333333333333  44688999999999999999999876 2  2223456666622111000        


Q ss_pred             hhhhhcchhhHHHHHHHhhCCCcceeehhhccc-------------cccc-cCCC-cEEEEEeCch---------hhhhh
Q 004021          234 KKWKEKSLQDKAVDISSILSPKKFRIDLTELGV-------------PLQM-LNAG-FKIVLKTRSA---------GVCDQ  289 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~-------------~~~~-~~~g-s~IivTTR~~---------~va~~  289 (779)
                                   .+.+.+..-. ++.+|++..             .+.. ...| .++|+||+..         .+.+.
T Consensus        90 -------------~~~~~~~~~d-lliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SR  155 (235)
T PRK08084         90 -------------EVLEGMEQLS-LVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASR  155 (235)
T ss_pred             -------------HHHHHhhhCC-EEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHH
Confidence                         0111111101 222333311             0100 1133 4799999853         23334


Q ss_pred             cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          290 MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       290 ~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      +. ..+++++++++++-.+++.+++.......+   +++..-|++.+.|-.-++..
T Consensus       156 l~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~---~~v~~~L~~~~~~d~r~l~~  208 (235)
T PRK08084        156 LDWGQIYKLQPLSDEEKLQALQLRARLRGFELP---EDVGRFLLKRLDREMRTLFM  208 (235)
T ss_pred             HhCCceeeecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhhcCCHHHHHH
Confidence            44 578999999999999999887755432222   57778888888876655543

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.77  E-value=0.00045  Score=72.70  Aligned_cols=164  Identities=16%  Similarity=0.202  Sum_probs=98.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhc---cccCCCCEEEEEEe--c----hHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFC---HQQHNFDVVIWAAV--Q----TFQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~---~~~~~F~~~~wv~v--~----~i~~~i~  225 (779)
                      .+++|.+..++.+.+.+..+. -...+.++|+.|+||||+|+.+++..-   ....|+|...|...  .    +-.+++.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~ir~~~   82 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDIRNII   82 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHHHHHH
Confidence            357899999999999987662 345778999999999999999988541   12456776666542  0    0111111


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehh----------hccccccccCCCcEEEEEeCchh-hhhhcC--C
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLT----------ELGVPLQMLNAGFKIVLKTRSAG-VCDQMD--S  292 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld----------~l~~~~~~~~~gs~IivTTR~~~-va~~~~--~  292 (779)
                      +.+...                  -...++|+.+..+          .+...+.....++.+|++|.+.+ +.....  .
T Consensus        83 ~~~~~~------------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc  144 (313)
T PRK05564         83 EEVNKK------------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRC  144 (313)
T ss_pred             HHHhcC------------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhc
Confidence            111110                  0112333322211          11122333346788888886643 323222  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ..+.+.++++++....+.+.....       -.+.+..++..++|.|..+..
T Consensus       145 ~~~~~~~~~~~~~~~~l~~~~~~~-------~~~~~~~l~~~~~g~~~~a~~  189 (313)
T PRK05564        145 QIYKLNRLSKEEIEKFISYKYNDI-------KEEEKKSAIAFSDGIPGKVEK  189 (313)
T ss_pred             eeeeCCCcCHHHHHHHHHHHhcCC-------CHHHHHHHHHHcCCCHHHHHH
Confidence            788999999999988776554211       134577889999999875543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.77  E-value=0.00088  Score=73.61  Aligned_cols=156  Identities=11%  Similarity=0.154  Sum_probs=99.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      ..-+.|+|..|+|||+|++++++.. .....--.+++++..++...+...++.. .         .....+.+.++.-. 
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~l-~~~~~~~~v~yv~~~~f~~~~~~~l~~~-~---------~~~~~~~~~~~~~d-  208 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNYI-ESNFSDLKVSYMSGDEFARKAVDILQKT-H---------KEIEQFKNEICQND-  208 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHHH-HHhCCCCeEEEEEHHHHHHHHHHHHHHh-h---------hHHHHHHHHhccCC-
Confidence            3568899999999999999999976 2122223456777777777777666431 0         11223334343322 


Q ss_pred             eeehhhcccccc--------------ccCCCcEEEEEeCch---------hhhhhcC-CceeEccCCChHHHHHHHHHHh
Q 004021          258 RIDLTELGVPLQ--------------MLNAGFKIVLKTRSA---------GVCDQMD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       258 ~~~ld~l~~~~~--------------~~~~gs~IivTTR~~---------~va~~~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      ++.+|++...-.              ....|..||+|+...         .+...+. .-.+.+++++.++-.+++.+++
T Consensus       209 vLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~  288 (450)
T PRK14087        209 VLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEI  288 (450)
T ss_pred             EEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHH
Confidence            455666532110              013456788887642         2233333 5677899999999999999988


Q ss_pred             hccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          314 ERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       314 ~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      ...+.. ..--+++..-|++.++|.|-.+..+.
T Consensus       289 ~~~gl~-~~l~~evl~~Ia~~~~gd~R~L~gaL  320 (450)
T PRK14087        289 KNQNIK-QEVTEEAINFISNYYSDDVRKIKGSV  320 (450)
T ss_pred             HhcCCC-CCCCHHHHHHHHHccCCCHHHHHHHH
Confidence            654311 11226788999999999998777554

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.76  E-value=4.5e-05  Score=80.40  Aligned_cols=78  Identities=27%  Similarity=0.481  Sum_probs=56.5

Q ss_pred             ccCCccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCC-cccccchhhccCccCcEeeccC
Q 004021          493 EWEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLT-HIRGLPQELKALEKLRYLNLEY  568 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~-~i~~lp~~~~~L~~L~~L~l~~  568 (779)
                      .+..+++|++++|.+..+|..|.   -|.+++|..++.+|..+.  .+|++|++++| .+..+|..      |++|+++.
T Consensus        50 ~~~~l~~L~Is~c~L~sLP~LP~sLtsL~Lsnc~nLtsLP~~LP--~nLe~L~Ls~Cs~L~sLP~s------Le~L~L~~  121 (426)
T PRK15386         50 EARASGRLYIKDCDIESLPVLPNELTEITIENCNNLTTLPGSIP--EGLEKLTVCHCPEISGLPES------VRSLEIKG  121 (426)
T ss_pred             HhcCCCEEEeCCCCCcccCCCCCCCcEEEccCCCCcccCCchhh--hhhhheEccCcccccccccc------cceEEeCC
Confidence            45678899999988888876554   488888767888887663  68999999988 78888864      55555554


Q ss_pred             C--cCCCCCchh
Q 004021          569 T--HYLSIIPHQ  578 (779)
Q Consensus       569 ~--~~l~~lp~~  578 (779)
                      +  ..+..+|.+
T Consensus       122 n~~~~L~~LPss  133 (426)
T PRK15386        122 SATDSIKNVPNG  133 (426)
T ss_pred             CCCcccccCcch
Confidence            3  235666664

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.74  E-value=0.0021  Score=74.28  Aligned_cols=162  Identities=22%  Similarity=0.302  Sum_probs=88.8

Q ss_pred             ccccchhhhHH---HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLP---RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~---~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      .+|+|.+..+.   .+.+.+..+  ....+.++|++|+||||||+.+++..   ...|.     .+......+       
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~--~~~slLL~GPpGtGKTTLA~aIA~~~---~~~f~-----~lna~~~~i-------   90 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKAD--RVGSLILYGPPGVGKTTLARIIANHT---RAHFS-----SLNAVLAGV-------   90 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHh---cCcce-----eehhhhhhh-------
Confidence            45789888774   455555554  56677899999999999999999876   34442     111110000       


Q ss_pred             cchhhhhcchhhHHHHHHHhh--CCCcceeehhhcccc--------ccccCCCcEEEEE--eCch--hhhhhc-C-Ccee
Q 004021          232 EDKKWKEKSLQDKAVDISSIL--SPKKFRIDLTELGVP--------LQMLNAGFKIVLK--TRSA--GVCDQM-D-SKNL  295 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L--~~kr~~~~ld~l~~~--------~~~~~~gs~IivT--TR~~--~va~~~-~-~~~~  295 (779)
                             .+..+......+.+  .+++..+.+|++...        ++....|+.++|+  |.+.  .+.... . ...+
T Consensus        91 -------~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g~IiLI~aTTenp~~~l~~aL~SR~~v~  163 (725)
T PRK13341         91 -------KDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSRSRLF  163 (725)
T ss_pred             -------HHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhcCceEEEEEecCCChHhhhhhHhhccccce
Confidence                   00111111121111  123334555555211        1112345555553  4442  122222 1 4678


Q ss_pred             EccCCChHHHHHHHHHHhhccC----CCCCCChHHHHHHHHHHhCCChh
Q 004021          296 EVYSLAHDEAWKLFQEMIERST----LDSHTSIPELAETLARECGRLPL  340 (779)
Q Consensus       296 ~l~~L~~~~a~~Lf~~~a~~~~----~~~~~~l~~~~~~I~~~c~glPL  340 (779)
                      .+++|+.++...++.+.+....    .....--++....|++.+.|..-
T Consensus       164 ~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R  212 (725)
T PRK13341        164 RLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDAR  212 (725)
T ss_pred             ecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHH
Confidence            9999999999999988765210    00111125667888888888543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.73  E-value=0.00046  Score=76.82  Aligned_cols=186  Identities=13%  Similarity=0.100  Sum_probs=97.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-C-CCCEEEEEEe-chHHHHHHHH----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-H-NFDVVIWAAV-QTFQDDIGKR----  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~-~F~~~~wv~v-~~i~~~i~~~----  227 (779)
                      .++||.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+...-.. . ......--|- -.....|...    
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpD   94 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVD   94 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCc
Confidence            468999999999999998762 235678999999999999999988762100 0 0000000000 0111111110    


Q ss_pred             -hCCCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhcc-----------ccccccCCCcE-EEEEeCchhhhhhcC--
Q 004021          228 -IGFSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELG-----------VPLQMLNAGFK-IVLKTRSAGVCDQMD--  291 (779)
Q Consensus       228 -l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~-----------~~~~~~~~gs~-IivTTR~~~va~~~~--  291 (779)
                       +..+........+..++.+.+...-...+| ...+|++.           ..+..-..+++ |++||....+...+-  
T Consensus        95 viEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLlpTIrSR  174 (700)
T PRK12323         95 YIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSR  174 (700)
T ss_pred             ceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhhhHHHHH
Confidence             000000000011111111111111112223 23333321           11111123444 555555566654433  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ...|.++.++.++..+.+.+.+...+...+   .+..+.|++.++|.|.-...
T Consensus       175 Cq~f~f~~ls~eei~~~L~~Il~~Egi~~d---~eAL~~IA~~A~Gs~RdALs  224 (700)
T PRK12323        175 CLQFNLKQMPPGHIVSHLDAILGEEGIAHE---VNALRLLAQAAQGSMRDALS  224 (700)
T ss_pred             HHhcccCCCChHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence            678999999999999999888765442221   45668899999998865443

>PRK05642 DNA replication initiation factor; Validated

Probab=97.72  E-value=0.0016  Score=65.24  Aligned_cols=140  Identities=17%  Similarity=0.272  Sum_probs=81.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      ...+.|+|..|+|||.|++++++.. .  ..-..++|++..++.....                     .+.+.+++-. 
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~-~--~~~~~v~y~~~~~~~~~~~---------------------~~~~~~~~~d-   99 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRF-E--QRGEPAVYLPLAELLDRGP---------------------ELLDNLEQYE-   99 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH-H--hCCCcEEEeeHHHHHhhhH---------------------HHHHhhhhCC-
Confidence            3678999999999999999999876 2  2224567777744432210                     0111111111 


Q ss_pred             eeehhhccc-------------ccc-ccCCCcEEEEEeCchh--h-------hhhcC-CceeEccCCChHHHHHHHHHHh
Q 004021          258 RIDLTELGV-------------PLQ-MLNAGFKIVLKTRSAG--V-------CDQMD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       258 ~~~ld~l~~-------------~~~-~~~~gs~IivTTR~~~--v-------a~~~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      .+.+|++..             .+. ....|..||+||+...  .       .+.+. ...+++++++.++-.+.++.++
T Consensus       100 ~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka  179 (234)
T PRK05642        100 LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRA  179 (234)
T ss_pred             EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHH
Confidence            112222210             010 0124678889887522  1       22222 4678999999999999999776


Q ss_pred             hccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          314 ERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       314 ~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      ......-+   +++..-|++++.|-.-++..+
T Consensus       180 ~~~~~~l~---~ev~~~L~~~~~~d~r~l~~~  208 (234)
T PRK05642        180 SRRGLHLT---DEVGHFILTRGTRSMSALFDL  208 (234)
T ss_pred             HHcCCCCC---HHHHHHHHHhcCCCHHHHHHH
Confidence            54432222   567777888887766555433

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

Probab=97.72  E-value=5.2e-06  Score=91.10  Aligned_cols=103  Identities=27%  Similarity=0.425  Sum_probs=82.7

Q ss_pred             ccccCCccEEEccccccccccc-Ccc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEe
Q 004021          491 VKEWEGAKRISLMANEIESLSE-IPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYL  564 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~-~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L  564 (779)
                      +..+.++..+++.+|.|..+.. ...     .|+|++| .|..+. .+..|+.|+.|++.+|.|+.++ .+..+++|+.+
T Consensus        91 l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N-~I~~i~-~l~~l~~L~~L~l~~N~i~~~~-~~~~l~~L~~l  167 (414)
T KOG0531|consen   91 LSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFN-KITKLE-GLSTLTLLKELNLSGNLISDIS-GLESLKSLKLL  167 (414)
T ss_pred             cccccceeeeeccccchhhcccchhhhhcchheecccc-cccccc-chhhccchhhheeccCcchhcc-CCccchhhhcc
Confidence            5566789999999999988776 332     3999999 888875 5778888999999999998886 35669999999


Q ss_pred             eccCCcCCCCCch-hhhcCCccCcEeeeccccCCC
Q 004021          565 NLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       565 ~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ++++| .+..+.. . ...+.+|+.+.+.+|.+..
T Consensus       168 ~l~~n-~i~~ie~~~-~~~~~~l~~l~l~~n~i~~  200 (414)
T KOG0531|consen  168 DLSYN-RIVDIENDE-LSELISLEELDLGGNSIRE  200 (414)
T ss_pred             cCCcc-hhhhhhhhh-hhhccchHHHhccCCchhc
Confidence            99999 5666766 2 3688899999999887664

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.0003  Score=78.10  Aligned_cols=181  Identities=14%  Similarity=0.090  Sum_probs=100.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .+++|.+..++.|.+++..+. -...+.++|++|+||||+|+.+++.. .-...+...+|.|...  ..+..........
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l-~c~~~~~~~cg~C~sc--~~i~~~~h~dv~e   89 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAV-NCSGEDPKPCGECESC--LAVRRGAHPDVLE   89 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHH-hccCCCCCCCCcChhh--HHHhcCCCCceEE
Confidence            458999999999988888762 33567999999999999999999877 2222233344444311  1111000000000


Q ss_pred             -h-hhhcchhhHHHHHHHhhC-----CCcceeehhhcc-----------ccccccCCCcEEEEEe-CchhhhhhcC--Cc
Q 004021          235 -K-WKEKSLQDKAVDISSILS-----PKKFRIDLTELG-----------VPLQMLNAGFKIVLKT-RSAGVCDQMD--SK  293 (779)
Q Consensus       235 -~-~~~~~~~~~~~~l~~~L~-----~kr~~~~ld~l~-----------~~~~~~~~gs~IivTT-R~~~va~~~~--~~  293 (779)
                       . ......++ +..+.+.+.     +++-.+++|+..           ..+......+.+|++| ....+...+.  ..
T Consensus        90 l~~~~~~~vd~-iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~  168 (504)
T PRK14963         90 IDAASNNSVED-VRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ  168 (504)
T ss_pred             ecccccCCHHH-HHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceE
Confidence             0 00011111 112222221     222244444431           1112222344545444 4444433333  57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .+++.+++.++....+.+.+...+...   -++....|++.++|.+--+.
T Consensus       169 ~~~f~~ls~~el~~~L~~i~~~egi~i---~~~Al~~ia~~s~GdlR~al  215 (504)
T PRK14963        169 HFRFRRLTEEEIAGKLRRLLEAEGREA---EPEALQLVARLADGAMRDAE  215 (504)
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHH
Confidence            889999999999999999886654322   25678899999999885443

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

Probab=97.70  E-value=4.1e-05  Score=73.89  Aligned_cols=47  Identities=28%  Similarity=0.415  Sum_probs=33.4

Q ss_pred             cccchhhhHHHHHHHHhc-cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITD-QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+||+++++++...+.. .....+.+.|+|.+|+|||+|.++++...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            379999999999999942 23456899999999999999999999888

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

Probab=97.67  E-value=1.6e-06  Score=94.33  Aligned_cols=128  Identities=26%  Similarity=0.273  Sum_probs=97.6

Q ss_pred             CccccccCCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchh-hccCcc
Q 004021          488 APKVKEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEK  560 (779)
Q Consensus       488 ~~~~~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~  560 (779)
                      +.+...|.++...+++.|.+..+.....      -|+|++| .+.+.- .+..|++|++|||++|.+..+|.- ...+ +
T Consensus       157 ~~ns~~Wn~L~~a~fsyN~L~~mD~SLqll~ale~LnLshN-k~~~v~-~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc-~  233 (1096)
T KOG1859|consen  157 ISNSPVWNKLATASFSYNRLVLMDESLQLLPALESLNLSHN-KFTKVD-NLRRLPKLKHLDLSYNCLRHVPQLSMVGC-K  233 (1096)
T ss_pred             cccchhhhhHhhhhcchhhHHhHHHHHHHHHHhhhhccchh-hhhhhH-HHHhcccccccccccchhccccccchhhh-h
Confidence            3444567888889999888776655443      3999999 777765 788899999999999999998863 2333 3


Q ss_pred             CcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       561 L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      |+.|.+++| .++.+-.  +.+|.+|+.||+++|-+.+             ...+.-|..|..|+.|.+.+|..
T Consensus       234 L~~L~lrnN-~l~tL~g--ie~LksL~~LDlsyNll~~-------------hseL~pLwsLs~L~~L~LeGNPl  291 (1096)
T KOG1859|consen  234 LQLLNLRNN-ALTTLRG--IENLKSLYGLDLSYNLLSE-------------HSELEPLWSLSSLIVLWLEGNPL  291 (1096)
T ss_pred             heeeeeccc-HHHhhhh--HHhhhhhhccchhHhhhhc-------------chhhhHHHHHHHHHHHhhcCCcc
Confidence            999999999 6787765  8999999999999987775             33444456667777777777654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.67  E-value=0.00026  Score=76.23  Aligned_cols=48  Identities=27%  Similarity=0.316  Sum_probs=39.0

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+++.++++.+.+...           -...+-+.++|++|+|||++|+++++..
T Consensus       122 ~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l  180 (364)
T TIGR01242       122 EDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET  180 (364)
T ss_pred             HHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC
Confidence            46899999999999887431           0124568999999999999999999877

Many proteins may score above the trusted cutoff because an internal

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.65  E-value=0.001  Score=74.28  Aligned_cols=182  Identities=12%  Similarity=0.094  Sum_probs=97.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCC---
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGF---  230 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~---  230 (779)
                      ..++|.+..++.|.+++..+. -...+.++|..|+||||+|+.+++.. .-....+..  .|- -...+.|...-..   
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~L-nC~~~~~~~--pCg~C~sC~~I~~g~hpDvi   90 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCL-NCETGVTST--PCEVCATCKAVNEGRFIDLI   90 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh-CCCcCCCCC--CCccCHHHHHHhcCCCCceE
Confidence            568999999999999998762 24678999999999999999998876 111101000  000 0111111110000   


Q ss_pred             --CcchhhhhcchhhHHHHHHHh-hCCCcceeehhhcc-----------ccccccCCCcEEEEEeCc-hhhhhh-cC-Cc
Q 004021          231 --SEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELG-----------VPLQMLNAGFKIVLKTRS-AGVCDQ-MD-SK  293 (779)
Q Consensus       231 --~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~-----------~~~~~~~~gs~IivTTR~-~~va~~-~~-~~  293 (779)
                        .........+..+....+... ..+++-...+|++-           ..+.....+.++|++|.+ ..+... .. ..
T Consensus        91 EIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd~~kIp~TIlSRCq  170 (702)
T PRK14960         91 EIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCL  170 (702)
T ss_pred             EecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECChHhhhHHHHHhhh
Confidence              000000000111111111111 11222133333321           111122245567776655 333222 22 57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .+++.+++.++..+.+.+.+...+...+   .+....|++.++|-+-.+.
T Consensus       171 ~feFkpLs~eEI~k~L~~Il~kEgI~id---~eAL~~IA~~S~GdLRdAL  217 (702)
T PRK14960        171 QFTLRPLAVDEITKHLGAILEKEQIAAD---QDAIWQIAESAQGSLRDAL  217 (702)
T ss_pred             eeeccCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHH
Confidence            8899999999999999888766543222   5667889999999775444

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.63  E-value=0.00092  Score=71.76  Aligned_cols=181  Identities=13%  Similarity=0.160  Sum_probs=95.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      .+++|.+..++.+.+.+..+. -...+.++|..|+||||+|+.+++.. .-...... -+..  -.....+.........
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~~l-~c~~~~~~~pc~~--c~~c~~~~~~~~~d~~   91 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAKSL-NCQNGITSNPCRK--CIICKEIEKGLCLDLI   91 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHHHh-cCCCCCCCCCCCC--CHHHHHHhcCCCCceE
Confidence            568999999999999887662 34567899999999999999999876 21111100 0000  0011111111000000


Q ss_pred             h-hh-hhcchhhHHHHHHHhhCC----Ccc-eeehhhcc-----------ccccccCCCcEEEEEeCc-hhhhhhcC--C
Q 004021          234 K-KW-KEKSLQDKAVDISSILSP----KKF-RIDLTELG-----------VPLQMLNAGFKIVLKTRS-AGVCDQMD--S  292 (779)
Q Consensus       234 ~-~~-~~~~~~~~~~~l~~~L~~----kr~-~~~ld~l~-----------~~~~~~~~gs~IivTTR~-~~va~~~~--~  292 (779)
                      + .. .....++ ...+.+.+..    .++ ...+|++.           ..+.......++|++|.+ ..+.....  .
T Consensus        92 ~~~~~~~~~v~~-ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~SRc  170 (363)
T PRK14961         92 EIDAASRTKVEE-MREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRC  170 (363)
T ss_pred             EecccccCCHHH-HHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHHhhc
Confidence            0 00 0001111 1122222111    111 22233221           111122245566666544 44443332  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      ..+++.+++.++..+.+.+.+...+...   -++.+..|++.++|.|-.+.
T Consensus       171 ~~~~~~~l~~~el~~~L~~~~~~~g~~i---~~~al~~ia~~s~G~~R~al  218 (363)
T PRK14961        171 LQFKLKIISEEKIFNFLKYILIKESIDT---DEYALKLIAYHAHGSMRDAL  218 (363)
T ss_pred             eEEeCCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHH
Confidence            7889999999999998888775543212   24667889999999886443

>PLN03025 replication factor C subunit; Provisional

Probab=97.62  E-value=0.00069  Score=71.44  Aligned_cols=162  Identities=16%  Similarity=0.161  Sum_probs=91.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKR  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~  227 (779)
                      .+++|.++.++.|.+++..+  ..+-+-++|.+|+||||+|+.+++...  ...|.. .++..       .+..+.+.+.
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~--~~~~lll~Gp~G~GKTtla~~la~~l~--~~~~~~-~~~eln~sd~~~~~~vr~~i~~   87 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDG--NMPNLILSGPPGTGKTTSILALAHELL--GPNYKE-AVLELNASDDRGIDVVRNKIKM   87 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHHh--cccCcc-ceeeecccccccHHHHHHHHHH
Confidence            45799998888888877765  455577999999999999999998761  122221 11111       0111111111


Q ss_pred             hCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhccc-----------cccccCCCcEEEEEeCc-hhhhhhcC--C
Q 004021          228 IGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGV-----------PLQMLNAGFKIVLKTRS-AGVCDQMD--S  292 (779)
Q Consensus       228 l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~-~~va~~~~--~  292 (779)
                      +...                 ...+ .++.-.+.+|++..           .+......+++++++.. ..+.....  .
T Consensus        88 ~~~~-----------------~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc  150 (319)
T PLN03025         88 FAQK-----------------KVTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRC  150 (319)
T ss_pred             HHhc-----------------cccCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhh
Confidence            1000                 0000 01111222333211           01112345667776654 23322222  4


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA  341 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa  341 (779)
                      ..++++++++++....+...+...+..-+   .+....|++.++|-.-.
T Consensus       151 ~~i~f~~l~~~~l~~~L~~i~~~egi~i~---~~~l~~i~~~~~gDlR~  196 (319)
T PLN03025        151 AIVRFSRLSDQEILGRLMKVVEAEKVPYV---PEGLEAIIFTADGDMRQ  196 (319)
T ss_pred             hcccCCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHH
Confidence            67899999999999999888766543222   56778999999986533

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.62  E-value=0.00092  Score=70.82  Aligned_cols=164  Identities=15%  Similarity=0.163  Sum_probs=92.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKR  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~  227 (779)
                      .+++|+++.++.+..++..+  ..+.+.++|.+|+||||+|+.+++...  ...+.. .++.+       .....+.+..
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~--~~~~~ll~G~~G~GKt~~~~~l~~~l~--~~~~~~-~~i~~~~~~~~~~~~~~~~i~~   91 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEK--NMPHLLFAGPPGTGKTTAALALARELY--GEDWRE-NFLELNASDERGIDVIRNKIKE   91 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHc--CCcccc-ceEEeccccccchHHHHHHHHH
Confidence            45899999999999998765  455679999999999999999998762  112211 12222       0111111111


Q ss_pred             hCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhc-----------cccccccCCCcEEEEEeCc-hhhhhhcC--Cc
Q 004021          228 IGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTEL-----------GVPLQMLNAGFKIVLKTRS-AGVCDQMD--SK  293 (779)
Q Consensus       228 l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l-----------~~~~~~~~~gs~IivTTR~-~~va~~~~--~~  293 (779)
                      +... .+. .              -.+++ .+.+|++           ...+......+.+|+++.. ..+.....  ..
T Consensus        92 ~~~~-~~~-~--------------~~~~~-vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~  154 (319)
T PRK00440         92 FART-APV-G--------------GAPFK-IIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCA  154 (319)
T ss_pred             HHhc-CCC-C--------------CCCce-EEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhh
Confidence            1000 000 0              00011 1111111           0111112234567766643 22222221  45


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .+++.+++.++....+...+...+..-+   ++....+++.++|.+--+.
T Consensus       155 ~~~~~~l~~~ei~~~l~~~~~~~~~~i~---~~al~~l~~~~~gd~r~~~  201 (319)
T PRK00440        155 VFRFSPLKKEAVAERLRYIAENEGIEIT---DDALEAIYYVSEGDMRKAI  201 (319)
T ss_pred             eeeeCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHH
Confidence            7899999999999999888765442222   5678899999999776543

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.62  E-value=0.002  Score=70.83  Aligned_cols=149  Identities=17%  Similarity=0.220  Sum_probs=91.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKK  256 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr  256 (779)
                      ..-+.|+|.+|+|||+||+++++.. . +.+.+ .++|++..++...+...+...        ...    .+.+.+..+.
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l-~-~~~~~~~v~yi~~~~f~~~~~~~~~~~--------~~~----~f~~~~~~~~  195 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYV-V-QNEPDLRVMYITSEKFLNDLVDSMKEG--------KLN----EFREKYRKKV  195 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHH-H-HhCCCCeEEEEEHHHHHHHHHHHHhcc--------cHH----HHHHHHHhcC
Confidence            4469999999999999999999987 2 22333 567788777777776655422        111    1222222222


Q ss_pred             ceeehhhccccc-------------c-ccCCCcEEEEEeCc-hh----h----hhhcC-CceeEccCCChHHHHHHHHHH
Q 004021          257 FRIDLTELGVPL-------------Q-MLNAGFKIVLKTRS-AG----V----CDQMD-SKNLEVYSLAHDEAWKLFQEM  312 (779)
Q Consensus       257 ~~~~ld~l~~~~-------------~-~~~~gs~IivTTR~-~~----v----a~~~~-~~~~~l~~L~~~~a~~Lf~~~  312 (779)
                      -.+.+|++....             . ....|..||+||.. ..    +    ...+. ...+.+++.+.+.-..++.+.
T Consensus       196 dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~  275 (440)
T PRK14088        196 DVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKM  275 (440)
T ss_pred             CEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHH
Confidence            244555543111             0 01245678888852 21    1    12222 457789999999999999988


Q ss_pred             hhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          313 IERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       313 a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      +.......+   +++..-|++.+.|..-.+.
T Consensus       276 ~~~~~~~l~---~ev~~~Ia~~~~~~~R~L~  303 (440)
T PRK14088        276 LEIEHGELP---EEVLNFVAENVDDNLRRLR  303 (440)
T ss_pred             HHhcCCCCC---HHHHHHHHhccccCHHHHH
Confidence            765432222   5678888888877554443

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

Probab=97.61  E-value=9.6e-06  Score=81.39  Aligned_cols=175  Identities=20%  Similarity=0.117  Sum_probs=87.3

Q ss_pred             cccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCCCCchhh-------------hcCCccCcEeeeccc
Q 004021          533 SSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLSIIPHQL-------------ISGFLKLEVLRLLEC  594 (779)
Q Consensus       533 ~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~lp~~~-------------i~~L~~L~~L~l~~~  594 (779)
                      ...++|++||||.|.+..     +-.-+..++.|++|+|.+| .++..-.+.             ++.-++|+++....|
T Consensus        89 ~~~~~L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~N~-Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~rN  167 (382)
T KOG1909|consen   89 LGCPKLQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLNNC-GLGPEAGGRLGRALFELAVNKKAASKPKLRVFICGRN  167 (382)
T ss_pred             hcCCceeEeeccccccCccchHHHHHHHHhccCHHHHhhhcC-CCChhHHHHHHHHHHHHHHHhccCCCcceEEEEeecc
Confidence            344567777777774432     2233566677777777777 333222211             223345666666666


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc---------cccCCCCCcccC--------------ccc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA---------VQKFFKYPKLDL--------------TWL  651 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~---------~~~~~~L~~L~~--------------~~l  651 (779)
                      +...          .........++..+.|+.+.+..|++..         +..+++|+.|++              ..+
T Consensus       168 rlen----------~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~LakaL  237 (382)
T KOG1909|consen  168 RLEN----------GGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALAKAL  237 (382)
T ss_pred             cccc----------ccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHHHHh
Confidence            5543          1112233334444555555555444321         123333333311              124


Q ss_pred             ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcc-----ccCCCCCCCCccEEee
Q 004021          652 VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS-----IYPNPLHFPKLKKIGV  726 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~-----l~~~~~~l~~L~~L~l  726 (779)
                      ..+++|+.|++++|..-..--     ..+   .+   ..-..+|+|+.|.+.++. ++.     +.......|.|..|++
T Consensus       238 ~s~~~L~El~l~dcll~~~Ga-----~a~---~~---al~~~~p~L~vl~l~gNe-It~da~~~la~~~~ek~dL~kLnL  305 (382)
T KOG1909|consen  238 SSWPHLRELNLGDCLLENEGA-----IAF---VD---ALKESAPSLEVLELAGNE-ITRDAALALAACMAEKPDLEKLNL  305 (382)
T ss_pred             cccchheeecccccccccccH-----HHH---HH---HHhccCCCCceeccCcch-hHHHHHHHHHHHHhcchhhHHhcC
Confidence            456778888888775422110     000   00   112347888888887742 221     1123345788888888


Q ss_pred             eCCC
Q 004021          727 YGCP  730 (779)
Q Consensus       727 ~~c~  730 (779)
                      ++|.
T Consensus       306 ngN~  309 (382)
T KOG1909|consen  306 NGNR  309 (382)
T ss_pred             Cccc
Confidence            8774

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

Probab=97.58  E-value=0.00018  Score=72.08  Aligned_cols=39  Identities=21%  Similarity=0.197  Sum_probs=34.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ....++|+|.+|+|||||++.+++.. .. .+|+.++|+.+
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l-~~-~~fdv~~~v~v   53 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAI-TK-NHPEVYLIVLL   53 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc-cc-ccCCeEEEEEE
Confidence            44789999999999999999999988 43 48999999996

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.57  E-value=0.00058  Score=73.99  Aligned_cols=180  Identities=11%  Similarity=0.062  Sum_probs=97.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~  232 (779)
                      .+++|.+..+..|..++..+  .+ ..+.++|..|+||||+|+.+++... -..... ..+..|  .-...+........
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~--ri~ha~Lf~GP~GtGKTTlAriLAk~Ln-ce~~~~~~pCg~C--~sC~~i~~g~~~dv   92 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSG--KIGHAYIFFGPRGVGKTTIARILAKRLN-CENPIGNEPCNEC--TSCLEITKGISSDV   92 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcC--CCCeEEEEECCCCCCHHHHHHHHHHhcC-cccccCccccCCC--cHHHHHHccCCccc
Confidence            45899999999999998877  44 4688999999999999999998762 111000 001111  11222222111100


Q ss_pred             ---c--hhhhhcchhhHHHHHHHhhCCCcc-eeehhhcc-----------ccccccCCCcEE-EEEeCchhhhhhcC--C
Q 004021          233 ---D--KKWKEKSLQDKAVDISSILSPKKF-RIDLTELG-----------VPLQMLNAGFKI-VLKTRSAGVCDQMD--S  292 (779)
Q Consensus       233 ---~--~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~-----------~~~~~~~~gs~I-ivTTR~~~va~~~~--~  292 (779)
                         +  ......+..+....+...-...+| ...+|++-           ..+......... +.||....+.....  .
T Consensus        93 iEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRC  172 (484)
T PRK14956         93 LEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRC  172 (484)
T ss_pred             eeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhh
Confidence               0  000011112222222211112233 33334331           111111123333 45555555544433  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ..|.+.+++.++..+.+.+.+...+...   -.+....|++.++|.+--+
T Consensus       173 q~~~f~~ls~~~i~~~L~~i~~~Egi~~---e~eAL~~Ia~~S~Gd~RdA  219 (484)
T PRK14956        173 QDFIFKKVPLSVLQDYSEKLCKIENVQY---DQEGLFWIAKKGDGSVRDM  219 (484)
T ss_pred             heeeecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCChHHHH
Confidence            6799999999999998888876544222   2567889999999987543

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

Probab=97.56  E-value=0.0039  Score=66.28  Aligned_cols=186  Identities=15%  Similarity=0.187  Sum_probs=113.6

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~~  226 (779)
                      ..+.+|+++++++...|..-  ...+.-+.|+|.+|+|||+.++.|.+.........+ +++|+.      .+++..|+.
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~-~~yINc~~~~t~~~i~~~i~~   95 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVE-VVYINCLELRTPYQVLSKILN   95 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCc-eEEEeeeeCCCHHHHHHHHHH
Confidence            44899999999999988752  223334899999999999999999998832222233 566666      678888998


Q ss_pred             HhCCCcchhhhhcchhhHHHHHHHhhCC--Ccceeehhhcccccc-----------cc-CCCcEEEE--EeCchhh----
Q 004021          227 RIGFSEDKKWKEKSLQDKAVDISSILSP--KKFRIDLTELGVPLQ-----------ML-NAGFKIVL--KTRSAGV----  286 (779)
Q Consensus       227 ~l~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l~~~~~-----------~~-~~gs~Iiv--TTR~~~v----  286 (779)
                      .++..+.   ...+..+....+.+.+..  +.+.+++|++.....           .. ..+++|+|  .+.+..+    
T Consensus        96 ~~~~~p~---~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~l  172 (366)
T COG1474          96 KLGKVPL---TGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYL  172 (366)
T ss_pred             HcCCCCC---CCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHh
Confidence            8863322   234455666667776654  455666666532211           11 12454443  4444332    


Q ss_pred             ----hhhcCCceeEccCCChHHHHHHHHHHhhc---cCCCCCCChHHHHHHHHHHhC-CChhHHHHH
Q 004021          287 ----CDQMDSKNLEVYSLAHDEAWKLFQEMIER---STLDSHTSIPELAETLARECG-RLPLALKTV  345 (779)
Q Consensus       287 ----a~~~~~~~~~l~~L~~~~a~~Lf~~~a~~---~~~~~~~~l~~~~~~I~~~c~-glPLai~~~  345 (779)
                          ....+...+..+|-+.+|-...+..++..   .. ..+++.-+.+..++..-+ -.-.||..+
T Consensus       173 d~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~-~~~~~vl~lia~~~a~~~GDAR~aidil  238 (366)
T COG1474         173 DPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAG-VIDDDVLKLIAALVAAESGDARKAIDIL  238 (366)
T ss_pred             hhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhhccCC-CcCccHHHHHHHHHHHcCccHHHHHHHH
Confidence                23333345778888899999998887643   22 223333344444444444 455666553

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.56  E-value=0.0033  Score=68.86  Aligned_cols=149  Identities=15%  Similarity=0.237  Sum_probs=90.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      ...+.|+|..|+|||+|++++++.. .....=..+++++..++...+...+...        .    ...+.+.+++-. 
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l-~~~~~~~~v~yi~~~~~~~~~~~~~~~~--------~----~~~~~~~~~~~d-  201 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEI-LENNPNAKVVYVSSEKFTNDFVNALRNN--------K----MEEFKEKYRSVD-  201 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHH-HHhCCCCcEEEEEHHHHHHHHHHHHHcC--------C----HHHHHHHHHhCC-
Confidence            4568899999999999999999987 2221113466777766666665554321        1    112233333222 


Q ss_pred             eeehhhccccc-------------c-ccCCCcEEEEEeCch--h-------hhhhcC-CceeEccCCChHHHHHHHHHHh
Q 004021          258 RIDLTELGVPL-------------Q-MLNAGFKIVLKTRSA--G-------VCDQMD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       258 ~~~ld~l~~~~-------------~-~~~~gs~IivTTR~~--~-------va~~~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      .+.+|++...-             . ....|..||+||...  .       +...+. ...+.+++.+.++-..++.+.+
T Consensus       202 lLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~  281 (405)
T TIGR00362       202 LLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKA  281 (405)
T ss_pred             EEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHH
Confidence            44455552210             0 012456788888642  1       222222 3568999999999999999988


Q ss_pred             hccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          314 ERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       314 ~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .......+   +++..-|++.+.|.+-.+.
T Consensus       282 ~~~~~~l~---~e~l~~ia~~~~~~~r~l~  308 (405)
T TIGR00362       282 EEEGLELP---DEVLEFIAKNIRSNVRELE  308 (405)
T ss_pred             HHcCCCCC---HHHHHHHHHhcCCCHHHHH
Confidence            76442222   5777888888888765444

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PF13173 AAA_14: AAA domain

Probab=97.56  E-value=0.0003  Score=63.21  Aligned_cols=110  Identities=27%  Similarity=0.304  Sum_probs=62.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      .+++.|.|+.|+|||||+++++++. .   ....+++++..+....-..             .. +..+.+.+....+..
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~-~---~~~~~~yi~~~~~~~~~~~-------------~~-~~~~~~~~~~~~~~~   63 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDL-L---PPENILYINFDDPRDRRLA-------------DP-DLLEYFLELIKPGKK   63 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh-c---ccccceeeccCCHHHHHHh-------------hh-hhHHHHHHhhccCCc
Confidence            3789999999999999999999887 2   3455667766221110000             00 012222222222333


Q ss_pred             eeehhhc---------cccccccCCCcEEEEEeCchhhhhh-----c-C-CceeEccCCChHHH
Q 004021          258 RIDLTEL---------GVPLQMLNAGFKIVLKTRSAGVCDQ-----M-D-SKNLEVYSLAHDEA  305 (779)
Q Consensus       258 ~~~ld~l---------~~~~~~~~~gs~IivTTR~~~va~~-----~-~-~~~~~l~~L~~~~a  305 (779)
                      .+.+|++         ...+.+..+..+|++|+.+......     . + ...+++.||+..|-
T Consensus        64 ~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   64 YIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             EEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            3444443         1222333456899999988665422     1 2 45678999987763

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=97.54  E-value=0.0044  Score=61.14  Aligned_cols=176  Identities=16%  Similarity=0.137  Sum_probs=97.4

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~  225 (779)
                      .+|+|.++-++++.=.+...   +..+--|-++|++|.||||||.-+++.. .  ..+.    ++-      ..=+..|+
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em-g--vn~k----~tsGp~leK~gDlaaiL   98 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL-G--VNLK----ITSGPALEKPGDLAAIL   98 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh-c--CCeE----ecccccccChhhHHHHH
Confidence            56899998888887776543   3466789999999999999999999987 2  2221    111      11122333


Q ss_pred             HHhCCCcchhhhhcchhhHH----HHHHHhhCCCcceeehhh------ccccccccCCCcEEEEEeCchhhhhhcC---C
Q 004021          226 KRIGFSEDKKWKEKSLQDKA----VDISSILSPKKFRIDLTE------LGVPLQMLNAGFKIVLKTRSAGVCDQMD---S  292 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~----~~l~~~L~~kr~~~~ld~------l~~~~~~~~~gs~IivTTR~~~va~~~~---~  292 (779)
                      ..+... + ..-.+....+.    +.+.-.+++-+..+....      +...++   +=+-|=.|||.-.+..-+.   .
T Consensus        99 t~Le~~-D-VLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLp---pFTLIGATTr~G~lt~PLrdRFG  173 (332)
T COG2255          99 TNLEEG-D-VLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLP---PFTLIGATTRAGMLTNPLRDRFG  173 (332)
T ss_pred             hcCCcC-C-eEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccCC---CeeEeeeccccccccchhHHhcC
Confidence            333221 0 00000011111    111111222111111100      011111   1122346898765544433   3


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      ...+++--+.+|-.+...+.+..-....+   ++.+.+|+++..|-|--+.-+
T Consensus       174 i~~rlefY~~~eL~~Iv~r~a~~l~i~i~---~~~a~eIA~rSRGTPRIAnRL  223 (332)
T COG2255         174 IIQRLEFYTVEELEEIVKRSAKILGIEID---EEAALEIARRSRGTPRIANRL  223 (332)
T ss_pred             CeeeeecCCHHHHHHHHHHHHHHhCCCCC---hHHHHHHHHhccCCcHHHHHH
Confidence            46688889999999999888755443332   577899999999999654433

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.53  E-value=0.0014  Score=75.73  Aligned_cols=182  Identities=15%  Similarity=0.112  Sum_probs=97.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEEEechHHHHHHHHhC---
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWAAVQTFQDDIGKRIG---  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv~v~~i~~~i~~~l~---  229 (779)
                      ..+||.+..++.|.+++..+  ++ ..+.++|..|+||||+|+.+++... -....+. -+-.|  .....|.....   
T Consensus        16 ddIIGQe~Iv~~LknaI~~~--rl~HAyLFtGPpGtGKTTLARiLAk~Ln-ce~~~~~~pCg~C--~sC~~i~~g~~~Dv   90 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQ--RLHHAYLFTGTRGVGKTSLARLFAKGLN-CEQGVTATPCGVC--SSCVEIAQGRFVDL   90 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhC--CCCeEEEEECCCCCCHHHHHHHHHHhcc-CccCCCCCCCCCc--hHHHHHhcCCCceE
Confidence            56899999999999998776  44 4568999999999999999998762 1111110 00000  11111111100   


Q ss_pred             --CCcchhhhhcchhhHHHHHHHh-hCCCcceeehhhccc-----------cccccCCCcEEEE-EeCchhhhhhcC--C
Q 004021          230 --FSEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELGV-----------PLQMLNAGFKIVL-KTRSAGVCDQMD--S  292 (779)
Q Consensus       230 --~~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~~-----------~~~~~~~gs~Iiv-TTR~~~va~~~~--~  292 (779)
                        .............++...+... ..+++-.+.+|++-.           .+-......++|+ ||....+...+-  .
T Consensus        91 iEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~TIlSRC  170 (944)
T PRK14949         91 IEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVTVLSRC  170 (944)
T ss_pred             EEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHHHHHhh
Confidence              0000000011112222222211 122222344444311           1111123445554 444455543322  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ..|++.+|+.++....+.+.+......   --.+....|++.++|.|--+..
T Consensus       171 q~f~fkpLs~eEI~~~L~~il~~EgI~---~edeAL~lIA~~S~Gd~R~ALn  219 (944)
T PRK14949        171 LQFNLKSLTQDEIGTQLNHILTQEQLP---FEAEALTLLAKAANGSMRDALS  219 (944)
T ss_pred             eEEeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHH
Confidence            789999999999999998877554322   1256788999999998854443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.52  E-value=0.0036  Score=69.42  Aligned_cols=172  Identities=15%  Similarity=0.237  Sum_probs=100.1

Q ss_pred             ccccchhhh--HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCc
Q 004021          155 QTIVGQEKL--LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~  232 (779)
                      ..++|....  ...+..+.........-+.|+|..|+|||+|++++++.. .....--.+++++...+...+...+... 
T Consensus       123 ~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~-~~~~~~~~v~yi~~~~~~~~~~~~~~~~-  200 (450)
T PRK00149        123 NFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYI-LEKNPNAKVVYVTSEKFTNDFVNALRNN-  200 (450)
T ss_pred             ccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHH-HHhCCCCeEEEEEHHHHHHHHHHHHHcC-
Confidence            334665432  233333333322234568999999999999999999987 2111123466777766666665555321 


Q ss_pred             chhhhhcchhhHHHHHHHhhCCCcceeehhhcccc----------cc----ccCCCcEEEEEeCchh---------hhhh
Q 004021          233 DKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP----------LQ----MLNAGFKIVLKTRSAG---------VCDQ  289 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~----------~~----~~~~gs~IivTTR~~~---------va~~  289 (779)
                             ..    ..+.+.++.- -++.+|++...          +.    ....|..||+||....         +...
T Consensus       201 -------~~----~~~~~~~~~~-dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SR  268 (450)
T PRK00149        201 -------TM----EEFKEKYRSV-DVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSR  268 (450)
T ss_pred             -------cH----HHHHHHHhcC-CEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhH
Confidence                   11    2223333321 14455555211          00    0124556888886531         2223


Q ss_pred             cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          290 MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       290 ~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      +. ...+++++.+.++-..++.+.+.......+   +++..-|++.+.|..-.+.
T Consensus       269 l~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~---~e~l~~ia~~~~~~~R~l~  320 (450)
T PRK00149        269 FEWGLTVDIEPPDLETRIAILKKKAEEEGIDLP---DEVLEFIAKNITSNVRELE  320 (450)
T ss_pred             hcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHcCcCCCHHHHH
Confidence            33 457899999999999999998865432222   5778888888888766443

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

Probab=97.50  E-value=2.6e-05  Score=89.40  Aligned_cols=122  Identities=25%  Similarity=0.228  Sum_probs=83.5

Q ss_pred             chhhc-ccccCceeeecCCccc--ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC
Q 004021          529 PSRIS-SLVSLHHLDLSLTHIR--GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN  605 (779)
Q Consensus       529 p~~i~-~L~~L~~L~L~~~~i~--~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~  605 (779)
                      |..++ -|++|+.|.+++-.+.  ++-.-..++++|..||++++ .++.+ .+ +++|+||+.|.+.+-.+..       
T Consensus       140 ~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~T-nI~nl-~G-IS~LknLq~L~mrnLe~e~-------  209 (699)
T KOG3665|consen  140 PKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGT-NISNL-SG-ISRLKNLQVLSMRNLEFES-------  209 (699)
T ss_pred             HHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCC-CccCc-HH-HhccccHHHHhccCCCCCc-------
Confidence            44554 4689999999886442  24444678889999999999 67888 44 9999999999998766653       


Q ss_pred             ccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccc
Q 004021          606 VLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEME  669 (779)
Q Consensus       606 ~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~  669 (779)
                            ...+.+|-+|++|+.|++|........   +....-+..-..||+|+.|+.|+....+
T Consensus       210 ------~~~l~~LF~L~~L~vLDIS~~~~~~~~---~ii~qYlec~~~LpeLrfLDcSgTdi~~  264 (699)
T KOG3665|consen  210 ------YQDLIDLFNLKKLRVLDISRDKNNDDT---KIIEQYLECGMVLPELRFLDCSGTDINE  264 (699)
T ss_pred             ------hhhHHHHhcccCCCeeeccccccccch---HHHHHHHHhcccCccccEEecCCcchhH
Confidence                  456778889999999999854322111   0000011222347889999888754433

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

Probab=97.45  E-value=3.1e-05  Score=77.82  Aligned_cols=187  Identities=18%  Similarity=0.136  Sum_probs=110.4

Q ss_pred             cchhhcccccCceeeecCC----cccccchh-------hccCccCcEeeccCCcCCCCCchh---hhcCCccCcEeeecc
Q 004021          528 LPSRISSLVSLHHLDLSLT----HIRGLPQE-------LKALEKLRYLNLEYTHYLSIIPHQ---LISGFLKLEVLRLLE  593 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~----~i~~lp~~-------~~~L~~L~~L~l~~~~~l~~lp~~---~i~~L~~L~~L~l~~  593 (779)
                      +-+.+.+.++|+.-+++.-    -..++|+.       +-..++|++|+||.|-.-..-+++   .+.++++|++|.+.+
T Consensus        50 i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~N  129 (382)
T KOG1909|consen   50 IAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLNN  129 (382)
T ss_pred             HHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeeccccccCccchHHHHHHHHhccCHHHHhhhc
Confidence            4455667778888888753    12345554       456679999999999554343433   367889999999999


Q ss_pred             ccCCCccccc-CCccCCCchhhHHhhcCCCCCCceeEEeecccc---------cccCCCCCccc-------C-------c
Q 004021          594 CGSEGVTKEE-GNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA---------VQKFFKYPKLD-------L-------T  649 (779)
Q Consensus       594 ~~~~~~~~~~-~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~---------~~~~~~L~~L~-------~-------~  649 (779)
                      |++...--.. +.-+-.  -......++-++|+.+....|....         +..++.|+.+.       +       .
T Consensus       130 ~Glg~~ag~~l~~al~~--l~~~kk~~~~~~Lrv~i~~rNrlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~e  207 (382)
T KOG1909|consen  130 CGLGPEAGGRLGRALFE--LAVNKKAASKPKLRVFICGRNRLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAE  207 (382)
T ss_pred             CCCChhHHHHHHHHHHH--HHHHhccCCCcceEEEEeeccccccccHHHHHHHHHhccccceEEEecccccCchhHHHHH
Confidence            9876410000 000000  0012223455788888888765532         24455666551       1       2


Q ss_pred             ccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc-----C-CCCCCCCccE
Q 004021          650 WLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY-----P-NPLHFPKLKK  723 (779)
Q Consensus       650 ~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~-----~-~~~~l~~L~~  723 (779)
                      .+.++|+|+.|+|..|.....--.        .+.    ..+..||+|+.|++.+|. ++.=-     . -....|+|+.
T Consensus       208 al~~~~~LevLdl~DNtft~egs~--------~La----kaL~s~~~L~El~l~dcl-l~~~Ga~a~~~al~~~~p~L~v  274 (382)
T KOG1909|consen  208 ALEHCPHLEVLDLRDNTFTLEGSV--------ALA----KALSSWPHLRELNLGDCL-LENEGAIAFVDALKESAPSLEV  274 (382)
T ss_pred             HHHhCCcceeeecccchhhhHHHH--------HHH----HHhcccchheeecccccc-cccccHHHHHHHHhccCCCCce
Confidence            345788888888888654322100        000    245678888889888873 32211     0 1224788888


Q ss_pred             EeeeCC
Q 004021          724 IGVYGC  729 (779)
Q Consensus       724 L~l~~c  729 (779)
                      |.+.+|
T Consensus       275 l~l~gN  280 (382)
T KOG1909|consen  275 LELAGN  280 (382)
T ss_pred             eccCcc
Confidence            888776

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.43  E-value=0.0027  Score=69.99  Aligned_cols=180  Identities=16%  Similarity=0.169  Sum_probs=93.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccC-CCCEEEEEEechHHHHHHH------
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQH-NFDVVIWAAVQTFQDDIGK------  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-~F~~~~wv~v~~i~~~i~~------  226 (779)
                      .+++|.+.....|...+..+  .+ ..+-++|++|+||||+|+.+++....... .+..+ -.  ......+..      
T Consensus        14 ~divGq~~i~~~L~~~i~~~--~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc-~~--c~~c~~i~~g~~~dv   88 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKN--SISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPC-NE--CRACRSIDEGTFMDV   88 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcC--CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCC-cc--cHHHHHHhcCCCCcc
Confidence            56899998888888877766  44 56889999999999999999887511000 00000 00  000001100      


Q ss_pred             -HhCCCcchhhhhcchhhHHHHHHHhhC-----CCcceeehhhc-----------cccccccCCCcEEEE-EeCchhhhh
Q 004021          227 -RIGFSEDKKWKEKSLQDKAVDISSILS-----PKKFRIDLTEL-----------GVPLQMLNAGFKIVL-KTRSAGVCD  288 (779)
Q Consensus       227 -~l~~~~~~~~~~~~~~~~~~~l~~~L~-----~kr~~~~ld~l-----------~~~~~~~~~gs~Iiv-TTR~~~va~  288 (779)
                       .+...     .....++ ...+.+...     +++-.+.+|++           ...+........+|+ ||....+..
T Consensus        89 ~el~aa-----~~~gid~-iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~Ilattn~~kl~~  162 (472)
T PRK14962         89 IELDAA-----SNRGIDE-IRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPP  162 (472)
T ss_pred             EEEeCc-----ccCCHHH-HHHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEEEEEeCChHhhhH
Confidence             00000     0000111 111111111     11112223322           111111122333333 443344544


Q ss_pred             hcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHHHH
Q 004021          289 QMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVGRA  348 (779)
Q Consensus       289 ~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g~~  348 (779)
                      ...  ...+.+.+++.++....+.+.+...+..-+   ++....|++.++| ++.|+..+-.+
T Consensus       163 ~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i~---~eal~~Ia~~s~GdlR~aln~Le~l  222 (472)
T PRK14962        163 TIISRCQVIEFRNISDELIIKRLQEVAEAEGIEID---REALSFIAKRASGGLRDALTMLEQV  222 (472)
T ss_pred             HHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            333  568899999999999998888755432222   5667888988865 56776666543

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.004  Score=69.41  Aligned_cols=173  Identities=15%  Similarity=0.113  Sum_probs=95.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc---C---------------CCCEEEEEE
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ---H---------------NFDVVIWAA  216 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~---------------~F~~~~wv~  216 (779)
                      .+++|.+..++.+...+..+. -...+-++|+.|+||||+|+.+++......   .               .|...+++.
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieid   94 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEID   94 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEee
Confidence            458999999999999987652 335678999999999999999987651100   0               111111211


Q ss_pred             echHHHHHHHHhCCCcchhhhhcchhhHHHHHHHh-hCCCcceeehhhcc-----------ccccccCCCcEEE-EEeCc
Q 004021          217 VQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELG-----------VPLQMLNAGFKIV-LKTRS  283 (779)
Q Consensus       217 v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~  283 (779)
                      ..       ..        ....+..+....+... ..+++-...+|++.           ..+......+.+| +||..
T Consensus        95 aa-------s~--------~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Ttd~  159 (546)
T PRK14957         95 AA-------SR--------TGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDY  159 (546)
T ss_pred             cc-------cc--------cCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEECCh
Confidence            10       00        0001111222222111 11222233333321           1111122344444 56555


Q ss_pred             hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHHHHHH
Q 004021          284 AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LALKTVG  346 (779)
Q Consensus       284 ~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai~~~g  346 (779)
                      ..+.....  ...+++.+++.++....+.+.+...+...   -++....|++.++|-+ -|+..+-
T Consensus       160 ~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi~~---e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        160 HKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINS---DEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             hhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            55543332  67889999999998888887665543222   2566788999999965 4554443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.38  E-value=0.0026  Score=72.02  Aligned_cols=183  Identities=13%  Similarity=0.103  Sum_probs=97.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhC----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIG----  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~----  229 (779)
                      .++||.+..++.|.+.+..+. -...+-++|..|+||||+|+.+++.... ...+...  -|- -..+..|...-.    
T Consensus        16 ~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c-~~~~~~~--pCg~C~~C~~i~~g~~~D~i   91 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNC-ETGITAT--PCGECDNCREIEQGRFVDLI   91 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhh-ccCCCCC--CCCCCHHHHHHHcCCCCCce
Confidence            568999999999999888762 2345789999999999999999887621 1110000  000 122222221100    


Q ss_pred             -CCcchhhhhcchhhHHHHHHHh-hCCCcceeehhhcc-----------ccccccCCCcE-EEEEeCchhhhhhcC--Cc
Q 004021          230 -FSEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELG-----------VPLQMLNAGFK-IVLKTRSAGVCDQMD--SK  293 (779)
Q Consensus       230 -~~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~-----------~~~~~~~~gs~-IivTTR~~~va~~~~--~~  293 (779)
                       ..........+..++...+... ..+++-...+|++.           ..+-......+ |++||....+...+-  ..
T Consensus        92 eidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~TI~SRC~  171 (647)
T PRK07994         92 EIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL  171 (647)
T ss_pred             eecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchHHHhhhe
Confidence             0000000111112222222111 12222233334331           11111123344 445555555543332  67


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      .|.+.+|+.++....+.+.+.......   -.+....|++.++|.+--+..
T Consensus       172 ~~~f~~Ls~~ei~~~L~~il~~e~i~~---e~~aL~~Ia~~s~Gs~R~Al~  219 (647)
T PRK07994        172 QFHLKALDVEQIRQQLEHILQAEQIPF---EPRALQLLARAADGSMRDALS  219 (647)
T ss_pred             EeeCCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHH
Confidence            899999999999999988775443222   245678899999997764443

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

Probab=97.38  E-value=0.00024  Score=66.15  Aligned_cols=56  Identities=25%  Similarity=0.271  Sum_probs=23.4

Q ss_pred             eeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          540 HLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       540 ~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      .+||++|.+..++ .|..+..|++|.+++| .+..+.+..-.-+++|..|.+.+|.+.
T Consensus        46 ~iDLtdNdl~~l~-~lp~l~rL~tLll~nN-rIt~I~p~L~~~~p~l~~L~LtnNsi~  101 (233)
T KOG1644|consen   46 AIDLTDNDLRKLD-NLPHLPRLHTLLLNNN-RITRIDPDLDTFLPNLKTLILTNNSIQ  101 (233)
T ss_pred             eecccccchhhcc-cCCCccccceEEecCC-cceeeccchhhhccccceEEecCcchh
Confidence            3444444443332 2334444444444444 344444431122334555555544433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.38  E-value=0.0032  Score=69.69  Aligned_cols=183  Identities=16%  Similarity=0.107  Sum_probs=97.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEE-Ee-chHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWA-AV-QTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv-~v-~~i~~~i~~~l~~~  231 (779)
                      .+++|.+..+..+...+..+. -...+-++|..|+||||+|+.+++.. .-...... ..+. |- ......|.......
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~L-nc~~~~~~~~~~~~C~~C~~C~~i~~~~h~D   98 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAV-NCSALITENTTIKTCEQCTNCISFNNHNHPD   98 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHh-cCccccccCcCcCCCCCChHHHHHhcCCCCc
Confidence            457999999999888777662 33578899999999999999999876 21111100 0000 00 11111111110000


Q ss_pred             -----cchhhhhcchhhHHHHHHHh-hCCCcceeehhhcc-----------ccccccCCCcEEE-EEeCchhhhhhcC--
Q 004021          232 -----EDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELG-----------VPLQMLNAGFKIV-LKTRSAGVCDQMD--  291 (779)
Q Consensus       232 -----~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~~~va~~~~--  291 (779)
                           ........+..+..+..... ..+++-...+|++.           ..+......+.+| +||+...+.....  
T Consensus        99 v~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~tI~SR  178 (507)
T PRK06645         99 IIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISR  178 (507)
T ss_pred             EEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhHHHHhc
Confidence                 00000011111111111110 11222233444431           1122222344544 4666566655443  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ...+++.+++.++....+.+.+...+...+   .+....|++.++|.+--+
T Consensus       179 c~~~ef~~ls~~el~~~L~~i~~~egi~ie---~eAL~~Ia~~s~GslR~a  226 (507)
T PRK06645        179 CQRYDLRRLSFEEIFKLLEYITKQENLKTD---IEALRIIAYKSEGSARDA  226 (507)
T ss_pred             ceEEEccCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHH
Confidence            567899999999999999998876542222   456788999999977444

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=97.37  E-value=0.0022  Score=69.64  Aligned_cols=48  Identities=31%  Similarity=0.328  Sum_probs=37.9

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..+++|.+.+.-.           -...+-|.++|.+|+|||++|+++++..
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el  241 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET  241 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            35689999999888876421           1234568899999999999999999976

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

Probab=97.36  E-value=2.3e-05  Score=67.91  Aligned_cols=78  Identities=29%  Similarity=0.494  Sum_probs=42.5

Q ss_pred             ccccccccccccchhhcc-cccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISS-LVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~-L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .+|++| .+..+|+.|.. .+.+..|++.+|.|+.+|.++..++.|+.|+++.| .+...|.- |..|.+|-.|+..+|.
T Consensus        58 i~ls~N-~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N-~l~~~p~v-i~~L~~l~~Lds~~na  134 (177)
T KOG4579|consen   58 ISLSDN-GFKKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFN-PLNAEPRV-IAPLIKLDMLDSPENA  134 (177)
T ss_pred             Eecccc-hhhhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccC-ccccchHH-HHHHHhHHHhcCCCCc
Confidence            455555 55555555433 23555556666666666655555666666666555 34555553 4445555555555544


Q ss_pred             CC
Q 004021          596 SE  597 (779)
Q Consensus       596 ~~  597 (779)
                      ..
T Consensus       135 ~~  136 (177)
T KOG4579|consen  135 RA  136 (177)
T ss_pred             cc
Confidence            33

>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=97.36  E-value=0.00015  Score=50.87  Aligned_cols=36  Identities=36%  Similarity=0.573  Sum_probs=30.3

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccch
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ  553 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~  553 (779)
                      |++++| .++.+|..|++|++|++|++++|.|+.+|.
T Consensus         6 L~l~~N-~i~~l~~~l~~l~~L~~L~l~~N~i~~i~~   41 (44)
T PF12799_consen    6 LDLSNN-QITDLPPELSNLPNLETLNLSNNPISDISP   41 (44)
T ss_dssp             EEETSS-S-SSHGGHGTTCTTSSEEEETSSCCSBEGG
T ss_pred             EEccCC-CCcccCchHhCCCCCCEEEecCCCCCCCcC
Confidence            566777 888898889999999999999999988763

...

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.36  E-value=0.03  Score=62.81  Aligned_cols=147  Identities=16%  Similarity=0.206  Sum_probs=89.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcce
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFR  258 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~  258 (779)
                      ..+.|+|..|+|||.|++++++... ....--.+++++..++..++...+...        .    ...+.+.+++-. +
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~-~~~~g~~V~Yitaeef~~el~~al~~~--------~----~~~f~~~y~~~D-L  380 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYAR-RLYPGTRVRYVSSEEFTNEFINSIRDG--------K----GDSFRRRYREMD-I  380 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHH-HhCCCCeEEEeeHHHHHHHHHHHHHhc--------c----HHHHHHHhhcCC-E
Confidence            4589999999999999999999872 111123466777766666665544321        1    111222222211 3


Q ss_pred             eehhhcccc-------------cc-ccCCCcEEEEEeCch---------hhhhhcC-CceeEccCCChHHHHHHHHHHhh
Q 004021          259 IDLTELGVP-------------LQ-MLNAGFKIVLKTRSA---------GVCDQMD-SKNLEVYSLAHDEAWKLFQEMIE  314 (779)
Q Consensus       259 ~~ld~l~~~-------------~~-~~~~gs~IivTTR~~---------~va~~~~-~~~~~l~~L~~~~a~~Lf~~~a~  314 (779)
                      +.+|++...             +. ....|..|||||+..         .+...+. .-.+++++.+.+.-..++.+++.
T Consensus       381 LlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        381 LLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             EEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence            444554211             00 013466799998862         2233333 56789999999999999999886


Q ss_pred             ccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          315 RSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       315 ~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ......+   +++..-|++.+.+..-.+
T Consensus       461 ~r~l~l~---~eVi~yLa~r~~rnvR~L  485 (617)
T PRK14086        461 QEQLNAP---PEVLEFIASRISRNIREL  485 (617)
T ss_pred             hcCCCCC---HHHHHHHHHhccCCHHHH
Confidence            6543332   566777777776654433

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

Probab=97.36  E-value=0.00033  Score=63.24  Aligned_cols=85  Identities=20%  Similarity=0.336  Sum_probs=54.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccc--cCCCCEEEEEEe------chHHHHHHHHhCCCcchhhhhcchhhHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQ--QHNFDVVIWAAV------QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDI  248 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~--~~~F~~~~wv~v------~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l  248 (779)
                      +.+++.|+|.+|+|||++++.+.+.....  ...-..++|+.+      ..+...|+..++....   ...+..++...+
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~l~~~~   79 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLK---SRQTSDELRSLL   79 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSS---STS-HHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCcccc---ccCCHHHHHHHH
Confidence            45789999999999999999999876210  001345668888      5788889988887622   134556666777


Q ss_pred             HHhhCCCcc-eeehhhc
Q 004021          249 SSILSPKKF-RIDLTEL  264 (779)
Q Consensus       249 ~~~L~~kr~-~~~ld~l  264 (779)
                      .+.+...+. .+++|++
T Consensus        80 ~~~l~~~~~~~lviDe~   96 (131)
T PF13401_consen   80 IDALDRRRVVLLVIDEA   96 (131)
T ss_dssp             HHHHHHCTEEEEEEETT
T ss_pred             HHHHHhcCCeEEEEeCh
Confidence            777776655 5555554

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.35  E-value=0.0039  Score=70.48  Aligned_cols=184  Identities=16%  Similarity=0.167  Sum_probs=95.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEEEe--chHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAV--QTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv~v--~~i~~~i~~~l~~~  231 (779)
                      .++||-+..++.|.+++..+. -...+-++|..|+||||+|+.+++..--.. ....+...-..  -..+..|...-..+
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D   94 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVD   94 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCc
Confidence            458999998999999888762 335678999999999999999977651000 00000000000  11222221100000


Q ss_pred             cchhhhhcchhhHHHHHHHhhC-------CCcc-eeehhhcc-----------ccccccCCCcEEEE-EeCchhhhhhcC
Q 004021          232 EDKKWKEKSLQDKAVDISSILS-------PKKF-RIDLTELG-----------VPLQMLNAGFKIVL-KTRSAGVCDQMD  291 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L~-------~kr~-~~~ld~l~-----------~~~~~~~~gs~Iiv-TTR~~~va~~~~  291 (779)
                       -...+.. ....++.+++.+.       ..+| ...+|++.           ..+.......++|+ ||....+....-
T Consensus        95 -~~eldaa-s~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~TIl  172 (618)
T PRK14951         95 -YTELDAA-SNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVL  172 (618)
T ss_pred             -eeecCcc-cccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHHHH
Confidence             0000000 0001111222221       1223 33334331           11111123445554 444444443322


Q ss_pred             --CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          292 --SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       292 --~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                        ...+++++++.++....+.+.+...+...+   .+....|++.++|.+--+..
T Consensus       173 SRc~~~~f~~Ls~eei~~~L~~i~~~egi~ie---~~AL~~La~~s~GslR~al~  224 (618)
T PRK14951        173 SRCLQFNLRPMAPETVLEHLTQVLAAENVPAE---PQALRLLARAARGSMRDALS  224 (618)
T ss_pred             HhceeeecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence              578999999999999999888765543222   46678899999997754443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.33  E-value=0.00027  Score=73.84  Aligned_cols=49  Identities=18%  Similarity=0.170  Sum_probs=37.9

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++++.+..= +.-+...|+|.+|+||||||+.+|+.. .. .+|+.++||.+
T Consensus       158 rvID~l~PI-GkGQR~lIvgppGvGKTTLaK~Ian~I-~~-nhFDv~~~VvL  206 (416)
T PRK09376        158 RIIDLIAPI-GKGQRGLIVAPPKAGKTVLLQNIANSI-TT-NHPEVHLIVLL  206 (416)
T ss_pred             eeeeeeccc-ccCceEEEeCCCCCChhHHHHHHHHHH-Hh-hcCCeEEEEEE
Confidence            344444331 134678999999999999999999988 43 38999999998

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

Probab=97.32  E-value=3.1e-05  Score=75.93  Aligned_cols=175  Identities=18%  Similarity=0.119  Sum_probs=111.0

Q ss_pred             CccEEEccccccccc------ccCccc--ccccccccccc-cchhhcccccCceeeecCC-ccccc--chhhccCccCcE
Q 004021          496 GAKRISLMANEIESL------SEIPTL--LSLRRNDSLTE-LPSRISSLVSLHHLDLSLT-HIRGL--PQELKALEKLRY  563 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l------~~~~~l--L~L~~~~~l~~-lp~~i~~L~~L~~L~L~~~-~i~~l--p~~~~~L~~L~~  563 (779)
                      .++++++++..|+.-      .....|  |+|.|+ .+.. +-..|.+=.+|+.|+|+.| ++++.  ---+.+++.|..
T Consensus       186 Rlq~lDLS~s~it~stl~~iLs~C~kLk~lSlEg~-~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~ll~~scs~L~~  264 (419)
T KOG2120|consen  186 RLQHLDLSNSVITVSTLHGILSQCSKLKNLSLEGL-RLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQLLLSSCSRLDE  264 (419)
T ss_pred             hhHHhhcchhheeHHHHHHHHHHHHhhhhcccccc-ccCcHHHHHHhccccceeeccccccccchhHHHHHHHhhhhHhh
Confidence            577888887766431      111112  777777 5543 4556778899999999998 67653  234789999999


Q ss_pred             eeccCCcCCCCCchhhhcC-CccCcEeeeccccCCCcccccCCccCCCchhhHHhh-cCCCCCCceeEEeecccccccCC
Q 004021          564 LNLEYTHYLSIIPHQLISG-FLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMREL-LGLKRLNVLSWSFRSSLAVQKFF  641 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~-L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~L~~L~~L~l~~~~~~~~~~~~  641 (779)
                      |+|++|......-.-.+.. =.+|..|+++|+.-.-            ....+..| ..+++|.+|+++.+..       
T Consensus       265 LNlsWc~l~~~~Vtv~V~hise~l~~LNlsG~rrnl------------~~sh~~tL~~rcp~l~~LDLSD~v~-------  325 (419)
T KOG2120|consen  265 LNLSWCFLFTEKVTVAVAHISETLTQLNLSGYRRNL------------QKSHLSTLVRRCPNLVHLDLSDSVM-------  325 (419)
T ss_pred             cCchHhhccchhhhHHHhhhchhhhhhhhhhhHhhh------------hhhHHHHHHHhCCceeeeccccccc-------
Confidence            9999994332221111111 2468888999875431            01223333 4678999999985432       


Q ss_pred             CCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCC
Q 004021          642 KYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGP  706 (779)
Q Consensus       642 ~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~  706 (779)
                       |+.=....+.+++.|++|.++.|..+.   +.       .+     -.+...|+|.+|++.+|-
T Consensus       326 -l~~~~~~~~~kf~~L~~lSlsRCY~i~---p~-------~~-----~~l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  326 -LKNDCFQEFFKFNYLQHLSLSRCYDII---PE-------TL-----LELNSKPSLVYLDVFGCV  374 (419)
T ss_pred             -cCchHHHHHHhcchheeeehhhhcCCC---hH-------He-----eeeccCcceEEEEecccc
Confidence             111112345678999999999986532   21       00     256788999999999873

>TIGR00763 lon ATP-dependent protease La

Probab=97.31  E-value=0.015  Score=68.89  Aligned_cols=49  Identities=29%  Similarity=0.412  Sum_probs=39.7

Q ss_pred             cccccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++|.++.++.|.+++...    ....+++.++|++|+|||++|+.+++..
T Consensus       319 ~~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l  371 (775)
T TIGR00763       319 DEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL  371 (775)
T ss_pred             hhhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            345789999999999876532    2234589999999999999999999886

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.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.31  E-value=0.0049  Score=66.38  Aligned_cols=167  Identities=14%  Similarity=0.177  Sum_probs=95.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc-c------------------CCCCEEEEE
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ-Q------------------HNFDVVIWA  215 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~------------------~~F~~~~wv  215 (779)
                      ..++|.+..++.+.+++..+. -...+-++|.+|+||||+|+.++...... .                  .+++. +++
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~~   91 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IEI   91 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEe
Confidence            457999999999999987662 23577899999999999999998775110 0                  12222 122


Q ss_pred             Eec-----hHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhc-----------cccccccCCCcEEEE
Q 004021          216 AVQ-----TFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTEL-----------GVPLQMLNAGFKIVL  279 (779)
Q Consensus       216 ~v~-----~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l-----------~~~~~~~~~gs~Iiv  279 (779)
                      ...     +-.+++...+...                  ....++| .+.+|++           ...+......+.+|+
T Consensus        92 ~~~~~~~~~~~~~l~~~~~~~------------------p~~~~~~-vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl  152 (355)
T TIGR02397        92 DAASNNGVDDIREILDNVKYA------------------PSSGKYK-VYIIDEVHMLSKSAFNALLKTLEEPPEHVVFIL  152 (355)
T ss_pred             eccccCCHHHHHHHHHHHhcC------------------cccCCce-EEEEeChhhcCHHHHHHHHHHHhCCccceeEEE
Confidence            110     0111222211110                  0011122 1222221           111212224556666


Q ss_pred             EeCchh-hhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          280 KTRSAG-VCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       280 TTR~~~-va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      +|.+.. +.....  ...+++.++++++....+...+...+...+   ++.+..+++.++|.|..+...
T Consensus       153 ~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i~---~~a~~~l~~~~~g~~~~a~~~  218 (355)
T TIGR02397       153 ATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIE---DEALELIARAADGSLRDALSL  218 (355)
T ss_pred             EeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCChHHHHHH
Confidence            665433 333322  467889999999999998887765442222   477888999999988766543

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.30  E-value=0.0027  Score=69.08  Aligned_cols=180  Identities=12%  Similarity=0.097  Sum_probs=95.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEE-----e--chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA-----V--QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~-----v--~~i~~~i~~  226 (779)
                      .+++|.+..++.|.+++..+  .+ ..+-++|+.|+||||+|..+++.. .-...++...|..     .  -.....+..
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~--~~~ha~lf~Gp~G~GKtt~A~~~a~~l-~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~   92 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMG--RVGHGYIFSGLRGVGKTTAARVFAKAV-NCQRMIDDADYLQEVTEPCGECESCRDFDA   92 (397)
T ss_pred             hhccChHHHHHHHHHHHHhC--CcceeEEEECCCCCCHHHHHHHHHHHh-cCCCCcCcccccccCCCCCCCCHHHHHHhc
Confidence            46899999999998888876  44 458899999999999999998876 2111111000000     0  011111111


Q ss_pred             HhCCCcchhh---hhcchhhHHHHHHHhhC------CCcceeehhhc-----------cccccccCCCcEEEEE-eCchh
Q 004021          227 RIGFSEDKKW---KEKSLQDKAVDISSILS------PKKFRIDLTEL-----------GVPLQMLNAGFKIVLK-TRSAG  285 (779)
Q Consensus       227 ~l~~~~~~~~---~~~~~~~~~~~l~~~L~------~kr~~~~ld~l-----------~~~~~~~~~gs~IivT-TR~~~  285 (779)
                      .-..+ -...   .....++. ..+.+.+.      ++|. +..|++           ...+....+.+.+|++ ++...
T Consensus        93 ~~~~n-~~~~~~~~~~~id~I-r~l~~~~~~~p~~~~~kv-vIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~k  169 (397)
T PRK14955         93 GTSLN-ISEFDAASNNSVDDI-RLLRENVRYGPQKGRYRV-YIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHK  169 (397)
T ss_pred             CCCCC-eEeecccccCCHHHH-HHHHHHHhhchhcCCeEE-EEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHH
Confidence            10000 0000   00011111 12223332      2222 222222           1122222345555554 45455


Q ss_pred             hhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          286 VCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       286 va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      +.....  ...+++.++++++....+...+...+..-   -.+.+..|++.++|.+--+.
T Consensus       170 l~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~i---~~~al~~l~~~s~g~lr~a~  226 (397)
T PRK14955        170 IPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISV---DADALQLIGRKAQGSMRDAQ  226 (397)
T ss_pred             hHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHH
Confidence            544333  46789999999999888888775433222   25778999999999775443

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

Probab=97.27  E-value=5e-05  Score=65.91  Aligned_cols=81  Identities=22%  Similarity=0.340  Sum_probs=63.3

Q ss_pred             CccEEEcccccccccccCcc-------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccC
Q 004021          496 GAKRISLMANEIESLSEIPT-------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEY  568 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~-------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~  568 (779)
                      .+..+++++|.++.+|....       .|+|++| .+..+|..+..++.|+.|+++.|.+...|..|..|.+|-.|+..+
T Consensus        54 el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~n-eisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~~L~~l~~Lds~~  132 (177)
T KOG4579|consen   54 ELTKISLSDNGFKKFPKKFTIKFPTATTLNLANN-EISDVPEELAAMPALRSLNLRFNPLNAEPRVIAPLIKLDMLDSPE  132 (177)
T ss_pred             eEEEEecccchhhhCCHHHhhccchhhhhhcchh-hhhhchHHHhhhHHhhhcccccCccccchHHHHHHHhHHHhcCCC
Confidence            55667888888877665321       4888888 888888888888888888888888888888888888888888888


Q ss_pred             CcCCCCCchh
Q 004021          569 THYLSIIPHQ  578 (779)
Q Consensus       569 ~~~l~~lp~~  578 (779)
                      | ....+|-.
T Consensus       133 n-a~~eid~d  141 (177)
T KOG4579|consen  133 N-ARAEIDVD  141 (177)
T ss_pred             C-ccccCcHH
Confidence            7 55666665

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.27  E-value=0.0039  Score=68.49  Aligned_cols=180  Identities=14%  Similarity=0.096  Sum_probs=93.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~  232 (779)
                      .++||.+..++.+.+.+..+  .+ ..+-++|..|+||||+|+.+++.. .-....+.-  -|- -.....|......+.
T Consensus        13 ~dliGQe~vv~~L~~a~~~~--ri~ha~Lf~Gp~G~GKTT~ArilAk~L-nC~~~~~~~--pCg~C~~C~~i~~~~~~Dv   87 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLN--KIPQSILLVGASGVGKTTCARIISLCL-NCSNGPTSD--PCGTCHNCISIKNSNHPDV   87 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcC--CCCceEEEECCCCccHHHHHHHHHHHH-cCcCCCCCC--CccccHHHHHHhccCCCCE
Confidence            56899999999888888766  44 478899999999999999998743 100000000  000 011111111110000


Q ss_pred             -----chhhhhcchhhHHHHHHHhhCCCcc-eeehhhc-----------cccccccCCCcEEEE-EeCchhhhhhcC--C
Q 004021          233 -----DKKWKEKSLQDKAVDISSILSPKKF-RIDLTEL-----------GVPLQMLNAGFKIVL-KTRSAGVCDQMD--S  292 (779)
Q Consensus       233 -----~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l-----------~~~~~~~~~gs~Iiv-TTR~~~va~~~~--~  292 (779)
                           .......+..+..+.....=-..+| ...+|++           ...+....+.+++|+ ||....+...+.  .
T Consensus        88 ~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~tI~SRc  167 (491)
T PRK14964         88 IEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRC  167 (491)
T ss_pred             EEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHHHHHHHhh
Confidence                 0000000111111111100001111 2222222           111111224455555 444455554433  6


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ..+.+.+++.++....+.+.+...+..-+   ++....|++.++|.+-.+
T Consensus       168 ~~~~f~~l~~~el~~~L~~ia~~Egi~i~---~eAL~lIa~~s~GslR~a  214 (491)
T PRK14964        168 QRFDLQKIPTDKLVEHLVDIAKKENIEHD---EESLKLIAENSSGSMRNA  214 (491)
T ss_pred             eeeecccccHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHH
Confidence            78899999999999999988876542222   566788999999877544

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.26  E-value=0.006  Score=65.61  Aligned_cols=164  Identities=12%  Similarity=0.086  Sum_probs=91.2

Q ss_pred             ccccchhhhHHHHHHHHhccCC--------CceEEEEEcCCCCcHHHHHHHHHhhhccc------------------cCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQK--------NRGIIGLYGIGGVGKTTLLKQVNNNFCHQ------------------QHN  208 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vi~I~G~gGvGKTtLA~~v~~~~~~~------------------~~~  208 (779)
                      ..++|.+..++.|.+.+..+..        -..-+-++|+.|+|||++|+.+++...-.                  ..|
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~h   84 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTH   84 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCC
Confidence            4579999999999999987521        24568899999999999999998754110                  011


Q ss_pred             CCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhC-----CCcceeehhhc-----------cccccccC
Q 004021          209 FDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILS-----PKKFRIDLTEL-----------GVPLQMLN  272 (779)
Q Consensus       209 F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~-----~kr~~~~ld~l-----------~~~~~~~~  272 (779)
                      .|. .++...              .   .....++ +..+.+...     +++-...+|++           ...+....
T Consensus        85 pD~-~~i~~~--------------~---~~i~i~~-iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep~  145 (394)
T PRK07940         85 PDV-RVVAPE--------------G---LSIGVDE-VRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEPP  145 (394)
T ss_pred             CCE-EEeccc--------------c---ccCCHHH-HHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcCC
Confidence            111 111110              0   0001111 111222211     11111222221           11111122


Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .+..+|++|.+ ..+....-  ...+.+.+++.++..+.+.+..+.     +   .+.+..+++.++|.|.....+
T Consensus       146 ~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~-----~---~~~a~~la~~s~G~~~~A~~l  213 (394)
T PRK07940        146 PRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV-----D---PETARRAARASQGHIGRARRL  213 (394)
T ss_pred             CCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC-----C---HHHHHHHHHHcCCCHHHHHHH
Confidence            35555655555 45544433  678899999999998888744311     1   456788999999999755443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.25  E-value=0.0051  Score=68.58  Aligned_cols=182  Identities=14%  Similarity=0.108  Sum_probs=93.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhC----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIG----  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~----  229 (779)
                      .++||-+..++.|.+++..+. -...+-++|+.|+||||+|+.+++.. .-...++..  -|- -.....|...-.    
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk~l-~c~~~~~~~--pCg~C~~C~~i~~g~~~d~~   91 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAKCL-NCEKGVSAN--PCNDCENCREIDEGRFPDLF   91 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHHHh-cCCCCCCcc--cCCCCHHHHHHhcCCCceEE
Confidence            458999999999999998762 23467899999999999999998866 111111100  000 011111110000    


Q ss_pred             -CCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhcc-----------ccccccCCCcEEEEE-eCchhhhhhcC--Cc
Q 004021          230 -FSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELG-----------VPLQMLNAGFKIVLK-TRSAGVCDQMD--SK  293 (779)
Q Consensus       230 -~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~-----------~~~~~~~~gs~IivT-TR~~~va~~~~--~~  293 (779)
                       ..........+..+....+...-...+| ...+|++.           ..+......+++|++ |....+.....  ..
T Consensus        92 eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd~~kl~~tI~SRc~  171 (509)
T PRK14958         92 EVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCL  171 (509)
T ss_pred             EEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECChHhchHHHHHHhh
Confidence             0000000001111111111111111233 22233321           111111234555554 44444443332  56


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .+++++++.++....+.+.+...+...+   .+....|++.++|.+.-+.
T Consensus       172 ~~~f~~l~~~~i~~~l~~il~~egi~~~---~~al~~ia~~s~GslR~al  218 (509)
T PRK14958        172 QFHLAQLPPLQIAAHCQHLLKEENVEFE---NAALDLLARAANGSVRDAL  218 (509)
T ss_pred             hhhcCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCcHHHHH
Confidence            7889999999988887777665442221   4567789999999775444

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.23  E-value=0.0072  Score=64.03  Aligned_cols=184  Identities=15%  Similarity=0.107  Sum_probs=100.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEE-Ee--chHHHHHHHH---
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWA-AV--QTFQDDIGKR---  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv-~v--~~i~~~i~~~---  227 (779)
                      ..++|.++..+.+...+..+. -...+-|+|..|+||||+|..+++...... ..+...... ..  ....+.|...   
T Consensus        23 ~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i~~~~hP  101 (351)
T PRK09112         23 TRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQIAQGAHP  101 (351)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHHHcCCCC
Confidence            568999999999999998772 334688999999999999999988762100 001111000 00  1233333221   


Q ss_pred             ----hCCCcchhh----hhcchhhHHHHHHHhhCC-----Ccceeehhhcc-----------ccccccCCCcE-EEEEeC
Q 004021          228 ----IGFSEDKKW----KEKSLQDKAVDISSILSP-----KKFRIDLTELG-----------VPLQMLNAGFK-IVLKTR  282 (779)
Q Consensus       228 ----l~~~~~~~~----~~~~~~~~~~~l~~~L~~-----kr~~~~ld~l~-----------~~~~~~~~gs~-IivTTR  282 (779)
                          +..+.++..    .....++ +..+.+++..     ++-.+.+|++.           ..+.....+.. |++|++
T Consensus       102 dl~~l~~~~~~~~~~~~~~I~vd~-iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~~~fiLit~~  180 (351)
T PRK09112        102 NLLHITRPFDEKTGKFKTAITVDE-IRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHS  180 (351)
T ss_pred             CEEEeecccccccccccccCCHHH-HHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCCceEEEEECC
Confidence                111000000    0111222 2344444432     22233333321           11111122344 455544


Q ss_pred             chhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          283 SAGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       283 ~~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      -..+.....  ...+.+.+++.++..+++.+.... .   . --.+....|++.++|.|.....+
T Consensus       181 ~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~-~---~-~~~~~~~~i~~~s~G~pr~Al~l  240 (351)
T PRK09112        181 SGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSS-Q---G-SDGEITEALLQRSKGSVRKALLL  240 (351)
T ss_pred             hhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcc-c---C-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            444443333  578999999999999999874321 1   1 11455788999999999866544

>PF14516 AAA_35: AAA-like domain

Probab=97.22  E-value=0.093  Score=55.51  Aligned_cols=185  Identities=16%  Similarity=0.203  Sum_probs=110.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---------------ch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---------------QT  219 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---------------~~  219 (779)
                      +..|+|...-+++.+.|.+.   ...+.|.|+-.+|||+|...+.+.. . +..+ .++++++               ..
T Consensus        11 ~~Yi~R~~~e~~~~~~i~~~---G~~~~I~apRq~GKTSll~~l~~~l-~-~~~~-~~v~id~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen   11 PFYIERPPAEQECYQEIVQP---GSYIRIKAPRQMGKTSLLLRLLERL-Q-QQGY-RCVYIDLQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             CcccCchHHHHHHHHHHhcC---CCEEEEECcccCCHHHHHHHHHHHH-H-HCCC-EEEEEEeecCCCcccCCHHHHHHH
Confidence            45689987788888888763   2689999999999999999998877 3 2344 3446666               23


Q ss_pred             HHHHHHHHhCCCc--chhhhh--cchhhHHHHHHHhh-C--CCcceeehhhccccccc-------------------cC-
Q 004021          220 FQDDIGKRIGFSE--DKKWKE--KSLQDKAVDISSIL-S--PKKFRIDLTELGVPLQM-------------------LN-  272 (779)
Q Consensus       220 i~~~i~~~l~~~~--~~~~~~--~~~~~~~~~l~~~L-~--~kr~~~~ld~l~~~~~~-------------------~~-  272 (779)
                      +...|.++++...  ...|..  .+......-+.+++ +  +++..+.+|++...+..                   .. 
T Consensus        85 ~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~  164 (331)
T PF14516_consen   85 FCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNP  164 (331)
T ss_pred             HHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCc
Confidence            4555666666542  111211  11122222333332 2  45665555554322210                   00 


Q ss_pred             -CCcEEEEEeCchhh---hhh----cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          273 -AGFKIVLKTRSAGV---CDQ----MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       273 -~gs~IivTTR~~~v---a~~----~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                       ..+-.+|...+...   ...    .. ...+.|++++.+|...|..++-..-.       ....++|...+||+|.-+.
T Consensus       165 ~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~~-------~~~~~~l~~~tgGhP~Lv~  237 (331)
T PF14516_consen  165 IWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEFS-------QEQLEQLMDWTGGHPYLVQ  237 (331)
T ss_pred             ccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccCC-------HHHHHHHHHHHCCCHHHHH
Confidence             11122333222111   111    11 45789999999999999887632211       3348999999999999999


Q ss_pred             HHHHHhcCC
Q 004021          344 TVGRAMKSQ  352 (779)
Q Consensus       344 ~~g~~l~~~  352 (779)
                      .++..+...
T Consensus       238 ~~~~~l~~~  246 (331)
T PF14516_consen  238 KACYLLVEE  246 (331)
T ss_pred             HHHHHHHHc
Confidence            999988763

>PRK06620 hypothetical protein; Validated

Probab=97.22  E-value=0.017  Score=56.84  Aligned_cols=68  Identities=9%  Similarity=0.046  Sum_probs=44.8

Q ss_pred             CCCcEEEEEeCchh-------hhhhcC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          272 NAGFKIVLKTRSAG-------VCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       272 ~~gs~IivTTR~~~-------va~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ..|..||+|++...       ..+.+. ..++++++++.++-..++.+.+.......+   +++..-|++.+.|---.+
T Consensus       111 e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~---~ev~~~L~~~~~~d~r~l  186 (214)
T PRK06620        111 EKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTIS---RQIIDFLLVNLPREYSKI  186 (214)
T ss_pred             hcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHccCCHHHH
Confidence            35678999987532       223333 458999999999988888887764332222   567777777777654443

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=97.21  E-value=0.009  Score=70.15  Aligned_cols=49  Identities=27%  Similarity=0.367  Sum_probs=40.9

Q ss_pred             cccccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+.+|.++.+++|+++|...    .....++.++|.+|+||||+|+.++...
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            456799999999999988742    2245689999999999999999999876

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.21  E-value=0.0055  Score=69.27  Aligned_cols=182  Identities=13%  Similarity=0.121  Sum_probs=95.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHH-----h
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKR-----I  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~-----l  228 (779)
                      .+++|.+..++.|.+++..+. -...+.++|..|+||||+|+.+++.. .-......  .-|- ......|...     +
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~L-nC~~~~~~--~pCg~C~sCr~i~~g~~~Dvl   91 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKSL-NCENAQHG--EPCGVCQSCTQIDAGRYVDLL   91 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHh-cccCCCCC--CCCcccHHHHHHhccCccceE
Confidence            568999999999999998762 23578999999999999999998765 11111000  0000 0011111100     0


Q ss_pred             CCCcchhhhhcchhhHHHHHHHh-hCCCcceeehhhccc-----------cccccCCCcEEEEEeCc-hhhhhhc-C-Cc
Q 004021          229 GFSEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELGV-----------PLQMLNAGFKIVLKTRS-AGVCDQM-D-SK  293 (779)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~-~~va~~~-~-~~  293 (779)
                      ...........+..+........ ..+++-.+.+|++..           .+......+++|++|.+ ..+.... + ..
T Consensus        92 EidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd~~kL~~TIrSRC~  171 (709)
T PRK08691         92 EIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCL  171 (709)
T ss_pred             EEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCCccccchHHHHHHh
Confidence            00000000000111111111100 112222333444311           11111234566666644 3333222 2 46


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .|.+.+++.++....+.+.+...+...+   .+....|++.++|.+.-+.
T Consensus       172 ~f~f~~Ls~eeI~~~L~~Il~kEgi~id---~eAL~~Ia~~A~GslRdAl  218 (709)
T PRK08691        172 QFVLRNMTAQQVADHLAHVLDSEKIAYE---PPALQLLGRAAAGSMRDAL  218 (709)
T ss_pred             hhhcCCCCHHHHHHHHHHHHHHcCCCcC---HHHHHHHHHHhCCCHHHHH
Confidence            7788899999999999988766543222   5678899999999875444

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

Probab=97.20  E-value=0.0045  Score=68.39  Aligned_cols=48  Identities=25%  Similarity=0.373  Sum_probs=41.5

Q ss_pred             ccccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+-+|.++-+++|++++.-+    ....++++.+|++|||||.+|+.++...
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~AL  462 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARAL  462 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHh
Confidence            34499999999999998643    3456899999999999999999999987

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.19  E-value=0.0085  Score=65.70  Aligned_cols=141  Identities=13%  Similarity=0.209  Sum_probs=83.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      ..-+.|+|..|+|||+|++++++.. .  ...-.+++++...+...+...+...            ....++..++... 
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~l-~--~~~~~v~yi~~~~f~~~~~~~l~~~------------~~~~f~~~~~~~d-  204 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHAL-R--ESGGKILYVRSELFTEHLVSAIRSG------------EMQRFRQFYRNVD-  204 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHHH-H--HcCCCEEEeeHHHHHHHHHHHHhcc------------hHHHHHHHcccCC-
Confidence            3568899999999999999999987 2  2223456676666655555554321            0112333333222 


Q ss_pred             eeehhhcccc-------------cc-ccCCCcEEEEEeCch---------hhhhhcC-CceeEccCCChHHHHHHHHHHh
Q 004021          258 RIDLTELGVP-------------LQ-MLNAGFKIVLKTRSA---------GVCDQMD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       258 ~~~ld~l~~~-------------~~-~~~~gs~IivTTR~~---------~va~~~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      .+.+|++...             +. -...|..||+||...         .+...+. ...+.+.+++.++-..++.+.+
T Consensus       205 vLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~  284 (445)
T PRK12422        205 ALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKA  284 (445)
T ss_pred             EEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHH
Confidence            3444444211             00 012466788888642         1222233 4678999999999999999887


Q ss_pred             hccCCCCCCChHHHHHHHHHHhCC
Q 004021          314 ERSTLDSHTSIPELAETLARECGR  337 (779)
Q Consensus       314 ~~~~~~~~~~l~~~~~~I~~~c~g  337 (779)
                      ......-+   +++..-|+..+.|
T Consensus       285 ~~~~~~l~---~evl~~la~~~~~  305 (445)
T PRK12422        285 EALSIRIE---ETALDFLIEALSS  305 (445)
T ss_pred             HHcCCCCC---HHHHHHHHHhcCC
Confidence            65442222   4555656666654

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.19  E-value=0.0001  Score=72.42  Aligned_cols=78  Identities=24%  Similarity=0.269  Sum_probs=42.4

Q ss_pred             cccccccccccc---chhhcccccCceeeecCCcccccchhh-ccCccCcEeeccCCcCCC--CCchhhhcCCccCcEee
Q 004021          517 LSLRRNDSLTEL---PSRISSLVSLHHLDLSLTHIRGLPQEL-KALEKLRYLNLEYTHYLS--IIPHQLISGFLKLEVLR  590 (779)
Q Consensus       517 L~L~~~~~l~~l---p~~i~~L~~L~~L~L~~~~i~~lp~~~-~~L~~L~~L~l~~~~~l~--~lp~~~i~~L~~L~~L~  590 (779)
                      |||.+| .|..-   -.-..+|++|++|+|+.|.+..--.++ -.+.+|++|-|.++. +.  .... ++..++.++.|+
T Consensus        76 lDL~~N-~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~-L~w~~~~s-~l~~lP~vtelH  152 (418)
T KOG2982|consen   76 LDLTGN-LISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTG-LSWTQSTS-SLDDLPKVTELH  152 (418)
T ss_pred             hhcccc-hhccHHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCC-CChhhhhh-hhhcchhhhhhh
Confidence            777777 55543   223456777777777777544321111 345667777776662 21  1111 245566666666


Q ss_pred             eccccCC
Q 004021          591 LLECGSE  597 (779)
Q Consensus       591 l~~~~~~  597 (779)
                      ++.|++.
T Consensus       153 mS~N~~r  159 (418)
T KOG2982|consen  153 MSDNSLR  159 (418)
T ss_pred             hccchhh
Confidence            6666443

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.19  E-value=0.00077  Score=61.96  Aligned_cols=55  Identities=25%  Similarity=0.357  Sum_probs=42.9

Q ss_pred             cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          158 VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +|++..++.+...+...  ..+.+.|+|.+|+|||++|+.+++.. .  ..-..++++..
T Consensus         1 ~~~~~~~~~i~~~~~~~--~~~~v~i~G~~G~GKT~l~~~i~~~~-~--~~~~~v~~~~~   55 (151)
T cd00009           1 VGQEEAIEALREALELP--PPKNLLLYGPPGTGKTTLARAIANEL-F--RPGAPFLYLNA   55 (151)
T ss_pred             CchHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHh-h--cCCCCeEEEeh
Confidence            47888899999888765  45789999999999999999999987 2  22234556655

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.17  E-value=0.0043  Score=69.33  Aligned_cols=185  Identities=13%  Similarity=0.100  Sum_probs=96.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCc-
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSE-  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~-  232 (779)
                      ..++|++..++.+.+++..+. -.+.+-++|+.|+||||+|+.+++.. .-....+..  .|- ...++.+........ 
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~L-~C~~~~~~~--~Cg~C~sCr~i~~~~h~Dii   91 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKAI-NCLNPKDGD--CCNSCSVCESINTNQSVDIV   91 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHh-cCCCCCCCC--CCcccHHHHHHHcCCCCceE
Confidence            568999999999999987662 23578899999999999999998876 111111000  000 112222211110000 


Q ss_pred             --c--hhhhhcchhhHHHHHHH--hhCCCcceeehhhcc-----------ccccccCCCcEEE-EEeCchhhhhhcC--C
Q 004021          233 --D--KKWKEKSLQDKAVDISS--ILSPKKFRIDLTELG-----------VPLQMLNAGFKIV-LKTRSAGVCDQMD--S  292 (779)
Q Consensus       233 --~--~~~~~~~~~~~~~~l~~--~L~~kr~~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~~~va~~~~--~  292 (779)
                        +  ......+.......+..  ...++| ...+|++.           ..+......+.+| +|+....+.....  .
T Consensus        92 eIdaas~igVd~IReIi~~~~~~P~~~~~K-VIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI~SRc  170 (605)
T PRK05896         92 ELDAASNNGVDEIRNIIDNINYLPTTFKYK-VYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRC  170 (605)
T ss_pred             EeccccccCHHHHHHHHHHHHhchhhCCcE-EEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHHHhhh
Confidence              0  00000011111111111  111222 23333321           1111112334444 4544455543322  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKTVGR  347 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~~g~  347 (779)
                      ..+++.+++.++....+...+...+...+   .+.+..+++.++|.+- |+..+-.
T Consensus       171 q~ieF~~Ls~~eL~~~L~~il~kegi~Is---~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        171 QRYNFKKLNNSELQELLKSIAKKEKIKIE---DNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             hhcccCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCcHHHHHHHHHH
Confidence            68899999999999998887765432222   4667889999999654 4444443

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

Probab=97.16  E-value=0.0013  Score=70.47  Aligned_cols=58  Identities=19%  Similarity=0.169  Sum_probs=49.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .++++.++..+.+...|...    +.|.++|++|+|||++|+.+++.. .....|+.+.||++
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l-~~~~~~~~v~~VtF  232 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLL-TGEKAPQRVNMVQF  232 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHh-cCCcccceeeEEee
Confidence            45788899999999998865    578889999999999999999887 44557888889988

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.14  E-value=0.003  Score=68.33  Aligned_cols=48  Identities=29%  Similarity=0.318  Sum_probs=39.0

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+++.++++.+.+...           -...+-|.++|.+|+|||++|+++++..
T Consensus       131 ~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~  189 (389)
T PRK03992        131 EDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET  189 (389)
T ss_pred             HHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh
Confidence            46789999999998876421           1245678999999999999999999876

>CHL00181 cbbX CbbX; Provisional

Probab=97.11  E-value=0.012  Score=60.66  Aligned_cols=48  Identities=19%  Similarity=0.247  Sum_probs=32.7

Q ss_pred             ccccchhhhHHHHHHHHh---c-------c---CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---D-------Q---QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~-------~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++|.++.+++|.++..   -       +   ......+.++|.+|+||||+|+.+++..
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~   83 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADIL   83 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            346887776665544421   1       0   1123357899999999999999998865

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.10  E-value=0.011  Score=62.88  Aligned_cols=181  Identities=10%  Similarity=0.064  Sum_probs=98.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCC------EEEEEEe-chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFD------VVIWAAV-QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~------~~~wv~v-~~i~~~i~~  226 (779)
                      ..++|.++.++.+.+.+..+. -...+-++|+.|+||||+|..+++..--.. ...+      ...-++- ....+.|..
T Consensus        19 ~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c~~i~~   97 (365)
T PRK07471         19 TALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRIAA   97 (365)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHHHHHHc
Confidence            568999999999999988772 234688999999999999998887652111 0000      0000010 112222211


Q ss_pred             HhCCCc--------chhh----hhcchhhHHHHHHHhhCCC----cc-eeehhhcc-----------ccccccCCCcEEE
Q 004021          227 RIGFSE--------DKKW----KEKSLQDKAVDISSILSPK----KF-RIDLTELG-----------VPLQMLNAGFKIV  278 (779)
Q Consensus       227 ~l~~~~--------~~~~----~~~~~~~~~~~l~~~L~~k----r~-~~~ld~l~-----------~~~~~~~~gs~Ii  278 (779)
                      .- .++        ++..    ....+++ +..+.+.+.-+    ++ .+.+|++.           ..+..-..++.+|
T Consensus        98 ~~-HPDl~~i~~~~~~~~~~~~~~I~Vdq-iR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~~~I  175 (365)
T PRK07471         98 GA-HGGLLTLERSWNEKGKRLRTVITVDE-VRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARSLFL  175 (365)
T ss_pred             cC-CCCeEEEecccccccccccccccHHH-HHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCeEEE
Confidence            10 000        0000    0011222 33344444322    12 33334321           1111122456667


Q ss_pred             EEeCch-hhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          279 LKTRSA-GVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       279 vTTR~~-~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      ++|.+. .+.....  ...+.+.+++.++..+++.+......       .+....+++.++|.|+.+..+
T Consensus       176 L~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~~-------~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        176 LVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDLP-------DDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             EEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccCC-------HHHHHHHHHHcCCCHHHHHHH
Confidence            777664 4433333  67889999999999999987642211       222378899999999866554

>PRK08118 topology modulation protein; Reviewed

Probab=97.10  E-value=0.00047  Score=64.93  Aligned_cols=36  Identities=36%  Similarity=0.647  Sum_probs=28.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEE
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIW  214 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~w  214 (779)
                      +.|.|+|++|+||||||+.+++...-..-+||..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            358999999999999999999987222356776665

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.09  E-value=0.01  Score=69.74  Aligned_cols=182  Identities=8%  Similarity=0.018  Sum_probs=94.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCC---
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGF---  230 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~---  230 (779)
                      .++||.+..++.|.+.+..+. -...+.++|..|+||||+|+.+++...-. ......  -|- -.-+..|...-..   
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~-~~~~~~--pCg~C~sC~~~~~g~~~~~d   90 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNCV-EGPTST--PCGECDSCVALAPGGPGSLD   90 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCcc-cCCCCC--CCcccHHHHHHHcCCCCCCc
Confidence            468999999999999998762 23467899999999999999998876211 111000  000 0111111111000   


Q ss_pred             ----CcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhc-----------cccccccCCCcEEE-EEeCchhhhhhcC--
Q 004021          231 ----SEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTEL-----------GVPLQMLNAGFKIV-LKTRSAGVCDQMD--  291 (779)
Q Consensus       231 ----~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l-----------~~~~~~~~~gs~Ii-vTTR~~~va~~~~--  291 (779)
                          .........+..++.+.+...-...+| .+.+|++           ...+..-...+.+| +||....+...+.  
T Consensus        91 v~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl~TIrSR  170 (824)
T PRK07764         91 VTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVIGTIRSR  170 (824)
T ss_pred             EEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHHHHhh
Confidence                000000001111111111110111222 2233332           11122222344444 4555555655443  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      ...|++..++.++..+.+.+.+...+...+   .+....|++.++|.+..+.
T Consensus       171 c~~v~F~~l~~~~l~~~L~~il~~EGv~id---~eal~lLa~~sgGdlR~Al  219 (824)
T PRK07764        171 THHYPFRLVPPEVMRGYLERICAQEGVPVE---PGVLPLVIRAGGGSVRDSL  219 (824)
T ss_pred             eeEEEeeCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHH
Confidence            678899999999999888887655442221   4566789999999774433

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

Probab=97.07  E-value=0.008  Score=66.82  Aligned_cols=48  Identities=31%  Similarity=0.412  Sum_probs=40.9

Q ss_pred             ccccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+-+|.++-+++|+++|.-.    .-.-+++++||++|||||+|++.++...
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al  374 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKAL  374 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHh
Confidence            34489999999999999643    2345799999999999999999999987

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.07  E-value=0.023  Score=61.41  Aligned_cols=165  Identities=12%  Similarity=0.137  Sum_probs=91.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc-----cCCCCEEE-EEEe-c----hHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ-----QHNFDVVI-WAAV-Q----TFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-----~~~F~~~~-wv~v-~----~i~~~  223 (779)
                      .+++|.+..++.+.+.+..+. -.+.+-++|.+|+||||+|+.+.+.....     ...|...+ -+.. .    +-...
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~   95 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDDIRN   95 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHHHHH
Confidence            457999999999999998762 34588899999999999999998875210     11122111 1110 0    11111


Q ss_pred             HHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhcc-----------ccccccCCCcEEEEEe-CchhhhhhcC
Q 004021          224 IGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELG-----------VPLQMLNAGFKIVLKT-RSAGVCDQMD  291 (779)
Q Consensus       224 i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~-----------~~~~~~~~gs~IivTT-R~~~va~~~~  291 (779)
                      +.+.+...                  ....++++ +.+|++.           ..+......+.+|++| ....+.....
T Consensus        96 l~~~~~~~------------------p~~~~~ki-viIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~  156 (367)
T PRK14970         96 LIDQVRIP------------------PQTGKYKI-YIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTIL  156 (367)
T ss_pred             HHHHHhhc------------------cccCCcEE-EEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHH
Confidence            22211100                  00111222 2222210           0111112334455444 4444433322


Q ss_pred             --CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          292 --SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       292 --~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                        ...++.+++++++....+...+...+...+   .+....|++.++|-+-.+
T Consensus       157 sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~i~---~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        157 SRCQIFDFKRITIKDIKEHLAGIAVKEGIKFE---DDALHIIAQKADGALRDA  206 (367)
T ss_pred             hcceeEecCCccHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhCCCCHHHH
Confidence              567899999999999998887765442222   567888899999865433

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.05  E-value=0.029  Score=63.16  Aligned_cols=186  Identities=14%  Similarity=0.151  Sum_probs=98.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~  233 (779)
                      .+++|.+..++.|.+.+..+. -...+-++|..|+||||+|+.+++.. .-....+..  -|- -.....|...-..+ -
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk~L-~C~~~~~~~--pCg~C~sC~~i~~g~hpD-v   90 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAKAL-NCETAPTGE--PCNTCEQCRKVTQGMHVD-V   90 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhc-cccCCCCCC--CCcccHHHHHHhcCCCCc-e
Confidence            457999888888888887651 24678899999999999999998876 211111000  000 01111111110000 0


Q ss_pred             hhhh---hcchhhHHHHHHHhh-----CCCcceeehhhcc-----------ccccccCCCcEEEEEe-CchhhhhhcC--
Q 004021          234 KKWK---EKSLQDKAVDISSIL-----SPKKFRIDLTELG-----------VPLQMLNAGFKIVLKT-RSAGVCDQMD--  291 (779)
Q Consensus       234 ~~~~---~~~~~~~~~~l~~~L-----~~kr~~~~ld~l~-----------~~~~~~~~gs~IivTT-R~~~va~~~~--  291 (779)
                      ...+   ....++ +..+.+.+     .+++-.+.+|++.           ..+........+|++| ....+...+.  
T Consensus        91 ~eId~a~~~~Id~-iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~SR  169 (624)
T PRK14959         91 VEIDGASNRGIDD-AKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSR  169 (624)
T ss_pred             EEEecccccCHHH-HHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHHhh
Confidence            0000   001111 11122211     1222233333321           1111112344455544 4355543332  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCC-hhHHHHHHHHh
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRL-PLALKTVGRAM  349 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~gl-PLai~~~g~~l  349 (779)
                      ...+++++++.++....+...+.......+   .+.+..|++.++|. -.|+..+...+
T Consensus       170 cq~i~F~pLs~~eL~~~L~~il~~egi~id---~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        170 CQHFTFTRLSEAGLEAHLTKVLGREGVDYD---PAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             hhccccCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            567899999999999999887765442222   56788899999995 46777766544

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.04  E-value=0.009  Score=68.32  Aligned_cols=182  Identities=14%  Similarity=0.114  Sum_probs=98.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCC---CCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHN---FDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~---F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      .+++|.+..++.|..++..+. -...+-++|..|+||||+|+.+++.. .-...   ++.+   .....+..|.......
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l-~c~~~~~~~~~c---~~c~~c~~i~~~~~~d   90 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAV-NCTTNDPKGRPC---GTCEMCRAIAEGSAVD   90 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHh-cCCCCCCCCCCC---ccCHHHHHHhcCCCCe
Confidence            568999999999998887662 23567899999999999999998876 21111   1100   0012333333221110


Q ss_pred             cch-hh-hhcchhhHHHHHHHhhCCCc-----ceeehhhc-----------cccccccCCCcEEEEEeC-chhhhhhcC-
Q 004021          232 EDK-KW-KEKSLQDKAVDISSILSPKK-----FRIDLTEL-----------GVPLQMLNAGFKIVLKTR-SAGVCDQMD-  291 (779)
Q Consensus       232 ~~~-~~-~~~~~~~~~~~l~~~L~~kr-----~~~~ld~l-----------~~~~~~~~~gs~IivTTR-~~~va~~~~-  291 (779)
                      .-+ .. .....++ ...+.+.+....     -.+.+|++           ...+......+.+|++|. ...+..... 
T Consensus        91 ~~~i~~~~~~~vd~-ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI~S  169 (585)
T PRK14950         91 VIEMDAASHTSVDD-AREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILS  169 (585)
T ss_pred             EEEEeccccCCHHH-HHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHHHh
Confidence            000 00 0011111 112222222111     12333332           111112223455555554 344443322 


Q ss_pred             -CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          292 -SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       292 -~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                       ...+.+..++.++....+.+.+...+...+   .+....|++.++|.+..+...
T Consensus       170 R~~~i~f~~l~~~el~~~L~~~a~~egl~i~---~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        170 RCQRFDFHRHSVADMAAHLRKIAAAEGINLE---PGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             ccceeeCCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHH
Confidence             467889999999999888888765442222   467889999999988655443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.04  E-value=0.021  Score=64.78  Aligned_cols=183  Identities=14%  Similarity=0.082  Sum_probs=98.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC--E-EEEEEe-chHHHHHHHHhCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD--V-VIWAAV-QTFQDDIGKRIGF  230 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~--~-~~wv~v-~~i~~~i~~~l~~  230 (779)
                      .+++|.+..++.|.+.+..+. -...+-++|..|+||||+|+.+++.. .-.....  + .+-.|- ..-...|...-..
T Consensus        24 ~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L-~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~  101 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARAL-NYEGPDGDGGPTIDLCGVGEHCQAIMEGRHV  101 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhh-CcCCccccCCCccccCcccHHHHHHhcCCCC
Confidence            568999999999999998762 23468899999999999999998876 1111100  0 000011 1122222221110


Q ss_pred             Ccch--hhhhcchhhHHHHHHHhhC------CCcceeehhhc-----------cccccccCCCcEEEE-EeCchhhhhhc
Q 004021          231 SEDK--KWKEKSLQDKAVDISSILS------PKKFRIDLTEL-----------GVPLQMLNAGFKIVL-KTRSAGVCDQM  290 (779)
Q Consensus       231 ~~~~--~~~~~~~~~~~~~l~~~L~------~kr~~~~ld~l-----------~~~~~~~~~gs~Iiv-TTR~~~va~~~  290 (779)
                      +.-+  .......++. ..+.+.++      ++| ..++|++           ...+..-..++.+|+ ||....+...+
T Consensus       102 Dv~e~~a~s~~gvd~I-ReIie~~~~~P~~a~~K-VvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kll~tI  179 (598)
T PRK09111        102 DVLEMDAASHTGVDDI-REIIESVRYRPVSARYK-VYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKVPVTV  179 (598)
T ss_pred             ceEEecccccCCHHHH-HHHHHHHHhchhcCCcE-EEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhhhHHH
Confidence            0000  0000111111 11222221      222 2333332           111112224455554 54445554333


Q ss_pred             C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          291 D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       291 ~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      .  ...+++..++.++....+.+.+.......+   .+....|++.++|.+.-+..
T Consensus       180 ~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i~---~eAl~lIa~~a~Gdlr~al~  232 (598)
T PRK09111        180 LSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVE---DEALALIARAAEGSVRDGLS  232 (598)
T ss_pred             HhheeEEEecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence            3  578899999999999999888765442222   46788999999998865544

>TIGR00767 rho transcription termination factor Rho

Probab=97.00  E-value=0.002  Score=67.91  Aligned_cols=39  Identities=15%  Similarity=0.153  Sum_probs=34.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .-..++|+|.+|+|||||++.+++.. . ..+|+..+||.+
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I-~-~nhfdv~v~VlL  205 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAI-T-RNHPEVELIVLL  205 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhh-c-ccCCceEEEEEE
Confidence            44689999999999999999999987 3 348999999999

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

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.97  E-value=0.017  Score=65.09  Aligned_cols=186  Identities=11%  Similarity=0.036  Sum_probs=97.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCC---
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGF---  230 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~---  230 (779)
                      .+++|.+..++.|.+++..+. -...+.++|..|+||||+|+.+++...- ....+..  -|- -.....|...-+.   
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c-~~~~~~~--pCg~C~~C~~i~~~~~~~~d   88 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILARSLNC-AQGPTAT--PCGVCESCVALAPNGPGSID   88 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcc-ccCCCCC--cccccHHHHHhhcccCCCce
Confidence            568999999999999998762 2345789999999999999999887511 1111000  000 0111111110000   


Q ss_pred             ----CcchhhhhcchhhHHHHHHHh--hCCCcceeehhhcc-----------ccccccCCCcE-EEEEeCchhhhhhcC-
Q 004021          231 ----SEDKKWKEKSLQDKAVDISSI--LSPKKFRIDLTELG-----------VPLQMLNAGFK-IVLKTRSAGVCDQMD-  291 (779)
Q Consensus       231 ----~~~~~~~~~~~~~~~~~l~~~--L~~kr~~~~ld~l~-----------~~~~~~~~gs~-IivTTR~~~va~~~~-  291 (779)
                          .........+..++...+...  ...+| ...+|++.           ..+........ |++||....+...+. 
T Consensus        89 vieidaas~~gvd~iRel~~~~~~~P~~~~~K-VvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll~TI~S  167 (584)
T PRK14952         89 VVELDAASHGGVDDTRELRDRAFYAPAQSRYR-IFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRS  167 (584)
T ss_pred             EEEeccccccCHHHHHHHHHHHHhhhhcCCce-EEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhHHHHHH
Confidence                000000001111111111111  11122 33333321           11111123444 445655566554433 


Q ss_pred             -CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHHHHHH
Q 004021          292 -SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKTVGRA  348 (779)
Q Consensus       292 -~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~~g~~  348 (779)
                       ...|++.+++.++..+.+.+.+...+...+   .+....|++.++|-+- |+..+-.+
T Consensus       168 Rc~~~~F~~l~~~~i~~~L~~i~~~egi~i~---~~al~~Ia~~s~GdlR~aln~Ldql  223 (584)
T PRK14952        168 RTHHYPFRLLPPRTMRALIARICEQEGVVVD---DAVYPLVIRAGGGSPRDTLSVLDQL  223 (584)
T ss_pred             hceEEEeeCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence             678999999999999888887765442222   4567888999999764 44444443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.96  E-value=0.02  Score=64.37  Aligned_cols=179  Identities=15%  Similarity=0.117  Sum_probs=92.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC--CEEEEEEechHHHHHHHHh----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF--DVVIWAAVQTFQDDIGKRI----  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F--~~~~wv~v~~i~~~i~~~l----  228 (779)
                      .+++|.+..++.+.+++..+. -...+-++|..|+||||+|+.+++.. .-....  ..+-.   -.....+...-    
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk~l-~c~~~~~~~pcg~---C~~C~~i~~~~~~d~   90 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAKSL-NCETGVTATPCGV---CSACLEIDSGRFVDL   90 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHHHh-cCCCCCCCCCCCC---CHHHHHHhcCCCCce
Confidence            568999999999999988762 23467899999999999999998776 111000  00000   00011110000    


Q ss_pred             -CCCcchhhhhcchhhHHHHHHHhh-----CCCcceeehhhccc-----------cccccCCCcEEEEEe-Cchhhhhhc
Q 004021          229 -GFSEDKKWKEKSLQDKAVDISSIL-----SPKKFRIDLTELGV-----------PLQMLNAGFKIVLKT-RSAGVCDQM  290 (779)
Q Consensus       229 -~~~~~~~~~~~~~~~~~~~l~~~L-----~~kr~~~~ld~l~~-----------~~~~~~~gs~IivTT-R~~~va~~~  290 (779)
                       .....   .....++. ..+.+..     .+++-...+|++..           .+......+.+|++| ....+...+
T Consensus        91 ~ei~~~---~~~~vd~i-r~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d~~kil~tI  166 (527)
T PRK14969         91 IEVDAA---SNTQVDAM-RELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTV  166 (527)
T ss_pred             eEeecc---ccCCHHHH-HHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCChhhCchhH
Confidence             00000   00111111 1111111     11111333333211           111112344555544 444443222


Q ss_pred             C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHHH
Q 004021          291 D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKTV  345 (779)
Q Consensus       291 ~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~~  345 (779)
                      .  ...+++++++.++..+.+.+.+...+...   -++....|++.++|.+- |+..+
T Consensus       167 ~SRc~~~~f~~l~~~~i~~~L~~il~~egi~~---~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        167 LSRCLQFNLKQMPPPLIVSHLQHILEQENIPF---DATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHHHHH
Confidence            2  56889999999999988888775443221   24567889999999775 44443

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

Probab=96.95  E-value=0.00063  Score=63.41  Aligned_cols=77  Identities=29%  Similarity=0.358  Sum_probs=59.5

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchhhcc-CccCcEeeccCCcCCCC---CchhhhcCCccCcEeee
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA-LEKLRYLNLEYTHYLSI---IPHQLISGFLKLEVLRL  591 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~-L~~L~~L~l~~~~~l~~---lp~~~i~~L~~L~~L~l  591 (779)
                      .+||++| .+..++ .+..+..|.+|.|++|+|+.+-+.+.. +++|+.|.|.+| .+..   +-+  +..+++|++|.+
T Consensus        46 ~iDLtdN-dl~~l~-~lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnN-si~~l~dl~p--La~~p~L~~Ltl  120 (233)
T KOG1644|consen   46 AIDLTDN-DLRKLD-NLPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNN-SIQELGDLDP--LASCPKLEYLTL  120 (233)
T ss_pred             eeccccc-chhhcc-cCCCccccceEEecCCcceeeccchhhhccccceEEecCc-chhhhhhcch--hccCCccceeee
Confidence            5889999 777665 566889999999999999998766654 567999999998 4443   433  567788888888


Q ss_pred             ccccCC
Q 004021          592 LECGSE  597 (779)
Q Consensus       592 ~~~~~~  597 (779)
                      -+|...
T Consensus       121 l~Npv~  126 (233)
T KOG1644|consen  121 LGNPVE  126 (233)
T ss_pred             cCCchh
Confidence            887655

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.92  E-value=0.015  Score=65.99  Aligned_cols=182  Identities=13%  Similarity=0.119  Sum_probs=95.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCc-eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEE------e-chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNR-GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA------V-QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~-~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~------v-~~i~~~i~~  226 (779)
                      .+++|.+..+..|.+.+..+  .+ ..+.++|+.|+||||+|+.+++.. .-...++...|-.      - -.....+..
T Consensus        16 ~eivGQe~i~~~L~~~i~~~--ri~ha~Lf~Gp~GvGKttlA~~lAk~L-~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~   92 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMD--RVGHGYIFSGLRGVGKTTAARVFAKAV-NCQRMIDDPVYLQEVTEPCGECESCRDFDA   92 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcC--CCCeeEEEECCCCCCHHHHHHHHHHHh-CCCCcCCccccccccCCCCccCHHHHHHhc
Confidence            56899999999999988765  44 458899999999999999998776 2111111000110      0 111111111


Q ss_pred             HhCCCcchhh---hhcchhhHHHHHHHhh------CCCcceeehhhcc-----------ccccccCCCcEEE-EEeCchh
Q 004021          227 RIGFSEDKKW---KEKSLQDKAVDISSIL------SPKKFRIDLTELG-----------VPLQMLNAGFKIV-LKTRSAG  285 (779)
Q Consensus       227 ~l~~~~~~~~---~~~~~~~~~~~l~~~L------~~kr~~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~~~  285 (779)
                      .-..+ -...   .....++.. .+.+.+      .++|. ..+|++.           ..+..-...+.+| +|++...
T Consensus        93 g~~~n-~~~~d~~s~~~vd~Ir-~l~e~~~~~P~~~~~KV-vIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~k  169 (620)
T PRK14954         93 GTSLN-ISEFDAASNNSVDDIR-QLRENVRYGPQKGRYRV-YIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHK  169 (620)
T ss_pred             cCCCC-eEEecccccCCHHHHH-HHHHHHHhhhhcCCCEE-EEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhh
Confidence            00000 0000   001111211 122222      23333 2222221           1111112334444 4555555


Q ss_pred             hhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHHHHH
Q 004021          286 VCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LALKTV  345 (779)
Q Consensus       286 va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai~~~  345 (779)
                      +...+.  ...+++.+++.++....+.+.+...+..-+   .+.+..|++.++|.. .|+..+
T Consensus       170 Ll~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I~---~eal~~La~~s~Gdlr~al~eL  229 (620)
T PRK14954        170 IPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQID---ADALQLIARKAQGSMRDAQSIL  229 (620)
T ss_pred             hhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHhCCCHHHHHHHH
Confidence            554433  678999999999988888877654332222   567889999999954 444433

>PRK08116 hypothetical protein; Validated

Probab=96.91  E-value=0.0059  Score=62.29  Aligned_cols=92  Identities=21%  Similarity=0.206  Sum_probs=56.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcce
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFR  258 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~  258 (779)
                      .-+.++|.+|+|||.||.++++.. .  ..-..++++++.+++..+.......     ...+    ...+.+.+.+-. +
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l-~--~~~~~v~~~~~~~ll~~i~~~~~~~-----~~~~----~~~~~~~l~~~d-l  181 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANEL-I--EKGVPVIFVNFPQLLNRIKSTYKSS-----GKED----ENEIIRSLVNAD-L  181 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH-H--HcCCeEEEEEHHHHHHHHHHHHhcc-----cccc----HHHHHHHhcCCC-E
Confidence            458899999999999999999987 2  2234577888777777776554322     1111    112333344333 5


Q ss_pred             eehhhcccccc------------c--cCCCcEEEEEeCc
Q 004021          259 IDLTELGVPLQ------------M--LNAGFKIVLKTRS  283 (779)
Q Consensus       259 ~~ld~l~~~~~------------~--~~~gs~IivTTR~  283 (779)
                      +++|+++..-.            +  -..|..+||||..
T Consensus       182 LviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        182 LILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             EEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            67777743210            0  1246678888863

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.88  E-value=0.024  Score=58.50  Aligned_cols=47  Identities=17%  Similarity=0.249  Sum_probs=31.8

Q ss_pred             cccchhhhHHHHHHHHh---cc----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCIT---DQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~---~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.++.+++|.+...   ..          .....-+.++|.+|+|||++|+.+++..
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l   82 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQIL   82 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHH
Confidence            46887776666555321   10          0112257899999999999998888766

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.86  E-value=0.0013  Score=68.49  Aligned_cols=47  Identities=21%  Similarity=0.387  Sum_probs=41.4

Q ss_pred             cccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.++.++++++++...    +...+++.++|++|+||||||..+++..
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l  102 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL  102 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999763    2346899999999999999999999887

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

>PRK07261 topology modulation protein; Provisional

Probab=96.85  E-value=0.0022  Score=60.73  Aligned_cols=23  Identities=30%  Similarity=0.680  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|+|++|+||||||+.+....
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            48999999999999999998765

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.85  E-value=0.044  Score=60.38  Aligned_cols=47  Identities=23%  Similarity=0.339  Sum_probs=39.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.+..++.+.+++..+. -...+-++|..|+||||+|+.+++..
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk~l   63 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAKAL   63 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            468999999999999997662 23567899999999999999998765

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.85  E-value=0.044  Score=52.87  Aligned_cols=60  Identities=20%  Similarity=0.179  Sum_probs=41.6

Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA  341 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa  341 (779)
                      ..+.+|++|++ ..+.....  ...+++.+++.++..+.+.+. +   ..     ++.+..|++.++|.|..
T Consensus       125 ~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~-g---i~-----~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       125 PNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ-G---IS-----EEAAELLLALAGGSPGA  187 (188)
T ss_pred             CCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc-C---CC-----HHHHHHHHHHcCCCccc
Confidence            34556666654 34433332  568899999999998888776 1   11     46788999999998853

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=96.83  E-value=0.1  Score=55.42  Aligned_cols=188  Identities=13%  Similarity=0.184  Sum_probs=111.4

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHH-HHHHhhhccccCCCCEEEEEEe---------chHHHHHHHHhC
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLL-KQVNNNFCHQQHNFDVVIWAAV---------QTFQDDIGKRIG  229 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA-~~v~~~~~~~~~~F~~~~wv~v---------~~i~~~i~~~l~  229 (779)
                      |.+..++|..||.+.  .-..|.|.|+-|+||+.|+ .++.++. +      .+..+..         ..+...++.++|
T Consensus         1 R~e~~~~L~~wL~e~--~~TFIvV~GPrGSGK~elV~d~~L~~r-~------~vL~IDC~~i~~ar~D~~~I~~lA~qvG   71 (431)
T PF10443_consen    1 RKEAIEQLKSWLNEN--PNTFIVVQGPRGSGKRELVMDHVLKDR-K------NVLVIDCDQIVKARGDAAFIKNLASQVG   71 (431)
T ss_pred             CchHHHHHHHHHhcC--CCeEEEEECCCCCCccHHHHHHHHhCC-C------CEEEEEChHhhhccChHHHHHHHHHhcC
Confidence            567889999999987  5579999999999999999 6665554 1      1555555         344555555554


Q ss_pred             CCcchhh---------------------hhcchhhHHH--------HHHH-------------hhCCCcc---------e
Q 004021          230 FSEDKKW---------------------KEKSLQDKAV--------DISS-------------ILSPKKF---------R  258 (779)
Q Consensus       230 ~~~~~~~---------------------~~~~~~~~~~--------~l~~-------------~L~~kr~---------~  258 (779)
                      .-+-=.|                     -..+.+....        .|++             .+++..|         .
T Consensus        72 Y~PvFsw~nSiss~IDLa~qGltGqKaGfSes~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PV  151 (431)
T PF10443_consen   72 YFPVFSWMNSISSFIDLAVQGLTGQKAGFSESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPV  151 (431)
T ss_pred             CCcchHHHHHHHHHHHHHHhhccccccCCCCChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCE
Confidence            3211000                     0011111111        1111             0111111         4


Q ss_pred             eehhhccccc----------------cccCCCcEEEEEeCchhhh----hhcC---CceeEccCCChHHHHHHHHHHhhc
Q 004021          259 IDLTELGVPL----------------QMLNAGFKIVLKTRSAGVC----DQMD---SKNLEVYSLAHDEAWKLFQEMIER  315 (779)
Q Consensus       259 ~~ld~l~~~~----------------~~~~~gs~IivTTR~~~va----~~~~---~~~~~l~~L~~~~a~~Lf~~~a~~  315 (779)
                      +++|++..--                ....+--+||++|-+....    ..+.   .+.+.|...+++.|.++...+...
T Consensus       152 VVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~~  231 (431)
T PF10443_consen  152 VVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLDE  231 (431)
T ss_pred             EEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhcc
Confidence            4555542110                0113455888888775543    3343   467789999999999999988765


Q ss_pred             cCCC------------CC-----CChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChh
Q 004021          316 STLD------------SH-----TSIPELAETLARECGRLPLALKTVGRAMKSQKKVG  356 (779)
Q Consensus       316 ~~~~------------~~-----~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~  356 (779)
                      ....            .+     .....-....+...||=-.-+..+++.++...++.
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p~  289 (431)
T PF10443_consen  232 DTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESPE  289 (431)
T ss_pred             cccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCHH
Confidence            3210            00     12334456778888998889999999888765543

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.83  E-value=0.017  Score=65.95  Aligned_cols=164  Identities=13%  Similarity=0.141  Sum_probs=93.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc--------------------ccCCCCEEEE
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH--------------------QQHNFDVVIW  214 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~--------------------~~~~F~~~~w  214 (779)
                      ..++|.+..++.|.+.+..+. -...+-++|..|+||||+|+.++....-                    ...+|+.. .
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~-~   94 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH-E   94 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE-E
Confidence            458999999999999998762 2346889999999999999998876510                    01133321 1


Q ss_pred             EEec-----hHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhc-----------cccccccCCCcEEE
Q 004021          215 AAVQ-----TFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTEL-----------GVPLQMLNAGFKIV  278 (779)
Q Consensus       215 v~v~-----~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l-----------~~~~~~~~~gs~Ii  278 (779)
                      +...     +-.++++.++...                  -...++|. ..+|++           ...+..-..++.+|
T Consensus        95 ld~~~~~~vd~Ir~li~~~~~~------------------P~~~~~KV-vIIdea~~Ls~~a~naLLK~LEepp~~tifI  155 (614)
T PRK14971         95 LDAASNNSVDDIRNLIEQVRIP------------------PQIGKYKI-YIIDEVHMLSQAAFNAFLKTLEEPPSYAIFI  155 (614)
T ss_pred             ecccccCCHHHHHHHHHHHhhC------------------cccCCcEE-EEEECcccCCHHHHHHHHHHHhCCCCCeEEE
Confidence            1110     0011111111000                  01112222 222221           11111112344544


Q ss_pred             -EEeCchhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          279 -LKTRSAGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       279 -vTTR~~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                       +||+...+.....  ...+++.+++.++....+.+.+...+...+   .+.+..|++.++|-.--+
T Consensus       156 L~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i~---~~al~~La~~s~gdlr~a  219 (614)
T PRK14971        156 LATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAE---PEALNVIAQKADGGMRDA  219 (614)
T ss_pred             EEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHH
Confidence             4555566654433  678999999999999999887765542222   456788999999966433

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.82  E-value=0.029  Score=57.31  Aligned_cols=47  Identities=21%  Similarity=0.217  Sum_probs=33.9

Q ss_pred             cccchhhhHHHHHHHHhc----------c---CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITD----------Q---QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~----------~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.+..+++|.+....          +   .+...-+.++|.+|+||||+|+.+++..
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l   66 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLF   66 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHH
Confidence            478988777666543211          1   2234567899999999999999998765

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.

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.80  E-value=0.001  Score=59.02  Aligned_cols=23  Identities=35%  Similarity=0.547  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.|.|++|+||||+|+.+++..
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            68999999999999999999876

...

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.79  E-value=0.0082  Score=71.35  Aligned_cols=46  Identities=17%  Similarity=0.322  Sum_probs=39.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.++.++++.|...  ...-+.++|.+|+||||+|..++++.
T Consensus       187 d~~iGr~~ei~~~i~~l~r~--~~~n~lLvG~pGvGKTal~~~La~~i  232 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRR--RQNNPILTGEAGVGKTAVVEGLALRI  232 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcC--CcCceeEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999988776  33445699999999999999999876

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.77  E-value=0.095  Score=55.88  Aligned_cols=150  Identities=16%  Similarity=0.253  Sum_probs=85.8

Q ss_pred             ccccchhhhH-HHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC--EEEEEEechHHHHHHHHhCC
Q 004021          155 QTIVGQEKLL-PRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD--VVIWAAVQTFQDDIGKRIGF  230 (779)
Q Consensus       155 ~~~vGr~~~~-~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~--~~~wv~v~~i~~~i~~~l~~  230 (779)
                      ..++|-.... ..+...+.+. ......+-|||..|.|||.|++++.+..   .....  .+++++......+++..+..
T Consensus        88 nFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign~~---~~~~~~a~v~y~~se~f~~~~v~a~~~  164 (408)
T COG0593          88 NFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGNEA---LANGPNARVVYLTSEDFTNDFVKALRD  164 (408)
T ss_pred             heeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHHHH---HhhCCCceEEeccHHHHHHHHHHHHHh
Confidence            3445544322 2333333332 2246789999999999999999999988   34444  45555556666555555432


Q ss_pred             CcchhhhhcchhhHHHHHHHhhCCCcceeehhhcc-------------cccc-ccCCCcEEEEEeCc---------hhhh
Q 004021          231 SEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELG-------------VPLQ-MLNAGFKIVLKTRS---------AGVC  287 (779)
Q Consensus       231 ~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~-------------~~~~-~~~~gs~IivTTR~---------~~va  287 (779)
                      .            ..+..++.. +-. ++..||+.             ..|. -...|-.||+|++.         ..+.
T Consensus       165 ~------------~~~~Fk~~y-~~d-lllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~  230 (408)
T COG0593         165 N------------EMEKFKEKY-SLD-LLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLR  230 (408)
T ss_pred             h------------hHHHHHHhh-ccC-eeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHH
Confidence            1            111222222 111 11122220             0010 01234489999965         2334


Q ss_pred             hhcC-CceeEccCCChHHHHHHHHHHhhccCCCCC
Q 004021          288 DQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSH  321 (779)
Q Consensus       288 ~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~  321 (779)
                      +.+. .-.+++.+.+.+.....+.+.+.......+
T Consensus       231 SR~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~  265 (408)
T COG0593         231 SRLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIP  265 (408)
T ss_pred             HHHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCC
Confidence            4445 678899999999999999998766554333

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=96.77  E-value=0.0097  Score=64.18  Aligned_cols=48  Identities=25%  Similarity=0.250  Sum_probs=38.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..+++|.+.+.-.           -...+-|.++|.+|.|||+||+++++..
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l  203 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT  203 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            45789999888888876421           1245678899999999999999999876

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

Probab=96.77  E-value=0.00069  Score=77.92  Aligned_cols=160  Identities=22%  Similarity=0.263  Sum_probs=88.4

Q ss_pred             cccCceeeecCCc-c-cccchhhc-cCccCcEeeccCCcCCC-CCchhhhcCCccCcEeeeccccCCCcccccCCccCCC
Q 004021          535 LVSLHHLDLSLTH-I-RGLPQELK-ALEKLRYLNLEYTHYLS-IIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDD  610 (779)
Q Consensus       535 L~~L~~L~L~~~~-i-~~lp~~~~-~L~~L~~L~l~~~~~l~-~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~  610 (779)
                      -.+|++|++++.. + ...|..++ .|++|++|.+.+-.... .+.. ...+++||..||++++++..            
T Consensus       121 r~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~-lc~sFpNL~sLDIS~TnI~n------------  187 (699)
T KOG3665|consen  121 RQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQ-LCASFPNLRSLDISGTNISN------------  187 (699)
T ss_pred             HHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHH-HhhccCccceeecCCCCccC------------
Confidence            3578888888763 2 23444554 47788888887653211 1112 24577888888888877653            


Q ss_pred             chhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCC
Q 004021          611 AEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSE  690 (779)
Q Consensus       611 ~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~  690 (779)
                          +..+++|++|+.|.+..-....   ..     .+..+.+|++|+.|++|........--      +...    .+.
T Consensus       188 ----l~GIS~LknLq~L~mrnLe~e~---~~-----~l~~LF~L~~L~vLDIS~~~~~~~~~i------i~qY----lec  245 (699)
T KOG3665|consen  188 ----LSGISRLKNLQVLSMRNLEFES---YQ-----DLIDLFNLKKLRVLDISRDKNNDDTKI------IEQY----LEC  245 (699)
T ss_pred             ----cHHHhccccHHHHhccCCCCCc---hh-----hHHHHhcccCCCeeeccccccccchHH------HHHH----HHh
Confidence                3556677777777665322111   11     122356789999999988554332200      0000    023


Q ss_pred             CCCCCCccEEEccCCCCCc-ccc-CCCCCCCCccEEeeeCCC
Q 004021          691 HNFFTQLESLGILYGPDLK-SIY-PNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       691 ~~~~~~L~~L~l~~~~~l~-~l~-~~~~~l~~L~~L~l~~c~  730 (779)
                      -..+|+|+.|+.++- .+. .+- .....-|+|+.+.+-+|.
T Consensus       246 ~~~LpeLrfLDcSgT-di~~~~le~ll~sH~~L~~i~~~~~~  286 (699)
T KOG3665|consen  246 GMVLPELRFLDCSGT-DINEEILEELLNSHPNLQQIAALDCL  286 (699)
T ss_pred             cccCccccEEecCCc-chhHHHHHHHHHhCccHhhhhhhhhh
Confidence            345899999998862 221 111 112244666666555443

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.75  E-value=0.046  Score=55.47  Aligned_cols=184  Identities=16%  Similarity=0.136  Sum_probs=99.4

Q ss_pred             ccccchh---hhHHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC----EEEEEEe------chH
Q 004021          155 QTIVGQE---KLLPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD----VVIWAAV------QTF  220 (779)
Q Consensus       155 ~~~vGr~---~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~----~~~wv~v------~~i  220 (779)
                      +..||..   +.++++.+++..+ ....+-+.|+|-+|.|||++++.+...+. ....-+    .++.|..      ..+
T Consensus        34 ~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp-~~~d~~~~~~PVv~vq~P~~p~~~~~  112 (302)
T PF05621_consen   34 DRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHP-PQSDEDAERIPVVYVQMPPEPDERRF  112 (302)
T ss_pred             CCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCC-CCCCCCCccccEEEEecCCCCChHHH
Confidence            4456654   3445555556554 33456799999999999999999997762 211111    2444444      778


Q ss_pred             HHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhccccc-----------------cccCCCcEEEEEeC
Q 004021          221 QDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELGVPL-----------------QMLNAGFKIVLKTR  282 (779)
Q Consensus       221 ~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~~~~-----------------~~~~~gs~IivTTR  282 (779)
                      ...|+.+++.+...   ..+...+.......++.-.. .++.|++-..+                 .+.-.-+-|.|-|+
T Consensus       113 Y~~IL~~lgaP~~~---~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~  189 (302)
T PF05621_consen  113 YSAILEALGAPYRP---RDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTR  189 (302)
T ss_pred             HHHHHHHhCcccCC---CCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccH
Confidence            99999999987432   22333344444444443333 34444442211                 11112334555555


Q ss_pred             chhhhhhc-----C-CceeEccCCChHHHH-HHHHHHhhcc--CCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          283 SAGVCDQM-----D-SKNLEVYSLAHDEAW-KLFQEMIERS--TLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       283 ~~~va~~~-----~-~~~~~l~~L~~~~a~-~Lf~~~a~~~--~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ...-+-..     + ...+.++....++-+ .|+......-  ...+.-...+++..|...++|+.=-+
T Consensus       190 ~A~~al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l  258 (302)
T PF05621_consen  190 EAYRALRTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGEL  258 (302)
T ss_pred             HHHHHhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHH
Confidence            42221111     1 356667776655444 3433221111  11222344788999999999986433

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

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

Probab=96.75  E-value=0.018  Score=67.95  Aligned_cols=46  Identities=24%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++++.|...  ...-+.++|.+|+|||++|+.+++..
T Consensus       182 ~~~igr~~ei~~~~~~L~~~--~~~n~lL~G~pG~GKT~l~~~la~~~  227 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRR--KKNNPLLVGEPGVGKTAIAEGLALRI  227 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999988766  33445799999999999999999876

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

Probab=96.73  E-value=0.046  Score=62.69  Aligned_cols=104  Identities=19%  Similarity=0.299  Sum_probs=63.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHH--HHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQ--DDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~--~~i~  225 (779)
                      ..++|.++.+..+.+.+...       .....+.-..|+.|||||.||++++...   -+.=+..+-+...+..  ..+.
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~L---fg~e~aliR~DMSEy~EkHsVS  567 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL---FGDEQALIRIDMSEYMEKHSVS  567 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHh---cCCCccceeechHHHHHHHHHH
Confidence            55899999999999988642       3345678889999999999999998876   1111233333333332  2344


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhccc
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELGV  266 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~~  266 (779)
                      +-+|.+++  +...+.   --.|-+..+.++| .+-+|++..
T Consensus       568 rLIGaPPG--YVGyee---GG~LTEaVRr~PySViLlDEIEK  604 (786)
T COG0542         568 RLIGAPPG--YVGYEE---GGQLTEAVRRKPYSVILLDEIEK  604 (786)
T ss_pred             HHhCCCCC--Cceecc---ccchhHhhhcCCCeEEEechhhh
Confidence            45565532  222221   2235566777888 334555533

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.73  E-value=0.057  Score=61.92  Aligned_cols=180  Identities=14%  Similarity=0.111  Sum_probs=94.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      ..++|.+..++.+.+++..+. -.+.+-++|+.|+||||+|+.+++..-.......+   -.. ..+...   .+...+-
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~---~pC-~~C~~~---~~~~~Dv   89 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLL---EPC-QECIEN---VNNSLDI   89 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCC---Cch-hHHHHh---hcCCCcE
Confidence            458999999999999998762 34567899999999999999998765110000000   000 000000   0000000


Q ss_pred             -hhhh---cchhhHHHHHHHhhC-----CCcceeehhhcc-----------ccccccCCCcE-EEEEeCchhhhhhcC--
Q 004021          235 -KWKE---KSLQDKAVDISSILS-----PKKFRIDLTELG-----------VPLQMLNAGFK-IVLKTRSAGVCDQMD--  291 (779)
Q Consensus       235 -~~~~---~~~~~~~~~l~~~L~-----~kr~~~~ld~l~-----------~~~~~~~~gs~-IivTTR~~~va~~~~--  291 (779)
                       ....   ...++ +..+.+.+.     +++-...+|++.           ..+........ |++||+...+.....  
T Consensus        90 ieidaasn~~vd~-IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl~TI~SR  168 (725)
T PRK07133         90 IEMDAASNNGVDE-IRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSR  168 (725)
T ss_pred             EEEeccccCCHHH-HHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhhHHHHhh
Confidence             0000   01111 122222222     111123333321           11111112333 555665566654332  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKTVG  346 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~~g  346 (779)
                      ...+.+.+++.++....+...+...+...+   .+.+..|++.++|.+- |+..+-
T Consensus       169 cq~ieF~~L~~eeI~~~L~~il~kegI~id---~eAl~~LA~lS~GslR~AlslLe  221 (725)
T PRK07133        169 VQRFNFRRISEDEIVSRLEFILEKENISYE---KNALKLIAKLSSGSLRDALSIAE  221 (725)
T ss_pred             ceeEEccCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHH
Confidence            568899999999999888887655432221   4567889999998664 444433

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.71  E-value=0.017  Score=63.90  Aligned_cols=48  Identities=27%  Similarity=0.349  Sum_probs=38.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..++++.+.+.-.           -...+-|.++|++|.|||++|+++++..
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL  240 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSL  240 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhh
Confidence            45678999999988876421           1234568899999999999999999987

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.69  E-value=0.012  Score=70.21  Aligned_cols=46  Identities=26%  Similarity=0.426  Sum_probs=39.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++++.|...  ...-+.++|.+|+|||++|..++...
T Consensus       179 ~~~igr~~ei~~~~~~L~r~--~~~n~lL~G~pGvGKTal~~~la~~i  224 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRR--TKNNPILIGEPGVGKTAIAEGLAQRI  224 (821)
T ss_pred             CCCCCcHHHHHHHHHHHccc--ccCCeEEECCCCCCHHHHHHHHHHHH
Confidence            34799999999999999866  33345699999999999999998876

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.69  E-value=0.081  Score=56.13  Aligned_cols=156  Identities=16%  Similarity=0.180  Sum_probs=98.6

Q ss_pred             cccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~  225 (779)
                      +..++||+.+++.+.+++...  .+...-+-|.|.+|.|||.+...++.+...-...| .++++..      ..++..|.
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~-~~v~inc~sl~~~~aiF~kI~  227 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSP-VTVYINCTSLTEASAIFKKIF  227 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccc-eeEEEeeccccchHHHHHHHH
Confidence            466899999999999999764  34567788999999999999999998872211222 3345544      45555555


Q ss_pred             HHh----CCCcchhhhhcchhhHHHHHHHhhCCCcc--eeehhhccc-----------cccc-cCCCcEEEEEeCchhh-
Q 004021          226 KRI----GFSEDKKWKEKSLQDKAVDISSILSPKKF--RIDLTELGV-----------PLQM-LNAGFKIVLKTRSAGV-  286 (779)
Q Consensus       226 ~~l----~~~~~~~~~~~~~~~~~~~l~~~L~~kr~--~~~ld~l~~-----------~~~~-~~~gs~IivTTR~~~v-  286 (779)
                      ..+    ..+       ....+....+..+.++.++  ++++|++..           .|.+ .-+++++|+.---..+ 
T Consensus       228 ~~~~q~~~s~-------~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslD  300 (529)
T KOG2227|consen  228 SSLLQDLVSP-------GTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLD  300 (529)
T ss_pred             HHHHHHhcCC-------chhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhh
Confidence            554    322       1124556677777777664  666665421           1221 2356666654321111 


Q ss_pred             -----h----hhcC--CceeEccCCChHHHHHHHHHHhhccC
Q 004021          287 -----C----DQMD--SKNLEVYSLAHDEAWKLFQEMIERST  317 (779)
Q Consensus       287 -----a----~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~  317 (779)
                           .    ...+  ...+..+|-+.++-.++|..+.....
T Consensus       301 lTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~  342 (529)
T KOG2227|consen  301 LTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEES  342 (529)
T ss_pred             HHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhccc
Confidence                 1    1012  45677888999999999998876543

>PRK12377 putative replication protein; Provisional

Probab=96.67  E-value=0.011  Score=59.24  Aligned_cols=49  Identities=18%  Similarity=0.173  Sum_probs=37.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRI  228 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l  228 (779)
                      ....+.++|.+|+|||+||.++++...   .....++++++.+++..|-...
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~~l~---~~g~~v~~i~~~~l~~~l~~~~  148 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGNRLL---AKGRSVIVVTVPDVMSRLHESY  148 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHH---HcCCCeEEEEHHHHHHHHHHHH
Confidence            346789999999999999999999882   3334468888877777665443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.66  E-value=0.095  Score=58.25  Aligned_cols=47  Identities=21%  Similarity=0.286  Sum_probs=39.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+++..+. -...+-++|..|+||||+|+.++...
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk~L   62 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAKVL   62 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            457999999999999998762 23466789999999999999998765

>PRK06696 uridine kinase; Validated

Probab=96.63  E-value=0.0029  Score=62.90  Aligned_cols=44  Identities=18%  Similarity=0.287  Sum_probs=36.4

Q ss_pred             chhhhHHHHHHHHhc-cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          159 GQEKLLPRVWRCITD-QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.+-+++|.+.+.. ..+...+|+|.|.+|+||||||+.+....
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l   46 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEI   46 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            366777888888765 23467899999999999999999999877

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.56  E-value=0.017  Score=57.77  Aligned_cols=63  Identities=16%  Similarity=0.193  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRI  228 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l  228 (779)
                      .+..+.++..........+.++|.+|+|||+||.++++...   ..-..++++++.++...+-...
T Consensus        84 al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~---~~g~~v~~it~~~l~~~l~~~~  146 (244)
T PRK07952         84 ALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELL---LRGKSVLIITVADIMSAMKDTF  146 (244)
T ss_pred             HHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHH---hcCCeEEEEEHHHHHHHHHHHH
Confidence            34444444443222345789999999999999999999872   2334667777777766665443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.56  E-value=0.089  Score=58.58  Aligned_cols=184  Identities=14%  Similarity=0.123  Sum_probs=94.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEEEechHHHHHHHHhCCCc-
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAVQTFQDDIGKRIGFSE-  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv~v~~i~~~i~~~l~~~~-  232 (779)
                      ..++|-+..++.+...+..+. -..++-++|..|+||||+|+.+++...... ..+.. +-+|  .-...+........ 
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~p-C~~C--~~C~~~~~~~h~dv~   89 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTP-CDTC--IQCQSALENRHIDII   89 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCC-Cccc--HHHHHHhhcCCCeEE
Confidence            458999999999999987662 334678999999999999999887651100 01000 0000  00111110000000 


Q ss_pred             -chhhhhcchhhHHHHHHHh--h-CCCcc-eeehhhcc-----------ccccccCCCcEEEEEeCc-hhhhhhcC--Cc
Q 004021          233 -DKKWKEKSLQDKAVDISSI--L-SPKKF-RIDLTELG-----------VPLQMLNAGFKIVLKTRS-AGVCDQMD--SK  293 (779)
Q Consensus       233 -~~~~~~~~~~~~~~~l~~~--L-~~kr~-~~~ld~l~-----------~~~~~~~~gs~IivTTR~-~~va~~~~--~~  293 (779)
                       .........++..+.+...  . ...++ ...+|++.           ..+......+++|++|.+ ..+.....  ..
T Consensus        90 eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd~~kL~~tI~SRc~  169 (535)
T PRK08451         90 EMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQ  169 (535)
T ss_pred             EeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECChhhCchHHHhhce
Confidence             0000000111111111110  0 00112 22233321           111112245666666654 33332222  57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .+++.+++.++....+.+.+...+...   -++....|++.++|.+--+...
T Consensus       170 ~~~F~~Ls~~ei~~~L~~Il~~EGi~i---~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        170 HFRFKQIPQNSIISHLKTILEKEGVSY---EPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             eEEcCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCcHHHHHHH
Confidence            889999999999999888776554222   2567889999999988555443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.53  E-value=0.016  Score=57.85  Aligned_cols=170  Identities=15%  Similarity=0.229  Sum_probs=97.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEE-EEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIW-AAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~w-v~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|.+..++-+.+.+...  ..+....+|++|.|||+-|.+++... --.+-|.+++- .++             ..+
T Consensus        36 de~~gQe~vV~~L~~a~~~~--~lp~~LFyGPpGTGKTStalafar~L-~~~~~~~~rvl~lna-------------Sde   99 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLRR--ILPHYLFYGPPGTGKTSTALAFARAL-NCEQLFPCRVLELNA-------------SDE   99 (346)
T ss_pred             HhhcchHHHHHHHHHHHhhc--CCceEEeeCCCCCcHhHHHHHHHHHh-cCccccccchhhhcc-------------ccc
Confidence            56799999999999999884  78899999999999999999998876 32344543321 111             000


Q ss_pred             hhhhhcc-hhhH---HHHHHHhh---CC---Ccc-eeehhhc-----------cccccccCCCcEEEEEeCc-hhhhhhc
Q 004021          234 KKWKEKS-LQDK---AVDISSIL---SP---KKF-RIDLTEL-----------GVPLQMLNAGFKIVLKTRS-AGVCDQM  290 (779)
Q Consensus       234 ~~~~~~~-~~~~---~~~l~~~L---~~---kr~-~~~ld~l-----------~~~~~~~~~gs~IivTTR~-~~va~~~  290 (779)
                         ...+ ..+.   ...+....   .+   .+| .+.+|+.           ..........++.+..|.. ..+...+
T Consensus       100 ---rGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi  176 (346)
T KOG0989|consen  100 ---RGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPL  176 (346)
T ss_pred             ---ccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHH
Confidence               0000 0000   00011001   01   111 2223322           1111122233444433333 3332222


Q ss_pred             C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHH
Q 004021          291 D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVG  346 (779)
Q Consensus       291 ~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g  346 (779)
                      .  ...|..++|.+++...-++..+...+.+.+   .+..+.|++.++| +--|+.++-
T Consensus       177 ~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d---~~al~~I~~~S~GdLR~Ait~Lq  232 (346)
T KOG0989|consen  177 VSRCQKFRFKKLKDEDIVDRLEKIASKEGVDID---DDALKLIAKISDGDLRRAITTLQ  232 (346)
T ss_pred             HhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCcHHHHHHHHH
Confidence            2  456788999999999999999887765444   5678899999998 555555543

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.46  E-value=0.025  Score=63.62  Aligned_cols=48  Identities=23%  Similarity=0.268  Sum_probs=34.8

Q ss_pred             ccccchhhhHHHHHHHHh---cc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++.+.+.   ..       ....+=+-++|++|+|||+||+++++..
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~  112 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA  112 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc
Confidence            457888877766655443   21       1233458899999999999999999876

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.43  E-value=0.054  Score=61.95  Aligned_cols=184  Identities=11%  Similarity=0.083  Sum_probs=94.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~  233 (779)
                      ..++|.+..++.|..++..+. -...+-++|..|+||||+|+.+++... -........--|. -..++.+......+.-
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~-c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~   93 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLN-CLNSDKPTPEPCGKCELCRAIAAGNALDVI   93 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhc-CCCcCCCCCCCCcccHHHHHHhcCCCccEE
Confidence            457999999999999988762 235678999999999999999998762 1111100000000 1222333222111000


Q ss_pred             --hhhhhcchhhHHHHHHHhhCCC----cc-eeehhhcc-----------ccccccCCCcEEE-EEeCchhhhhhcC--C
Q 004021          234 --KKWKEKSLQDKAVDISSILSPK----KF-RIDLTELG-----------VPLQMLNAGFKIV-LKTRSAGVCDQMD--S  292 (779)
Q Consensus       234 --~~~~~~~~~~~~~~l~~~L~~k----r~-~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~~~va~~~~--~  292 (779)
                        ........++. ..+.+.....    ++ .+.+|++.           ..+..-.....+| +|+....+...+.  .
T Consensus        94 ei~~~~~~~vd~I-Reii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTIrSRc  172 (620)
T PRK14948         94 EIDAASNTGVDNI-RELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRC  172 (620)
T ss_pred             EEeccccCCHHHH-HHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHHHhhe
Confidence              00000111111 1111211111    11 22333221           1111111233444 4544444443333  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ..+.+..++.++....+.+.+...+...+   .+....|++.++|.+..+..
T Consensus       173 ~~~~f~~l~~~ei~~~L~~ia~kegi~is---~~al~~La~~s~G~lr~A~~  221 (620)
T PRK14948        173 QRFDFRRIPLEAMVQHLSEIAEKESIEIE---PEALTLVAQRSQGGLRDAES  221 (620)
T ss_pred             eEEEecCCCHHHHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCCHHHHHH
Confidence            67788899999988888877765432211   46688999999997765543

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.43  E-value=0.0063  Score=58.83  Aligned_cols=51  Identities=22%  Similarity=0.276  Sum_probs=37.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      +++|.++|+.|+||||.+..++... ..+  -..+..++.       .+-++..++.++.+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~-~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARL-KLK--GKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHH-HHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHH-hhc--cccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            4799999999999999998888877 322  446777777       34566667777754

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 ....

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.41  E-value=0.035  Score=56.79  Aligned_cols=47  Identities=28%  Similarity=0.318  Sum_probs=37.6

Q ss_pred             cccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+=|-++.+++|.+.+.-+           =..++=|-++|++|.|||-||++|+++.
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T  209 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT  209 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc
Confidence            4567899999988876421           1245668899999999999999999987

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

Probab=96.38  E-value=0.00048  Score=71.06  Aligned_cols=226  Identities=21%  Similarity=0.211  Sum_probs=107.5

Q ss_pred             cccccccccccc-chhh-cccccCceeeecCC-ccccc--chhhccCccCcEeeccCCcCCCC--CchhhhcCCccCcEe
Q 004021          517 LSLRRNDSLTEL-PSRI-SSLVSLHHLDLSLT-HIRGL--PQELKALEKLRYLNLEYTHYLSI--IPHQLISGFLKLEVL  589 (779)
Q Consensus       517 L~L~~~~~l~~l-p~~i-~~L~~L~~L~L~~~-~i~~l--p~~~~~L~~L~~L~l~~~~~l~~--lp~~~i~~L~~L~~L  589 (779)
                      |.+.+|..++.- -.++ ..+.+|++|++..| .++..  -.-...+++|++|++++|..++.  +.. ...+..+|+.+
T Consensus       169 L~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~kL~~lNlSwc~qi~~~gv~~-~~rG~~~l~~~  247 (483)
T KOG4341|consen  169 LALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAEGCRKLKYLNLSWCPQISGNGVQA-LQRGCKELEKL  247 (483)
T ss_pred             hhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHHhhhhHHHhhhccCchhhcCcchH-Hhccchhhhhh
Confidence            577777444431 1122 35678888888885 45542  22234678889999998865543  222 24566667777


Q ss_pred             eeccccCCCcc---------cccCC-------ccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccc-c
Q 004021          590 RLLECGSEGVT---------KEEGN-------VLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL-V  652 (779)
Q Consensus       590 ~l~~~~~~~~~---------~~~~~-------~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l-~  652 (779)
                      .+.+|.-.+..         .++-.       ...+  ......-..+..|+.|+.+.        +.++....+..+ .
T Consensus       248 ~~kGC~e~~le~l~~~~~~~~~i~~lnl~~c~~lTD--~~~~~i~~~c~~lq~l~~s~--------~t~~~d~~l~aLg~  317 (483)
T KOG4341|consen  248 SLKGCLELELEALLKAAAYCLEILKLNLQHCNQLTD--EDLWLIACGCHALQVLCYSS--------CTDITDEVLWALGQ  317 (483)
T ss_pred             hhcccccccHHHHHHHhccChHhhccchhhhccccc--hHHHHHhhhhhHhhhhcccC--------CCCCchHHHHHHhc
Confidence            66665322200         00000       0000  00000001122333333331        111111111111 2


Q ss_pred             cccCcceEEeccccccceeccc--------------ccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-----cC
Q 004021          653 FVQNLKELEIIVCTEMEEIICV--------------DKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-----YP  713 (779)
Q Consensus       653 ~l~~L~~L~L~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-----~~  713 (779)
                      +.++|+.|.++.|......-..              +.++.+..  ..+-....++|.|+.|.++.|.....-     ..
T Consensus       318 ~~~~L~~l~l~~c~~fsd~~ft~l~rn~~~Le~l~~e~~~~~~d--~tL~sls~~C~~lr~lslshce~itD~gi~~l~~  395 (483)
T KOG4341|consen  318 HCHNLQVLELSGCQQFSDRGFTMLGRNCPHLERLDLEECGLITD--GTLASLSRNCPRLRVLSLSHCELITDEGIRHLSS  395 (483)
T ss_pred             CCCceEEEeccccchhhhhhhhhhhcCChhhhhhcccccceehh--hhHhhhccCCchhccCChhhhhhhhhhhhhhhhh
Confidence            3456666666666543332100              00000000  000123356888999999887665543     22


Q ss_pred             CCCCCCCccEEeeeCCCCCCCCC--CCCCCcccccEEEechHhh
Q 004021          714 NPLHFPKLKKIGVYGCPKLKKLP--INSSSAKERRVVIEGLKEW  755 (779)
Q Consensus       714 ~~~~l~~L~~L~l~~c~~L~~lP--~~~~~~~~~~l~i~~~~~~  755 (779)
                      ...++..|+.+.+.+||.+..--  ..-....++.+++.+|...
T Consensus       396 ~~c~~~~l~~lEL~n~p~i~d~~Le~l~~c~~Leri~l~~~q~v  439 (483)
T KOG4341|consen  396 SSCSLEGLEVLELDNCPLITDATLEHLSICRNLERIELIDCQDV  439 (483)
T ss_pred             ccccccccceeeecCCCCchHHHHHHHhhCcccceeeeechhhh
Confidence            33467789999999998765411  1111223366777777544

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.37  E-value=0.15  Score=49.97  Aligned_cols=166  Identities=16%  Similarity=0.190  Sum_probs=90.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHHHhCCCcchhhh-hcchhhHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGKRIGFSEDKKWK-EKSLQDKAVDISS  250 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~~l~~~~~~~~~-~~~~~~~~~~l~~  250 (779)
                      +.+++.++|--|.|||.++++..... .  +.=-+++.+..     ..+...|...+..+  ..+. ....++....+..
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~-~--~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~--p~~~~~~~~e~~~~~L~a  124 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASL-N--EDQVAVVVIDKPTLSDATLLEAIVADLESQ--PKVNVNAVLEQIDRELAA  124 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhc-C--CCceEEEEecCcchhHHHHHHHHHHHhccC--ccchhHHHHHHHHHHHHH
Confidence            45699999999999999999665554 1  11112222222     55667777777653  1111 1123334444444


Q ss_pred             hhC-CCc-ceeehhhc---ccc-------cc----ccCCCcEEEEEeC----c---hhhhhhcC--Cce-eEccCCChHH
Q 004021          251 ILS-PKK-FRIDLTEL---GVP-------LQ----MLNAGFKIVLKTR----S---AGVCDQMD--SKN-LEVYSLAHDE  304 (779)
Q Consensus       251 ~L~-~kr-~~~~ld~l---~~~-------~~----~~~~gs~IivTTR----~---~~va~~~~--~~~-~~l~~L~~~~  304 (779)
                      ..+ ++| .....|+.   ...       |.    ....--+|+..-.    .   ..+.....  ... |++.|++.++
T Consensus       125 l~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~~~~  204 (269)
T COG3267         125 LVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLTEAE  204 (269)
T ss_pred             HHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcChHH
Confidence            443 455 32222211   000       00    0001112222211    0   11112222  223 8999999999


Q ss_pred             HHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHH
Q 004021          305 AWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGR  347 (779)
Q Consensus       305 a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~  347 (779)
                      ...++..+..+...+.+---.+....|.....|.|.+|..++.
T Consensus       205 t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         205 TGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             HHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            9998888876654333333356778899999999999987654

>PRK07667 uridine kinase; Provisional

Probab=96.37  E-value=0.0051  Score=59.59  Aligned_cols=39  Identities=26%  Similarity=0.486  Sum_probs=32.5

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.+.+.+....+...+|+|-|.+|+||||+|+.+....
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l   41 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENM   41 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            456777776655566899999999999999999999876

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.35  E-value=0.078  Score=60.15  Aligned_cols=181  Identities=13%  Similarity=0.102  Sum_probs=92.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .+++|.+..++.+.+++..+. -.+.+-++|..|+||||+|+.+++.. .-...-+.. -...-.....|......+ -.
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAkal-~c~~~~~~~-pC~~C~~C~~i~~g~~~d-v~   91 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAKAV-NCLNPPDGE-PCNECEICKAITNGSLMD-VI   91 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh-cCCCCCCCC-CCCccHHHHHHhcCCCCC-eE
Confidence            568999999999999998763 33567789999999999999998765 111100000 000001122221110000 00


Q ss_pred             hhhh---cchhhHHHHHHHhhC----CCcc-eeehhhcc-----------ccccccCCCcE-EEEEeCchhhhhhcC--C
Q 004021          235 KWKE---KSLQDKAVDISSILS----PKKF-RIDLTELG-----------VPLQMLNAGFK-IVLKTRSAGVCDQMD--S  292 (779)
Q Consensus       235 ~~~~---~~~~~~~~~l~~~L~----~kr~-~~~ld~l~-----------~~~~~~~~gs~-IivTTR~~~va~~~~--~  292 (779)
                      ..+.   ...+ .+..+.+...    ..+| ...+|++.           ..+........ |+.||....+.....  .
T Consensus        92 eidaas~~~vd-~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~tI~SRc  170 (559)
T PRK05563         92 EIDAASNNGVD-EIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPATILSRC  170 (559)
T ss_pred             EeeccccCCHH-HHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcHHHHhHh
Confidence            0000   0111 1112222211    1112 22233221           11111112333 444555555544332  5


Q ss_pred             ceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          293 KNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       293 ~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      ..+...+++.++....+...+...+...+   .+....|++.++|-+.-+.
T Consensus       171 ~~~~f~~~~~~ei~~~L~~i~~~egi~i~---~~al~~ia~~s~G~~R~al  218 (559)
T PRK05563        171 QRFDFKRISVEDIVERLKYILDKEGIEYE---DEALRLIARAAEGGMRDAL  218 (559)
T ss_pred             eEEecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHH
Confidence            67889999999999888887765442222   4667888999998775443

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=96.33  E-value=0.011  Score=52.31  Aligned_cols=117  Identities=15%  Similarity=0.181  Sum_probs=63.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF  257 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~  257 (779)
                      .+-|.|.|.+|+||||||.+++...     .|   -|+++.++.++=--.-+.+..-+...-+.+.+.+.|...+.+..+
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~-----~~---~~i~isd~vkEn~l~~gyDE~y~c~i~DEdkv~D~Le~~m~~Gg~   78 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKT-----GL---EYIEISDLVKENNLYEGYDEEYKCHILDEDKVLDELEPLMIEGGN   78 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHh-----CC---ceEehhhHHhhhcchhcccccccCccccHHHHHHHHHHHHhcCCc
Confidence            4568899999999999999998654     22   255553333221001111111111234556667777777766666


Q ss_pred             eeehhhccccccccCCCcEEEEEeCchhhhhhcCCceeEccCCChH
Q 004021          258 RIDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHD  303 (779)
Q Consensus       258 ~~~ld~l~~~~~~~~~gs~IivTTR~~~va~~~~~~~~~l~~L~~~  303 (779)
                      ..+|-.- ..||..--.--+++||-+..+-..+..+.|.-..+.+.
T Consensus        79 IVDyHgC-d~FperwfdlVvVLr~~~s~LY~RL~sRgY~e~Ki~eN  123 (176)
T KOG3347|consen   79 IVDYHGC-DFFPERWFDLVVVLRTPNSVLYDRLKSRGYSEKKIKEN  123 (176)
T ss_pred             EEeeccc-CccchhheeEEEEEecCchHHHHHHHHcCCCHHHHhhh
Confidence            6666542 22333223335666776666555554444544444333

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.30  E-value=0.068  Score=60.42  Aligned_cols=180  Identities=11%  Similarity=0.084  Sum_probs=93.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~  233 (779)
                      .+++|-+..++.+..++..+. -.+.+-++|..|+||||+|+.+++.. .-.......  -|- -.....|...-.....
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk~L-~c~~~~~~~--pC~~C~~C~~i~~~~~~dv~   91 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFARCL-NCVNGPTPM--PCGECSSCKSIDNDNSLDVI   91 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhh-ccccCCCCC--CCccchHHHHHHcCCCCCeE
Confidence            468999999999999998762 33568899999999999999998876 111100000  000 0011111110000000


Q ss_pred             --hhhhhcchhhHHHHHHHhh------CCCcceeehhhc-----------cccccccCCCcEEEEE-eCchhhhhhcC--
Q 004021          234 --KKWKEKSLQDKAVDISSIL------SPKKFRIDLTEL-----------GVPLQMLNAGFKIVLK-TRSAGVCDQMD--  291 (779)
Q Consensus       234 --~~~~~~~~~~~~~~l~~~L------~~kr~~~~ld~l-----------~~~~~~~~~gs~IivT-TR~~~va~~~~--  291 (779)
                        ........++.. .+.+.+      .+++ ...+|++           ...+......+.+|.+ |....+.....  
T Consensus        92 ~idgas~~~vddIr-~l~e~~~~~p~~~~~K-VvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~~tI~SR  169 (563)
T PRK06647         92 EIDGASNTSVQDVR-QIKEEIMFPPASSRYR-VYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSR  169 (563)
T ss_pred             EecCcccCCHHHHH-HHHHHHHhchhcCCCE-EEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhHHHHHHh
Confidence              000001111111 111111      1122 2222221           1112112234445444 44444543333  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      ...+++.+++.++-...+.+.+...+...   -++....|++.++|.+-.+.
T Consensus       170 c~~~~f~~l~~~el~~~L~~i~~~egi~i---d~eAl~lLa~~s~GdlR~al  218 (563)
T PRK06647        170 CQHFNFRLLSLEKIYNMLKKVCLEDQIKY---EDEALKWIAYKSTGSVRDAY  218 (563)
T ss_pred             ceEEEecCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHcCCCHHHHH
Confidence            56789999999999888888775544222   25677889999999775444

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.28  E-value=0.11  Score=59.33  Aligned_cols=182  Identities=12%  Similarity=0.105  Sum_probs=93.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      .+++|.+..++.|.+.+..+. -...+-++|..|+||||+|+.+++.... ....+. -+=.  ......|...-..+ -
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak~l~c-~~~~~~~~c~~--c~~c~~i~~g~~~d-~   90 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAKALNC-EQGLTAEPCNV--CPPCVEITEGRSVD-V   90 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhcC-CCCCCCCCCCc--cHHHHHHhcCCCCC-e
Confidence            568999999999999988762 2356789999999999999999877511 111000 0000  01111111100000 0


Q ss_pred             hhhh---hcchhhHHHHHHHhhCC----Ccc-eeehhhcc-----------ccccccCCCcEEE-EEeCchhhhhhcC--
Q 004021          234 KKWK---EKSLQDKAVDISSILSP----KKF-RIDLTELG-----------VPLQMLNAGFKIV-LKTRSAGVCDQMD--  291 (779)
Q Consensus       234 ~~~~---~~~~~~~~~~l~~~L~~----kr~-~~~ld~l~-----------~~~~~~~~gs~Ii-vTTR~~~va~~~~--  291 (779)
                      ...+   ....++ +..+.+.++-    .+| ...+|++.           ..+......+.+| +||....+.....  
T Consensus        91 ~eid~~s~~~v~~-ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI~SR  169 (576)
T PRK14965         91 FEIDGASNTGVDD-IRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSR  169 (576)
T ss_pred             eeeeccCccCHHH-HHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHHHHh
Confidence            0000   000111 1112222211    112 22223221           1111112344444 5555555654433  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHHHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LALKTV  345 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai~~~  345 (779)
                      ...+++.+++.++....+...+...+...+   .+....|++.++|.. .|+..+
T Consensus       170 c~~~~f~~l~~~~i~~~L~~i~~~egi~i~---~~al~~la~~a~G~lr~al~~L  221 (576)
T PRK14965        170 CQRFDFRRIPLQKIVDRLRYIADQEGISIS---DAALALVARKGDGSMRDSLSTL  221 (576)
T ss_pred             hhhhhcCCCCHHHHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence            567889999999998888877655442222   466788999999855 454444

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.28  E-value=0.088  Score=61.54  Aligned_cols=46  Identities=26%  Similarity=0.401  Sum_probs=38.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++++.|...  ...-+.++|.+|+|||++|+.+++..
T Consensus       186 ~~liGR~~ei~~~i~iL~r~--~~~n~LLvGppGvGKT~lae~la~~i  231 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhcc--CCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999998875  22344589999999999999999875

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

Probab=96.26  E-value=0.0019  Score=63.00  Aligned_cols=83  Identities=22%  Similarity=0.164  Sum_probs=41.9

Q ss_pred             cccCceeeecCCcccccchhhccCccCcEeeccCC--cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCch
Q 004021          535 LVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT--HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAE  612 (779)
Q Consensus       535 L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~--~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~  612 (779)
                      +.+|+.|++.+..++.+- .+-.|++|+.|.++.|  .-...++.- ..++++|++|++++|++.-             .
T Consensus        42 ~~~le~ls~~n~gltt~~-~~P~Lp~LkkL~lsdn~~~~~~~l~vl-~e~~P~l~~l~ls~Nki~~-------------l  106 (260)
T KOG2739|consen   42 FVELELLSVINVGLTTLT-NFPKLPKLKKLELSDNYRRVSGGLEVL-AEKAPNLKVLNLSGNKIKD-------------L  106 (260)
T ss_pred             ccchhhhhhhccceeecc-cCCCcchhhhhcccCCcccccccceeh-hhhCCceeEEeecCCcccc-------------c
Confidence            344444444444433321 2334566666666666  222333332 3455667777776666552             2


Q ss_pred             hhHHhhcCCCCCCceeEEee
Q 004021          613 PLMRELLGLKRLNVLSWSFR  632 (779)
Q Consensus       613 ~~~~~l~~L~~L~~L~l~~~  632 (779)
                      ..+..+..+.+|..|++..+
T Consensus       107 stl~pl~~l~nL~~Ldl~n~  126 (260)
T KOG2739|consen  107 STLRPLKELENLKSLDLFNC  126 (260)
T ss_pred             cccchhhhhcchhhhhcccC
Confidence            33444555556666665543

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.24  E-value=0.0076  Score=54.31  Aligned_cols=44  Identities=23%  Similarity=0.460  Sum_probs=36.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      +|.|.|.+|+||||+|+.++++.   .-.     .|+...++++|++..+.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~---gl~-----~vsaG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHL---GLK-----LVSAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHh---CCc-----eeeccHHHHHHHHHcCCC
Confidence            68999999999999999999987   122     355578999999998876

>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=96.16  E-value=0.0026  Score=37.01  Aligned_cols=22  Identities=32%  Similarity=0.529  Sum_probs=14.6

Q ss_pred             cCceeeecCCcccccchhhccC
Q 004021          537 SLHHLDLSLTHIRGLPQELKAL  558 (779)
Q Consensus       537 ~L~~L~L~~~~i~~lp~~~~~L  558 (779)
                      +|++|+|++|.++.+|++|++|
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT-
T ss_pred             CccEEECCCCcCEeCChhhcCC
Confidence            4677777777777777666543

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 ....

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.15  E-value=0.0061  Score=66.91  Aligned_cols=47  Identities=19%  Similarity=0.347  Sum_probs=40.8

Q ss_pred             cccchhhhHHHHHHHHhc----cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITD----QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +++|.++.+++|++.|..    -+...+++.++|++|+||||||+.+++-.
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            579999999999999943    24456899999999999999999999876

>CHL00176 ftsH cell division protein; Validated

Probab=96.14  E-value=0.083  Score=60.55  Aligned_cols=48  Identities=25%  Similarity=0.253  Sum_probs=34.7

Q ss_pred             ccccchhhhHHHHHHHH---hccC-------CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCI---TDQQ-------KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L---~~~~-------~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++.+.+   ...+       ...+-|.++|.+|+|||+||+++++..
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~  240 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA  240 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            45788877666655543   3321       124568999999999999999998876

>PHA00729 NTP-binding motif containing protein

Probab=96.13  E-value=0.016  Score=56.58  Aligned_cols=35  Identities=20%  Similarity=0.286  Sum_probs=27.3

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++.+...  +...|.|.|.+|+||||||..+.+..
T Consensus         7 ~~~~~l~~~--~f~nIlItG~pGvGKT~LA~aLa~~l   41 (226)
T PHA00729          7 KIVSAYNNN--GFVSAVIFGKQGSGKTTYALKVARDV   41 (226)
T ss_pred             HHHHHHhcC--CeEEEEEECCCCCCHHHHHHHHHHHH
Confidence            344445444  55678999999999999999998875

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.13  E-value=0.22  Score=52.36  Aligned_cols=66  Identities=12%  Similarity=0.128  Sum_probs=45.0

Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .++.+|+||.+ ..+.....  ...+.+.+++.+++.+.+.......       ..+.+..++..++|.|..+..+
T Consensus       135 ~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~~-------~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        135 GDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPES-------DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             CCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhcccC-------ChHHHHHHHHHcCCCHHHHHHH
Confidence            45666666666 44544433  5788999999999998887653111       1344667899999999765544

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

Probab=96.10  E-value=0.032  Score=57.51  Aligned_cols=70  Identities=20%  Similarity=0.380  Sum_probs=56.7

Q ss_pred             cccccchhhhHHHHHHHHhccCCC-ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQKN-RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIGK  226 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~~-~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~~  226 (779)
                      ++.|.+|+.++..+..++.+.+.. +..|-|+|-.|.|||.+.+.+.+..   ..+   .+|+++      +.++..|+.
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~---n~~---~vw~n~~ecft~~~lle~IL~   78 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKL---NLE---NVWLNCVECFTYAILLEKILN   78 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhc---CCc---ceeeehHHhccHHHHHHHHHH
Confidence            477899999999999999877543 3456899999999999999999876   223   468888      667888888


Q ss_pred             HhC
Q 004021          227 RIG  229 (779)
Q Consensus       227 ~l~  229 (779)
                      +.+
T Consensus        79 ~~~   81 (438)
T KOG2543|consen   79 KSQ   81 (438)
T ss_pred             Hhc
Confidence            875

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.08  E-value=0.0076  Score=54.32  Aligned_cols=36  Identities=28%  Similarity=0.371  Sum_probs=27.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEE
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWA  215 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv  215 (779)
                      .--|.|.||+|+||||+++.+.+.. +. ..|...-++
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L-~~-~g~kvgGf~   40 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL-RE-KGYKVGGFI   40 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH-Hh-cCceeeeEE
Confidence            3468999999999999999999887 32 336543333

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.08  E-value=0.033  Score=63.29  Aligned_cols=48  Identities=21%  Similarity=0.338  Sum_probs=40.3

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++..++...   ....+++.|+|.+|+||||+++.++...
T Consensus        84 del~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        84 HELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             HHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            56899999999999998764   2234689999999999999999998765

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=96.03  E-value=0.15  Score=53.34  Aligned_cols=180  Identities=13%  Similarity=0.152  Sum_probs=96.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc-------------cCCCCEEEEEEe----
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ-------------QHNFDVVIWAAV----  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-------------~~~F~~~~wv~v----  217 (779)
                      ..++|.+..++.+.+.+..+. -.+..-++|..|+||+++|..+++..-..             ..|.| ..|+.-    
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPD-l~~i~p~~~~   81 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPD-LLWVEPTYQH   81 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCC-EEEEeccccc
Confidence            457999999999999998762 24789999999999999998887764111             11222 233321    


Q ss_pred             --chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcc------eeehh--hc--------cccccccCCCcEEEE
Q 004021          218 --QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKF------RIDLT--EL--------GVPLQMLNAGFKIVL  279 (779)
Q Consensus       218 --~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~------~~~ld--~l--------~~~~~~~~~gs~Iiv  279 (779)
                        ..+-.+-+...+.. .........+ .+..+.+.+..+.+      .+.++  .+        ...+-.-.++.-|++
T Consensus        82 ~g~~~~~~~~~~~~~~-~~~~~~I~id-~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp~~~fILi  159 (314)
T PRK07399         82 QGKLITASEAEEAGLK-RKAPPQIRLE-QIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPGNGTLILI  159 (314)
T ss_pred             cccccchhhhhhcccc-ccccccCcHH-HHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCCCCeEEEE
Confidence              00101111111100 0000001111 22344444543333      22221  11        111111113333444


Q ss_pred             EeCchhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          280 KTRSAGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       280 TTR~~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      |++-..+.....  ...+.+.++++++..+.+.+......      .......++..++|.|..+..
T Consensus       160 ~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~------~~~~~~~l~~~a~Gs~~~al~  220 (314)
T PRK07399        160 APSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI------LNINFPELLALAQGSPGAAIA  220 (314)
T ss_pred             ECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc------chhHHHHHHHHcCCCHHHHHH
Confidence            544455555443  67889999999999999987643211      111236889999999976554

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.01  E-value=0.012  Score=63.89  Aligned_cols=44  Identities=11%  Similarity=0.187  Sum_probs=39.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||++.++.+...+..+    .-|-|.|.+|+|||++|+.+....
T Consensus        20 ~~i~gre~vI~lll~aalag----~hVLL~GpPGTGKT~LAraLa~~~   63 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAF   63 (498)
T ss_pred             hhccCcHHHHHHHHHHHccC----CCEEEECCCChhHHHHHHHHHHHh
Confidence            45899999999999988766    567899999999999999999876

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.00  E-value=0.058  Score=54.30  Aligned_cols=39  Identities=23%  Similarity=0.284  Sum_probs=29.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccc--cCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQ--QHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~--~~~F~~~~wv~v  217 (779)
                      -++|-++|++|.|||+|.++++++. .+  .+.+....-+.+
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkL-SIR~~~~y~~~~liEi  217 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKL-SIRTNDRYYKGQLIEI  217 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhh-eeeecCccccceEEEE
Confidence            4789999999999999999999987 43  334444444444

>PRK10536 hypothetical protein; Provisional

Probab=95.97  E-value=0.034  Score=55.21  Aligned_cols=44  Identities=18%  Similarity=0.224  Sum_probs=37.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+.+|......++.++.+.    .+|.+.|..|.|||+||.+++.+.
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~----~lV~i~G~aGTGKT~La~a~a~~~   98 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK----QLIFATGEAGCGKTWISAAKAAEA   98 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC----CeEEEECCCCCCHHHHHHHHHHHH
Confidence            34578888888888888764    599999999999999999998864

>PRK06547 hypothetical protein; Provisional

Probab=95.94  E-value=0.011  Score=55.79  Aligned_cols=34  Identities=21%  Similarity=0.161  Sum_probs=27.1

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +...+...  ...+|+|.|.+|+||||+|+.+....
T Consensus         6 ~~~~~~~~--~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547          6 IAARLCGG--GMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             HHHHhhcC--CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            33444433  67899999999999999999998765

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.94  E-value=0.1  Score=57.39  Aligned_cols=39  Identities=33%  Similarity=0.476  Sum_probs=27.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+|+|+|.+|+||||++..++... ..+.....+..++.
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa~l-a~~~~gkkVaLIdt  388 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQRF-AAQHAPRDVALVTT  388 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH-HHhcCCCceEEEec
Confidence            4799999999999999999988765 21222234555554

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

Probab=95.93  E-value=0.0046  Score=60.40  Aligned_cols=63  Identities=27%  Similarity=0.390  Sum_probs=46.5

Q ss_pred             ccccCceeeecCC--ccc-ccchhhccCccCcEeeccCCcC--CCCCchhhhcCCccCcEeeeccccCCC
Q 004021          534 SLVSLHHLDLSLT--HIR-GLPQELKALEKLRYLNLEYTHY--LSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       534 ~L~~L~~L~L~~~--~i~-~lp~~~~~L~~L~~L~l~~~~~--l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      .|++|++|.++.|  ++. .++.-..++++|++|++++|..  ++.+++  +..+.+|..|+++.|....
T Consensus        63 ~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~p--l~~l~nL~~Ldl~n~~~~~  130 (260)
T KOG2739|consen   63 KLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRP--LKELENLKSLDLFNCSVTN  130 (260)
T ss_pred             CcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccch--hhhhcchhhhhcccCCccc
Confidence            5778999999988  443 3666666779999999999842  334555  6778888888888886553

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.93  E-value=0.23  Score=53.64  Aligned_cols=38  Identities=21%  Similarity=0.393  Sum_probs=28.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...+|.++|.+|+||||+|..++... . +..+ .++.|+.
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l-~-~~G~-kV~lV~~  136 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYY-Q-RKGF-KPCLVCA  136 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH-H-HCCC-CEEEEcC
Confidence            46899999999999999999988766 3 2223 4555655

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.89  E-value=0.32  Score=51.74  Aligned_cols=39  Identities=26%  Similarity=0.322  Sum_probs=28.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++.++|+.|+||||++..++... ..+.....+..++.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~-~~~~G~~~V~lit~  175 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARC-VMRFGASKVALLTT  175 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHhcCCCeEEEEec
Confidence            4799999999999999999998876 21212245666666

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.83  E-value=0.17  Score=49.47  Aligned_cols=48  Identities=23%  Similarity=0.393  Sum_probs=38.7

Q ss_pred             ccccchhhhHHH---HHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPR---VWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~---l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++||.++.+.+   |+++|.++    +-.++-|-.+|++|.|||-+|+++++..
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc
Confidence            457898877654   66777664    3457889999999999999999999987

>PRK05541 adenylylsulfate kinase; Provisional

Probab=95.78  E-value=0.012  Score=56.05  Aligned_cols=38  Identities=29%  Similarity=0.455  Sum_probs=30.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...+|.+.|+.|+||||+|+.++...   ...+...+++..
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l---~~~~~~~~~~~~   43 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERL---KLKYSNVIYLDG   43 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHH---HHcCCcEEEEec
Confidence            45699999999999999999999987   345555555543

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=95.76  E-value=0.0076  Score=53.94  Aligned_cols=22  Identities=45%  Similarity=0.789  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|.+|+||||+|+++....
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999998873

...

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.76  E-value=0.14  Score=60.74  Aligned_cols=48  Identities=25%  Similarity=0.260  Sum_probs=36.2

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..+++|.+.+.-           +-...+-|.++|.+|+|||++|+++++..
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~  511 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES  511 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            3467888888877776542           11234558899999999999999999976

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.73  E-value=0.31  Score=53.20  Aligned_cols=38  Identities=29%  Similarity=0.358  Sum_probs=28.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+.+|.++|.+|+||||+|..++... .. ..+ .++.|+.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L-~~-~g~-kV~lV~~  131 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYF-KK-KGL-KVGLVAA  131 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH-HH-cCC-eEEEecC
Confidence            46799999999999999999999877 32 223 4444555

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=95.73  E-value=0.83  Score=45.05  Aligned_cols=47  Identities=21%  Similarity=0.382  Sum_probs=37.7

Q ss_pred             ccccchhhhHHHHHHHHh---ccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|..++.|++-..   .+. ...-+-+||..|.|||++++++.+.+
T Consensus        27 ~~L~Gie~Qk~~l~~Nt~~Fl~G~-pannvLL~G~rGtGKSSlVkall~~y   76 (249)
T PF05673_consen   27 DDLIGIERQKEALIENTEQFLQGL-PANNVLLWGARGTGKSSLVKALLNEY   76 (249)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHcCC-CCcceEEecCCCCCHHHHHHHHHHHH
Confidence            678999999988877543   232 44567789999999999999999887

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.70  E-value=0.014  Score=58.20  Aligned_cols=27  Identities=33%  Similarity=0.561  Sum_probs=24.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....+|+|.|..|+|||||++.+....
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l   57 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALL   57 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            467899999999999999999998876

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.65  E-value=0.012  Score=70.15  Aligned_cols=46  Identities=20%  Similarity=0.424  Sum_probs=39.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.+++++++.|...  ...-+.++|.+|+|||++|..++...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~--~~~n~lL~G~pGvGKT~l~~~la~~i  223 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRI  223 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcC--CcCceEEECCCCCCHHHHHHHHHHHh
Confidence            34799999999999999776  34456699999999999999999876

>PRK08233 hypothetical protein; Provisional

Probab=95.64  E-value=0.01  Score=56.99  Aligned_cols=25  Identities=32%  Similarity=0.534  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|.+|+||||||..++...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            4789999999999999999998876

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.63  E-value=0.034  Score=53.61  Aligned_cols=75  Identities=20%  Similarity=0.240  Sum_probs=44.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHH-----HHHHhCCCcchhhhhcchhhHHHHHHHh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDD-----IGKRIGFSEDKKWKEKSLQDKAVDISSI  251 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~-----i~~~l~~~~~~~~~~~~~~~~~~~l~~~  251 (779)
                      .+.+|+|.|.+|+||||+|+.++..+   ...  .+.-++......+     ........ -..+..-+.+-+.+.|...
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~---~~~--~~~~I~~D~YYk~~~~~~~~~~~~~n-~d~p~A~D~dLl~~~L~~L   80 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQL---GVE--KVVVISLDDYYKDQSHLPFEERNKIN-YDHPEAFDLDLLIEHLKDL   80 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHh---CcC--cceEeeccccccchhhcCHhhcCCcC-ccChhhhcHHHHHHHHHHH
Confidence            45799999999999999999999988   323  1222222111111     11111111 1112345566677788888


Q ss_pred             hCCCcc
Q 004021          252 LSPKKF  257 (779)
Q Consensus       252 L~~kr~  257 (779)
                      ++++..
T Consensus        81 ~~g~~v   86 (218)
T COG0572          81 KQGKPV   86 (218)
T ss_pred             HcCCcc
Confidence            888774

>PRK04040 adenylate kinase; Provisional

Probab=95.62  E-value=0.036  Score=53.24  Aligned_cols=47  Identities=21%  Similarity=0.398  Sum_probs=35.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCC
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGF  230 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~  230 (779)
                      ..+|+|+|++|+||||+++.+.... .  ..+   -+++..++...++...+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l-~--~~~---~~~~~g~~~~~~a~~~g~   48 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKL-K--EDY---KIVNFGDVMLEVAKEEGL   48 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHh-c--cCC---eEEecchHHHHHHHHcCC
Confidence            3689999999999999999998876 2  122   235556777777776664

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.61  E-value=0.051  Score=56.46  Aligned_cols=98  Identities=16%  Similarity=0.136  Sum_probs=56.8

Q ss_pred             HHHHHh-ccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcchh
Q 004021          167 VWRCIT-DQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSLQ  242 (779)
Q Consensus       167 l~~~L~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~~  242 (779)
                      |-..|. .+=+.-+++-|+|.+|+||||||.+++...   ...-..++|++. ..+-...++.++.+.+.-  ....+.+
T Consensus        43 LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~---~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~e  119 (325)
T cd00983          43 LDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEA---QKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGE  119 (325)
T ss_pred             HHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHH---HHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHH
Confidence            334444 332345799999999999999999987765   233456788888 333345566665542111  0122344


Q ss_pred             hHHHHHHHhhCCCcc-eeehhhcccc
Q 004021          243 DKAVDISSILSPKKF-RIDLTELGVP  267 (779)
Q Consensus       243 ~~~~~l~~~L~~kr~-~~~ld~l~~~  267 (779)
                      +....+...++...+ ++++|.+...
T Consensus       120 q~l~i~~~li~s~~~~lIVIDSvaal  145 (325)
T cd00983         120 QALEIADSLVRSGAVDLIVVDSVAAL  145 (325)
T ss_pred             HHHHHHHHHHhccCCCEEEEcchHhh
Confidence            455555444444434 5566665443

RecA couples ATP hydrolysis to DNA strand exchange.

>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=95.59  E-value=0.011  Score=46.36  Aligned_cols=23  Identities=35%  Similarity=0.605  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|..|+||||+|+.+.+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998874

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.

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

Probab=95.58  E-value=0.0025  Score=71.78  Aligned_cols=15  Identities=13%  Similarity=0.401  Sum_probs=9.7

Q ss_pred             CCccEEeeeCCCCCC
Q 004021          719 PKLKKIGVYGCPKLK  733 (779)
Q Consensus       719 ~~L~~L~l~~c~~L~  733 (779)
                      .+|+.|.+..|....
T Consensus       401 ~~l~~L~l~~~~~~t  415 (482)
T KOG1947|consen  401 DSLRVLNLSDCRLVT  415 (482)
T ss_pred             CccceEecccCcccc
Confidence            336777777776544

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

Probab=95.57  E-value=0.01  Score=57.60  Aligned_cols=23  Identities=48%  Similarity=0.709  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ||+|.|.+|+||||+|+.+....
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L   23 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQIL   23 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            79999999999999999999887

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 ....

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.56  E-value=0.0011  Score=64.77  Aligned_cols=35  Identities=29%  Similarity=0.367  Sum_probs=16.4

Q ss_pred             ccccCceeeecCCcccccchhhccCccCcEeeccCC
Q 004021          534 SLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT  569 (779)
Q Consensus       534 ~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~  569 (779)
                      +|+.|++|.|+-|.|+.|. .+..+++|+.|+|+.|
T Consensus        39 kMp~lEVLsLSvNkIssL~-pl~rCtrLkElYLRkN   73 (388)
T KOG2123|consen   39 KMPLLEVLSLSVNKISSLA-PLQRCTRLKELYLRKN   73 (388)
T ss_pred             hcccceeEEeeccccccch-hHHHHHHHHHHHHHhc
Confidence            4444555555544444442 2444444444444444

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.54  E-value=0.012  Score=57.89  Aligned_cols=26  Identities=35%  Similarity=0.510  Sum_probs=23.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|.+|+||||||+.++...
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            56799999999999999999998876

>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=95.53  E-value=0.075  Score=48.28  Aligned_cols=112  Identities=15%  Similarity=0.157  Sum_probs=85.4

Q ss_pred             CCcccccchhhHHHHHHHHHhhhhcchhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCchhHHHHHHHHHHH
Q 004021            2 GNLISTSLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKL   81 (779)
Q Consensus         2 ~~~~~~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~~~~~~~~~~~Wl~~l~~~   81 (779)
                      |+.++.|+++.+++.+...+.+...-...++.-++.|...++.+.-++++++..-..-+        ..-+.-++++.+.
T Consensus         3 ~eL~~gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld--------~~~~ee~e~L~~~   74 (147)
T PF05659_consen    3 AELVGGAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVELD--------RPRQEEIERLKEL   74 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcC--------CchhHHHHHHHHH
Confidence            56788888999999999999999999999999999999999999999999766533222        2225667888899


Q ss_pred             HHHHHHHHHHHHHHhhhhhcCCCCccccccccchHHHHHHHHHHHHHHH
Q 004021           82 GTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLN  130 (779)
Q Consensus        82 ~~d~ed~ld~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~i~~~~  130 (779)
                      ..+++++++.|..-.         .+++...++.+++|+++.+.+....
T Consensus        75 L~~g~~LV~k~sk~~---------r~n~~kk~~y~~Ki~~le~~l~~f~  114 (147)
T PF05659_consen   75 LEKGKELVEKCSKVR---------RWNLYKKPRYARKIEELEESLRRFI  114 (147)
T ss_pred             HHHHHHHHHHhcccc---------HHHHHhhHhHHHHHHHHHHHHHHHh
Confidence            999999998764211         1234455667788887777777653

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 [].

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

Probab=95.52  E-value=0.13  Score=60.87  Aligned_cols=49  Identities=31%  Similarity=0.427  Sum_probs=39.1

Q ss_pred             cccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++|.++.++.+.+.+...       .....++.++|+.|+|||+||+.++...
T Consensus       453 ~~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l  508 (731)
T TIGR02639       453 KAKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL  508 (731)
T ss_pred             hcceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh
Confidence            356789999999998887642       1233468899999999999999998876

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

Probab=95.50  E-value=0.017  Score=55.12  Aligned_cols=46  Identities=28%  Similarity=0.322  Sum_probs=39.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++||-++.++.+.-...++  +.+-+.|.||+|+||||-+..+++..
T Consensus        27 ~dIVGNe~tv~rl~via~~g--nmP~liisGpPG~GKTTsi~~LAr~L   72 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKEG--NMPNLIISGPPGTGKTTSILCLAREL   72 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHcC--CCCceEeeCCCCCchhhHHHHHHHHH
Confidence            46899999999887777666  78889999999999999998888776

>PRK10867 signal recognition particle protein; Provisional

Probab=95.46  E-value=0.33  Score=52.85  Aligned_cols=39  Identities=23%  Similarity=0.353  Sum_probs=28.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+.+|.++|.+|+||||.|..++... ..+ .-..++.|+.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l-~~~-~G~kV~lV~~  137 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYL-KKK-KKKKVLLVAA  137 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH-HHh-cCCcEEEEEc
Confidence            46899999999999999998888766 222 1233555555

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.46  E-value=0.026  Score=50.29  Aligned_cols=41  Identities=22%  Similarity=0.274  Sum_probs=30.1

Q ss_pred             hhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          162 KLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       162 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.+++.+.|...=....+|.+.|.-|+||||+++.+++..
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            34445555554422234699999999999999999999876

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.

>TIGR00235 udk uridine kinase

Probab=95.43  E-value=0.014  Score=57.33  Aligned_cols=26  Identities=35%  Similarity=0.535  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+||||||+.++...
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~~l   30 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYEQL   30 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45799999999999999999998876

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK06762 hypothetical protein; Provisional

Probab=95.43  E-value=0.014  Score=55.15  Aligned_cols=25  Identities=36%  Similarity=0.531  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998775

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.42  E-value=0.019  Score=60.69  Aligned_cols=47  Identities=15%  Similarity=0.067  Sum_probs=39.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++..+.+..++..+. -..++.++|.+|+||||+|+.+++..
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~~~   67 (316)
T PHA02544         21 DECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCNEV   67 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            567999999999999988652 34677779999999999999998875

>PTZ00301 uridine kinase; Provisional

Probab=95.41  E-value=0.014  Score=56.98  Aligned_cols=25  Identities=28%  Similarity=0.578  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|.+|+||||||+.+.+..
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l   27 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSEL   27 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHH
Confidence            4799999999999999999998765

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

Probab=95.39  E-value=0.011  Score=57.86  Aligned_cols=93  Identities=20%  Similarity=0.102  Sum_probs=46.0

Q ss_pred             hhcccccCceeeecCCcccc-cch----hhccCccCcEeeccCCcCCCCCchhhhc-------------CCccCcEeeec
Q 004021          531 RISSLVSLHHLDLSLTHIRG-LPQ----ELKALEKLRYLNLEYTHYLSIIPHQLIS-------------GFLKLEVLRLL  592 (779)
Q Consensus       531 ~i~~L~~L~~L~L~~~~i~~-lp~----~~~~L~~L~~L~l~~~~~l~~lp~~~i~-------------~L~~L~~L~l~  592 (779)
                      .+-++++|+..+|+.|.+.. .|+    .|++-+.|.+|.+++| .++.+..+-|+             .-+.|++....
T Consensus        87 aLlkcp~l~~v~LSDNAfg~~~~e~L~d~is~~t~l~HL~l~Nn-GlGp~aG~rigkal~~la~nKKaa~kp~Le~vicg  165 (388)
T COG5238          87 ALLKCPRLQKVDLSDNAFGSEFPEELGDLISSSTDLVHLKLNNN-GLGPIAGGRIGKALFHLAYNKKAADKPKLEVVICG  165 (388)
T ss_pred             HHhcCCcceeeeccccccCcccchHHHHHHhcCCCceeEEeecC-CCCccchhHHHHHHHHHHHHhhhccCCCceEEEec
Confidence            34556666777776664432 222    3455566667777666 34433322122             23445555555


Q ss_pred             cccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          593 ECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       593 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      .|++...+          .......|....+|+.+.+..|++
T Consensus       166 rNRlengs----------~~~~a~~l~sh~~lk~vki~qNgI  197 (388)
T COG5238         166 RNRLENGS----------KELSAALLESHENLKEVKIQQNGI  197 (388)
T ss_pred             cchhccCc----------HHHHHHHHHhhcCceeEEeeecCc
Confidence            55544311          112222344445666666665554

>TIGR02012 tigrfam_recA protein RecA

Probab=95.38  E-value=0.078  Score=55.06  Aligned_cols=96  Identities=14%  Similarity=0.132  Sum_probs=54.3

Q ss_pred             HHHHh-ccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcchhh
Q 004021          168 WRCIT-DQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSLQD  243 (779)
Q Consensus       168 ~~~L~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~~~  243 (779)
                      -..|. .+=+.-+++-|+|.+|+||||||.++....   ...-..++|++. ..+-...++.++.+...-  ....+.++
T Consensus        44 D~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~---~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq  120 (321)
T TIGR02012        44 DLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEA---QKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQ  120 (321)
T ss_pred             HHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHH---HHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHH
Confidence            34443 332355799999999999999999987766   233456788888 333334455665541110  12233444


Q ss_pred             HHHHHHHhhCCCcc-eeehhhccc
Q 004021          244 KAVDISSILSPKKF-RIDLTELGV  266 (779)
Q Consensus       244 ~~~~l~~~L~~kr~-~~~ld~l~~  266 (779)
                      ....+...++...+ ++++|.+..
T Consensus       121 ~l~~~~~li~~~~~~lIVIDSv~a  144 (321)
T TIGR02012       121 ALEIAETLVRSGAVDIIVVDSVAA  144 (321)
T ss_pred             HHHHHHHHhhccCCcEEEEcchhh
Confidence            44444444443333 455565543

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK09354 recA recombinase A; Provisional

Probab=95.35  E-value=0.079  Score=55.52  Aligned_cols=98  Identities=13%  Similarity=0.128  Sum_probs=57.9

Q ss_pred             HHHHHh-ccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcchh
Q 004021          167 VWRCIT-DQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSLQ  242 (779)
Q Consensus       167 l~~~L~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~~  242 (779)
                      |-..|. .+=..-+++-|+|.+|+||||||.+++...   ...-..++||+. ..+-...++.++.+.+.-  ....+.+
T Consensus        48 LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~---~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~E  124 (349)
T PRK09354         48 LDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEA---QKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGE  124 (349)
T ss_pred             HHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHH---HHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHH
Confidence            334454 333355799999999999999999987765   234467889998 334445666666542111  1223344


Q ss_pred             hHHHHHHHhhCCCcc-eeehhhcccc
Q 004021          243 DKAVDISSILSPKKF-RIDLTELGVP  267 (779)
Q Consensus       243 ~~~~~l~~~L~~kr~-~~~ld~l~~~  267 (779)
                      +....+...++...+ ++++|.+...
T Consensus       125 q~l~i~~~li~s~~~~lIVIDSvaaL  150 (349)
T PRK09354        125 QALEIADTLVRSGAVDLIVVDSVAAL  150 (349)
T ss_pred             HHHHHHHHHhhcCCCCEEEEeChhhh
Confidence            445545444444333 5566665433

>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=95.35  E-value=0.014  Score=53.43  Aligned_cols=23  Identities=39%  Similarity=0.576  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.+.|++|+||||+|+.+....
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            68899999999999999998765

...

>PRK03839 putative kinase; Provisional

Probab=95.31  E-value=0.014  Score=55.81  Aligned_cols=23  Identities=43%  Similarity=0.654  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+++..
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999999986

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.24  E-value=0.24  Score=53.34  Aligned_cols=150  Identities=18%  Similarity=0.141  Sum_probs=74.8

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechH--------HHHHHHHhCCCcchhhhhcchhhHHHH
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTF--------QDDIGKRIGFSEDKKWKEKSLQDKAVD  247 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i--------~~~i~~~l~~~~~~~~~~~~~~~~~~~  247 (779)
                      ....-+.+.|.+|+|||+||..++..     ..|..+--++..++        ...|-+.+....... -..-.-+-+++
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~~-----S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~-lsiivvDdiEr  609 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIALS-----SDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSP-LSIIVVDDIER  609 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHhh-----cCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCc-ceEEEEcchhh
Confidence            35667788999999999999999765     46776544444111        111111111000000 00000000111


Q ss_pred             HHHhh-CCCcc-eeehhhc---cccccccCCCcEEEEEeCchhhhhhcC-----CceeEccCCCh-HHHHHHHHHHhhcc
Q 004021          248 ISSIL-SPKKF-RIDLTEL---GVPLQMLNAGFKIVLKTRSAGVCDQMD-----SKNLEVYSLAH-DEAWKLFQEMIERS  316 (779)
Q Consensus       248 l~~~L-~~kr~-~~~ld~l---~~~~~~~~~gs~IivTTR~~~va~~~~-----~~~~~l~~L~~-~~a~~Lf~~~a~~~  316 (779)
                      |.++. -+-|| ..++..+   ....|..++.--|+-||-...|...|+     ...|+++.++. ++..+.++..-.  
T Consensus       610 LiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~n~--  687 (744)
T KOG0741|consen  610 LLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEELNI--  687 (744)
T ss_pred             hhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHHHccC--
Confidence            11111 12222 1111111   111122233344566888888988887     46789999987 677777665421  


Q ss_pred             CCCCCCChHHHHHHHHHHh
Q 004021          317 TLDSHTSIPELAETLAREC  335 (779)
Q Consensus       317 ~~~~~~~l~~~~~~I~~~c  335 (779)
                        -.+.+.+.++.+...+|
T Consensus       688 --fsd~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  688 --FSDDEVRAIAEQLLSKK  704 (744)
T ss_pred             --CCcchhHHHHHHHhccc
Confidence              12344566677777666

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.24  E-value=0.076  Score=53.31  Aligned_cols=48  Identities=17%  Similarity=0.214  Sum_probs=33.6

Q ss_pred             HHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCC----CCEEEEEEe
Q 004021          169 RCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHN----FDVVIWAAV  217 (779)
Q Consensus       169 ~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~----F~~~~wv~v  217 (779)
                      +.|.++=..-.++.|+|.+|+|||+||.+++... .....    -..++|++.
T Consensus        10 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~-~~~~~~~g~~~~viyi~~   61 (235)
T cd01123          10 ELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTV-QLPIELGGLEGKAVYIDT   61 (235)
T ss_pred             hhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHe-eCccccCCCCccEEEEeC
Confidence            3344333345799999999999999999997543 11221    367889988

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 .

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=95.24  E-value=0.042  Score=54.33  Aligned_cols=36  Identities=31%  Similarity=0.432  Sum_probs=30.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      -.++|+|..|+|||||+..+....   ...|+++++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~---~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYL---RHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhh---cccCCEEEEEec
Confidence            467899999999999999998877   678888877765

This is thought to be an ATPase involved in viral DNA packaging [].

>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=95.22  E-value=0.016  Score=52.04  Aligned_cols=22  Identities=41%  Similarity=0.505  Sum_probs=20.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|+|.+|+||||+|+.+++..
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            5799999999999999999987

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 ....

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.19  E-value=0.017  Score=55.67  Aligned_cols=26  Identities=27%  Similarity=0.342  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++|.|.|++|+||||+|+.++...
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            46799999999999999999998765

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.16  E-value=0.022  Score=68.27  Aligned_cols=46  Identities=20%  Similarity=0.435  Sum_probs=38.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.++++++..|...  ...-+.++|.+|+|||++|..++++.
T Consensus       173 ~~~igr~~ei~~~~~~l~r~--~~~n~lL~G~pGvGKT~l~~~la~~i  218 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRR--TKNNPVLIGEPGVGKTAIVEGLAQRI  218 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcC--CCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            34799999999999999776  33445589999999999999998876

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.

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

Probab=95.15  E-value=0.016  Score=56.70  Aligned_cols=81  Identities=25%  Similarity=0.281  Sum_probs=57.4

Q ss_pred             cccccccccc-----ccchhhcccccCceeeecCCcc----cccc-------hhhccCccCcEeeccCCcCCCCCchh--
Q 004021          517 LSLRRNDSLT-----ELPSRISSLVSLHHLDLSLTHI----RGLP-------QELKALEKLRYLNLEYTHYLSIIPHQ--  578 (779)
Q Consensus       517 L~L~~~~~l~-----~lp~~i~~L~~L~~L~L~~~~i----~~lp-------~~~~~L~~L~~L~l~~~~~l~~lp~~--  578 (779)
                      ++|||| .+.     .+...|.+-.+|+..+++.-..    .++|       +.+-+|++|+..+|+.|-+-...|+.  
T Consensus        35 vdLSGN-tigtEA~e~l~~~ia~~~~L~vvnfsd~ftgr~kde~~~~L~~Ll~aLlkcp~l~~v~LSDNAfg~~~~e~L~  113 (388)
T COG5238          35 VDLSGN-TIGTEAMEELCNVIANVRNLRVVNFSDAFTGRDKDELYSNLVMLLKALLKCPRLQKVDLSDNAFGSEFPEELG  113 (388)
T ss_pred             EeccCC-cccHHHHHHHHHHHhhhcceeEeehhhhhhcccHHHHHHHHHHHHHHHhcCCcceeeeccccccCcccchHHH
Confidence            455555 443     2455677778899888876421    2244       34678999999999999766666653  


Q ss_pred             -hhcCCccCcEeeeccccCCC
Q 004021          579 -LISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       579 -~i~~L~~L~~L~l~~~~~~~  598 (779)
                       .|++-+.|.||.+++|++-.
T Consensus       114 d~is~~t~l~HL~l~NnGlGp  134 (388)
T COG5238         114 DLISSSTDLVHLKLNNNGLGP  134 (388)
T ss_pred             HHHhcCCCceeEEeecCCCCc
Confidence             46788999999999997654

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.12  E-value=0.027  Score=51.01  Aligned_cols=36  Identities=28%  Similarity=0.299  Sum_probs=27.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+.|+|.+|+||||+|+.+++..   ......++++..
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~---~~~~~~~~~~~~   38 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAREL---GPPGGGVIYIDG   38 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhcc---CCCCCCEEEECC
Confidence            578999999999999999999887   222233555555

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.10  E-value=0.4  Score=53.19  Aligned_cols=48  Identities=25%  Similarity=0.282  Sum_probs=34.2

Q ss_pred             ccccchhhhHHHHHHHHh---c-----cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---D-----QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~-----~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..++.+.+...   .     +-...+-|-++|++|.|||.+|+++++..
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~  283 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW  283 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            456787776666554321   1     11234668899999999999999999876

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.10  E-value=0.3  Score=57.94  Aligned_cols=48  Identities=27%  Similarity=0.295  Sum_probs=37.9

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.+..++++.+.+.-.           -...+-|.++|.+|+|||+||+++++..
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~  236 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEA  236 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHh
Confidence            34789999999988876421           1234568899999999999999999876

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK00625 shikimate kinase; Provisional

Probab=95.05  E-value=0.02  Score=54.11  Aligned_cols=23  Identities=35%  Similarity=0.379  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.++||+|+||||+++.+.+..
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l   24 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999998876

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=95.02  E-value=0.032  Score=51.16  Aligned_cols=36  Identities=28%  Similarity=0.249  Sum_probs=27.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+|-|.|.+|+||||||+++.+.. .  ..-..+.++..
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L-~--~~g~~~~~LDg   38 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRL-F--ARGIKVYLLDG   38 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHH-H--HTTS-EEEEEH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH-H--HcCCcEEEecC
Confidence            589999999999999999999988 2  33344545544

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 ....

>PRK05439 pantothenate kinase; Provisional

Probab=95.01  E-value=0.11  Score=53.71  Aligned_cols=28  Identities=36%  Similarity=0.380  Sum_probs=24.2

Q ss_pred             CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          175 QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       175 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+..-+|+|.|.+|+||||+|+.+....
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~~l  110 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQALL  110 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3466799999999999999999988765

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.97  E-value=0.0023  Score=62.60  Aligned_cols=95  Identities=23%  Similarity=0.260  Sum_probs=67.0

Q ss_pred             CCccEEEcccccccccccCc---c--cccccccccccccchhhcccccCceeeecCCcccccc--hhhccCccCcEeecc
Q 004021          495 EGAKRISLMANEIESLSEIP---T--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP--QELKALEKLRYLNLE  567 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~---~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp--~~~~~L~~L~~L~l~  567 (779)
                      .+++.|++.++.+.++.-..   .  +|.||-| .|+.+. .+..+++|+.|+|+.|.|..+-  ..+.+|++|++|-|.
T Consensus        19 ~~vkKLNcwg~~L~DIsic~kMp~lEVLsLSvN-kIssL~-pl~rCtrLkElYLRkN~I~sldEL~YLknlpsLr~LWL~   96 (388)
T KOG2123|consen   19 ENVKKLNCWGCGLDDISICEKMPLLEVLSLSVN-KISSLA-PLQRCTRLKELYLRKNCIESLDELEYLKNLPSLRTLWLD   96 (388)
T ss_pred             HHhhhhcccCCCccHHHHHHhcccceeEEeecc-ccccch-hHHHHHHHHHHHHHhcccccHHHHHHHhcCchhhhHhhc
Confidence            34555666666665544221   1  4677777 777663 4678899999999999888764  357899999999998


Q ss_pred             CCcCCCCCchh----hhcCCccCcEeee
Q 004021          568 YTHYLSIIPHQ----LISGFLKLEVLRL  591 (779)
Q Consensus       568 ~~~~l~~lp~~----~i~~L~~L~~L~l  591 (779)
                      .|.....-+..    ++.-|+||+.|+-
T Consensus        97 ENPCc~~ag~nYR~~VLR~LPnLkKLDn  124 (388)
T KOG2123|consen   97 ENPCCGEAGQNYRRKVLRVLPNLKKLDN  124 (388)
T ss_pred             cCCcccccchhHHHHHHHHcccchhccC
Confidence            88765554442    4667888888863

>PRK06217 hypothetical protein; Validated

Probab=94.96  E-value=0.021  Score=54.76  Aligned_cols=23  Identities=30%  Similarity=0.411  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+++....
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999876

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=94.87  E-value=1.5  Score=43.61  Aligned_cols=214  Identities=14%  Similarity=0.201  Sum_probs=115.8

Q ss_pred             ccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc---ccCCCCEEEEEEe----------------
Q 004021          157 IVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH---QQHNFDVVIWAAV----------------  217 (779)
Q Consensus       157 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~---~~~~F~~~~wv~v----------------  217 (779)
                      +.++++....+......+  +.+-.-++|+.|.||-|.+..+.+..-.   .+-.-+...|.+-                
T Consensus        15 l~~~~e~~~~Lksl~~~~--d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHl   92 (351)
T KOG2035|consen   15 LIYHEELANLLKSLSSTG--DFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHL   92 (351)
T ss_pred             cccHHHHHHHHHHhcccC--CCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceE
Confidence            577777777777766544  7888999999999999988777665411   0112244444443                


Q ss_pred             -----------chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCccee-eh---hhcc--------ccccccCCC
Q 004021          218 -----------QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRI-DL---TELG--------VPLQMLNAG  274 (779)
Q Consensus       218 -----------~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~-~l---d~l~--------~~~~~~~~g  274 (779)
                                 +-+.++|+++......               .+.-..+.|.. ++   |.+-        .....-...
T Consensus        93 EitPSDaG~~DRvViQellKevAQt~q---------------ie~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~  157 (351)
T KOG2035|consen   93 EITPSDAGNYDRVVIQELLKEVAQTQQ---------------IETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSN  157 (351)
T ss_pred             EeChhhcCcccHHHHHHHHHHHHhhcc---------------hhhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcC
Confidence                       1223333333221100               00001223322 11   1110        001112356


Q ss_pred             cEEEEEeCch-hhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHHHH-h
Q 004021          275 FKIVLKTRSA-GVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVGRA-M  349 (779)
Q Consensus       275 s~IivTTR~~-~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g~~-l  349 (779)
                      +|+|+...+. .+.....  ...+.+...+++|-...+.+.+...+...+   .+++++|+++++| +--|+-++-.. +
T Consensus       158 ~RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp---~~~l~rIa~kS~~nLRrAllmlE~~~~  234 (351)
T KOG2035|consen  158 CRLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP---KELLKRIAEKSNRNLRRALLMLEAVRV  234 (351)
T ss_pred             ceEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc---HHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            7777654432 2222222  456789999999999999998877664444   7889999999988 44555443221 1


Q ss_pred             cCC--------CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCC
Q 004021          350 KSQ--------KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLS  391 (779)
Q Consensus       350 ~~~--------~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~  391 (779)
                      .+.        -..-+|+-+........-..... ..+..+-..=|+-|.
T Consensus       235 ~n~~~~a~~~~i~~~dWe~~i~e~a~~i~~eQs~-~~L~~vR~~LYeLL~  283 (351)
T KOG2035|consen  235 NNEPFTANSQVIPKPDWEIYIQEIARVILKEQSP-AKLLEVRGRLYELLS  283 (351)
T ss_pred             ccccccccCCCCCCccHHHHHHHHHHHHHhccCH-HHHHHHHHHHHHHHh
Confidence            111        13458988877665543221111 244444444455554

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=94.87  E-value=0.022  Score=54.09  Aligned_cols=25  Identities=28%  Similarity=0.462  Sum_probs=23.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|-||=|+||||||+.++++.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l   28 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHL   28 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHh
Confidence            4689999999999999999999987

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.85  E-value=0.15  Score=50.76  Aligned_cols=47  Identities=21%  Similarity=0.152  Sum_probs=33.6

Q ss_pred             HHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC------CEEEEEEe
Q 004021          168 WRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF------DVVIWAAV  217 (779)
Q Consensus       168 ~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F------~~~~wv~v  217 (779)
                      -+.|.++=....++.|+|.+|+|||+||.+++...   ...-      ..++|++.
T Consensus         9 D~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~---~~~~~~~g~~~~v~yi~~   61 (226)
T cd01393           9 DELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEA---QLPGELGGLEGKVVYIDT   61 (226)
T ss_pred             HHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHh---hcccccCCCcceEEEEec
Confidence            33444433355799999999999999999987665   1222      56788887

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.80  E-value=0.043  Score=58.39  Aligned_cols=48  Identities=23%  Similarity=0.313  Sum_probs=38.9

Q ss_pred             ccccchhhhHHHHHHHHhcc------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+.-.+...            +...+-|.++|++|+|||++|+.++...
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l   71 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLA   71 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            56899999999887776642            1124678999999999999999999876

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.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=94.79  E-value=0.018  Score=50.37  Aligned_cols=27  Identities=41%  Similarity=0.604  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhhccccCCCC
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFD  210 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~~~~~~~F~  210 (779)
                      |-|+|.+|+||||+|+.++...   ...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~~~---~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSL---GLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHT---T--EE
T ss_pred             EeeECCCccHHHHHHHHHHHHc---CCcee
Confidence            5789999999999999999887   55664

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.78  E-value=0.043  Score=53.97  Aligned_cols=39  Identities=23%  Similarity=0.311  Sum_probs=31.8

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...+++.|+|.+|+|||++|.+++...   ...-..++|++.
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~---~~~g~~v~yi~~   48 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNA---ARQGKKVVYIDT   48 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH---HhCCCeEEEEEC
Confidence            345799999999999999999988766   233567888887

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK00131 aroK shikimate kinase; Reviewed

Probab=94.78  E-value=0.027  Score=53.50  Aligned_cols=26  Identities=27%  Similarity=0.362  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|.|+|++|+||||+|+.++...
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l   28 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRL   28 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999999876

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=94.78  E-value=0.032  Score=54.66  Aligned_cols=26  Identities=35%  Similarity=0.615  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+..|.++||+|+||||..+.++.+.
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl   43 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHL   43 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHH
Confidence            45688999999999999999999877

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.75  E-value=0.3  Score=49.80  Aligned_cols=157  Identities=13%  Similarity=0.164  Sum_probs=88.4

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~  225 (779)
                      ..++|-.++..++-.++...  .++-.-|.|+|+.|.|||+|...+..+..+..++|   +-|..       +-.+..|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~---l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENF---LLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeE---EEEEECccchhhHHHHHHHH
Confidence            45799999999999888753  23556788999999999999887776642334444   33333       22344444


Q ss_pred             HHhCCCcch-hhhhcchhhHHHHHHHhhCCCc------ceeehhhcc---cc---------c----cccCCCcEEEEEeC
Q 004021          226 KRIGFSEDK-KWKEKSLQDKAVDISSILSPKK------FRIDLTELG---VP---------L----QMLNAGFKIVLKTR  282 (779)
Q Consensus       226 ~~l~~~~~~-~~~~~~~~~~~~~l~~~L~~kr------~~~~ld~l~---~~---------~----~~~~~gs~IivTTR  282 (779)
                      .++...... .....+..+....+...|+.+-      +..++|++.   .+         |    ....+-|-|-+|||
T Consensus       101 rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttr  180 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTR  180 (408)
T ss_pred             HHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecc
Confidence            444221000 0122333444455555554321      233443331   11         1    12346677788999


Q ss_pred             chh-------hhhhcCCc-eeEccCCChHHHHHHHHHHhh
Q 004021          283 SAG-------VCDQMDSK-NLEVYSLAHDEAWKLFQEMIE  314 (779)
Q Consensus       283 ~~~-------va~~~~~~-~~~l~~L~~~~a~~Lf~~~a~  314 (779)
                      -.-       |-.....+ ++-++.++-++...++++...
T Consensus       181 ld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  181 LDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             ccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhc
Confidence            632       22223333 445677788888888877663

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.74  E-value=0.021  Score=54.78  Aligned_cols=23  Identities=30%  Similarity=0.446  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ||.|+|++|+||||+|+.++...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58899999999999999998865

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.73  E-value=1.5  Score=45.85  Aligned_cols=64  Identities=14%  Similarity=0.033  Sum_probs=43.7

Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .++.+|++|.+ ..+.....  ...+.+.+++.+++.+.+... +     .+   ...+..++..++|.|+.+..+
T Consensus       142 ~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~-~-----~~---~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        142 PGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQ-G-----VS---ERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             CCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHc-C-----CC---hHHHHHHHHHcCCCHHHHHHH
Confidence            46666666654 55554443  678899999999998887653 1     11   233678899999999876544

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.72  E-value=0.065  Score=46.80  Aligned_cols=48  Identities=17%  Similarity=0.324  Sum_probs=36.2

Q ss_pred             ccccchhhhHHHHHHHHhc----c-CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD----Q-QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|..-..+.+++.+.+    . ...+-|++.+|..|+|||.+|+.+++..
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            4568877666666666653    2 3355699999999999999998888773

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

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.72  E-value=0.3  Score=46.76  Aligned_cols=25  Identities=32%  Similarity=0.460  Sum_probs=21.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.|++|+|+.|+|||||.+.+..-.
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~LE   52 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGLE   52 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCc
Confidence            4699999999999999999986543

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=94.71  E-value=0.059  Score=53.69  Aligned_cols=49  Identities=22%  Similarity=0.255  Sum_probs=35.7

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEec
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQ  218 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~  218 (779)
                      |-+.|..+=....++.|+|.+|+|||++|.+++....   ..-..++|++..
T Consensus        12 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~---~~~~~v~yi~~e   60 (225)
T PRK09361         12 LDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAA---KNGKKVIYIDTE   60 (225)
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEECC
Confidence            3344444433557999999999999999999987762   334678888873

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=94.70  E-value=0.29  Score=53.15  Aligned_cols=126  Identities=25%  Similarity=0.266  Sum_probs=67.3

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhc
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEK  239 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~  239 (779)
                      |..-..++.+.+...  . .++.|.|+-++||||+++.+....   .+.   .+++...++...-              .
T Consensus        22 ~~~~~~~l~~~~~~~--~-~i~~i~GpR~~GKTtll~~l~~~~---~~~---~iy~~~~d~~~~~--------------~   78 (398)
T COG1373          22 RRKLLPRLIKKLDLR--P-FIILILGPRQVGKTTLLKLLIKGL---LEE---IIYINFDDLRLDR--------------I   78 (398)
T ss_pred             HHhhhHHHHhhcccC--C-cEEEEECCccccHHHHHHHHHhhC---Ccc---eEEEEecchhcch--------------h
Confidence            334445555554444  2 299999999999999997776655   222   5555552211000              0


Q ss_pred             chhhHHHHHHHhhCCCcceee---------hhhccccccccCCCcEEEEEeCchhh-----hhhc-C-CceeEccCCChH
Q 004021          240 SLQDKAVDISSILSPKKFRID---------LTELGVPLQMLNAGFKIVLKTRSAGV-----CDQM-D-SKNLEVYSLAHD  303 (779)
Q Consensus       240 ~~~~~~~~l~~~L~~kr~~~~---------ld~l~~~~~~~~~gs~IivTTR~~~v-----a~~~-~-~~~~~l~~L~~~  303 (779)
                      ...+....+...-..++..+.         |+.....+.+.++. +|++|+-+..+     +... | ...+++.||+..
T Consensus        79 ~l~d~~~~~~~~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~  157 (398)
T COG1373          79 ELLDLLRAYIELKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFR  157 (398)
T ss_pred             hHHHHHHHHHHhhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHH
Confidence            000111111111111333333         33333334444555 88988877554     3333 3 567899999998


Q ss_pred             HHHHHH
Q 004021          304 EAWKLF  309 (779)
Q Consensus       304 ~a~~Lf  309 (779)
                      |-..+-
T Consensus       158 Efl~~~  163 (398)
T COG1373         158 EFLKLK  163 (398)
T ss_pred             HHHhhc
Confidence            887653

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=94.69  E-value=0.12  Score=61.79  Aligned_cols=49  Identities=27%  Similarity=0.391  Sum_probs=39.9

Q ss_pred             cccccchhhhHHHHHHHHhc-------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITD-------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++|.+..++.+.+.+..       +.....++.++|+.|+|||.||++++...
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l  620 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL  620 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            35789999999999998853       12234578999999999999999998766

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.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=94.68  E-value=0.97  Score=50.75  Aligned_cols=154  Identities=12%  Similarity=0.157  Sum_probs=87.5

Q ss_pred             ccccchhhhHHHHHHHHhc---cCCCceEEEEEcCCCCcHHHHHHHHHhhhcc--ccCCCCEEEEEEe--------chHH
Q 004021          155 QTIVGQEKLLPRVWRCITD---QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH--QQHNFDVVIWAAV--------QTFQ  221 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~--~~~~F~~~~wv~v--------~~i~  221 (779)
                      ..+-+|+.+..+|.+.+..   +++..+.+-|.|.+|+|||..+..|.+....  .++.-....+|.+        .++.
T Consensus       396 ~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y  475 (767)
T KOG1514|consen  396 ESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIY  475 (767)
T ss_pred             ccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHH
Confidence            4567899999999998864   2344568999999999999999999885410  1222222223333        6677


Q ss_pred             HHHHHHhCCCcchhhhhcchhhHHHHHHHhhC---CCcc--e---eehhhccc--------ccc-ccCCCcEEEEEeCc-
Q 004021          222 DDIGKRIGFSEDKKWKEKSLQDKAVDISSILS---PKKF--R---IDLTELGV--------PLQ-MLNAGFKIVLKTRS-  283 (779)
Q Consensus       222 ~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~---~kr~--~---~~ld~l~~--------~~~-~~~~gs~IivTTR~-  283 (779)
                      ..|...+...      ........+.+..+..   .++-  .   ..+|.+..        .|. ...++||++|.+=. 
T Consensus       476 ~~I~~~lsg~------~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~IaN  549 (767)
T KOG1514|consen  476 EKIWEALSGE------RVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIAN  549 (767)
T ss_pred             HHHHHhcccC------cccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEecc
Confidence            8888877654      1122333444444443   2222  2   22333322        122 23578887776521 


Q ss_pred             ----------hhhhhhcCCceeEccCCChHHHHHHHHHHhh
Q 004021          284 ----------AGVCDQMDSKNLEVYSLAHDEAWKLFQEMIE  314 (779)
Q Consensus       284 ----------~~va~~~~~~~~~l~~L~~~~a~~Lf~~~a~  314 (779)
                                ..|+..+|...+...|-++.+-.++...+..
T Consensus       550 TmdlPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~  590 (767)
T KOG1514|consen  550 TMDLPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLK  590 (767)
T ss_pred             cccCHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhc
Confidence                      1223334444556666666665555555443

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.68  E-value=0.068  Score=54.57  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=35.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT  219 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~  219 (779)
                      +..+++.|.|.+|+|||++|.++....   ......++||+...
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~---~~~ge~vlyvs~~e   61 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEG---AREGEPVLYVSTEE   61 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHH---HhcCCcEEEEEecC
Confidence            356899999999999999999998877   35588899999933

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=94.67  E-value=0.023  Score=54.17  Aligned_cols=23  Identities=39%  Similarity=0.635  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|.+|+||||+|+.++...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~~   23 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRIL   23 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999998875

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.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.65  E-value=0.056  Score=57.59  Aligned_cols=49  Identities=22%  Similarity=0.319  Sum_probs=39.5

Q ss_pred             cccccchhhhHHHHHHHHhcc------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..++|.++.++.+..++...            +....-|.++|++|+|||+||+.++...
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l   74 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            356899999999998888541            1124678999999999999999998876

>PRK12608 transcription termination factor Rho; Provisional

Probab=94.63  E-value=0.12  Score=54.32  Aligned_cols=65  Identities=15%  Similarity=0.123  Sum_probs=43.6

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEEEe-------chHHHHHHHHhCC
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWAAV-------QTFQDDIGKRIGF  230 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv~v-------~~i~~~i~~~l~~  230 (779)
                      ...++++.+..-. ....+.|+|.+|+|||||++.+++...  ..+-+. ++|+.+       .++.+.+...+..
T Consensus       119 ~~~RvID~l~PiG-kGQR~LIvG~pGtGKTTLl~~la~~i~--~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vva  191 (380)
T PRK12608        119 LSMRVVDLVAPIG-KGQRGLIVAPPRAGKTVLLQQIAAAVA--ANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYA  191 (380)
T ss_pred             hhHhhhhheeecC-CCceEEEECCCCCCHHHHHHHHHHHHH--hcCCCceEEEEEecCCCCCHHHHHHHHhhhEEe
Confidence            3445777776421 335679999999999999999998762  234454 356666       5566666665554

>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=94.61  E-value=0.049  Score=51.22  Aligned_cols=46  Identities=20%  Similarity=0.304  Sum_probs=34.8

Q ss_pred             ccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          157 IVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       157 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +||.+..+.++.+.+..-.....-|-|+|-.|+||+.+|+.+++.-
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            4788888999888887643233556699999999999999998865

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 ....

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.61  E-value=0.68  Score=55.57  Aligned_cols=48  Identities=29%  Similarity=0.422  Sum_probs=38.8

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+.+...       .....++.++|..|+|||++|+.+++..
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            56899999999998888642       1223578899999999999999998765

>PRK00889 adenylylsulfate kinase; Provisional

Probab=94.56  E-value=0.037  Score=52.68  Aligned_cols=26  Identities=23%  Similarity=0.452  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|+|.+|+||||+|+.++...
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l   28 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKL   28 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45699999999999999999999876

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.54  E-value=0.028  Score=51.55  Aligned_cols=20  Identities=45%  Similarity=0.690  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 004021          180 IIGLYGIGGVGKTTLLKQVN  199 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~  199 (779)
                      .|+|.|.||+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999987

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=94.53  E-value=0.078  Score=52.40  Aligned_cols=52  Identities=21%  Similarity=0.285  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...++++.+....++..+|+|.|.||+||+||.-++.... ..+  =..++-+.|
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~-~~~--g~~VaVlAV   65 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIREL-RER--GKRVAVLAV   65 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHH-HHT--T--EEEEEE
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHH-hhc--CCceEEEEE
Confidence            4566777776655577899999999999999999988877 322  223455555

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>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=94.52  E-value=0.056  Score=52.18  Aligned_cols=54  Identities=15%  Similarity=0.206  Sum_probs=36.5

Q ss_pred             chhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          159 GQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+..+-...++.|.+    ..++.+.|.+|.|||.||.+.+-+. -..+.|+.++++.-
T Consensus         4 p~~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al~~-v~~g~~~kiii~Rp   57 (205)
T PF02562_consen    4 PKNEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAALEL-VKEGEYDKIIITRP   57 (205)
T ss_dssp             --SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHHHH-HHTTS-SEEEEEE-
T ss_pred             CCCHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHHHH-HHhCCCcEEEEEec
Confidence            445556667777773    3699999999999999999988665 34588888877754

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK13947 shikimate kinase; Provisional

Probab=94.49  E-value=0.032  Score=52.91  Aligned_cols=23  Identities=43%  Similarity=0.507  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|+|++|+||||+|+.+++..
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999876

>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=94.49  E-value=0.038  Score=52.70  Aligned_cols=23  Identities=39%  Similarity=0.767  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|.+|+||||||+.+....
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l   23 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQL   23 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=94.48  E-value=0.026  Score=55.77  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|.+|+||||+|+.+....
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l   23 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALL   23 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999876

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.47  E-value=0.027  Score=54.88  Aligned_cols=23  Identities=39%  Similarity=0.660  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|.+|+||||||+.+....
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999997764

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.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=94.45  E-value=0.029  Score=48.39  Aligned_cols=22  Identities=41%  Similarity=0.768  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |-|+|.+|+|||+||+.++.+.
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            4689999999999999988776

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

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.44  E-value=0.12  Score=53.57  Aligned_cols=87  Identities=13%  Similarity=0.204  Sum_probs=53.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchhh--hhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKKW--KEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~~--~~~~~~~~~~~l~~~L~  253 (779)
                      .-+++-|+|..|+||||||..+....   +..-..++|+.. ..+-...+..++.+.+.-.  .+...++....+.+.++
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia~~---q~~g~~~a~ID~e~~ld~~~a~~lGvdl~rllv~~P~~~E~al~~~e~lir  128 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIAEA---QKQGGICAFIDAEHALDPEYAESLGVDLDRLLVVQPDTGEQALWIAEQLIR  128 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH---HHTT-EEEEEESSS---HHHHHHTT--GGGEEEEE-SSHHHHHHHHHHHHH
T ss_pred             cCceEEEeCCCCCchhhhHHHHHHhh---hcccceeEEecCcccchhhHHHhcCccccceEEecCCcHHHHHHHHHHHhh
Confidence            45799999999999999999988766   334567899999 5566677777776533211  23344555555555555


Q ss_pred             CCcc-eeehhhccc
Q 004021          254 PKKF-RIDLTELGV  266 (779)
Q Consensus       254 ~kr~-~~~ld~l~~  266 (779)
                      ...+ .+++|.+..
T Consensus       129 sg~~~lVVvDSv~a  142 (322)
T PF00154_consen  129 SGAVDLVVVDSVAA  142 (322)
T ss_dssp             TTSESEEEEE-CTT
T ss_pred             cccccEEEEecCcc
Confidence            5444 555666543

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.41  E-value=0.21  Score=52.81  Aligned_cols=38  Identities=34%  Similarity=0.417  Sum_probs=28.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++|+++|.+|+||||++..++... . ...+ .+..++.
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L-~-~~Gk-kVglI~a  277 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQF-H-GKKK-TVGFITT  277 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHH-H-HcCC-cEEEEec
Confidence            45799999999999999999998776 2 2222 3445555

>cd01394 radB RadB

Probab=94.40  E-value=0.086  Score=52.20  Aligned_cols=48  Identities=17%  Similarity=0.180  Sum_probs=33.7

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      |-+.|..+=....++.|.|.+|+||||+|.+++...   ...-..++|++.
T Consensus         8 LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~---~~~g~~v~yi~~   55 (218)
T cd01394           8 LDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVET---AGQGKKVAYIDT   55 (218)
T ss_pred             HHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHH---HhcCCeEEEEEC
Confidence            444444333355799999999999999999998776   222345677765

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=94.39  E-value=0.035  Score=53.08  Aligned_cols=24  Identities=33%  Similarity=0.488  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+|+.|+|||||++.+....
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~   25 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARL   25 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            478999999999999999998765

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.

>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=94.39  E-value=0.03  Score=51.40  Aligned_cols=23  Identities=35%  Similarity=0.576  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.|.|.+|+||||+|+.+....
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998865

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=94.34  E-value=0.048  Score=55.87  Aligned_cols=26  Identities=27%  Similarity=0.258  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.+|+|.|..|+||||+|+.+..-.
T Consensus        61 ~p~IIGIaG~~GSGKSTlar~L~~ll   86 (290)
T TIGR00554        61 IPYIISIAGSVAVGKSTTARILQALL   86 (290)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            56799999999999999998876654

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.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=94.34  E-value=0.058  Score=54.02  Aligned_cols=39  Identities=26%  Similarity=0.543  Sum_probs=33.3

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++..+....++..+|+|.|.||+||+||.-.+...+
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l   75 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGREL   75 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHH
Confidence            457777777766688999999999999999998888777

>PRK13949 shikimate kinase; Provisional

Probab=94.32  E-value=0.038  Score=52.14  Aligned_cols=23  Identities=43%  Similarity=0.443  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|+|++|+||||+++.+++..
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999876

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.31  E-value=0.037  Score=52.65  Aligned_cols=24  Identities=25%  Similarity=0.393  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.+.|++|+||||+|+.+....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            589999999999999999998775

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=94.30  E-value=0.098  Score=53.47  Aligned_cols=38  Identities=32%  Similarity=0.463  Sum_probs=29.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++|.++|.+|+||||++..++... .  ..-..+.+++.
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~l-~--~~g~~V~li~~  108 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANKL-K--KQGKSVLLAAG  108 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH-H--hcCCEEEEEeC
Confidence            56899999999999999999998776 2  22235666665

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.28  E-value=0.11  Score=52.93  Aligned_cols=26  Identities=31%  Similarity=0.404  Sum_probs=24.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+|.|+|.+|+|||||+..+.+..
T Consensus       103 ~~~~v~l~G~pGsGKTTLl~~l~~~l  128 (290)
T PRK10463        103 KQLVLNLVSSPGSGKTTLLTETLMRL  128 (290)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            78999999999999999999999876

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=94.27  E-value=0.065  Score=61.16  Aligned_cols=70  Identities=14%  Similarity=0.215  Sum_probs=53.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHHHhC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGKRIG  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~~l~  229 (779)
                      ..++|.++.++.|...+...    +.+.++|.+|+||||+|+.+.+...  ..+++..+|..-     ..+++.++..++
T Consensus        31 ~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~~l~--~~~~~~~~~~~np~~~~~~~~~~v~~~~G  104 (637)
T PRK13765         31 DQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAELLP--KEELQDILVYPNPEDPNNPKIRTVPAGKG  104 (637)
T ss_pred             HHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHHHcC--hHhHHHheEeeCCCcchHHHHHHHHHhcC
Confidence            56899999988888777655    4688999999999999999998762  345677888776     455555655544


Q ss_pred             C
Q 004021          230 F  230 (779)
Q Consensus       230 ~  230 (779)
                      .
T Consensus       105 ~  105 (637)
T PRK13765        105 K  105 (637)
T ss_pred             H
Confidence            3

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=94.24  E-value=0.71  Score=44.85  Aligned_cols=47  Identities=26%  Similarity=0.343  Sum_probs=34.1

Q ss_pred             cccc-hhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVG-QEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vG-r~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++| .+..+++|.+.+.-+           -..++=+.++|++|.|||-||++|+++.
T Consensus       147 eMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht  205 (404)
T KOG0728|consen  147 EMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT  205 (404)
T ss_pred             HHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc
Confidence            3455 577777777665321           1245667899999999999999999876

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=94.23  E-value=0.056  Score=52.17  Aligned_cols=23  Identities=39%  Similarity=0.590  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+|.|-||+||||+|..+....
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l   24 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRL   24 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHH
Confidence            68999999999999999966655

>PRK04328 hypothetical protein; Provisional

Probab=94.23  E-value=0.22  Score=50.33  Aligned_cols=48  Identities=19%  Similarity=0.130  Sum_probs=34.1

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      |-+.|..+=..-.++.|.|.+|+|||+||.++....   -..-..++|++.
T Consensus        12 LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~---~~~ge~~lyis~   59 (249)
T PRK04328         12 MDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNG---LQMGEPGVYVAL   59 (249)
T ss_pred             HHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHH---HhcCCcEEEEEe
Confidence            334444432345799999999999999999876654   123456888988

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.22  E-value=0.034  Score=51.37  Aligned_cols=23  Identities=35%  Similarity=0.593  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.|.|++|+||||+|+.+....
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999997764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=94.21  E-value=0.069  Score=48.48  Aligned_cols=37  Identities=22%  Similarity=0.448  Sum_probs=26.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++|.|+|..|+|||||++.+.+.. . +..+...+..+.
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l-~-~~g~~v~~ik~~   37 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINEL-K-RRGYRVAVIKHT   37 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHH-H-HTT--EEEEEE-
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-h-HcCCceEEEEEc
Confidence            489999999999999999999988 2 345555545544

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=94.19  E-value=0.18  Score=51.68  Aligned_cols=55  Identities=24%  Similarity=0.292  Sum_probs=42.5

Q ss_pred             cccccchhhhHH---HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC
Q 004021          154 EQTIVGQEKLLP---RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF  209 (779)
Q Consensus       154 ~~~~vGr~~~~~---~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F  209 (779)
                      ...+||..+..+   -+++.+..+.-.-+.|-|+|++|.|||+||..+.+.. -..-.|
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eL-G~dvPF   95 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIAREL-GEDVPF   95 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHh-CCCCCc
Confidence            456899876554   4666777665567899999999999999999999988 444556

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=94.18  E-value=0.059  Score=51.27  Aligned_cols=46  Identities=24%  Similarity=0.372  Sum_probs=33.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      ..-+.++|..|+|||.||.++.+...  ... ..+.|+++.+++..+-.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~--~~g-~~v~f~~~~~L~~~l~~   92 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAI--RKG-YSVLFITASDLLDELKQ   92 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHH--HTT---EEEEEHHHHHHHHHC
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhc--cCC-cceeEeecCceeccccc
Confidence            35699999999999999999998873  222 34677888777776643

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.17  E-value=0.1  Score=59.83  Aligned_cols=70  Identities=17%  Similarity=0.232  Sum_probs=49.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHHHhC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGKRIG  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~~l~  229 (779)
                      ..++|.++.++.+...+...    +-+.++|++|+||||+|+.+.+.. . ...|...+++.-     ..++..++..++
T Consensus        18 ~~viG~~~a~~~l~~a~~~~----~~~ll~G~pG~GKT~la~~la~~l-~-~~~~~~~~~~~n~~~~~~~~~~~v~~~~g   91 (608)
T TIGR00764        18 DQVIGQEEAVEIIKKAAKQK----RNVLLIGEPGVGKSMLAKAMAELL-P-DEELEDILVYPNPEDPNMPRIVEVPAGEG   91 (608)
T ss_pred             hhccCHHHHHHHHHHHHHcC----CCEEEECCCCCCHHHHHHHHHHHc-C-chhheeEEEEeCCCCCchHHHHHHHHhhc
Confidence            56799999888887777655    245599999999999999999877 2 223333333333     456666666655


Q ss_pred             C
Q 004021          230 F  230 (779)
Q Consensus       230 ~  230 (779)
                      .
T Consensus        92 ~   92 (608)
T TIGR00764        92 R   92 (608)
T ss_pred             h
Confidence            3

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=94.17  E-value=0.039  Score=52.33  Aligned_cols=23  Identities=35%  Similarity=0.515  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|.+|+||||+|+.+.+..
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999875

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.11  E-value=1.4  Score=49.33  Aligned_cols=52  Identities=31%  Similarity=0.328  Sum_probs=37.9

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF  209 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F  209 (779)
                      .++=|.++-+.++.+.+.-+           -...+=|-.+|+||.|||++|+++++..   +-.|
T Consensus       434 ~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~---~~nF  496 (693)
T KOG0730|consen  434 DDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEA---GMNF  496 (693)
T ss_pred             hhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhh---cCCe
Confidence            44455777776666554321           2356788899999999999999999987   5555

>PRK14530 adenylate kinase; Provisional

Probab=94.11  E-value=0.042  Score=54.27  Aligned_cols=24  Identities=33%  Similarity=0.405  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.|+|++|+||||+|+.++...
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998776

>PRK08181 transposase; Validated

Probab=94.09  E-value=0.11  Score=52.82  Aligned_cols=45  Identities=18%  Similarity=0.215  Sum_probs=34.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      .-+.++|.+|+|||.||.++.+...   .....+.|+++.++...+..
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~---~~g~~v~f~~~~~L~~~l~~  151 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALI---ENGWRVLFTRTTDLVQKLQV  151 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHH---HcCCceeeeeHHHHHHHHHH
Confidence            4589999999999999999998772   23345677777666666643

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=94.08  E-value=0.12  Score=52.47  Aligned_cols=64  Identities=20%  Similarity=0.214  Sum_probs=40.8

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc----CCCCEEEEEEe-----chHHHHHHHHhCC
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ----HNFDVVIWAAV-----QTFQDDIGKRIGF  230 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~~F~~~~wv~v-----~~i~~~i~~~l~~  230 (779)
                      .|-+.|.++=....++=|+|.+|+|||+||..++-.. ...    +.=..++|++-     .+-+.+|++..+.
T Consensus        26 ~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~-~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~~~~~   98 (256)
T PF08423_consen   26 SLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNV-QLPEEIGGLGGKVVYIDTEGTFSPERLQQIAERFGL   98 (256)
T ss_dssp             HHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHT-TSGGCTTSSSSEEEEEESSSSS-HHHHHHHHHHTTS
T ss_pred             HHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHh-hcccccccCCCceEEEeCCCCCCHHHHHHHhhcccc
Confidence            3444554432244699999999999999998876443 111    12246899998     3344566665543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=94.07  E-value=0.073  Score=51.06  Aligned_cols=37  Identities=35%  Similarity=0.476  Sum_probs=30.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .++|.|+|+.|+|||||+..+....   ...|...++.+-
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~---~~~~~~~v~~TT   38 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEF---PDKFGRVVSHTT   38 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHS---TTTEEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc---ccccccceeecc
Confidence            4789999999999999999999987   567765555554

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=94.06  E-value=0.69  Score=46.38  Aligned_cols=23  Identities=30%  Similarity=0.576  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|..|+||||+|+.+.+..
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l   23 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIF   23 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999998876

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.03  E-value=0.081  Score=53.45  Aligned_cols=50  Identities=20%  Similarity=0.240  Sum_probs=39.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIG  229 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~  229 (779)
                      ...=+.++|.+|+|||.||.++.++..   ..--.+.++++.++..++.....
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~---~~g~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELL---KAGISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHH---HcCCeEEEEEHHHHHHHHHHHHh
Confidence            446788999999999999999999982   33345778888888887776554

>PRK13948 shikimate kinase; Provisional

Probab=94.03  E-value=0.056  Score=51.46  Aligned_cols=26  Identities=19%  Similarity=0.293  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+.|.++|+.|+||||+++.+.+..
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~l   34 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRAL   34 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            45789999999999999999998876

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=94.01  E-value=0.051  Score=52.49  Aligned_cols=25  Identities=32%  Similarity=0.347  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.++.+.
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998875

>PRK06835 DNA replication protein DnaC; Validated

Probab=94.01  E-value=0.12  Score=54.10  Aligned_cols=45  Identities=20%  Similarity=0.288  Sum_probs=34.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      .-+.++|..|+|||.||.++++...   ..-..++++++.+++..+..
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~---~~g~~V~y~t~~~l~~~l~~  228 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELL---DRGKSVIYRTADELIEILRE  228 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHH---HCCCeEEEEEHHHHHHHHHH
Confidence            6799999999999999999999872   22236778888776666644

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=93.99  E-value=0.043  Score=49.89  Aligned_cols=22  Identities=36%  Similarity=0.498  Sum_probs=20.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.++|.+|+|||+||+.+++..
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~   23 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALL   23 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999999876

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.

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.98  E-value=0.05  Score=53.29  Aligned_cols=29  Identities=21%  Similarity=0.425  Sum_probs=24.0

Q ss_pred             ccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          173 DQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       173 ~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ++....++|.|+|.+|+|||||++.+...
T Consensus         8 ~~~~~~~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738          8 NKPAKPLLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             CCCCCCeEEEEECcCCCCHHHHHHHHHhc
Confidence            33446789999999999999999998754

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=93.97  E-value=0.056  Score=50.64  Aligned_cols=26  Identities=31%  Similarity=0.431  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++++|+|..|+|||||++.+....
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l   30 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPAL   30 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHH
Confidence            56799999999999999999998876

>PLN02318 phosphoribulokinase/uridine kinase

Probab=93.95  E-value=0.069  Score=59.22  Aligned_cols=35  Identities=23%  Similarity=0.393  Sum_probs=27.3

Q ss_pred             HHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          168 WRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       168 ~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.+....+++.+|+|.|..|+||||||+.+....
T Consensus        55 ~qlL~~~~~~riIIGIaGpSGSGKTTLAk~LaglL   89 (656)
T PLN02318         55 CQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLNFM   89 (656)
T ss_pred             HHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHhhC
Confidence            33444344467899999999999999999998654

>PRK08939 primosomal protein DnaI; Reviewed

Probab=93.95  E-value=0.14  Score=53.23  Aligned_cols=67  Identities=19%  Similarity=0.227  Sum_probs=46.4

Q ss_pred             chhhhHHHHHHHHhccC--CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHh
Q 004021          159 GQEKLLPRVWRCITDQQ--KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRI  228 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~~--~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l  228 (779)
                      +|....+...+++..-.  ...+-+-++|..|+|||.||.++++...  +.. ..+.++++..++..+....
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~--~~g-~~v~~~~~~~l~~~lk~~~  203 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA--KKG-VSSTLLHFPEFIRELKNSI  203 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH--HcC-CCEEEEEHHHHHHHHHHHH
Confidence            45555555566665321  1346788999999999999999999983  233 3467788877777776554

>PRK03846 adenylylsulfate kinase; Provisional

Probab=93.92  E-value=0.06  Score=52.40  Aligned_cols=26  Identities=19%  Similarity=0.415  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|++|+||||||+.+....
T Consensus        23 ~~~~i~i~G~~GsGKSTla~~l~~~l   48 (198)
T PRK03846         23 KGVVLWFTGLSGSGKSTVAGALEEAL   48 (198)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            56799999999999999999998876

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=93.91  E-value=1.9  Score=45.52  Aligned_cols=46  Identities=13%  Similarity=0.150  Sum_probs=35.2

Q ss_pred             cccc-hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVG-QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vG-r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++| .+..++.+.+.+..+. -....-++|..|+||||+|..+.+..
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~-l~ha~Lf~G~~G~gk~~~a~~la~~l   52 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR-LSHAYLFEGAKGTGKKATALWLAKSL   52 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHH
Confidence            3567 6667777777776552 34577999999999999999987765

>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=93.90  E-value=0.037  Score=29.77  Aligned_cols=16  Identities=44%  Similarity=0.683  Sum_probs=7.2

Q ss_pred             cCceeeecCCcccccc
Q 004021          537 SLHHLDLSLTHIRGLP  552 (779)
Q Consensus       537 ~L~~L~L~~~~i~~lp  552 (779)
                      +|+.|+|++|+++++|
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            4566666666665554

...

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=93.90  E-value=0.11  Score=58.58  Aligned_cols=45  Identities=29%  Similarity=0.406  Sum_probs=37.1

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .+++|.+..++.+...+...  ...-|-|+|.+|+|||++|+.+++.
T Consensus        65 ~~iiGqs~~i~~l~~al~~~--~~~~vLi~Ge~GtGKt~lAr~i~~~  109 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGP--NPQHVIIYGPPGVGKTAAARLVLEE  109 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCC--CCceEEEECCCCCCHHHHHHHHHHH
Confidence            35899999999998877554  3455679999999999999999864

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.87  E-value=0.15  Score=51.29  Aligned_cols=57  Identities=18%  Similarity=0.148  Sum_probs=38.2

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      |-+.|..+=....++.|.|.+|+|||++|.++....   -..-..++||+...-..++.+
T Consensus        10 LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~---~~~ge~~lyvs~ee~~~~i~~   66 (237)
T TIGR03877        10 MDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNG---LQMGEPGIYVALEEHPVQVRR   66 (237)
T ss_pred             HHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHH---HHcCCcEEEEEeeCCHHHHHH
Confidence            334454443356799999999999999999876654   123467888888443334433

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>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=93.86  E-value=0.049  Score=50.48  Aligned_cols=22  Identities=36%  Similarity=0.510  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|+|++|+||||+|+.+....
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            6899999999999999998775

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=93.84  E-value=0.19  Score=52.83  Aligned_cols=26  Identities=27%  Similarity=0.464  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.++|++|+||||++..+++..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l  164 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYL  164 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            46899999999999999998888766

>TIGR03263 guanyl_kin guanylate kinase

Probab=93.84  E-value=0.049  Score=52.10  Aligned_cols=24  Identities=38%  Similarity=0.461  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|+.|+||||||+.++...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            589999999999999999998864

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.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=93.84  E-value=0.052  Score=49.18  Aligned_cols=23  Identities=52%  Similarity=0.784  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|+|+.|+|||||++.+....
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~~   23 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEF   23 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhcC
Confidence            37899999999999999998875

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.

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

Probab=93.82  E-value=0.14  Score=45.57  Aligned_cols=60  Identities=15%  Similarity=0.236  Sum_probs=29.9

Q ss_pred             hhcccccCceeeecCCcccccchh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecc
Q 004021          531 RISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE  593 (779)
Q Consensus       531 ~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~  593 (779)
                      .|.+..+|+.+.+.. .++.++.. |.++++|+.+.+..+  +..++...+..+.+|+.+.+..
T Consensus         7 ~F~~~~~l~~i~~~~-~~~~I~~~~F~~~~~l~~i~~~~~--~~~i~~~~F~~~~~l~~i~~~~   67 (129)
T PF13306_consen    7 AFYNCSNLESITFPN-TIKKIGENAFSNCTSLKSINFPNN--LTSIGDNAFSNCKSLESITFPN   67 (129)
T ss_dssp             TTTT-TT--EEEETS-T--EE-TTTTTT-TT-SEEEESST--TSCE-TTTTTT-TT-EEEEETS
T ss_pred             HHhCCCCCCEEEECC-CeeEeChhhccccccccccccccc--ccccceeeeecccccccccccc
Confidence            355666777777664 35555443 666667777777654  5666666566666677776643

>PF13245 AAA_19: Part of AAA domain

Probab=93.80  E-value=0.19  Score=40.11  Aligned_cols=51  Identities=22%  Similarity=0.218  Sum_probs=29.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccc-cCCCCEEEEEEe-chHHHHHHHHh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQ-QHNFDVVIWAAV-QTFQDDIGKRI  228 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~~F~~~~wv~v-~~i~~~i~~~l  228 (779)
                      .+++.|.|.+|.|||+++.......... ...-+.++.++. ....+.|.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            3678889999999995554444333121 122334555555 55555665555

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

Probab=93.79  E-value=0.0059  Score=63.31  Aligned_cols=211  Identities=22%  Similarity=0.237  Sum_probs=109.0

Q ss_pred             cccccccccc--ccchhhcccccCceeeecCC-cccc--cchhhccCccCcEeeccCCcCCCCCchh-hhcCCccCcEee
Q 004021          517 LSLRRNDSLT--ELPSRISSLVSLHHLDLSLT-HIRG--LPQELKALEKLRYLNLEYTHYLSIIPHQ-LISGFLKLEVLR  590 (779)
Q Consensus       517 L~L~~~~~l~--~lp~~i~~L~~L~~L~L~~~-~i~~--lp~~~~~L~~L~~L~l~~~~~l~~lp~~-~i~~L~~L~~L~  590 (779)
                      |.|+|+..+.  .+-..-.+.++++.|++.+| .++.  +-.--..+.+|++|++..|..++...-. ....+++|.+|+
T Consensus       143 LSlrG~r~v~~sslrt~~~~CpnIehL~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~kL~~lN  222 (483)
T KOG4341|consen  143 LSLRGCRAVGDSSLRTFASNCPNIEHLALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAEGCRKLKYLN  222 (483)
T ss_pred             ccccccccCCcchhhHHhhhCCchhhhhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHHhhhhHHHhh
Confidence            6666663332  22333456778888888877 3433  2222346788888888887655533221 234678888888


Q ss_pred             eccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc-------ccCCCCCccc------Cc----cc--
Q 004021          591 LLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV-------QKFFKYPKLD------LT----WL--  651 (779)
Q Consensus       591 l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~-------~~~~~L~~L~------~~----~l--  651 (779)
                      ++.|.--.          +  ...-.-..+..+|+.+...++....+       ..+.-+.+++      +.    |.  
T Consensus       223 lSwc~qi~----------~--~gv~~~~rG~~~l~~~~~kGC~e~~le~l~~~~~~~~~i~~lnl~~c~~lTD~~~~~i~  290 (483)
T KOG4341|consen  223 LSWCPQIS----------G--NGVQALQRGCKELEKLSLKGCLELELEALLKAAAYCLEILKLNLQHCNQLTDEDLWLIA  290 (483)
T ss_pred             hccCchhh----------c--CcchHHhccchhhhhhhhcccccccHHHHHHHhccChHhhccchhhhccccchHHHHHh
Confidence            88774221          0  11112233344455554443222111       0000011110      00    00  


Q ss_pred             ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC--CCCCCCccEEeeeCC
Q 004021          652 VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN--PLHFPKLKKIGVYGC  729 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~--~~~l~~L~~L~l~~c  729 (779)
                      ..+..|+.|..++|..+.+.+-.              .-..+.++|+.|.++.|..+......  ..+.+.|+.+++..|
T Consensus       291 ~~c~~lq~l~~s~~t~~~d~~l~--------------aLg~~~~~L~~l~l~~c~~fsd~~ft~l~rn~~~Le~l~~e~~  356 (483)
T KOG4341|consen  291 CGCHALQVLCYSSCTDITDEVLW--------------ALGQHCHNLQVLELSGCQQFSDRGFTMLGRNCPHLERLDLEEC  356 (483)
T ss_pred             hhhhHhhhhcccCCCCCchHHHH--------------HHhcCCCceEEEeccccchhhhhhhhhhhcCChhhhhhccccc
Confidence            23456677777776654433210              12245688999999988877665442  236788888888888


Q ss_pred             CCCCCC--C-CCCCCcccccEEEechH
Q 004021          730 PKLKKL--P-INSSSAKERRVVIEGLK  753 (779)
Q Consensus       730 ~~L~~l--P-~~~~~~~~~~l~i~~~~  753 (779)
                      .....-  - .......++.+.++.|.
T Consensus       357 ~~~~d~tL~sls~~C~~lr~lslshce  383 (483)
T KOG4341|consen  357 GLITDGTLASLSRNCPRLRVLSLSHCE  383 (483)
T ss_pred             ceehhhhHhhhccCCchhccCChhhhh
Confidence            654322  1 11122333666666443

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=93.79  E-value=0.096  Score=50.27  Aligned_cols=44  Identities=27%  Similarity=0.289  Sum_probs=33.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..+..+.-...+.    .=+.++|.+|+|||++|+.+..-.
T Consensus         3 ~dI~GQe~aKrAL~iAAaG~----h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAGG----HHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHCC------EEEES-CCCTHHHHHHHHHHCS
T ss_pred             hhhcCcHHHHHHHHHHHcCC----CCeEEECCCCCCHHHHHHHHHHhC
Confidence            45789888888877666654    578899999999999999987544

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=93.79  E-value=0.059  Score=48.99  Aligned_cols=47  Identities=30%  Similarity=0.452  Sum_probs=32.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      .+++.|+|.+|+||||+.+.+-...  +..     -.|+...+.-+++...+..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l--~~~-----~ivNyG~~Mle~A~k~glv   50 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL--VKH-----KIVNYGDLMLEIAKKKGLV   50 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH--hhc-----eeeeHhHHHHHHHHHhCCc
Confidence            5799999999999999998776543  111     1133366777777776665

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=93.79  E-value=0.28  Score=45.90  Aligned_cols=26  Identities=35%  Similarity=0.432  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.++-|+|..|.|||||.+.+|...
T Consensus        27 ~Gef~fl~GpSGAGKSTllkLi~~~e   52 (223)
T COG2884          27 KGEFVFLTGPSGAGKSTLLKLIYGEE   52 (223)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhhh
Confidence            34689999999999999999999876

>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=93.78  E-value=0.09  Score=54.52  Aligned_cols=48  Identities=21%  Similarity=0.369  Sum_probs=42.4

Q ss_pred             ccccchhhhHHHHHHHHhcc----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|+|.++.++++++.+...    +..-+|+-++|+.|.||||||..+.+-.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~l  112 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGL  112 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999763    3466899999999999999999998877

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=93.78  E-value=0.28  Score=51.23  Aligned_cols=65  Identities=15%  Similarity=0.123  Sum_probs=41.7

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc----CCCCEEEEEEe-----chHHHHHHHHhCCC
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ----HNFDVVIWAAV-----QTFQDDIGKRIGFS  231 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~----~~F~~~~wv~v-----~~i~~~i~~~l~~~  231 (779)
                      .|-+.|..+=...+++-|+|.+|+|||+|+.+++-.. ...    ..=..++||+.     .+-+.++++.++.+
T Consensus        84 ~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~-~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~g~d  157 (313)
T TIGR02238        84 ALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTA-QLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERFGVD  157 (313)
T ss_pred             HHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHH-hcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHcCCC
Confidence            3444555443355799999999999999998876432 111    11247899998     23345567666654

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>TIGR01069 mutS2 MutS2 family protein

Probab=93.75  E-value=0.99  Score=53.28  Aligned_cols=25  Identities=24%  Similarity=0.326  Sum_probs=21.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      +.+++.|.|+.|.|||||.+.+...
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHH
Confidence            3479999999999999999988755

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=93.74  E-value=0.27  Score=54.19  Aligned_cols=175  Identities=14%  Similarity=0.153  Sum_probs=95.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEEEe-chHHHHHHHHhCCCc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAV-QTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv~v-~~i~~~i~~~l~~~~  232 (779)
                      ++++|.+.-...|.+.+..+. -..-....|.-|+||||+|+-++...--.. ...+.    |- -...+.|...-..+ 
T Consensus        16 ~evvGQe~v~~~L~nal~~~r-i~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~eP----C~~C~~Ck~I~~g~~~D-   89 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGR-IAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEP----CGKCISCKEINEGSLID-   89 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCc-chhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCc----chhhhhhHhhhcCCccc-
Confidence            457999999999999998762 234566789999999999999887651111 11110    00 12223332220000 


Q ss_pred             chhhhhcchhhHHHHHHHhhCCCcc--------eeehhhc-----------cccccccCCCc-EEEEEeCchhhhhhcC-
Q 004021          233 DKKWKEKSLQDKAVDISSILSPKKF--------RIDLTEL-----------GVPLQMLNAGF-KIVLKTRSAGVCDQMD-  291 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~kr~--------~~~ld~l-----------~~~~~~~~~gs-~IivTTR~~~va~~~~-  291 (779)
                      --.++. .-...++.+++..+.-.|        ...+|++           ...+..--..- -|+.||--..+....- 
T Consensus        90 viEiDa-ASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~TIlS  168 (515)
T COG2812          90 VIEIDA-ASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILS  168 (515)
T ss_pred             chhhhh-hhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchhhhh
Confidence            000000 011234444444433222        2233332           11111111222 3555666666654433 


Q ss_pred             -CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh
Q 004021          292 -SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP  339 (779)
Q Consensus       292 -~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP  339 (779)
                       ...|.++.++.++-...+...+.......+   ++....|++..+|..
T Consensus       169 Rcq~f~fkri~~~~I~~~L~~i~~~E~I~~e---~~aL~~ia~~a~Gs~  214 (515)
T COG2812         169 RCQRFDFKRLDLEEIAKHLAAILDKEGINIE---EDALSLIARAAEGSL  214 (515)
T ss_pred             ccccccccCCCHHHHHHHHHHHHHhcCCccC---HHHHHHHHHHcCCCh
Confidence             688999999999999988888876654333   455667777777644

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.73  E-value=0.82  Score=50.41  Aligned_cols=139  Identities=21%  Similarity=0.224  Sum_probs=74.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe--chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCC
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV--QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPK  255 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v--~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~k  255 (779)
                      ..=|-+||++|.|||-||++|+|..   .-.|     ++|  .+++..-.            ..+.....+..++.=...
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVANEa---g~NF-----isVKGPELlNkYV------------GESErAVR~vFqRAR~sa  604 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVANEA---GANF-----ISVKGPELLNKYV------------GESERAVRQVFQRARASA  604 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhhhc---cCce-----EeecCHHHHHHHh------------hhHHHHHHHHHHHhhcCC
Confidence            4557899999999999999999987   4555     555  33322211            111111111111111122


Q ss_pred             cceeehhhcccc----------------------cc--ccCCCcEEEEEeCchhhhhh----cC--CceeEccCCChHHH
Q 004021          256 KFRIDLTELGVP----------------------LQ--MLNAGFKIVLKTRSAGVCDQ----MD--SKNLEVYSLAHDEA  305 (779)
Q Consensus       256 r~~~~ld~l~~~----------------------~~--~~~~gs~IivTTR~~~va~~----~~--~~~~~l~~L~~~~a  305 (779)
                      .+.+-+|++...                      +.  ....|--||-.|...++...    .|  +...-++.-+.+|=
T Consensus       605 PCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR  684 (802)
T KOG0733|consen  605 PCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEER  684 (802)
T ss_pred             CeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHHHH
Confidence            332222222111                      00  11245556777776665322    13  56667788888888


Q ss_pred             HHHHHHHhhc--cCCCCCCChHHHHHHHHHHhCCC
Q 004021          306 WKLFQEMIER--STLDSHTSIPELAETLARECGRL  338 (779)
Q Consensus       306 ~~Lf~~~a~~--~~~~~~~~l~~~~~~I~~~c~gl  338 (779)
                      ..+++.....  .....+-++.++++.  .+|.|.
T Consensus       685 ~~ILK~~tkn~k~pl~~dVdl~eia~~--~~c~gf  717 (802)
T KOG0733|consen  685 VAILKTITKNTKPPLSSDVDLDEIARN--TKCEGF  717 (802)
T ss_pred             HHHHHHHhccCCCCCCcccCHHHHhhc--ccccCC
Confidence            9999888763  333445566666543  345543

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.71  E-value=0.4  Score=44.93  Aligned_cols=35  Identities=26%  Similarity=0.338  Sum_probs=26.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEE
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA  216 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~  216 (779)
                      -.+++|.|..|.|||||.+.++...    ....+.+++.
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~----~~~~G~v~~~   60 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLY----KPDSGEILVD   60 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC----CCCCeEEEEC
Confidence            4689999999999999999998765    2334555543

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=93.70  E-value=0.16  Score=50.93  Aligned_cols=57  Identities=18%  Similarity=0.051  Sum_probs=38.0

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      +-+.|..+=....++.|+|.+|+|||+||.++.....   ..=..++|++..+-..++++
T Consensus        14 LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~---~~g~~~~y~~~e~~~~~~~~   70 (234)
T PRK06067         14 LDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGAL---KQGKKVYVITTENTSKSYLK   70 (234)
T ss_pred             HHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHH---hCCCEEEEEEcCCCHHHHHH
Confidence            3344444433567999999999999999999866541   23357888888433344444

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=93.70  E-value=0.52  Score=55.76  Aligned_cols=24  Identities=25%  Similarity=0.345  Sum_probs=20.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      +.+++.|.|+.+.||||+.+.+.-
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl  349 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGL  349 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHH
Confidence            457899999999999999988753

>PRK13975 thymidylate kinase; Provisional

Probab=93.69  E-value=0.059  Score=52.37  Aligned_cols=24  Identities=38%  Similarity=0.487  Sum_probs=22.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|+.|+||||+|+.++...
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l   26 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKL   26 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999999987

>PRK14527 adenylate kinase; Provisional

Probab=93.69  E-value=0.063  Score=51.93  Aligned_cols=26  Identities=19%  Similarity=0.373  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|+|.+|+||||+|+.++...
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~~~   30 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQEL   30 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998776

>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=93.69  E-value=0.11  Score=51.91  Aligned_cols=73  Identities=14%  Similarity=0.170  Sum_probs=58.7

Q ss_pred             HHHHHHHHHhhhhcchhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCchhHHHHHHHHHHHHHHHHHHHHHH
Q 004021           13 LFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTELQQVR   92 (779)
Q Consensus        13 ~~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~~~~~~~~~~~Wl~~l~~~~~d~ed~ld~~   92 (779)
                      +++.|-++.......+..++.+++-+++|++++|.||+.+      ++... ... ...+..+.++-..||++|.++|-+
T Consensus       301 lL~NLkdfq~rysdSlaflKnQiqvIQ~elesLqpFLk~V------~ee~~-nkh-~~~ed~a~~ii~kAyevEYVVDaC  372 (402)
T PF12061_consen  301 LLKNLKDFQGRYSDSLAFLKNQIQVIQTELESLQPFLKHV------VEEPH-NKH-DTNEDCATQIIRKAYEVEYVVDAC  372 (402)
T ss_pred             HHhhHHHHhccccchHHHHHHHHHHHHHHHHHhhHHHHHH------Hhccc-hhh-hhhhhHHHHHHHHHhheeeeeehh
Confidence            6667777777777778889999999999999999999985      44432 122 348999999999999999999876


Q ss_pred             H
Q 004021           93 A   93 (779)
Q Consensus        93 ~   93 (779)
                      .
T Consensus       373 i  373 (402)
T PF12061_consen  373 I  373 (402)
T ss_pred             h
Confidence            3

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.

>PRK00300 gmk guanylate kinase; Provisional

Probab=93.68  E-value=0.061  Score=52.71  Aligned_cols=26  Identities=35%  Similarity=0.382  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+||||||+.++...
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34789999999999999999998875

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=93.66  E-value=0.092  Score=55.23  Aligned_cols=46  Identities=24%  Similarity=0.366  Sum_probs=37.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+||.++.+..++-.+.++  ...-|.|.|..|+|||||++.+..-.
T Consensus         4 ~~ivgq~~~~~al~~~~~~~--~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         4 TAIVGQDEMKLALLLNVIDP--KIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             cccccHHHHHHHHHHHhcCC--CCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            45799999998887777765  44567799999999999999997544

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.

>TIGR00959 ffh signal recognition particle protein

Probab=93.63  E-value=0.32  Score=52.89  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.++.++|.+|+||||.|..++...
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l  123 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYL  123 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH
Confidence            46799999999999999998888775

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.

>PRK06526 transposase; Provisional

Probab=93.63  E-value=0.052  Score=54.79  Aligned_cols=44  Identities=23%  Similarity=0.346  Sum_probs=31.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIG  225 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~  225 (779)
                      .-+.|+|.+|+|||+||.++.+...  +..+ .+.|++..++...+.
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~--~~g~-~v~f~t~~~l~~~l~  142 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRAC--QAGH-RVLFATAAQWVARLA  142 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHH--HCCC-chhhhhHHHHHHHHH
Confidence            5689999999999999999988762  2223 345555555555554

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=93.62  E-value=0.17  Score=53.00  Aligned_cols=39  Identities=23%  Similarity=0.428  Sum_probs=30.5

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+.+.+....+...+|+|.|.+|+|||||+..+....
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l   80 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHL   80 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            345666555434467899999999999999999988776

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=93.60  E-value=0.15  Score=48.40  Aligned_cols=23  Identities=39%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.++|++|+||||+++.++...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~   24 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68899999999999999998876

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=93.59  E-value=0.29  Score=52.33  Aligned_cols=51  Identities=24%  Similarity=0.274  Sum_probs=36.5

Q ss_pred             HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEec
Q 004021          165 PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQ  218 (779)
Q Consensus       165 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~  218 (779)
                      .++-+.|..+=..-.++.|.|.+|+|||||+.+++....   ..-..++|++..
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a---~~g~~VlYvs~E  119 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA---KRGGKVLYVSGE  119 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHH---hcCCeEEEEECC
Confidence            444455544433457999999999999999999988762   223567888873

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK13946 shikimate kinase; Provisional

Probab=93.59  E-value=0.065  Score=51.43  Aligned_cols=25  Identities=24%  Similarity=0.449  Sum_probs=22.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|.++|++|+||||+|+.+++..
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~L   34 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATML   34 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHc
Confidence            3579999999999999999999886

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=93.58  E-value=0.065  Score=50.74  Aligned_cols=25  Identities=32%  Similarity=0.405  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|.|+|+.|+||||+|+.+.+..
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHc
Confidence            3569999999999999999998875

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=93.57  E-value=0.083  Score=49.32  Aligned_cols=35  Identities=31%  Similarity=0.442  Sum_probs=28.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++.|+|.+|+||||+|..+....   ...-..++|++.
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~---~~~~~~v~~~~~   35 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNI---ATKGGKVVYVDI   35 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHH---HhcCCEEEEEEC
Confidence            46899999999999999998876   223456777777

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PLN02200 adenylate kinase family protein

Probab=93.54  E-value=0.071  Score=53.22  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.++...
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998765

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.49  E-value=3.4  Score=44.12  Aligned_cols=52  Identities=19%  Similarity=0.298  Sum_probs=36.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      .+.||-.+|.-|.||||.|..+++.+ +  .+=..+.-|+.       -+-++.++++.+.+
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~~l-k--k~~~kvllVaaD~~RpAA~eQL~~La~q~~v~  157 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAKYL-K--KKGKKVLLVAADTYRPAAIEQLKQLAEQVGVP  157 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHHHH-H--HcCCceEEEecccCChHHHHHHHHHHHHcCCc
Confidence            46799999999999999999999888 2  22223444444       34466677777655

>PRK09183 transposase/IS protein; Provisional

Probab=93.48  E-value=0.12  Score=52.45  Aligned_cols=43  Identities=23%  Similarity=0.225  Sum_probs=29.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      ..+.|+|.+|+|||+||.++++...  ... ..+.+++..++...+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~--~~G-~~v~~~~~~~l~~~l  145 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAV--RAG-IKVRFTTAADLLLQL  145 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHH--HcC-CeEEEEeHHHHHHHH
Confidence            5678999999999999999987752  122 234455655554444

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=93.48  E-value=0.11  Score=50.09  Aligned_cols=37  Identities=22%  Similarity=0.094  Sum_probs=27.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT  219 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~  219 (779)
                      ++.|.|.+|+|||+||.++.....   ..=..++|++...
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~---~~g~~v~~~s~e~   37 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGL---ARGEPGLYVTLEE   37 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHH---HCCCcEEEEECCC
Confidence            367899999999999999877652   2224577888733

A related protein is found in archaea.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=93.46  E-value=0.11  Score=56.18  Aligned_cols=49  Identities=24%  Similarity=0.337  Sum_probs=37.0

Q ss_pred             cccccchhhhHHHHHHHHhcc--------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ--------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~--------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..++|.+..++.+...+...              .....-|.++|.+|+|||++|+.++...
T Consensus        70 ~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l  132 (412)
T PRK05342         70 DQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL  132 (412)
T ss_pred             hhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh
Confidence            356899999998886655221              0123568999999999999999998765

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=93.46  E-value=0.067  Score=47.00  Aligned_cols=22  Identities=36%  Similarity=0.567  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|+|..|+|||||.+.+....
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            7899999999999999998765

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.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=93.45  E-value=1.2  Score=49.05  Aligned_cols=48  Identities=25%  Similarity=0.315  Sum_probs=37.8

Q ss_pred             ccccchhhhHHHHHHHHhc---c-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD---Q-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++=|.+..+.++.+.+..   .       =...+=|-+||++|.|||.||+++++..
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel  247 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL  247 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc
Confidence            4567889888888887653   1       1234567899999999999999999987

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=93.45  E-value=0.06  Score=49.62  Aligned_cols=23  Identities=30%  Similarity=0.651  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.|+|.+|+||||+|+.+....
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l   23 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKL   23 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            57899999999999999998876

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.43  E-value=0.053  Score=50.89  Aligned_cols=22  Identities=27%  Similarity=0.570  Sum_probs=19.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|+|++|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999998875

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.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=93.40  E-value=0.1  Score=50.83  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.||||||+.+..-.
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhccc
Confidence            34689999999999999999998755

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=93.39  E-value=0.099  Score=54.87  Aligned_cols=46  Identities=26%  Similarity=0.384  Sum_probs=36.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+.-.+.+.  +..-+-+.|.+|+||||+|+.+.+-.
T Consensus         8 ~~i~Gq~~~~~~l~~~~~~~--~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          8 SAIVGQEEMKQAMVLTAIDP--GIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             HHhCCHHHHHHHHHHHHhcc--CCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            56799999998887655433  33458899999999999999997654

>TIGR01287 nifH nitrogenase iron protein

Probab=93.35  E-value=0.062  Score=55.45  Aligned_cols=24  Identities=33%  Similarity=0.703  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|+|+|-||+||||+|..++...
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~L   24 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAAL   24 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHHH
Confidence            478999999999999999998877

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=93.35  E-value=0.12  Score=57.52  Aligned_cols=58  Identities=24%  Similarity=0.404  Sum_probs=44.6

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+++--.+-++++..||...   ....+++.+.|++|+||||.++.+++..     .|+.+-|.+-
T Consensus        19 ~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el-----g~~v~Ew~np   79 (519)
T PF03215_consen   19 DELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL-----GFEVQEWINP   79 (519)
T ss_pred             HHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh-----CCeeEEecCC
Confidence            34555567788999998763   3345799999999999999999999876     4677777654

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.32  E-value=0.83  Score=47.56  Aligned_cols=47  Identities=21%  Similarity=0.205  Sum_probs=34.0

Q ss_pred             cccchhhhHHHHHHHHhcc----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.|.++.++-|.+...-+          ...-+-|..+|++|.|||-||++||..-
T Consensus       213 DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc  269 (491)
T KOG0738|consen  213 DIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATEC  269 (491)
T ss_pred             hhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhh
Confidence            3566666666665554321          2345678899999999999999999876

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.32  E-value=0.067  Score=51.45  Aligned_cols=24  Identities=33%  Similarity=0.465  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+|+.|+|||||++.++...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            478999999999999999997764

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=93.32  E-value=4.5  Score=42.38  Aligned_cols=62  Identities=13%  Similarity=0.015  Sum_probs=41.9

Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      .++.+|++|.+ ..+....-  ...+.+.+++.++..+.+.......        ...+...++.++|.|+.+
T Consensus       136 ~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~~~--------~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        136 PNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSAE--------ISEILTALRINYGRPLLA  200 (325)
T ss_pred             CCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhccC--------hHHHHHHHHHcCCCHHHH
Confidence            45556666654 45554433  5788999999999998887654211        123567788999999644

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=93.32  E-value=0.11  Score=55.03  Aligned_cols=44  Identities=27%  Similarity=0.431  Sum_probs=37.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|+++.+..+...+..+    +-+-+.|.+|+|||+||+.++...
T Consensus        24 ~~~~g~~~~~~~~l~a~~~~----~~vll~G~PG~gKT~la~~lA~~l   67 (329)
T COG0714          24 KVVVGDEEVIELALLALLAG----GHVLLEGPPGVGKTLLARALARAL   67 (329)
T ss_pred             CeeeccHHHHHHHHHHHHcC----CCEEEECCCCccHHHHHHHHHHHh
Confidence            34799888888888887766    568899999999999999999887

>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=93.31  E-value=0.068  Score=52.67  Aligned_cols=24  Identities=33%  Similarity=0.690  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|-||+||||++..++...
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~~l   24 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAAL   24 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHHHH
Confidence            579999999999999999888877

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PRK06921 hypothetical protein; Provisional

Probab=93.30  E-value=0.17  Score=51.66  Aligned_cols=46  Identities=26%  Similarity=0.317  Sum_probs=33.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      ...-+.++|..|+|||.||.++++.. . +..-..+++++..+++..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l-~-~~~g~~v~y~~~~~l~~~l  161 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANEL-M-RKKGVPVLYFPFVEGFGDL  161 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHH-h-hhcCceEEEEEHHHHHHHH
Confidence            35678999999999999999999987 2 2213456777765555544

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=93.27  E-value=0.091  Score=52.51  Aligned_cols=32  Identities=28%  Similarity=0.315  Sum_probs=22.2

Q ss_pred             EEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          183 LYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       183 I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      |+|++|+||||+++.+.+..   ...-..++-|+.
T Consensus         1 ViGpaGSGKTT~~~~~~~~~---~~~~~~~~~vNL   32 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL---ESNGRDVYIVNL   32 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH---TTT-S-EEEEE-
T ss_pred             CCCCCCCCHHHHHHHHHHHH---HhccCCceEEEc
Confidence            68999999999999999887   233334555555

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.26  E-value=0.12  Score=52.62  Aligned_cols=36  Identities=31%  Similarity=0.357  Sum_probs=26.3

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -++++..++..+    .-|-+.|.+|+|||++|+.+++..
T Consensus        10 l~~~~l~~l~~g----~~vLL~G~~GtGKT~lA~~la~~l   45 (262)
T TIGR02640        10 VTSRALRYLKSG----YPVHLRGPAGTGKTTLAMHVARKR   45 (262)
T ss_pred             HHHHHHHHHhcC----CeEEEEcCCCCCHHHHHHHHHHHh
Confidence            344555555444    456689999999999999998754

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=93.24  E-value=0.12  Score=58.57  Aligned_cols=48  Identities=17%  Similarity=0.257  Sum_probs=36.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |..+.|.+-.+.|.++.........+|.|+|++|+||||+|+.++...
T Consensus       369 P~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~~L  416 (568)
T PRK05537        369 PEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMVKL  416 (568)
T ss_pred             ChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHHHh
Confidence            445667766666666655544455689999999999999999999887

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=93.22  E-value=0.099  Score=55.01  Aligned_cols=46  Identities=26%  Similarity=0.382  Sum_probs=38.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+||.++.+..|...+.++  .+.-|.|.|..|+||||+|+.+++-.
T Consensus        17 ~~ivGq~~~k~al~~~~~~p--~~~~vli~G~~GtGKs~~ar~~~~~l   62 (350)
T CHL00081         17 TAIVGQEEMKLALILNVIDP--KIGGVMIMGDRGTGKSTTIRALVDLL   62 (350)
T ss_pred             HHHhChHHHHHHHHHhccCC--CCCeEEEEcCCCCCHHHHHHHHHHHH
Confidence            56799999999988888776  55556699999999999999997665

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.20  E-value=0.24  Score=49.49  Aligned_cols=48  Identities=17%  Similarity=0.149  Sum_probs=33.4

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +-+.|..+=..-.++.|.|.+|+||||||.++.....   ..-..++|++.
T Consensus         9 LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~---~~g~~~~~is~   56 (229)
T TIGR03881         9 LDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGL---RDGDPVIYVTT   56 (229)
T ss_pred             HHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHH---hcCCeEEEEEc
Confidence            3334433323457999999999999999998776541   22357788887

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=93.19  E-value=0.56  Score=53.77  Aligned_cols=63  Identities=13%  Similarity=0.139  Sum_probs=42.2

Q ss_pred             EEEEeCchhhhhh----cC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          277 IVLKTRSAGVCDQ----MD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       277 IivTTR~~~va~~----~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      ++-+|+..++...    .|  ++.+.++.-+.....++|.-++......  .+..++++ |+...-|.+=|.
T Consensus       453 ~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~--~e~~dl~~-~a~~t~gf~gad  521 (774)
T KOG0731|consen  453 VLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLD--DEDVDLSK-LASLTPGFSGAD  521 (774)
T ss_pred             EEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCC--cchhhHHH-HHhcCCCCcHHH
Confidence            4446776666432    23  6788888888889999999888765532  33455566 877777776443

>PRK05973 replicative DNA helicase; Provisional

Probab=93.16  E-value=0.24  Score=49.21  Aligned_cols=39  Identities=15%  Similarity=0.088  Sum_probs=29.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEec
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQ  218 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~  218 (779)
                      ...++.|.|.+|+|||++|.++.....  + .=..+++++.+
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~~a--~-~Ge~vlyfSlE  101 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVEAM--K-SGRTGVFFTLE  101 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHH--h-cCCeEEEEEEe
Confidence            447899999999999999999877652  2 23457788883

>PRK04182 cytidylate kinase; Provisional

Probab=93.15  E-value=0.078  Score=50.61  Aligned_cols=43  Identities=23%  Similarity=0.380  Sum_probs=30.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCC
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGF  230 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~  230 (779)
                      +|.|.|+.|+||||+|+.++... .    +   -+++..++...+.+..+.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~l-g----~---~~id~~~~~~~~~~~~g~   44 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKL-G----L---KHVSAGEIFRELAKERGM   44 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc-C----C---cEecHHHHHHHHHHHcCC
Confidence            68999999999999999998876 1    1   123334566666655443

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=93.15  E-value=0.084  Score=48.97  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-|.++||.|+||||+.+++++..
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L   26 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKAL   26 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHc
Confidence            347899999999999999999887

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=93.15  E-value=0.35  Score=49.06  Aligned_cols=46  Identities=24%  Similarity=0.219  Sum_probs=34.9

Q ss_pred             HHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          169 RCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       169 ~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +.|..+=+..+++=|+|..|+||||+|.+++-..   +..-..++|++.
T Consensus        51 ~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~a---q~~g~~a~fIDt   96 (279)
T COG0468          51 EALGGGLPRGRITEIYGPESSGKTTLALQLVANA---QKPGGKAAFIDT   96 (279)
T ss_pred             HHhcCCcccceEEEEecCCCcchhhHHHHHHHHh---hcCCCeEEEEeC
Confidence            3344433456899999999999999999887665   444558899998

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=93.14  E-value=0.076  Score=49.86  Aligned_cols=22  Identities=55%  Similarity=0.667  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|.+|+|||||++.+.+..
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            6899999999999999999877

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=93.13  E-value=0.073  Score=48.35  Aligned_cols=45  Identities=22%  Similarity=0.329  Sum_probs=33.3

Q ss_pred             cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          158 VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ||+...++++.+.+..-.....-|.|.|-.|+||+++|+.+++..
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~   45 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYS   45 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhc
Confidence            577777788877776532244667899999999999999998876

>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=93.12  E-value=0.051  Score=29.24  Aligned_cols=17  Identities=29%  Similarity=0.618  Sum_probs=9.2

Q ss_pred             CCccEEeeeCCCCCCCCC
Q 004021          719 PKLKKIGVYGCPKLKKLP  736 (779)
Q Consensus       719 ~~L~~L~l~~c~~L~~lP  736 (779)
                      ++|+.|++++|. |++||
T Consensus         1 ~~L~~L~l~~n~-L~~lP   17 (17)
T PF13504_consen    1 PNLRTLDLSNNR-LTSLP   17 (17)
T ss_dssp             TT-SEEEETSS---SSE-
T ss_pred             CccCEEECCCCC-CCCCc
Confidence            467777777776 66665

...

>TIGR00750 lao LAO/AO transport system ATPase

Probab=93.11  E-value=0.11  Score=54.07  Aligned_cols=38  Identities=26%  Similarity=0.406  Sum_probs=29.1

Q ss_pred             HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          165 PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       165 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++.+....+...+|+|.|.+|+|||||+..+....
T Consensus        21 ~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~~~   58 (300)
T TIGR00750        21 KQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMEL   58 (300)
T ss_pred             HHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            34444444434467899999999999999999988766

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=93.10  E-value=0.15  Score=53.12  Aligned_cols=49  Identities=27%  Similarity=0.321  Sum_probs=35.3

Q ss_pred             cccccchhhhHH---HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLP---RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~---~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+||..+..+   -+++.+..+.-.-+.|-+.|++|.|||+||..+++..
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eL   74 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKEL   74 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHC
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHh
Confidence            356899876554   4566666664456889999999999999999999988

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=93.08  E-value=0.07  Score=50.08  Aligned_cols=38  Identities=24%  Similarity=0.328  Sum_probs=24.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhC
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIG  229 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~  229 (779)
                      |+|.|..|+|||||++.+...      .+   .||  .+..+.+.....
T Consensus         2 I~i~G~~stGKTTL~~~L~~~------g~---~~v--~E~ar~~~~~~~   39 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR------GY---PVV--PEYAREIIEEGG   39 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH------T----EEE----TTHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHHc------CC---eEE--eecHHHHHHHhc
Confidence            789999999999999999764      22   233  555556665544

>PRK04296 thymidine kinase; Provisional

Probab=93.07  E-value=0.2  Score=48.32  Aligned_cols=101  Identities=19%  Similarity=0.129  Sum_probs=53.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCC
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSP  254 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~  254 (779)
                      .++.|+|..|.||||+|..++.+. .  .+-..++.+.-    ......++.+++.... ........+....+.+  ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~-~--~~g~~v~i~k~~~d~~~~~~~i~~~lg~~~~-~~~~~~~~~~~~~~~~--~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNY-E--ERGMKVLVFKPAIDDRYGEGKVVSRIGLSRE-AIPVSSDTDIFELIEE--EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHH-H--HcCCeEEEEeccccccccCCcEecCCCCccc-ceEeCChHHHHHHHHh--hC
Confidence            577899999999999999988876 2  22223333311    1223345555553211 1111223344444444  33


Q ss_pred             Ccc-eeehhhcccc--------ccc-cCCCcEEEEEeCchh
Q 004021          255 KKF-RIDLTELGVP--------LQM-LNAGFKIVLKTRSAG  285 (779)
Q Consensus       255 kr~-~~~ld~l~~~--------~~~-~~~gs~IivTTR~~~  285 (779)
                      ..+ .+.+|++.-.        ... ...|..||+|.++.+
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l~~~g~~vi~tgl~~~  117 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVLDDLGIPVICYGLDTD  117 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHHHHcCCeEEEEecCcc
Confidence            344 4555554211        111 346788999988744

>PRK15453 phosphoribulokinase; Provisional

Probab=93.05  E-value=0.097  Score=52.76  Aligned_cols=26  Identities=31%  Similarity=0.514  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|.+|+||||+|+.+.+..
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~if   29 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEKIF   29 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            56799999999999999999998766

>PRK13695 putative NTPase; Provisional

Probab=93.01  E-value=0.12  Score=48.98  Aligned_cols=23  Identities=43%  Similarity=0.645  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+|+|.+|+|||||++.+++..
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999998876

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.01  E-value=0.67  Score=49.73  Aligned_cols=40  Identities=20%  Similarity=0.256  Sum_probs=29.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhcccc--CCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ--HNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~--~~F~~~~wv~v  217 (779)
                      ..++|.++|..|+||||.+..++... ...  .+-..+..++.
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~-~~~~~~~g~~V~lit~  214 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIY-GINSDDKSLNIKIITI  214 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH-HhhhccCCCeEEEEec
Confidence            45799999999999999999988776 211  12235666766

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=93.00  E-value=2.6  Score=46.46  Aligned_cols=48  Identities=17%  Similarity=0.214  Sum_probs=33.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGK  226 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~  226 (779)
                      ...++.|-|.+|+|||++|..++... .. .+-..++|++.    .++...++.
T Consensus       193 ~g~liviag~pg~GKT~~al~ia~~~-a~-~~g~~v~~fSlEm~~~~l~~Rl~~  244 (421)
T TIGR03600       193 KGDLIVIGARPSMGKTTLALNIAENV-AL-REGKPVLFFSLEMSAEQLGERLLA  244 (421)
T ss_pred             CCceEEEEeCCCCCHHHHHHHHHHHH-HH-hCCCcEEEEECCCCHHHHHHHHHH
Confidence            34688999999999999999998665 21 22345778887    445444443

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

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

Probab=93.00  E-value=0.33  Score=43.21  Aligned_cols=39  Identities=13%  Similarity=0.158  Sum_probs=21.8

Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      .|.++++|+.+.+..+  +..++...+..+++|+.+.+..+
T Consensus         7 ~F~~~~~l~~i~~~~~--~~~I~~~~F~~~~~l~~i~~~~~   45 (129)
T PF13306_consen    7 AFYNCSNLESITFPNT--IKKIGENAFSNCTSLKSINFPNN   45 (129)
T ss_dssp             TTTT-TT--EEEETST----EE-TTTTTT-TT-SEEEESST
T ss_pred             HHhCCCCCCEEEECCC--eeEeChhhccccccccccccccc
Confidence            3667778888887643  56777776777778888877653

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=92.99  E-value=0.11  Score=50.94  Aligned_cols=26  Identities=27%  Similarity=0.474  Sum_probs=24.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++++|+++|..|+|||||..++.+..
T Consensus        21 ~~~~i~~~G~~gsGKTTli~~l~~~~   46 (207)
T TIGR00073        21 GLVVLNFMSSPGSGKTTLIEKLIDNL   46 (207)
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHH
Confidence            78999999999999999999998875

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=92.97  E-value=2.3  Score=51.06  Aligned_cols=48  Identities=29%  Similarity=0.423  Sum_probs=38.6

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+.+...       ......+.++|+.|+|||+||+.+++..
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l  563 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYF  563 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            56899999999999888632       2223466789999999999999998865

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=92.95  E-value=0.093  Score=44.70  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHH
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVN  199 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~  199 (779)
                      -..++|+|..|.|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4689999999999999999975

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

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=92.94  E-value=0.072  Score=54.01  Aligned_cols=23  Identities=39%  Similarity=0.665  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|.+.|++|+||||+|+.+....
T Consensus         1 LIvl~G~pGSGKST~a~~La~~l   23 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKKL   23 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999877

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=92.93  E-value=0.094  Score=50.64  Aligned_cols=23  Identities=43%  Similarity=0.463  Sum_probs=20.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      ..+|+|+|+.|+||||.|+.+..
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            36899999999999999998865

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=92.92  E-value=0.08  Score=55.12  Aligned_cols=24  Identities=38%  Similarity=0.483  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +++.+.|-|||||||+|.+.+-..
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~   25 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALAL   25 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHH
Confidence            688999999999999998887666

...

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=92.92  E-value=0.13  Score=53.50  Aligned_cols=37  Identities=27%  Similarity=0.363  Sum_probs=27.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+++.+.|.|||||||+|.+.+-...   .....++-|++
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA---~~g~kvLlvSt   38 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLA---ESGKKVLLVST   38 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHH---HcCCcEEEEEe
Confidence            47899999999999999999766552   22244777766

>PTZ00088 adenylate kinase 1; Provisional

Probab=92.91  E-value=0.083  Score=52.38  Aligned_cols=23  Identities=35%  Similarity=0.488  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+++..
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            38899999999999999998876

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=92.91  E-value=0.39  Score=50.57  Aligned_cols=65  Identities=17%  Similarity=0.111  Sum_probs=41.2

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc--c-cCCCCEEEEEEe-----chHHHHHHHHhCCC
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH--Q-QHNFDVVIWAAV-----QTFQDDIGKRIGFS  231 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~--~-~~~F~~~~wv~v-----~~i~~~i~~~l~~~  231 (779)
                      |-+.|..+=....++-|+|.+|+|||+|+..++-....  . ...-..++|++.     .+-+.++++.++..
T Consensus       115 LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~g~d  187 (344)
T PLN03187        115 LDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERFGMD  187 (344)
T ss_pred             HHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHcCCC
Confidence            33445444335578899999999999999887643201  0 111247899998     33445566666654

>PLN02348 phosphoribulokinase

Probab=92.90  E-value=0.2  Score=53.08  Aligned_cols=27  Identities=30%  Similarity=0.586  Sum_probs=24.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +...+|+|.|.+|+||||+|+.+.+..
T Consensus        47 ~~p~IIGIaG~SGSGKSTfA~~L~~~L   73 (395)
T PLN02348         47 DGTVVIGLAADSGCGKSTFMRRLTSVF   73 (395)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            366899999999999999999999877

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=92.89  E-value=0.16  Score=44.61  Aligned_cols=26  Identities=31%  Similarity=0.410  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...||.+.|-=|+||||+++.++...
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~l   39 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARAL   39 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHc
Confidence            34899999999999999999998876

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=92.88  E-value=0.17  Score=54.62  Aligned_cols=49  Identities=22%  Similarity=0.344  Sum_probs=37.5

Q ss_pred             cccccchhhhHHHHHHHHhc----------cC--C----CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITD----------QQ--K----NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~----------~~--~----~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..++|.++.++.+...+..          ..  .    ....|.++|++|+|||++|+.++...
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l  140 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL  140 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc
Confidence            46789999999988776621          11  0    12578999999999999999998765

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=92.88  E-value=0.37  Score=50.86  Aligned_cols=66  Identities=17%  Similarity=0.188  Sum_probs=42.4

Q ss_pred             HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc---c-CCCCEEEEEEe-----chHHHHHHHHhCCC
Q 004021          165 PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ---Q-HNFDVVIWAAV-----QTFQDDIGKRIGFS  231 (779)
Q Consensus       165 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~-~~F~~~~wv~v-----~~i~~~i~~~l~~~  231 (779)
                      ..|-+.|..+=....++-|.|.+|+|||+||..++-.. ..   . ..-..++|++.     .+-+.+|++.++..
T Consensus       110 ~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~-~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~~~~~~  184 (342)
T PLN03186        110 RELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTC-QLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAERFGLN  184 (342)
T ss_pred             HHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHh-hcchhhCCCCceEEEEECCCCccHHHHHHHHHHcCCC
Confidence            33444455443356789999999999999998877443 11   1 11236899999     23355667766554

>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=92.87  E-value=0.041  Score=31.91  Aligned_cols=22  Identities=36%  Similarity=0.597  Sum_probs=16.8

Q ss_pred             cCcEeeccCCcCCCCCchhhhcCC
Q 004021          560 KLRYLNLEYTHYLSIIPHQLISGF  583 (779)
Q Consensus       560 ~L~~L~l~~~~~l~~lp~~~i~~L  583 (779)
                      +|++|++++| .++.+|++ |++|
T Consensus         1 ~L~~Ldls~n-~l~~ip~~-~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGN-NLTSIPSS-FSNL   22 (22)
T ss_dssp             TESEEEETSS-EESEEGTT-TTT-
T ss_pred             CccEEECCCC-cCEeCChh-hcCC
Confidence            5889999999 67788887 6553

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 ....

>PRK14737 gmk guanylate kinase; Provisional

Probab=92.85  E-value=0.1  Score=50.06  Aligned_cols=26  Identities=15%  Similarity=0.355  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|+|++|+|||||++.+....
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45789999999999999999998765

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=92.85  E-value=0.093  Score=49.60  Aligned_cols=43  Identities=23%  Similarity=0.445  Sum_probs=30.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCC
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGF  230 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~  230 (779)
                      +|+|.|..|+||||+|+.+.+..     .|.   +++...+...++...+.
T Consensus         2 iI~i~G~~GSGKstia~~la~~l-----g~~---~~~~~~~~~~~~~~~g~   44 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKL-----SLK---LISAGDIFRELAAKMGL   44 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc-----CCc---eecHHHHHHHHHHHcCC
Confidence            79999999999999999998765     122   23334556666655443

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=92.85  E-value=1.8  Score=50.30  Aligned_cols=47  Identities=21%  Similarity=0.235  Sum_probs=32.3

Q ss_pred             cccchhhhHHHHHHHH---hcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCI---TDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L---~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.|.+..++++.+.+   ...       ..-.+-|.++|.+|.|||++|+.+++..
T Consensus       153 di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~  209 (644)
T PRK10733        153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA  209 (644)
T ss_pred             HHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc
Confidence            4567776665555443   221       0112348999999999999999998876

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=92.82  E-value=0.13  Score=55.37  Aligned_cols=48  Identities=25%  Similarity=0.303  Sum_probs=37.1

Q ss_pred             ccccchhh---hHHHHHHHHhccC-------CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEK---LLPRVWRCITDQQ-------KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~---~~~~l~~~L~~~~-------~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++-|-|+   ++++|+++|.++.       .-++=|-++|++|.|||-||++|+...
T Consensus       304 ~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  304 EDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             ccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc
Confidence            34567764   5677888888752       234568899999999999999999876

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=92.82  E-value=0.094  Score=49.64  Aligned_cols=24  Identities=29%  Similarity=0.318  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|.|+|+.|+||||+|+.+++..
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~l   26 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQAL   26 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            358889999999999999999876

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=92.81  E-value=0.086  Score=48.83  Aligned_cols=23  Identities=26%  Similarity=0.512  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |++|+|..|+|||||+.++....
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l   23 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKAL   23 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999999877

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=92.78  E-value=0.1  Score=53.81  Aligned_cols=40  Identities=35%  Similarity=0.490  Sum_probs=28.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++|+|+|.+|+||||++..++... ..+..-..+..|+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~-~~~~g~~~V~li~~  232 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARF-VLEHGNKKVALITT  232 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH-HHHcCCCeEEEEEC
Confidence            35799999999999999999998776 22211134556665

>PRK14532 adenylate kinase; Provisional

Probab=92.77  E-value=0.088  Score=50.77  Aligned_cols=35  Identities=17%  Similarity=0.215  Sum_probs=26.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHH
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDD  223 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~  223 (779)
                      |.|.|++|+||||+|+.++...     .   ..+++..++++.
T Consensus         3 i~~~G~pGsGKsT~a~~la~~~-----g---~~~is~~d~lr~   37 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVEER-----G---MVQLSTGDMLRA   37 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc-----C---CeEEeCcHHHHH
Confidence            7789999999999999998765     1   345566555544

>PRK06761 hypothetical protein; Provisional

Probab=92.76  E-value=0.14  Score=52.18  Aligned_cols=24  Identities=33%  Similarity=0.505  Sum_probs=22.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.|.|.+|+||||+|+.+++..
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~L   27 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDIL   27 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            689999999999999999999887

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=92.71  E-value=0.095  Score=43.88  Aligned_cols=23  Identities=43%  Similarity=0.661  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.+.|.+|+||||++..++...
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l   23 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAAL   23 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            47889999999999999998887

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=92.70  E-value=1.3  Score=50.17  Aligned_cols=48  Identities=31%  Similarity=0.387  Sum_probs=37.7

Q ss_pred             ccccchhhhHHHHHHHHhcc----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++=|.++.+.+|.+-+.-+          -....=|-++|++|.|||-+|++|+...
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEc  729 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATEC  729 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhc
Confidence            56678899999998877531          1123467899999999999999999876

>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]

Probab=92.70  E-value=0.21  Score=45.53  Aligned_cols=36  Identities=17%  Similarity=0.353  Sum_probs=29.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      -+.|+|-||+||+++.+.+|.-.-  .+.+...+||+.
T Consensus        22 K~vivGng~VGKssmiqryCkgif--TkdykktIgvdf   57 (246)
T KOG4252|consen   22 KFVIVGNGSVGKSSMIQRYCKGIF--TKDYKKTIGVDF   57 (246)
T ss_pred             EEEEECCCccchHHHHHHHhcccc--ccccccccchhh
Confidence            467999999999999999997542  556778889887

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=92.70  E-value=4.2  Score=42.94  Aligned_cols=63  Identities=11%  Similarity=0.005  Sum_probs=42.0

Q ss_pred             CCcEEEEEeCc-hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          273 AGFKIVLKTRS-AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       273 ~gs~IivTTR~-~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .++-+|++|.+ ..+.....  ...+.+.+++.+++.+.+.+..+.     +   .+.+..+++.++|.|..+.
T Consensus       137 ~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~~-----~---~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        137 ENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVTM-----S---QDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             CCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccCC-----C---HHHHHHHHHHcCCCHHHHH
Confidence            45555555554 55655533  567899999999998887654211     1   3446788999999996543

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

Probab=92.68  E-value=0.15  Score=58.66  Aligned_cols=45  Identities=24%  Similarity=0.530  Sum_probs=37.0

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++||+++++++++.|.....+-+|  ++|-+|||||++|.-++.+.
T Consensus       171 PvIGRd~EI~r~iqIL~RR~KNNPv--LiGEpGVGKTAIvEGLA~rI  215 (786)
T COG0542         171 PVIGRDEEIRRTIQILSRRTKNNPV--LVGEPGVGKTAIVEGLAQRI  215 (786)
T ss_pred             CCcChHHHHHHHHHHHhccCCCCCe--EecCCCCCHHHHHHHHHHHH
Confidence            3699999999999999876434443  58999999999998887776

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=92.65  E-value=0.18  Score=56.48  Aligned_cols=26  Identities=35%  Similarity=0.464  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-++.-++|++|+||||||.-++++.
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqa  350 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQA  350 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhc
Confidence            45799999999999999999998865

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=92.65  E-value=0.093  Score=50.84  Aligned_cols=22  Identities=32%  Similarity=0.469  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|++|+||||+|+.++...
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999998765

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=92.65  E-value=0.67  Score=54.36  Aligned_cols=101  Identities=18%  Similarity=0.302  Sum_probs=66.2

Q ss_pred             ccccchhhhHHHHHHHHhcc----C--CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----Q--KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRI  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----~--~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l  228 (779)
                      ..++|.++.+..|.+.+...    .  .......+.|+-|+|||-||++++...   -+..+..+-++..+... +.+.+
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~---Fgse~~~IriDmse~~e-vskli  637 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYV---FGSEENFIRLDMSEFQE-VSKLI  637 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHH---cCCccceEEechhhhhh-hhhcc
Confidence            56789999999999888653    1  145678899999999999999998876   34444444444455555 44444


Q ss_pred             CCCcchhhhhcchhhHHHHHHHhhCCCccee-ehhhc
Q 004021          229 GFSEDKKWKEKSLQDKAVDISSILSPKKFRI-DLTEL  264 (779)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~-~ld~l  264 (779)
                      +.++     ..-..+....|.+.++.+.|.. -+|+|
T Consensus       638 gsp~-----gyvG~e~gg~LteavrrrP~sVVLfdeI  669 (898)
T KOG1051|consen  638 GSPP-----GYVGKEEGGQLTEAVKRRPYSVVLFEEI  669 (898)
T ss_pred             CCCc-----ccccchhHHHHHHHHhcCCceEEEEech
Confidence            5541     1112233446888899999933 34444

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=92.64  E-value=0.094  Score=54.20  Aligned_cols=24  Identities=29%  Similarity=0.596  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|-||+||||+|..++...
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~~L   25 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAAAL   25 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            578999999999999999988877

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=92.63  E-value=1.1  Score=50.41  Aligned_cols=53  Identities=28%  Similarity=0.273  Sum_probs=36.4

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD  210 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~  210 (779)
                      ..+.|.+..++.+.+.+.-           +-...+.+-++|++|.|||.||+++++..   ...|-
T Consensus       242 ~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~---~~~fi  305 (494)
T COG0464         242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALES---RSRFI  305 (494)
T ss_pred             ehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhC---CCeEE
Confidence            3445666666555554421           12355689999999999999999999965   44553

>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=92.61  E-value=0.098  Score=51.82  Aligned_cols=24  Identities=38%  Similarity=0.556  Sum_probs=21.6

Q ss_pred             eEEEEEcC-CCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGI-GGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~-gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|. ||+||||++..++.-.
T Consensus         2 ~~iai~s~kGGvG~TTltAnLA~aL   26 (243)
T PF06564_consen    2 KVIAIVSPKGGVGKTTLTANLAWAL   26 (243)
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHH
Confidence            58999996 9999999999998877

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.

>PRK13236 nitrogenase reductase; Reviewed

Probab=92.61  E-value=0.11  Score=54.10  Aligned_cols=26  Identities=35%  Similarity=0.567  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++|++.|-|||||||.|..++.-.
T Consensus         5 ~~~~~~~~GKGGVGKTt~a~NLA~~L   30 (296)
T PRK13236          5 NIRQIAFYGKGGIGKSTTSQNTLAAM   30 (296)
T ss_pred             CceEEEEECCCcCCHHHHHHHHHHHH
Confidence            67999999999999999998888776

>PRK13768 GTPase; Provisional

Probab=92.61  E-value=0.15  Score=51.73  Aligned_cols=24  Identities=38%  Similarity=0.498  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.|.||+||||++..+....
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~l   26 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDWL   26 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHHH
Confidence            578999999999999998888766

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=92.61  E-value=0.0076  Score=57.49  Aligned_cols=76  Identities=24%  Similarity=0.165  Sum_probs=44.2

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ||++.| .+..+-..|+.++.|..|+++.|.|..+|..++.+..++++++..| .++..|.+ +++++.+++++.-++.
T Consensus        47 ld~~s~-r~vn~~~n~s~~t~~~rl~~sknq~~~~~~d~~q~~e~~~~~~~~n-~~~~~p~s-~~k~~~~k~~e~k~~~  122 (326)
T KOG0473|consen   47 LDLSSN-RLVNLGKNFSILTRLVRLDLSKNQIKFLPKDAKQQRETVNAASHKN-NHSQQPKS-QKKEPHPKKNEQKKTE  122 (326)
T ss_pred             ehhhhh-HHHhhccchHHHHHHHHHhccHhhHhhChhhHHHHHHHHHHHhhcc-chhhCCcc-ccccCCcchhhhccCc
Confidence            555555 5555555555556666666666666666666666666666665555 45556655 5666666666555543

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=92.56  E-value=0.11  Score=49.38  Aligned_cols=24  Identities=25%  Similarity=0.393  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|+|..|.||||+++.++...
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l   27 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALF   27 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhc
Confidence            589999999999999999999876

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=92.54  E-value=0.099  Score=53.84  Aligned_cols=24  Identities=33%  Similarity=0.696  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|-|||||||+|..++...
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~~L   25 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAAL   25 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHH
Confidence            578889999999999999988776

>PTZ00494 tuzin-like protein; Provisional

Probab=92.53  E-value=3.4  Score=44.20  Aligned_cols=153  Identities=14%  Similarity=0.055  Sum_probs=90.3

Q ss_pred             cccccchhhhHHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---chHHHHHHHHhC
Q 004021          154 EQTIVGQEKLLPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---QTFQDDIGKRIG  229 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~~i~~~i~~~l~  229 (779)
                      ...+|.|+.+-..+.+.|..- ...++++.+.|.-|.||++|.+...... .     -..++|.+   ++-++.+.+.++
T Consensus       370 ~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE-~-----~paV~VDVRg~EDtLrsVVKALg  443 (664)
T PTZ00494        370 EAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVE-G-----VALVHVDVGGTEDTLRSVVRALG  443 (664)
T ss_pred             cccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHc-C-----CCeEEEEecCCcchHHHHHHHhC
Confidence            367899999888888888763 3478999999999999999999877655 2     23567777   889999999998


Q ss_pred             CCcchhhhhcchhhHHHHH---HHhhCCCcceeeh--------hhc---cccccccCCCcEEEEEeCchhhhhhc---C-
Q 004021          230 FSEDKKWKEKSLQDKAVDI---SSILSPKKFRIDL--------TEL---GVPLQMLNAGFKIVLKTRSAGVCDQM---D-  291 (779)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~l---~~~L~~kr~~~~l--------d~l---~~~~~~~~~gs~IivTTR~~~va~~~---~-  291 (779)
                      .+.-+ .-.+-++-..+..   .....++.-++++        ..+   ...+.....-|.|++---.+.+.-..   . 
T Consensus       444 V~nve-~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLREGssL~RVYnE~vaLacDrRlCHvv~EVplESLT~~n~~LPR  522 (664)
T PTZ00494        444 VSNVE-VCGDLLGFVEEAMRGATVKASDGVPFLVMRLREGSDLGRVYGEVVSLVSDCQACHIVLAVPMKALTPLNVSSRR  522 (664)
T ss_pred             CCChh-hhccHHHHHHHHHHHHHHhcCCCCCEEEEEeccCCcHHHHHHHHHHHHccchhheeeeechHhhhchhhccCcc
Confidence            87221 1111111111111   1112222222221        111   01122333456666544333332111   1 


Q ss_pred             CceeEccCCChHHHHHHHHHHh
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                      -..|.+++++..+|.+.-.+..
T Consensus       523 LDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        523 LDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             ceeEecCCcCHHHHHHHHhccc
Confidence            3578899999999988766553

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.51  E-value=0.38  Score=50.78  Aligned_cols=38  Identities=37%  Similarity=0.427  Sum_probs=29.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++++++|..|+||||++..++... ..+  -..+.+|+.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l-~~~--g~~V~lIta  242 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQL-LKQ--NRTVGFITT  242 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH-HHc--CCeEEEEeC
Confidence            46799999999999999999998766 222  235667777

>TIGR00665 DnaB replicative DNA helicase

Probab=92.49  E-value=4.1  Score=45.11  Aligned_cols=48  Identities=15%  Similarity=0.166  Sum_probs=33.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGK  226 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~  226 (779)
                      ...++.|-|.+|+|||++|..++.+... ... ..++|++.    .++...++.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~-~~g-~~vl~~SlEm~~~~i~~R~~~  245 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAI-KEG-KPVAFFSLEMSAEQLAMRMLS  245 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHH-hCC-CeEEEEeCcCCHHHHHHHHHH
Confidence            3468999999999999999998876521 222 36788888    444444443

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.43  E-value=0.19  Score=52.53  Aligned_cols=26  Identities=31%  Similarity=0.558  Sum_probs=23.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+++|++|+||||++..++...
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l  138 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKY  138 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            46899999999999999999998877

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=92.38  E-value=0.1  Score=53.63  Aligned_cols=24  Identities=33%  Similarity=0.702  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|-||+||||+|..++...
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~~L   25 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSAAL   25 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHHHH
Confidence            578888999999999999998877

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.

>PRK14531 adenylate kinase; Provisional

Probab=92.37  E-value=0.12  Score=49.55  Aligned_cols=24  Identities=21%  Similarity=0.209  Sum_probs=21.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|.|.|++|+||||+|+.++...
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358899999999999999998876

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=92.36  E-value=0.21  Score=50.79  Aligned_cols=38  Identities=18%  Similarity=0.357  Sum_probs=29.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+++.|.|.+|+|||++|.+++....   ..=..+++++.
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a---~~Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQA---SRGNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHH---hCCCcEEEEEe
Confidence            457999999999999999999866541   22346777877

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=92.35  E-value=0.11  Score=49.07  Aligned_cols=24  Identities=38%  Similarity=0.534  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.+.|.+|+||||+|++++...
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L   25 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKEL   25 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHH
Confidence            467889999999999999998876

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=92.35  E-value=0.15  Score=52.01  Aligned_cols=24  Identities=25%  Similarity=0.551  Sum_probs=22.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|.+|+|||||+..+....
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~~L   25 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVDRL   25 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            589999999999999999999887

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.33  E-value=0.5  Score=52.11  Aligned_cols=58  Identities=21%  Similarity=0.247  Sum_probs=39.6

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      +.++-+.|..+=..-.++.|.|.+|+|||||+.+++....   ..-..++|++..+-..++
T Consensus        66 i~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a---~~g~~vlYvs~Ees~~qi  123 (446)
T PRK11823         66 IGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLA---AAGGKVLYVSGEESASQI  123 (446)
T ss_pred             cHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHH---hcCCeEEEEEccccHHHH
Confidence            3455555554433457999999999999999999988762   223467888884433444

>cd01878 HflX HflX subfamily

Probab=92.30  E-value=0.25  Score=48.27  Aligned_cols=26  Identities=23%  Similarity=0.333  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|+|+|.+|+|||||...+.+..
T Consensus        40 ~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          40 GIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHhcch
Confidence            45789999999999999999988754

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.

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=92.29  E-value=3.9  Score=40.18  Aligned_cols=54  Identities=24%  Similarity=0.282  Sum_probs=40.5

Q ss_pred             cccccc--ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          149 IELPLE--QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       149 ~~~~~~--~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.|++  +++-|.+..++++++.+.-+           -..++=|..+|++|.|||-+|++.+...
T Consensus       163 DekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT  229 (424)
T KOG0652|consen  163 DEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQT  229 (424)
T ss_pred             ccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhc
Confidence            444443  45778999999999987421           1235567899999999999999987765

>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=92.27  E-value=0.12  Score=50.21  Aligned_cols=23  Identities=39%  Similarity=0.642  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|+.|+||||+++.+++..
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l   24 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERL   24 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999887

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=92.26  E-value=0.13  Score=47.92  Aligned_cols=25  Identities=40%  Similarity=0.462  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++.|.|+.|+|||||+++++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4688999999999999999998764

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=92.25  E-value=0.5  Score=54.94  Aligned_cols=99  Identities=14%  Similarity=0.168  Sum_probs=61.0

Q ss_pred             HHHHHHh-ccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcch
Q 004021          166 RVWRCIT-DQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSL  241 (779)
Q Consensus       166 ~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~  241 (779)
                      .|-..|. .+=...+++-|.|.+|+||||||.+++...   ...=..++|+.. ..+-...++.++.+.+.-  ....+.
T Consensus        47 ~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a---~~~G~~v~yId~E~t~~~~~A~~lGvDl~~llv~~~~~~  123 (790)
T PRK09519         47 ALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANA---QAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTG  123 (790)
T ss_pred             HHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHH---HHcCCcEEEECCccchhHHHHHHcCCChhHeEEecCCCH
Confidence            4444454 332356799999999999999998876554   122356789988 334446778887652211  122334


Q ss_pred             hhHHHHHHHhhCCCcc-eeehhhcccc
Q 004021          242 QDKAVDISSILSPKKF-RIDLTELGVP  267 (779)
Q Consensus       242 ~~~~~~l~~~L~~kr~-~~~ld~l~~~  267 (779)
                      ++....+...++...+ ++++|.+...
T Consensus       124 E~~l~~i~~lv~~~~~~LVVIDSI~aL  150 (790)
T PRK09519        124 EQALEIADMLIRSGALDIVVIDSVAAL  150 (790)
T ss_pred             HHHHHHHHHHhhcCCCeEEEEcchhhh
Confidence            5555556666666555 5667766433

>PRK10646 ADP-binding protein; Provisional

Probab=92.24  E-value=0.26  Score=45.04  Aligned_cols=42  Identities=24%  Similarity=0.253  Sum_probs=30.8

Q ss_pred             hhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          161 EKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       161 ~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +++.+++-+.|...-....+|.+.|-=|+||||+++.+++..
T Consensus        11 ~~~t~~l~~~la~~l~~g~vi~L~GdLGaGKTtf~rgl~~~L   52 (153)
T PRK10646         11 EQATLDLGARVAKACDGATVIYLYGDLGAGKTTFSRGFLQAL   52 (153)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            345555555554432233689999999999999999998876

>PRK08840 replicative DNA helicase; Provisional

Probab=92.21  E-value=5.8  Score=44.01  Aligned_cols=49  Identities=14%  Similarity=0.097  Sum_probs=33.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGKR  227 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~~  227 (779)
                      ...++.|-|.+|+|||++|..++... ..+ +-..+++++.    .++...++..
T Consensus       216 ~g~LiviaarPg~GKTafalnia~~~-a~~-~~~~v~~fSlEMs~~ql~~Rlla~  268 (464)
T PRK08840        216 GSDLIIVAARPSMGKTTFAMNLCENA-AMD-QDKPVLIFSLEMPAEQLMMRMLAS  268 (464)
T ss_pred             CCceEEEEeCCCCchHHHHHHHHHHH-HHh-CCCeEEEEeccCCHHHHHHHHHHh
Confidence            34688899999999999998888765 222 2235667777    4455555444

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=92.18  E-value=0.12  Score=55.91  Aligned_cols=26  Identities=27%  Similarity=0.409  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+.|+|+|..|+||||||+++++..
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~~  243 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANIF  243 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999998875

>PRK12338 hypothetical protein; Provisional

Probab=92.18  E-value=0.14  Score=52.96  Aligned_cols=26  Identities=19%  Similarity=0.368  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.+|.|.|.+|+||||+|+.++...
T Consensus         3 ~p~ii~i~G~sGsGKST~a~~la~~l   28 (319)
T PRK12338          3 KPYVILIGSASGIGKSTIASELARTL   28 (319)
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHC
Confidence            35799999999999999999998876

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=92.17  E-value=0.11  Score=49.68  Aligned_cols=21  Identities=48%  Similarity=0.626  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      +|+|.|+.|+||||+|+.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999866

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=92.17  E-value=0.24  Score=49.35  Aligned_cols=38  Identities=21%  Similarity=0.291  Sum_probs=26.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...++.|.|.+|+||||||.+++....  +.. ..+++++.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~--~~g-~~~~yi~~   60 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFL--QNG-YSVSYVST   60 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH--hCC-CcEEEEeC
Confidence            446999999999999999876655441  122 34566666

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=92.17  E-value=0.51  Score=49.40  Aligned_cols=65  Identities=15%  Similarity=0.165  Sum_probs=40.3

Q ss_pred             HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc---cC-CCCEEEEEEech-----HHHHHHHHhCC
Q 004021          165 PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ---QH-NFDVVIWAAVQT-----FQDDIGKRIGF  230 (779)
Q Consensus       165 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~~-~F~~~~wv~v~~-----i~~~i~~~l~~  230 (779)
                      ..+-+.|..+=....++.|+|.+|+|||||+..++... ..   .. .-..++|++...     -+..+++.++.
T Consensus        83 ~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~-~~~~~~Gg~~~~vvyIdtE~~f~~~Rl~~ia~~~~~  156 (316)
T TIGR02239        83 KELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTC-QLPIDQGGGEGKALYIDTEGTFRPERLLAIAERYGL  156 (316)
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHH-hhhhhcCCCCceEEEEECCCCCCHHHHHHHHHHcCC
Confidence            34444455443356899999999999999999887532 11   11 123578988822     23445555544

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.14  E-value=0.3  Score=53.34  Aligned_cols=39  Identities=28%  Similarity=0.399  Sum_probs=28.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .+++.++|++|+||||++..++... .....-..+..|+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~-~~~~~g~~V~li~~  259 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARY-ALLYGKKKVALITL  259 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHhcCCCeEEEEEC
Confidence            3699999999999999999887766 20122345666776

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=92.12  E-value=0.22  Score=50.30  Aligned_cols=38  Identities=39%  Similarity=0.655  Sum_probs=28.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v  217 (779)
                      .-+.++|.|..|+||||||+.+++..   +.+|+ .++++-+
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i---~~~~~~~~V~~~i  106 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNI---AKAHGGYSVFAGV  106 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHH---HhcCCCEEEEEEe
Confidence            34678999999999999999999987   34454 4444443

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>PRK08506 replicative DNA helicase; Provisional

Probab=92.12  E-value=6.3  Score=43.94  Aligned_cols=48  Identities=15%  Similarity=0.117  Sum_probs=34.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGKR  227 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~~  227 (779)
                      .-.++.|-|.+|+|||++|..++....  +.. ..+++++.    .++...++..
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~~~--~~g-~~V~~fSlEMs~~ql~~Rlla~  242 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALKAL--NQD-KGVAFFSLEMPAEQLMLRMLSA  242 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHHHH--hcC-CcEEEEeCcCCHHHHHHHHHHH
Confidence            346899999999999999999987762  222 35677787    4455555443

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=92.11  E-value=0.17  Score=46.63  Aligned_cols=26  Identities=23%  Similarity=0.530  Sum_probs=23.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|-+.|.+|.||||+|.+++...
T Consensus        22 ~~~viW~TGLSGsGKSTiA~ale~~L   47 (197)
T COG0529          22 KGAVIWFTGLSGSGKSTIANALEEKL   47 (197)
T ss_pred             CCeEEEeecCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999999887

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=92.11  E-value=0.33  Score=50.34  Aligned_cols=43  Identities=14%  Similarity=0.191  Sum_probs=32.0

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++=..+....+..++..+    +-|.|.|.+|+||||+|+.++...
T Consensus        46 ~y~f~~~~~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~lA~~l   88 (327)
T TIGR01650        46 AYLFDKATTKAICAGFAYD----RRVMVQGYHGTGKSTHIEQIAARL   88 (327)
T ss_pred             CccCCHHHHHHHHHHHhcC----CcEEEEeCCCChHHHHHHHHHHHH
Confidence            3333444555677777544    468999999999999999999876

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK01184 hypothetical protein; Provisional

Probab=92.10  E-value=0.13  Score=49.48  Aligned_cols=21  Identities=38%  Similarity=0.669  Sum_probs=17.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      .+|+|+|++|+||||+|+ ++.
T Consensus         2 ~~i~l~G~~GsGKsT~a~-~~~   22 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSK-IAR   22 (184)
T ss_pred             cEEEEECCCCCCHHHHHH-HHH
Confidence            489999999999999987 444

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.10  E-value=0.2  Score=48.71  Aligned_cols=24  Identities=29%  Similarity=0.459  Sum_probs=21.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|+|..|+||||++..+....
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~   25 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYI   25 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999887766

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PLN02165 adenylate isopentenyltransferase

Probab=92.09  E-value=0.14  Score=53.11  Aligned_cols=26  Identities=23%  Similarity=0.471  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+||||||..++...
T Consensus        42 ~g~iivIiGPTGSGKStLA~~LA~~l   67 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSVDLATRF   67 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHc
Confidence            45699999999999999999998875

>PRK14528 adenylate kinase; Provisional

Probab=92.05  E-value=0.14  Score=49.22  Aligned_cols=24  Identities=29%  Similarity=0.271  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.|.|++|+||||+|+.++...
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            458899999999999999998765

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=92.05  E-value=0.14  Score=47.18  Aligned_cols=25  Identities=32%  Similarity=0.581  Sum_probs=23.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|++|+|..|+|||||...+....
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L   26 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKL   26 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHH
Confidence            4799999999999999999998877

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=92.05  E-value=0.74  Score=42.54  Aligned_cols=103  Identities=18%  Similarity=0.179  Sum_probs=55.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-ch----HHHHHHHHhC--------CC-----cchhhhhcc
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QT----FQDDIGKRIG--------FS-----EDKKWKEKS  240 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~----i~~~i~~~l~--------~~-----~~~~~~~~~  240 (779)
                      .+|-|++..|.||||+|...+-+..  ...+ .+.++.. +.    =-..+++.+.        ..     .+.......
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~--~~g~-~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRAL--GHGY-RVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH--HCCC-eEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHH
Confidence            4788899899999999988877662  2222 3444444 10    1122333331        00     000000011


Q ss_pred             hhhHHHHHHHhhCCCcc-eeehhhcccc--------------ccccCCCcEEEEEeCch
Q 004021          241 LQDKAVDISSILSPKKF-RIDLTELGVP--------------LQMLNAGFKIVLKTRSA  284 (779)
Q Consensus       241 ~~~~~~~l~~~L~~kr~-~~~ld~l~~~--------------~~~~~~gs~IivTTR~~  284 (779)
                      ..+.....++.+....| ++++|++..+              +.....+..||+|.|+.
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            12233445556666666 6677776443              22334677999999984

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=92.04  E-value=0.11  Score=46.96  Aligned_cols=25  Identities=36%  Similarity=0.577  Sum_probs=22.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++...
T Consensus        11 g~~~~i~G~nGsGKStLl~~l~g~~   35 (137)
T PF00005_consen   11 GEIVAIVGPNGSGKSTLLKALAGLL   35 (137)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEEccCCCccccceeeecccc
Confidence            3689999999999999999998766

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 ....

>PRK13235 nifH nitrogenase reductase; Reviewed

Probab=91.98  E-value=0.12  Score=53.11  Aligned_cols=24  Identities=29%  Similarity=0.628  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|-||+||||+|..++...
T Consensus         2 ~~iav~~KGGVGKTT~~~nLA~~L   25 (274)
T PRK13235          2 RKVAIYGKGGIGKSTTTQNTVAGL   25 (274)
T ss_pred             CEEEEeCCCCccHHHHHHHHHHHH
Confidence            578999999999999999888776

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=91.98  E-value=0.24  Score=58.00  Aligned_cols=48  Identities=27%  Similarity=0.360  Sum_probs=39.0

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.|.+.+...       ......+-++|+.|+|||++|+.++...
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l  512 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh
Confidence            45799999999999988631       2234578999999999999999998876

>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=91.96  E-value=0.26  Score=45.46  Aligned_cols=37  Identities=19%  Similarity=0.253  Sum_probs=29.5

Q ss_pred             hhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          161 EKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       161 ~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.+++|.+.|.+     +++.++|..|+|||||...+....
T Consensus        23 ~~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   23 GEGIEELKELLKG-----KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CcCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHHHHhhc
Confidence            3456677776643     689999999999999999988764

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=91.95  E-value=0.88  Score=47.96  Aligned_cols=99  Identities=19%  Similarity=0.208  Sum_probs=58.0

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH---HHHhCCCcchhhhhc
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI---GKRIGFSEDKKWKEK  239 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i---~~~l~~~~~~~~~~~  239 (779)
                      ...++-+.|..+=-.-.+|.|-|-+|+|||||..+++.+..   ..- .+.+|+-++-..+|   ++.++.+. ....- 
T Consensus        78 g~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA---~~~-~vLYVsGEES~~QiklRA~RL~~~~-~~l~l-  151 (456)
T COG1066          78 GIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA---KRG-KVLYVSGEESLQQIKLRADRLGLPT-NNLYL-  151 (456)
T ss_pred             ChHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHH---hcC-cEEEEeCCcCHHHHHHHHHHhCCCc-cceEE-
Confidence            34556666655433447999999999999999999999882   222 78888884443333   45566441 11111 


Q ss_pred             chhhHHHHHHHhhCCCcc-eeehhhcccc
Q 004021          240 SLQDKAVDISSILSPKKF-RIDLTELGVP  267 (779)
Q Consensus       240 ~~~~~~~~l~~~L~~kr~-~~~ld~l~~~  267 (779)
                      -.+...+.+.+.+..++. +.+.|.+...
T Consensus       152 ~aEt~~e~I~~~l~~~~p~lvVIDSIQT~  180 (456)
T COG1066         152 LAETNLEDIIAELEQEKPDLVVIDSIQTL  180 (456)
T ss_pred             ehhcCHHHHHHHHHhcCCCEEEEecccee
Confidence            112223334444444444 6666766443

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=91.94  E-value=0.11  Score=51.33  Aligned_cols=24  Identities=46%  Similarity=0.529  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-|.|+|.+|+|||||+..+.++.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            568999999999999999998765

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=91.94  E-value=0.21  Score=49.82  Aligned_cols=57  Identities=18%  Similarity=0.166  Sum_probs=34.8

Q ss_pred             HHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHH
Q 004021          169 RCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKR  227 (779)
Q Consensus       169 ~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~  227 (779)
                      +.|..+=....++.|.|.+|+|||+||.++.....+  ..=+.++||+..+-.+++.+.
T Consensus        10 ~~l~GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~--~~ge~vlyvs~ee~~~~l~~~   66 (226)
T PF06745_consen   10 ELLGGGIPKGSVVLISGPPGSGKTTLALQFLYNGLK--NFGEKVLYVSFEEPPEELIEN   66 (226)
T ss_dssp             HHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHHHH--HHT--EEEEESSS-HHHHHHH
T ss_pred             HhhcCCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhh--hcCCcEEEEEecCCHHHHHHH
Confidence            334333234579999999999999999987654411  113467888884433444443

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR01351 adk adenylate kinases

Probab=91.94  E-value=0.13  Score=50.63  Aligned_cols=22  Identities=32%  Similarity=0.519  Sum_probs=19.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|++|+||||+|+.++...
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6799999999999999998765

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=91.93  E-value=0.57  Score=49.59  Aligned_cols=39  Identities=28%  Similarity=0.371  Sum_probs=27.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .++|+++|+.||||||-...++.++ .....=..+..++.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~-~~~~~~~kVaiITt  241 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARY-VMLKKKKKVAIITT  241 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHH-HhhccCcceEEEEe
Confidence            6899999999999987655555554 11233345677777

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=91.91  E-value=0.14  Score=46.09  Aligned_cols=24  Identities=42%  Similarity=0.448  Sum_probs=21.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.++|..|+|||||++++-...
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            467899999999999999997755

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

>PRK13233 nifH nitrogenase reductase; Reviewed

Probab=91.90  E-value=0.13  Score=53.04  Aligned_cols=24  Identities=33%  Similarity=0.652  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|-|||||||+|..++...
T Consensus         3 ~vIav~~KGGVGKTT~a~nLA~~L   26 (275)
T PRK13233          3 RKIAIYGKGGIGKSTTTQNTAAAM   26 (275)
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Confidence            688999999999999999888776

>PRK08356 hypothetical protein; Provisional

Probab=91.88  E-value=0.16  Score=49.34  Aligned_cols=22  Identities=36%  Similarity=0.474  Sum_probs=19.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHH
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVN  199 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~  199 (779)
                      ..+|+|.|++|+||||+|+.+.
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            3579999999999999999983

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=91.85  E-value=0.23  Score=48.77  Aligned_cols=26  Identities=35%  Similarity=0.544  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.++...
T Consensus        25 ~G~~~~i~G~nGsGKSTLl~~l~G~~   50 (210)
T cd03269          25 KGEIFGLLGPNGAGKTTTIRMILGII   50 (210)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            34689999999999999999998765

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=91.84  E-value=0.12  Score=47.76  Aligned_cols=35  Identities=20%  Similarity=0.331  Sum_probs=25.9

Q ss_pred             EEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHH
Q 004021          183 LYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIG  225 (779)
Q Consensus       183 I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~  225 (779)
                      |+|++|+||||+|+.++.+.     .|   ..+++.++++..+
T Consensus         1 i~G~PgsGK~t~~~~la~~~-----~~---~~is~~~llr~~~   35 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRY-----GL---VHISVGDLLREEI   35 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHH-----TS---EEEEHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHhc-----Cc---ceechHHHHHHHH
Confidence            78999999999999999876     22   3456655555443

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.84  E-value=0.4  Score=47.64  Aligned_cols=55  Identities=18%  Similarity=0.111  Sum_probs=36.0

Q ss_pred             HHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHH
Q 004021          168 WRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIG  225 (779)
Q Consensus       168 ~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~  225 (779)
                      -+.|..+=....++.|.|.+|+|||++|.+++....   ..=..++|++...-..++.
T Consensus         6 D~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~---~~g~~~~y~s~e~~~~~l~   60 (224)
T TIGR03880         6 DEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGL---KNGEKAMYISLEEREERIL   60 (224)
T ss_pred             HHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHH---hCCCeEEEEECCCCHHHHH
Confidence            334433323457999999999999999998876641   2235677888733333333

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=91.84  E-value=0.52  Score=49.64  Aligned_cols=51  Identities=18%  Similarity=0.241  Sum_probs=34.6

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCC----CCEEEEEEe
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHN----FDVVIWAAV  217 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~----F~~~~wv~v  217 (779)
                      .+.+.|..+=....++-|+|.+|+|||++|.+++... .....    =..++||+.
T Consensus        90 ~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~-~~~~~~gg~~~~~~yi~t  144 (317)
T PRK04301         90 ELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNV-QLPEEKGGLEGKAVYIDT  144 (317)
T ss_pred             HHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHh-ccccccCCCCceEEEEeC
Confidence            3334444433356799999999999999999988654 11111    147889988

>PRK02496 adk adenylate kinase; Provisional

Probab=91.81  E-value=0.14  Score=49.16  Aligned_cols=23  Identities=22%  Similarity=0.260  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+....
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=91.81  E-value=0.14  Score=53.57  Aligned_cols=24  Identities=29%  Similarity=0.381  Sum_probs=21.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.+.|.+|+||||+|+.+..+.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHC
Confidence            578899999999999999997765

>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=91.80  E-value=0.17  Score=47.04  Aligned_cols=24  Identities=42%  Similarity=0.704  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++++|+|..|+|||||+..+....
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~~l   25 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIPAL   25 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            589999999999999999999876

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.

>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=91.80  E-value=0.14  Score=44.72  Aligned_cols=21  Identities=29%  Similarity=0.585  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |+|+|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999974

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 ....

>PRK00279 adk adenylate kinase; Reviewed

Probab=91.79  E-value=0.15  Score=50.38  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.++...
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=91.78  E-value=0.14  Score=47.87  Aligned_cols=23  Identities=35%  Similarity=0.430  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+++|.+|+|||||+..+.+..
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            47899999999999999987654

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

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=91.78  E-value=0.24  Score=49.00  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||++.++.-.
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~Gl~   53 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILGIE   53 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4689999999999999999998765

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.76  E-value=0.4  Score=51.88  Aligned_cols=39  Identities=31%  Similarity=0.371  Sum_probs=27.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+|+++|..|+||||++..++... ......+.+..++.
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~-~~~~~~~~v~~i~~  229 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARA-VIRHGADKVALLTT  229 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHhcCCCeEEEEec
Confidence            4799999999999999999887654 11222344555555

>PHA02244 ATPase-like protein

Probab=91.74  E-value=0.2  Score=52.59  Aligned_cols=44  Identities=16%  Similarity=0.245  Sum_probs=29.9

Q ss_pred             ccccchhhhH----HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLL----PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~----~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.....    ..+..++..+    .-|-|+|.+|+|||+||+++++..
T Consensus        96 ~~~ig~sp~~~~~~~ri~r~l~~~----~PVLL~GppGtGKTtLA~aLA~~l  143 (383)
T PHA02244         96 TTKIASNPTFHYETADIAKIVNAN----IPVFLKGGAGSGKNHIAEQIAEAL  143 (383)
T ss_pred             CcccCCCHHHHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHh
Confidence            3456654433    3444444433    346789999999999999999876

>smart00072 GuKc Guanylate kinase homologues

Probab=91.74  E-value=0.19  Score=48.19  Aligned_cols=25  Identities=44%  Similarity=0.539  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|.|+|+.|+|||||+..+....
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhcC
Confidence            3689999999999999999998765

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=91.74  E-value=0.23  Score=45.67  Aligned_cols=23  Identities=35%  Similarity=0.746  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|++.|.+|+||||++..+....
T Consensus         1 ~i~~~G~~GsGKTt~~~~l~~~~   23 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITAL   23 (148)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHH
Confidence            47899999999999999998776

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=91.71  E-value=0.25  Score=47.70  Aligned_cols=25  Identities=36%  Similarity=0.632  Sum_probs=22.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||++.+....
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G~~   42 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNGLL   42 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3689999999999999999998765

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.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=91.70  E-value=0.16  Score=49.24  Aligned_cols=24  Identities=33%  Similarity=0.408  Sum_probs=22.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|+|.|..|+||||+|+.+++..
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l   27 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLL   27 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            579999999999999999999887

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PLN02796 D-glycerate 3-kinase

Probab=91.69  E-value=0.17  Score=52.80  Aligned_cols=26  Identities=35%  Similarity=0.401  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+-+|+|.|..|+||||||+.+....
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~lL  124 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVYLF  124 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHh
Confidence            45689999999999999999999877

>PRK05748 replicative DNA helicase; Provisional

Probab=91.67  E-value=5.7  Score=44.08  Aligned_cols=49  Identities=14%  Similarity=0.130  Sum_probs=34.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGKR  227 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~~  227 (779)
                      .-.++.|-|.+|+|||++|..+..+. ..+.. ..+++++.    .++...++..
T Consensus       202 ~G~livIaarpg~GKT~~al~ia~~~-a~~~g-~~v~~fSlEms~~~l~~R~l~~  254 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFALNIAQNV-ATKTD-KNVAIFSLEMGAESLVMRMLCA  254 (448)
T ss_pred             CCceEEEEeCCCCCchHHHHHHHHHH-HHhCC-CeEEEEeCCCCHHHHHHHHHHH
Confidence            44689999999999999999998765 21212 35677887    4455555433

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=91.67  E-value=0.25  Score=50.92  Aligned_cols=54  Identities=17%  Similarity=0.207  Sum_probs=38.9

Q ss_pred             cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEE
Q 004021          158 VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVI  213 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~  213 (779)
                      -+|..+..--+++|.++  ++..|.+.|.+|.|||.||.+..=..--.++.|..++
T Consensus       227 ~prn~eQ~~ALdlLld~--dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~Kii  280 (436)
T COG1875         227 RPRNAEQRVALDLLLDD--DIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKII  280 (436)
T ss_pred             CcccHHHHHHHHHhcCC--CCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEE
Confidence            34666666677888888  8999999999999999999765432213355665443

>TIGR02016 BchX chlorophyllide reductase iron protein subunit X

Probab=91.67  E-value=0.15  Score=53.05  Aligned_cols=24  Identities=33%  Similarity=0.631  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|+|-||+||||+|..++...
T Consensus         1 ~vIav~gKGGvGKTT~a~nLA~~L   24 (296)
T TIGR02016         1 RIIAIYGKGGSGKSFTTTNLSHMM   24 (296)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999998877

This model represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or "iron" protein.

---

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	779
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-42
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	3e-41
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-34
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	4e-14
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	5e-10
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	5e-06
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	7e-10
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-08
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-08
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	3e-04
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	4e-09
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-07
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	2e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	6e-05
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	1e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-07
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-06
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-06
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-06
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-05
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	2e-08
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	1e-06
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	6e-06
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	2e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-08
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	3e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-06
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	9e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-04
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	1e-07
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	1e-06
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	4e-06
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	4e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-07
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	4e-07
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	3e-06
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-05
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-04
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-07
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-07
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	7e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-07
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	2e-07
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	2e-05
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	9e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	2e-07
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	7e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-07
1o6v_A	466	Internalin A; bacterial infection, extracellular r	2e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	4e-06
1o6v_A	466	Internalin A; bacterial infection, extracellular r	5e-05
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	3e-07
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	3e-06
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	3e-06
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	4e-06
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	2e-05
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	6e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	6e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-05
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	8e-04
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-07
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	7e-07
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	4e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-04
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	4e-07
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-07
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	5e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	7e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	4e-05
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	5e-07
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	8e-07
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	5e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-05
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	6e-07
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	5e-06
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	6e-06
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	6e-07
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	2e-06
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	6e-07
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-06
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	2e-06
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	4e-04
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	9e-07
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	4e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	6e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	7e-04
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	1e-06
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-06
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	5e-05
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	5e-04
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	6e-05
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-04
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-04
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	8e-06
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	9e-05
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-04
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	2e-06
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	5e-06
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	3e-06
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	1e-05
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	4e-06
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	4e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	4e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	6e-05
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	7e-04
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	8e-06
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	1e-05
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	1e-05
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	2e-05
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	3e-05
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	3e-05
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	3e-05
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	4e-04
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	4e-05
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	5e-05
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	2e-04
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	4e-05
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	4e-05
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	6e-05
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	7e-05
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	5e-05
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	4e-04
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	5e-05
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	5e-05
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	2e-04
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	6e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	1e-04
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	1e-04
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	6e-04
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	1e-04
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	2e-04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	3e-04
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	3e-04
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	8e-04
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	8e-04

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  162 bits (412), Expect = 2e-42
 Identities = 68/468 (14%), Positives = 154/468 (32%), Gaps = 74/468 (15%)

Query: 157 IVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF-DVVIWA 215
            V ++KL+  + + ++  +   G + ++G+ G GK+ L  +   +    +  F   V W 
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 216 AV-QTFQDD-----------IGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTE 263
           +V +  +             + +   FS+      +  +D+   +  ++  K  R     
Sbjct: 186 SVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDR---LRILMLRKHPRS---- 238

Query: 264 LGV--------PLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVY---SLAHDEAWKLFQEM 312
           L +         L+  ++  +I+L TR   V D +      V    SL  ++  ++    
Sbjct: 239 LLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILS-- 296

Query: 313 IERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTF 372
                      +PE A ++ +EC   PL +  +G  ++        E  +++++      
Sbjct: 297 --LFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN--RWEYYLKQLQNKQFKR 352

Query: 373 SGMEENVFLR-----LKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMA 427
                +         +  S + L  D ++       +  +D K+P + L   W  E    
Sbjct: 353 IRKSSSYDYEALDEAMSISVEMLRED-IKDYYTDLSILQKDVKVPTKVLCILWDMETEEV 411

Query: 428 DFDRGCEFINDLLHACLLEEEGDDHV---KMHDMIREMSLWIA-WTIEKEKKNFL----- 478
           +     + + + ++  LL  + +       +HD+  +         ++   K  +     
Sbjct: 412 E-----DILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQR 466

Query: 479 -VRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLS----LRRNDSLTELPSRIS 533
             +      +      W     ++      +   E+  L+     ++    L      I 
Sbjct: 467 YHQPHTLSPDQEDCMYW--YNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIH 524

Query: 534 SLVSLHH-LDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLI 580
             V   H LD     +    QE  +L           H L   P   I
Sbjct: 525 EFVEYRHILDEKDCAVSENFQEFLSL---------NGHLLGRQPFPNI 563

>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 =  158 bits (401), Expect = 3e-41
 Identities = 58/431 (13%), Positives = 128/431 (29%), Gaps = 50/431 (11%)

Query: 76  EDVQKLGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYG--REVVELTDRVINLNKDG 133
           +  + +    T L+++    +            L+  +NY     + +  +  I+   + 
Sbjct: 39  DHSELISKMSTRLERIA-NFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINE 97

Query: 134 EKIAVVVEKAPDGAAIE---------LPLEQTIVGQEKLLPRVWRCITD-QQKNRGIIGL 183
             +   V  AP  +            +P + T   +E  + RV + + +    +   + L
Sbjct: 98  PDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFL 157

Query: 184 YGIGGVGKTTLLKQV-NNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKKWKEKSL 241
           +G  G GK+ +  Q  + +      N+D ++W     T                  E  L
Sbjct: 158 HGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDL 217

Query: 242 QDKAVDISSILSPKKFRIDLTELGVPLQML----------------NAGFKIVLKTRSAG 285
            +    +  + S    R+    L      L                    + ++ TR   
Sbjct: 218 LNFP-SVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVE 276

Query: 286 VCDQMDSK--NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK 343
           + +        +EV SL  DE +   +       +       ++           P  L 
Sbjct: 277 ISNAASQTCEFIEVTSLEIDECYDFLEAY--GMPMPVGEKEEDVLNKTIELSSGNPATLM 334

Query: 344 TVGRAMKSQKKVGDRERAIEKMRTSAST-----FSGMEENVFLRLKFSYDSLSMDKLRSC 398
              ++ +  K      +   K+ +              +++ + L+   + LS D+ RS 
Sbjct: 335 MFFKSCEP-KTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLS-DEDRSA 392

Query: 399 LLYCCLYPEDYKIPKRSLIDYWISEGFMAD----FDRGCEFINDLLHACLLEEEGDDHV- 453
           L +  + P    IP +        +    +     D   + +  L     L       V 
Sbjct: 393 LAFAVVMPPGVDIPVKLWSCVIPVDICSNEEEQLDDEVADRLKRLSKRGALLSGKRMPVL 452

Query: 454 --KMHDMIREM 462
             K+  +I   
Sbjct: 453 TFKIDHIIHMF 463

>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 =  140 bits (353), Expect = 3e-34
 Identities = 100/635 (15%), Positives = 202/635 (31%), Gaps = 144/635 (22%)

Query: 31  LKKNLEGLKTE--MRKLTRTR--DDLVNKVEVEEQPRR------TRRTNRVAGWLEDVQK 80
              N +    +   + +      D ++   +      R      +++   V  ++E+V +
Sbjct: 29  FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLR 88

Query: 81  LGTEFTELQQVRAQEMDRLCLGGLCSKNLVSSYNYGREVVELTDRVINLNKDGEKIAVVV 140
           +  +F  +  ++ ++             +   Y   R      DR+ N N+         
Sbjct: 89  INYKFL-MSPIKTEQRQP--------SMMTRMYIEQR------DRLYNDNQ--------- 124

Query: 141 EKAPDGAAIELPLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNN 200
                         +  V + +   ++ + + + +  + ++ + G+ G GKT +   V  
Sbjct: 125 -----------VFAKYNVSRLQPYLKLRQALLELRPAKNVL-IDGVLGSGKTWVALDVCL 172

Query: 201 NFCHQQHNFDVVIWAAV-------------QTFQDDIGK----RIGFSEDKKWKEKSLQD 243
           ++  Q      + W  +             Q     I      R   S + K +  S+Q 
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 244 KAVDISSILSPKKFRIDLTEL-GV----PLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVY 298
           +   +  +L  K +   L  L  V         N   KI+L TR   V D + +      
Sbjct: 233 E---LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289

Query: 299 SLAH-------DEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKS 351
           SL H       DE   L  + ++    D    +P             P  L  +  +++ 
Sbjct: 290 SLDHHSMTLTPDEVKSLLLKYLDCRPQD----LPREV------LTTNPRRLSIIAESIRD 339

Query: 352 QKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKI 411
                D  + +   + +              ++ S + L   + R       ++P    I
Sbjct: 340 GLATWDNWKHVNCDKLTTI------------IESSLNVLEPAEYRKMFDRLSVFPPSAHI 387

Query: 412 PKRSLIDYWISEGFMADFDRGCEFINDLLHA-CLLEEEGDDH-VKMHDMIREMSLWIAWT 469
           P   L   W     +   D     + + LH   L+E++  +  + +  +  E+ +     
Sbjct: 388 PTILLSLIWFD---VIKSD--VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV----K 438

Query: 470 IEKEKKNFLVRAGVKLTEAPKVKEWEGAKRISL-------------MANEIESLSEIPTL 516
           +E E    L R+ V     PK  + +      L                  E ++    +
Sbjct: 439 LENEYA--LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV 496

Query: 517 -LSLR------RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT 569
            L  R      R+DS T   +  S L +L  L     +I     + +     R +N    
Sbjct: 497 FLDFRFLEQKIRHDS-TAWNASGSILNTLQQLKFYKPYICDNDPKYE-----RLVN-AIL 549

Query: 570 HYLSIIPHQLI-SGFLKLEVLRL-LECGSEGVTKE 602
            +L  I   LI S +  L  LR+ L    E + +E
Sbjct: 550 DFLPKIEENLICSKYTDL--LRIALMAEDEAIFEE 582

>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 = 56.4 bits (135), Expect = 3e-08
 Identities = 86/591 (14%), Positives = 175/591 (29%), Gaps = 163/591 (27%)

Query: 204 HQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTE 263
           HQ    D++       F+D       F ++   K+  +QD      SILS ++    +  
Sbjct: 14  HQYQYKDIL-----SVFEDA------FVDNFDCKD--VQDM---PKSILSKEEID-HIIM 56

Query: 264 LGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTS 323
               +      F  +L  +   V   ++        L  +  +      I+         
Sbjct: 57  SKDAVSGTLRLFWTLLSKQEEMVQKFVEE------VLRINYKF--LMSPIKTEQRQPSMM 108

Query: 324 IPELAETLARECGRLPLALK-TVGRAMKSQKKVGDRERAIEKMRTSAS-TFSGMEENVFL 381
                E   R      +  K  V R     +      +A+ ++R + +    G+      
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNVSR----LQPYLKLRQALLELRPAKNVLIDGV------ 158

Query: 382 RLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLH 441
            L      +++D   S  + C +   D+KI       +W++       +   E +  LL+
Sbjct: 159 -LGSGKTWVALDVCLSYKVQCKM---DFKI-------FWLNLKNCNSPETVLEMLQKLLY 207

Query: 442 --ACLLEEEGDDH----VKMHDMIREMSLWIAWTIEKEKKNFLVRAGVKLTEAPKVKEWE 495
                     D      +++H +  E+   +    +  +   LV   V            
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS--KPYENCLLVLLNV----------QN 255

Query: 496 GAKRISLMANEIESLS-EIPTLLSLRRNDSLTE-LPSRISSLVSLHHLDLSLTHIRGLPQ 553
                   A    + +     LL   R   +T+ L +  ++ +SL H  ++LT     P 
Sbjct: 256 --------AKAWNAFNLSCKILL-TTRFKQVTDFLSAATTTHISLDHHSMTLT-----PD 301

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEP 613
           E+K+L  L+YL+         +P ++++                               P
Sbjct: 302 EVKSL-LLKYLDCR----PQDLPREVLTTN-----------------------------P 327

Query: 614 LMRELLG-LKRLNVLSWSFRSSLAVQKFFKYP---KLDLTWLVFVQNLKELEIIVCTEME 669
               ++    R  + +W           +K+    KL       +  L+  E     +  
Sbjct: 328 RRLSIIAESIRDGLATW---------DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL 378

Query: 670 EIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP----NPLH-------F 718
            +         + I  I+            L +++  D+         N LH        
Sbjct: 379 SV-----FPPSAHIPTIL------------LSLIWF-DVIKSDVMVVVNKLHKYSLVEKQ 420

Query: 719 PKLKKIGVYGCPKLKKLPINSSSAKERRVV-----IEGLKEWWEELQWEDQ 764
           PK   I +       K+ + +  A  R +V      +          + DQ
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471

>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 = 75.6 bits (186), Expect = 4e-14
 Identities = 66/467 (14%), Positives = 152/467 (32%), Gaps = 60/467 (12%)

Query: 152 PLEQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF-D 210
                 V ++KL+  + + +       G + +YG+ G GK+ L  +   +    +  F  
Sbjct: 121 QRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSG 180

Query: 211 VVIW--------AAVQTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFR---- 258
            V W        + +     ++  R+   E    +     ++A D   +L  +K      
Sbjct: 181 GVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLL 240

Query: 259 -IDLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKNLEVY---SLAHDEAWKLFQEMIE 314
            +D       L+  +   +I+L TR   V D +      V     L  ++  ++    + 
Sbjct: 241 ILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVN 300

Query: 315 RSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGD------RERAIEKMRTS 368
                    +P  A ++ +EC   PL +  +G  ++             + +  +++R S
Sbjct: 301 MKK----EDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKS 356

Query: 369 ASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMAD 428
           +S      +     +  S + L  + ++       +  +D K+P + L   W  E    +
Sbjct: 357 SSYDYEALDEA---MSISVEMLR-EDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVE 412

Query: 429 FDRGCEFINDLLHACLLEEEGDD---HVKMHDMIRE---------MSLWIAWTIEKEKKN 476
                + + + ++  LL    +       +HD+  +         +       + + ++ 
Sbjct: 413 -----DILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRY 467

Query: 477 FLVRAGVKLTEAPK--VKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISS 534
           +         E               + M  E+ +L     + SL       +  + +  
Sbjct: 468 YQPHTLSPDQEDCMYWYNFLAYHMASANMHKELCAL-----MFSLDW----IKAKTELVG 518

Query: 535 LVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLIS 581
              L H  ++  HI    ++    E  +       H L   P   I 
Sbjct: 519 PAHLIHEFVAYRHILD-EKDCAVCENFQEFLSLNGHLLGRQPFPNIV 564

>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 = 60.7 bits (148), Expect = 5e-10
 Identities = 57/279 (20%), Positives = 94/279 (33%), Gaps = 57/279 (20%)

Query: 474 KKNFLVRAGVKLTEAPKVKE---WEGAKRISLMANEIESL-SEIPTLLSLRR----NDSL 525
                 R G  L     + E     G   + L +  +     +   L  L+        L
Sbjct: 57  NPQIETRTGRALKATADLLEDATQPGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGL 116

Query: 526 TELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQL------ 579
            ELP  +     L  L L+   +R LP  + +L +LR L++     L+ +P  L      
Sbjct: 117 MELPDTMQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDAS 176

Query: 580 --ISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV 637
               G + L+ LRL   G   +     N            L  LK L  +  S  S+L  
Sbjct: 177 GEHQGLVNLQSLRLEWTGIRSLPASIAN------------LQNLKSLK-IRNSPLSAL-- 221

Query: 638 QKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQL 697
                     +  L     L+EL++  CT +                 I G        L
Sbjct: 222 ------GP-AIHHL---PKLEELDLRGCTALRN------------YPPIFGG----RAPL 255

Query: 698 ESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLP 736
           + L +    +L ++  +     +L+K+ + GC  L +LP
Sbjct: 256 KRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLP 294

>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 = 48.4 bits (116), Expect = 5e-06
 Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 7/84 (8%)

Query: 505 NEIESL-SEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSL-THIRGLPQELKA 557
             + +             L L+   +L  LP  I  L  L  LDL    ++  LP  +  
Sbjct: 240 TALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQ 299

Query: 558 LEKLRYLNLEYTHYLSIIPHQLIS 581
           L     + +       +  H+ ++
Sbjct: 300 LPANCIILVPPHLQAQLDQHRPVA 323

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 58.1 bits (141), Expect = 4e-09
 Identities = 19/143 (13%), Positives = 40/143 (27%), Gaps = 17/143 (11%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + ++L  N I  +           L L  N  L  +     S   +  + L    +  + 
Sbjct: 172 EHLNLQYNFIYDVKGQVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNNKLVLIE 230

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVL-----------RLLECGSEGVTK 601
           + L+  + L + +L    +         S   +++ +              EC    +  
Sbjct: 231 KALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGH 290

Query: 602 EEGNVLCDDAEPLMRELLGLKRL 624
                  D   P    L+ L   
Sbjct: 291 YGAYCCEDLPAPFADRLIALGHH 313

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 52.3 bits (126), Expect = 3e-07
 Identities = 19/111 (17%), Positives = 44/111 (39%), Gaps = 6/111 (5%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL--LSLRRNDSLTELPSRISSLVSLHHL 541
            L E   ++     + + L  N ++ L   P++  L    N +++ +           ++
Sbjct: 69  VLYETLDLESLSTLRTLDLNNNYVQELLVGPSIETLHAANN-NISRVSCSR--GQGKKNI 125

Query: 542 DLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L+   I  L   +     +++YL+L+     ++   +L +    LE L L
Sbjct: 126 YLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNL 176

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 49.2 bits (118), Expect = 2e-06
 Identities = 14/99 (14%), Positives = 37/99 (37%), Gaps = 13/99 (13%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + ++L +N +    ++ +L     L L  N  + EL        S+  L  +  +I  + 
Sbjct: 61  ELLNLSSNVLYETLDLESLSTLRTLDLNNN-YVQELL----VGPSIETLHAANNNISRVS 115

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                 +  + + L     ++++         +++ L L
Sbjct: 116 CS--RGQGKKNIYLANNK-ITMLRDLDEGCRSRVQYLDL 151

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 48.8 bits (117), Expect = 3e-06
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 12/91 (13%)

Query: 509 SLSEIP------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLP-QELKALEK 560
           ++ EI        +  +  + SL +  + +  S  ++  LDLS   +  +   +L    K
Sbjct: 1   AIHEIKQNGNRYKIEKVTDS-SLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTK 59

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L  LNL     L       +     L  L L
Sbjct: 60  LELLNLSSNV-LYETLD--LESLSTLRTLDL 87

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 45.0 bits (107), Expect = 6e-05
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 7/93 (7%)

Query: 501 SLMANEIESLSEIPTLLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIRGLPQELKAL 558
            L   +    S +   L L+ N  +  +      +S  +L HL+L    I  +  ++   
Sbjct: 134 MLRDLDEGCRSRV-QYLDLKLN-EIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-F 190

Query: 559 EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            KL+ L+L     L+ +  +       +  + L
Sbjct: 191 AKLKTLDLSSNK-LAFMGPE-FQSAAGVTWISL 221

>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 = 57.4 bits (139), Expect = 1e-08
 Identities = 48/282 (17%), Positives = 90/282 (31%), Gaps = 71/282 (25%)

Query: 498 KRISLMANEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ 553
             +    + I  ++ I  L  L +    ++++T L   +S   +L +L      +  L  
Sbjct: 45  TSLDCHNSSITDMTGIEKLTGLTKLICTSNNITTLD--LSQNTNLTYLACDSNKLTNLD- 101

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEP 613
            +  L KL YLN +    L+ +    +S    L  L               N L +    
Sbjct: 102 -VTPLTKLTYLNCDTNK-LTKLD---VSQNPLLTYLNC-----------ARNTLTEI--- 142

Query: 614 LMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD-------------------LTWLVFV 654
              ++    +L  L       +         +L                    L  L   
Sbjct: 143 ---DVSHNTQLTELDCHLNKKITKLDVTPQTQLTTLDCSFNKITELDVSQNKLLNRLNCD 199

Query: 655 QN-LKELEIIVCTEMEEIIC---------VDKLR-----DVSD--ISEIIGSEHNFFTQL 697
            N + +L++    ++  + C         V  L      D S   ++E+  S     ++L
Sbjct: 200 TNNITKLDLNQNIQLTFLDCSSNKLTEIDVTPLTQLTYFDCSVNPLTELDVST---LSKL 256

Query: 698 ESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINS 739
            +L      DL  I  +  H  +L      GC K+K+L +  
Sbjct: 257 TTL-HCIQTDLLEI--DLTHNTQLIYFQAEGCRKIKELDVTH 295

>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 = 57.3 bits (139), Expect = 1e-08
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 4/91 (4%)

Query: 505 NEIESLSEIPTL--LSLRRND--SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK 560
               S  ++P+L  L L RN                SL +LDLS   +  +      LE+
Sbjct: 338 GNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQ 397

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L +L+ ++++   +    +      L  L +
Sbjct: 398 LEHLDFQHSNLKQMSEFSVFLSLRNLIYLDI 428

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 56.6 bits (137), Expect = 2e-08
 Identities = 47/230 (20%), Positives = 71/230 (30%), Gaps = 56/230 (24%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGL-PQELKALE 559
           +  +IP         L L  N  L  L S    S   L  LDLS   I+ +     ++L 
Sbjct: 18  NFYKIPDNLPFSTKNLDLSFN-PLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLS 76

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELL 619
            L  L L      S+      SG   L+ L                 L       +  L 
Sbjct: 77  HLSTLILTGNPIQSLALG-AFSGLSSLQKLVA-----------VETNLASLENFPIGHLK 124

Query: 620 GLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRD 679
            LK LN ++ +   S  + ++F              NL  LE +               D
Sbjct: 125 TLKELN-VAHNLIQSFKLPEYF-------------SNLTNLEHL---------------D 155

Query: 680 VSD--ISEIIGSEHNFFTQLESLGI---LYGPDLKSIYPNPLHFPKLKKI 724
           +S   I  I  ++     Q+  L +   L    +  I P      +L K+
Sbjct: 156 LSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKL 205

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 53.9 bits (130), Expect = 1e-07
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 505 NEIESLSEIPTLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGL-PQELKALEKLR 562
              +SLS + + L L  N  +  L     S L SL  L    T++  L    +  L+ L+
Sbjct: 70  GAYQSLSHL-STLILTGN-PIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLK 127

Query: 563 YLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            LN+ +    S    +  S    LE L L
Sbjct: 128 ELNVAHNLIQSFKLPEYFSNLTNLEHLDL 156

>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 = 50.8 bits (122), Expect = 1e-06
 Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 501 SLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL-PQELKALE 559
            L +    S  E+  +L L R +  T       SL  L  L L+   I+ L       L 
Sbjct: 42  HLGSYSFFSFPEL-QVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLS 100

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L+ L    T+ L+ + +  I     L+ L +
Sbjct: 101 SLQKLVAVETN-LASLENFPIGHLKTLKELNV 131

>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 = 50.0 bits (120), Expect = 2e-06
 Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 499 RISLMANEIESLSEIPTLLSLRRNDSLTEL--PSRISSLVSLHHLDLSLTHIRGL-PQEL 555
            +  M++    L ++   L  + + +L ++   S   SL +L +LD+S TH R       
Sbjct: 384 GVITMSSNFLGLEQL-EHLDFQHS-NLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIF 441

Query: 556 KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             L  L  L +    +       + +    L  L L
Sbjct: 442 NGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDL 477

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 49.6 bits (119), Expect = 3e-06
 Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 508 ESLSEIPTL--LSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGL-PQELKALEKLRY 563
           +  +E+  L  L L +   L +L     +SL SL  L++S  +   L     K L  L+ 
Sbjct: 464 DIFTELRNLTFLDLSQC-QLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQV 522

Query: 564 LNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L+    H ++    +L      L  L L
Sbjct: 523 LDYSLNHIMTSKKQELQHFPSSLAFLNL 550

>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 = 47.3 bits (113), Expect = 1e-05
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 7/89 (7%)

Query: 508 ESLSEIPTL--LSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLR 562
              + + +L  L +  N S  E  LP   + L +L  LDLS   +  L P    +L  L+
Sbjct: 439 GIFNGLSSLEVLKMAGN-SFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQ 497

Query: 563 YLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            LN+ + +    +          L+VL  
Sbjct: 498 VLNMSHNN-FFSLDTFPYKCLNSLQVLDY 525

>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 = 55.8 bits (135), Expect = 2e-08
 Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESLSE----IPTL--LSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIR 549
           K + L  N + ++S     +  L  L  + + +L ++       SL +L +LD+S TH R
Sbjct: 81  KYLDLSFNGVITMSSNFLGLEQLEHLDFQHS-NLKQMSEFSVFLSLRNLIYLDISHTHTR 139

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                    L  L  L +    +       + +    L  L L
Sbjct: 140 VAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDL 182

>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 = 50.0 bits (120), Expect = 1e-06
 Identities = 25/105 (23%), Positives = 46/105 (43%), Gaps = 9/105 (8%)

Query: 496 GAKRISLMANEIESL-----SEIPTL--LSLRRND-SLTELPSRI-SSLVSLHHLDLSLT 546
            A R+ L +N+++SL      ++  L  LSL  N  S     S+      SL +LDLS  
Sbjct: 29  SATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFN 88

Query: 547 HIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +  +      LE+L +L+ ++++   +    +      L  L +
Sbjct: 89  GVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDI 133

>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 = 47.7 bits (114), Expect = 6e-06
 Identities = 18/103 (17%), Positives = 33/103 (32%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
             + +               + +L  L +  N         I + L +L  LDLS   + 
Sbjct: 129 IYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLE 188

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L      +L  L+ LN+ + +    +          L+VL  
Sbjct: 189 QLSPTAFNSLSSLQVLNMSHNN-FFSLDTFPYKCLNSLQVLDY 230

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri} Length = 306

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 5/80 (6%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
           T L L +   L +L     +SL SL  L++S  +   L     K L  L+ L+    H +
Sbjct: 178 TFLDLSQC-QLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNH-I 235

Query: 573 SIIPHQLISGFLK-LEVLRL 591
                Q +  F   L  L L
Sbjct: 236 MTSKKQELQHFPSSLAFLNL 255

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 55.4 bits (134), Expect = 5e-08
 Identities = 17/94 (18%), Positives = 36/94 (38%), Gaps = 9/94 (9%)

Query: 505 NEIESLSEIPTL-----LSLRRNDSLTEL--PSRISSLVSLHHLDLSLTHIRGLPQELKA 557
           ++ ++L++ P       + +  N +L      + +  +  L  L+     + G      +
Sbjct: 293 DDWQALADAPVGEKIQIIYIGYN-NLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGS 351

Query: 558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             KL  LNL Y   ++ IP        ++E L  
Sbjct: 352 EIKLASLNLAYNQ-ITEIPANFCGFTEQVENLSF 384

>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 = 50.4 bits (121), Expect = 2e-06
 Identities = 14/96 (14%), Positives = 40/96 (41%), Gaps = 10/96 (10%)

Query: 505 NEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ---------EL 555
            + ++L ++ T + +    +LT+LP+ + +L  +  ++++        Q         + 
Sbjct: 243 LKWDNLKDL-TDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADA 301

Query: 556 KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
              EK++ + + Y +  +      +    KL +L  
Sbjct: 302 PVGEKIQIIYIGYNNLKTFPVETSLQKMKKLGMLEC 337

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 49.7 bits (119), Expect = 3e-06
 Identities = 19/95 (20%), Positives = 34/95 (35%), Gaps = 11/95 (11%)

Query: 505 NEIESLSEIPTLLSLRRNDSLTELPS--RISSLVSLHHLDLSLTHIRGLPQELKALEKLR 562
              ++   + T + LR N  LT+L    R ++L  L  +DLS       P +      L+
Sbjct: 482 ENFKNTYLL-TSIDLRFN-KLTKLSDDFRATTLPYLVGIDLSYNSFSKFPTQPLNSSTLK 539

Query: 563 YLNLEYTHYLS------IIPHQLISGFLKLEVLRL 591
              +               P + I+    L  L++
Sbjct: 540 GFGIRNQRDAQGNRTLREWP-EGITLCPSLTQLQI 573

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 49.3 bits (118), Expect = 4e-06
 Identities = 14/104 (13%), Positives = 40/104 (38%), Gaps = 10/104 (9%)

Query: 498 KRISLMANEI--ESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLS-LTHIRGLPQE 554
           ++  +  +    E++ E     +            +  +L  L  +++    ++  LP  
Sbjct: 209 RQFYMGNSPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTF 268

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFL-------KLEVLRL 591
           LKAL +++ +N+     +S    +     L       K++++ +
Sbjct: 269 LKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYI 312

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 48.9 bits (117), Expect = 5e-06
 Identities = 15/93 (16%), Positives = 36/93 (38%), Gaps = 8/93 (8%)

Query: 505 NEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALE 559
            +  + S +           + N +L E P  I+   SL  L +    IR + +++    
Sbjct: 530 TQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQIGSNDIRKVNEKI--TP 587

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL 592
            +  L+++    +SI     +  +++  +  L 
Sbjct: 588 NISVLDIKDNPNISIDL-SYVCPYIEAGMYMLF 619

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.8 bits (109), Expect = 4e-05
 Identities = 7/99 (7%), Positives = 27/99 (27%), Gaps = 5/99 (5%)

Query: 499 RISLMANEIESLSEIPTL----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
           R+      ++              +  +     +       +    +     +I  + + 
Sbjct: 142 RMHYQKTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQIGQLSNNITFVSKA 201

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE 593
           +  L KLR   +  + +++    +        E  +  +
Sbjct: 202 VMRLTKLRQFYMGNSPFVAENICEAWE-NENSEYAQQYK 239

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.8 bits (109), Expect = 5e-05
 Identities = 31/238 (13%), Positives = 62/238 (26%), Gaps = 38/238 (15%)

Query: 515 TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYT 569
           T LSL    +   +P  I  L  L  L L     +       P+ + A            
Sbjct: 84  TGLSLEGFGASGRVPDAIGQLTELEVLALGSHGEKVNERLFGPKGISANMSDEQKQKMRM 143

Query: 570 HYLSIIPHQLISG-FLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLS 628
           HY            F  L    +     +                + +      +   + 
Sbjct: 144 HYQKTFVDYDPREDFSDLIKDCINSDPQQK--------------SIKKSSRITLKDTQIG 189

Query: 629 WSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEI----IVCTEMEEIICVDKLRDVSDIS 684
               +   V K      + LT       L++  +     V   + E    +   + +   
Sbjct: 190 QLSNNITFVSKAV----MRLT------KLRQFYMGNSPFVAENICEAWENENS-EYAQQY 238

Query: 685 EIIGSEHNFFTQLESLGILYGPDLKSIYPNPL-HFPKLKKIGVYGCPKLKKLPINSSS 741
           +    + +    L  + +   P+L  + P  L   P+++ I V    +          
Sbjct: 239 KTEDLKWDNLKDLTDVEVYNCPNLTKL-PTFLKALPEMQLINVACN-RGISGEQLKDD 294

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 45.0 bits (107), Expect = 9e-05
 Identities = 18/117 (15%), Positives = 37/117 (31%), Gaps = 24/117 (20%)

Query: 498 KRISLMANEIESLSEIP--------TLLSLRRN-------DSLTELPSRISSLVSLHHLD 542
           + +S   N+++ +  I         + +    N        +   L       +++  ++
Sbjct: 380 ENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSIN 439

Query: 543 LSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFL-------KLEVLRL 591
           LS   I   P+E       L  +NL     L+ IP   +            L  + L
Sbjct: 440 LSNNQISKFPKELFSTGSPLSSINLMGNM-LTEIPKNSLKDENENFKNTYLLTSIDL 495

>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 = 43.5 bits (103), Expect = 2e-04
 Identities = 13/96 (13%), Positives = 35/96 (36%), Gaps = 11/96 (11%)

Query: 505 NEIESLSEIPTLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQ--ELKALEKL 561
               S  ++   L+L  N  +TE+P+        + +L  +   ++ +P   + K++  +
Sbjct: 347 PAFGSEIKL-ASLNLAYN-QITEIPANFCGFTEQVENLSFAHNKLKYIPNIFDAKSVSVM 404

Query: 562 RYLNLEYTHYLSIIPHQL------ISGFLKLEVLRL 591
             ++  Y    S+               + +  + L
Sbjct: 405 SAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSINL 440

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 54.0 bits (130), Expect = 1e-07
 Identities = 26/92 (28%), Positives = 35/92 (38%), Gaps = 11/92 (11%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALE 559
           +L E+P        LL+L  N  +  +       L  L  L LS  HIR +       L 
Sbjct: 54  NLREVPDGISTNTRLLNLHEN-QIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLA 112

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  L L     L+ IP+       KL+ L L
Sbjct: 113 NLNTLELFDNR-LTTIPNGAFVYLSKLKELWL 143

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 50.5 bits (121), Expect = 1e-06
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 9/101 (8%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGL 551
           + ++L    +  +  +  L     L L  N  L+ +       L+ L  L +  + I+ +
Sbjct: 188 RYLNLAMCNLREIPNLTPLIKLDELDLSGN-HLSAIRPGSFQGLMHLQKLWMIQSQIQVI 246

Query: 552 PQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +     L+ L  +NL + + L+++PH L +    LE + L
Sbjct: 247 ERNAFDNLQSLVEINLAHNN-LTLLPHDLFTPLHHLERIHL 286

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 49.0 bits (117), Expect = 4e-06
 Identities = 27/103 (26%), Positives = 37/103 (35%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           + + L  N I ++       +  L  L L  N  LT +P+     L  L  L L    I 
Sbjct: 91  EILQLSRNHIRTIEIGAFNGLANLNTLELFDN-RLTTIPNGAFVYLSKLKELWLRNNPIE 149

Query: 550 GLPQEL-KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +P      +  LR L+L     LS I      G   L  L L
Sbjct: 150 SIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNL 192

>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 = 29/104 (27%), Positives = 48/104 (46%), Gaps = 14/104 (13%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLS-LTHI 548
             + L  N + ++       +  L  L LR N  +  +PS   + + SL  LDL  L  +
Sbjct: 115 NTLELFDNRLTTIPNGAFVYLSKLKELWLRNN-PIESIPSYAFNRIPSLRRLDLGELKRL 173

Query: 549 RGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             + +   + L  LRYLNL   + L  IP+  ++  +KL+ L L
Sbjct: 174 SYISEGAFEGLSNLRYLNLAMCN-LREIPN--LTPLIKLDELDL 214

>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 = 54.1 bits (130), Expect = 1e-07
 Identities = 21/144 (14%), Positives = 42/144 (29%), Gaps = 17/144 (11%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + ++L  N I  +           L L  N  L  +     S   +  + L    +  + 
Sbjct: 172 EHLNLQYNFIYDVKGQVVFAKLKTLDLSSN-KLAFMGPEFQSAAGVTWISLRNNKLVLIE 230

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVL-----------RLLECGSEGVTK 601
           + L+  + L + +L    +         S   +++ +              EC    +  
Sbjct: 231 KALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGH 290

Query: 602 EEGNVLCDDAEPLMRELLGLKRLN 625
                  D   P    L+ LKR  
Sbjct: 291 YGAYCCEDLPAPFADRLIALKRKE 314

>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 = 52.2 bits (125), Expect = 4e-07
 Identities = 20/111 (18%), Positives = 45/111 (40%), Gaps = 6/111 (5%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL--LSLRRNDSLTELPSRISSLVSLHHL 541
            L E   ++     + + L  N ++ L   P++  L    N +++ +    S      ++
Sbjct: 69  VLYETLDLESLSTLRTLDLNNNYVQELLVGPSIETLHAANN-NISRVSC--SRGQGKKNI 125

Query: 542 DLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L+   I  L   +     +++YL+L+     ++   +L +    LE L L
Sbjct: 126 YLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNL 176

>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 = 49.5 bits (118), Expect = 3e-06
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 12/91 (13%)

Query: 509 SLSEIP------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGL-PQELKALEK 560
           ++ EI        +  +  + SL +  + +  S  ++  LDLS   +  +   +L    K
Sbjct: 1   AIHEIKQNGNRYKIEKVTDS-SLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTK 59

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L  LNL     L       +     L  L L
Sbjct: 60  LELLNLSSNV-LYETLD--LESLSTLRTLDL 87

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 13/91 (14%), Positives = 34/91 (37%), Gaps = 11/91 (12%)

Query: 505 NEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK 560
           N +    ++ +L +LR     N+ + EL        S+  L  +  +I  +       + 
Sbjct: 68  NVLYETLDLESLSTLRTLDLNNNYVQELL----VGPSIETLHAANNNISRVSCS--RGQG 121

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            + + L     ++++         +++ L L
Sbjct: 122 KKNIYLANNK-ITMLRDLDEGCRSRVQYLDL 151

>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 = 44.5 bits (105), Expect = 1e-04
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 7/93 (7%)

Query: 501 SLMANEIESLSEIPTLLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIRGLPQELKAL 558
            L   +    S +   L L+ N  +  +      +S  +L HL+L    I  +  ++   
Sbjct: 134 MLRDLDEGCRSRV-QYLDLKLN-EIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-F 190

Query: 559 EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            KL+ L+L     L+ +  +       +  + L
Sbjct: 191 AKLKTLDLSSNK-LAFMGPE-FQSAAGVTWISL 221

>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 = 53.3 bits (129), Expect = 1e-07
 Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 9/100 (9%)

Query: 496 GAKRISLMANEIESLSEIPTLLSLRRND----SLTELPSRISSLVSLHHLDLSLTHIRGL 551
           GA  ++ +   I  +     L    R      S+T++ +    L S+  L ++   +  +
Sbjct: 1   GAATLATLPAPINQIFPDADLAEGIRAVLQKASVTDVVT-QEELESITKLVVAGEKVASI 59

Query: 552 PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
              ++ L  L YLNL       I P   +S  +KL  L +
Sbjct: 60  Q-GIEYLTNLEYLNLNGNQITDISP---LSNLVKLTNLYI 95

>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 = 53.3 bits (129), Expect = 1e-07
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 10/99 (10%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
             + +  N+I  +S +  L     L L  + +++++   +++L  ++ L+L   H     
Sbjct: 91  TNLYIGTNKITDISALQNLTNLRELYLNED-NISDISP-LANLTKMYSLNLGANHNLSDL 148

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             L  +  L YL +  +    + P   I+    L  L L
Sbjct: 149 SPLSNMTGLNYLTVTESKVKDVTP---IANLTDLYSLSL 184

>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 = 47.9 bits (115), Expect = 7e-06
 Identities = 16/99 (16%), Positives = 41/99 (41%), Gaps = 9/99 (9%)

Query: 498 KRISLMANEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLSLTHIRGL-P 552
             + +  N+I  ++ +  L  L+     ++ ++++   +++L  L+ L L+   +     
Sbjct: 246 TWLEIGTNQISDINAVKDLTKLKMLNVGSNQISDISV-LNNLSQLNSLFLNNNQLGNEDM 304

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           + +  L  L  L L   H   I P   ++   K++    
Sbjct: 305 EVIGGLTNLTTLFLSQNHITDIRP---LASLSKMDSADF 340

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 46.4 bits (111), Expect = 2e-05
 Identities = 17/99 (17%), Positives = 43/99 (43%), Gaps = 11/99 (11%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
             +++  ++++ ++ I  L     LSL  N  + ++   ++SL SLH+    +  I  + 
Sbjct: 158 NYLTVTESKVKDVTPIANLTDLYSLSLNYN-QIEDISP-LASLTSLHYFTAYVNQITDIT 215

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             +  + +L  L +       + P   ++   +L  L +
Sbjct: 216 -PVANMTRLNSLKIGNNKITDLSP---LANLSQLTWLEI 250

>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 = 43.7 bits (104), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           K +++ +N+I  +S +  L     L L  N    E    I  L +L  L LS  HI  + 
Sbjct: 268 KMLNVGSNQISDISVLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNHITDIR 327

Query: 553 QELKALEKLRYLNLEY 568
             L +L K+   +   
Sbjct: 328 -PLASLSKMDSADFAN 342

>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 = 54.0 bits (130), Expect = 1e-07
 Identities = 28/103 (27%), Positives = 42/103 (40%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           K + L  N+I  +            +L L+ +  +  +      SL SL HLDLS  H+ 
Sbjct: 29  KSLDLSFNKITYIGHGDLRACANLQVLILKSS-RINTIEGDAFYSLGSLEHLDLSDNHLS 87

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L       L  L+YLNL    Y ++    L      L+ LR+
Sbjct: 88  SLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRI 130

>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 = 53.6 bits (129), Expect = 2e-07
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 517 LSLRRN--DSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI 574
           L L +N   S+ +    + +L +L  LD+S      +P   +  EK+R+LNL  T  + +
Sbjct: 366 LVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSSTG-IRV 424

Query: 575 IPHQLISGFLKLEVLRL 591
           +   +      LEVL +
Sbjct: 425 VKTCI---PQTLEVLDV 438

>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 = 47.0 bits (112), Expect = 2e-05
 Identities = 17/101 (16%), Positives = 39/101 (38%), Gaps = 10/101 (9%)

Query: 501 SLMANEIESLSEIPTL--LSLRRND----SLTELPSRI-SSLVSLHHLDLSLTHIRGLPQ 553
               +E + +SE+  +  +++RR       L    S + S L  +  + +  + +  +P 
Sbjct: 268 DFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPC 327

Query: 554 E-LKALEKLRYLNLEYT--HYLSIIPHQLISGFLKLEVLRL 591
              + L+ L +L+L         +        +  L+ L L
Sbjct: 328 SFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVL 368

>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 = 41.6 bits (98), Expect = 9e-04
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 17/108 (15%)

Query: 498 KRISLMANEIESL-----SEIPTL--LSLRRNDSLTEL----PSRISSLVSLHHLDLS-- 544
           KRI++  +++  +       + +L  L L  N  + E      +   +  SL  L LS  
Sbjct: 313 KRITVENSKVFLVPCSFSQHLKSLEFLDLSENL-MVEEYLKNSACKGAWPSLQTLVLSQN 371

Query: 545 -LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  ++   + L  L+ L  L++        +P        K+  L L
Sbjct: 372 HLRSMQKTGEILLTLKNLTSLDISRNT-FHPMPDS-CQWPEKMRFLNL 417

>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 = 34/201 (16%), Positives = 65/201 (32%), Gaps = 28/201 (13%)

Query: 498 KRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG 550
             + L  NE+E +   P         L +  N  L  L      + +L  LDLS  H+  
Sbjct: 257 VEVDLSYNELEKIMYHPFVKMQRLERLYISNN-RLVALNLYGQPIPTLKVLDLSHNHLLH 315

Query: 551 LPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL-CD 609
           + +     ++L  L L++ + +  +    +S    L+ L L             N   C+
Sbjct: 316 VERNQPQFDRLENLYLDH-NSIVTLK---LSTHHTLKNLTL-----------SHNDWDCN 360

Query: 610 DAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEME 669
               L R +     ++      +    ++      + D  +L  +     L  +V     
Sbjct: 361 SLRALFRNVARP-AVDDADQHCKIDYQLEHGLCCKESDKPYLDRLLQYIALTSVVEKVQR 419

Query: 670 E---IICVDKLRDVSDISEII 687
                   D +  V  +S  I
Sbjct: 420 AQGRCSATDTINSVQSLSHYI 440

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 597

 Score = 48.4 bits (115), Expect = 7e-06
 Identities = 12/79 (15%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
            +++ + + ++ +LP+ +  S   +  L+L+   I  +          ++ L + +   +
Sbjct: 54  KIVTFKNS-TMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNA-I 111

Query: 573 SIIPHQLISGFLKLEVLRL 591
             +P  +      L VL L
Sbjct: 112 RYLPPHVFQNVPLLTVLVL 130

>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 = 53.0 bits (128), Expect = 2e-07
 Identities = 20/113 (17%), Positives = 39/113 (34%), Gaps = 11/113 (9%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSL 538
            +T+     + +    +      I+S+  +  L     ++   N  LT++   + +L  L
Sbjct: 35  NVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNN-QLTDITP-LKNLTKL 92

Query: 539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             + ++   I  +   L  L  L  L L       I P   +     L  L L
Sbjct: 93  VDILMNNNQIADIT-PLANLTNLTGLTLFNNQITDIDP---LKNLTNLNRLEL 141

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 49.6 bits (119), Expect = 2e-06
 Identities = 28/99 (28%), Positives = 44/99 (44%), Gaps = 11/99 (11%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + +    N+I  ++ +  L     LSL  N  L ++ + ++SL +L  LDL+   I  L 
Sbjct: 202 ESLIATNNQISDITPLGILTNLDELSLNGN-QLKDIGT-LASLTNLTDLDLANNQISNLA 259

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             L  L KL  L L      +I P   ++G   L  L L
Sbjct: 260 -PLSGLTKLTELKLGANQISNISP---LAGLTALTNLEL 294

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 49.6 bits (119), Expect = 3e-06
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 9/98 (9%)

Query: 498 KRISLMANEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ 553
             + L  N++E +S I  L +L       ++++++   +SSL  L  L      +  +  
Sbjct: 290 TNLELNENQLEDISPISNLKNLTYLTLYFNNISDISP-VSSLTKLQRLFFYNNKVSDVS- 347

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  L  + +L+  +     + P   ++   ++  L L
Sbjct: 348 SLANLTNINWLSAGHNQISDLTP---LANLTRITQLGL 382

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 48.8 bits (117), Expect = 4e-06
 Identities = 23/113 (20%), Positives = 47/113 (41%), Gaps = 11/113 (9%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSL 538
           +++    +        + L AN+I ++S +  L     L L  N  L ++   IS+L +L
Sbjct: 254 QISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNEN-QLEDISP-ISNLKNL 311

Query: 539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +L L   +I  +   + +L KL+ L       +S +    ++    +  L  
Sbjct: 312 TYLTLYFNNISDIS-PVSSLTKLQRLFFYNNK-VSDVSS--LANLTNINWLSA 360

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 45.7 bits (109), Expect = 5e-05
 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 9/91 (9%)

Query: 505 NEIESLSEIPTLLSLRRND----SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK 560
             I  +     L    +      ++T+  S  + L  +  L      I+ +   ++ L  
Sbjct: 12  TPINQIFTDTALAEKMKTVLGKTNVTDTVS-QTDLDQVTTLQADRLGIKSID-GVEYLNN 69

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L  +N      L+ I    +    KL  + +
Sbjct: 70  LTQINFSNNQ-LTDITP--LKNLTKLVDILM 97

>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 = 52.8 bits (127), Expect = 3e-07
 Identities = 24/92 (26%), Positives = 33/92 (35%), Gaps = 11/92 (11%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALE 559
            LSE+P         L+L  N ++  + +     L  L  L L    IR +       L 
Sbjct: 65  GLSEVPQGIPSNTRYLNLMEN-NIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLA 123

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  L L     L++IP        KL  L L
Sbjct: 124 SLNTLELFDNW-LTVIPSGAFEYLSKLRELWL 154

>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 = 49.7 bits (119), Expect = 3e-06
 Identities = 28/109 (25%), Positives = 45/109 (41%), Gaps = 11/109 (10%)

Query: 495 EGAKRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLT 546
              + ++LM N I+ +       +  L  L L RN S+ ++     + L SL+ L+L   
Sbjct: 75  SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRN-SIRQIEVGAFNGLASLNTLELFDN 133

Query: 547 HIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC 594
            +  +P    + L KLR L L     +  IP    +    L  L L E 
Sbjct: 134 WLTVIPSGAFEYLSKLRELWLRNNP-IESIPSYAFNRVPSLMRLDLGEL 181

>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 = 49.4 bits (118), Expect = 3e-06
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSII 575
           L+L    ++ ++P+ ++ LV L  L++S  H   +       L  L+ L +  +  +S+I
Sbjct: 201 LNLGMC-NIKDMPN-LTPLVGLEELEMSGNHFPEIRPGSFHGLSSLKKLWVMNSQ-VSLI 257

Query: 576 PHQLISGFLKLEVLRL 591
                 G   L  L L
Sbjct: 258 ERNAFDGLASLVELNL 273

>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 = 49.0 bits (117), Expect = 4e-06
 Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 9/101 (8%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGL 551
           K ++L    I+ +  +  L     L +  N    E+       L SL  L +  + +  +
Sbjct: 199 KYLNLGMCNIKDMPNLTPLVGLEELEMSGN-HFPEIRPGSFHGLSSLKKLWVMNSQVSLI 257

Query: 552 PQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +     L  L  LNL + + LS +PH L +    L  L L
Sbjct: 258 ERNAFDGLASLVELNLAHNN-LSSLPHDLFTPLRYLVELHL 297

>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 = 46.7 bits (111), Expect = 2e-05
 Identities = 26/103 (25%), Positives = 36/103 (34%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           + + L  N I  +       + +L  L L  N  LT +PS     L  L  L L    I 
Sbjct: 102 EVLQLGRNSIRQIEVGAFNGLASLNTLELFDN-WLTVIPSGAFEYLSKLRELWLRNNPIE 160

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +P      +  L  L+L     L  I      G   L+ L L
Sbjct: 161 SIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNL 203

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 53.0 bits (127), Expect = 3e-07
 Identities = 17/108 (15%), Positives = 38/108 (35%), Gaps = 11/108 (10%)

Query: 494 WEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG--- 550
            + AK+         +L ++ T + L    ++T+LP  +  L  L  L+++         
Sbjct: 474 SDYAKQYENEELSWSNLKDL-TDVELYNCPNMTQLPDFLYDLPELQSLNIACNRGISAAQ 532

Query: 551 -------LPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                  L  +     K++   + Y +         +   +KL +L  
Sbjct: 533 LKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDC 580

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 52.6 bits (126), Expect = 4e-07
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 10/85 (11%)

Query: 515 TLLSLRRNDSLTELPSRI--SSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYL 572
           T + LR N  LT L      ++L  L ++D+S       P +     +L+   + +    
Sbjct: 731 TTIDLRFN-KLTSLSDDFRATTLPYLSNMDVSYNCFSSFPTQPLNSSQLKAFGIRHQRDA 789

Query: 573 S------IIPHQLISGFLKLEVLRL 591
                    P   I+    L  L++
Sbjct: 790 EGNRILRQWPTG-ITTCPSLIQLQI 813

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 51.0 bits (122), Expect = 1e-06
 Identities = 16/104 (15%), Positives = 33/104 (31%), Gaps = 13/104 (12%)

Query: 498 KRISLMANEIESLSEIPTL--------LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIR 549
           +   +  N +E      +L        L    N  +  L +   + V L  L L    I 
Sbjct: 551 QIFYMGYNNLEEFPASASLQKMVKLGLLDCVHN-KVRHLEA-FGTNVKLTDLKLDYNQIE 608

Query: 550 GLPQEL-KALEKLRYLNLEYTHYLSIIPHQL-ISGFLKLEVLRL 591
            +P++     +++  L   +   L  IP+         +  +  
Sbjct: 609 EIPEDFCAFTDQVEGLGFSHNK-LKYIPNIFNAKSVYVMGSVDF 651

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 50.6 bits (121), Expect = 2e-06
 Identities = 16/93 (17%), Positives = 36/93 (38%), Gaps = 8/93 (8%)

Query: 505 NEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALE 559
            +  + S++             N  L + P+ I++  SL  L +    IR + ++L    
Sbjct: 770 TQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSNDIRKVDEKL--TP 827

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL 592
           +L  L++        I    +  +++  +  LL
Sbjct: 828 QLYILDIADNP-NISIDVTSVCPYIEAGMYVLL 859

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 48.7 bits (116), Expect = 6e-06
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 11/87 (12%)

Query: 509 SLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA--LEKLRYLNL 566
            ++ IP        +SL        +   L  +DL    +  L  + +A  L  L  +++
Sbjct: 708 LMTSIP-------ENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDV 760

Query: 567 EYTHYLSIIPHQLISGFLKLEVLRLLE 593
            Y    S  P Q      +L+   +  
Sbjct: 761 SYNC-FSSFPTQ-PLNSSQLKAFGIRH 785

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 48.7 bits (116), Expect = 6e-06
 Identities = 16/101 (15%), Positives = 30/101 (29%), Gaps = 20/101 (19%)

Query: 509 SLSEIP----------TLLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIRGLPQEL- 555
            + EIP            L    N  L  +P+     S+  +  +D S   I    + + 
Sbjct: 606 QIEEIPEDFCAFTDQVEGLGFSHN-KLKYIPNIFNAKSVYVMGSVDFSYNKIGSEGRNIS 664

Query: 556 -----KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                        + L Y   +   P +L +    +  + L
Sbjct: 665 CSMDDYKGINASTVTLSYNE-IQKFPTELFATGSPISTIIL 704

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 13/96 (13%), Positives = 29/96 (30%), Gaps = 12/96 (12%)

Query: 505 NEIESLSEIPTLLSLRRND------SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKAL 558
            E++ + +  + +SL+          +T +   I  L  L  +  + +        +   
Sbjct: 412 PEMKPIKKD-SRISLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVDWE 470

Query: 559 EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC 594
           +     N +Y            S    L  + L  C
Sbjct: 471 D----ANSDYAKQYENEELS-WSNLKDLTDVELYNC 501

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 42.2 bits (99), Expect = 8e-04
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 515 TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI 574
           T LSL    +   +P  I  L  L  L           +     E    ++ E  H + +
Sbjct: 326 TGLSLAGFGAKGRVPDAIGQLTELKVLSFGTHSETVSGRLFGDEELTPDMSEERKHRIRM 385

Query: 575 IPHQLISGFL-KLEVLRLLE 593
              ++   +  +L +  LL+
Sbjct: 386 HYKKMFLDYDQRLNLSDLLQ 405

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 52.7 bits (127), Expect = 3e-07
 Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 3/76 (3%)

Query: 517 LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSII 575
           ++L+++     + S        L  LDL+ TH+  LP  L  L  L+ L L        +
Sbjct: 259 INLQKH-YFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANK-FENL 316

Query: 576 PHQLISGFLKLEVLRL 591
                S F  L  L +
Sbjct: 317 CQISASNFPSLTHLSI 332

>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 = 51.6 bits (124), Expect = 7e-07
 Identities = 47/206 (22%), Positives = 70/206 (33%), Gaps = 51/206 (24%)

Query: 508 ESLSEIPTL--LSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGLP---QELKALEKL 561
            S S  P+L  LS++ N    EL +  + +L +L  LDLS   I        +L+ L  L
Sbjct: 319 ISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHL 378

Query: 562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCD-DAEPLMRELLG 620
           + LNL Y      +  +      +LE+L L               L   DA+   + L  
Sbjct: 379 QSLNLSYNE-PLSLKTEAFKECPQLELLDL-----------AFTRLKVKDAQSPFQNLHL 426

Query: 621 LKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDV 680
           LK LN LS S     + Q F                L  L+ +               ++
Sbjct: 427 LKVLN-LSHSLLDISSEQLF--------------DGLPALQHL---------------NL 456

Query: 681 SD--ISEIIGSEHNFFTQLESLGILY 704
                 +    + N    L  L IL 
Sbjct: 457 QGNHFPKGNIQKTNSLQTLGRLEILV 482

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 49.2 bits (118), Expect = 4e-06
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIR 549
           + +    N + ++           T L L R   +  +      S   L  L L+   + 
Sbjct: 36  ECLEFSFNVLPTIQNTTFSRLINLTFLDLTRC-QIYWIHEDTFQSQHRLDTLVLTANPLI 94

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            + +  L   + L++L    T  +S I    +     LE L L
Sbjct: 95  FMAETALSGPKALKHLFFIQTG-ISSIDFIPLHNQKTLESLYL 136

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 26/101 (25%), Positives = 45/101 (44%), Gaps = 10/101 (9%)

Query: 500 ISLMANEIESLSEIPTLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKA 557
                N +++L  +  +L L     L+ +     +SL  ++H+DLS   +     E L  
Sbjct: 465 NIQKTNSLQTLGRL-EILVLSFC-DLSSIDQHAFTSLKMMNHVDLSHNRLTSSSIEALSH 522

Query: 558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL----LEC 594
           L+ + YLNL   H +SII   L+    +   + L    L+C
Sbjct: 523 LKGI-YLNLASNH-ISIILPSLLPILSQQRTINLRQNPLDC 561

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 50.3 bits (121), Expect = 4e-07
 Identities = 19/100 (19%), Positives = 41/100 (41%), Gaps = 8/100 (8%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL- 551
           K +++      + + I  L     L +   D  ++    +S L SL  LD+S +      
Sbjct: 69  KDLTINNIHATNYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSI 128

Query: 552 PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             ++  L K+  ++L Y   ++ I    +    +L+ L +
Sbjct: 129 LTKINTLPKVNSIDLSYNGAITDIMP--LKTLPELKSLNI 166

>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 = 52.3 bits (126), Expect = 5e-07
 Identities = 21/103 (20%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEI-----ESLSEIPTL--LSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIR 549
             + +  N I     E   ++P L  L+L+ N  L++L  +  +   +L  L L    I+
Sbjct: 52  TSLDVGFNTISKLEPELCQKLPMLKVLNLQHN-ELSQLSDKTFAFCTNLTELHLMSNSIQ 110

Query: 550 GL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +        + L  L+L +    S            L+ L L
Sbjct: 111 KIKNNPFVKQKNLITLDLSHNGLSSTKLG-TQVQLENLQELLL 152

>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 = 50.8 bits (122), Expect = 1e-06
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 5/78 (6%)

Query: 515 TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLS 573
            +        LT++P  + +  ++  L+L+   +R L         +L  L++ +   +S
Sbjct: 7   EVADCSHL-KLTQVPDDLPT--NITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNT-IS 62

Query: 574 IIPHQLISGFLKLEVLRL 591
            +  +L      L+VL L
Sbjct: 63  KLEPELCQKLPMLKVLNL 80

>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 = 50.0 bits (120), Expect = 2e-06
 Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 12/96 (12%)

Query: 508 ESLSEIPTL--LSLRRN--DSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLR 562
            S + +P+L  L LRR    ++   PS    L +L  LDLS  +I  +  + L+ LEKL 
Sbjct: 448 NSFALVPSLQRLMLRRVALKNVDSSPSPFQPLRNLTILDLSNNNIANINDDMLEGLEKLE 507

Query: 563 YLNLEYTHYLSI-------IPHQLISGFLKLEVLRL 591
            L+L++ +   +        P   + G   L +L L
Sbjct: 508 ILDLQHNNLARLWKHANPGGPIYFLKGLSHLHILNL 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 = 48.8 bits (117), Expect = 5e-06
 Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 7/86 (8%)

Query: 515 TLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
            +L+L  N    E+P      L  L  +DL L ++  LP         L+ LNL+     
Sbjct: 539 HILNLESN-GFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQKNLIT 597

Query: 573 SIIPHQLISGFLKLEVLRL----LEC 594
           S+        F  L  L +     +C
Sbjct: 598 SVEKKVFGPAFRNLTELDMRFNPFDC 623

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 48.5 bits (116), Expect = 7e-06
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 5/82 (6%)

Query: 515 TLLSLRRND-SLTELPSRI---SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYT 569
             LSL  +  SL  L +      +   LH L+L+   I  +  +    L  L  L+L   
Sbjct: 356 KYLSLSNSFTSLRTLTNETFVSLAHSPLHILNLTKNKISKIESDAFSWLGHLEVLDLGLN 415

Query: 570 HYLSIIPHQLISGFLKLEVLRL 591
                +  Q   G   +  + L
Sbjct: 416 EIGQELTGQEWRGLENIFEIYL 437

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 46.5 bits (111), Expect = 3e-05
 Identities = 25/113 (22%), Positives = 43/113 (38%), Gaps = 20/113 (17%)

Query: 498 KRISLMANEIESLSEIP---------TLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTH 547
           + +SL  +++ + S            T+L L  N +L  + +   + L  L +  L   +
Sbjct: 225 RNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYN-NLNVVGNDSFAWLPQLEYFFLEYNN 283

Query: 548 IRGL-PQELKALEKLRYLNLEYTHY--------LSIIPHQLISGFLKLEVLRL 591
           I+ L    L  L  +RYLNL+ +          L  I          LE L +
Sbjct: 284 IQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNM 336

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 46.1 bits (110), Expect = 4e-05
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSI 574
           L  L ++ +       +  L  LH L+L       +P E  K L +L+ ++L   + L+ 
Sbjct: 516 LARLWKHANPGGPIYFLKGLSHLHILNLESNGFDEIPVEVFKDLFELKIIDLGLNN-LNT 574

Query: 575 IPHQLISGFLKLEVLRL 591
           +P  + +  + L+ L L
Sbjct: 575 LPASVFNNQVSLKSLNL 591

>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 = 52.0 bits (125), Expect = 5e-07
 Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 10/103 (9%)

Query: 498 KRISLMANEIESL-SEIPTL-----LSLRRNDSLTELPSRI--SSLVSLHHLDLSLTHIR 549
           K + L  N + ++ S    L     L  + + +L ++       SL +L +LD+S TH R
Sbjct: 376 KYLDLSFNGVITMSSNFLGLEQLEHLDFQHS-NLKQMSEFSVFLSLRNLIYLDISHTHTR 434

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                    L  L  L +    +       + +    L  L L
Sbjct: 435 VAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDL 477

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 51.6 bits (124), Expect = 8e-07
 Identities = 39/239 (16%), Positives = 67/239 (28%), Gaps = 47/239 (19%)

Query: 521 RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQL 579
              +  ++P  +    S  +LDLS   +R L      +  +L+ L+L     +  I    
Sbjct: 15  MELNFYKIPDNLPF--STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCE-IQTIEDGA 71

Query: 580 ISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK 639
                 L  L L            GN +   A      L  L++L     +  +SL    
Sbjct: 72  YQSLSHLSTLIL-----------TGNPIQSLALGAFSGLSSLQKLV-AVETNLASLENFP 119

Query: 640 FFKYPKL-----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSD--ISEI 686
                 L                 +  NL  LE +               D+S   I  I
Sbjct: 120 IGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHL---------------DLSSNKIQSI 164

Query: 687 IGSEHNFFTQLESLGI---LYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA 742
             ++     Q+  L +   L    +  I P      +L K+ +        +       
Sbjct: 165 YCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQG 223

>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 = 49.3 bits (118), Expect = 4e-06
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 4/91 (4%)

Query: 505 NEIESLSEIPTL--LSLRRND--SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK 560
               S  ++P+L  L L RN                SL +LDLS   +  +      LE+
Sbjct: 338 GNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQ 397

Query: 561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L +L+ ++++   +    +      L  L +
Sbjct: 398 LEHLDFQHSNLKQMSEFSVFLSLRNLIYLDI 428

>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 = 49.3 bits (118), Expect = 4e-06
 Identities = 47/266 (17%), Positives = 77/266 (28%), Gaps = 42/266 (15%)

Query: 498 KRISLMANEIESLSEIPTL--------LSLRRNDSLTELPSR-ISSLVSLH----HLDLS 544
           K +++  N I+S               L L  N  +  +    +  L  +      LDLS
Sbjct: 127 KELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSN-KIQSIYCTDLRVLHQMPLLNLSLDLS 185

Query: 545 LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEG 604
           L  +  +        +L  L L        +    I G   LEV RL+            
Sbjct: 186 LNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRN-----E 240

Query: 605 NVLCDDAEPLMREL--LGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL----------- 651
             L    +  +  L  L ++   +    +     +  F     +    L           
Sbjct: 241 GNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDF 300

Query: 652 VFVQNLKELEIIVCTEMEEIICVDKLRDVS--DISEIIGSEHNFFTQLESLGILYGPDLK 709
            +    + LE++ C   +      KL+ +     +   G        L SL  L   DL 
Sbjct: 301 SYNFGWQHLELVNCKFGQ--FPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFL---DLS 355

Query: 710 SIYPNPLHFPKLKKIGVYGCPKLKKL 735
               N L F        +G   LK L
Sbjct: 356 R---NGLSFKGCCSQSDFGTTSLKYL 378

>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 = 48.9 bits (117), Expect = 5e-06
 Identities = 40/216 (18%), Positives = 69/216 (31%), Gaps = 26/216 (12%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
           + L L  N  +  L     S L SL  L    T++  L    +  L+ L+ LN+ +    
Sbjct: 79  STLILTGN-PIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQ 137

Query: 573 SIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL----CDDAEPLMRELLGLKRLNVLS 628
           S    +  S    LE L L             N +    C D   L +  L    L+ LS
Sbjct: 138 SFKLPEYFSNLTNLEHLDL-----------SSNKIQSIYCTDLRVLHQMPLLNLSLD-LS 185

Query: 629 WSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEII--VCTEMEEIICVD-KLRDVSDISE 685
            +  + +    F    ++ L  L    N   L ++      +  +      L +  +   
Sbjct: 186 LNPMNFIQPGAF---KEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGN 242

Query: 686 IIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKL 721
           +   + +    L +L I     L  +         L
Sbjct: 243 LEKFDKSALEGLCNLTIEE-FRLAYLDYYLDDIIDL 277

>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 = 46.2 bits (110), Expect = 4e-05
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 5/80 (6%)

Query: 515 TLLSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHY 571
            +L +  N S  E  LP   + L +L  LDLS   +  L      +L  L+ LN+     
Sbjct: 448 EVLKMAGN-SFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASNQ- 505

Query: 572 LSIIPHQLISGFLKLEVLRL 591
           L  +P  +      L+ + L
Sbjct: 506 LKSVPDGIFDRLTSLQKIWL 525

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 51.6 bits (124), Expect = 6e-07
 Identities = 25/115 (21%), Positives = 47/115 (40%), Gaps = 12/115 (10%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRISSLV 536
            LT+   +  + G   + L  NE+E +       +  L  L +  N  L  L      + 
Sbjct: 237 NLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNN-RLVALNLYGQPIP 295

Query: 537 SLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           +L  LDLS  H+  + +     ++L  L L++ + +  +    +S    L+ L L
Sbjct: 296 TLKVLDLSHNHLLHVERNQPQFDRLENLYLDH-NSIVTLK---LSTHHTLKNLTL 346

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 48.5 bits (116), Expect = 5e-06
 Identities = 12/79 (15%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
            +++ + + ++ +LP+ +  S   +  L+L+   I  +          ++ L + +   +
Sbjct: 48  KIVTFKNS-TMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNA-I 105

Query: 573 SIIPHQLISGFLKLEVLRL 591
             +P  +      L VL L
Sbjct: 106 RYLPPHVFQNVPLLTVLVL 124

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 48.1 bits (115), Expect = 6e-06
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEIESL-----SEIPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           K ++   + +  L          +  L+L     + E+ +   +   ++  L +    IR
Sbjct: 48  KIVTFKNSTMRKLPAALLDSFRQVELLNLNDL-QIEEIDTYAFAYAHTIQKLYMGFNAIR 106

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            LP    + +  L  L LE    LS +P  +     KL  L +
Sbjct: 107 YLPPHVFQNVPLLTVLVLERND-LSSLPRGIFHNTPKLTTLSM 148

>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 = 51.6 bits (124), Expect = 6e-07
 Identities = 49/252 (19%), Positives = 90/252 (35%), Gaps = 35/252 (13%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           + + L +N ++ +       +  L  L +  N  +  L   +   L +L  L++    + 
Sbjct: 83  RTLGLRSNRLKLIPLGVFTGLSNLTKLDISEN-KIVILLDYMFQDLYNLKSLEVGDNDLV 141

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLC 608
            +       L  L  L LE  + L+ IP + +S    L VLRL               + 
Sbjct: 142 YISHRAFSGLNSLEQLTLEKCN-LTSIPTEALSHLHGLIVLRL-----------RHLNIN 189

Query: 609 DDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQN-LKELEIIVCTE 667
              +   + L  LK L +  W +  ++     +    L+LT L      L  +  +    
Sbjct: 190 AIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLY---GLNLTSLSITHCNLTAVPYLAVRH 246

Query: 668 MEEIICVDKLRDVSDISEIIGSEHNFFTQLESLG--ILYGPDLKSIYPNPL-HFPKLKKI 724
           +  +  ++ L   + IS I   E +   +L  L    L G  L  + P        L+ +
Sbjct: 247 LVYLRFLN-LSY-NPISTI---EGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVL 301

Query: 725 GVYGCPKLKKLP 736
            V G  +L  L 
Sbjct: 302 NVSGN-QLTTLE 312

>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 = 50.1 bits (120), Expect = 2e-06
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           + + L  N I++L++      P L  L L  N  ++ +     ++L +L  L L    ++
Sbjct: 35  RLLDLGKNRIKTLNQDEFASFPHLEELELNEN-IVSAVEPGAFNNLFNLRTLGLRSNRLK 93

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +P      L  L  L++     + I+   +      L+ L +
Sbjct: 94  LIPLGVFTGLSNLTKLDISENK-IVILLDYMFQDLYNLKSLEV 135

>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 = 52.0 bits (125), Expect = 6e-07
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 505 NEIESLSEIPTL--LSLRRNDSLTELPS---RISSLVSLHHLDLSLTHIRGLPQELKALE 559
           +       +P+L  L L RN +L+             SL HLDLS      +      LE
Sbjct: 341 SISFKKVALPSLSYLDLSRN-ALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLE 399

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           +L++L+ +++    +          KL  L +
Sbjct: 400 ELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDI 431

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 51.2 bits (123), Expect = 1e-06
 Identities = 18/77 (23%), Positives = 26/77 (33%), Gaps = 3/77 (3%)

Query: 517 LSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSI 574
           L L  N  +        S L SL +L    T +  L    +  L  L+ LN+ +    S 
Sbjct: 85  LILTGN-PIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSC 143

Query: 575 IPHQLISGFLKLEVLRL 591
                 S    L  + L
Sbjct: 144 KLPAYFSNLTNLVHVDL 160

>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 = 50.4 bits (121), Expect = 2e-06
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 515 TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLS 573
                     L+++P  I S  S  ++DLS   ++ L         +L++L+L     + 
Sbjct: 14  ITYQCMDQ-KLSKVPDDIPS--STKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCE-IE 69

Query: 574 IIPHQLISGFLKLEVLRL 591
            I  +   G   L  L L
Sbjct: 70  TIEDKAWHGLHHLSNLIL 87

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 21/109 (19%), Positives = 34/109 (31%), Gaps = 14/109 (12%)

Query: 498 KRISLMANEIESLSEIPTL--------LSLRRNDSLTELPSRI-----SSLVSLHHLDLS 544
           K++++  N I S               + L  N  +  +          +      LD+S
Sbjct: 131 KKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYN-YIQTITVNDLQFLRENPQVNLSLDMS 189

Query: 545 LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE 593
           L  I  +  +     KL  L L      S I    +     L V RL+ 
Sbjct: 190 LNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLIL 238

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 51.1 bits (123), Expect = 9e-07
 Identities = 27/106 (25%), Positives = 39/106 (36%), Gaps = 25/106 (23%)

Query: 505 NEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKAL--- 558
             + SL    P L  L    N SLTELP    SL SL   + +L  +  LP  L+ L   
Sbjct: 81  LGLSSLPELPPHLESLVASCN-SLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVS 139

Query: 559 -------------EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                          L+ ++++    L  +P    S    LE +  
Sbjct: 140 NNQLEKLPELQNSSFLKIIDVDNNS-LKKLPDLPPS----LEFIAA 180

>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 = 23/98 (23%), Positives = 40/98 (40%), Gaps = 13/98 (13%)

Query: 498 KRISLMANEIESLSEIPTLLSLR----RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ 553
           + + +  N++E L E+     L+     N+SL +LP    SL     +      +  LP 
Sbjct: 134 EYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLE---FIAAGNNQLEELP- 189

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           EL+ L  L  +  +    L  +P   +S    LE +  
Sbjct: 190 ELQNLPFLTAIYADNNS-LKKLPDLPLS----LESIVA 222

>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 = 49.6 bits (119), Expect = 2e-06
 Identities = 30/125 (24%), Positives = 46/125 (36%), Gaps = 23/125 (18%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHH 540
            L E P+++       I    N +++L    P+L  L++R N  LT+LP    SL  L  
Sbjct: 226 ILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDN-YLTDLPELPQSLTFLDV 284

Query: 541 LDLSLTHIRGLPQELKAL--------------EKLRYLNLEYTHYLSIIPHQLISGFLKL 586
            +   + +  LP  L  L                L  LN+     L  +P        +L
Sbjct: 285 SENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNK-LIELPALP----PRL 339

Query: 587 EVLRL 591
           E L  
Sbjct: 340 ERLIA 344

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 48.8 bits (117), Expect = 4e-06
 Identities = 21/111 (18%), Positives = 41/111 (36%), Gaps = 11/111 (9%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHH 540
           +L + P+++     K I +  N ++ L    P+L  ++   N  L ELP  + +L  L  
Sbjct: 142 QLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNN-QLEELPE-LQNLPFLTA 199

Query: 541 LDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           +      ++ LP        L  +       L  +P   +     L  +  
Sbjct: 200 IYADNNSLKKLPDLPL---SLESIVAGNNI-LEELPE--LQNLPFLTTIYA 244

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 48.5 bits (116), Expect = 6e-06
 Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 6/94 (6%)

Query: 498 KRISLMANEIESL-SEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELK 556
           K++ +  N +        ++  LR N  L E+P    +L     L +    +R  P   +
Sbjct: 360 KQLHVEYNPLREFPDIPESVEDLRMNSHLAEVPELPQNL---KQLHVETNPLREFPDIPE 416

Query: 557 ALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLR 590
           ++E LR  +                  L+ +V  
Sbjct: 417 SVEDLRMNSERVVDPYEFAHETTDK--LEDDVFE 448

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 47.3 bits (113), Expect = 1e-05
 Identities = 23/111 (20%), Positives = 39/111 (35%), Gaps = 13/111 (11%)

Query: 498 KRISLMANEIESLSEIP---TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
             I    N ++ L ++P     +    N  L ELP  + +L  L  +      ++ LP  
Sbjct: 198 TAIYADNNSLKKLPDLPLSLESIVAGNN-ILEELPE-LQNLPFLTTIYADNNLLKTLPDL 255

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN 605
             +LE L   +   T         L      L  L + E    G+++   N
Sbjct: 256 PPSLEALNVRDNYLT--------DLPELPQSLTFLDVSENIFSGLSELPPN 298

>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 = 41.9 bits (99), Expect = 7e-04
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 16/97 (16%)

Query: 498 KRISLMANEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
           + +++  N++  L +  P L  L    N  L E+P       +L  L +    +R  P  
Sbjct: 320 EELNVSNNKLIELPALPPRLERLIASFN-HLAEVPE---LPQNLKQLHVEYNPLREFPDI 375

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +++E LR  +      L+ +P         L+ L +
Sbjct: 376 PESVEDLRMNSH-----LAEVPELP----QNLKQLHV 403

>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 = 51.3 bits (123), Expect = 1e-06
 Identities = 37/217 (17%), Positives = 75/217 (34%), Gaps = 52/217 (23%)

Query: 501 SLMANEIESLSEIPTLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKAL 558
           SL +   E+L ++  +L+L  N  + ++       L +L  L+LS   +  L       L
Sbjct: 280 SLNSRVFETLKDL-KVLNLAYN-KINKIADEAFYGLDNLQVLNLSYNLLGELYSSNFYGL 337

Query: 559 EKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMREL 618
            K+ Y++L+  H ++II  Q      KL+ L L +                     +  +
Sbjct: 338 PKVAYIDLQKNH-IAIIQDQTFKFLEKLQTLDLRDN-------------------ALTTI 377

Query: 619 LGLKRLNVLSWSFRSSLAVQK-FFKYPKLDLTW--------LVFVQNLKELEIIVCTEME 669
             +  +  +  S    + + K       + L+         L F+  +  L+I+      
Sbjct: 378 HFIPSIPDIFLSGNKLVTLPKINLTANLIHLSENRLENLDILYFLLRVPHLQIL------ 431

Query: 670 EIICVDKLRDVSD--ISEIIGSEHNFFTQLESLGILY 704
                     ++    S    S     ++  SL  L+
Sbjct: 432 ---------ILNQNRFSSC--SGDQTPSENPSLEQLF 457

>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 = 49.4 bits (118), Expect = 4e-06
 Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 5/81 (6%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLS---LTHIRGLPQELKALEKLRYLNLEYTH 570
            +L L  +  +  L       L  L  L L    L+         + L+ L  L+L    
Sbjct: 76  RILDLGSS-KIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQ 134

Query: 571 YLSIIPHQLISGFLKLEVLRL 591
             S+  H        L+ +  
Sbjct: 135 IRSLYLHPSFGKLNSLKSIDF 155

>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 = 46.0 bits (109), Expect = 5e-05
 Identities = 37/212 (17%), Positives = 65/212 (30%), Gaps = 52/212 (24%)

Query: 521 RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQL 579
           R  +LT++P  +++      L LS  +IR +       LE+L+ L L   +    I  + 
Sbjct: 12  RFCNLTQVPQVLNTT---ERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEA 68

Query: 580 ISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK 639
                 L +L L             + +        + L  L  L  L +   S   ++ 
Sbjct: 69  FRNLPNLRILDL-----------GSSKIYFLHPDAFQGLFHLFELR-LYFCGLSDAVLKD 116

Query: 640 FFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSD--ISEIIGSEHNFFTQL 697
            +         L   + L  L                  D+S   I  +    H  F +L
Sbjct: 117 GY------FRNL---KALTRL------------------DLSKNQIRSL--YLHPSFGKL 147

Query: 698 ESLGILY--GPDLKSIYPN---PLHFPKLKKI 724
            SL  +      +  +  +   PL    L   
Sbjct: 148 NSLKSIDFSSNQIFLVCEHELEPLQGKTLSFF 179

>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 = 42.5 bits (100), Expect = 5e-04
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 505 NEIESLSEIPTLLSLR-RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE--LKALEKL 561
           N + ++  IP++  +    + L  LP      ++ + + LS   +  L     L  +  L
Sbjct: 372 NALTTIHFIPSIPDIFLSGNKLVTLPKI---NLTANLIHLSENRLENLDILYFLLRVPHL 428

Query: 562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           + L L    + S    Q  S    LE L L
Sbjct: 429 QILILNQNRFSSCSGDQTPSENPSLEQLFL 458

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 8/95 (8%)

Query: 498 KRISLMANEIESLSEIP---TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
           K + +  N + SL  +P     L +  N  LT LP   S L     L +    +  LP+ 
Sbjct: 224 KELIVSGNRLTSLPVLPSELKELMVSGN-RLTSLPMLPSGL---LSLSVYRNQLTRLPES 279

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVL 589
           L  L     +NLE    LS    Q +         
Sbjct: 280 LIHLSSETTVNLEGNP-LSERTLQALREITSAPGY 313

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 26/112 (23%), Positives = 40/112 (35%), Gaps = 23/112 (20%)

Query: 498 KRISLMANEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
             + +  N + SL +  P L  L +  N  LT LP     L+ L      LTH+  LP  
Sbjct: 64  TTLVIPDNNLTSLPALPPELRTLEVSGN-QLTSLPVLPPGLLELSIFSNPLTHLPALPSG 122

Query: 555 LKALE--------------KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL 592
           L  L                L+ L++     L+ +P    +   +L  L   
Sbjct: 123 LCKLWIFGNQLTSLPVLPPGLQELSVSDNQ-LASLP----ALPSELCKLWAY 169

>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 = 45.7 bits (108), Expect = 6e-05
 Identities = 26/104 (25%), Positives = 38/104 (36%), Gaps = 23/104 (22%)

Query: 505 NEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALE-- 559
           N++ SL      L  LS+  N  L  LP+  S L  L   +  LT +  LP  LK L   
Sbjct: 171 NQLTSLPMLPSGLQELSVSDN-QLASLPTLPSELYKLWAYNNRLTSLPALPSGLKELIVS 229

Query: 560 ------------KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
                       +L+ L +     L+ +P         L  L +
Sbjct: 230 GNRLTSLPVLPSELKELMVSGNR-LTSLPMLPSG----LLSLSV 268

>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 = 43.7 bits (103), Expect = 2e-04
 Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 15/100 (15%)

Query: 498 KRISLMANEIESL-SEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
            ++ +  N++ SL    P L  LS+  N  L  LP+  S L  L   +  LT    LP  
Sbjct: 124 CKLWIFGNQLTSLPVLPPGLQELSVSDN-QLASLPALPSELCKLWAYNNQLTS---LPML 179

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC 594
                 L+ L++     L+ +P    +   +L  L     
Sbjct: 180 ---PSGLQELSVSDNQ-LASLP----TLPSELYKLWAYNN 211

>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 = 43.7 bits (103), Expect = 2e-04
 Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 15/107 (14%)

Query: 492 KEWEGAKRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRISSLVSLHHLDLS 544
             W  A            + ++         +L++  +  LT LP  + +   +  L + 
Sbjct: 13  SAWRRAAPAEESRGRAAVVQKMRACLNNGNAVLNVGES-GLTTLPDCLPA--HITTLVIP 69

Query: 545 LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             ++  LP       +LR L +     L+ +P  L  G L+L +   
Sbjct: 70  DNNLTSLPALPP---ELRTLEVSGNQ-LTSLPV-LPPGLLELSIFSN 111

>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 = 50.7 bits (122), Expect = 2e-06
 Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 1/77 (1%)

Query: 516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSII 575
           L S   N   + + S + SL  L  L LS +HI G     K    L  L+L        +
Sbjct: 57  LSSKPLNVGFSAVSSSLLSLTGLESLFLSNSHINGSVSGFKCSASLTSLDLSRNSLSGPV 116

Query: 576 PHQL-ISGFLKLEVLRL 591
                +     L+ L +
Sbjct: 117 TTLTSLGSCSGLKFLNV 133

>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 = 48.4 bits (116), Expect = 8e-06
 Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 6/88 (6%)

Query: 508 ESLSEIPTL--LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRY 563
           + L  + TL  L L  N  LT E+PS +S+  +L+ + LS   + G +P+ +  LE L  
Sbjct: 460 QELMYVKTLETLILDFN-DLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAI 518

Query: 564 LNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           L L    +   IP + +     L  L L
Sbjct: 519 LKLSNNSFSGNIPAE-LGDCRSLIWLDL 545

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 46.8 bits (112), Expect = 2e-05
 Identities = 21/88 (23%), Positives = 29/88 (32%), Gaps = 6/88 (6%)

Query: 509 SLSEIPTL--LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL---PQELKALEKLRY 563
           SL  +  L  L L  +     +        SL  LDLS   + G       L +   L++
Sbjct: 72  SLLSLTGLESLFLSNSHINGSVSG-FKCSASLTSLDLSRNSLSGPVTTLTSLGSCSGLKF 130

Query: 564 LNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           LN+                   LEVL L
Sbjct: 131 LNVSSNTLDFPGKVSGGLKLNSLEVLDL 158

>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 = 45.7 bits (109), Expect = 5e-05
 Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 6/88 (6%)

Query: 508 ESLSEIPTL--LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRY 563
            SL  +  L  L L  N  L  E+P  +  + +L  L L    + G +P  L     L +
Sbjct: 436 SSLGSLSKLRDLKLWLN-MLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNW 494

Query: 564 LNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           ++L        IP   I     L +L+L
Sbjct: 495 ISLSNNRLTGEIPKW-IGRLENLAILKL 521

>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 = 45.3 bits (108), Expect = 6e-05
 Identities = 24/90 (26%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 506 EIESLSEIPTL--LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKL 561
            I  L +   L  L +  N  L+ +    IS+   L  L++S     G +P     L+ L
Sbjct: 215 GIPFLGDCSALQHLDISGN-KLSGDFSRAISTCTELKLLNISSNQFVGPIPPLP--LKSL 271

Query: 562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           +YL+L    +   IP  L      L  L L
Sbjct: 272 QYLSLAENKFTGEIPDFLSGACDTLTGLDL 301

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 44.9 bits (107), Expect = 9e-05
 Identities = 22/80 (27%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 515 TLLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIRG-LPQE-LKALEKLRYLNLEYTHY 571
           T L L  N      +P    S   L  L LS  +  G LP + L  +  L+ L+L +  +
Sbjct: 297 TGLDLSGN-HFYGAVPPFFGSCSLLESLALSSNNFSGELPMDTLLKMRGLKVLDLSFNEF 355

Query: 572 LSIIPHQLISGFLKLEVLRL 591
              +P  L +    L  L L
Sbjct: 356 SGELPESLTNLSASLLTLDL 375

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 43.0 bits (102), Expect = 4e-04
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 515 TLLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRYLNLEYTHYL 572
             L L+ N   T ++P  +S+   L  L LS  ++ G +P  L +L KLR L L     L
Sbjct: 397 QELYLQNN-GFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNM-L 454

Query: 573 S-IIPHQLISGFLKLEVLRL 591
              IP + +     LE L L
Sbjct: 455 EGEIPQE-LMYVKTLETLIL 473

>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 = 48.8 bits (117), Expect = 2e-06
 Identities = 18/106 (16%), Positives = 49/106 (46%), Gaps = 13/106 (12%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLT-HI 548
           + + L+   + ++       +P +  + +  + +L +L S    +L  + H+++  T ++
Sbjct: 34  QTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNL 93

Query: 549 RGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE 593
             +  + LK L  L++L +  T  L + P   ++     ++  +LE
Sbjct: 94  TYIDPDALKELPLLKFLGIFNTG-LKMFPD--LTKVYSTDIFFILE 136

>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 = 47.7 bits (114), Expect = 5e-06
 Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 10/92 (10%)

Query: 509 SLSEIPTL------LSLRRNDSLTELPSRI-SSLVSLHHLDLSL-THIRGLPQEL-KALE 559
            +  IP+L      L L     L  +PS   S+L ++  + +S+   ++ L       L 
Sbjct: 22  DIQRIPSLPPSTQTLKLIET-HLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLS 80

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           K+ ++ +  T  L+ I    +     L+ L +
Sbjct: 81  KVTHIEIRNTRNLTYIDPDALKELPLLKFLGI 112

>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 = 48.8 bits (117), Expect = 3e-06
 Identities = 23/103 (22%), Positives = 37/103 (35%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
             + L    ++ L       +  L  L L+ N +L  LP      L +L HL L    I 
Sbjct: 108 HTLHLDRCGLQELGPGLFRGLAALQYLYLQDN-ALQALPDDTFRDLGNLTHLFLHGNRIS 166

Query: 550 GLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            +P+   + L  L  L L     ++ +         +L  L L
Sbjct: 167 SVPERAFRGLHSLDRLLLHQNR-VAHVHPHAFRDLGRLMTLYL 208

>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 = 46.5 bits (111), Expect = 1e-05
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQE-LKALE 559
            L  +P         + L  N  ++ +P+    +  +L  L L    +  +       L 
Sbjct: 22  GLQAVPVGIPAASQRIFLHGN-RISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLA 80

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  L+L     L  +      G  +L  L L
Sbjct: 81  LLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL 112

>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 = 49.0 bits (117), Expect = 4e-06
 Identities = 45/249 (18%), Positives = 80/249 (32%), Gaps = 35/249 (14%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           + + L +N I ++ E     + +L  L L  N  L+ L S     L SL  L+L     +
Sbjct: 79  QALVLTSNGINTIEEDSFSSLGSLEHLDLSYN-YLSNLSSSWFKPLSSLTFLNLLGNPYK 137

Query: 550 GLPQE--LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL 607
            L +      L KL+ L +      + I  +  +G   LE L +           + + L
Sbjct: 138 TLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEI-----------DASDL 186

Query: 608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL----VFVQNLKELEII 663
                  ++ +  +  L  L       L          ++   L    +   +  EL   
Sbjct: 187 QSYEPKSLKSIQNVSHLI-LHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTG 245

Query: 664 VCTEMEEIICVDKLRDVSDISEIIGSEHNFF---TQLESLGILYGPDLKSIYPNPLH-FP 719
                  +I     R+V    E +          + L  L       LKS+         
Sbjct: 246 E---TNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLELE-FSRNQLKSVPDGIFDRLT 301

Query: 720 KLKKIGVYG 728
            L+KI ++ 
Sbjct: 302 SLQKIWLHT 310

>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 = 48.6 bits (116), Expect = 4e-06
 Identities = 32/110 (29%), Positives = 45/110 (40%), Gaps = 10/110 (9%)

Query: 496 GAKRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTH 547
             K + L  N I  +S            L L  N  +  +     SSL SL HLDLS  +
Sbjct: 53  AVKSLDLSNNRITYISNSDLQRCVNLQALVLTSN-GINTIEEDSFSSLGSLEHLDLSYNY 111

Query: 548 IRGLPQEL-KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS 596
           +  L     K L  L +LNL    Y ++    L S   KL++LR+    +
Sbjct: 112 LSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDT 161

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 49.2 bits (117), Expect = 4e-06
 Identities = 26/172 (15%), Positives = 53/172 (30%), Gaps = 12/172 (6%)

Query: 498 KRISLMANEIESLSEIP---TLLSLRRNDSLTELPSRISSLVSL----HHLDLSLTHIRG 550
           + +S+  N++  L E+P     L +  N  L  LP+                     I  
Sbjct: 163 EVLSVRNNQLTFLPELPESLEALDVSTNL-LESLPAVPVRNHHSEETEIFFRCRENRITH 221

Query: 551 LPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDD 610
           +P+ + +L+    + LE    LS    + +S                    ++  +    
Sbjct: 222 IPENILSLDPTCTIILEDNP-LSSRIRESLSQQTAQPDYHGPRIYFSMSDGQQNTLHRPL 280

Query: 611 AEPLMRELLGLKRLNVLSW--SFRSSLAVQKFFKYPKLDLTWLVFVQNLKEL 660
           A+ +       K+ +V     +F        F  +    L+  V  +N    
Sbjct: 281 ADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLD-RLSDTVSARNTSGF 331

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 45.3 bits (107), Expect = 6e-05
 Identities = 31/129 (24%), Positives = 49/129 (37%), Gaps = 24/129 (18%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESL-SEIP---TLLSLRRNDSLTELPSRISSLVSLH 539
           +     K         + L    + SL   +P   T+L + +N +L  LP   +SL  L 
Sbjct: 48  EAVSLLKECLINQFSELQLNRLNLSSLPDNLPPQITVLEITQN-ALISLPELPASLEYLD 106

Query: 540 HLDLSLTHIRGLPQELKALE--------------KLRYLNLEYTHYLSIIPHQLISGFLK 585
             D  L+ +  LP  LK L+               L Y+N +    L+++P    S    
Sbjct: 107 ACDNRLSTLPELPASLKHLDVDNNQLTMLPELPALLEYINADNNQ-LTMLPELPTS---- 161

Query: 586 LEVLRLLEC 594
           LEVL +   
Sbjct: 162 LEVLSVRNN 170

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 41.9 bits (98), Expect = 7e-04
 Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 12/97 (12%)

Query: 498 KRISLMANEIESLSEIPTLL---SLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE 554
           K + +  N++  L E+P LL   +   N  LT LP   +   SL  L +    +  LP+ 
Sbjct: 123 KHLDVDNNQLTMLPELPALLEYINADNN-QLTMLPELPT---SLEVLSVRNNQLTFLPEL 178

Query: 555 LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
               E L  L++     L  +P  +       E   +
Sbjct: 179 ---PESLEALDVSTNL-LESLP-AVPVRNHHSEETEI 210

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 47.9 bits (114), Expect = 8e-06
 Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 12/104 (11%)

Query: 498 KRISLMANEIESLSEIP--------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHI 548
             + L  N +  L              L L  N  L  + S     + +L +LDLS  H+
Sbjct: 42  ALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHN-HLNFISSEAFVPVPNLRYLDLSSNHL 100

Query: 549 RGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             L +     L+ L  L L   H + ++         +L+ L L
Sbjct: 101 HTLDEFLFSDLQALEVLLLYNNH-IVVVDRNAFEDMAQLQKLYL 143

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 47.1 bits (113), Expect = 1e-05
 Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 14/105 (13%)

Query: 499 RISLMANEIESLSEIP---------TLLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHI 548
            + L    +     IP           L +   ++L   +P  I+ L  LH+L ++ T++
Sbjct: 54  NLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNV 113

Query: 549 RG-LPQELKALEKLRYLNLEYTHYLS-IIPHQLISGFLKLEVLRL 591
            G +P  L  ++ L  L+  Y   LS  +P   IS    L  +  
Sbjct: 114 SGAIPDFLSQIKTLVTLDFSYNA-LSGTLPPS-ISSLPNLVGITF 156

>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 = 47.0 bits (112), Expect = 1e-05
 Identities = 33/158 (20%), Positives = 54/158 (34%), Gaps = 22/158 (13%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           K +SL  N I  ++ +  L     L L  N  +T++   +S L  L  L L    I  + 
Sbjct: 115 KSLSLEHNGISDINGLVHLPQLESLYLGNN-KITDITV-LSRLTKLDTLSLEDNQISDIV 172

Query: 553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAE 612
             L  L KL+ L L   H   +     ++G   L+VL L                 +   
Sbjct: 173 -PLAGLTKLQNLYLSKNHISDLRA---LAGLKNLDVLEL-----------FSQECLNKPI 217

Query: 613 PLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTW 650
                L+    +     S  +   +     Y K ++ W
Sbjct: 218 NHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKW 255

>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 = 45.8 bits (109), Expect = 2e-05
 Identities = 30/103 (29%), Positives = 45/103 (43%), Gaps = 11/103 (10%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           +RI L  N+I  L+      + +L  L L  N  +TELP  +   L SL  L L+   I 
Sbjct: 59  RRIDLSNNQISELAPDAFQGLRSLNSLVLYGN-KITELPKSLFEGLFSLQLLLLNANKIN 117

Query: 550 GLPQEL-KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L  +  + L  L  L+L Y + L  I     S    ++ + L
Sbjct: 118 CLRVDAFQDLHNLNLLSL-YDNKLQTIAKGTFSPLRAIQTMHL 159

>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 = 46.0 bits (109), Expect = 3e-05
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 514 PTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYL 572
             +   + +  +TE+PS +    +   L   LT +R + +        L  + +     L
Sbjct: 11  NRVFLCQES-KVTEIPSDLPR--NAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVL 67

Query: 573 SIIPHQLISGFLKLEVLRLLEC 594
            +I   + S   KL  +R+ + 
Sbjct: 68  EVIEADVFSNLPKLHEIRIEKA 89

>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 = 46.0 bits (109), Expect = 3e-05
 Identities = 34/248 (13%), Positives = 62/248 (25%), Gaps = 48/248 (19%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSRI-SSLVSLHHLDLS----LTHIRGLPQELK 556
            ++EIP         L       L  +     S    L  +++S    L  I        
Sbjct: 20  KVTEIPSDLPRNAIELRFVLT-KLRVIQKGAFSGFGDLEKIEISQNDVLEVIE--ADVFS 76

Query: 557 ALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMR 616
            L KL  + +E  + L  I  +       L+ L +               +    +    
Sbjct: 77  NLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLI-----------SNTGIKHLPDVHKI 125

Query: 617 ELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQN------------LKELEIIV 664
             L    L++       ++    F          L   +N             +  E+ +
Sbjct: 126 HSLQKVLLDIQDNINIHTIERNSFVGLSFE-SVILWLNKNGIQEIHNSAFNGTQLDELNL 184

Query: 665 CTEME-EIICVDKLRDVSDISEIIGS-------EHNFFTQLESLGILYGPDLKSIYPNPL 716
                 E +  D     S    +  S              L+ L      +LK + P   
Sbjct: 185 SDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKL-PTLE 243

Query: 717 HFPKLKKI 724
               L + 
Sbjct: 244 KLVALMEA 251

>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 = 46.3 bits (110), Expect = 3e-05
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQEL-KALEKLRYLNLEYTHYL 572
             L+L +N  + ++       L  L  L+LS   +  +   + + L+KL  L+L Y H +
Sbjct: 302 EQLTLAQN-EINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKLEVLDLSYNH-I 359

Query: 573 SIIPHQLISGFLKLEVLRL 591
             +  Q   G   L+ L L
Sbjct: 360 RALGDQSFLGLPNLKELAL 378

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 5/81 (6%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRG--LPQEL-KALEKLRYLNLEYTH 570
            +L L  N    +L +   + L +L  L L+  ++ G  L     K L  L  L L   +
Sbjct: 82  IILKLDYN-QFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNN 140

Query: 571 YLSIIPHQLISGFLKLEVLRL 591
              I P        +  VL L
Sbjct: 141 IKKIQPASFFLNMRRFHVLDL 161

>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 = 45.4 bits (108), Expect = 4e-05
 Identities = 18/103 (17%), Positives = 42/103 (40%), Gaps = 12/103 (11%)

Query: 498 KRISLMANEIESL-----SEIPTL--LSLRRND-SLTELPSRI-SSLVSLHHLDLSLTHI 548
           + + +  NEI  +     + +  +  + L  N    + + +     +  L ++ ++ T+I
Sbjct: 124 QELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNI 183

Query: 549 RGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             +PQ L     L  L+L+    ++ +    + G   L  L L
Sbjct: 184 TTIPQGL--PPSLTELHLDGNK-ITKVDAASLKGLNNLAKLGL 223

>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 = 45.0 bits (107), Expect = 5e-05
 Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 16/104 (15%)

Query: 502 LMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQ 553
           L  N+I  +       +  L  L L  N S++ + +   ++   L  L L+   +  +P 
Sbjct: 199 LDGNKITKVDAASLKGLNNLAKLGLSFN-SISAVDNGSLANTPHLRELHLNNNKLVKVPG 257

Query: 554 ELKALEKLRYLNLEYTHYLSII------PHQLISGFLKLEVLRL 591
            L   + ++ + L   + +S I      P    +       + L
Sbjct: 258 GLADHKYIQVVYLHNNN-ISAIGSNDFCPPGYNTKKASYSGVSL 300

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A* Length = 330

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 20/105 (19%), Positives = 46/105 (43%), Gaps = 12/105 (11%)

Query: 495 EGAKRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLT 546
                + L  N+I  + +     +  L  L L  N  ++++     + LV L  L LS  
Sbjct: 52  PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINN-KISKISPGAFAPLVKLERLYLSKN 110

Query: 547 HIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            ++ LP+++   + L+ L +     ++ +   + +G  ++ V+ L
Sbjct: 111 QLKELPEKM--PKTLQELRVHENE-ITKVRKSVFNGLNQMIVVEL 152

>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 = 45.1 bits (107), Expect = 4e-05
 Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 10/101 (9%)

Query: 498 KRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG 550
             + L  N + + S          T L+L R   LT+L     +L  L  LDLS   ++ 
Sbjct: 34  TILHLSENLLYTFSLATLMPYTRLTQLNLDRA-ELTKLQV-DGTLPVLGTLDLSHNQLQS 91

Query: 551 LPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           LP   + L  L  L++ +   L+ +P   + G  +L+ L L
Sbjct: 92  LPLLGQTLPALTVLDVSFNR-LTSLPLGALRGLGELQELYL 131

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 16/104 (15%)

Query: 502 LMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQ 553
           L  N+I+++          L  L L  N  +  + +   S L +L  L L    +  +P 
Sbjct: 200 LDHNKIQAIELEDLLRYSKLYRLGLGHN-QIRMIENGSLSFLPTLRELHLDNNKLSRVPA 258

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISG------FLKLEVLRL 591
            L  L+ L+ + L   + ++ +                   + L
Sbjct: 259 GLPDLKLLQVVYLHTNN-ITKVGVNDFCPVGFGVKRAYYNGISL 301

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 12/104 (11%)

Query: 496 GAKRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTH 547
               + L  N+I  L +     +  L  L L  N  ++++  +  S L  L  L +S  H
Sbjct: 55  DTTLLDLQNNDISELRKDDFKGLQHLYALVLVNN-KISKIHEKAFSPLRKLQKLYISKNH 113

Query: 548 IRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           +  +P  L     L  L +     +  +P  + SG   +  + +
Sbjct: 114 LVEIPPNL--PSSLVELRIHDNR-IRKVPKGVFSGLRNMNCIEM 154

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 44.6 bits (106), Expect = 7e-05
 Identities = 18/102 (17%), Positives = 42/102 (41%), Gaps = 11/102 (10%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRND-SLTELPSRISSLVSLHHLDLSLTHIR 549
             + +  N I  + +     +  +  + +  N    +         + L++L +S   + 
Sbjct: 126 VELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGLKLNYLRISEAKLT 185

Query: 550 GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
           G+P++L   E L  L+L++   +  I  + +  + KL  L L
Sbjct: 186 GIPKDL--PETLNELHLDHNK-IQAIELEDLLRYSKLYRLGL 224

>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 = 45.6 bits (108), Expect = 5e-05
 Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 501 SLMANEIESLSEIPTLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQELKALE 559
            L  ++I SLS++  +L +  N  +  L   +      L +LDLS   +  +        
Sbjct: 35  ELWTSDILSLSKL-RILIISHN-RIQYLDISVFKFNQELEYLDLSHNKLVKIS--CHPTV 90

Query: 560 KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            L++L+L +  + ++   +      +L+ L L
Sbjct: 91  NLKHLDLSFNAFDALPICKEFGNMSQLKFLGL 122

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens} Length = 520

 Score = 42.9 bits (101), Expect = 4e-04
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 5/81 (6%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQELKA---LEKLRYLNLEYTH 570
             L    N  LT+        L  L  L L +  ++ L +  +    ++ L+ L++    
Sbjct: 327 LHLDFSNN-LLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNS 385

Query: 571 YLSIIPHQLISGFLKLEVLRL 591
                     S    L  L +
Sbjct: 386 VSYDEKKGDCSWTKSLLSLNM 406

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 25/81 (30%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 517 LSLRRNDSLTELPSRISSL----VSLHHLDLSLTHIRGLPQELKA--LEKLRYLNLEYTH 570
           L+LR    +       S+L    V L  LDLS   +R            +L  LNL +T 
Sbjct: 206 LALRNA-GMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTG 264

Query: 571 YLSIIPHQLISGFLKLEVLRL 591
            L  +P  L +   KL VL L
Sbjct: 265 -LKQVPKGLPA---KLSVLDL 281

>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 = 45.9 bits (108), Expect = 5e-05
 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 9/114 (7%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSL 538
            +++   +      + + L  N+I  ++ +  L     LSL  N  ++++   ++ L  L
Sbjct: 120 GISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDN-QISDIVP-LAGLTKL 177

Query: 539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL 592
            +L LS  HI  L + L  L+ L  L L     L+   +   S  +    ++  
Sbjct: 178 QNLYLSKNHISDL-RALAGLKNLDVLELFSQECLNKPINHQ-SNLVVPNTVKNT 229

>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 = 43.9 bits (103), Expect = 2e-04
 Identities = 33/113 (29%), Positives = 54/113 (47%), Gaps = 11/113 (9%)

Query: 484 KLTEAPKVKEWEGAKRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSL 538
            +T+A    E     +I    ++I+S+  I  L     L L  N  LT++   +++L +L
Sbjct: 32  SVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNK-LTDI-KPLTNLKNL 89

Query: 539 HHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
             L L    I+ L   LK L+KL+ L+LE+   +S I    +    +LE L L
Sbjct: 90  GWLFLDENKIKDL-SSLKDLKKLKSLSLEHNG-ISDING--LVHLPQLESLYL 138

>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 = 42.4 bits (99), Expect = 6e-04
 Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 9/98 (9%)

Query: 498 KRISLMANEIESLSEIPTLLSLRRND----SLTELPSRISSLVSLHHLDLSLTHIRGLPQ 553
                ++  I+ +          +++    S+T+  +  + L S+  +  + + I+ + Q
Sbjct: 2   GETITVSTPIKQIFPDDAFAETIKDNLKKKSVTDAVT-QNELNSIDQIIANNSDIKSV-Q 59

Query: 554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL 591
            ++ L  +  L L       I P   ++    L  L L
Sbjct: 60  GIQYLPNVTKLFLNGNKLTDIKP---LTNLKNLGWLFL 94

>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 = 43.9 bits (104), Expect = 1e-04
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + +S+   ++  L+ +  L     L    N  ++++   ++SL +L  + L    I  + 
Sbjct: 154 QYLSIGNAQVSDLTPLANLSKLTTLKADDN-KISDISP-LASLPNLIEVHLKNNQISDVS 211

Query: 553 QELKALEKLRYLNLEY 568
             L     L  + L  
Sbjct: 212 -PLANTSNLFIVTLTN 226

>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 = 43.8 bits (104), Expect = 1e-04
 Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQEL-KALEKLRYLNLEYTHYL 572
           + L L  N  +  L     S L SL  L    T++  L       L+ L+ LN+ +    
Sbjct: 79  STLILTGN-PIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQ 137

Query: 573 SIIPHQLISGFLKLEVLRL 591
           S    +  S    LE L L
Sbjct: 138 SFKLPEYFSNLTNLEHLDL 156

>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 = 41.5 bits (98), Expect = 6e-04
 Identities = 23/107 (21%), Positives = 44/107 (41%), Gaps = 15/107 (14%)

Query: 498 KRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHI 548
           +++  +   + SL   P         L++  N  +         S+L +L HLDLS   I
Sbjct: 103 QKLVAVETNLASLENFPIGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNKI 161

Query: 549 RGLPQE-LKALEKLRYLNLE---YTHYLSIIPHQLISGFLKLEVLRL 591
           + +    L+ L ++  LNL      + ++ I        ++L+ L L
Sbjct: 162 QSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKE-IRLKELAL 207

>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 = 43.1 bits (102), Expect = 1e-04
 Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 11/104 (10%)

Query: 498 KRISLMANEIESLSE-----IPTL--LSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIR 549
           ++I+   N+I  + E        +  + L  N  L  +  ++   L SL  L L    I 
Sbjct: 60  RKINFSNNKITDIEEGAFEGASGVNEILLTSN-RLENVQHKMFKGLESLKTLMLRSNRIT 118

Query: 550 GLPQEL-KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL 592
            +  +    L  +R L+L Y + ++ +          L  L LL
Sbjct: 119 CVGNDSFIGLSSVRLLSL-YDNQITTVAPGAFDTLHSLSTLNLL 161

>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 = 44.1 bits (104), Expect = 2e-04
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 515 TLLSLRRNDSLTELPSRI-SSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLS 573
            +L L  N  +  L   +      L +LD+S   ++ +      +  LR+L+L +  +  
Sbjct: 79  RVLRLSHN-RIRSLDFHVFLFNQDLEYLDVSHNRLQNIS--CCPMASLRHLDLSFNDFDV 135

Query: 574 IIPHQLISGFLKLEVLRL 591
           +   +      KL  L L
Sbjct: 136 LPVCKEFGNLTKLTFLGL 153

>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 = 43.2 bits (101), Expect = 3e-04
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 514 PTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLS 573
             +L L   D LT L   +  L+ + HLDLS   +R LP  L AL  L  L     + L 
Sbjct: 443 VRVLHLAHKD-LTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASD-NALE 499

Query: 574 IIPHQLISGFLKLEVLRL 591
            +    ++   +L+ L L
Sbjct: 500 NVDG--VANLPRLQELLL 515

>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 = 43.2 bits (101), Expect = 3e-04
 Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 28/103 (27%)

Query: 493 EWEGAKRISLMANEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLS---L 545
           E+   + + L   ++  L  +  LL +      ++ L  LP  +++L  L  L  S   L
Sbjct: 439 EYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNAL 498

Query: 546 THIRGLPQ---------------------ELKALEKLRYLNLE 567
            ++ G+                        L +  +L  LNL+
Sbjct: 499 ENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQ 541

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 41.2 bits (97), Expect = 8e-04
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
            R+ L  NE+     +  L     LS+R N  L  +   +  L  L  LDL    I    
Sbjct: 109 SRLFLDNNELRDTDSLIHLKNLEILSIRNN-KLKSIVM-LGFLSKLEVLDLHGNEITNTG 166

Query: 553 QELKALEKLRYLNLEY 568
             L  L+K+ +++L  
Sbjct: 167 -GLTRLKKVNWIDLTG 181

>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 = 22/77 (28%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 498 KRISLMANEIESLSEIPTL-----LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP 552
           + +S +   + S++ +P L     L L  N     L        +L HL+LS   I+ L 
Sbjct: 45  EFLSTINVGLTSIANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLS 104

Query: 553 Q--ELKALEKLRYLNLE 567
               LK LE L+ L+L 
Sbjct: 105 TIEPLKKLENLKSLDLF 121

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	779
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.86
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.8
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.74
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.74
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.72
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.71
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.71
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.71
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.7
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.7
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.7
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.7
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.69
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.69
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.69
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.69
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.69
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.68
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.68
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.68
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.68
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.68
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.67
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.67
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.67
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.67
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.66
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.65
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.65
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.65
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.65
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.64
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.64
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.64
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.64
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.64
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.64
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.63
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.63
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.63
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.63
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.63
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.63
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.62
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.62
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.62
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.61
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.61
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.61
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.61
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.61
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.6
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.6
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.6
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.59
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.59
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.59
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.59
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.58
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.58
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.58
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.58
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.58
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.58
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.57
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.57
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.57
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.56
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.56
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.56
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.55
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.55
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.55
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.54
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.54
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.53
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.52
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.52
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.51
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.51
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.51
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.5
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.49
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.48
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.47
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.47
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.46
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.46
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.46
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.46
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.45
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.44
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.44
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.44
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.43
2fna_A	357	Conserved hypothetical protein; structural genomic	99.42
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.42
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.42
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.42
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.41
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.41
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.41
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.4
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.39
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.38
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.38
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.37
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.37
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.35
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.33
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.29
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.27
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.26
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.23
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.22
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.21
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.21
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.21
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.2
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.18
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.15
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.15
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.13
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.13
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.11
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.11
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.1
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.09
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.09
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.09
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.08
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.06
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.06
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.02
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.02
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.01
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.99
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.98
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.97
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.96
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.95
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.95
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.94
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.87
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.86
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.84
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.74
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.7
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.69
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.65
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.6
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.6
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.46
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.43
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.37
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.34
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.25
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.24
3bos_A	242	Putative DNA replication factor; P-loop containing	98.13
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.11
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.1
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.1
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.07
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.03
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.99
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.91
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.88
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.85
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.78
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.77
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.76
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.73
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.7
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.67
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.65
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.56
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.55
3pvs_A	447	Replication-associated recombination protein A; ma	97.53
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.52
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.51
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.5
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.49
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.45
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.43
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.42
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.41
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.4
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.38
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.37
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.34
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.33
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.3
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.3
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.27
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.25
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.25
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.06
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.05
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.99
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.97
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.94
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.92
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.91
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.76
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.7
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.69
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.68
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	96.57
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.56
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.53
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.38
3co5_A	143	Putative two-component system transcriptional RES	96.29
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	96.12
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.09
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.89
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.87
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.84
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.84
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.77
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.72
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	95.71
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.68
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	95.63
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.59
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.55
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.55
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.55
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.31
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	95.25
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.24
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	95.23
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.22
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.2
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.14
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.14
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.11
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.07
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.05
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.04
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	95.02
2qgz_A	308	Helicase loader, putative primosome component; str	94.98
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	94.96
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	94.93
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	94.9
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	94.87
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	94.86
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.84
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	94.8
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	94.79
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.78
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.7
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.64
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	94.64
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.54
2xxa_A	433	Signal recognition particle protein; protein trans	94.53
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.53
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.52
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.51
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.51
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.51
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.51
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.48
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.46
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.44
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.44
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	94.41
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.41
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.4
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.39
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	94.32
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.31
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.3
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.3
1via_A	175	Shikimate kinase; structural genomics, transferase	94.3
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.28
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.23
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.23
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.21
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.21
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.21
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.18
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.15
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.14
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	94.13
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	94.1
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	94.08
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.07
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.07
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.04
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.01
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	93.99
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	93.99
3io5_A	333	Recombination and repair protein; storage dimer, i	93.98
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.92
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.92
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	93.92
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	93.91
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	93.9
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.89
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.88
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.88
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	93.88
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	93.85
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	93.85
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.74
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	93.74
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	93.74
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.73
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.72
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.71
2vli_A	183	Antibiotic resistance protein; transferase, tunica	93.65
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.65
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	93.65
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	93.64
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	93.62
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.62
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	93.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	93.59
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.52
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	93.5
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	93.48
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.46
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	93.43
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.39
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.37
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.34
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	93.34
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	93.34
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.31
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.27
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	93.25
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.21
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.2
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.2
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.16
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.13
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.13
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.09
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.09
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	93.03
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.02
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.01
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.0
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.99
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.99
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.94
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	92.93
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.89
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	92.88
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.88
1tue_A	212	Replication protein E1; helicase, replication, E1E	92.86
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	92.78
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	92.76
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	92.75
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	92.69
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	92.66
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.51
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	92.49
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	92.45
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	92.4
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.38
2cvh_A	220	DNA repair and recombination protein RADB; filamen	92.38
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	92.36
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	92.35
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.32
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.3
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.27
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	92.27
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.27
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.24
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.22
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	92.21
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	92.21
4a74_A	231	DNA repair and recombination protein RADA; hydrola	92.17
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	92.14
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	92.12
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	92.06
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	92.03
3end_A	307	Light-independent protochlorophyllide reductase ir	92.02
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.01
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	91.98
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	91.93
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.93
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	91.87
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	91.86
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.79
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.71
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	91.66
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.64
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.62
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	91.59
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	91.58
1b0u_A	262	Histidine permease; ABC transporter, transport pro	91.56
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	91.47
2og2_A	359	Putative signal recognition particle receptor; nuc	91.41
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	91.38
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.31
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	91.26
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	91.26
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	91.18
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.17
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.16
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.14
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.14
1sgw_A	214	Putative ABC transporter; structural genomics, P p	91.08
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.08
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.05
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.05
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	91.04
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	90.97
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	90.94
1g6h_A	257	High-affinity branched-chain amino acid transport	90.93
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	90.91
2r6a_A	454	DNAB helicase, replicative helicase; replication,	90.88
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	90.87
2ged_A	193	SR-beta, signal recognition particle receptor beta	90.87
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	90.83
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	90.82
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	90.82
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	90.79
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	90.73
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	90.65
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	90.62
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	90.61
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	90.6
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	90.58
1u94_A	356	RECA protein, recombinase A; homologous recombinat	90.57
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	90.57
2wji_A	165	Ferrous iron transport protein B homolog; membrane	90.54
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	90.52
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	90.5
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	90.49
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.44
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	90.39
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.35
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	90.33
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	90.27
2eyu_A	261	Twitching motility protein PILT; pilus retraction	90.25
2ghi_A	260	Transport protein; multidrug resistance protein, M	90.25
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.14
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	90.12
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.09
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	90.04
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	90.04
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	89.99
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	89.95
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	89.9
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	89.88
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	89.86
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	89.86
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	89.8
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	89.77
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	89.72
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	89.71
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	89.71
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	89.69
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	89.57
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	89.42
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	89.39
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	89.36
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	89.28
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	89.27
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	89.16
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	89.14
1nrj_B	218	SR-beta, signal recognition particle receptor beta	89.07
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	89.01
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	88.98
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	88.94
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	88.91
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	88.87
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	88.86
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	88.84
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	88.78
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	88.76
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	88.75
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	88.75
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	88.73
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	88.66
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	88.63
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	88.62
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	88.62
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	88.59
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	88.58
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	88.58
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	88.58
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	88.57
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	88.57
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	88.55
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	88.54
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	88.53
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	88.51
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	88.43
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	88.38
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	88.36
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	88.34
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	88.34

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=7.5e-44  Score=403.41  Aligned_cols=299  Identities=15%  Similarity=0.158  Sum_probs=237.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHh--hhccccCCCCEEEEEEe--------chHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNN--NFCHQQHNFDVVIWAAV--------QTFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~--~~~~~~~~F~~~~wv~v--------~~i~~~  223 (779)
                      +..+||++++++|.++|..+ +...++|+|+||||+||||||+++|+  +. +++.+|++++||++        ..++..
T Consensus       128 ~~~~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~-~~~~~F~~~~wv~vs~~~~~~~~~~~~~  206 (549)
T 2a5y_B          128 MTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQ-LIGINYDSIVWLKDSGTAPKSTFDLFTD  206 (549)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSS-TBTTTBSEEEEEECCCCSTTHHHHHHHH
T ss_pred             CccCCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhH-HHhccCCcEEEEEECCCCCCCHHHHHHH
Confidence            34359999999999999765 44689999999999999999999998  44 66899999999998        246778


Q ss_pred             HHHHhCCCcc----hhhhhcchhhHHHHHHHhhCCC-cceeehhhcccccc---ccCCCcEEEEEeCchhhhhhcC--Cc
Q 004021          224 IGKRIGFSED----KKWKEKSLQDKAVDISSILSPK-KFRIDLTELGVPLQ---MLNAGFKIVLKTRSAGVCDQMD--SK  293 (779)
Q Consensus       224 i~~~l~~~~~----~~~~~~~~~~~~~~l~~~L~~k-r~~~~ld~l~~~~~---~~~~gs~IivTTR~~~va~~~~--~~  293 (779)
                      |+.+++....    ......+.+++...+++.|+++ ||++++|+++..-.   ...+||+||||||+..|+..++  ..
T Consensus       207 il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~~~~gs~ilvTTR~~~v~~~~~~~~~  286 (549)
T 2a5y_B          207 ILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCE  286 (549)
T ss_dssp             HHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSCEE
T ss_pred             HHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhcccccCCCEEEEEcCCHHHHHHcCCCCe
Confidence            8888875411    0112234456788999999996 99999999976421   1338999999999999998875  36


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCC
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFS  373 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~  373 (779)
                      .|+|++|++++||+||.++++...  .++.+++++++|+++|+|+||||+++|+.++.+    .|... +.+....+...
T Consensus       287 ~~~l~~L~~~ea~~Lf~~~a~~~~--~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~----~w~~~-~~l~~~l~~~~  359 (549)
T 2a5y_B          287 FIEVTSLEIDECYDFLEAYGMPMP--VGEKEEDVLNKTIELSSGNPATLMMFFKSCEPK----TFEKM-AQLNNKLESRG  359 (549)
T ss_dssp             EEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSS----SHHHH-HHHHHHHHHHC
T ss_pred             EEECCCCCHHHHHHHHHHHhcCCC--CchhHHHHHHHHHHHhCCChHHHHHHHHHhccc----hHHHH-HHhHHHhhccc
Confidence            799999999999999999987653  246788899999999999999999999999764    25443 44444322211


Q ss_pred             CchHHHHHHHHHHHhcCCccchhhhhh-----------hccccCCCcccChHHHHHHHHHc--CCCcch-------hhHH
Q 004021          374 GMEENVFLRLKFSYDSLSMDKLRSCLL-----------YCCLYPEDYKIPKRSLIDYWISE--GFMADF-------DRGC  433 (779)
Q Consensus       374 ~~~~~i~~~l~~sy~~L~~~~~k~cf~-----------~~s~fp~~~~i~~~~Li~~W~a~--g~~~~~-------~~~~  433 (779)
                        ...+..++.+||+.||+ ++|.||+           |||+||+++.|+    +++|+|+  ||+...       +.+.
T Consensus       360 --~~~i~~~l~~Sy~~L~~-~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~~  432 (549)
T 2a5y_B          360 --LVGVECITPYSYKSLAM-ALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVAD  432 (549)
T ss_dssp             --SSTTCCCSSSSSSSHHH-HHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHHH
T ss_pred             --HHHHHHHHhcccccccH-HHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHHH
Confidence              13577788999999998 8999999           999999999999    8999999  888642       3444


Q ss_pred             HHHHHHHHccccccc---CCCcEEechHHHHHHHHHHhh
Q 004021          434 EFINDLLHACLLEEE---GDDHVKMHDMIREMSLWIAWT  469 (779)
Q Consensus       434 ~~l~~L~~~sll~~~---~~~~~~mHdlv~~~a~~~~~~  469 (779)
                       +|++|+++||++..   ...+|+|||+||+||++++.+
T Consensus       433 -~l~~L~~rsLl~~~~~~~~~~~~mHdlv~~~a~~~~~~  470 (549)
T 2a5y_B          433 -RLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDA  470 (549)
T ss_dssp             -HHHHTTTBSSCSEEECSSSCEEECCHHHHHHHHTTSCT
T ss_pred             -HHHHHHHcCCeeEecCCCceEEEeChHHHHHHHHHHHH
Confidence             99999999999986   345799999999999988866

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=4.3e-37  Score=385.74  Aligned_cols=305  Identities=16%  Similarity=0.256  Sum_probs=248.5

Q ss_pred             cccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccC-CCCEEEEEEec--------hHHHHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH-NFDVVIWAAVQ--------TFQDDI  224 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-~F~~~~wv~v~--------~i~~~i  224 (779)
                      .+.||||++++++|.++|...++..++|+|+||||+||||||+++|++...+.. .|+.++||++.        ..+..+
T Consensus       123 ~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~  202 (1249)
T 3sfz_A          123 PVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNL  202 (1249)
T ss_dssp             CSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHH
T ss_pred             CceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHH
Confidence            467999999999999999876667899999999999999999999998522244 45788899981        235556


Q ss_pred             HHHhCCCcc-hhhhhcchhhHHHHHHHhhCCC--cceeehhhcccc--ccccCCCcEEEEEeCchhhhhhc-C-CceeEc
Q 004021          225 GKRIGFSED-KKWKEKSLQDKAVDISSILSPK--KFRIDLTELGVP--LQMLNAGFKIVLKTRSAGVCDQM-D-SKNLEV  297 (779)
Q Consensus       225 ~~~l~~~~~-~~~~~~~~~~~~~~l~~~L~~k--r~~~~ld~l~~~--~~~~~~gs~IivTTR~~~va~~~-~-~~~~~l  297 (779)
                      +..+..... ......+.++....++..+.++  |+++++|++...  +...++||+||||||++.++..+ + ...+++
T Consensus       203 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~~~~~~ilvTtR~~~~~~~~~~~~~~~~~  282 (1249)
T 3sfz_A          203 CMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPV  282 (1249)
T ss_dssp             HHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTTCSSCEEEEEESSTTTTTTCCSCBCCEEC
T ss_pred             HHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhhcCCCEEEEEcCCHHHHHhhcCCceEEEe
Confidence            666654311 1112345677888899999887  999999998764  33457899999999999998653 4 678899


Q ss_pred             cC-CChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcC----
Q 004021          298 YS-LAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTF----  372 (779)
Q Consensus       298 ~~-L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~----  372 (779)
                      ++ |++++|++||...++...    +.+++++++|+++|+|+||||+++|++|+.+.  ..|...++.+....+..    
T Consensus       283 ~~~l~~~~a~~l~~~~~~~~~----~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~--~~~~~~l~~l~~~~~~~~~~~  356 (1249)
T 3sfz_A          283 ESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYLRQLQNKQFKRIRKS  356 (1249)
T ss_dssp             CSSCCHHHHHHHHHHHHTSCS----TTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS--SCHHHHHHHHHSCCCCCSSCT
T ss_pred             cCCCCHHHHHHHHHHhhCCCh----hhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh--hHHHHHHHHHhhhhhhhcccc
Confidence            96 999999999999885433    44567899999999999999999999998754  57999998887764321    


Q ss_pred             -CCchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHHHHHHcccccccCCC
Q 004021          373 -SGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEEGDD  451 (779)
Q Consensus       373 -~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~~L~~~sll~~~~~~  451 (779)
                       ....+.+..++.+||+.||+ ++|.||+|||+||+++.|+++.++.+|.+++     +.++.++++|+++||++....+
T Consensus       357 ~~~~~~~~~~~l~~s~~~L~~-~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~~-----~~~~~~l~~L~~~sl~~~~~~~  430 (1249)
T 3sfz_A          357 SSYDYEALDEAMSISVEMLRE-DIKDYYTDLSILQKDVKVPTKVLCVLWDLET-----EEVEDILQEFVNKSLLFCNRNG  430 (1249)
T ss_dssp             TCTTHHHHHHHHHHHHHTSCT-TTHHHHHHGGGSCTTCCEEHHHHHHHHTCCH-----HHHHHHHHHHHHTTSCEEEESS
T ss_pred             cccchHHHHHHHHHHHHhCCH-HHHHHHHHhCccCCCCeeCHHHHHHHhCCCH-----HHHHHHHHHHHhccceEEecCC
Confidence             11225799999999999999 8999999999999999999999999997764     7889999999999999987333


Q ss_pred             ---cEEechHHHHHHHHHHhhh
Q 004021          452 ---HVKMHDMIREMSLWIAWTI  470 (779)
Q Consensus       452 ---~~~mHdlv~~~a~~~~~~~  470 (779)
                         +|+|||+||+||+..+.++
T Consensus       431 ~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          431 KSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             SSEEEECCHHHHHHHHHHTGGG
T ss_pred             CceEEEecHHHHHHHHhhhhHH
Confidence               5999999999999987654

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=1.6e-36  Score=345.73  Aligned_cols=279  Identities=15%  Similarity=0.204  Sum_probs=219.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCE-EEEEEe------chHHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDV-VIWAAV------QTFQDDIGKR  227 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~-~~wv~v------~~i~~~i~~~  227 (779)
                      +..|||++++++|.++|...+ ..++|+|+||||+||||||+++|++. +++.+|+. ++|+++      ..++..|+..
T Consensus       128 k~~VGRe~eLeeL~elL~~~d-~~RVV~IvGmGGIGKTTLAk~Vy~d~-rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~l  205 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSY-KVQCKMDFKIFWLNLKNCNSPETVLEMLQKL  205 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHHCC-SSCEEEECCSTTSSHHHHHHHHHHHC-HHHHHHSSCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhccC-CCeEEEEEcCCCccHHHHHHHHHHhh-HHHHhCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            345999999999999998643 47999999999999999999999876 66788986 999999      3455555554


Q ss_pred             hCCCc---chh-----hhhcchhhHHHHHHHhh---CCCcceeehhhcccccc--ccCCCcEEEEEeCchhhhhhcC-Cc
Q 004021          228 IGFSE---DKK-----WKEKSLQDKAVDISSIL---SPKKFRIDLTELGVPLQ--MLNAGFKIVLKTRSAGVCDQMD-SK  293 (779)
Q Consensus       228 l~~~~---~~~-----~~~~~~~~~~~~l~~~L---~~kr~~~~ld~l~~~~~--~~~~gs~IivTTR~~~va~~~~-~~  293 (779)
                      ++...   ...     ....+.++....+++.|   .++|+++++||+.....  ...+||+||||||++.++..+. ..
T Consensus       206 L~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~pGSRILVTTRd~~Va~~l~g~~  285 (1221)
T 1vt4_I          206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT  285 (1221)
T ss_dssp             HHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHHSSCCEEEECSCSHHHHHHHHHS
T ss_pred             HhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhCCCeEEEEeccChHHHHhcCCCe
Confidence            32110   000     01123445566777766   78999999999876421  2348999999999999987554 44


Q ss_pred             eeEcc------CCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCC-ChhHHHHHHHHHh
Q 004021          294 NLEVY------SLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQK-KVGDRERAIEKMR  366 (779)
Q Consensus       294 ~~~l~------~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~-~~~~w~~~~~~l~  366 (779)
                      .|.++      +|+.+|||+||.+.....       ..++..+|   |+|+||||+++|+.|+.+. +..+|...     
T Consensus       286 vy~LeL~d~dL~LS~eEA~eLF~~~~g~~-------~eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~~-----  350 (1221)
T 1vt4_I          286 TTHISLDHHSMTLTPDEVKSLLLKYLDCR-------PQDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHV-----  350 (1221)
T ss_dssp             SCEEEECSSSSCCCHHHHHHHHHHHHCCC-------TTTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHHC-----
T ss_pred             EEEecCccccCCcCHHHHHHHHHHHcCCC-------HHHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhcC-----
Confidence            67777      999999999999984321       12334444   9999999999999999863 67788652     


Q ss_pred             cccCcCCCchHHHHHHHHHHHhcCCccch-hhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHHHHHHcccc
Q 004021          367 TSASTFSGMEENVFLRLKFSYDSLSMDKL-RSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLL  445 (779)
Q Consensus       367 ~~~~~~~~~~~~i~~~l~~sy~~L~~~~~-k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~~L~~~sll  445 (779)
                              ....+..+|.+||+.||+ +. |.||++||+||+++.|+++.++.+|+++|.    +.+..+|++|+++||+
T Consensus       351 --------~~~~I~aaLelSYd~Lp~-eelK~cFL~LAIFPed~~I~~elLa~LW~aeGe----edAe~~L~eLvdRSLL  417 (1221)
T 1vt4_I          351 --------NCDKLTTIIESSLNVLEP-AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIK----SDVMVVVNKLHKYSLV  417 (1221)
T ss_dssp             --------SCHHHHHHHHHHHHHSCT-THHHHHHHHTTSSCTTSCEEHHHHHHHHCSSCS----HHHHHHHHHHHTSSSS
T ss_pred             --------ChhHHHHHHHHHHHhCCH-HHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCCH----HHHHHHHHHHHhhCCE
Confidence                    125899999999999999 78 999999999999999999999999999872    5688999999999999


Q ss_pred             ccc-CCCcEEechHHHHHH
Q 004021          446 EEE-GDDHVKMHDMIREMS  463 (779)
Q Consensus       446 ~~~-~~~~~~mHdlv~~~a  463 (779)
                      +.. ...+|+|||++++++
T Consensus       418 q~d~~~~rYrMHDLllELr  436 (1221)
T 1vt4_I          418 EKQPKESTISIPSIYLELK  436 (1221)
T ss_dssp             SBCSSSSEEBCCCHHHHHH
T ss_pred             EEeCCCCEEEehHHHHHHh
Confidence            986 467899999999855

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=6.6e-34  Score=327.16  Aligned_cols=301  Identities=16%  Similarity=0.266  Sum_probs=235.7

Q ss_pred             cccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc-cCCC-CEEEEEEe-----chHHHHH--
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ-QHNF-DVVIWAAV-----QTFQDDI--  224 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~~F-~~~~wv~v-----~~i~~~i--  224 (779)
                      .+.||||+.++++|.++|....+..++|+|+||||+||||||++++++. .+ ..+| ++++|+++     ..+...+  
T Consensus       123 ~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~-~~~~~~f~~~v~wv~~~~~~~~~~~~~l~~  201 (591)
T 1z6t_A          123 PVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDH-SLLEGCFPGGVHWVSVGKQDKSGLLMKLQN  201 (591)
T ss_dssp             CSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCH-HHHHHHCTTCEEEEEEESCCHHHHHHHHHH
T ss_pred             CCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhch-hHHHhhCCCceEEEECCCCchHHHHHHHHH
Confidence            3679999999999999998655578999999999999999999999886 44 5678 58999999     2233333  


Q ss_pred             -HHHhCCCcc-hhhhhcchhhHHHHHHHhhCC--Ccceeehhhcccc--ccccCCCcEEEEEeCchhhhhhcCCceeEc-
Q 004021          225 -GKRIGFSED-KKWKEKSLQDKAVDISSILSP--KKFRIDLTELGVP--LQMLNAGFKIVLKTRSAGVCDQMDSKNLEV-  297 (779)
Q Consensus       225 -~~~l~~~~~-~~~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l~~~--~~~~~~gs~IivTTR~~~va~~~~~~~~~l-  297 (779)
                       +..++.... ......+.+.....+...+.+  +++++++||+...  +....+|++||||||+..++..++...+++ 
T Consensus       202 l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l~~~~~ilvTsR~~~~~~~~~~~~~~v~  281 (591)
T 1z6t_A          202 LCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVP  281 (591)
T ss_dssp             HHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTTCSSCEEEEEESCGGGGTTCCSCEEEEE
T ss_pred             HHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHhcCCCeEEEECCCcHHHHhcCCCceEee
Confidence             334442100 011234556677778888876  7899999998543  233468999999999999887655344554 


Q ss_pred             --cCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCc----
Q 004021          298 --YSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSAST----  371 (779)
Q Consensus       298 --~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~----  371 (779)
                        ++|+.+||++||...++...    ....+.+.+|+++|+|+||||..+|+.++.+  ..+|...++.+......    
T Consensus       282 ~l~~L~~~ea~~L~~~~~~~~~----~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~--~~~w~~~l~~l~~~~~~~~~~  355 (591)
T 1z6t_A          282 VESSLGKEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGALLRDF--PNRWEYYLKQLQNKQFKRIRK  355 (591)
T ss_dssp             CCSSCCHHHHHHHHHHHHTSCG----GGSCTHHHHHHHHHTTCHHHHHHHHHHHHHS--TTCHHHHHHHHHSCCCCCSSC
T ss_pred             cCCCCCHHHHHHHHHHHhCCCc----ccccHHHHHHHHHhCCCcHHHHHHHHHHhcC--chhHHHHHHHHHHhHHHHhhh
Confidence              58999999999999987532    2234678999999999999999999999874  34799888888765322    


Q ss_pred             -CCCchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCcchhhHHHHHHHHHHccccccc--
Q 004021          372 -FSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMADFDRGCEFINDLLHACLLEEE--  448 (779)
Q Consensus       372 -~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~~~~~~~~~l~~L~~~sll~~~--  448 (779)
                       .......+..++..||+.||+ +.|.||++||+||+++.|+.+.+..+|.+++     +.+..++++|+++||++..  
T Consensus       356 ~~~~~~~~l~~~l~~s~~~L~~-~~~~~l~~la~f~~~~~i~~~~l~~l~~~~~-----~~~~~~l~~L~~~~Ll~~~~~  429 (591)
T 1z6t_A          356 SSSYDYEALDEAMSISVEMLRE-DIKDYYTDLSILQKDVKVPTKVLCILWDMET-----EEVEDILQEFVNKSLLFCDRN  429 (591)
T ss_dssp             CCSSCCHHHHHHHHHHHHTSCT-TTHHHHHHGGGCCTTCCEEHHHHHHHHTCCH-----HHHHHHHHHHHHTTSSEEEEE
T ss_pred             ccccchHHHHHHHHHHHHhCCH-HHHHHHHHccccCCCCccCHHHHHHHhccCH-----HHHHHHHHHHHhCcCeEEecC
Confidence             112235899999999999999 8999999999999999999999999997653     5678899999999999865  


Q ss_pred             -CCCcEEechHHHHHHHHHH
Q 004021          449 -GDDHVKMHDMIREMSLWIA  467 (779)
Q Consensus       449 -~~~~~~mHdlv~~~a~~~~  467 (779)
                       ...+|+||+++|++++...
T Consensus       430 ~~~~~~~~H~lv~~~~~~~~  449 (591)
T 1z6t_A          430 GKSFRYYLHDLQVDFLTEKN  449 (591)
T ss_dssp             TTEEEEECCHHHHHHHHHHT
T ss_pred             CCccEEEEcHHHHHHHHhhh
Confidence             2347999999999999874

>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=99.86  E-value=3e-21  Score=203.96  Aligned_cols=222  Identities=20%  Similarity=0.294  Sum_probs=182.2

Q ss_pred             CCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccC
Q 004021          495 EGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEY  568 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~  568 (779)
                      ..++.|++++|.+..+|....      .|+|++| .+..+|..++++++|++|+|++|.++.+|..++++++|++|++++
T Consensus        81 ~~l~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~n-~l~~lp~~~~~l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L~L~~  159 (328)
T 4fcg_A           81 PGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAA-GLMELPDTMQQFAGLETLTLARNPLRALPASIASLNRLRELSIRA  159 (328)
T ss_dssp             TTCCEEEEESSCCSSCCSCGGGGTTCSEEEEESS-CCCCCCSCGGGGTTCSEEEEESCCCCCCCGGGGGCTTCCEEEEEE
T ss_pred             cceeEEEccCCCchhcChhhhhCCCCCEEECCCC-CccchhHHHhccCCCCEEECCCCccccCcHHHhcCcCCCEEECCC
Confidence            578899999999888876432      3899999 888999999999999999999999999999999999999999999


Q ss_pred             CcCCCCCchhhhcC---------CccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccccc
Q 004021          569 THYLSIIPHQLISG---------FLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK  639 (779)
Q Consensus       569 ~~~l~~lp~~~i~~---------L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~  639 (779)
                      |..++.+|.. ++.         +++|++|++++|.+..               .+..++.+++|+.|+++.|...    
T Consensus       160 n~~~~~~p~~-~~~~~~~~~~~~l~~L~~L~L~~n~l~~---------------lp~~l~~l~~L~~L~L~~N~l~----  219 (328)
T 4fcg_A          160 CPELTELPEP-LASTDASGEHQGLVNLQSLRLEWTGIRS---------------LPASIANLQNLKSLKIRNSPLS----  219 (328)
T ss_dssp             ETTCCCCCSC-SEEEC-CCCEEESTTCCEEEEEEECCCC---------------CCGGGGGCTTCCEEEEESSCCC----
T ss_pred             CCCccccChh-HhhccchhhhccCCCCCEEECcCCCcCc---------------chHhhcCCCCCCEEEccCCCCC----
Confidence            8788888886 554         9999999999998764               4456788999999999966433    


Q ss_pred             CCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCC
Q 004021          640 FFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFP  719 (779)
Q Consensus       640 ~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~  719 (779)
                           .+ ++.++.+++|+.|+|++|+..+.++.                .++.+++|+.|+|++|+.++.+|..+..++
T Consensus       220 -----~l-~~~l~~l~~L~~L~Ls~n~~~~~~p~----------------~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~  277 (328)
T 4fcg_A          220 -----AL-GPAIHHLPKLEELDLRGCTALRNYPP----------------IFGGRAPLKRLILKDCSNLLTLPLDIHRLT  277 (328)
T ss_dssp             -----CC-CGGGGGCTTCCEEECTTCTTCCBCCC----------------CTTCCCCCCEEECTTCTTCCBCCTTGGGCT
T ss_pred             -----cC-chhhccCCCCCEEECcCCcchhhhHH----------------HhcCCCCCCEEECCCCCchhhcchhhhcCC
Confidence                 32 34678899999999999988776654                678899999999999999999999999999


Q ss_pred             CccEEeeeCCCCCCCCCCCCCCccc-ccEEEechHhhhhhCcc
Q 004021          720 KLKKIGVYGCPKLKKLPINSSSAKE-RRVVIEGLKEWWEELQW  761 (779)
Q Consensus       720 ~L~~L~l~~c~~L~~lP~~~~~~~~-~~l~i~~~~~~~~~l~w  761 (779)
                      +|++|++++|+.++.+|..+...+. +.+.+.  ..+.+.+.+
T Consensus       278 ~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~l~--~~~~~~l~~  318 (328)
T 4fcg_A          278 QLEKLDLRGCVNLSRLPSLIAQLPANCIILVP--PHLQAQLDQ  318 (328)
T ss_dssp             TCCEEECTTCTTCCCCCGGGGGSCTTCEEECC--GGGSCC---
T ss_pred             CCCEEeCCCCCchhhccHHHhhccCceEEeCC--HHHHHHHhh
Confidence            9999999999999999988766544 444433  444444433

>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=99.80  E-value=1.7e-19  Score=190.53  Aligned_cols=201  Identities=21%  Similarity=0.291  Sum_probs=166.4

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .|+|++| .+..+|..++++++|++|+|++|.++.+|..++++++|++|++++| .+..+|.. ++++++|++|++++|.
T Consensus        85 ~L~L~~n-~l~~lp~~l~~l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~n-~l~~lp~~-l~~l~~L~~L~L~~n~  161 (328)
T 4fcg_A           85 ALELRSV-PLPQFPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARN-PLRALPAS-IASLNRLRELSIRACP  161 (328)
T ss_dssp             EEEEESS-CCSSCCSCGGGGTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEESC-CCCCCCGG-GGGCTTCCEEEEEEET
T ss_pred             EEEccCC-CchhcChhhhhCCCCCEEECCCCCccchhHHHhccCCCCEEECCCC-ccccCcHH-HhcCcCCCEEECCCCC
Confidence            4899999 9999999999999999999999999999999999999999999999 67899997 9999999999999987


Q ss_pred             CCC-cccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccc
Q 004021          596 SEG-VTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       596 ~~~-~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      ..+ +|..+..      ......++.+++|+.|+++.|...         .+ +.+++.+++|+.|+|++|... .++. 
T Consensus       162 ~~~~~p~~~~~------~~~~~~~~~l~~L~~L~L~~n~l~---------~l-p~~l~~l~~L~~L~L~~N~l~-~l~~-  223 (328)
T 4fcg_A          162 ELTELPEPLAS------TDASGEHQGLVNLQSLRLEWTGIR---------SL-PASIANLQNLKSLKIRNSPLS-ALGP-  223 (328)
T ss_dssp             TCCCCCSCSEE------EC-CCCEEESTTCCEEEEEEECCC---------CC-CGGGGGCTTCCEEEEESSCCC-CCCG-
T ss_pred             CccccChhHhh------ccchhhhccCCCCCEEECcCCCcC---------cc-hHhhcCCCCCCEEEccCCCCC-cCch-
Confidence            654 1211110      011123556999999999977543         22 456888999999999997643 3433 


Q ss_pred             ccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc-ccEEEech
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE-RRVVIEGL  752 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~-~~l~i~~~  752 (779)
                                     .++.+++|+.|++++|+....+|..++.+++|++|++++|+.+..+|..+...+. +.+.+.+|
T Consensus       224 ---------------~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~~~~l~~L~~L~L~~n  287 (328)
T 4fcg_A          224 ---------------AIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGC  287 (328)
T ss_dssp             ---------------GGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTTGGGCTTCCEEECTTC
T ss_pred             ---------------hhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchhhhcCCCCCEEeCCCC
Confidence                           5678999999999999888999999999999999999999999999987765544 89999876

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.74  E-value=9.8e-18  Score=182.03  Aligned_cols=252  Identities=17%  Similarity=0.141  Sum_probs=122.8

Q ss_pred             cccCCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCc
Q 004021          492 KEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLR  562 (779)
Q Consensus       492 ~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~  562 (779)
                      ..+++++.|++.+|.+..++...     .  .|+|++| .+..+ |..|+++++|++|++++|.++.+|.. ++++++|+
T Consensus        66 ~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~  144 (390)
T 3o6n_A           66 DSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFN-AIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLT  144 (390)
T ss_dssp             HHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             cccccCcEEECCCCcccccChhhccCCCCcCEEECCCC-CCCcCCHHHhcCCCCCCEEECCCCccCcCCHHHhcCCCCCc
Confidence            34456666666666655544311     1  2666666 55555 33456666666666666666666655 36666666


Q ss_pred             EeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCC--CchhhHHhhcCCCCCCceeEEeeccccc--c
Q 004021          563 YLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCD--DAEPLMRELLGLKRLNVLSWSFRSSLAV--Q  638 (779)
Q Consensus       563 ~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~L~~L~~L~l~~~~~~~~--~  638 (779)
                      +|++++| .+..+++..++++++|++|++++|.+..++......+..  .....+..+...++|+.|+++.+....+  .
T Consensus       145 ~L~L~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~L~~L~l~~n~l~~~~~~~~L~~L~l~~n~l~~~~~~  223 (390)
T 3o6n_A          145 TLSMSNN-NLERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIPSLFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGP  223 (390)
T ss_dssp             EEECCSS-CCCBCCTTTTSSCTTCCEEECCSSCCSBCCGGGCTTCSEEECCSSCCSEEECCSSCSEEECCSSCCCEEECC
T ss_pred             EEECCCC-ccCccChhhccCCCCCCEEECCCCcCCccccccccccceeecccccccccCCCCcceEEECCCCeeeecccc
Confidence            6666666 345554444566666666666666555422111100000  0000001111222333333333322211  1


Q ss_pred             cCCCCCcc--------cCcccccccCcceEEeccccccceeccccc-----------ccCcccchhhccCCCCCCCCccE
Q 004021          639 KFFKYPKL--------DLTWLVFVQNLKELEIIVCTEMEEIICVDK-----------LRDVSDISEIIGSEHNFFTQLES  699 (779)
Q Consensus       639 ~~~~L~~L--------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~L~~  699 (779)
                      .+++|+.|        .++++..+++|+.|+|++|......+....           ...+..++    .....+++|+.
T Consensus       224 ~~~~L~~L~l~~n~l~~~~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~----~~~~~l~~L~~  299 (390)
T 3o6n_A          224 VNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVALN----LYGQPIPTLKV  299 (390)
T ss_dssp             CCSSCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSCCEEECCSSCCCEEE----CSSSCCTTCCE
T ss_pred             ccccccEEECCCCCCcccHHHcCCCCccEEECCCCcCCCcChhHccccccCCEEECCCCcCcccC----cccCCCCCCCE
Confidence            12233333        223455566666666666543222221000           00001111    23455677777


Q ss_pred             EEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          700 LGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       700 L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      |+++++ .+..++.....+++|++|++++|+ +..+|.. ....++.+.+.++
T Consensus       300 L~L~~n-~l~~~~~~~~~l~~L~~L~L~~N~-i~~~~~~-~~~~L~~L~l~~N  349 (390)
T 3o6n_A          300 LDLSHN-HLLHVERNQPQFDRLENLYLDHNS-IVTLKLS-THHTLKNLTLSHN  349 (390)
T ss_dssp             EECCSS-CCCCCGGGHHHHTTCSEEECCSSC-CCCCCCC-TTCCCSEEECCSS
T ss_pred             EECCCC-cceecCccccccCcCCEEECCCCc-cceeCch-hhccCCEEEcCCC
Confidence            777764 566666666667777777777764 6666632 2234477777653

>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=99.74  E-value=1e-17  Score=192.21  Aligned_cols=263  Identities=16%  Similarity=0.152  Sum_probs=150.5

Q ss_pred             cCcccccCcc--ccccCCccEEEcccccccccccCc-----c--cccccccccccccch-hhcccccCceeeecCCcccc
Q 004021          481 AGVKLTEAPK--VKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRG  550 (779)
Q Consensus       481 ~~~~~~~~~~--~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~  550 (779)
                      .+..+..+|.  +..++.++.|++++|.+..++...     .  .|+|++| .+..+|+ .|+++++|++|+|++|.++.
T Consensus        59 ~~~~l~~lp~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~  137 (597)
T 3oja_B           59 KNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFN-AIRYLPPHVFQNVPLLTVLVLERNDLSS  137 (597)
T ss_dssp             SSCEESEECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCC
T ss_pred             eCCCCCCcCHHHHccCCCCcEEECCCCCCCCCChHHhcCCCCCCEEECCCC-cCCCCCHHHHcCCCCCCEEEeeCCCCCC
Confidence            3333444443  345678888888888887765421     1  3888888 7777744 46888888888888888888


Q ss_pred             cchh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccC--CCchhhHHhhcCCCCCCce
Q 004021          551 LPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLC--DDAEPLMRELLGLKRLNVL  627 (779)
Q Consensus       551 lp~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~L~~L~~L  627 (779)
                      +|.. |+++++|++|++++| .+..+|+..++++++|++|++++|.+..++......+.  +.....+..+....+|+.|
T Consensus       138 l~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~l~~L~~L~l~~n~l~~l~~~~~L~~L  216 (597)
T 3oja_B          138 LPRGIFHNTPKLTTLSMSNN-NLERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIPSLFHANVSYNLLSTLAIPIAVEEL  216 (597)
T ss_dssp             CCTTTTTTCTTCCEEECCSS-CCCBCCTTTTTTCTTCCEEECTTSCCSBCCGGGCTTCSEEECCSSCCSEEECCTTCSEE
T ss_pred             CCHHHhccCCCCCEEEeeCC-cCCCCChhhhhcCCcCcEEECcCCCCCCcChhhhhhhhhhhcccCccccccCCchhhee
Confidence            8876 488888888888888 56666665588888888888888877764322111000  0000011122233344444


Q ss_pred             eEEeeccccc--ccCCCCCcc--------cCcccccccCcceEEeccccccceeccccc-----------ccCcccchhh
Q 004021          628 SWSFRSSLAV--QKFFKYPKL--------DLTWLVFVQNLKELEIIVCTEMEEIICVDK-----------LRDVSDISEI  686 (779)
Q Consensus       628 ~l~~~~~~~~--~~~~~L~~L--------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~-----------~~~~~~~~~~  686 (779)
                      +++.|....+  ...++|+.|        .++++..+++|+.|+|++|.....++....           ...+..++  
T Consensus       217 ~ls~n~l~~~~~~~~~~L~~L~L~~n~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~l~--  294 (597)
T 3oja_B          217 DASHNSINVVRGPVNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVALN--  294 (597)
T ss_dssp             ECCSSCCCEEECSCCSCCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSCCEEECTTSCCCEEE--
T ss_pred             eccCCcccccccccCCCCCEEECCCCCCCCChhhccCCCCCEEECCCCccCCCCHHHhcCccCCCEEECCCCCCCCCC--
Confidence            4444433222  111233333        234455566666666666443322221000           00001111  


Q ss_pred             ccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          687 IGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       687 ~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                        .....+++|+.|+|+++ .+..+|..+..+++|+.|++++|+ +..+|... ...++.+.+.++
T Consensus       295 --~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~l~~L~~L~L~~N~-l~~~~~~~-~~~L~~L~l~~N  355 (597)
T 3oja_B          295 --LYGQPIPTLKVLDLSHN-HLLHVERNQPQFDRLENLYLDHNS-IVTLKLST-HHTLKNLTLSHN  355 (597)
T ss_dssp             --CSSSCCTTCCEEECCSS-CCCCCGGGHHHHTTCSEEECCSSC-CCCCCCCT-TCCCSEEECCSS
T ss_pred             --cccccCCCCcEEECCCC-CCCccCcccccCCCCCEEECCCCC-CCCcChhh-cCCCCEEEeeCC
Confidence              23455777777777774 556666666677778888887764 66666332 234577777653

>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=99.72  E-value=1.5e-16  Score=168.48  Aligned_cols=225  Identities=16%  Similarity=0.169  Sum_probs=155.5

Q ss_pred             CCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccchhhccCccCcEeec
Q 004021          495 EGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNL  566 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l  566 (779)
                      ..++.|++++|.+..++..     +.  .|+|++| .+..+ |..|+++++|++|++++|.++.+|..+.  ++|++|++
T Consensus        52 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~--~~L~~L~l  128 (330)
T 1xku_A           52 PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINN-KISKISPGAFAPLVKLERLYLSKNQLKELPEKMP--KTLQELRV  128 (330)
T ss_dssp             TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCC--TTCCEEEC
T ss_pred             CCCeEEECCCCcCCEeChhhhccCCCCCEEECCCC-cCCeeCHHHhcCCCCCCEEECCCCcCCccChhhc--ccccEEEC
Confidence            4677777777777666542     11  3777777 66665 6677777777777777777777776654  67777777


Q ss_pred             cCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccc--cCCCCC
Q 004021          567 EYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ--KFFKYP  644 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~--~~~~L~  644 (779)
                      ++| .+..++...+.++++|++|++++|.+..            ....+..+..+++|+.|+++.+....++  ..++|+
T Consensus       129 ~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~------------~~~~~~~~~~l~~L~~L~l~~n~l~~l~~~~~~~L~  195 (330)
T 1xku_A          129 HEN-EITKVRKSVFNGLNQMIVVELGTNPLKS------------SGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLT  195 (330)
T ss_dssp             CSS-CCCBBCHHHHTTCTTCCEEECCSSCCCG------------GGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCS
T ss_pred             CCC-cccccCHhHhcCCccccEEECCCCcCCc------------cCcChhhccCCCCcCEEECCCCccccCCccccccCC
Confidence            777 5666666557777788888777776642            1234456777888888888877665442  124555


Q ss_pred             cc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC
Q 004021          645 KL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN  714 (779)
Q Consensus       645 ~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~  714 (779)
                      .|          .+..+..+++|+.|+|++|.. ..++.               ..+..+++|+.|+++++ .+..+|..
T Consensus       196 ~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l-~~~~~---------------~~~~~l~~L~~L~L~~N-~l~~lp~~  258 (330)
T 1xku_A          196 ELHLDGNKITKVDAASLKGLNNLAKLGLSFNSI-SAVDN---------------GSLANTPHLRELHLNNN-KLVKVPGG  258 (330)
T ss_dssp             EEECTTSCCCEECTGGGTTCTTCCEEECCSSCC-CEECT---------------TTGGGSTTCCEEECCSS-CCSSCCTT
T ss_pred             EEECCCCcCCccCHHHhcCCCCCCEEECCCCcC-ceeCh---------------hhccCCCCCCEEECCCC-cCccCChh
Confidence            55          345677888999999988654 44433               35678899999999985 67888888


Q ss_pred             CCCCCCccEEeeeCCCCCCCCCCCCCC--------cccccEEEechH
Q 004021          715 PLHFPKLKKIGVYGCPKLKKLPINSSS--------AKERRVVIEGLK  753 (779)
Q Consensus       715 ~~~l~~L~~L~l~~c~~L~~lP~~~~~--------~~~~~l~i~~~~  753 (779)
                      +..+++|++|++++| .++.+|.....        .....+.+.+.+
T Consensus       259 l~~l~~L~~L~l~~N-~i~~~~~~~f~~~~~~~~~~~l~~l~l~~N~  304 (330)
T 1xku_A          259 LADHKYIQVVYLHNN-NISAIGSNDFCPPGYNTKKASYSGVSLFSNP  304 (330)
T ss_dssp             TTTCSSCCEEECCSS-CCCCCCTTSSSCSSCCTTSCCCSEEECCSSS
T ss_pred             hccCCCcCEEECCCC-cCCccChhhcCCcccccccccccceEeecCc
Confidence            889999999999987 48888754321        223566666543

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.71  E-value=1e-16  Score=164.46  Aligned_cols=193  Identities=22%  Similarity=0.271  Sum_probs=155.6

Q ss_pred             CccEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCcccccchh-hccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~  569 (779)
                      ..+.++++++.+..+|...+    .|+|++| .+..+|. .|.++++|++|++++|.++.+|.. +.++++|++|++++|
T Consensus        17 ~~~~l~~~~~~l~~ip~~~~~~l~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n   95 (270)
T 2o6q_A           17 NKNSVDCSSKKLTAIPSNIPADTKKLDLQSN-KLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDN   95 (270)
T ss_dssp             TTTEEECTTSCCSSCCSCCCTTCSEEECCSS-CCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCSS
T ss_pred             CCCEEEccCCCCCccCCCCCCCCCEEECcCC-CCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEECCCC
Confidence            46789999998888876432    5999999 8888865 799999999999999999999876 488999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLT  649 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~  649 (779)
                       .+..+|...+.++++|++|++++|.+..              ..+..++.+++|+.|+++.|         +++.+...
T Consensus        96 -~l~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~Ls~n---------~l~~~~~~  151 (270)
T 2o6q_A           96 -KLQALPIGVFDQLVNLAELRLDRNQLKS--------------LPPRVFDSLTKLTYLSLGYN---------ELQSLPKG  151 (270)
T ss_dssp             -CCCCCCTTTTTTCSSCCEEECCSSCCCC--------------CCTTTTTTCTTCCEEECCSS---------CCCCCCTT
T ss_pred             -cCCcCCHhHcccccCCCEEECCCCccCe--------------eCHHHhCcCcCCCEEECCCC---------cCCccCHh
Confidence             6788888768899999999999998875              23345778899999999854         34444445


Q ss_pred             ccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeC
Q 004021          650 WLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYG  728 (779)
Q Consensus       650 ~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~  728 (779)
                      .+..+++|+.|+|++|. +..++.               ..+..+++|+.|+++++ .++.++.. +..+++|+.|++++
T Consensus       152 ~~~~l~~L~~L~L~~n~-l~~~~~---------------~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~  214 (270)
T 2o6q_A          152 VFDKLTSLKELRLYNNQ-LKRVPE---------------GAFDKLTELKTLKLDNN-QLKRVPEGAFDSLEKLKMLQLQE  214 (270)
T ss_dssp             TTTTCTTCCEEECCSSC-CSCCCT---------------TTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCS
T ss_pred             HccCCcccceeEecCCc-CcEeCh---------------hHhccCCCcCEEECCCC-cCCcCCHHHhccccCCCEEEecC
Confidence            57788999999999864 444433               35678899999999985 67777764 56789999999998


Q ss_pred             CC
Q 004021          729 CP  730 (779)
Q Consensus       729 c~  730 (779)
                      +|
T Consensus       215 N~  216 (270)
T 2o6q_A          215 NP  216 (270)
T ss_dssp             SC
T ss_pred             CC
Confidence            76

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.71  E-value=1.1e-17  Score=175.60  Aligned_cols=223  Identities=13%  Similarity=0.146  Sum_probs=138.6

Q ss_pred             CccEEEcccccccc---cccCcc------cccccc-ccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcE
Q 004021          496 GAKRISLMANEIES---LSEIPT------LLSLRR-NDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRY  563 (779)
Q Consensus       496 ~lr~l~l~~~~~~~---l~~~~~------lL~L~~-~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~  563 (779)
                      .++.|++++|.+..   +|....      .|+|++ | .+. .+|..|+++++|++|++++|.++ .+|..+.++++|++
T Consensus        51 ~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n-~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~  129 (313)
T 1ogq_A           51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGIN-NLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEET-TEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             eEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCC-cccccCChhHhcCCCCCEEECcCCeeCCcCCHHHhCCCCCCE
Confidence            56677777776653   333211      367774 5 444 56777777777777777777776 56777777777777


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCC-CCCceeEEeeccc-----cc
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLK-RLNVLSWSFRSSL-----AV  637 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~-~L~~L~l~~~~~~-----~~  637 (779)
                      |++++|.....+|.. ++++++|++|++++|.+.+              ..+..+..++ +|+.|+++.|...     .+
T Consensus       130 L~Ls~N~l~~~~p~~-~~~l~~L~~L~L~~N~l~~--------------~~p~~l~~l~~~L~~L~L~~N~l~~~~~~~~  194 (313)
T 1ogq_A          130 LDFSYNALSGTLPPS-ISSLPNLVGITFDGNRISG--------------AIPDSYGSFSKLFTSMTISRNRLTGKIPPTF  194 (313)
T ss_dssp             EECCSSEEESCCCGG-GGGCTTCCEEECCSSCCEE--------------ECCGGGGCCCTTCCEEECCSSEEEEECCGGG
T ss_pred             EeCCCCccCCcCChH-HhcCCCCCeEECcCCcccC--------------cCCHHHhhhhhcCcEEECcCCeeeccCChHH
Confidence            777777433356665 7777777777777776652              2344555555 6666666655432     11


Q ss_pred             ccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCC
Q 004021          638 QKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPD  707 (779)
Q Consensus       638 ~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~  707 (779)
                      ..++ |+.|          .+..+..+++|+.|+|++|.....+                 ..+..+++|++|+++++.-
T Consensus       195 ~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~-----------------~~~~~l~~L~~L~Ls~N~l  256 (313)
T 1ogq_A          195 ANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDL-----------------GKVGLSKNLNGLDLRNNRI  256 (313)
T ss_dssp             GGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCBG-----------------GGCCCCTTCCEEECCSSCC
T ss_pred             hCCc-ccEEECcCCcccCcCCHHHhcCCCCCEEECCCCceeeec-----------------CcccccCCCCEEECcCCcc
Confidence            2222 4433          3345667788888888876543222                 1355678888888887543


Q ss_pred             CccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          708 LKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       708 l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      ...+|..+..+++|++|++++|+--..+|.......++.+.+.++
T Consensus       257 ~~~~p~~l~~l~~L~~L~Ls~N~l~~~ip~~~~l~~L~~l~l~~N  301 (313)
T 1ogq_A          257 YGTLPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYANN  301 (313)
T ss_dssp             EECCCGGGGGCTTCCEEECCSSEEEEECCCSTTGGGSCGGGTCSS
T ss_pred             cCcCChHHhcCcCCCEEECcCCcccccCCCCccccccChHHhcCC
Confidence            336677777888888888888764446776533333455555444

>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=99.71  E-value=7.6e-17  Score=166.86  Aligned_cols=196  Identities=19%  Similarity=0.144  Sum_probs=161.5

Q ss_pred             ccccCCccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccchhhccCccCcEee
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLN  565 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~  565 (779)
                      ...+.+++.+++.++.+..+|...+    .|+|++| .+..+ |..|.++++|++|+|++|.++.+|.. +.+++|++|+
T Consensus         6 ~~~l~~l~~l~~~~~~l~~ip~~~~~~l~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~-~~l~~L~~L~   83 (290)
T 1p9a_G            6 VSKVASHLEVNCDKRNLTALPPDLPKDTTILHLSEN-LLYTFSLATLMPYTRLTQLNLDRAELTKLQVD-GTLPVLGTLD   83 (290)
T ss_dssp             EECSTTCCEEECTTSCCSSCCSCCCTTCCEEECTTS-CCSEEEGGGGTTCTTCCEEECTTSCCCEEECC-SCCTTCCEEE
T ss_pred             ccccCCccEEECCCCCCCcCCCCCCCCCCEEEcCCC-cCCccCHHHhhcCCCCCEEECCCCccCcccCC-CCCCcCCEEE
Confidence            3455688999999999988876433    5999999 88877 67899999999999999999998875 8999999999


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| .+..+|.. +..+++|++|++++|.+..              ..+..+..+++|+.|+++.|         +++.
T Consensus        84 Ls~N-~l~~l~~~-~~~l~~L~~L~l~~N~l~~--------------l~~~~~~~l~~L~~L~L~~N---------~l~~  138 (290)
T 1p9a_G           84 LSHN-QLQSLPLL-GQTLPALTVLDVSFNRLTS--------------LPLGALRGLGELQELYLKGN---------ELKT  138 (290)
T ss_dssp             CCSS-CCSSCCCC-TTTCTTCCEEECCSSCCCC--------------CCSSTTTTCTTCCEEECTTS---------CCCC
T ss_pred             CCCC-cCCcCchh-hccCCCCCEEECCCCcCcc--------------cCHHHHcCCCCCCEEECCCC---------CCCc
Confidence            9999 68899986 8999999999999998875              22345778899999999854         3444


Q ss_pred             ccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEe
Q 004021          646 LDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIG  725 (779)
Q Consensus       646 L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~  725 (779)
                      +.+..+..+++|+.|+|++|. +..++.               ..+..+++|+.|+|++ +.++.+|.....+++|+.|+
T Consensus       139 ~~~~~~~~l~~L~~L~L~~N~-l~~l~~---------------~~~~~l~~L~~L~L~~-N~l~~ip~~~~~~~~L~~l~  201 (290)
T 1p9a_G          139 LPPGLLTPTPKLEKLSLANNN-LTELPA---------------GLLNGLENLDTLLLQE-NSLYTIPKGFFGSHLLPFAF  201 (290)
T ss_dssp             CCTTTTTTCTTCCEEECTTSC-CSCCCT---------------TTTTTCTTCCEEECCS-SCCCCCCTTTTTTCCCSEEE
T ss_pred             cChhhcccccCCCEEECCCCc-CCccCH---------------HHhcCcCCCCEEECCC-CcCCccChhhcccccCCeEE
Confidence            445557788999999999864 455544               3567899999999998 57889999888899999999


Q ss_pred             eeCCC
Q 004021          726 VYGCP  730 (779)
Q Consensus       726 l~~c~  730 (779)
                      ++++|
T Consensus       202 L~~Np  206 (290)
T 1p9a_G          202 LHGNP  206 (290)
T ss_dssp             CCSCC
T ss_pred             eCCCC
Confidence            99876

>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=99.70  E-value=1.8e-16  Score=167.84  Aligned_cols=221  Identities=20%  Similarity=0.242  Sum_probs=171.2

Q ss_pred             CCccEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCccccc-chhhccCccCcEeeccC
Q 004021          495 EGAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEY  568 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~  568 (779)
                      ..++.+++.++.+..+|....    .|+|++| .++.+|. .|+++++|++|++++|.++.+ |..++++++|++|++++
T Consensus        31 c~l~~l~~~~~~l~~lp~~~~~~l~~L~L~~n-~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~  109 (330)
T 1xku_A           31 CHLRVVQCSDLGLEKVPKDLPPDTALLDLQNN-KITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSK  109 (330)
T ss_dssp             EETTEEECTTSCCCSCCCSCCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS
T ss_pred             CCCeEEEecCCCccccCccCCCCCeEEECCCC-cCCEeChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEECCC
Confidence            368899999999888876432    5999999 8998865 799999999999999999987 78899999999999999


Q ss_pred             CcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc-------cccCC
Q 004021          569 THYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA-------VQKFF  641 (779)
Q Consensus       569 ~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~-------~~~~~  641 (779)
                      | .++.+|.. +.  ++|++|++++|.+..              .....+..+++|+.|+++.+....       +..++
T Consensus       110 n-~l~~l~~~-~~--~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~  171 (330)
T 1xku_A          110 N-QLKELPEK-MP--KTLQELRVHENEITK--------------VRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMK  171 (330)
T ss_dssp             S-CCSBCCSS-CC--TTCCEEECCSSCCCB--------------BCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCT
T ss_pred             C-cCCccChh-hc--ccccEEECCCCcccc--------------cCHhHhcCCccccEEECCCCcCCccCcChhhccCCC
Confidence            9 68899986 43  799999999998874              345568889999999999876532       34456


Q ss_pred             CCCcccCcc--c-----ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-
Q 004021          642 KYPKLDLTW--L-----VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-  713 (779)
Q Consensus       642 ~L~~L~~~~--l-----~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-  713 (779)
                      +|+.|.+..  +     ...++|+.|++++|. +..++.               ..+..+++|+.|+++++ .+..++. 
T Consensus       172 ~L~~L~l~~n~l~~l~~~~~~~L~~L~l~~n~-l~~~~~---------------~~~~~l~~L~~L~Ls~n-~l~~~~~~  234 (330)
T 1xku_A          172 KLSYIRIADTNITTIPQGLPPSLTELHLDGNK-ITKVDA---------------ASLKGLNNLAKLGLSFN-SISAVDNG  234 (330)
T ss_dssp             TCCEEECCSSCCCSCCSSCCTTCSEEECTTSC-CCEECT---------------GGGTTCTTCCEEECCSS-CCCEECTT
T ss_pred             CcCEEECCCCccccCCccccccCCEEECCCCc-CCccCH---------------HHhcCCCCCCEEECCCC-cCceeChh
Confidence            666652110  1     112677788887754 333322               36778999999999985 5666655 


Q ss_pred             CCCCCCCccEEeeeCCCCCCCCCCCCCCcc-cccEEEech
Q 004021          714 NPLHFPKLKKIGVYGCPKLKKLPINSSSAK-ERRVVIEGL  752 (779)
Q Consensus       714 ~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~-~~~l~i~~~  752 (779)
                      .+..+++|++|++++| .+..+|..+...+ ++.+.+.++
T Consensus       235 ~~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~~L~l~~N  273 (330)
T 1xku_A          235 SLANTPHLRELHLNNN-KLVKVPGGLADHKYIQVVYLHNN  273 (330)
T ss_dssp             TGGGSTTCCEEECCSS-CCSSCCTTTTTCSSCCEEECCSS
T ss_pred             hccCCCCCCEEECCCC-cCccCChhhccCCCcCEEECCCC
Confidence            5678999999999998 5889998776544 488888765

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.70  E-value=1.8e-16  Score=167.85  Aligned_cols=224  Identities=18%  Similarity=0.175  Sum_probs=147.3

Q ss_pred             CCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccchhhccCccCcEeec
Q 004021          495 EGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNL  566 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l  566 (779)
                      +.++.|++++|.+..++..     +.  .|+|++| .+..+ |..|+++++|++|++++|.++.+|..+.  ++|++|++
T Consensus        54 ~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~L~l  130 (332)
T 2ft3_A           54 PDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNN-KISKIHEKAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVELRI  130 (332)
T ss_dssp             TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCCEECGGGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCEEEC
T ss_pred             CCCeEEECCCCcCCccCHhHhhCCCCCcEEECCCC-ccCccCHhHhhCcCCCCEEECCCCcCCccCcccc--ccCCEEEC
Confidence            4677777777777665431     11  3777777 66665 6667777777777777777777776655  67777777


Q ss_pred             cCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccc--cCCCCC
Q 004021          567 EYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ--KFFKYP  644 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~--~~~~L~  644 (779)
                      ++| .+..+|...+.++++|++|++++|.+...            ...+..+..+ +|+.|+++.+....++  ..++|+
T Consensus       131 ~~n-~i~~~~~~~~~~l~~L~~L~l~~n~l~~~------------~~~~~~~~~l-~L~~L~l~~n~l~~l~~~~~~~L~  196 (332)
T 2ft3_A          131 HDN-RIRKVPKGVFSGLRNMNCIEMGGNPLENS------------GFEPGAFDGL-KLNYLRISEAKLTGIPKDLPETLN  196 (332)
T ss_dssp             CSS-CCCCCCSGGGSSCSSCCEEECCSCCCBGG------------GSCTTSSCSC-CCSCCBCCSSBCSSCCSSSCSSCS
T ss_pred             CCC-ccCccCHhHhCCCccCCEEECCCCccccC------------CCCcccccCC-ccCEEECcCCCCCccCccccCCCC
Confidence            777 56666665567777777777777766420            1233445555 6777777766554432  123444


Q ss_pred             cc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC
Q 004021          645 KL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN  714 (779)
Q Consensus       645 ~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~  714 (779)
                      .|          .+..+..+++|+.|+|++|.. ..++.               ..+..+++|+.|+++++ .+..+|..
T Consensus       197 ~L~l~~n~i~~~~~~~l~~l~~L~~L~L~~N~l-~~~~~---------------~~~~~l~~L~~L~L~~N-~l~~lp~~  259 (332)
T 2ft3_A          197 ELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQI-RMIEN---------------GSLSFLPTLRELHLDNN-KLSRVPAG  259 (332)
T ss_dssp             CCBCCSSCCCCCCTTSSTTCTTCSCCBCCSSCC-CCCCT---------------TGGGGCTTCCEEECCSS-CCCBCCTT
T ss_pred             EEECCCCcCCccCHHHhcCCCCCCEEECCCCcC-CcCCh---------------hHhhCCCCCCEEECCCC-cCeecChh
Confidence            44          334577788888888888643 33332               25678899999999984 67888888


Q ss_pred             CCCCCCccEEeeeCCCCCCCCCCCCC--------CcccccEEEechH
Q 004021          715 PLHFPKLKKIGVYGCPKLKKLPINSS--------SAKERRVVIEGLK  753 (779)
Q Consensus       715 ~~~l~~L~~L~l~~c~~L~~lP~~~~--------~~~~~~l~i~~~~  753 (779)
                      +..+++|++|++++| .++.+|....        ...++.+.+.+++
T Consensus       260 l~~l~~L~~L~l~~N-~l~~~~~~~~~~~~~~~~~~~l~~L~l~~N~  305 (332)
T 2ft3_A          260 LPDLKLLQVVYLHTN-NITKVGVNDFCPVGFGVKRAYYNGISLFNNP  305 (332)
T ss_dssp             GGGCTTCCEEECCSS-CCCBCCTTSSSCSSCCSSSCCBSEEECCSSS
T ss_pred             hhcCccCCEEECCCC-CCCccChhHccccccccccccccceEeecCc
Confidence            888999999999986 4777775322        1223667776654

>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=99.70  E-value=1.8e-16  Score=175.47  Aligned_cols=214  Identities=21%  Similarity=0.194  Sum_probs=139.8

Q ss_pred             CCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCcEee
Q 004021          495 EGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~  565 (779)
                      ..++.|++++|.+..++...     .  .|+|++| .+..+ |..|.++++|++|+|++|.++.+|.. +.++++|++|+
T Consensus        75 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~  153 (452)
T 3zyi_A           75 SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRN-SIRQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRELW  153 (452)
T ss_dssp             TTCSEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCCEEE
T ss_pred             CCccEEECcCCcCceECHHHcCCCCCCCEEECCCC-ccCCcChhhccCcccCCEEECCCCcCCccChhhhcccCCCCEEE
Confidence            46777777777776653321     1  3777777 66665 35667777777777777777776654 66677777777


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| .+..+|...+.++++|++|++++|....             ......+..+++|+.|+++.|....         
T Consensus       154 L~~N-~l~~~~~~~~~~l~~L~~L~l~~~~~l~-------------~i~~~~~~~l~~L~~L~L~~n~l~~---------  210 (452)
T 3zyi_A          154 LRNN-PIESIPSYAFNRVPSLMRLDLGELKKLE-------------YISEGAFEGLFNLKYLNLGMCNIKD---------  210 (452)
T ss_dssp             CCSC-CCCEECTTTTTTCTTCCEEECCCCTTCC-------------EECTTTTTTCTTCCEEECTTSCCSS---------
T ss_pred             CCCC-CcceeCHhHHhcCCcccEEeCCCCCCcc-------------ccChhhccCCCCCCEEECCCCcccc---------
Confidence            7777 4666666556777777777777644332             1223346677777777777554332         


Q ss_pred             ccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc-CCCCCCCCccEE
Q 004021          646 LDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY-PNPLHFPKLKKI  724 (779)
Q Consensus       646 L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~-~~~~~l~~L~~L  724 (779)
                        .+.+..+++|+.|+|++|.. ..++.               ..+..+++|+.|+++++ .+..++ ..+..+++|+.|
T Consensus       211 --~~~~~~l~~L~~L~Ls~N~l-~~~~~---------------~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L  271 (452)
T 3zyi_A          211 --MPNLTPLVGLEELEMSGNHF-PEIRP---------------GSFHGLSSLKKLWVMNS-QVSLIERNAFDGLASLVEL  271 (452)
T ss_dssp             --CCCCTTCTTCCEEECTTSCC-SEECG---------------GGGTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEE
T ss_pred             --cccccccccccEEECcCCcC-cccCc---------------ccccCccCCCEEEeCCC-cCceECHHHhcCCCCCCEE
Confidence              23456778889999988654 34433               36778889999999884 555554 456678999999


Q ss_pred             eeeCCCCCCCCCCCC-CC-cccccEEEech
Q 004021          725 GVYGCPKLKKLPINS-SS-AKERRVVIEGL  752 (779)
Q Consensus       725 ~l~~c~~L~~lP~~~-~~-~~~~~l~i~~~  752 (779)
                      ++++| ++..+|... .. ..++.+.+.++
T Consensus       272 ~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N  300 (452)
T 3zyi_A          272 NLAHN-NLSSLPHDLFTPLRYLVELHLHHN  300 (452)
T ss_dssp             ECCSS-CCSCCCTTSSTTCTTCCEEECCSS
T ss_pred             ECCCC-cCCccChHHhccccCCCEEEccCC
Confidence            99887 677887643 22 23477777643

>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=99.70  E-value=2e-16  Score=168.77  Aligned_cols=115  Identities=25%  Similarity=0.348  Sum_probs=89.8

Q ss_pred             EEcCcccccCccccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccch
Q 004021          479 VRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ  553 (779)
Q Consensus       479 ~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~  553 (779)
                      ...+..+..++.+..++++++|++++|.+..++....     .|++++| .+..+| .+.++++|++|++++|.++.+|.
T Consensus        50 ~l~~~~i~~~~~~~~~~~L~~L~l~~n~i~~~~~~~~l~~L~~L~L~~n-~i~~~~-~~~~l~~L~~L~l~~n~i~~~~~  127 (347)
T 4fmz_A           50 VVAGEKVASIQGIEYLTNLEYLNLNGNQITDISPLSNLVKLTNLYIGTN-KITDIS-ALQNLTNLRELYLNEDNISDISP  127 (347)
T ss_dssp             ECCSSCCCCCTTGGGCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSS-CCCCCG-GGTTCTTCSEEECTTSCCCCCGG
T ss_pred             EEeCCccccchhhhhcCCccEEEccCCccccchhhhcCCcCCEEEccCC-cccCch-HHcCCCcCCEEECcCCcccCchh
Confidence            3344555566667778889999999888877765322     3888888 888876 58888999999999998888876


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                       +.++++|++|++++|..+..++.  +..+++|++|++.+|.+..
T Consensus       128 -~~~l~~L~~L~l~~n~~~~~~~~--~~~l~~L~~L~l~~~~~~~  169 (347)
T 4fmz_A          128 -LANLTKMYSLNLGANHNLSDLSP--LSNMTGLNYLTVTESKVKD  169 (347)
T ss_dssp             -GTTCTTCCEEECTTCTTCCCCGG--GTTCTTCCEEECCSSCCCC
T ss_pred             -hccCCceeEEECCCCCCcccccc--hhhCCCCcEEEecCCCcCC
Confidence             88888999999988866666655  7888888888888887765

>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=99.69  E-value=1.2e-16  Score=170.44  Aligned_cols=247  Identities=16%  Similarity=0.138  Sum_probs=140.3

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhh
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQEL  555 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~  555 (779)
                      .+..+..++.+..+.++++|++.+|.+..++....     .|++++| .+..+|. +.++++|++|++++|.....+..+
T Consensus        74 ~~n~i~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~l~~L~~L~l~~n-~i~~~~~-~~~l~~L~~L~l~~n~~~~~~~~~  151 (347)
T 4fmz_A           74 NGNQITDISPLSNLVKLTNLYIGTNKITDISALQNLTNLRELYLNED-NISDISP-LANLTKMYSLNLGANHNLSDLSPL  151 (347)
T ss_dssp             CSSCCCCCGGGTTCTTCCEEECCSSCCCCCGGGTTCTTCSEEECTTS-CCCCCGG-GTTCTTCCEEECTTCTTCCCCGGG
T ss_pred             cCCccccchhhhcCCcCCEEEccCCcccCchHHcCCCcCCEEECcCC-cccCchh-hccCCceeEEECCCCCCcccccch
Confidence            34445555556677788888888887777654322     3788888 7777765 777888888888887444434447


Q ss_pred             ccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC-------ccCCCchhhHHhhcCCCCCCcee
Q 004021          556 KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN-------VLCDDAEPLMRELLGLKRLNVLS  628 (779)
Q Consensus       556 ~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~-------~~~~~~~~~~~~l~~L~~L~~L~  628 (779)
                      .++++|++|++++| .+..++.  +..+++|++|++++|.+..++. +..       .+.++.......+..+++|+.|+
T Consensus       152 ~~l~~L~~L~l~~~-~~~~~~~--~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~l~~n~l~~~~~~~~~~~L~~L~  227 (347)
T 4fmz_A          152 SNMTGLNYLTVTES-KVKDVTP--IANLTDLYSLSLNYNQIEDISP-LASLTSLHYFTAYVNQITDITPVANMTRLNSLK  227 (347)
T ss_dssp             TTCTTCCEEECCSS-CCCCCGG--GGGCTTCSEEECTTSCCCCCGG-GGGCTTCCEEECCSSCCCCCGGGGGCTTCCEEE
T ss_pred             hhCCCCcEEEecCC-CcCCchh--hccCCCCCEEEccCCccccccc-ccCCCccceeecccCCCCCCchhhcCCcCCEEE
Confidence            77888888888877 4566665  6777888888888777665321 000       00000001111145556666666


Q ss_pred             EEeeccccc---ccCCCCCcc--------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCc
Q 004021          629 WSFRSSLAV---QKFFKYPKL--------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQL  697 (779)
Q Consensus       629 l~~~~~~~~---~~~~~L~~L--------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L  697 (779)
                      ++.|....+   ..+++|+.|        ..+.+..+++|+.|++++|.. ..+                 ..+..+++|
T Consensus       228 l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~l-~~~-----------------~~~~~l~~L  289 (347)
T 4fmz_A          228 IGNNKITDLSPLANLSQLTWLEIGTNQISDINAVKDLTKLKMLNVGSNQI-SDI-----------------SVLNNLSQL  289 (347)
T ss_dssp             CCSSCCCCCGGGTTCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSSCC-CCC-----------------GGGGGCTTC
T ss_pred             ccCCccCCCcchhcCCCCCEEECCCCccCCChhHhcCCCcCEEEccCCcc-CCC-----------------hhhcCCCCC
Confidence            665544332   233334333        123344555566666655432 221                 134566777


Q ss_pred             cEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          698 ESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       698 ~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      +.|++++|.-....+..+..+++|++|++++|+ +..+|.......++.+.+.++
T Consensus       290 ~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~-l~~~~~~~~l~~L~~L~l~~N  343 (347)
T 4fmz_A          290 NSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNH-ITDIRPLASLSKMDSADFANQ  343 (347)
T ss_dssp             SEEECCSSCCCGGGHHHHHTCTTCSEEECCSSS-CCCCGGGGGCTTCSEESSSCC
T ss_pred             CEEECcCCcCCCcChhHhhccccCCEEEccCCc-cccccChhhhhccceeehhhh
Confidence            777777653322333344567777777777765 555544222223355555443

>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=99.69  E-value=1.7e-16  Score=164.25  Aligned_cols=197  Identities=16%  Similarity=0.144  Sum_probs=111.1

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccc-hhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcC
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~  571 (779)
                      +.++..++.+..+|....    .|+|++| .+..+| ..|.++++|++|++++|.++.+ |..+.++++|++|++++|..
T Consensus        14 ~~~~c~~~~l~~ip~~~~~~l~~L~l~~n-~i~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~   92 (285)
T 1ozn_A           14 VTTSCPQQGLQAVPVGIPAASQRIFLHGN-RISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQ   92 (285)
T ss_dssp             CEEECCSSCCSSCCTTCCTTCSEEECTTS-CCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTT
T ss_pred             eEEEcCcCCcccCCcCCCCCceEEEeeCC-cCCccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCC
Confidence            345555555555443211    3666666 566554 3466667777777777766665 55566677777777776643


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccc
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL  651 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l  651 (779)
                      ++.+++..+..+++|++|++++|.+..              ..+..+..+++|+.|+++.|.         +..+.+..+
T Consensus        93 l~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~n~---------l~~~~~~~~  149 (285)
T 1ozn_A           93 LRSVDPATFHGLGRLHTLHLDRCGLQE--------------LGPGLFRGLAALQYLYLQDNA---------LQALPDDTF  149 (285)
T ss_dssp             CCCCCTTTTTTCTTCCEEECTTSCCCC--------------CCTTTTTTCTTCCEEECCSSC---------CCCCCTTTT
T ss_pred             ccccCHHHhcCCcCCCEEECCCCcCCE--------------ECHhHhhCCcCCCEEECCCCc---------ccccCHhHh
Confidence            555544336666777777777666553              223345566666666666432         223333345


Q ss_pred             ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEeeeCCC
Q 004021          652 VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c~  730 (779)
                      ..+++|+.|+|++|. +..++.               ..+..+++|+.|+++++ .+..+ +..+..+++|+.|++++| 
T Consensus       150 ~~l~~L~~L~l~~n~-l~~~~~---------------~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n-  211 (285)
T 1ozn_A          150 RDLGNLTHLFLHGNR-ISSVPE---------------RAFRGLHSLDRLLLHQN-RVAHVHPHAFRDLGRLMTLYLFAN-  211 (285)
T ss_dssp             TTCTTCCEEECCSSC-CCEECT---------------TTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSS-
T ss_pred             ccCCCccEEECCCCc-ccccCH---------------HHhcCccccCEEECCCC-cccccCHhHccCcccccEeeCCCC-
Confidence            556666666666643 333332               23555666666666663 34433 445556666666666665 


Q ss_pred             CCCCCC
Q 004021          731 KLKKLP  736 (779)
Q Consensus       731 ~L~~lP  736 (779)
                      .+..+|
T Consensus       212 ~l~~~~  217 (285)
T 1ozn_A          212 NLSALP  217 (285)
T ss_dssp             CCSCCC
T ss_pred             cCCcCC
Confidence            355555

>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=99.69  E-value=2.4e-16  Score=174.53  Aligned_cols=197  Identities=21%  Similarity=0.230  Sum_probs=163.4

Q ss_pred             ccccCCccEEEcccccccccccCc-----c--cccccccccccccchh-hcccccCceeeecCCcccccch-hhccCccC
Q 004021          491 VKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGLPQ-ELKALEKL  561 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~~-i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L  561 (779)
                      +..+.+++.|++++|.+..++...     .  .|+|++| .+..+|.. |.++++|++|+|++|.++.+|. .+.++++|
T Consensus        95 ~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L  173 (452)
T 3zyi_A           95 FRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDN-WLTVIPSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSL  173 (452)
T ss_dssp             TTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCSBCCTTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTC
T ss_pred             cCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCC-cCCccChhhhcccCCCCEEECCCCCcceeCHhHHhcCCcc
Confidence            456789999999999998776432     2  3999999 89988664 8899999999999999999876 68999999


Q ss_pred             cEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCC
Q 004021          562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFF  641 (779)
Q Consensus       562 ~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~  641 (779)
                      ++|++++|..++.+|.+.+.++++|++|++++|.+..+                ..+..+++|+.|+++.|         
T Consensus       174 ~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~----------------~~~~~l~~L~~L~Ls~N---------  228 (452)
T 3zyi_A          174 MRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDM----------------PNLTPLVGLEELEMSGN---------  228 (452)
T ss_dssp             CEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCCSSC----------------CCCTTCTTCCEEECTTS---------
T ss_pred             cEEeCCCCCCccccChhhccCCCCCCEEECCCCccccc----------------ccccccccccEEECcCC---------
Confidence            99999998889999987789999999999999988751                24778899999999844         


Q ss_pred             CCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCC
Q 004021          642 KYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPK  720 (779)
Q Consensus       642 ~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~  720 (779)
                      ++..+.+..+..+++|+.|+|++|.. ..++.               ..+..+++|+.|+|+++ .+..++.. +..+++
T Consensus       229 ~l~~~~~~~~~~l~~L~~L~L~~n~l-~~~~~---------------~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~  291 (452)
T 3zyi_A          229 HFPEIRPGSFHGLSSLKKLWVMNSQV-SLIER---------------NAFDGLASLVELNLAHN-NLSSLPHDLFTPLRY  291 (452)
T ss_dssp             CCSEECGGGGTTCTTCCEEECTTSCC-CEECT---------------TTTTTCTTCCEEECCSS-CCSCCCTTSSTTCTT
T ss_pred             cCcccCcccccCccCCCEEEeCCCcC-ceECH---------------HHhcCCCCCCEEECCCC-cCCccChHHhccccC
Confidence            45555567788899999999999654 44433               36788999999999984 77777764 457999


Q ss_pred             ccEEeeeCCC
Q 004021          721 LKKIGVYGCP  730 (779)
Q Consensus       721 L~~L~l~~c~  730 (779)
                      |+.|++++||
T Consensus       292 L~~L~L~~Np  301 (452)
T 3zyi_A          292 LVELHLHHNP  301 (452)
T ss_dssp             CCEEECCSSC
T ss_pred             CCEEEccCCC
Confidence            9999999875

>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=99.69  E-value=1.1e-16  Score=167.55  Aligned_cols=228  Identities=19%  Similarity=0.162  Sum_probs=161.6

Q ss_pred             CcccccCccccccCCccEEEcccccccccccCc--c-----ccccccccccccc---chhhcccccCceeeecCCccccc
Q 004021          482 GVKLTEAPKVKEWEGAKRISLMANEIESLSEIP--T-----LLSLRRNDSLTEL---PSRISSLVSLHHLDLSLTHIRGL  551 (779)
Q Consensus       482 ~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~--~-----lL~L~~~~~l~~l---p~~i~~L~~L~~L~L~~~~i~~l  551 (779)
                      +..+..+|. .....+++|++++|.+..++...  .     .|+|++| .+..+   |..+..+++|++|++++|.+..+
T Consensus        16 ~~~l~~ip~-~~~~~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~l   93 (306)
T 2z66_A           16 SKGLTSVPT-GIPSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSN-GLSFKGCCSQSDFGTTSLKYLDLSFNGVITM   93 (306)
T ss_dssp             SSCCSSCCS-CCCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSS-CCCEEEEEEHHHHSCSCCCEEECCSCSEEEE
T ss_pred             CCCcccCCC-CCCCCCCEEECCCCccCccCHhHhhccccCCEEECCCC-ccCcccCcccccccccccCEEECCCCccccC
Confidence            334455554 22357888899888888776532  1     3888888 77654   67777888888999988888888


Q ss_pred             chhhccCccCcEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEE
Q 004021          552 PQELKALEKLRYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       552 p~~~~~L~~L~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                      |..+.++++|++|++++| .+..++. ..+..+++|++|++++|.+..              ..+..+..+++|+.|+++
T Consensus        94 ~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~  158 (306)
T 2z66_A           94 SSNFLGLEQLEHLDFQHS-NLKQMSEFSVFLSLRNLIYLDISHTHTRV--------------AFNGIFNGLSSLEVLKMA  158 (306)
T ss_dssp             EEEEETCTTCCEEECTTS-EEESSTTTTTTTTCTTCCEEECTTSCCEE--------------CSTTTTTTCTTCCEEECT
T ss_pred             hhhcCCCCCCCEEECCCC-cccccccchhhhhccCCCEEECCCCcCCc--------------cchhhcccCcCCCEEECC
Confidence            888888888899988888 5666664 337888888888888887653              334456778888888887


Q ss_pred             eecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcc
Q 004021          631 FRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS  710 (779)
Q Consensus       631 ~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~  710 (779)
                      .|....        ...+..+..+++|+.|+|++|.. ..++.               ..+..+++|+.|+++++ .+..
T Consensus       159 ~n~l~~--------~~~~~~~~~l~~L~~L~Ls~n~l-~~~~~---------------~~~~~l~~L~~L~L~~N-~l~~  213 (306)
T 2z66_A          159 GNSFQE--------NFLPDIFTELRNLTFLDLSQCQL-EQLSP---------------TAFNSLSSLQVLNMSHN-NFFS  213 (306)
T ss_dssp             TCEEGG--------GEECSCCTTCTTCCEEECTTSCC-CEECT---------------TTTTTCTTCCEEECTTS-CCSB
T ss_pred             CCcccc--------ccchhHHhhCcCCCEEECCCCCc-CCcCH---------------HHhcCCCCCCEEECCCC-ccCc
Confidence            554321        01245567788999999998654 44433               36778899999999984 5666


Q ss_pred             ccC-CCCCCCCccEEeeeCCCCCCCCCCCCCCc--ccccEEEec
Q 004021          711 IYP-NPLHFPKLKKIGVYGCPKLKKLPINSSSA--KERRVVIEG  751 (779)
Q Consensus       711 l~~-~~~~l~~L~~L~l~~c~~L~~lP~~~~~~--~~~~l~i~~  751 (779)
                      ++. .+..+++|+.|++++|+--...|..+...  .++.+.+.+
T Consensus       214 ~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~~L~~L~L~~  257 (306)
T 2z66_A          214 LDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQ  257 (306)
T ss_dssp             CCSGGGTTCTTCCEEECTTSCCCBCSSSSCCCCCTTCCEEECTT
T ss_pred             cChhhccCcccCCEeECCCCCCcccCHHHHHhhhccCCEEEccC
Confidence            654 45678999999999986544455544443  346676654

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.69  E-value=3e-17  Score=172.09  Aligned_cols=215  Identities=14%  Similarity=0.151  Sum_probs=161.4

Q ss_pred             cccccCCccEEEccc-cccc-ccccCc----c--ccccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCc
Q 004021          490 KVKEWEGAKRISLMA-NEIE-SLSEIP----T--LLSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALE  559 (779)
Q Consensus       490 ~~~~~~~lr~l~l~~-~~~~-~l~~~~----~--lL~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~  559 (779)
                      .+..+..+++|++++ |.+. .+|...    .  .|+|++| .+. .+|..|+++++|++|++++|.++ .+|..+.+++
T Consensus        71 ~l~~l~~L~~L~L~~~n~l~~~~p~~l~~l~~L~~L~Ls~n-~l~~~~p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~  149 (313)
T 1ogq_A           71 SLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHT-NVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLP  149 (313)
T ss_dssp             GGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEE-CCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCT
T ss_pred             hHhCCCCCCeeeCCCCCcccccCChhHhcCCCCCEEECcCC-eeCCcCCHHHhCCCCCCEEeCCCCccCCcCChHHhcCC
Confidence            456778899999984 7665 344322    2  4899999 777 67989999999999999999988 6888999999


Q ss_pred             cCcEeeccCCcCCCCCchhhhcCCc-cCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc---
Q 004021          560 KLRYLNLEYTHYLSIIPHQLISGFL-KLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL---  635 (779)
Q Consensus       560 ~L~~L~l~~~~~l~~lp~~~i~~L~-~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~---  635 (779)
                      +|++|++++|.....+|.. +++++ +|++|++++|.+.+              ..+..+..++ |+.|+++.|...   
T Consensus       150 ~L~~L~L~~N~l~~~~p~~-l~~l~~~L~~L~L~~N~l~~--------------~~~~~~~~l~-L~~L~Ls~N~l~~~~  213 (313)
T 1ogq_A          150 NLVGITFDGNRISGAIPDS-YGSFSKLFTSMTISRNRLTG--------------KIPPTFANLN-LAFVDLSRNMLEGDA  213 (313)
T ss_dssp             TCCEEECCSSCCEEECCGG-GGCCCTTCCEEECCSSEEEE--------------ECCGGGGGCC-CSEEECCSSEEEECC
T ss_pred             CCCeEECcCCcccCcCCHH-HhhhhhcCcEEECcCCeeec--------------cCChHHhCCc-ccEEECcCCcccCcC
Confidence            9999999999433378887 88888 99999999988763              2344455554 777777665543   


Q ss_pred             --ccccCCCCCcc---------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccC
Q 004021          636 --AVQKFFKYPKL---------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILY  704 (779)
Q Consensus       636 --~~~~~~~L~~L---------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~  704 (779)
                        .+..+++|+.|         .++.+..+++|++|+|++|...+.++.                .+..+++|+.|++++
T Consensus       214 ~~~~~~l~~L~~L~L~~N~l~~~~~~~~~l~~L~~L~Ls~N~l~~~~p~----------------~l~~l~~L~~L~Ls~  277 (313)
T 1ogq_A          214 SVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQ----------------GLTQLKFLHSLNVSF  277 (313)
T ss_dssp             GGGCCTTSCCSEEECCSSEECCBGGGCCCCTTCCEEECCSSCCEECCCG----------------GGGGCTTCCEEECCS
T ss_pred             CHHHhcCCCCCEEECCCCceeeecCcccccCCCCEEECcCCcccCcCCh----------------HHhcCcCCCEEECcC
Confidence              23445556555         234467789999999999765444443                677899999999999


Q ss_pred             CCCCccccCCCCCCCCccEEeeeCCCCCCCCCCC
Q 004021          705 GPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPIN  738 (779)
Q Consensus       705 ~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~  738 (779)
                      +.-...+|.. ..+++|+.|++.+++.+...|..
T Consensus       278 N~l~~~ip~~-~~l~~L~~l~l~~N~~lc~~p~~  310 (313)
T 1ogq_A          278 NNLCGEIPQG-GNLQRFDVSAYANNKCLCGSPLP  310 (313)
T ss_dssp             SEEEEECCCS-TTGGGSCGGGTCSSSEEESTTSS
T ss_pred             CcccccCCCC-ccccccChHHhcCCCCccCCCCC
Confidence            6443366654 78999999999999988876653

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.68  E-value=3.1e-16  Score=172.95  Aligned_cols=213  Identities=19%  Similarity=0.219  Sum_probs=127.1

Q ss_pred             CCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCcccccch-hhccCccCcEee
Q 004021          495 EGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~  565 (779)
                      ..++.|++++|.+..++...     .  .|+|++| .+..+ |..|.++++|++|+|++|.++.+|. .|.++++|++|+
T Consensus        64 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n-~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~  142 (440)
T 3zyj_A           64 TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRN-HIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKELW  142 (440)
T ss_dssp             TTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSS-CCCEECGGGGTTCSSCCEEECCSSCCSSCCTTTSCSCSSCCEEE
T ss_pred             CCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCC-cCCccChhhccCCccCCEEECCCCcCCeeCHhHhhccccCceee
Confidence            46677777777666554321     1  2677777 66665 3556667777777777777766665 366677777777


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| .+..+|...+.++++|++|++.+|....             ......+..+++|+.|+++.|....+        
T Consensus       143 L~~N-~i~~~~~~~~~~l~~L~~L~l~~~~~l~-------------~i~~~~~~~l~~L~~L~L~~n~l~~~--------  200 (440)
T 3zyj_A          143 LRNN-PIESIPSYAFNRIPSLRRLDLGELKRLS-------------YISEGAFEGLSNLRYLNLAMCNLREI--------  200 (440)
T ss_dssp             CCSC-CCCEECTTTTTTCTTCCEEECCCCTTCC-------------EECTTTTTTCSSCCEEECTTSCCSSC--------
T ss_pred             CCCC-cccccCHHHhhhCcccCEeCCCCCCCcc-------------eeCcchhhcccccCeecCCCCcCccc--------
Confidence            7776 4566666556667777777776643332             12223466677777777765543322        


Q ss_pred             ccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-CCCCCCCccEE
Q 004021          646 LDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-NPLHFPKLKKI  724 (779)
Q Consensus       646 L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-~~~~l~~L~~L  724 (779)
                         +.+..+++|+.|+|++|. +..++.               ..+..+++|+.|+++++ .+..++. .+..+++|+.|
T Consensus       201 ---~~~~~l~~L~~L~Ls~N~-l~~~~~---------------~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L  260 (440)
T 3zyj_A          201 ---PNLTPLIKLDELDLSGNH-LSAIRP---------------GSFQGLMHLQKLWMIQS-QIQVIERNAFDNLQSLVEI  260 (440)
T ss_dssp             ---CCCTTCSSCCEEECTTSC-CCEECT---------------TTTTTCTTCCEEECTTC-CCCEECTTSSTTCTTCCEE
T ss_pred             ---cccCCCcccCEEECCCCc-cCccCh---------------hhhccCccCCEEECCCC-ceeEEChhhhcCCCCCCEE
Confidence               234566777777777753 333433               35666777777777763 4555543 44567777777


Q ss_pred             eeeCCCCCCCCCCCC-CC-cccccEEEec
Q 004021          725 GVYGCPKLKKLPINS-SS-AKERRVVIEG  751 (779)
Q Consensus       725 ~l~~c~~L~~lP~~~-~~-~~~~~l~i~~  751 (779)
                      ++++| ++..+|... .. ..++.+.+.+
T Consensus       261 ~L~~N-~l~~~~~~~~~~l~~L~~L~L~~  288 (440)
T 3zyj_A          261 NLAHN-NLTLLPHDLFTPLHHLERIHLHH  288 (440)
T ss_dssp             ECTTS-CCCCCCTTTTSSCTTCCEEECCS
T ss_pred             ECCCC-CCCccChhHhccccCCCEEEcCC
Confidence            77775 466666543 21 2335565553

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.68  E-value=4.1e-16  Score=172.01  Aligned_cols=212  Identities=18%  Similarity=0.186  Sum_probs=167.8

Q ss_pred             ccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccc-hhhccCccCcEeeccCCc
Q 004021          497 AKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLNLEYTH  570 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~l~~~~  570 (779)
                      .+.++..++.+..+|....    .|+|++| .+..+ |..|.++++|++|+|++|.++.++ ..|.++++|++|+|++| 
T Consensus        45 ~~~v~c~~~~l~~iP~~~~~~l~~L~L~~n-~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n-  122 (440)
T 3zyj_A           45 FSKVICVRKNLREVPDGISTNTRLLNLHEN-QIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDN-  122 (440)
T ss_dssp             SCEEECCSCCCSSCCSCCCTTCSEEECCSC-CCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSS-
T ss_pred             CCEEEeCCCCcCcCCCCCCCCCcEEEccCC-cCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCC-
Confidence            4578888888888876533    6999999 88887 578999999999999999999876 56999999999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTW  650 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~  650 (779)
                      .++.+|.+.+..+++|++|++++|.+..              .....+..+++|+.|+++.        ...+..+....
T Consensus       123 ~l~~~~~~~~~~l~~L~~L~L~~N~i~~--------------~~~~~~~~l~~L~~L~l~~--------~~~l~~i~~~~  180 (440)
T 3zyj_A          123 RLTTIPNGAFVYLSKLKELWLRNNPIES--------------IPSYAFNRIPSLRRLDLGE--------LKRLSYISEGA  180 (440)
T ss_dssp             CCSSCCTTTSCSCSSCCEEECCSCCCCE--------------ECTTTTTTCTTCCEEECCC--------CTTCCEECTTT
T ss_pred             cCCeeCHhHhhccccCceeeCCCCcccc--------------cCHHHhhhCcccCEeCCCC--------CCCcceeCcch
Confidence            7889998778999999999999998874              2334577899999999874        23455555556


Q ss_pred             cccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEeeeCC
Q 004021          651 LVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGVYGC  729 (779)
Q Consensus       651 l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c  729 (779)
                      +..+++|+.|+|++|.. ..+                 ..+..+++|+.|+|+++ .+..+ +..+..+++|+.|++++|
T Consensus       181 ~~~l~~L~~L~L~~n~l-~~~-----------------~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~n  241 (440)
T 3zyj_A          181 FEGLSNLRYLNLAMCNL-REI-----------------PNLTPLIKLDELDLSGN-HLSAIRPGSFQGLMHLQKLWMIQS  241 (440)
T ss_dssp             TTTCSSCCEEECTTSCC-SSC-----------------CCCTTCSSCCEEECTTS-CCCEECTTTTTTCTTCCEEECTTC
T ss_pred             hhcccccCeecCCCCcC-ccc-----------------cccCCCcccCEEECCCC-ccCccChhhhccCccCCEEECCCC
Confidence            78899999999999753 333                 24678999999999995 66666 557778999999999987


Q ss_pred             CCCCCCCC-CCCC-cccccEEEech
Q 004021          730 PKLKKLPI-NSSS-AKERRVVIEGL  752 (779)
Q Consensus       730 ~~L~~lP~-~~~~-~~~~~l~i~~~  752 (779)
                      . +..++. .+.. .+++.+.++++
T Consensus       242 ~-l~~~~~~~~~~l~~L~~L~L~~N  265 (440)
T 3zyj_A          242 Q-IQVIERNAFDNLQSLVEINLAHN  265 (440)
T ss_dssp             C-CCEECTTSSTTCTTCCEEECTTS
T ss_pred             c-eeEEChhhhcCCCCCCEEECCCC
Confidence            4 666554 3333 33477777654

>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=99.68  E-value=3.4e-16  Score=161.96  Aligned_cols=206  Identities=19%  Similarity=0.200  Sum_probs=163.4

Q ss_pred             cccccCccccccCCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCc-cccc-c
Q 004021          483 VKLTEAPKVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTH-IRGL-P  552 (779)
Q Consensus       483 ~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~-i~~l-p  552 (779)
                      ..+..+|. .....+++|++++|.+..++...     .  .|+|++| .+..+ |..|.++++|++|++++|. ++.+ |
T Consensus        21 ~~l~~ip~-~~~~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~~l~~~~~   98 (285)
T 1ozn_A           21 QGLQAVPV-GIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSN-VLARIDAAAFTGLALLEQLDLSDNAQLRSVDP   98 (285)
T ss_dssp             SCCSSCCT-TCCTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSCTTCCCCCT
T ss_pred             CCcccCCc-CCCCCceEEEeeCCcCCccCHHHcccCCCCCEEECCCC-ccceeCHhhcCCccCCCEEeCCCCCCccccCH
Confidence            34455553 23468999999999998876431     2  4999999 88887 7889999999999999997 8888 6


Q ss_pred             hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEee
Q 004021          553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFR  632 (779)
Q Consensus       553 ~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~  632 (779)
                      ..+.++++|++|++++| .+..+++..+.++++|++|++++|.+..              .....++.+++|+.|+++.|
T Consensus        99 ~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~n  163 (285)
T 1ozn_A           99 ATFHGLGRLHTLHLDRC-GLQELGPGLFRGLAALQYLYLQDNALQA--------------LPDDTFRDLGNLTHLFLHGN  163 (285)
T ss_dssp             TTTTTCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECCSSCCCC--------------CCTTTTTTCTTCCEEECCSS
T ss_pred             HHhcCCcCCCEEECCCC-cCCEECHhHhhCCcCCCEEECCCCcccc--------------cCHhHhccCCCccEEECCCC
Confidence            77999999999999999 5677765558999999999999998875              22344778999999999855


Q ss_pred             cccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          633 SSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       633 ~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                               +++.+....+..+++|+.|++++|.. ..+..               ..+..+++|+.|+++++ .+..++
T Consensus       164 ---------~l~~~~~~~~~~l~~L~~L~l~~n~l-~~~~~---------------~~~~~l~~L~~L~l~~n-~l~~~~  217 (285)
T 1ozn_A          164 ---------RISSVPERAFRGLHSLDRLLLHQNRV-AHVHP---------------HAFRDLGRLMTLYLFAN-NLSALP  217 (285)
T ss_dssp             ---------CCCEECTTTTTTCTTCCEEECCSSCC-CEECT---------------TTTTTCTTCCEEECCSS-CCSCCC
T ss_pred             ---------cccccCHHHhcCccccCEEECCCCcc-cccCH---------------hHccCcccccEeeCCCC-cCCcCC
Confidence                     34445455678899999999999764 44433               36788999999999985 666666


Q ss_pred             C-CCCCCCCccEEeeeCCCC
Q 004021          713 P-NPLHFPKLKKIGVYGCPK  731 (779)
Q Consensus       713 ~-~~~~l~~L~~L~l~~c~~  731 (779)
                      . .+..+++|+.|++++++-
T Consensus       218 ~~~~~~l~~L~~L~l~~N~~  237 (285)
T 1ozn_A          218 TEALAPLRALQYLRLNDNPW  237 (285)
T ss_dssp             HHHHTTCTTCCEEECCSSCE
T ss_pred             HHHcccCcccCEEeccCCCc
Confidence            4 366899999999999863

>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=99.68  E-value=4.8e-16  Score=173.56  Aligned_cols=237  Identities=17%  Similarity=0.195  Sum_probs=166.8

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+..+..+|.. -...++.|++++|.+..++..     +.  .|+|++| .+..+ |..|+++++|++|+|++|.++.+|
T Consensus        19 ~~~~l~~ip~~-~~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n-~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~   96 (477)
T 2id5_A           19 HRKRFVAVPEG-IPTETRLLDLGKNRIKTLNQDEFASFPHLEELELNEN-IVSAVEPGAFNNLFNLRTLGLRSNRLKLIP   96 (477)
T ss_dssp             CSCCCSSCCSC-CCTTCSEEECCSSCCCEECTTTTTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECCSSCCCSCC
T ss_pred             CCCCcCcCCCC-CCCCCcEEECCCCccceECHhHccCCCCCCEEECCCC-ccCEeChhhhhCCccCCEEECCCCcCCccC
Confidence            34445555542 235889999999998877532     11  3899999 88876 778999999999999999999988


Q ss_pred             hh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEe
Q 004021          553 QE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSF  631 (779)
Q Consensus       553 ~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~  631 (779)
                      .. |.++++|++|++++| .+..+++..+.++++|++|++++|.+..              ..+..+..+++|+.|+++.
T Consensus        97 ~~~~~~l~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~  161 (477)
T 2id5_A           97 LGVFTGLSNLTKLDISEN-KIVILLDYMFQDLYNLKSLEVGDNDLVY--------------ISHRAFSGLNSLEQLTLEK  161 (477)
T ss_dssp             TTSSTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEEECCTTCCE--------------ECTTSSTTCTTCCEEEEES
T ss_pred             cccccCCCCCCEEECCCC-ccccCChhHccccccCCEEECCCCccce--------------eChhhccCCCCCCEEECCC
Confidence            65 688999999999999 5566655458899999999999987764              3344567788888888887


Q ss_pred             eccccc-----ccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCC
Q 004021          632 RSSLAV-----QKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQ  696 (779)
Q Consensus       632 ~~~~~~-----~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  696 (779)
                      |....+     ..+++|+.|          ....+..+++|+.|++++|+.+..++.                ......+
T Consensus       162 n~l~~~~~~~l~~l~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~----------------~~~~~~~  225 (477)
T 2id5_A          162 CNLTSIPTEALSHLHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTP----------------NCLYGLN  225 (477)
T ss_dssp             CCCSSCCHHHHTTCTTCCEEEEESCCCCEECTTCSCSCTTCCEEEEECCTTCCEECT----------------TTTTTCC
T ss_pred             CcCcccChhHhcccCCCcEEeCCCCcCcEeChhhcccCcccceeeCCCCccccccCc----------------ccccCcc
Confidence            665432     345555555          223456677888888888777666654                2233458


Q ss_pred             ccEEEccCCCCCccccC-CCCCCCCccEEeeeCCCCCCCCCCC-CCC-cccccEEEech
Q 004021          697 LESLGILYGPDLKSIYP-NPLHFPKLKKIGVYGCPKLKKLPIN-SSS-AKERRVVIEGL  752 (779)
Q Consensus       697 L~~L~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~~L~~lP~~-~~~-~~~~~l~i~~~  752 (779)
                      |+.|+++++ .++.++. .+..+++|+.|++++|+ +..+|.. +.. ..++.+.+.++
T Consensus       226 L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~~~~~~l~~L~~L~L~~n  282 (477)
T 2id5_A          226 LTSLSITHC-NLTAVPYLAVRHLVYLRFLNLSYNP-ISTIEGSMLHELLRLQEIQLVGG  282 (477)
T ss_dssp             CSEEEEESS-CCCSCCHHHHTTCTTCCEEECCSSC-CCEECTTSCTTCTTCCEEECCSS
T ss_pred             ccEEECcCC-cccccCHHHhcCccccCeeECCCCc-CCccChhhccccccCCEEECCCC
Confidence            888888874 5666663 45678889999998875 6666543 222 23477777654

>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=99.68  E-value=1.4e-16  Score=166.69  Aligned_cols=210  Identities=20%  Similarity=0.227  Sum_probs=164.4

Q ss_pred             cCcccccCcc--ccccCCccEEEccccccccccc-------Ccc--cccccccccccccchhhcccccCceeeecCCccc
Q 004021          481 AGVKLTEAPK--VKEWEGAKRISLMANEIESLSE-------IPT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIR  549 (779)
Q Consensus       481 ~~~~~~~~~~--~~~~~~lr~l~l~~~~~~~l~~-------~~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~  549 (779)
                      .+..+..++.  +..+.+++.|++++|.+..+..       ...  .|+|++| .+..+|..+.++++|++|++++|.++
T Consensus        36 ~~n~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n-~i~~l~~~~~~l~~L~~L~l~~n~l~  114 (306)
T 2z66_A           36 ESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFN-GVITMSSNFLGLEQLEHLDFQHSNLK  114 (306)
T ss_dssp             CSSCCCCCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHHHSCSCCCEEECCSC-SEEEEEEEEETCTTCCEEECTTSEEE
T ss_pred             CCCccCccCHhHhhccccCCEEECCCCccCcccCcccccccccccCEEECCCC-ccccChhhcCCCCCCCEEECCCCccc
Confidence            3444555554  4678899999999998875521       112  4999999 99999999999999999999999999


Q ss_pred             ccch--hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCce
Q 004021          550 GLPQ--ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVL  627 (779)
Q Consensus       550 ~lp~--~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L  627 (779)
                      .+|.  .+.++++|++|++++| .+..+++..+.++++|++|++++|.+..             ...+..+..+++|+.|
T Consensus       115 ~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~-------------~~~~~~~~~l~~L~~L  180 (306)
T 2z66_A          115 QMSEFSVFLSLRNLIYLDISHT-HTRVAFNGIFNGLSSLEVLKMAGNSFQE-------------NFLPDIFTELRNLTFL  180 (306)
T ss_dssp             SSTTTTTTTTCTTCCEEECTTS-CCEECSTTTTTTCTTCCEEECTTCEEGG-------------GEECSCCTTCTTCCEE
T ss_pred             ccccchhhhhccCCCEEECCCC-cCCccchhhcccCcCCCEEECCCCcccc-------------ccchhHHhhCcCCCEE
Confidence            9875  7999999999999999 4555555458999999999999998763             2355668889999999


Q ss_pred             eEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCC
Q 004021          628 SWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPD  707 (779)
Q Consensus       628 ~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~  707 (779)
                      +++.|         ++..+.+.++..+++|+.|+|++|.. ..++.               ..+..+++|+.|+++++.-
T Consensus       181 ~Ls~n---------~l~~~~~~~~~~l~~L~~L~L~~N~l-~~~~~---------------~~~~~l~~L~~L~L~~N~l  235 (306)
T 2z66_A          181 DLSQC---------QLEQLSPTAFNSLSSLQVLNMSHNNF-FSLDT---------------FPYKCLNSLQVLDYSLNHI  235 (306)
T ss_dssp             ECTTS---------CCCEECTTTTTTCTTCCEEECTTSCC-SBCCS---------------GGGTTCTTCCEEECTTSCC
T ss_pred             ECCCC---------CcCCcCHHHhcCCCCCCEEECCCCcc-CccCh---------------hhccCcccCCEeECCCCCC
Confidence            99844         44555566788899999999999754 33333               2567899999999999654


Q ss_pred             CccccCCCCCCC-CccEEeeeCCC
Q 004021          708 LKSIYPNPLHFP-KLKKIGVYGCP  730 (779)
Q Consensus       708 l~~l~~~~~~l~-~L~~L~l~~c~  730 (779)
                      ....+..+..+| +|++|++++|+
T Consensus       236 ~~~~~~~~~~~~~~L~~L~L~~N~  259 (306)
T 2z66_A          236 MTSKKQELQHFPSSLAFLNLTQND  259 (306)
T ss_dssp             CBCSSSSCCCCCTTCCEEECTTCC
T ss_pred             cccCHHHHHhhhccCCEEEccCCC
Confidence            444555667775 99999999886

>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=99.67  E-value=3.8e-16  Score=174.33  Aligned_cols=223  Identities=20%  Similarity=0.194  Sum_probs=174.3

Q ss_pred             ccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCc
Q 004021          497 AKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTH  570 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~  570 (779)
                      .+.+..+++.+..+|...+    .|+|++| .+..+ |..|.++++|++|+|++|.++.+ |..|.++++|++|+|++| 
T Consensus        13 ~~~v~c~~~~l~~ip~~~~~~l~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n-   90 (477)
T 2id5_A           13 DRAVLCHRKRFVAVPEGIPTETRLLDLGKN-RIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSN-   90 (477)
T ss_dssp             TTEEECCSCCCSSCCSCCCTTCSEEECCSS-CCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS-
T ss_pred             CCEEEeCCCCcCcCCCCCCCCCcEEECCCC-ccceECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCC-
Confidence            3567888888888776433    6999999 89887 67899999999999999999987 778999999999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc-----cccCCCCCc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA-----VQKFFKYPK  645 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~-----~~~~~~L~~  645 (779)
                      .+..+|.+.++++++|++|++++|.+..              ..+..+..+++|+.|+++.|....     +..+++|+.
T Consensus        91 ~l~~~~~~~~~~l~~L~~L~Ls~n~i~~--------------~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~  156 (477)
T 2id5_A           91 RLKLIPLGVFTGLSNLTKLDISENKIVI--------------LLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQ  156 (477)
T ss_dssp             CCCSCCTTSSTTCTTCCEEECTTSCCCE--------------ECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCE
T ss_pred             cCCccCcccccCCCCCCEEECCCCcccc--------------CChhHccccccCCEEECCCCccceeChhhccCCCCCCE
Confidence            6889998768999999999999998874              345567889999999999876543     345566666


Q ss_pred             cc----------CcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCC
Q 004021          646 LD----------LTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNP  715 (779)
Q Consensus       646 L~----------~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~  715 (779)
                      |.          ...+..+++|+.|+|++|.. ..++.               ..+..+++|+.|++++++.+..++...
T Consensus       157 L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n~i-~~~~~---------------~~~~~l~~L~~L~l~~~~~~~~~~~~~  220 (477)
T 2id5_A          157 LTLEKCNLTSIPTEALSHLHGLIVLRLRHLNI-NAIRD---------------YSFKRLYRLKVLEISHWPYLDTMTPNC  220 (477)
T ss_dssp             EEEESCCCSSCCHHHHTTCTTCCEEEEESCCC-CEECT---------------TCSCSCTTCCEEEEECCTTCCEECTTT
T ss_pred             EECCCCcCcccChhHhcccCCCcEEeCCCCcC-cEeCh---------------hhcccCcccceeeCCCCccccccCccc
Confidence            61          12366778888888888543 33433               367788999999999988888888877


Q ss_pred             CCCCCccEEeeeCCCCCCCCCCC-C-CCcccccEEEech
Q 004021          716 LHFPKLKKIGVYGCPKLKKLPIN-S-SSAKERRVVIEGL  752 (779)
Q Consensus       716 ~~l~~L~~L~l~~c~~L~~lP~~-~-~~~~~~~l~i~~~  752 (779)
                      ...++|+.|++++| ++..+|.. + ....++.+.+.++
T Consensus       221 ~~~~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~Ls~n  258 (477)
T 2id5_A          221 LYGLNLTSLSITHC-NLTAVPYLAVRHLVYLRFLNLSYN  258 (477)
T ss_dssp             TTTCCCSEEEEESS-CCCSCCHHHHTTCTTCCEEECCSS
T ss_pred             ccCccccEEECcCC-cccccCHHHhcCccccCeeECCCC
Confidence            77789999999987 57788732 2 2234477777654

>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=99.67  E-value=1.1e-16  Score=171.13  Aligned_cols=242  Identities=20%  Similarity=0.198  Sum_probs=143.9

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+..+..+|. .-.+.+++|++++|.+..++..     +.  .|+|++| .+..+ |..|+++++|++|++++|.++.+|
T Consensus        39 ~~~~l~~iP~-~~~~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~  116 (353)
T 2z80_A           39 SSGSLNSIPS-GLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSN-GINTIEEDSFSSLGSLEHLDLSYNYLSNLS  116 (353)
T ss_dssp             CSTTCSSCCT-TCCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECCSSCCSSCC
T ss_pred             CCCCcccccc-cccccCcEEECCCCcCcccCHHHhccCCCCCEEECCCC-ccCccCHhhcCCCCCCCEEECCCCcCCcCC
Confidence            3444555554 2235788999998888877652     11  3888888 88876 556888899999999999888888


Q ss_pred             hh-hccCccCcEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEE
Q 004021          553 QE-LKALEKLRYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       553 ~~-~~~L~~L~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                      .. ++++++|++|++++| .++.+|. ..++++++|++|++++|....             ...+..++.+++|+.|+++
T Consensus       117 ~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~~l~~L~~L~l~~n~~~~-------------~~~~~~~~~l~~L~~L~l~  182 (353)
T 2z80_A          117 SSWFKPLSSLTFLNLLGN-PYKTLGETSLFSHLTKLQILRVGNMDTFT-------------KIQRKDFAGLTFLEELEID  182 (353)
T ss_dssp             HHHHTTCTTCSEEECTTC-CCSSSCSSCSCTTCTTCCEEEEEESSSCC-------------EECTTTTTTCCEEEEEEEE
T ss_pred             HhHhCCCccCCEEECCCC-CCcccCchhhhccCCCCcEEECCCCcccc-------------ccCHHHccCCCCCCEEECC
Confidence            76 788899999999988 6778887 447888999999998874221             2234557778888888888


Q ss_pred             eeccccc-----ccCCCCCcccC----------cccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCC
Q 004021          631 FRSSLAV-----QKFFKYPKLDL----------TWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFT  695 (779)
Q Consensus       631 ~~~~~~~-----~~~~~L~~L~~----------~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  695 (779)
                      .|.....     ..+++|+.|.+          ..+..+++|+.|++++|......+.        .+     ......+
T Consensus       183 ~n~l~~~~~~~l~~l~~L~~L~l~~n~l~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~--------~l-----~~~~~~~  249 (353)
T 2z80_A          183 ASDLQSYEPKSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFS--------EL-----STGETNS  249 (353)
T ss_dssp             ETTCCEECTTTTTTCSEEEEEEEECSCSTTHHHHHHHHTTTEEEEEEESCBCTTCCCC-------------------CCC
T ss_pred             CCCcCccCHHHHhccccCCeecCCCCccccchhhhhhhcccccEEECCCCcccccccc--------cc-----ccccccc
Confidence            7654322     22223333311          1122355566666655433221110        00     0111223


Q ss_pred             CccEEEccCCCC----CccccCCCCCCCCccEEeeeCCCCCCCCCCCC-CC-cccccEEEech
Q 004021          696 QLESLGILYGPD----LKSIYPNPLHFPKLKKIGVYGCPKLKKLPINS-SS-AKERRVVIEGL  752 (779)
Q Consensus       696 ~L~~L~l~~~~~----l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~-~~-~~~~~l~i~~~  752 (779)
                      .++.+++.++.-    +..+|..+..+++|++|++++| +++.+|... .. ..++.+.+.++
T Consensus       250 ~l~~l~L~~~~l~~~~l~~l~~~l~~l~~L~~L~Ls~N-~l~~i~~~~~~~l~~L~~L~L~~N  311 (353)
T 2z80_A          250 LIKKFTFRNVKITDESLFQVMKLLNQISGLLELEFSRN-QLKSVPDGIFDRLTSLQKIWLHTN  311 (353)
T ss_dssp             CCCEEEEESCBCCHHHHHHHHHHHHTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             hhhccccccccccCcchhhhHHHHhcccCCCEEECCCC-CCCccCHHHHhcCCCCCEEEeeCC
Confidence            333333333210    0112333445677777777776 466777653 22 23366666643

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.67  E-value=1.5e-16  Score=188.10  Aligned_cols=102  Identities=24%  Similarity=0.318  Sum_probs=47.2

Q ss_pred             cccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |++++| .+. .+|..++.+++|++|++++|.++ .+|..++++++|++|++++|.....+|.. ++.+++|++|++++|
T Consensus       447 L~L~~n-~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~-~~~l~~L~~L~L~~N  524 (768)
T 3rgz_A          447 LKLWLN-MLEGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKW-IGRLENLAILKLSNN  524 (768)
T ss_dssp             EECCSS-CCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGG-GGGCTTCCEEECCSS
T ss_pred             EECCCC-cccCcCCHHHcCCCCceEEEecCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChH-HhcCCCCCEEECCCC
Confidence            444444 333 33444444444444444444443 23444444444444444444322234443 444444444444444


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      .+.+              ..+..++.+++|+.|+++.|..
T Consensus       525 ~l~~--------------~~p~~l~~l~~L~~L~Ls~N~l  550 (768)
T 3rgz_A          525 SFSG--------------NIPAELGDCRSLIWLDLNTNLF  550 (768)
T ss_dssp             CCEE--------------ECCGGGGGCTTCCEEECCSSEE
T ss_pred             cccC--------------cCCHHHcCCCCCCEEECCCCcc
Confidence            4332              3445566666666666665543

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.67  E-value=4.5e-16  Score=168.86  Aligned_cols=241  Identities=17%  Similarity=0.161  Sum_probs=155.6

Q ss_pred             ccCCccEEEcccccccccccCc-----c--cccccccccccccc-hhhcccccCceeeecCCcccccch-hhccCccCcE
Q 004021          493 EWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRY  563 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~  563 (779)
                      .+.+++++++.++.+..+|...     .  .|+|++| .+..+| ..|+++++|++|++++|.++.+|+ .++++++|++
T Consensus        43 ~l~~l~~l~l~~~~l~~l~~~~~~~l~~L~~L~L~~n-~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  121 (390)
T 3o6n_A           43 TLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDL-QIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTV  121 (390)
T ss_dssp             GGCCCSEEEEESCEESEECTHHHHHCCCCSEEECTTS-CCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCE
T ss_pred             ccCCceEEEecCCchhhCChhHhcccccCcEEECCCC-cccccChhhccCCCCcCEEECCCCCCCcCCHHHhcCCCCCCE
Confidence            4578999999999999888642     2  4999999 888875 489999999999999999999865 4899999999


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc--ccCC
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV--QKFF  641 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~--~~~~  641 (779)
                      |++++| .++.+|.+.++++++|++|++++|.+..+              .+..++.+++|+.|+++.|....+  ..++
T Consensus       122 L~L~~n-~l~~l~~~~~~~l~~L~~L~L~~n~l~~~--------------~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~  186 (390)
T 3o6n_A          122 LVLERN-DLSSLPRGIFHNTPKLTTLSMSNNNLERI--------------EDDTFQATTSLQNLQLSSNRLTHVDLSLIP  186 (390)
T ss_dssp             EECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCBC--------------CTTTTSSCTTCCEEECCSSCCSBCCGGGCT
T ss_pred             EECCCC-ccCcCCHHHhcCCCCCcEEECCCCccCcc--------------ChhhccCCCCCCEEECCCCcCCcccccccc
Confidence            999999 68899998679999999999999988752              233456666777777766554332  3344


Q ss_pred             CCCccc-----Cccccc---------------------ccCcceEEeccccccceecccccccCcc-------cchhhcc
Q 004021          642 KYPKLD-----LTWLVF---------------------VQNLKELEIIVCTEMEEIICVDKLRDVS-------DISEIIG  688 (779)
Q Consensus       642 ~L~~L~-----~~~l~~---------------------l~~L~~L~L~~~~~~~~~~~~~~~~~~~-------~~~~~~~  688 (779)
                      +|+.|.     +..+..                     .++|+.|++++|.... ++.........       .+....+
T Consensus       187 ~L~~L~l~~n~l~~~~~~~~L~~L~l~~n~l~~~~~~~~~~L~~L~l~~n~l~~-~~~l~~l~~L~~L~Ls~n~l~~~~~  265 (390)
T 3o6n_A          187 SLFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTD-TAWLLNYPGLVEVDLSYNELEKIMY  265 (390)
T ss_dssp             TCSEEECCSSCCSEEECCSSCSEEECCSSCCCEEECCCCSSCCEEECCSSCCCC-CGGGGGCTTCSEEECCSSCCCEEES
T ss_pred             ccceeecccccccccCCCCcceEEECCCCeeeeccccccccccEEECCCCCCcc-cHHHcCCCCccEEECCCCcCCCcCh
Confidence            444431     111122                     2455666665543221 11100000000       0000011


Q ss_pred             CCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCc-ccccEEEech
Q 004021          689 SEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA-KERRVVIEGL  752 (779)
Q Consensus       689 ~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~-~~~~l~i~~~  752 (779)
                      ..+..+++|+.|++++ +.+..++.....+|+|++|++++| .+..+|..+... .++.+.+.++
T Consensus       266 ~~~~~l~~L~~L~L~~-n~l~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~l~~L~~L~L~~N  328 (390)
T 3o6n_A          266 HPFVKMQRLERLYISN-NRLVALNLYGQPIPTLKVLDLSHN-HLLHVERNQPQFDRLENLYLDHN  328 (390)
T ss_dssp             GGGTTCSSCCEEECCS-SCCCEEECSSSCCTTCCEEECCSS-CCCCCGGGHHHHTTCSEEECCSS
T ss_pred             hHccccccCCEEECCC-CcCcccCcccCCCCCCCEEECCCC-cceecCccccccCcCCEEECCCC
Confidence            3455566677777766 355666665566777777777766 466666543322 2355665544

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.66  E-value=4.4e-16  Score=179.70  Aligned_cols=237  Identities=12%  Similarity=0.130  Sum_probs=149.9

Q ss_pred             cCcccccCcc---ccccCCccEEEccccccc-ccccCcc-----cccccccccccccchhhccccc-CceeeecCCcccc
Q 004021          481 AGVKLTEAPK---VKEWEGAKRISLMANEIE-SLSEIPT-----LLSLRRNDSLTELPSRISSLVS-LHHLDLSLTHIRG  550 (779)
Q Consensus       481 ~~~~~~~~~~---~~~~~~lr~l~l~~~~~~-~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~-L~~L~L~~~~i~~  550 (779)
                      .+..+..+|.   +..+.+++.|++++|.+. .+|....     .|+|++| .+..+|..++++++ |++|++++|.++.
T Consensus       313 ~~n~l~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip~~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~~L~~L~Ls~N~l~~  391 (636)
T 4eco_A          313 GYNNLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGSEIKLASLNLAYN-QITEIPANFCGFTEQVENLSFAHNKLKY  391 (636)
T ss_dssp             CSSCCSSCCCHHHHTTCTTCCEEECCSCCCEEECCCCEEEEEESEEECCSS-EEEECCTTSEEECTTCCEEECCSSCCSS
T ss_pred             CCCcCCccCchhhhccCCCCCEEeCcCCcCccchhhhCCCCCCCEEECCCC-ccccccHhhhhhcccCcEEEccCCcCcc
Confidence            3334445554   456667777777777776 5652211     2777777 66677777777777 7777777777777


Q ss_pred             cchhhccCc--cCcEeeccCCcCCCCCchhhhc-------CCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCC
Q 004021          551 LPQELKALE--KLRYLNLEYTHYLSIIPHQLIS-------GFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGL  621 (779)
Q Consensus       551 lp~~~~~L~--~L~~L~l~~~~~l~~lp~~~i~-------~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L  621 (779)
                      +|..+..+.  +|++|++++|.....+|.. +.       .+.+|++|++++|.+..+|              ...+..+
T Consensus       392 lp~~~~~~~l~~L~~L~Ls~N~l~~~~p~~-l~~~~~~~~~~~~L~~L~Ls~N~l~~lp--------------~~~~~~l  456 (636)
T 4eco_A          392 IPNIFDAKSVSVMSAIDFSYNEIGSVDGKN-FDPLDPTPFKGINVSSINLSNNQISKFP--------------KELFSTG  456 (636)
T ss_dssp             CCSCCCTTCSSCEEEEECCSSCTTTTTTCS-SCTTCSSCCCCCCEEEEECCSSCCCSCC--------------THHHHTT
T ss_pred             cchhhhhcccCccCEEECcCCcCCCcchhh-hcccccccccCCCCCEEECcCCccCcCC--------------HHHHccC
Confidence            776666544  6777777777443444443 55       5667777777777665422              1223456


Q ss_pred             CCCCceeEEeeccccccc------------CCCCCcc---------cCcccc--cccCcceEEeccccccceeccccccc
Q 004021          622 KRLNVLSWSFRSSLAVQK------------FFKYPKL---------DLTWLV--FVQNLKELEIIVCTEMEEIICVDKLR  678 (779)
Q Consensus       622 ~~L~~L~l~~~~~~~~~~------------~~~L~~L---------~~~~l~--~l~~L~~L~L~~~~~~~~~~~~~~~~  678 (779)
                      ++|+.|+++.|....++.            +++|+.|         .+..+.  .+++|+.|+|++|.... ++.     
T Consensus       457 ~~L~~L~Ls~N~l~~i~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N~l~~-ip~-----  530 (636)
T 4eco_A          457 SPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYNSFSK-FPT-----  530 (636)
T ss_dssp             CCCSEEECCSSCCSBCCSSSSEETTEECTTGGGCCEEECCSSCCCBCCGGGSTTTCTTCCEEECCSSCCSS-CCC-----
T ss_pred             CCCCEEECCCCCCCCcCHHHhccccccccccCCccEEECcCCcCCccChhhhhccCCCcCEEECCCCCCCC-cCh-----
Confidence            777777777665543311            1144444         123344  67788888888765433 433     


Q ss_pred             CcccchhhccCCCCCCCCccEEEccC------CCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          679 DVSDISEIIGSEHNFFTQLESLGILY------GPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       679 ~~~~~~~~~~~~~~~~~~L~~L~l~~------~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                                 .+..+++|+.|+|++      +.-...+|..+..+++|++|++++|. ++.+|..+. ..++.+.++++
T Consensus       531 -----------~~~~l~~L~~L~Ls~N~~ls~N~l~~~~p~~l~~l~~L~~L~Ls~N~-l~~ip~~~~-~~L~~L~Ls~N  597 (636)
T 4eco_A          531 -----------QPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPSLTQLQIGSND-IRKVNEKIT-PNISVLDIKDN  597 (636)
T ss_dssp             -----------GGGGCSSCCEEECCSCBCTTCCBCCCCCCTTGGGCSSCCEEECCSSC-CCBCCSCCC-TTCCEEECCSC
T ss_pred             -----------hhhcCCCCCEEECCCCcccccCcccccChHHHhcCCCCCEEECCCCc-CCccCHhHh-CcCCEEECcCC
Confidence                       556788888888854      33355677777788888888888875 588887655 45577777765

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.65  E-value=1.1e-15  Score=179.72  Aligned_cols=235  Identities=13%  Similarity=0.115  Sum_probs=135.7

Q ss_pred             CccEEEccccccccccc--Cc-c-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCcc-CcEeec
Q 004021          496 GAKRISLMANEIESLSE--IP-T-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK-LRYLNL  566 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~--~~-~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~-L~~L~l  566 (779)
                      +++.|++++|.+..+|.  .. .     .|+|++| .+..+| .|+++++|++|+|++|.+..+|..+.++++ |++|++
T Consensus       549 ~L~~L~Ls~N~L~~ip~~~~l~~L~~L~~L~Ls~N-~l~~lp-~~~~L~~L~~L~Ls~N~l~~lp~~l~~l~~~L~~L~L  626 (876)
T 4ecn_A          549 KIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHN-KVRHLE-AFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGF  626 (876)
T ss_dssp             TCCEEECCSSCCCBCCCHHHHTTCTTCCEEECTTS-CCCBCC-CCCTTSEESEEECCSSCCSCCCTTSCEECTTCCEEEC
T ss_pred             CccEEEeeCCcCCccCChhhhhcCCCCCEEECCCC-Ccccch-hhcCCCcceEEECcCCccccchHHHhhccccCCEEEC
Confidence            55666666665555554  11 1     2556666 555555 555666666666666655556655666655 666666


Q ss_pred             cCCcCCCCCchhhhcCCcc--CcEeeeccccCCCcccccC---------C----ccCC-CchhhHHh-hcCCCCCCceeE
Q 004021          567 EYTHYLSIIPHQLISGFLK--LEVLRLLECGSEGVTKEEG---------N----VLCD-DAEPLMRE-LLGLKRLNVLSW  629 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~--L~~L~l~~~~~~~~~~~~~---------~----~~~~-~~~~~~~~-l~~L~~L~~L~l  629 (779)
                      ++| .+..+|.. +..+..  |++|++++|.+.+.+..+.         +    .+.. .....+.. +..+++|+.|++
T Consensus       627 s~N-~L~~lp~~-~~~~~~~~L~~L~Ls~N~l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~L~~lp~~~~~~l~~L~~L~L  704 (876)
T 4ecn_A          627 SHN-KLKYIPNI-FNAKSVYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPISTIIL  704 (876)
T ss_dssp             CSS-CCCSCCSC-CCTTCSSCEEEEECCSSCTTTTSSSCSSCTTTCCCCCEEEEECCSSCCCSCCHHHHHTTCCCSEEEC
T ss_pred             cCC-CCCcCchh-hhccccCCCCEEECcCCcCCCccccchhhhccccCCCcCEEEccCCcCCccCHHHHccCCCCCEEEC
Confidence            665 34455543 444432  5566665555543211111         0    0000 00112222 336777888888


Q ss_pred             Eeeccccccc------------CCCCCcc---------cCcccc--cccCcceEEeccccccceecccccccCcccchhh
Q 004021          630 SFRSSLAVQK------------FFKYPKL---------DLTWLV--FVQNLKELEIIVCTEMEEIICVDKLRDVSDISEI  686 (779)
Q Consensus       630 ~~~~~~~~~~------------~~~L~~L---------~~~~l~--~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~  686 (779)
                      +.|....++.            +++|+.|         .+..+.  .+++|+.|+|++|.... ++              
T Consensus       705 s~N~L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~L~~lp~~l~~~~l~~L~~L~Ls~N~L~~-lp--------------  769 (876)
T 4ecn_A          705 SNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYNCFSS-FP--------------  769 (876)
T ss_dssp             CSCCCSCCCTTSSSCTTSCCTTGGGCCEEECCSSCCCCCCGGGSTTTCTTCCEEECCSSCCSS-CC--------------
T ss_pred             CCCcCCccChHHhccccccccccCCccEEECCCCCCccchHHhhhccCCCcCEEEeCCCCCCc-cc--------------
Confidence            7766543321            1144444         223344  67788888887765433 33              


Q ss_pred             ccCCCCCCCCccEEEccC------CCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEechH
Q 004021          687 IGSEHNFFTQLESLGILY------GPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGLK  753 (779)
Q Consensus       687 ~~~~~~~~~~L~~L~l~~------~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~~  753 (779)
                        ..+..+++|+.|+|++      +.-...+|..+..+++|+.|++++|. +..+|..+. ..++.+.+++++
T Consensus       770 --~~l~~L~~L~~L~Ls~N~~ls~N~l~~~ip~~l~~L~~L~~L~Ls~N~-L~~Ip~~l~-~~L~~LdLs~N~  838 (876)
T 4ecn_A          770 --TQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSND-IRKVDEKLT-PQLYILDIADNP  838 (876)
T ss_dssp             --CGGGGCTTCCEEECCCCBCTTCCBCCCCCCTTGGGCSSCCEEECCSSC-CCBCCSCCC-SSSCEEECCSCT
T ss_pred             --hhhhcCCCCCEEECCCCCCcccccccccChHHHhcCCCCCEEECCCCC-CCccCHhhc-CCCCEEECCCCC
Confidence              3566889999999976      33355677778889999999999885 588998765 356888887764

>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=99.65  E-value=2.2e-16  Score=168.82  Aligned_cols=213  Identities=19%  Similarity=0.173  Sum_probs=158.5

Q ss_pred             ccccCCccEEEcccccccccccC-----cc--cccccccccccccchh-hcccccCceeeecCCcccccch--hhccCcc
Q 004021          491 VKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGLPQ--ELKALEK  560 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~lp~~-i~~L~~L~~L~L~~~~i~~lp~--~~~~L~~  560 (779)
                      +..+.+++.|++++|.+..++..     +.  .|+|++| .++.+|.. ++++++|++|++++|.++.+|.  .+.++++
T Consensus        72 ~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~  150 (353)
T 2z80_A           72 LQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYN-YLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTK  150 (353)
T ss_dssp             TTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCSSCCHHHHTTCTTCSEEECTTCCCSSSCSSCSCTTCTT
T ss_pred             hccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCC-cCCcCCHhHhCCCccCCEEECCCCCCcccCchhhhccCCC
Confidence            56778999999999998877542     12  4999999 99999776 8999999999999999999987  6899999


Q ss_pred             CcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc---
Q 004021          561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV---  637 (779)
Q Consensus       561 L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~---  637 (779)
                      |++|++++|..+..+++..++++++|++|++++|.+.+              ..+..++.+++|+.|+++.|....+   
T Consensus       151 L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~l~~l~~L~~L~l~~n~l~~~~~~  216 (353)
T 2z80_A          151 LQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQS--------------YEPKSLKSIQNVSHLILHMKQHILLLEI  216 (353)
T ss_dssp             CCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCE--------------ECTTTTTTCSEEEEEEEECSCSTTHHHH
T ss_pred             CcEEECCCCccccccCHHHccCCCCCCEEECCCCCcCc--------------cCHHHHhccccCCeecCCCCccccchhh
Confidence            99999999966777766558999999999999998775              2345566677777777776655332   


Q ss_pred             --ccCCCCCcccC-------------cccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEc
Q 004021          638 --QKFFKYPKLDL-------------TWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGI  702 (779)
Q Consensus       638 --~~~~~L~~L~~-------------~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l  702 (779)
                        ..+++|+.|.+             +.....+.++.++++.+.....-.        ..++    ..+..+++|+.|++
T Consensus       217 ~~~~~~~L~~L~L~~n~l~~~~~~~l~~~~~~~~l~~l~L~~~~l~~~~l--------~~l~----~~l~~l~~L~~L~L  284 (353)
T 2z80_A          217 FVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDESL--------FQVM----KLLNQISGLLELEF  284 (353)
T ss_dssp             HHHHTTTEEEEEEESCBCTTCCCC------CCCCCCEEEEESCBCCHHHH--------HHHH----HHHHTCTTCCEEEC
T ss_pred             hhhhcccccEEECCCCccccccccccccccccchhhccccccccccCcch--------hhhH----HHHhcccCCCEEEC
Confidence              22455555511             112235667888887754322110        0111    34678999999999


Q ss_pred             cCCCCCccccCCC-CCCCCccEEeeeCCCC
Q 004021          703 LYGPDLKSIYPNP-LHFPKLKKIGVYGCPK  731 (779)
Q Consensus       703 ~~~~~l~~l~~~~-~~l~~L~~L~l~~c~~  731 (779)
                      +++ .++.+|... ..+++|++|++++|+-
T Consensus       285 s~N-~l~~i~~~~~~~l~~L~~L~L~~N~~  313 (353)
T 2z80_A          285 SRN-QLKSVPDGIFDRLTSLQKIWLHTNPW  313 (353)
T ss_dssp             CSS-CCCCCCTTTTTTCTTCCEEECCSSCB
T ss_pred             CCC-CCCccCHHHHhcCCCCCEEEeeCCCc
Confidence            984 788888875 7899999999999863

>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=99.65  E-value=1.2e-15  Score=174.95  Aligned_cols=225  Identities=16%  Similarity=0.117  Sum_probs=152.9

Q ss_pred             cCcccccCc--cccccCCccEEEcccccccccccCc-----c--cccccccccccccchh-hcccccCceeeecCCcccc
Q 004021          481 AGVKLTEAP--KVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRG  550 (779)
Q Consensus       481 ~~~~~~~~~--~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~~-i~~L~~L~~L~L~~~~i~~  550 (779)
                      .+..+..++  .+..+.+++.|++++|.+..++...     .  .|+|++| .+..+|.. |+++++|++|+|++|.++.
T Consensus        83 ~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~Ls~N~l~~  161 (597)
T 3oja_B           83 NDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERN-DLSSLPRGIFHNTPKLTTLSMSNNNLER  161 (597)
T ss_dssp             TTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCB
T ss_pred             CCCCCCCCChHHhcCCCCCCEEECCCCcCCCCCHHHHcCCCCCCEEEeeCC-CCCCCCHHHhccCCCCCEEEeeCCcCCC
Confidence            333444433  4567789999999999998876542     1  4999999 99999876 5899999999999999988


Q ss_pred             cch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCc-------------------ccccCC-----
Q 004021          551 LPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGV-------------------TKEEGN-----  605 (779)
Q Consensus       551 lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~-------------------~~~~~~-----  605 (779)
                      +|+ .|+++++|++|++++| .+..+|.   +.+++|++|++++|.+.++                   +.....     
T Consensus       162 ~~~~~~~~l~~L~~L~L~~N-~l~~~~~---~~l~~L~~L~l~~n~l~~l~~~~~L~~L~ls~n~l~~~~~~~~~~L~~L  237 (597)
T 3oja_B          162 IEDDTFQATTSLQNLQLSSN-RLTHVDL---SLIPSLFHANVSYNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTIL  237 (597)
T ss_dssp             CCTTTTTTCTTCCEEECTTS-CCSBCCG---GGCTTCSEEECCSSCCSEEECCTTCSEEECCSSCCCEEECSCCSCCCEE
T ss_pred             CChhhhhcCCcCcEEECcCC-CCCCcCh---hhhhhhhhhhcccCccccccCCchhheeeccCCcccccccccCCCCCEE
Confidence            765 6999999999999999 5677664   4566666666666554432                   111111     


Q ss_pred             ccCCCchhhHHhhcCCCCCCceeEEeecccc-----cccCCCCCccc---------CcccccccCcceEEecccccccee
Q 004021          606 VLCDDAEPLMRELLGLKRLNVLSWSFRSSLA-----VQKFFKYPKLD---------LTWLVFVQNLKELEIIVCTEMEEI  671 (779)
Q Consensus       606 ~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~-----~~~~~~L~~L~---------~~~l~~l~~L~~L~L~~~~~~~~~  671 (779)
                      .+.++....+..+..+++|+.|+++.|....     +..+++|+.|.         +..+..+++|+.|+|++|... .+
T Consensus       238 ~L~~n~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~~L~Ls~N~l~-~i  316 (597)
T 3oja_B          238 KLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLVALNLYGQPIPTLKVLDLSHNHLL-HV  316 (597)
T ss_dssp             ECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSCCEEECTTSCCCEEECSSSCCTTCCEEECCSSCCC-CC
T ss_pred             ECCCCCCCCChhhccCCCCCEEECCCCccCCCCHHHhcCccCCCEEECCCCCCCCCCcccccCCCCcEEECCCCCCC-cc
Confidence            1111111223556677788888887665532     23455555551         122344667777777775432 33


Q ss_pred             cccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCC
Q 004021          672 ICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       672 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                      +.                .+..+++|+.|+|+++ .+..++  ...+++|+.|++++||
T Consensus       317 ~~----------------~~~~l~~L~~L~L~~N-~l~~~~--~~~~~~L~~L~l~~N~  356 (597)
T 3oja_B          317 ER----------------NQPQFDRLENLYLDHN-SIVTLK--LSTHHTLKNLTLSHND  356 (597)
T ss_dssp             GG----------------GHHHHTTCSEEECCSS-CCCCCC--CCTTCCCSEEECCSSC
T ss_pred             Cc----------------ccccCCCCCEEECCCC-CCCCcC--hhhcCCCCEEEeeCCC
Confidence            32                4567899999999995 566664  6689999999999986

>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=99.65  E-value=4.9e-16  Score=179.05  Aligned_cols=234  Identities=15%  Similarity=0.108  Sum_probs=144.4

Q ss_pred             ccccCccccccCCccEEEcccccccccccC--cc--cccccccccccccchhhcccccCceeeecCCccccc---chhhc
Q 004021          484 KLTEAPKVKEWEGAKRISLMANEIESLSEI--PT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL---PQELK  556 (779)
Q Consensus       484 ~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~--~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~l---p~~~~  556 (779)
                      ....++.+..+.+++.|++.+|.+..+|..  +.  .|++++|..+..+  .++.+++|++|++++|.++.+   |..+.
T Consensus       296 ~~~~l~~l~~~~~L~~L~l~~n~l~~lp~~~l~~L~~L~l~~n~~~~~~--~~~~l~~L~~L~ls~n~l~~~~~~~~~~~  373 (606)
T 3vq2_A          296 SIKYLEDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISF--KKVALPSLSYLDLSRNALSFSGCCSYSDL  373 (606)
T ss_dssp             CCCCCCCCCTTCCCSEEEEESCCCSSCCCCCCSSCCEEEEESCSSCEEC--CCCCCTTCCEEECCSSCEEEEEECCHHHH
T ss_pred             cchhhhhccccccCCEEEcccccCcccccCCCCccceeeccCCcCccch--hhccCCCCCEEECcCCccCCCcchhhhhc
Confidence            334444455556667777777666655532  11  2555555222222  445666666666666666554   55666


Q ss_pred             cCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc
Q 004021          557 ALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA  636 (779)
Q Consensus       557 ~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~  636 (779)
                      .+++|++|++++| .+..+|.. +..+++|++|++++|.+.+             ......+..+++|+.|+++.|....
T Consensus       374 ~~~~L~~L~L~~n-~l~~~~~~-~~~l~~L~~L~l~~n~l~~-------------~~~~~~~~~l~~L~~L~l~~n~l~~  438 (606)
T 3vq2_A          374 GTNSLRHLDLSFN-GAIIMSAN-FMGLEELQHLDFQHSTLKR-------------VTEFSAFLSLEKLLYLDISYTNTKI  438 (606)
T ss_dssp             CCSCCCEEECCSC-SEEEECCC-CTTCTTCCEEECTTSEEES-------------TTTTTTTTTCTTCCEEECTTSCCEE
T ss_pred             cCCcccEeECCCC-ccccchhh-ccCCCCCCeeECCCCccCC-------------ccChhhhhccccCCEEECcCCCCCc
Confidence            6666666666666 35556644 6666666666666665553             1111345566666666666554422


Q ss_pred             -----cccCCCCCcc-----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEE
Q 004021          637 -----VQKFFKYPKL-----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESL  700 (779)
Q Consensus       637 -----~~~~~~L~~L-----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L  700 (779)
                           +..+++|+.|           .+..+..+++|+.|+|++|... .++.               ..+..+++|+.|
T Consensus       439 ~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~-~~~~---------------~~~~~l~~L~~L  502 (606)
T 3vq2_A          439 DFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLE-QISW---------------GVFDTLHRLQLL  502 (606)
T ss_dssp             CCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCC-EECT---------------TTTTTCTTCCEE
T ss_pred             cchhhhcCCCCCCEEECCCCcCCCcchHHhhccCCCCCEEECCCCcCC-ccCh---------------hhhcccccCCEE
Confidence                 2334445444           2345677889999999887544 3333               367789999999


Q ss_pred             EccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcc--cccEEEec
Q 004021          701 GILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAK--ERRVVIEG  751 (779)
Q Consensus       701 ~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~--~~~l~i~~  751 (779)
                      +++++.-....|..+..+++|+.|++++|. ++.+|..+...+  ++.+.+.+
T Consensus       503 ~Ls~N~l~~~~~~~~~~l~~L~~L~l~~N~-l~~~p~~~~~l~~~L~~l~l~~  554 (606)
T 3vq2_A          503 NMSHNNLLFLDSSHYNQLYSLSTLDCSFNR-IETSKGILQHFPKSLAFFNLTN  554 (606)
T ss_dssp             ECCSSCCSCEEGGGTTTCTTCCEEECTTSC-CCCEESCGGGSCTTCCEEECCS
T ss_pred             ECCCCcCCCcCHHHccCCCcCCEEECCCCc-CcccCHhHhhhcccCcEEEccC
Confidence            999864433346677889999999999885 888998765542  57777765

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.64  E-value=1.6e-15  Score=155.36  Aligned_cols=192  Identities=20%  Similarity=0.241  Sum_probs=154.4

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      .++++++ .++.+|..+.  .+|++|++++|.++.+|. .|.++++|++|++++| .++.+|.+.+.++++|++|++++|
T Consensus        20 ~l~~~~~-~l~~ip~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~i~~~~~~~l~~L~~L~l~~n   95 (270)
T 2o6q_A           20 SVDCSSK-KLTAIPSNIP--ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDN-KLQTLPAGIFKELKNLETLWVTDN   95 (270)
T ss_dssp             EEECTTS-CCSSCCSCCC--TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSS-CCSCCCTTTTSSCTTCCEEECCSS
T ss_pred             EEEccCC-CCCccCCCCC--CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCC-ccCeeChhhhcCCCCCCEEECCCC
Confidence            4889999 8999998775  689999999999999886 6999999999999999 688999886789999999999999


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      .+..              ..+..+..+++|+.|+++.+.         ++.+.+..+..+++|++|+|++|. +..++. 
T Consensus        96 ~l~~--------------~~~~~~~~l~~L~~L~l~~n~---------l~~~~~~~~~~l~~L~~L~Ls~n~-l~~~~~-  150 (270)
T 2o6q_A           96 KLQA--------------LPIGVFDQLVNLAELRLDRNQ---------LKSLPPRVFDSLTKLTYLSLGYNE-LQSLPK-  150 (270)
T ss_dssp             CCCC--------------CCTTTTTTCSSCCEEECCSSC---------CCCCCTTTTTTCTTCCEEECCSSC-CCCCCT-
T ss_pred             cCCc--------------CCHhHcccccCCCEEECCCCc---------cCeeCHHHhCcCcCCCEEECCCCc-CCccCH-
Confidence            8875              223456788999999998543         444445567889999999999965 444443 


Q ss_pred             ccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCCCC-CCC-cccccEEEec
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLPIN-SSS-AKERRVVIEG  751 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP~~-~~~-~~~~~l~i~~  751 (779)
                                    ..+..+++|+.|+++++ .+..++.. +..+++|++|++++| .++.+|.. +.. ..++.+.+.+
T Consensus       151 --------------~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~  214 (270)
T 2o6q_A          151 --------------GVFDKLTSLKELRLYNN-QLKRVPEGAFDKLTELKTLKLDNN-QLKRVPEGAFDSLEKLKMLQLQE  214 (270)
T ss_dssp             --------------TTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCS
T ss_pred             --------------hHccCCcccceeEecCC-cCcEeChhHhccCCCcCEEECCCC-cCCcCCHHHhccccCCCEEEecC
Confidence                          35778999999999984 67777764 567999999999997 68888875 332 3447888875


Q ss_pred             h
Q 004021          752 L  752 (779)
Q Consensus       752 ~  752 (779)
                      +
T Consensus       215 N  215 (270)
T 2o6q_A          215 N  215 (270)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=4.5e-16  Score=159.71  Aligned_cols=104  Identities=23%  Similarity=0.321  Sum_probs=53.1

Q ss_pred             ccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchh-hccCccCcEe
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYL  564 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L  564 (779)
                      ...+.+++.|.+.+|.+..++....     .|+|++| .+..+| .++++++|++|++++|.++.+|.. ++++++|++|
T Consensus        37 ~~~l~~L~~L~l~~~~i~~~~~l~~l~~L~~L~l~~n-~l~~~~-~l~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L  114 (272)
T 3rfs_A           37 QNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGN-KLHDIS-ALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKEL  114 (272)
T ss_dssp             HHHHTTCCEEECTTSCCCCCTTGGGCTTCCEEECTTS-CCCCCG-GGTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEE
T ss_pred             cccccceeeeeeCCCCcccccccccCCCCcEEECCCC-CCCCch-hhcCCCCCCEEECCCCccCccChhHhcCCcCCCEE
Confidence            3445677777777666554432211     2555555 444433 445555555555555555554433 3555555555


Q ss_pred             eccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          565 NLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       565 ~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      ++++| .+..+|+..++++++|++|++++|.+.
T Consensus       115 ~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~  146 (272)
T 3rfs_A          115 VLVEN-QLQSLPDGVFDKLTNLTYLNLAHNQLQ  146 (272)
T ss_dssp             ECTTS-CCCCCCTTTTTTCTTCCEEECCSSCCC
T ss_pred             ECCCC-cCCccCHHHhccCCCCCEEECCCCccC
Confidence            55555 344444443455555555555555444

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.64  E-value=8e-16  Score=162.95  Aligned_cols=219  Identities=19%  Similarity=0.228  Sum_probs=168.3

Q ss_pred             CccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCccccc-chhhccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~  569 (779)
                      .++.++++++.+..+|....    .|+|++| .+..+ |..|+++++|++|++++|.++.+ |..++++++|++|++++|
T Consensus        34 ~l~~l~~~~~~l~~ip~~~~~~l~~L~l~~n-~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n  112 (332)
T 2ft3_A           34 HLRVVQCSDLGLKAVPKEISPDTTLLDLQNN-DISELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQKLYISKN  112 (332)
T ss_dssp             ETTEEECCSSCCSSCCSCCCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSCCCEECGGGSTTCTTCCEEECCSS
T ss_pred             cCCEEECCCCCccccCCCCCCCCeEEECCCC-cCCccCHhHhhCCCCCcEEECCCCccCccCHhHhhCcCCCCEEECCCC
Confidence            68899999999988876433    5999999 88888 55899999999999999999987 778999999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc-------ccCCC
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV-------QKFFK  642 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~-------~~~~~  642 (779)
                       .+..+|.. +.  ++|++|++++|.+..              .....+..+++|+.|+++.|.....       ..+ +
T Consensus       113 -~l~~l~~~-~~--~~L~~L~l~~n~i~~--------------~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l-~  173 (332)
T 2ft3_A          113 -HLVEIPPN-LP--SSLVELRIHDNRIRK--------------VPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-K  173 (332)
T ss_dssp             -CCCSCCSS-CC--TTCCEEECCSSCCCC--------------CCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSC-C
T ss_pred             -cCCccCcc-cc--ccCCEEECCCCccCc--------------cCHhHhCCCccCCEEECCCCccccCCCCcccccCC-c
Confidence             68899986 44  899999999998875              2234478899999999998766421       222 5


Q ss_pred             CCcccCc--ccc-----cccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-C
Q 004021          643 YPKLDLT--WLV-----FVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-N  714 (779)
Q Consensus       643 L~~L~~~--~l~-----~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-~  714 (779)
                      |+.|.+.  .+.     ..++|+.|++++|.. ..++.               ..+..+++|+.|+++++ .+..++. .
T Consensus       174 L~~L~l~~n~l~~l~~~~~~~L~~L~l~~n~i-~~~~~---------------~~l~~l~~L~~L~L~~N-~l~~~~~~~  236 (332)
T 2ft3_A          174 LNYLRISEAKLTGIPKDLPETLNELHLDHNKI-QAIEL---------------EDLLRYSKLYRLGLGHN-QIRMIENGS  236 (332)
T ss_dssp             CSCCBCCSSBCSSCCSSSCSSCSCCBCCSSCC-CCCCT---------------TSSTTCTTCSCCBCCSS-CCCCCCTTG
T ss_pred             cCEEECcCCCCCccCccccCCCCEEECCCCcC-CccCH---------------HHhcCCCCCCEEECCCC-cCCcCChhH
Confidence            5555211  011     125788888887543 33322               36778999999999984 6666655 5


Q ss_pred             CCCCCCccEEeeeCCCCCCCCCCCCCCcc-cccEEEech
Q 004021          715 PLHFPKLKKIGVYGCPKLKKLPINSSSAK-ERRVVIEGL  752 (779)
Q Consensus       715 ~~~l~~L~~L~l~~c~~L~~lP~~~~~~~-~~~l~i~~~  752 (779)
                      +..+++|++|++++| ++..+|..+...+ ++.+.+.++
T Consensus       237 ~~~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~~L~l~~N  274 (332)
T 2ft3_A          237 LSFLPTLRELHLDNN-KLSRVPAGLPDLKLLQVVYLHTN  274 (332)
T ss_dssp             GGGCTTCCEEECCSS-CCCBCCTTGGGCTTCCEEECCSS
T ss_pred             hhCCCCCCEEECCCC-cCeecChhhhcCccCCEEECCCC
Confidence            678999999999987 5889998765544 488888754

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.64  E-value=1e-15  Score=180.94  Aligned_cols=79  Identities=30%  Similarity=0.357  Sum_probs=40.3

Q ss_pred             cccccccccc-ccchhhcccccCceeeecCCccc-ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLT-ELPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |++++| .+. .+|..++++++|++|++++|.++ .+|..++++++|++|++++|.....+|.. ++.+++|++|++++|
T Consensus       399 L~L~~n-~l~~~~p~~l~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~-~~~l~~L~~L~L~~N  476 (768)
T 3rgz_A          399 LYLQNN-GFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQE-LMYVKTLETLILDFN  476 (768)
T ss_dssp             EECCSS-EEEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCCSCCCGG-GGGCTTCCEEECCSS
T ss_pred             EECCCC-ccccccCHHHhcCCCCCEEECcCCcccCcccHHHhcCCCCCEEECCCCcccCcCCHH-HcCCCCceEEEecCC
Confidence            555555 433 34555555555555555555544 34555555555555555555333344443 555555555555555


Q ss_pred             cCC
Q 004021          595 GSE  597 (779)
Q Consensus       595 ~~~  597 (779)
                      .+.
T Consensus       477 ~l~  479 (768)
T 3rgz_A          477 DLT  479 (768)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            444

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.64  E-value=1e-15  Score=179.93  Aligned_cols=59  Identities=19%  Similarity=0.283  Sum_probs=37.4

Q ss_pred             CCCCccEEEccCCCCCccccCCCCCCCCccEEeeeC------CCCCCCCCCCCCCcc-cccEEEech
Q 004021          693 FFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYG------CPKLKKLPINSSSAK-ERRVVIEGL  752 (779)
Q Consensus       693 ~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~------c~~L~~lP~~~~~~~-~~~l~i~~~  752 (779)
                      .+++|+.|+|+++ .+..+|..+..+++|+.|++++      |.-...+|..+...+ ++.+.+++|
T Consensus       751 ~l~~L~~L~Ls~N-~L~~lp~~l~~L~~L~~L~Ls~N~~ls~N~l~~~ip~~l~~L~~L~~L~Ls~N  816 (876)
T 4ecn_A          751 TLPYLSNMDVSYN-CFSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSN  816 (876)
T ss_dssp             TCTTCCEEECCSS-CCSSCCCGGGGCTTCCEEECCCCBCTTCCBCCCCCCTTGGGCSSCCEEECCSS
T ss_pred             cCCCcCEEEeCCC-CCCccchhhhcCCCCCEEECCCCCCcccccccccChHHHhcCCCCCEEECCCC
Confidence            6777777777763 5556766667777777777765      333455666554433 366666654

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.64  E-value=1e-15  Score=153.93  Aligned_cols=193  Identities=15%  Similarity=0.158  Sum_probs=140.6

Q ss_pred             cccccccccccccch-hhcccccCceeeecCCc-ccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeec
Q 004021          516 LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTH-IRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL  592 (779)
Q Consensus       516 lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~-i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~  592 (779)
                      .|+|++| .++.+|. .|.++++|++|++++|. ++.+|. .|.++++|++|++++|..++.+|+..+.++++|++|+++
T Consensus        35 ~L~l~~n-~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~~L~l~  113 (239)
T 2xwt_C           35 TLKLIET-HLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFLGIF  113 (239)
T ss_dssp             EEEEESC-CCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTCCEEEEE
T ss_pred             EEEEeCC-cceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCCEEeCC
Confidence            4777777 7777765 68889999999999996 888876 688999999999998337788887668889999999999


Q ss_pred             cccCCCcccccCCccCCCchhhHHhhcCCCCCC---ceeEEeecccccccCCCCCcccCcccccccCcc-eEEecccccc
Q 004021          593 ECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLN---VLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLK-ELEIIVCTEM  668 (779)
Q Consensus       593 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~---~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~-~L~L~~~~~~  668 (779)
                      +|.+..+|                .+..+++|+   .|+++.|        +++..+.+..+..+++|+ .|++++|. +
T Consensus       114 ~n~l~~lp----------------~~~~l~~L~~L~~L~l~~N--------~~l~~i~~~~~~~l~~L~~~L~l~~n~-l  168 (239)
T 2xwt_C          114 NTGLKMFP----------------DLTKVYSTDIFFILEITDN--------PYMTSIPVNAFQGLCNETLTLKLYNNG-F  168 (239)
T ss_dssp             EECCCSCC----------------CCTTCCBCCSEEEEEEESC--------TTCCEECTTTTTTTBSSEEEEECCSCC-C
T ss_pred             CCCCcccc----------------ccccccccccccEEECCCC--------cchhhcCcccccchhcceeEEEcCCCC-C
Confidence            98877521                155566666   8888854        144455455677888899 99998854 4


Q ss_pred             ceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCC-CCccEEeeeCCCCCCCCCCCCCCccccc
Q 004021          669 EEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHF-PKLKKIGVYGCPKLKKLPINSSSAKERR  746 (779)
Q Consensus       669 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l-~~L~~L~l~~c~~L~~lP~~~~~~~~~~  746 (779)
                      ..++.               ..+.. ++|+.|+++++..++.++.. +..+ ++|+.|+++++ .++.+|.. ....++.
T Consensus       169 ~~i~~---------------~~~~~-~~L~~L~L~~n~~l~~i~~~~~~~l~~~L~~L~l~~N-~l~~l~~~-~~~~L~~  230 (239)
T 2xwt_C          169 TSVQG---------------YAFNG-TKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDVSQT-SVTALPSK-GLEHLKE  230 (239)
T ss_dssp             CEECT---------------TTTTT-CEEEEEECTTCTTCCEECTTTTTTCSBCCSEEECTTC-CCCCCCCT-TCTTCSE
T ss_pred             cccCH---------------hhcCC-CCCCEEEcCCCCCcccCCHHHhhccccCCcEEECCCC-ccccCChh-HhccCce
Confidence            45554               23334 78999999886568777653 4567 88999999885 57888876 3334466


Q ss_pred             EEEech
Q 004021          747 VVIEGL  752 (779)
Q Consensus       747 l~i~~~  752 (779)
                      +.+.++
T Consensus       231 L~l~~~  236 (239)
T 2xwt_C          231 LIARNT  236 (239)
T ss_dssp             EECTTC
T ss_pred             eeccCc
Confidence            666544

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.63  E-value=1.2e-15  Score=159.44  Aligned_cols=194  Identities=19%  Similarity=0.266  Sum_probs=154.6

Q ss_pred             ccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEee
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLN  565 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~  565 (779)
                      ...+.+++.|++.+|.+..++....     .|+|++| .+..+|. +.++++|++|++++|.++.+| .+.++++|++|+
T Consensus        37 ~~~l~~L~~L~l~~~~i~~l~~~~~l~~L~~L~L~~n-~i~~~~~-~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~L~  113 (308)
T 1h6u_A           37 QADLDGITTLSAFGTGVTTIEGVQYLNNLIGLELKDN-QITDLAP-LKNLTKITELELSGNPLKNVS-AIAGLQSIKTLD  113 (308)
T ss_dssp             HHHHHTCCEEECTTSCCCCCTTGGGCTTCCEEECCSS-CCCCCGG-GTTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEE
T ss_pred             HHHcCCcCEEEeeCCCccCchhhhccCCCCEEEccCC-cCCCChh-HccCCCCCEEEccCCcCCCch-hhcCCCCCCEEE
Confidence            3456789999999998887765432     3999999 8998887 999999999999999999987 689999999999


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| .+..+|.  +..+++|++|++++|.+..               . ..+..+++|+.|+++.|...         .
T Consensus       114 l~~n-~l~~~~~--l~~l~~L~~L~l~~n~l~~---------------~-~~l~~l~~L~~L~l~~n~l~---------~  165 (308)
T 1h6u_A          114 LTST-QITDVTP--LAGLSNLQVLYLDLNQITN---------------I-SPLAGLTNLQYLSIGNAQVS---------D  165 (308)
T ss_dssp             CTTS-CCCCCGG--GTTCTTCCEEECCSSCCCC---------------C-GGGGGCTTCCEEECCSSCCC---------C
T ss_pred             CCCC-CCCCchh--hcCCCCCCEEECCCCccCc---------------C-ccccCCCCccEEEccCCcCC---------C
Confidence            9999 6788876  8999999999999998775               1 12778899999999865433         2


Q ss_pred             ccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEe
Q 004021          646 LDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIG  725 (779)
Q Consensus       646 L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~  725 (779)
                      +  +.+..+++|+.|++++|.. ..++                 .+..+++|+.|+++++ .+..++. +..+++|+.|+
T Consensus       166 ~--~~l~~l~~L~~L~l~~n~l-~~~~-----------------~l~~l~~L~~L~L~~N-~l~~~~~-l~~l~~L~~L~  223 (308)
T 1h6u_A          166 L--TPLANLSKLTTLKADDNKI-SDIS-----------------PLASLPNLIEVHLKNN-QISDVSP-LANTSNLFIVT  223 (308)
T ss_dssp             C--GGGTTCTTCCEEECCSSCC-CCCG-----------------GGGGCTTCCEEECTTS-CCCBCGG-GTTCTTCCEEE
T ss_pred             C--hhhcCCCCCCEEECCCCcc-CcCh-----------------hhcCCCCCCEEEccCC-ccCcccc-ccCCCCCCEEE
Confidence            2  2267789999999999654 3331                 3567899999999985 6677764 67899999999


Q ss_pred             eeCCCCCCCCCCC
Q 004021          726 VYGCPKLKKLPIN  738 (779)
Q Consensus       726 l~~c~~L~~lP~~  738 (779)
                      +++|+ +..+|..
T Consensus       224 l~~N~-i~~~~~~  235 (308)
T 1h6u_A          224 LTNQT-ITNQPVF  235 (308)
T ss_dssp             EEEEE-EECCCEE
T ss_pred             ccCCe-eecCCee
Confidence            99875 6666643

>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=99.63  E-value=2.5e-15  Score=167.05  Aligned_cols=253  Identities=19%  Similarity=0.236  Sum_probs=124.2

Q ss_pred             cccccCccccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhcc
Q 004021          483 VKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA  557 (779)
Q Consensus       483 ~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~  557 (779)
                      ..+..++.+..+.++++|++++|.+..++....     .|++++| .+..+|. ++++++|++|++++|.++.+|. +.+
T Consensus        56 ~~i~~l~~~~~l~~L~~L~Ls~n~l~~~~~~~~l~~L~~L~l~~n-~l~~~~~-~~~l~~L~~L~L~~n~l~~~~~-~~~  132 (466)
T 1o6v_A           56 LGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNN-QIADITP-LANLTNLTGLTLFNNQITDIDP-LKN  132 (466)
T ss_dssp             SCCCCCTTGGGCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSSCCCCCGG-GTT
T ss_pred             CCCccCcchhhhcCCCEEECCCCccCCchhhhccccCCEEECCCC-ccccChh-hcCCCCCCEEECCCCCCCCChH-HcC
Confidence            334445555566677777777776666554221     2666666 6666655 6667777777777766666654 666


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC-------ccCCCchhhHHhhcCCCCCCceeEE
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN-------VLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~-------~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                      +++|++|++++| .+..+|.  ++++++|++|++.+ .....+. +.+       .+.++....+..+..+++|+.|+++
T Consensus       133 l~~L~~L~l~~n-~l~~~~~--~~~l~~L~~L~l~~-~~~~~~~-~~~l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~  207 (466)
T 1o6v_A          133 LTNLNRLELSSN-TISDISA--LSGLTSLQQLSFGN-QVTDLKP-LANLTTLERLDISSNKVSDISVLAKLTNLESLIAT  207 (466)
T ss_dssp             CTTCSEEEEEEE-EECCCGG--GTTCTTCSEEEEEE-SCCCCGG-GTTCTTCCEEECCSSCCCCCGGGGGCTTCSEEECC
T ss_pred             CCCCCEEECCCC-ccCCChh--hccCCcccEeecCC-cccCchh-hccCCCCCEEECcCCcCCCChhhccCCCCCEEEec
Confidence            666777776666 3455543  45555555554432 1111000 000       0000000111224444555555555


Q ss_pred             eeccccc---ccCCCCCcc--------cCcccccccCcceEEeccccccceecccccc----------cCcccchhhccC
Q 004021          631 FRSSLAV---QKFFKYPKL--------DLTWLVFVQNLKELEIIVCTEMEEIICVDKL----------RDVSDISEIIGS  689 (779)
Q Consensus       631 ~~~~~~~---~~~~~L~~L--------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~----------~~~~~~~~~~~~  689 (779)
                      .+....+   ..+++|+.|        ..+.+..+++|+.|++++|.... ++.....          ..+..+     .
T Consensus       208 ~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~~n~l~~-~~~~~~l~~L~~L~l~~n~l~~~-----~  281 (466)
T 1o6v_A          208 NNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISN-LAPLSGLTKLTELKLGANQISNI-----S  281 (466)
T ss_dssp             SSCCCCCGGGGGCTTCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCC-CGGGTTCTTCSEEECCSSCCCCC-----G
T ss_pred             CCcccccccccccCCCCEEECCCCCcccchhhhcCCCCCEEECCCCcccc-chhhhcCCCCCEEECCCCccCcc-----c
Confidence            4433222   223344433        12334455555555555543221 1110000          000111     1


Q ss_pred             CCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          690 EHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       690 ~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      .+..+++|+.|+++++ .+..++. ...+++|+.|++++|. +..++.......++.+.+.+|
T Consensus       282 ~~~~l~~L~~L~L~~n-~l~~~~~-~~~l~~L~~L~L~~n~-l~~~~~~~~l~~L~~L~l~~n  341 (466)
T 1o6v_A          282 PLAGLTALTNLELNEN-QLEDISP-ISNLKNLTYLTLYFNN-ISDISPVSSLTKLQRLFFYNN  341 (466)
T ss_dssp             GGTTCTTCSEEECCSS-CCSCCGG-GGGCTTCSEEECCSSC-CSCCGGGGGCTTCCEEECCSS
T ss_pred             cccCCCccCeEEcCCC-cccCchh-hcCCCCCCEEECcCCc-CCCchhhccCccCCEeECCCC
Confidence            2455667777777763 4454443 5567778888887774 555444223334466776655

>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=99.63  E-value=2.1e-15  Score=167.35  Aligned_cols=61  Identities=18%  Similarity=0.336  Sum_probs=46.5

Q ss_pred             CCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEeeeCCCCCCCCCCCC-CC-cccccEEEec
Q 004021          689 SEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGVYGCPKLKKLPINS-SS-AKERRVVIEG  751 (779)
Q Consensus       689 ~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c~~L~~lP~~~-~~-~~~~~l~i~~  751 (779)
                      ..+..+++|+.|+|+++ .+..+ +..+..+++|++|++++| +++.+|... .. ..++.+.+.+
T Consensus       341 ~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~  404 (455)
T 3v47_A          341 RMFENLDKLEVLDLSYN-HIRALGDQSFLGLPNLKELALDTN-QLKSVPDGIFDRLTSLQKIWLHT  404 (455)
T ss_dssp             GGGTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCS
T ss_pred             hHhcCcccCCEEECCCC-cccccChhhccccccccEEECCCC-ccccCCHhHhccCCcccEEEccC
Confidence            35678899999999985 55655 557788999999999986 588888753 33 3458888874

>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=99.63  E-value=1.7e-15  Score=155.86  Aligned_cols=194  Identities=22%  Similarity=0.181  Sum_probs=97.0

Q ss_pred             CCccEEEcccccccccccC-----cc--cccccccccccccch-hhcccccCceeeecCCcccccc-hhhccCccCcEee
Q 004021          495 EGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~  565 (779)
                      ..+++|++++|.+..++..     +.  .|+|++| .+..+|. .+.++++|++|++++|.++.++ ..+.++++|++|+
T Consensus        28 ~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~  106 (276)
T 2z62_A           28 FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLV  106 (276)
T ss_dssp             TTCCEEECTTCCCCEECTTTTTTCTTCSEEECTTC-CCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEE
T ss_pred             CCccEEECCCCcccccCHhHhccccCCcEEECCCC-cCCccCHHHccCCcCCCEEECCCCccCccChhhhcCCccccEEE
Confidence            3566666666666554431     11  2556665 5555432 4555666666666666555544 3455566666666


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| .+..++...++++++|++|++++|.+..             ...+..++.+++|+.|+++.|.         +..
T Consensus       107 l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~-------------~~l~~~~~~l~~L~~L~Ls~N~---------l~~  163 (276)
T 2z62_A          107 AVET-NLASLENFPIGHLKTLKELNVAHNLIQS-------------FKLPEYFSNLTNLEHLDLSSNK---------IQS  163 (276)
T ss_dssp             CTTS-CCCCSTTCCCTTCTTCCEEECCSSCCCC-------------CCCCGGGGGCTTCCEEECCSSC---------CCE
T ss_pred             CCCC-CccccCchhcccCCCCCEEECcCCccce-------------ecCchhhccCCCCCEEECCCCC---------CCc
Confidence            6655 3444444225555666666666555442             1123445555566666655332         222


Q ss_pred             ccCcccccccCcc----eEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCC
Q 004021          646 LDLTWLVFVQNLK----ELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPK  720 (779)
Q Consensus       646 L~~~~l~~l~~L~----~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~  720 (779)
                      +.+..+..+++|+    .|++++|. +..++.                ......+|+.|+++++ .++.++.. +..+++
T Consensus       164 ~~~~~~~~l~~L~~l~l~L~ls~n~-l~~~~~----------------~~~~~~~L~~L~L~~n-~l~~~~~~~~~~l~~  225 (276)
T 2z62_A          164 IYCTDLRVLHQMPLLNLSLDLSLNP-MNFIQP----------------GAFKEIRLKELALDTN-QLKSVPDGIFDRLTS  225 (276)
T ss_dssp             ECGGGGHHHHTCTTCCEEEECCSSC-CCEECT----------------TSSCSCCEEEEECCSS-CCSCCCTTTTTTCCS
T ss_pred             CCHHHhhhhhhccccceeeecCCCc-ccccCc----------------cccCCCcccEEECCCC-ceeecCHhHhccccc
Confidence            2223333344444    55555533 233322                1122335666666653 35555543 245666


Q ss_pred             ccEEeeeCCC
Q 004021          721 LKKIGVYGCP  730 (779)
Q Consensus       721 L~~L~l~~c~  730 (779)
                      |+.|++++++
T Consensus       226 L~~L~l~~N~  235 (276)
T 2z62_A          226 LQKIWLHTNP  235 (276)
T ss_dssp             CCEEECCSSC
T ss_pred             ccEEEccCCc
Confidence            6666666543

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.63  E-value=6.7e-16  Score=178.15  Aligned_cols=240  Identities=16%  Similarity=0.196  Sum_probs=158.4

Q ss_pred             ccccCCccEEEccccc-ccc--cccC----------cc--cccccccccccccch--hhcccccCceeeecCCccc-ccc
Q 004021          491 VKEWEGAKRISLMANE-IES--LSEI----------PT--LLSLRRNDSLTELPS--RISSLVSLHHLDLSLTHIR-GLP  552 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~-~~~--l~~~----------~~--lL~L~~~~~l~~lp~--~i~~L~~L~~L~L~~~~i~-~lp  552 (779)
                      +..+.+++.|++++|. +..  +|..          +.  .|+|++| .+..+|.  .++++++|++|++++|.++ .+|
T Consensus       269 l~~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n-~l~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip  347 (636)
T 4eco_A          269 LKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYN-NLKTFPVETSLQKMKKLGMLECLYNQLEGKLP  347 (636)
T ss_dssp             TTTCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSS-CCSSCCCHHHHTTCTTCCEEECCSCCCEEECC
T ss_pred             HhcCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCC-cCCccCchhhhccCCCCCEEeCcCCcCccchh
Confidence            4567788888888887 653  4432          12  4888888 7778888  7888888888888888888 788


Q ss_pred             hhhccCccCcEeeccCCcCCCCCchhhhcCCcc-CcEeeeccccCCCcccccCC---------ccCCC--chhhHHhhc-
Q 004021          553 QELKALEKLRYLNLEYTHYLSIIPHQLISGFLK-LEVLRLLECGSEGVTKEEGN---------VLCDD--AEPLMRELL-  619 (779)
Q Consensus       553 ~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~-L~~L~l~~~~~~~~~~~~~~---------~~~~~--~~~~~~~l~-  619 (779)
                       .++++++|++|++++| .+..+|.. ++++++ |++|++++|.+..+|..+..         .+..+  ....+..+. 
T Consensus       348 -~~~~l~~L~~L~L~~N-~l~~lp~~-l~~l~~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N~l~~~~p~~l~~  424 (636)
T 4eco_A          348 -AFGSEIKLASLNLAYN-QITEIPAN-FCGFTEQVENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEIGSVDGKNFDP  424 (636)
T ss_dssp             -CCEEEEEESEEECCSS-EEEECCTT-SEEECTTCCEEECCSSCCSSCCSCCCTTCSSCEEEEECCSSCTTTTTTCSSCT
T ss_pred             -hhCCCCCCCEEECCCC-ccccccHh-hhhhcccCcEEEccCCcCcccchhhhhcccCccCEEECcCCcCCCcchhhhcc
Confidence             7888888888888888 56688876 788888 88888888877765543221         01110  112233444 


Q ss_pred             ------CCCCCCceeEEeecccccc-----cCCCCCcccC----------cccc-------cccCcceEEecccccccee
Q 004021          620 ------GLKRLNVLSWSFRSSLAVQ-----KFFKYPKLDL----------TWLV-------FVQNLKELEIIVCTEMEEI  671 (779)
Q Consensus       620 ------~L~~L~~L~l~~~~~~~~~-----~~~~L~~L~~----------~~l~-------~l~~L~~L~L~~~~~~~~~  671 (779)
                            .+++|+.|+++.|....++     .+++|+.|.+          ..+.       ++++|+.|+|++|... .+
T Consensus       425 ~~~~~~~~~~L~~L~Ls~N~l~~lp~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~-~l  503 (636)
T 4eco_A          425 LDPTPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLT-KL  503 (636)
T ss_dssp             TCSSCCCCCCEEEEECCSSCCCSCCTHHHHTTCCCSEEECCSSCCSBCCSSSSEETTEECTTGGGCCEEECCSSCCC-BC
T ss_pred             cccccccCCCCCEEECcCCccCcCCHHHHccCCCCCEEECCCCCCCCcCHHHhccccccccccCCccEEECcCCcCC-cc
Confidence                  5667788888776654432     2455555511          1111       1226677777665432 33


Q ss_pred             cccccccCcccchhhccCCCC--CCCCccEEEccCCCCCccccCCCCCCCCccEEeeeC------CCCCCCCCCCCCCcc
Q 004021          672 ICVDKLRDVSDISEIIGSEHN--FFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYG------CPKLKKLPINSSSAK  743 (779)
Q Consensus       672 ~~~~~~~~~~~~~~~~~~~~~--~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~------c~~L~~lP~~~~~~~  743 (779)
                      +.                .+.  .+++|+.|+|+++ .+..+|..+..+++|+.|++++      |.-...+|..+...+
T Consensus       504 p~----------------~~~~~~l~~L~~L~Ls~N-~l~~ip~~~~~l~~L~~L~Ls~N~~ls~N~l~~~~p~~l~~l~  566 (636)
T 4eco_A          504 SD----------------DFRATTLPYLVGIDLSYN-SFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCP  566 (636)
T ss_dssp             CG----------------GGSTTTCTTCCEEECCSS-CCSSCCCGGGGCSSCCEEECCSCBCTTCCBCCCCCCTTGGGCS
T ss_pred             Ch----------------hhhhccCCCcCEEECCCC-CCCCcChhhhcCCCCCEEECCCCcccccCcccccChHHHhcCC
Confidence            32                343  7888999999884 5666888888889999998854      444667887665543


Q ss_pred             -cccEEEech
Q 004021          744 -ERRVVIEGL  752 (779)
Q Consensus       744 -~~~l~i~~~  752 (779)
                       ++.+.++++
T Consensus       567 ~L~~L~Ls~N  576 (636)
T 4eco_A          567 SLTQLQIGSN  576 (636)
T ss_dssp             SCCEEECCSS
T ss_pred             CCCEEECCCC
Confidence             377777765

>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=99.63  E-value=3.6e-15  Score=165.69  Aligned_cols=256  Identities=19%  Similarity=0.216  Sum_probs=122.2

Q ss_pred             cccccCccccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccch----
Q 004021          483 VKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ----  553 (779)
Q Consensus       483 ~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~----  553 (779)
                      ..+..++.+..+.++++|++.+|.+..++....     .|++++| .+..+|. +.++++|++|++++|.+..+|.    
T Consensus        78 n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~L~~n-~l~~~~~-~~~l~~L~~L~l~~n~l~~~~~~~~l  155 (466)
T 1o6v_A           78 NQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNN-QITDIDP-LKNLTNLNRLELSSNTISDISALSGL  155 (466)
T ss_dssp             SCCCCCGGGTTCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSS-CCCCCGG-GTTCTTCSEEEEEEEEECCCGGGTTC
T ss_pred             CccCCchhhhccccCCEEECCCCccccChhhcCCCCCCEEECCCC-CCCCChH-HcCCCCCCEEECCCCccCCChhhccC
Confidence            334444445556667777777666665543211     2666666 6666654 6666666666666666555442    


Q ss_pred             ----------------hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCccc-ccCC-----ccCCCc
Q 004021          554 ----------------ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTK-EEGN-----VLCDDA  611 (779)
Q Consensus       554 ----------------~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~-~~~~-----~~~~~~  611 (779)
                                      .+.++++|++|++++| .+..++.  +.++++|++|++++|.+...+. ....     .+.++.
T Consensus       156 ~~L~~L~l~~~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~--l~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~  232 (466)
T 1o6v_A          156 TSLQQLSFGNQVTDLKPLANLTTLERLDISSN-KVSDISV--LAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQ  232 (466)
T ss_dssp             TTCSEEEEEESCCCCGGGTTCTTCCEEECCSS-CCCCCGG--GGGCTTCSEEECCSSCCCCCGGGGGCTTCCEEECCSSC
T ss_pred             CcccEeecCCcccCchhhccCCCCCEEECcCC-cCCCChh--hccCCCCCEEEecCCcccccccccccCCCCEEECCCCC
Confidence                            1444555555555555 3444443  5555566666665555444211 0000     011111


Q ss_pred             hhhHHhhcCCCCCCceeEEeeccccc---ccCCCCCcc--------cCcccccccCcceEEeccccccceecccccc---
Q 004021          612 EPLMRELLGLKRLNVLSWSFRSSLAV---QKFFKYPKL--------DLTWLVFVQNLKELEIIVCTEMEEIICVDKL---  677 (779)
Q Consensus       612 ~~~~~~l~~L~~L~~L~l~~~~~~~~---~~~~~L~~L--------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~---  677 (779)
                      ...+..+..+++|+.|+++.|....+   ..+++|+.|        ..+.+..+++|+.|++++|.. ..++.....   
T Consensus       233 l~~~~~l~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~L~~n~l-~~~~~~~~l~~L  311 (466)
T 1o6v_A          233 LKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQL-EDISPISNLKNL  311 (466)
T ss_dssp             CCCCGGGGGCTTCSEEECCSSCCCCCGGGTTCTTCSEEECCSSCCCCCGGGTTCTTCSEEECCSSCC-SCCGGGGGCTTC
T ss_pred             cccchhhhcCCCCCEEECCCCccccchhhhcCCCCCEEECCCCccCccccccCCCccCeEEcCCCcc-cCchhhcCCCCC
Confidence            11122344555555555555443322   233333333        112244455555555555432 111110000   


Q ss_pred             -------cCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEe
Q 004021          678 -------RDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIE  750 (779)
Q Consensus       678 -------~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~  750 (779)
                             ..+...     ..+..+++|+.|+++++ .+..++ ....+++|+.|++++|+ +..++.......++.+.+.
T Consensus       312 ~~L~L~~n~l~~~-----~~~~~l~~L~~L~l~~n-~l~~~~-~l~~l~~L~~L~l~~n~-l~~~~~~~~l~~L~~L~l~  383 (466)
T 1o6v_A          312 TYLTLYFNNISDI-----SPVSSLTKLQRLFFYNN-KVSDVS-SLANLTNINWLSAGHNQ-ISDLTPLANLTRITQLGLN  383 (466)
T ss_dssp             SEEECCSSCCSCC-----GGGGGCTTCCEEECCSS-CCCCCG-GGTTCTTCCEEECCSSC-CCBCGGGTTCTTCCEEECC
T ss_pred             CEEECcCCcCCCc-----hhhccCccCCEeECCCC-ccCCch-hhccCCCCCEEeCCCCc-cCccchhhcCCCCCEEecc
Confidence                   000000     12345667777777764 444442 45567778888887775 3333332223334666665


Q ss_pred             ch
Q 004021          751 GL  752 (779)
Q Consensus       751 ~~  752 (779)
                      ++
T Consensus       384 ~n  385 (466)
T 1o6v_A          384 DQ  385 (466)
T ss_dssp             CE
T ss_pred             CC
Confidence            54

>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=99.62  E-value=2e-15  Score=167.43  Aligned_cols=80  Identities=24%  Similarity=0.345  Sum_probs=46.0

Q ss_pred             cccccccccccc-chhhcccccCceeeecCCcccc-cchh--hccCccCcEeeccCCcCCCCC-chhhhcCCccCcEeee
Q 004021          517 LSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRG-LPQE--LKALEKLRYLNLEYTHYLSII-PHQLISGFLKLEVLRL  591 (779)
Q Consensus       517 L~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~-lp~~--~~~L~~L~~L~l~~~~~l~~l-p~~~i~~L~~L~~L~l  591 (779)
                      |+|++| .+..+ |..|+++++|++|++++|.++. +|..  ++++++|++|++++|. +..+ |...++++++|++|++
T Consensus        84 L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~~~l~~L~~L~L  161 (455)
T 3v47_A           84 LKLDYN-QFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNN-IKKIQPASFFLNMRRFHVLDL  161 (455)
T ss_dssp             EECTTC-TTCEECTTTTTTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSB-CCSCCCCGGGGGCTTCCEEEC
T ss_pred             EeCCCC-ccCccChhhccCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCc-cCccCcccccCCCCcccEEeC
Confidence            666666 55544 5556666666666666666554 3333  5666666666666663 3433 3333556666666666


Q ss_pred             ccccCCC
Q 004021          592 LECGSEG  598 (779)
Q Consensus       592 ~~~~~~~  598 (779)
                      ++|.+.+
T Consensus       162 ~~n~l~~  168 (455)
T 3v47_A          162 TFNKVKS  168 (455)
T ss_dssp             TTCCBSC
T ss_pred             CCCcccc
Confidence            6665554

>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=99.62  E-value=2.4e-15  Score=174.32  Aligned_cols=60  Identities=8%  Similarity=-0.025  Sum_probs=38.3

Q ss_pred             CCCCCCCCccEEEccCCCCCccccC-CCCCCCCccEEeeeCCCCCCCCC-CCCCCc--ccccEEEe
Q 004021          689 SEHNFFTQLESLGILYGPDLKSIYP-NPLHFPKLKKIGVYGCPKLKKLP-INSSSA--KERRVVIE  750 (779)
Q Consensus       689 ~~~~~~~~L~~L~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~~L~~lP-~~~~~~--~~~~l~i~  750 (779)
                      ..+.++++|+.|+|++ +.+..++. .+..+++|+.|++++|. +..+| ..+...  +++.+.+.
T Consensus       512 ~~f~~l~~L~~L~Ls~-N~l~~l~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~l~~l~~~L~~L~L~  575 (635)
T 4g8a_A          512 TAFNSLSSLQVLNMSH-NNFFSLDTFPYKCLNSLQVLDYSLNH-IMTSKKQELQHFPSSLAFLNLT  575 (635)
T ss_dssp             TTTTTCTTCCEEECTT-SCCCBCCCGGGTTCTTCCEEECTTSC-CCBCCSSCTTCCCTTCCEEECT
T ss_pred             HHHcCCCCCCEEECCC-CcCCCCChhHHhCCCCCCEEECCCCc-CCCCCHHHHHhhhCcCCEEEee
Confidence            3566777777777777 35666654 35567888888888764 55554 334332  34777776

>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=99.62  E-value=2.2e-15  Score=151.40  Aligned_cols=200  Identities=13%  Similarity=0.153  Sum_probs=153.7

Q ss_pred             cccCccccccCCccEEEcccccccccccCc-----c--ccccccccc-ccccch-hhcccccCceeeecC-Ccccccch-
Q 004021          485 LTEAPKVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDS-LTELPS-RISSLVSLHHLDLSL-THIRGLPQ-  553 (779)
Q Consensus       485 ~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~-l~~lp~-~i~~L~~L~~L~L~~-~~i~~lp~-  553 (779)
                      +..+|.  -...++.|++++|.+..++...     .  .|++++| . ++.+|. .|.++++|++|++++ |.++.+|. 
T Consensus        23 l~~ip~--~~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n-~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~   99 (239)
T 2xwt_C           23 IQRIPS--LPPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSID-VTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPD   99 (239)
T ss_dssp             CSSCCC--CCTTCCEEEEESCCCSEECTTTTTTCTTCCEEEEECC-SSCCEECTTTEESCTTCCEEEEEEETTCCEECTT
T ss_pred             ccccCC--CCCcccEEEEeCCcceEECHHHccCCCCCcEEeCCCC-CCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHH
Confidence            455555  3358999999999998887632     1  3999999 6 888865 789999999999998 89999875 


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCc---Eeeeccc-cCCCcccccCCccCCCchhhHHhhcCCCCCC-cee
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLE---VLRLLEC-GSEGVTKEEGNVLCDDAEPLMRELLGLKRLN-VLS  628 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~---~L~l~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~-~L~  628 (779)
                      .|.++++|++|++++| .++.+|.  ++.+++|+   +|++++| .+..              .....+..+++|+ .|+
T Consensus       100 ~f~~l~~L~~L~l~~n-~l~~lp~--~~~l~~L~~L~~L~l~~N~~l~~--------------i~~~~~~~l~~L~~~L~  162 (239)
T 2xwt_C          100 ALKELPLLKFLGIFNT-GLKMFPD--LTKVYSTDIFFILEITDNPYMTS--------------IPVNAFQGLCNETLTLK  162 (239)
T ss_dssp             SEECCTTCCEEEEEEE-CCCSCCC--CTTCCBCCSEEEEEEESCTTCCE--------------ECTTTTTTTBSSEEEEE
T ss_pred             HhCCCCCCCEEeCCCC-CCccccc--cccccccccccEEECCCCcchhh--------------cCcccccchhcceeEEE
Confidence            5889999999999999 6788887  78888888   9999998 6664              2233477888999 999


Q ss_pred             EEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCC-CCccEEEccCCCC
Q 004021          629 WSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFF-TQLESLGILYGPD  707 (779)
Q Consensus       629 l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~L~~L~l~~~~~  707 (779)
                      ++.|.         ++.+....+.. ++|+.|+|++|..+..++.               ..+..+ ++|+.|++++ +.
T Consensus       163 l~~n~---------l~~i~~~~~~~-~~L~~L~L~~n~~l~~i~~---------------~~~~~l~~~L~~L~l~~-N~  216 (239)
T 2xwt_C          163 LYNNG---------FTSVQGYAFNG-TKLDAVYLNKNKYLTVIDK---------------DAFGGVYSGPSLLDVSQ-TS  216 (239)
T ss_dssp             CCSCC---------CCEECTTTTTT-CEEEEEECTTCTTCCEECT---------------TTTTTCSBCCSEEECTT-CC
T ss_pred             cCCCC---------CcccCHhhcCC-CCCCEEEcCCCCCcccCCH---------------HHhhccccCCcEEECCC-Cc
Confidence            88554         33332333333 7899999999765677655               466778 9999999998 57


Q ss_pred             CccccCCCCCCCCccEEeeeCCCCC
Q 004021          708 LKSIYPNPLHFPKLKKIGVYGCPKL  732 (779)
Q Consensus       708 l~~l~~~~~~l~~L~~L~l~~c~~L  732 (779)
                      ++.+|..  .|++|+.|.+.+|..|
T Consensus       217 l~~l~~~--~~~~L~~L~l~~~~~l  239 (239)
T 2xwt_C          217 VTALPSK--GLEHLKELIARNTWTL  239 (239)
T ss_dssp             CCCCCCT--TCTTCSEEECTTC---
T ss_pred             cccCChh--HhccCceeeccCccCC
Confidence            7877765  7899999999988754

>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=99.61  E-value=2.5e-15  Score=173.09  Aligned_cols=220  Identities=18%  Similarity=0.132  Sum_probs=124.0

Q ss_pred             CccEEEcccccccccccCc-----c--cccccccccccccchhhcccccCceeeecCCccccc-chhhccCccCcEeecc
Q 004021          496 GAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLE  567 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~  567 (779)
                      .++.+++.+|.+..++...     .  .|++++| .+..+|..++++++|++|++++|.++.+ |..+.++++|++|+++
T Consensus       255 ~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~lp~~l~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~  333 (606)
T 3t6q_A          255 SVESINLQKHYFFNISSNTFHCFSGLQELDLTAT-HLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIK  333 (606)
T ss_dssp             EEEEEECTTCCCSSCCTTTTTTCTTCSEEECTTS-CCSCCCSSCCSCTTCCEEECTTCCCSBGGGGCGGGCTTCSEEECC
T ss_pred             ceeEEEeecCccCccCHHHhccccCCCEEeccCC-ccCCCChhhcccccCCEEECccCCcCcCchhhhhccCcCCEEECC
Confidence            5677777777776665431     1  3777777 7777777777777888888887777765 4467777777888877


Q ss_pred             CCcCCCCCchhhhcCCccCcEeeeccccCCCcc---cccCC-------ccCCC--chhhHHhhcCCCCCCceeEEeeccc
Q 004021          568 YTHYLSIIPHQLISGFLKLEVLRLLECGSEGVT---KEEGN-------VLCDD--AEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       568 ~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~---~~~~~-------~~~~~--~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      +|.....+|.+.++++++|++|++++|.+....   ..+.+       .+.++  ....+..+..+++|+.|+++.|...
T Consensus       334 ~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~  413 (606)
T 3t6q_A          334 GNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLK  413 (606)
T ss_dssp             SCSSCCBCCSSTTTTCTTCCEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCSCEEECTTTTTTCTTCSEEECTTCCEE
T ss_pred             CCCcccccchhhhhccCcCCEEECCCCccccccCcchhcccCCCCCEEECCCCcCCcCCHHHhcCCccCCeEECCCCcCC
Confidence            775444666655677777777777777665421   00100       00000  0122333444555555555444332


Q ss_pred             c------cccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccE
Q 004021          636 A------VQKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLES  699 (779)
Q Consensus       636 ~------~~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~  699 (779)
                      .      +..+++|+.|          .+..+..+++|+.|+|++|...+..+.        .     ...+..+++|+.
T Consensus       414 ~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~--------~-----~~~~~~l~~L~~  480 (606)
T 3t6q_A          414 VKDAQSPFQNLHLLKVLNLSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQ--------K-----TNSLQTLGRLEI  480 (606)
T ss_dssp             CCTTCCTTTTCTTCCEEECTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEEC--------S-----SCGGGGCTTCCE
T ss_pred             CcccchhhhCcccCCEEECCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccc--------c-----chhhccCCCccE
Confidence            1      2223333333          122344455555555555443221110        0     023556777777


Q ss_pred             EEccCCCCCccc-cCCCCCCCCccEEeeeCCC
Q 004021          700 LGILYGPDLKSI-YPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       700 L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c~  730 (779)
                      |+++++ .+..+ +..+..+++|++|++++|.
T Consensus       481 L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~N~  511 (606)
T 3t6q_A          481 LVLSFC-DLSSIDQHAFTSLKMMNHVDLSHNR  511 (606)
T ss_dssp             EECTTS-CCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             EECCCC-ccCccChhhhccccCCCEEECCCCc
Confidence            777775 34444 4456677777777777764

>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=99.61  E-value=4.1e-15  Score=152.99  Aligned_cols=208  Identities=20%  Similarity=0.233  Sum_probs=159.5

Q ss_pred             EEcccccccccccC----cccccccccccccccch-hhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCC
Q 004021          500 ISLMANEIESLSEI----PTLLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLS  573 (779)
Q Consensus       500 l~l~~~~~~~l~~~----~~lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~  573 (779)
                      +...+..+..+|..    ...|+|++| .++.+|. .|.++++|++|++++|.++.+|. .+.++++|++|++++| .+.
T Consensus        12 ~~c~~~~l~~ip~~l~~~l~~L~ls~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~   89 (276)
T 2z62_A           12 YQCMELNFYKIPDNLPFSTKNLDLSFN-PLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGN-PIQ   89 (276)
T ss_dssp             EECTTSCCSSCCSSSCTTCCEEECTTC-CCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTC-CCC
T ss_pred             EEecCCCccccCCCCCCCccEEECCCC-cccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCC-ccC
Confidence            44445555555543    225999999 8998865 89999999999999999999876 6899999999999999 577


Q ss_pred             CCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCccc-Ccccc
Q 004021          574 IIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD-LTWLV  652 (779)
Q Consensus       574 ~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~-~~~l~  652 (779)
                      .++...+.++++|++|++.+|.+..              .....++.+++|+.|+++.|.         +..+. +..+.
T Consensus        90 ~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~n~---------l~~~~l~~~~~  146 (276)
T 2z62_A           90 SLALGAFSGLSSLQKLVAVETNLAS--------------LENFPIGHLKTLKELNVAHNL---------IQSFKLPEYFS  146 (276)
T ss_dssp             EECTTTTTTCTTCCEEECTTSCCCC--------------STTCCCTTCTTCCEEECCSSC---------CCCCCCCGGGG
T ss_pred             ccChhhhcCCccccEEECCCCCccc--------------cCchhcccCCCCCEEECcCCc---------cceecCchhhc
Confidence            7776558999999999999998775              222247789999999998554         33332 56788


Q ss_pred             cccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCcc----EEEccCCCCCccccCCCCCCCCccEEeeeC
Q 004021          653 FVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLE----SLGILYGPDLKSIYPNPLHFPKLKKIGVYG  728 (779)
Q Consensus       653 ~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~----~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~  728 (779)
                      .+++|+.|++++|.. ..++.               ..+..+++|+    .|++++ +.+..++......++|++|++++
T Consensus       147 ~l~~L~~L~Ls~N~l-~~~~~---------------~~~~~l~~L~~l~l~L~ls~-n~l~~~~~~~~~~~~L~~L~L~~  209 (276)
T 2z62_A          147 NLTNLEHLDLSSNKI-QSIYC---------------TDLRVLHQMPLLNLSLDLSL-NPMNFIQPGAFKEIRLKELALDT  209 (276)
T ss_dssp             GCTTCCEEECCSSCC-CEECG---------------GGGHHHHTCTTCCEEEECCS-SCCCEECTTSSCSCCEEEEECCS
T ss_pred             cCCCCCEEECCCCCC-CcCCH---------------HHhhhhhhccccceeeecCC-CcccccCccccCCCcccEEECCC
Confidence            899999999999654 44433               2344455555    899998 57888888777778999999999


Q ss_pred             CCCCCCCCCCC-C-CcccccEEEe
Q 004021          729 CPKLKKLPINS-S-SAKERRVVIE  750 (779)
Q Consensus       729 c~~L~~lP~~~-~-~~~~~~l~i~  750 (779)
                      |. ++.+|... . ..+++.+.+.
T Consensus       210 n~-l~~~~~~~~~~l~~L~~L~l~  232 (276)
T 2z62_A          210 NQ-LKSVPDGIFDRLTSLQKIWLH  232 (276)
T ss_dssp             SC-CSCCCTTTTTTCCSCCEEECC
T ss_pred             Cc-eeecCHhHhcccccccEEEcc
Confidence            75 88888754 3 2344888887

>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=99.61  E-value=1.1e-14  Score=165.69  Aligned_cols=236  Identities=21%  Similarity=0.150  Sum_probs=159.6

Q ss_pred             EEEEcCcccccCccccccCCccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCCcccccch
Q 004021          477 FLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ  553 (779)
Q Consensus       477 ~~~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~  553 (779)
                      .+...+..+..+|.... ++++.|++++|.+..+|....   .|+|++| .++.+|.   .+++|++|++++|.++.+|.
T Consensus        44 ~L~ls~n~L~~lp~~l~-~~L~~L~L~~N~l~~lp~~l~~L~~L~Ls~N-~l~~lp~---~l~~L~~L~Ls~N~l~~l~~  118 (622)
T 3g06_A           44 VLNVGESGLTTLPDCLP-AHITTLVIPDNNLTSLPALPPELRTLEVSGN-QLTSLPV---LPPGLLELSIFSNPLTHLPA  118 (622)
T ss_dssp             EEECCSSCCSCCCSCCC-TTCSEEEECSCCCSCCCCCCTTCCEEEECSC-CCSCCCC---CCTTCCEEEECSCCCCCCCC
T ss_pred             EEEecCCCcCccChhhC-CCCcEEEecCCCCCCCCCcCCCCCEEEcCCC-cCCcCCC---CCCCCCEEECcCCcCCCCCC
Confidence            34445555666665322 789999999999998887433   4999999 8999987   78999999999999999987


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC----ccCCCchhhHHhhcCCCCCCceeE
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPLMRELLGLKRLNVLSW  629 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~L~~L~~L~l  629 (779)
                         .+++|++|++++| .++.+|..    +++|++|++++|.+..++....+    .+.++....+.  ..+++|+.|++
T Consensus       119 ---~l~~L~~L~L~~N-~l~~lp~~----l~~L~~L~Ls~N~l~~l~~~~~~L~~L~L~~N~l~~l~--~~~~~L~~L~L  188 (622)
T 3g06_A          119 ---LPSGLCKLWIFGN-QLTSLPVL----PPGLQELSVSDNQLASLPALPSELCKLWAYNNQLTSLP--MLPSGLQELSV  188 (622)
T ss_dssp             ---CCTTCCEEECCSS-CCSCCCCC----CTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSCCC--CCCTTCCEEEC
T ss_pred             ---CCCCcCEEECCCC-CCCcCCCC----CCCCCEEECcCCcCCCcCCccCCCCEEECCCCCCCCCc--ccCCCCcEEEC
Confidence               6788999999999 67888874    48899999999988775432222    11111111111  34577888888


Q ss_pred             Eeecccccc-cCCCCCcccC-----ccc-ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEc
Q 004021          630 SFRSSLAVQ-KFFKYPKLDL-----TWL-VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGI  702 (779)
Q Consensus       630 ~~~~~~~~~-~~~~L~~L~~-----~~l-~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l  702 (779)
                      +.|....++ .+++|+.|.+     ..+ ..+++|+.|+|++|. +..++                   ..+++|+.|++
T Consensus       189 s~N~l~~l~~~~~~L~~L~L~~N~l~~l~~~~~~L~~L~Ls~N~-L~~lp-------------------~~l~~L~~L~L  248 (622)
T 3g06_A          189 SDNQLASLPTLPSELYKLWAYNNRLTSLPALPSGLKELIVSGNR-LTSLP-------------------VLPSELKELMV  248 (622)
T ss_dssp             CSSCCSCCCCCCTTCCEEECCSSCCSSCCCCCTTCCEEECCSSC-CSCCC-------------------CCCTTCCEEEC
T ss_pred             CCCCCCCCCCccchhhEEECcCCcccccCCCCCCCCEEEccCCc-cCcCC-------------------CCCCcCcEEEC
Confidence            877665542 2344555411     001 123677788887753 33232                   34578888888


Q ss_pred             cCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccc-ccEEEech
Q 004021          703 LYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKE-RRVVIEGL  752 (779)
Q Consensus       703 ~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~-~~l~i~~~  752 (779)
                      +++ .++.+|.   .+++|+.|++++| ++..+|..+...+. +.+.+.++
T Consensus       249 s~N-~L~~lp~---~~~~L~~L~Ls~N-~L~~lp~~l~~l~~L~~L~L~~N  294 (622)
T 3g06_A          249 SGN-RLTSLPM---LPSGLLSLSVYRN-QLTRLPESLIHLSSETTVNLEGN  294 (622)
T ss_dssp             CSS-CCSCCCC---CCTTCCEEECCSS-CCCSCCGGGGGSCTTCEEECCSC
T ss_pred             CCC-CCCcCCc---ccccCcEEeCCCC-CCCcCCHHHhhccccCEEEecCC
Confidence            874 6777766   5688888888887 57788876554433 77777655

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.61  E-value=1.6e-14  Score=172.49  Aligned_cols=117  Identities=21%  Similarity=0.223  Sum_probs=70.4

Q ss_pred             EcCcccccCccccccCCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCccccc
Q 004021          480 RAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGL  551 (779)
Q Consensus       480 ~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~l  551 (779)
                      .....+..+|.  ...++++|++++|.+..++...     .  .|+|++|..+..+ |..|++|++|++|+|++|.+..+
T Consensus        11 cs~~~L~~vP~--lp~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~   88 (844)
T 3j0a_A           11 YRFCNLTQVPQ--VLNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFL   88 (844)
T ss_dssp             ESCCCSSCCCS--SCTTCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTCCCCEE
T ss_pred             ccCCCCCCCCC--CCCCcCEEECCCCcCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCCcCccc
Confidence            34455666666  4567888888888776654221     1  3667666334445 55667777777777777766665


Q ss_pred             -chhhccCccCcEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCC
Q 004021          552 -PQELKALEKLRYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       552 -p~~~~~L~~L~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~  598 (779)
                       |..|+++++|++|+|++|.....+|. ..++++++|++|++++|.+.+
T Consensus        89 ~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~  137 (844)
T 3j0a_A           89 HPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRS  137 (844)
T ss_dssp             CTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCC
T ss_pred             CHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccc
Confidence             55666666677777666632222332 225566666666666666554

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.61  E-value=6.2e-15  Score=151.17  Aligned_cols=176  Identities=20%  Similarity=0.204  Sum_probs=141.6

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |++++| .+..++ .+..+++|++|++++|.++.++ .+.++++|++|++++| .++.+|+..++++++|++|++++|.+
T Consensus        46 L~l~~~-~i~~~~-~l~~l~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l  121 (272)
T 3rfs_A           46 IIANNS-DIKSVQ-GIQYLPNVRYLALGGNKLHDIS-ALKELTNLTYLILTGN-QLQSLPNGVFDKLTNLKELVLVENQL  121 (272)
T ss_dssp             EECTTS-CCCCCT-TGGGCTTCCEEECTTSCCCCCG-GGTTCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECTTSCC
T ss_pred             eeeCCC-Cccccc-ccccCCCCcEEECCCCCCCCch-hhcCCCCCCEEECCCC-ccCccChhHhcCCcCCCEEECCCCcC
Confidence            889999 888776 5899999999999999999876 7899999999999999 67888887679999999999999988


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      ..              ..+..++.+++|+.|+++.|.         +..+.+..+..+++|+.|++++|.. ..++.   
T Consensus       122 ~~--------------~~~~~~~~l~~L~~L~L~~n~---------l~~~~~~~~~~l~~L~~L~l~~n~l-~~~~~---  174 (272)
T 3rfs_A          122 QS--------------LPDGVFDKLTNLTYLNLAHNQ---------LQSLPKGVFDKLTNLTELDLSYNQL-QSLPE---  174 (272)
T ss_dssp             CC--------------CCTTTTTTCTTCCEEECCSSC---------CCCCCTTTTTTCTTCCEEECCSSCC-CCCCT---
T ss_pred             Cc--------------cCHHHhccCCCCCEEECCCCc---------cCccCHHHhccCccCCEEECCCCCc-CccCH---
Confidence            75              233447788999999998553         4444455678899999999999754 44433   


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCC
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLP  736 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP  736 (779)
                                  ..+..+++|+.|+++++ .+..++.. +..+++|+.|++++|+-....|
T Consensus       175 ------------~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~~~~~~~  222 (272)
T 3rfs_A          175 ------------GVFDKLTQLKDLRLYQN-QLKSVPDGVFDRLTSLQYIWLHDNPWDCTCP  222 (272)
T ss_dssp             ------------TTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSCBCCCTT
T ss_pred             ------------HHhcCCccCCEEECCCC-cCCccCHHHHhCCcCCCEEEccCCCccccCc
Confidence                        35678999999999985 56666654 5789999999999986544444

>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=99.60  E-value=4.9e-15  Score=153.24  Aligned_cols=187  Identities=20%  Similarity=0.164  Sum_probs=152.5

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccc-hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++++++ .++.+|..+.  .+|++|+|++|.++.++ ..+.++++|++|++++| .++.+|.  .+.+++|++|++++|.
T Consensus        15 l~~~~~-~l~~ip~~~~--~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~--~~~l~~L~~L~Ls~N~   88 (290)
T 1p9a_G           15 VNCDKR-NLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRA-ELTKLQV--DGTLPVLGTLDLSHNQ   88 (290)
T ss_dssp             EECTTS-CCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTS-CCCEEEC--CSCCTTCCEEECCSSC
T ss_pred             EECCCC-CCCcCCCCCC--CCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCC-ccCcccC--CCCCCcCCEEECCCCc
Confidence            788998 9999998775  79999999999999874 57999999999999999 6888887  4899999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +..               .+..+..+++|+.|+++.|         +++.+.+..+..+++|+.|+|++|. +..++.  
T Consensus        89 l~~---------------l~~~~~~l~~L~~L~l~~N---------~l~~l~~~~~~~l~~L~~L~L~~N~-l~~~~~--  141 (290)
T 1p9a_G           89 LQS---------------LPLLGQTLPALTVLDVSFN---------RLTSLPLGALRGLGELQELYLKGNE-LKTLPP--  141 (290)
T ss_dssp             CSS---------------CCCCTTTCTTCCEEECCSS---------CCCCCCSSTTTTCTTCCEEECTTSC-CCCCCT--
T ss_pred             CCc---------------CchhhccCCCCCEEECCCC---------cCcccCHHHHcCCCCCCEEECCCCC-CCccCh--
Confidence            875               3345678899999999854         4455555678889999999999965 444444  


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCC-CCCCCccEEeeeCCCCCCCCCCCCCCcc-cccEEEec
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNP-LHFPKLKKIGVYGCPKLKKLPINSSSAK-ERRVVIEG  751 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~-~~l~~L~~L~l~~c~~L~~lP~~~~~~~-~~~l~i~~  751 (779)
                                   ..+..+++|+.|++++ +.++.++... ..+++|+.|++++| .++.+|..+.... ++.+.+.+
T Consensus       142 -------------~~~~~l~~L~~L~L~~-N~l~~l~~~~~~~l~~L~~L~L~~N-~l~~ip~~~~~~~~L~~l~L~~  204 (290)
T 1p9a_G          142 -------------GLLTPTPKLEKLSLAN-NNLTELPAGLLNGLENLDTLLLQEN-SLYTIPKGFFGSHLLPFAFLHG  204 (290)
T ss_dssp             -------------TTTTTCTTCCEEECTT-SCCSCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCCCSEEECCS
T ss_pred             -------------hhcccccCCCEEECCC-CcCCccCHHHhcCcCCCCEEECCCC-cCCccChhhcccccCCeEEeCC
Confidence                         3567899999999998 5788888765 57999999999986 5889998765543 37777764

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.60  E-value=9.4e-16  Score=160.75  Aligned_cols=195  Identities=17%  Similarity=0.164  Sum_probs=103.3

Q ss_pred             cccccccccc-ccchhh--cccccCceeeecCCcccccchhhccC-----ccCcEeeccCCcCCCCCchhhhcCCccCcE
Q 004021          517 LSLRRNDSLT-ELPSRI--SSLVSLHHLDLSLTHIRGLPQELKAL-----EKLRYLNLEYTHYLSIIPHQLISGFLKLEV  588 (779)
Q Consensus       517 L~L~~~~~l~-~lp~~i--~~L~~L~~L~L~~~~i~~lp~~~~~L-----~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~  588 (779)
                      |+|++| .+. .+|..+  +.+++|++|+|++|.++.+|..++.+     ++|++|++++| .+..+|+..++++++|++
T Consensus       100 L~L~~n-~l~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~~~~~~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~  177 (312)
T 1wwl_A          100 LTLENL-EVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQA-HSLNFSCEQVRVFPALST  177 (312)
T ss_dssp             EEEEEE-BCBSCCCCCSSSCCSCCCSEEEEESCBCSSSSSHHHHHHTTCCTTCCEEEEESC-SCCCCCTTTCCCCSSCCE
T ss_pred             EEccCC-cccchhHHHHHHhcCCCccEEEccCCCCcchhHHHHHHHHhhcCCCcEEEeeCC-CCccchHHHhccCCCCCE
Confidence            455555 444 345554  56666666666666666666555555     66666666666 445555333666666666


Q ss_pred             eeeccccCCCcccccCCccCCCchhhHHhh--cCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          589 LRLLECGSEGVTKEEGNVLCDDAEPLMREL--LGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       589 L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l--~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                      |++++|.+.+            ....+..+  +.+++|+.|+++.|....++      .+....+..+++|+.|+|++|.
T Consensus       178 L~Ls~N~l~~------------~~~~~~~~~~~~l~~L~~L~L~~N~l~~~~------~~~~~~~~~l~~L~~L~Ls~N~  239 (312)
T 1wwl_A          178 LDLSDNPELG------------ERGLISALCPLKFPTLQVLALRNAGMETPS------GVCSALAAARVQLQGLDLSHNS  239 (312)
T ss_dssp             EECCSCTTCH------------HHHHHHHSCTTSCTTCCEEECTTSCCCCHH------HHHHHHHHTTCCCSEEECTTSC
T ss_pred             EECCCCCcCc------------chHHHHHHHhccCCCCCEEECCCCcCcchH------HHHHHHHhcCCCCCEEECCCCc
Confidence            6666665432            01123333  55666666666644322110      1111122355677777777654


Q ss_pred             ccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCccccc
Q 004021          667 EMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERR  746 (779)
Q Consensus       667 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~  746 (779)
                      ....++.               ..+..+++|+.|++++ +.++.+|....  ++|++|++++| +++.+|.......++.
T Consensus       240 l~~~~~~---------------~~~~~l~~L~~L~Ls~-N~l~~ip~~~~--~~L~~L~Ls~N-~l~~~p~~~~l~~L~~  300 (312)
T 1wwl_A          240 LRDAAGA---------------PSCDWPSQLNSLNLSF-TGLKQVPKGLP--AKLSVLDLSYN-RLDRNPSPDELPQVGN  300 (312)
T ss_dssp             CCSSCCC---------------SCCCCCTTCCEEECTT-SCCSSCCSSCC--SEEEEEECCSS-CCCSCCCTTTSCEEEE
T ss_pred             CCcccch---------------hhhhhcCCCCEEECCC-CccChhhhhcc--CCceEEECCCC-CCCCChhHhhCCCCCE
Confidence            3332211               1334466777777776 34556665543  67777777665 4666665222222344


Q ss_pred             EEEe
Q 004021          747 VVIE  750 (779)
Q Consensus       747 l~i~  750 (779)
                      +.+.
T Consensus       301 L~L~  304 (312)
T 1wwl_A          301 LSLK  304 (312)
T ss_dssp             EECT
T ss_pred             Eecc
Confidence            4444

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.60  E-value=1.4e-15  Score=169.42  Aligned_cols=205  Identities=17%  Similarity=0.121  Sum_probs=131.2

Q ss_pred             cCCccEEEcccccccccccC-----cc--cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeec
Q 004021          494 WEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNL  566 (779)
Q Consensus       494 ~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l  566 (779)
                      +++++.|++++|.+..++..     +.  .|+|++| .+..+++ ++++++|++|+|++|.++.+|..    ++|++|++
T Consensus        33 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~-l~~l~~L~~L~Ls~N~l~~l~~~----~~L~~L~L  106 (487)
T 3oja_A           33 AWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSN-VLYETLD-LESLSTLRTLDLNNNYVQELLVG----PSIETLHA  106 (487)
T ss_dssp             GGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTTS-CCEEEEE-CTTCTTCCEEECCSSEEEEEEEC----TTCCEEEC
T ss_pred             CCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeCC-CCCCCcc-cccCCCCCEEEecCCcCCCCCCC----CCcCEEEC
Confidence            34788888888887766532     11  3888888 7776654 78888888888888888777642    67888888


Q ss_pred             cCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcc
Q 004021          567 EYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL  646 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L  646 (779)
                      ++| .+..+|..   .+++|++|++++|.+.+              ..+..++.+++|+.|+++.|.         +...
T Consensus       107 ~~N-~l~~~~~~---~l~~L~~L~L~~N~l~~--------------~~~~~~~~l~~L~~L~Ls~N~---------l~~~  159 (487)
T 3oja_A          107 ANN-NISRVSCS---RGQGKKNIYLANNKITM--------------LRDLDEGCRSRVQYLDLKLNE---------IDTV  159 (487)
T ss_dssp             CSS-CCCCEEEC---CCSSCEEEECCSSCCCS--------------GGGBCGGGGSSEEEEECTTSC---------CCEE
T ss_pred             cCC-cCCCCCcc---ccCCCCEEECCCCCCCC--------------CCchhhcCCCCCCEEECCCCC---------CCCc
Confidence            887 55666553   46778888888877764              234455667777888777443         3333


Q ss_pred             cCcccc-cccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEe
Q 004021          647 DLTWLV-FVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIG  725 (779)
Q Consensus       647 ~~~~l~-~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~  725 (779)
                      .+..+. .+++|+.|+|++|.. ..++                 ....+++|+.|+|++ +.+..++..+..+++|+.|+
T Consensus       160 ~~~~l~~~l~~L~~L~Ls~N~l-~~~~-----------------~~~~l~~L~~L~Ls~-N~l~~~~~~~~~l~~L~~L~  220 (487)
T 3oja_A          160 NFAELAASSDTLEHLNLQYNFI-YDVK-----------------GQVVFAKLKTLDLSS-NKLAFMGPEFQSAAGVTWIS  220 (487)
T ss_dssp             EGGGGGGGTTTCCEEECTTSCC-CEEE-----------------CCCCCTTCCEEECCS-SCCCEECGGGGGGTTCSEEE
T ss_pred             ChHHHhhhCCcccEEecCCCcc-cccc-----------------ccccCCCCCEEECCC-CCCCCCCHhHcCCCCccEEE
Confidence            334443 567777777777543 3332                 223467777777776 35666666666677777777


Q ss_pred             eeCCCCCCCCCCCCCCc-ccccEEEec
Q 004021          726 VYGCPKLKKLPINSSSA-KERRVVIEG  751 (779)
Q Consensus       726 l~~c~~L~~lP~~~~~~-~~~~l~i~~  751 (779)
                      +++| .+..+|..+... .++.+.+.+
T Consensus       221 Ls~N-~l~~lp~~l~~l~~L~~L~l~~  246 (487)
T 3oja_A          221 LRNN-KLVLIEKALRFSQNLEHFDLRG  246 (487)
T ss_dssp             CTTS-CCCEECTTCCCCTTCCEEECTT
T ss_pred             ecCC-cCcccchhhccCCCCCEEEcCC
Confidence            7765 356666655443 235566554

>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=99.59  E-value=5.1e-15  Score=170.54  Aligned_cols=220  Identities=20%  Similarity=0.172  Sum_probs=157.4

Q ss_pred             cCcccccCccccccCCccEEEcccccc-cccc--cCcc--ccccccccccccc---chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEI-ESLS--EIPT--LLSLRRNDSLTEL---PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~-~~l~--~~~~--lL~L~~~~~l~~l---p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+..+..+|.. .+..++.|++.+|.. ..++  ..+.  .|++++| .+..+   |..+..+++|++|++++|.++.+|
T Consensus       315 ~~n~l~~lp~~-~l~~L~~L~l~~n~~~~~~~~~~l~~L~~L~ls~n-~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~  392 (606)
T 3vq2_A          315 IRCQLKQFPTL-DLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRN-ALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMS  392 (606)
T ss_dssp             ESCCCSSCCCC-CCSSCCEEEEESCSSCEECCCCCCTTCCEEECCSS-CEEEEEECCHHHHCCSCCCEEECCSCSEEEEC
T ss_pred             ccccCcccccC-CCCccceeeccCCcCccchhhccCCCCCEEECcCC-ccCCCcchhhhhccCCcccEeECCCCccccch
Confidence            34444566655 777888888888732 2221  1112  3888888 76655   777888888888888888888888


Q ss_pred             hhhccCccCcEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEe
Q 004021          553 QELKALEKLRYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSF  631 (779)
Q Consensus       553 ~~~~~L~~L~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~  631 (779)
                      ..+.++++|++|++++|. +..+++ ..+..+++|++|++++|.+..              ..+..++.+++|+.|+++.
T Consensus       393 ~~~~~l~~L~~L~l~~n~-l~~~~~~~~~~~l~~L~~L~l~~n~l~~--------------~~~~~~~~l~~L~~L~l~~  457 (606)
T 3vq2_A          393 ANFMGLEELQHLDFQHST-LKRVTEFSAFLSLEKLLYLDISYTNTKI--------------DFDGIFLGLTSLNTLKMAG  457 (606)
T ss_dssp             CCCTTCTTCCEEECTTSE-EESTTTTTTTTTCTTCCEEECTTSCCEE--------------CCTTTTTTCTTCCEEECTT
T ss_pred             hhccCCCCCCeeECCCCc-cCCccChhhhhccccCCEEECcCCCCCc--------------cchhhhcCCCCCCEEECCC
Confidence            888888888888888884 444433 337788888888888887663              2344566667777777766


Q ss_pred             ecccc------cccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCC
Q 004021          632 RSSLA------VQKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFT  695 (779)
Q Consensus       632 ~~~~~------~~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  695 (779)
                      |....      +..+++|+.|          .+.++..+++|+.|+|++|.....++.                .+..++
T Consensus       458 n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~----------------~~~~l~  521 (606)
T 3vq2_A          458 NSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSS----------------HYNQLY  521 (606)
T ss_dssp             CEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSCEEGG----------------GTTTCT
T ss_pred             CcCCCcchHHhhccCCCCCEEECCCCcCCccChhhhcccccCCEEECCCCcCCCcCHH----------------HccCCC
Confidence            55432      2344555555          455688899999999999865554433                678899


Q ss_pred             CccEEEccCCCCCccccCCCCCCC-CccEEeeeCCCCCCC
Q 004021          696 QLESLGILYGPDLKSIYPNPLHFP-KLKKIGVYGCPKLKK  734 (779)
Q Consensus       696 ~L~~L~l~~~~~l~~l~~~~~~l~-~L~~L~l~~c~~L~~  734 (779)
                      +|+.|+|+++ .++.+|..+..++ +|++|++++||-...
T Consensus       522 ~L~~L~l~~N-~l~~~p~~~~~l~~~L~~l~l~~N~~~c~  560 (606)
T 3vq2_A          522 SLSTLDCSFN-RIETSKGILQHFPKSLAFFNLTNNSVACI  560 (606)
T ss_dssp             TCCEEECTTS-CCCCEESCGGGSCTTCCEEECCSCCCCCS
T ss_pred             cCCEEECCCC-cCcccCHhHhhhcccCcEEEccCCCcccC
Confidence            9999999995 6889998888887 599999999875443

>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=99.59  E-value=2.4e-15  Score=171.16  Aligned_cols=106  Identities=20%  Similarity=0.235  Sum_probs=59.4

Q ss_pred             cccCCccEEEcccccccccccCc-----c--cccccccccccccchh-hcccccCceeeecCCcccc--cchhhccCccC
Q 004021          492 KEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRG--LPQELKALEKL  561 (779)
Q Consensus       492 ~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~~-i~~L~~L~~L~L~~~~i~~--lp~~~~~L~~L  561 (779)
                      ..+.++++|++++|.+..++...     .  .|+|++| .+..+|.. |+++++|++|++++|.++.  .|..++++++|
T Consensus        47 ~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L  125 (549)
T 2z81_A           47 RACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDN-HLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNL  125 (549)
T ss_dssp             SSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTS-CCCSCCHHHHTTCTTCCEEECTTCCCSSSCSSCSCTTCTTC
T ss_pred             hcCCcccEEECCCCCcCccChhhccccccCCEEECCCC-ccCccCHHHhccCCCCcEEECCCCcccccchhhhhhccCCc
Confidence            34455566666655555444211     1  2666666 55555433 6666666666666666653  34556666666


Q ss_pred             cEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          562 RYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       562 ~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ++|++++|..+..+|...++++++|++|++++|.+.+
T Consensus       126 ~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~  162 (549)
T 2z81_A          126 QTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRN  162 (549)
T ss_dssp             CEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCE
T ss_pred             cEEECCCCccccccCHhhhhcccccCeeeccCCcccc
Confidence            6666666644555554336666666666666665554

>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=99.59  E-value=9.9e-15  Score=164.78  Aligned_cols=112  Identities=21%  Similarity=0.207  Sum_probs=85.5

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+..+..+|..- ..++++|++++|.+..++..     ..  .|+|++| .+..+ |..|+++++|++|+|++|.++.+|
T Consensus         8 s~n~l~~ip~~~-~~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~lp   85 (520)
T 2z7x_B            8 SKNGLIHVPKDL-SQKTTILNISQNYISELWTSDILSLSKLRILIISHN-RIQYLDISVFKFNQELEYLDLSHNKLVKIS   85 (520)
T ss_dssp             TTSCCSSCCCSC-CTTCSEEECCSSCCCCCCHHHHTTCTTCCEEECCSS-CCCEEEGGGGTTCTTCCEEECCSSCCCEEE
T ss_pred             CCCCcccccccc-cccccEEECCCCcccccChhhccccccccEEecCCC-ccCCcChHHhhcccCCCEEecCCCceeecC
Confidence            344555555422 27889999999988776531     12  4899999 88877 778899999999999999998888


Q ss_pred             hhhccCccCcEeeccCCcCCCC--CchhhhcCCccCcEeeeccccCCC
Q 004021          553 QELKALEKLRYLNLEYTHYLSI--IPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       553 ~~~~~L~~L~~L~l~~~~~l~~--lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ..  .+++|++|++++| .+..  +|.. ++++++|++|++++|.+..
T Consensus        86 ~~--~l~~L~~L~L~~N-~l~~~~~p~~-~~~l~~L~~L~L~~n~l~~  129 (520)
T 2z7x_B           86 CH--PTVNLKHLDLSFN-AFDALPICKE-FGNMSQLKFLGLSTTHLEK  129 (520)
T ss_dssp             CC--CCCCCSEEECCSS-CCSSCCCCGG-GGGCTTCCEEEEEESSCCG
T ss_pred             cc--ccCCccEEeccCC-ccccccchhh-hccCCcceEEEecCcccch
Confidence            77  8889999999998 4554  5665 8889999999988887653

>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=99.59  E-value=9.9e-15  Score=152.48  Aligned_cols=183  Identities=21%  Similarity=0.243  Sum_probs=147.9

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .|++++| .+..+| .+..+++|++|++++|.++.+|. +.++++|++|++++| .++.+|.  +..+++|++|++++|.
T Consensus        45 ~L~l~~~-~i~~l~-~~~~l~~L~~L~L~~n~i~~~~~-~~~l~~L~~L~L~~n-~l~~~~~--~~~l~~L~~L~l~~n~  118 (308)
T 1h6u_A           45 TLSAFGT-GVTTIE-GVQYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGN-PLKNVSA--IAGLQSIKTLDLTSTQ  118 (308)
T ss_dssp             EEECTTS-CCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSC-CCSCCGG--GTTCTTCCEEECTTSC
T ss_pred             EEEeeCC-CccCch-hhhccCCCCEEEccCCcCCCChh-HccCCCCCEEEccCC-cCCCchh--hcCCCCCCEEECCCCC
Confidence            3899999 899888 69999999999999999999988 999999999999999 5788874  8999999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +..                +..+..+++|+.|+++.|...         .+  +.+..+++|+.|++++|.. ..+    
T Consensus       119 l~~----------------~~~l~~l~~L~~L~l~~n~l~---------~~--~~l~~l~~L~~L~l~~n~l-~~~----  166 (308)
T 1h6u_A          119 ITD----------------VTPLAGLSNLQVLYLDLNQIT---------NI--SPLAGLTNLQYLSIGNAQV-SDL----  166 (308)
T ss_dssp             CCC----------------CGGGTTCTTCCEEECCSSCCC---------CC--GGGGGCTTCCEEECCSSCC-CCC----
T ss_pred             CCC----------------chhhcCCCCCCEEECCCCccC---------cC--ccccCCCCccEEEccCCcC-CCC----
Confidence            874                123888999999999866433         22  2367889999999999753 332    


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                                   ..+..+++|+.|+++++ .+..++. ...+++|++|++++| .+..+|.......++.+.+.++
T Consensus       167 -------------~~l~~l~~L~~L~l~~n-~l~~~~~-l~~l~~L~~L~L~~N-~l~~~~~l~~l~~L~~L~l~~N  227 (308)
T 1h6u_A          167 -------------TPLANLSKLTTLKADDN-KISDISP-LASLPNLIEVHLKNN-QISDVSPLANTSNLFIVTLTNQ  227 (308)
T ss_dssp             -------------GGGTTCTTCCEEECCSS-CCCCCGG-GGGCTTCCEEECTTS-CCCBCGGGTTCTTCCEEEEEEE
T ss_pred             -------------hhhcCCCCCCEEECCCC-ccCcChh-hcCCCCCCEEEccCC-ccCccccccCCCCCCEEEccCC
Confidence                         13678899999999984 6777765 678999999999997 4777775333344577777755

>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=99.58  E-value=5.5e-15  Score=166.91  Aligned_cols=96  Identities=25%  Similarity=0.221  Sum_probs=85.6

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccc-hhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcC
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~  571 (779)
                      +++++++|.++.+|....    .|+|++| .+..+| ..|.++++|++|+|++|.++.+ |..|+++++|++|++++| .
T Consensus         3 ~~l~ls~n~l~~ip~~~~~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N-~   80 (520)
T 2z7x_B            3 FLVDRSKNGLIHVPKDLSQKTTILNISQN-YISELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHN-K   80 (520)
T ss_dssp             CEEECTTSCCSSCCCSCCTTCSEEECCSS-CCCCCCHHHHTTCTTCCEEECCSSCCCEEEGGGGTTCTTCCEEECCSS-C
T ss_pred             ceEecCCCCcccccccccccccEEECCCC-cccccChhhccccccccEEecCCCccCCcChHHhhcccCCCEEecCCC-c
Confidence            679999999998886433    5999999 888875 6899999999999999999987 678999999999999999 6


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCC
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ++.+|..   .+++|++|++++|.+.+
T Consensus        81 l~~lp~~---~l~~L~~L~L~~N~l~~  104 (520)
T 2z7x_B           81 LVKISCH---PTVNLKHLDLSFNAFDA  104 (520)
T ss_dssp             CCEEECC---CCCCCSEEECCSSCCSS
T ss_pred             eeecCcc---ccCCccEEeccCCcccc
Confidence            8899984   89999999999999876

>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=99.58  E-value=1.2e-14  Score=147.05  Aligned_cols=100  Identities=21%  Similarity=0.306  Sum_probs=51.5

Q ss_pred             CccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~  569 (779)
                      ..++++++++.+..+|....    .|+|++| .+..+ |..|.++++|++|+|++|.++.++.. +.++++|++|++++|
T Consensus        15 ~~~~l~~~~~~l~~~p~~~~~~l~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n   93 (251)
T 3m19_A           15 GKKEVDCQGKSLDSVPSGIPADTEKLDLQST-GLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANN   93 (251)
T ss_dssp             GGTEEECTTCCCSSCCSCCCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTS
T ss_pred             CCeEEecCCCCccccCCCCCCCCCEEEccCC-CcCccCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEECCCC
Confidence            34566666666655554322    3555555 45444 22455555555555555555554332 455555555555555


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                       .++.+|...+..+++|++|++++|.+.
T Consensus        94 -~l~~~~~~~~~~l~~L~~L~L~~N~l~  120 (251)
T 3m19_A           94 -QLASLPLGVFDHLTQLDKLYLGGNQLK  120 (251)
T ss_dssp             -CCCCCCTTTTTTCTTCCEEECCSSCCC
T ss_pred             -cccccChhHhcccCCCCEEEcCCCcCC
Confidence             344454443455555555555555444

>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=99.58  E-value=1.3e-14  Score=169.47  Aligned_cols=115  Identities=21%  Similarity=0.229  Sum_probs=88.4

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccCc-----c--ccccccccccccc-chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+..+..+|..- ...+++|++++|.+..++...     .  .|+|++| .+..+ |..|+++++|++|+|++|.++.+|
T Consensus        12 s~~~L~~ip~~~-~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~   89 (680)
T 1ziw_A           12 SHLKLTQVPDDL-PTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFN-TISKLEPELCQKLPMLKVLNLQHNELSQLS   89 (680)
T ss_dssp             CSSCCSSCCSCS-CTTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSS-CCCCCCTTHHHHCTTCCEEECCSSCCCCCC
T ss_pred             CCCCcccccccc-CCCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCC-ccCccCHHHHhcccCcCEEECCCCccCccC
Confidence            344555566422 268899999999888776531     1  3888888 77776 677888999999999999888888


Q ss_pred             h-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          553 Q-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       553 ~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      . .|+++++|++|++++| .+..+|+..++++++|++|++++|.+.+
T Consensus        90 ~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~l~~  135 (680)
T 1ziw_A           90 DKTFAFCTNLTELHLMSN-SIQKIKNNPFVKQKNLITLDLSHNGLSS  135 (680)
T ss_dssp             TTTTTTCTTCSEEECCSS-CCCCCCSCTTTTCTTCCEEECCSSCCSC
T ss_pred             hhhhccCCCCCEEECCCC-ccCccChhHccccCCCCEEECCCCcccc
Confidence            7 4888999999999988 5677775558889999999998887765

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.58  E-value=1e-14  Score=160.93  Aligned_cols=101  Identities=23%  Similarity=0.277  Sum_probs=54.1

Q ss_pred             cccCccccccCCccEEEcccccccccccC--cc--cccccccccccccchhhcccccCceeeecCCcccccchhhccCcc
Q 004021          485 LTEAPKVKEWEGAKRISLMANEIESLSEI--PT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEK  560 (779)
Q Consensus       485 ~~~~~~~~~~~~lr~l~l~~~~~~~l~~~--~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~  560 (779)
                      +..+|.+..+..+++|++++|.+..++-.  +.  .|++++| .+..+|  ++++++|++|++++|.++.+|  ++++++
T Consensus        54 l~~~~~l~~l~~L~~L~Ls~n~l~~~~~~~l~~L~~L~Ls~N-~l~~~~--~~~l~~L~~L~L~~N~l~~l~--~~~l~~  128 (457)
T 3bz5_A           54 ITDMTGIEKLTGLTKLICTSNNITTLDLSQNTNLTYLACDSN-KLTNLD--VTPLTKLTYLNCDTNKLTKLD--VSQNPL  128 (457)
T ss_dssp             CCCCTTGGGCTTCSEEECCSSCCSCCCCTTCTTCSEEECCSS-CCSCCC--CTTCTTCCEEECCSSCCSCCC--CTTCTT
T ss_pred             cccChhhcccCCCCEEEccCCcCCeEccccCCCCCEEECcCC-CCceee--cCCCCcCCEEECCCCcCCeec--CCCCCc
Confidence            33344445555666666666666554311  11  2566666 555554  555666666666666655554  555566


Q ss_pred             CcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          561 LRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       561 L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |++|++++| .++.+|   ++.+++|++|++++|
T Consensus       129 L~~L~l~~N-~l~~l~---l~~l~~L~~L~l~~n  158 (457)
T 3bz5_A          129 LTYLNCARN-TLTEID---VSHNTQLTELDCHLN  158 (457)
T ss_dssp             CCEEECTTS-CCSCCC---CTTCTTCCEEECTTC
T ss_pred             CCEEECCCC-ccceec---cccCCcCCEEECCCC
Confidence            666666555 344442   445555555555554

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.58  E-value=6.9e-15  Score=126.99  Aligned_cols=84  Identities=17%  Similarity=0.223  Sum_probs=75.3

Q ss_pred             cchhhHHHHHHHHHhhhhcchhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCchhHHHHHHHHHHHHHHHHH
Q 004021            8 SLPPDLFSRTLHRVGEQANYVWGLKKNLEGLKTEMRKLTRTRDDLVNKVEVEEQPRRTRRTNRVAGWLEDVQKLGTEFTE   87 (779)
Q Consensus         8 ~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~~ae~~~~~~~~~~~~~Wl~~l~~~~~d~ed   87 (779)
                      |+++.+++||.+++.+|+.++.++++++++|+++|+.|+++|.+       |+.+.....+++++.|+++||+++||+||
T Consensus         1 a~v~~ll~KL~~ll~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~d-------a~~~~~~~~d~~vk~W~~~vrdlaYD~ED   73 (115)
T 3qfl_A            1 AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIK-------IGEVPREQLDSQDKLWADEVRELSYVIED   73 (115)
T ss_dssp             CTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HTTSCGGGCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHH-------HHHhccccCCHHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999998       66552115789999999999999999999


Q ss_pred             HHHHHHHHhhh
Q 004021           88 LQQVRAQEMDR   98 (779)
Q Consensus        88 ~ld~~~~~~~~   98 (779)
                      ++|+|.++...
T Consensus        74 ~iD~f~~~~~~   84 (115)
T 3qfl_A           74 VVDKFLVQVDG   84 (115)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhcc
Confidence            99999988753

>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=99.58  E-value=7.7e-15  Score=169.07  Aligned_cols=239  Identities=18%  Similarity=0.153  Sum_probs=133.1

Q ss_pred             cccCCccEEEcccccccccccCcc------ccccccccccccc-chhhcccccCceeeecCCccc-ccchh-hccCccCc
Q 004021          492 KEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIR-GLPQE-LKALEKLR  562 (779)
Q Consensus       492 ~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~-~lp~~-~~~L~~L~  562 (779)
                      ..+.+++.|++++|.+..+|....      .|++++| .+..+ |..++++++|++|++++|.+. .+|.. +.++++|+
T Consensus       275 ~~l~~L~~L~l~~n~l~~lp~~l~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~  353 (606)
T 3t6q_A          275 HCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSAN-KFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLR  353 (606)
T ss_dssp             TTCTTCSEEECTTSCCSCCCSSCCSCTTCCEEECTTC-CCSBGGGGCGGGCTTCSEEECCSCSSCCBCCSSTTTTCTTCC
T ss_pred             ccccCCCEEeccCCccCCCChhhcccccCCEEECccC-CcCcCchhhhhccCcCCEEECCCCCcccccchhhhhccCcCC
Confidence            344555556665555555543321      2555555 44443 334555555555555555443 23332 44555555


Q ss_pred             EeeccCCcCCCCC---chhhhcCCccCcEeeeccccCCCcccccCC--------ccCCCc---hhhHHhhcCCCCCCcee
Q 004021          563 YLNLEYTHYLSII---PHQLISGFLKLEVLRLLECGSEGVTKEEGN--------VLCDDA---EPLMRELLGLKRLNVLS  628 (779)
Q Consensus       563 ~L~l~~~~~l~~l---p~~~i~~L~~L~~L~l~~~~~~~~~~~~~~--------~~~~~~---~~~~~~l~~L~~L~~L~  628 (779)
                      +|++++| .+..+   |.. ++.+++|++|++++|.+...+.....        .+.++.   ......+..+++|+.|+
T Consensus       354 ~L~l~~n-~l~~~~~~~~~-~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~  431 (606)
T 3t6q_A          354 ELDLSHD-DIETSDCCNLQ-LRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLN  431 (606)
T ss_dssp             EEECCSS-CCCEEEESTTT-TTTCTTCCEEECCSCSCEEECTTTTTTCTTCSEEECTTCCEECCTTCCTTTTCTTCCEEE
T ss_pred             EEECCCC-ccccccCcchh-cccCCCCCEEECCCCcCCcCCHHHhcCCccCCeEECCCCcCCCcccchhhhCcccCCEEE
Confidence            5555554 23332   222 44455555555554444332211111        000000   11122367788888888


Q ss_pred             EEeecccc-----cccCCCCCccc-------------CcccccccCcceEEeccccccceecccccccCcccchhhccCC
Q 004021          629 WSFRSSLA-----VQKFFKYPKLD-------------LTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSE  690 (779)
Q Consensus       629 l~~~~~~~-----~~~~~~L~~L~-------------~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~  690 (779)
                      ++.|....     +..+++|+.|.             +..+..+++|+.|+|++|... .++.               ..
T Consensus       432 l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~l~~L~~L~Ls~n~l~-~~~~---------------~~  495 (606)
T 3t6q_A          432 LSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLS-SIDQ---------------HA  495 (606)
T ss_dssp             CTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEECSSCGGGGCTTCCEEECTTSCCC-EECT---------------TT
T ss_pred             CCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccccchhhccCCCccEEECCCCccC-ccCh---------------hh
Confidence            88776533     34566676661             134778999999999997654 4433               36


Q ss_pred             CCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCC-CCC-cccccEEEec
Q 004021          691 HNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPIN-SSS-AKERRVVIEG  751 (779)
Q Consensus       691 ~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~-~~~-~~~~~l~i~~  751 (779)
                      +..+++|+.|+++++.-....+..+..+++| .|++++|. +..+|.. +.. ..++.+.+.+
T Consensus       496 ~~~l~~L~~L~Ls~N~l~~~~~~~l~~l~~L-~L~L~~N~-l~~~~~~~~~~l~~L~~L~l~~  556 (606)
T 3t6q_A          496 FTSLKMMNHVDLSHNRLTSSSIEALSHLKGI-YLNLASNH-ISIILPSLLPILSQQRTINLRQ  556 (606)
T ss_dssp             TTTCTTCCEEECCSSCCCGGGGGGGTTCCSC-EEECCSSC-CCCCCGGGHHHHHTSSEEECTT
T ss_pred             hccccCCCEEECCCCccCcCChhHhCccccc-EEECcCCc-ccccCHhhcccCCCCCEEeCCC
Confidence            7889999999999964444455677789999 99999985 6666543 222 2336777764

>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=99.57  E-value=1.8e-14  Score=164.23  Aligned_cols=137  Identities=22%  Similarity=0.248  Sum_probs=97.6

Q ss_pred             EEEEcCcccccCccccccCCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcc
Q 004021          477 FLVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHI  548 (779)
Q Consensus       477 ~~~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i  548 (779)
                      .+-..+..+..+|.. -...+++|++++|.+..++..     +.  .|+|++| .++.+ |..|+++++|++|+|++|.+
T Consensus        35 ~l~ls~~~L~~ip~~-~~~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l  112 (562)
T 3a79_B           35 MVDYSNRNLTHVPKD-LPPRTKALSLSQNSISELRMPDISFLSELRVLRLSHN-RIRSLDFHVFLFNQDLEYLDVSHNRL  112 (562)
T ss_dssp             EEECTTSCCCSCCTT-SCTTCCEEECCSSCCCCCCGGGTTTCTTCCEEECCSC-CCCEECTTTTTTCTTCCEEECTTSCC
T ss_pred             EEEcCCCCCccCCCC-CCCCcCEEECCCCCccccChhhhccCCCccEEECCCC-CCCcCCHHHhCCCCCCCEEECCCCcC
Confidence            333445556666642 236888999998888877632     11  3889998 88877 67788899999999999988


Q ss_pred             cccchhhccCccCcEeeccCCcCCCCCc--hhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCc
Q 004021          549 RGLPQELKALEKLRYLNLEYTHYLSIIP--HQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNV  626 (779)
Q Consensus       549 ~~lp~~~~~L~~L~~L~l~~~~~l~~lp--~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~  626 (779)
                      +.+|..  .+++|++|++++| .+..+|  .. ++++++|++|++++|.+..              ..+..+..+ +|+.
T Consensus       113 ~~lp~~--~l~~L~~L~Ls~N-~l~~l~~p~~-~~~l~~L~~L~L~~n~l~~--------------~~~~~l~~L-~L~~  173 (562)
T 3a79_B          113 QNISCC--PMASLRHLDLSFN-DFDVLPVCKE-FGNLTKLTFLGLSAAKFRQ--------------LDLLPVAHL-HLSC  173 (562)
T ss_dssp             CEECSC--CCTTCSEEECCSS-CCSBCCCCGG-GGGCTTCCEEEEECSBCCT--------------TTTGGGTTS-CEEE
T ss_pred             CccCcc--ccccCCEEECCCC-CccccCchHh-hcccCcccEEecCCCcccc--------------Cchhhhhhc-eeeE
Confidence            888877  7889999999988 566654  44 8889999999998887763              122333333 3477


Q ss_pred             eeEEeecc
Q 004021          627 LSWSFRSS  634 (779)
Q Consensus       627 L~l~~~~~  634 (779)
                      |+++.|..
T Consensus       174 L~L~~n~l  181 (562)
T 3a79_B          174 ILLDLVSY  181 (562)
T ss_dssp             EEEEESSC
T ss_pred             EEeecccc
Confidence            77776544

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.57  E-value=2.8e-15  Score=157.53  Aligned_cols=203  Identities=16%  Similarity=0.119  Sum_probs=115.8

Q ss_pred             CCccEEEcccccccccccC-----cc--cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeecc
Q 004021          495 EGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLE  567 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~  567 (779)
                      .++++|++++|.+..++..     +.  .|+|++| .+..+++ +.++++|++|++++|.++.+|.    +++|++|+++
T Consensus        34 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~-~~~l~~L~~L~Ls~n~l~~l~~----~~~L~~L~l~  107 (317)
T 3o53_A           34 WNVKELDLSGNPLSQISAADLAPFTKLELLNLSSN-VLYETLD-LESLSTLRTLDLNNNYVQELLV----GPSIETLHAA  107 (317)
T ss_dssp             GGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTTS-CCEEEEE-ETTCTTCCEEECCSSEEEEEEE----CTTCCEEECC
T ss_pred             CCCCEEECcCCccCcCCHHHhhCCCcCCEEECCCC-cCCcchh-hhhcCCCCEEECcCCccccccC----CCCcCEEECC
Confidence            4677777777777655421     11  3777777 6665554 7777777777777777766652    3667777777


Q ss_pred             CCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCccc
Q 004021          568 YTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD  647 (779)
Q Consensus       568 ~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~  647 (779)
                      +| .+..++..   .+++|++|++++|.+..              ..+..++.+++|+.|+++.|..         ..+.
T Consensus       108 ~n-~l~~~~~~---~~~~L~~L~l~~N~l~~--------------~~~~~~~~l~~L~~L~Ls~N~l---------~~~~  160 (317)
T 3o53_A          108 NN-NISRVSCS---RGQGKKNIYLANNKITM--------------LRDLDEGCRSRVQYLDLKLNEI---------DTVN  160 (317)
T ss_dssp             SS-CCSEEEEC---CCSSCEEEECCSSCCCS--------------GGGBCTGGGSSEEEEECTTSCC---------CEEE
T ss_pred             CC-ccCCcCcc---ccCCCCEEECCCCCCCC--------------ccchhhhccCCCCEEECCCCCC---------Cccc
Confidence            76 45555543   35667777777776654              2223455566677777664432         2222


Q ss_pred             Cccc-ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEee
Q 004021          648 LTWL-VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGV  726 (779)
Q Consensus       648 ~~~l-~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l  726 (779)
                      +..+ ..+++|+.|+|++|. +..++                 ....+++|+.|++++ +.+..++..+..+++|+.|++
T Consensus       161 ~~~~~~~l~~L~~L~L~~N~-l~~~~-----------------~~~~l~~L~~L~Ls~-N~l~~l~~~~~~l~~L~~L~L  221 (317)
T 3o53_A          161 FAELAASSDTLEHLNLQYNF-IYDVK-----------------GQVVFAKLKTLDLSS-NKLAFMGPEFQSAAGVTWISL  221 (317)
T ss_dssp             GGGGGGGTTTCCEEECTTSC-CCEEE-----------------CCCCCTTCCEEECCS-SCCCEECGGGGGGTTCSEEEC
T ss_pred             HHHHhhccCcCCEEECCCCc-Ccccc-----------------cccccccCCEEECCC-CcCCcchhhhcccCcccEEEC
Confidence            2233 345666666666644 23221                 122356666666665 345555555556666666666


Q ss_pred             eCCCCCCCCCCCCCCc-ccccEEEe
Q 004021          727 YGCPKLKKLPINSSSA-KERRVVIE  750 (779)
Q Consensus       727 ~~c~~L~~lP~~~~~~-~~~~l~i~  750 (779)
                      ++| .++.+|..+... .++.+.+.
T Consensus       222 ~~N-~l~~l~~~~~~l~~L~~L~l~  245 (317)
T 3o53_A          222 RNN-KLVLIEKALRFSQNLEHFDLR  245 (317)
T ss_dssp             TTS-CCCEECTTCCCCTTCCEEECT
T ss_pred             cCC-cccchhhHhhcCCCCCEEEcc
Confidence            665 455566544333 22555554

>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=99.57  E-value=1.8e-14  Score=145.77  Aligned_cols=171  Identities=23%  Similarity=0.291  Sum_probs=137.8

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      .++++++ .+..+|..+.  .+|++|+|++|.++.++. .+.++++|++|++++| .+..+++..+..+++|++|++++|
T Consensus        18 ~l~~~~~-~l~~~p~~~~--~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L~~n   93 (251)
T 3m19_A           18 EVDCQGK-SLDSVPSGIP--ADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYN-QLQTLSAGVFDDLTELGTLGLANN   93 (251)
T ss_dssp             EEECTTC-CCSSCCSCCC--TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECTTS
T ss_pred             EEecCCC-CccccCCCCC--CCCCEEEccCCCcCccCHhHhcCcccCCEEECCCC-cCCccCHhHhccCCcCCEEECCCC
Confidence            3788888 8999998776  689999999999988765 5899999999999999 677777766899999999999999


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      .+..              ..+..+..+++|+.|+++.|.         ++.+.+..+..+++|+.|+|++|. +..++. 
T Consensus        94 ~l~~--------------~~~~~~~~l~~L~~L~L~~N~---------l~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~-  148 (251)
T 3m19_A           94 QLAS--------------LPLGVFDHLTQLDKLYLGGNQ---------LKSLPSGVFDRLTKLKELRLNTNQ-LQSIPA-  148 (251)
T ss_dssp             CCCC--------------CCTTTTTTCTTCCEEECCSSC---------CCCCCTTTTTTCTTCCEEECCSSC-CCCCCT-
T ss_pred             cccc--------------cChhHhcccCCCCEEEcCCCc---------CCCcChhHhccCCcccEEECcCCc-CCccCH-
Confidence            8875              233456788999999998554         444444556788999999999964 444443 


Q ss_pred             ccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-CCCCCCCccEEeeeCCC
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-NPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~  730 (779)
                                    ..+..+++|+.|+|++ +.+..++. .+..+++|+.|++++|+
T Consensus       149 --------------~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~l~~N~  190 (251)
T 3m19_A          149 --------------GAFDKLTNLQTLSLST-NQLQSVPHGAFDRLGKLQTITLFGNQ  190 (251)
T ss_dssp             --------------TTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSCC
T ss_pred             --------------HHcCcCcCCCEEECCC-CcCCccCHHHHhCCCCCCEEEeeCCc
Confidence                          3577899999999998 46777776 56689999999999876

>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=99.56  E-value=3.2e-14  Score=162.07  Aligned_cols=108  Identities=24%  Similarity=0.313  Sum_probs=72.5

Q ss_pred             CcccccCc--cccccCCccEEEcccccccccccCc-----c--cccccccccccccchhhcccccCceeeecCCcccccc
Q 004021          482 GVKLTEAP--KVKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       482 ~~~~~~~~--~~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      +..+..++  .+..+.++++|++++|.+..++...     .  .|+|++| .+..+|..  .+++|++|++++|.++.+|
T Consensus        61 ~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~lp~~--~l~~L~~L~Ls~N~l~~l~  137 (562)
T 3a79_B           61 QNSISELRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVSHN-RLQNISCC--PMASLRHLDLSFNDFDVLP  137 (562)
T ss_dssp             SSCCCCCCGGGTTTCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECTTS-CCCEECSC--CCTTCSEEECCSSCCSBCC
T ss_pred             CCCccccChhhhccCCCccEEECCCCCCCcCCHHHhCCCCCCCEEECCCC-cCCccCcc--ccccCCEEECCCCCccccC
Confidence            33444443  3456677888888888777664321     1  3788888 77777766  7788888888888777654


Q ss_pred             --hhhccCccCcEeeccCCcCCCCCchhhhcCCccC--cEeeeccccC
Q 004021          553 --QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKL--EVLRLLECGS  596 (779)
Q Consensus       553 --~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L--~~L~l~~~~~  596 (779)
                        ..++++++|++|++++| .+...  . +..+++|  ++|++++|.+
T Consensus       138 ~p~~~~~l~~L~~L~L~~n-~l~~~--~-~~~l~~L~L~~L~L~~n~l  181 (562)
T 3a79_B          138 VCKEFGNLTKLTFLGLSAA-KFRQL--D-LLPVAHLHLSCILLDLVSY  181 (562)
T ss_dssp             CCGGGGGCTTCCEEEEECS-BCCTT--T-TGGGTTSCEEEEEEEESSC
T ss_pred             chHhhcccCcccEEecCCC-ccccC--c-hhhhhhceeeEEEeecccc
Confidence              67888888888888877 34432  1 4455555  8888887766

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.56  E-value=3e-14  Score=157.13  Aligned_cols=101  Identities=20%  Similarity=0.218  Sum_probs=88.1

Q ss_pred             cccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEe
Q 004021          490 KVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYL  564 (779)
Q Consensus       490 ~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L  564 (779)
                      .+..+.++++|++++|.+..+|....     .|+|++| .++.+|  ++++++|++|++++|.++.+|  ++++++|++|
T Consensus        37 ~~~~l~~L~~L~Ls~n~l~~~~~l~~l~~L~~L~Ls~n-~l~~~~--~~~l~~L~~L~Ls~N~l~~~~--~~~l~~L~~L  111 (457)
T 3bz5_A           37 SEEQLATLTSLDCHNSSITDMTGIEKLTGLTKLICTSN-NITTLD--LSQNTNLTYLACDSNKLTNLD--VTPLTKLTYL  111 (457)
T ss_dssp             EHHHHTTCCEEECCSSCCCCCTTGGGCTTCSEEECCSS-CCSCCC--CTTCTTCSEEECCSSCCSCCC--CTTCTTCCEE
T ss_pred             ChhHcCCCCEEEccCCCcccChhhcccCCCCEEEccCC-cCCeEc--cccCCCCCEEECcCCCCceee--cCCCCcCCEE
Confidence            44567899999999999988764322     4999999 899887  899999999999999999986  8999999999


Q ss_pred             eccCCcCCCCCchhhhcCCccCcEeeeccccCCCc
Q 004021          565 NLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGV  599 (779)
Q Consensus       565 ~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~  599 (779)
                      ++++| .++.+|   ++.+++|++|++++|.+.++
T Consensus       112 ~L~~N-~l~~l~---~~~l~~L~~L~l~~N~l~~l  142 (457)
T 3bz5_A          112 NCDTN-KLTKLD---VSQNPLLTYLNCARNTLTEI  142 (457)
T ss_dssp             ECCSS-CCSCCC---CTTCTTCCEEECTTSCCSCC
T ss_pred             ECCCC-cCCeec---CCCCCcCCEEECCCCcccee
Confidence            99999 677775   78999999999999998864

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.56  E-value=1.1e-14  Score=152.58  Aligned_cols=195  Identities=18%  Similarity=0.221  Sum_probs=151.0

Q ss_pred             ccCCccEEEcccccccc-cccCc------c--cccccccccccccchhhccc-----ccCceeeecCCcccccc-hhhcc
Q 004021          493 EWEGAKRISLMANEIES-LSEIP------T--LLSLRRNDSLTELPSRISSL-----VSLHHLDLSLTHIRGLP-QELKA  557 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~-l~~~~------~--lL~L~~~~~l~~lp~~i~~L-----~~L~~L~L~~~~i~~lp-~~~~~  557 (779)
                      .+.++++|++++|.+.. +|...      .  .|+|++| .+..+|..++++     ++|++|++++|.+..+| ..+++
T Consensus        93 ~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~~  171 (312)
T 1wwl_A           93 GISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNV-SWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRV  171 (312)
T ss_dssp             TTSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEESC-BCSSSSSHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCCC
T ss_pred             CcCCccEEEccCCcccchhHHHHHHhcCCCccEEEccCC-CCcchhHHHHHHHHhhcCCCcEEEeeCCCCccchHHHhcc
Confidence            35789999999999873 55432      1  3999999 898889889888     99999999999999987 78999


Q ss_pred             CccCcEeeccCCcCCCC--Cchhhh--cCCccCcEeeeccccCCCcccccCCccCCCchhhH-HhhcCCCCCCceeEEee
Q 004021          558 LEKLRYLNLEYTHYLSI--IPHQLI--SGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLM-RELLGLKRLNVLSWSFR  632 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~--lp~~~i--~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~L~~L~~L~l~~~  632 (779)
                      +++|++|++++|...+.  +|.. +  +.+++|++|++++|.+..+            ...+ .-+..+++|+.|+++.|
T Consensus       172 l~~L~~L~Ls~N~l~~~~~~~~~-~~~~~l~~L~~L~L~~N~l~~~------------~~~~~~~~~~l~~L~~L~Ls~N  238 (312)
T 1wwl_A          172 FPALSTLDLSDNPELGERGLISA-LCPLKFPTLQVLALRNAGMETP------------SGVCSALAAARVQLQGLDLSHN  238 (312)
T ss_dssp             CSSCCEEECCSCTTCHHHHHHHH-SCTTSCTTCCEEECTTSCCCCH------------HHHHHHHHHTTCCCSEEECTTS
T ss_pred             CCCCCEEECCCCCcCcchHHHHH-HHhccCCCCCEEECCCCcCcch------------HHHHHHHHhcCCCCCEEECCCC
Confidence            99999999999953333  3444 4  8999999999999988741            1222 33467899999999966


Q ss_pred             cccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          633 SSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       633 ~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                      ......        ..+.+..+++|+.|+|++|.. ..++.                .+.  ++|+.|++++ +.++.+|
T Consensus       239 ~l~~~~--------~~~~~~~l~~L~~L~Ls~N~l-~~ip~----------------~~~--~~L~~L~Ls~-N~l~~~p  290 (312)
T 1wwl_A          239 SLRDAA--------GAPSCDWPSQLNSLNLSFTGL-KQVPK----------------GLP--AKLSVLDLSY-NRLDRNP  290 (312)
T ss_dssp             CCCSSC--------CCSCCCCCTTCCEEECTTSCC-SSCCS----------------SCC--SEEEEEECCS-SCCCSCC
T ss_pred             cCCccc--------chhhhhhcCCCCEEECCCCcc-Chhhh----------------hcc--CCceEEECCC-CCCCCCh
Confidence            543221        123455678999999999754 45543                332  8999999998 5788886


Q ss_pred             CCCCCCCCccEEeeeCCC
Q 004021          713 PNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       713 ~~~~~l~~L~~L~l~~c~  730 (779)
                      . ...+++|++|++++++
T Consensus       291 ~-~~~l~~L~~L~L~~N~  307 (312)
T 1wwl_A          291 S-PDELPQVGNLSLKGNP  307 (312)
T ss_dssp             C-TTTSCEEEEEECTTCT
T ss_pred             h-HhhCCCCCEEeccCCC
Confidence            6 7899999999999875

>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=99.55  E-value=2.3e-14  Score=152.77  Aligned_cols=224  Identities=15%  Similarity=0.135  Sum_probs=147.5

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCcccc-cch-hhccCccCcEeeccCCc
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRG-LPQ-ELKALEKLRYLNLEYTH  570 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~-lp~-~~~~L~~L~~L~l~~~~  570 (779)
                      +.+..++++++++|...+    -|+|++| .|+.+|. .|.+|++|++|+|++|.+.+ +|. .|.+|++|+.+...++.
T Consensus        12 ~~v~C~~~~Lt~iP~~l~~~l~~L~Ls~N-~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N   90 (350)
T 4ay9_X           12 RVFLCQESKVTEIPSDLPRNAIELRFVLT-KLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKAN   90 (350)
T ss_dssp             TEEEEESTTCCSCCTTCCTTCSEEEEESC-CCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEET
T ss_pred             CEEEecCCCCCccCcCcCCCCCEEEccCC-cCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCC
Confidence            456666777777765432    4888888 8888875 57889999999999998744 554 47888888765544443


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCC--------ccCC--Cc-hhhHHhhcCC-CCCCceeEEeecccccc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN--------VLCD--DA-EPLMRELLGL-KRLNVLSWSFRSSLAVQ  638 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~--------~~~~--~~-~~~~~~l~~L-~~L~~L~l~~~~~~~~~  638 (779)
                      .+..+|++.+..+++|++|++++|.+..++.....        ...+  .. ......+..+ ..++.|+++.|      
T Consensus        91 ~l~~l~~~~f~~l~~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N------  164 (350)
T 4ay9_X           91 NLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKN------  164 (350)
T ss_dssp             TCCEECTTSBCCCTTCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSS------
T ss_pred             cccccCchhhhhccccccccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhccccc------
Confidence            78888777688899999999998887764321110        0000  00 0000111122 12333444322      


Q ss_pred             cCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCC
Q 004021          639 KFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHF  718 (779)
Q Consensus       639 ~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l  718 (779)
                         .++.+. +.....++|+.|.+++++.++.++.               ..+..+++|+.|++++ +.++.+|..  .|
T Consensus       165 ---~i~~i~-~~~f~~~~L~~l~l~~~n~l~~i~~---------------~~f~~l~~L~~LdLs~-N~l~~lp~~--~~  222 (350)
T 4ay9_X          165 ---GIQEIH-NSAFNGTQLDELNLSDNNNLEELPN---------------DVFHGASGPVILDISR-TRIHSLPSY--GL  222 (350)
T ss_dssp             ---CCCEEC-TTSSTTEEEEEEECTTCTTCCCCCT---------------TTTTTEECCSEEECTT-SCCCCCCSS--SC
T ss_pred             ---cccCCC-hhhccccchhHHhhccCCcccCCCH---------------HHhccCcccchhhcCC-CCcCccChh--hh
Confidence               223322 2223456788888888777777765               4678899999999998 578888764  58


Q ss_pred             CCccEEeeeCCCCCCCCCCCCCCcccccEEEe
Q 004021          719 PKLKKIGVYGCPKLKKLPINSSSAKERRVVIE  750 (779)
Q Consensus       719 ~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~  750 (779)
                      .+|+.|.+.+|++++.+|..-....++.+.+.
T Consensus       223 ~~L~~L~~l~~~~l~~lP~l~~l~~L~~l~l~  254 (350)
T 4ay9_X          223 ENLKKLRARSTYNLKKLPTLEKLVALMEASLT  254 (350)
T ss_dssp             TTCCEEECTTCTTCCCCCCTTTCCSCCEEECS
T ss_pred             ccchHhhhccCCCcCcCCCchhCcChhhCcCC
Confidence            89999999999999999975444455777765

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.55  E-value=3.1e-14  Score=162.68  Aligned_cols=252  Identities=16%  Similarity=0.141  Sum_probs=171.4

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccC-----cc--ccccccccccccc-chhhcccccCceeeecCCcccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEI-----PT--LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~-----~~--lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      .+.++..+|.. -...+++|++++|.+..++..     +.  .|+|++| .+..+ |..|+++++|++|+|++|.++.+|
T Consensus        15 ~~~~l~~ip~~-l~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n-~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~   92 (570)
T 2z63_A           15 MELNFYKIPDN-LPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPIQSLA   92 (570)
T ss_dssp             CSSCCSSCCSS-SCSSCCEEECCSCCCCEECTTTTTTCSSCCEEECTTC-CCCEECTTTTTTCTTCCEEECTTCCCCEEC
T ss_pred             CCCCccccCCC-ccccccEEEccCCccCccChhHhhCCCCceEEECCCC-cCCccCcccccCchhCCEEeCcCCcCCccC
Confidence            34455566642 235799999999998877543     12  4999999 88887 557899999999999999998876


Q ss_pred             -hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEe
Q 004021          553 -QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSF  631 (779)
Q Consensus       553 -~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~  631 (779)
                       ..|+++++|++|++++| .+..+|...++++++|++|++++|.+..             ...+..++++++|+.|+++.
T Consensus        93 ~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~L~~n~l~~-------------~~lp~~~~~l~~L~~L~l~~  158 (570)
T 2z63_A           93 LGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAHNLIQS-------------FKLPEYFSNLTNLEHLDLSS  158 (570)
T ss_dssp             TTTTTTCTTCCEEECTTS-CCCCSTTCSCTTCTTCCEEECCSSCCCC-------------CCCCGGGGGCTTCCEEECTT
T ss_pred             HhhhcCcccccccccccc-ccccCCCccccccccccEEecCCCccce-------------ecChhhhcccCCCCEEeCcC
Confidence             57999999999999999 6788887448999999999999998764             23466788899999999987


Q ss_pred             eccccc-----ccCCCC----Ccc----------cCcccccccCcceEEeccccccc-----------------------
Q 004021          632 RSSLAV-----QKFFKY----PKL----------DLTWLVFVQNLKELEIIVCTEME-----------------------  669 (779)
Q Consensus       632 ~~~~~~-----~~~~~L----~~L----------~~~~l~~l~~L~~L~L~~~~~~~-----------------------  669 (779)
                      +....+     ..+.+|    ..|          .+..+.. .+|+.|++++|....                       
T Consensus       159 n~l~~~~~~~~~~l~~L~~~~~~L~l~~n~l~~~~~~~~~~-~~L~~L~l~~n~~~~~~~~~~~~~l~~l~~~~l~~~~~  237 (570)
T 2z63_A          159 NKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKE-IRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEF  237 (570)
T ss_dssp             SCCCEECGGGGHHHHTCTTCCCEEECTTCCCCEECTTTTTT-CEEEEEEEESCCSCTTHHHHHHHTTTTCEEEEEEEEEC
T ss_pred             CccceecHHHccchhccchhhhhcccCCCCceecCHHHhcc-CcceeEecccccccccchhhhhcCccccceeeeccccc
Confidence            654332     223333    222          2222222 267778777752110                       


Q ss_pred             -------eeccccccc------------CcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCC
Q 004021          670 -------EIICVDKLR------------DVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       670 -------~~~~~~~~~------------~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                             .+......+            ....+....+..+..+++|+.|+++++ .+..+|.....+ +|++|++++|.
T Consensus       238 ~~~~~l~~~~~~~~~~l~~l~l~~l~l~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~l~~l~~~~~~~-~L~~L~l~~n~  315 (570)
T 2z63_A          238 RNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSV-TIERVKDFSYNF-GWQHLELVNCK  315 (570)
T ss_dssp             CCCSSCEECCTTTTGGGGGSEEEEEEEEETTEEESCSTTTTGGGTTCSEEEEESC-EECSCCBCCSCC-CCSEEEEESCB
T ss_pred             cCchhhhhcchhhhccccccchhhhhhhcchhhhhhchhhhcCcCcccEEEecCc-cchhhhhhhccC-CccEEeeccCc
Confidence                   000000000            000011111235667899999999985 567788877777 99999999985


Q ss_pred             CCCCCCCCCCCcccccEEEechH
Q 004021          731 KLKKLPINSSSAKERRVVIEGLK  753 (779)
Q Consensus       731 ~L~~lP~~~~~~~~~~l~i~~~~  753 (779)
                       +..+|.. ....++.+.+.++.
T Consensus       316 -~~~l~~~-~l~~L~~L~l~~n~  336 (570)
T 2z63_A          316 -FGQFPTL-KLKSLKRLTFTSNK  336 (570)
T ss_dssp             -CSSCCBC-BCSSCCEEEEESCB
T ss_pred             -ccccCcc-cccccCEEeCcCCc
Confidence             6688873 33455888887654

>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=99.55  E-value=6.4e-14  Score=163.65  Aligned_cols=115  Identities=19%  Similarity=0.200  Sum_probs=90.0

Q ss_pred             cccccCcc--ccccCCccEEEcccccccccccCc-----c--cccccccccccccch-hhcccccCceeeecCCcccccc
Q 004021          483 VKLTEAPK--VKEWEGAKRISLMANEIESLSEIP-----T--LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLP  552 (779)
Q Consensus       483 ~~~~~~~~--~~~~~~lr~l~l~~~~~~~l~~~~-----~--lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp  552 (779)
                      ..+..++.  +..+.++++|++++|.+..++...     .  .|+|++| .+..+|. .|+++++|++|++++|.++.+|
T Consensus        35 n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~  113 (680)
T 1ziw_A           35 NQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQHN-ELSQLSDKTFAFCTNLTELHLMSNSIQKIK  113 (680)
T ss_dssp             SCCCCCCGGGGGGGTTCSEEECCSSCCCCCCTTHHHHCTTCCEEECCSS-CCCCCCTTTTTTCTTCSEEECCSSCCCCCC
T ss_pred             CCCCCcCHHHHhCCCcCcEEECCCCccCccCHHHHhcccCcCEEECCCC-ccCccChhhhccCCCCCEEECCCCccCccC
Confidence            33444442  567789999999999887764421     1  4899999 8888876 5899999999999999998887


Q ss_pred             -hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCc
Q 004021          553 -QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGV  599 (779)
Q Consensus       553 -~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~  599 (779)
                       ..|+++++|++|++++| .+..++++.++++++|++|++++|.+.++
T Consensus       114 ~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n~l~~~  160 (680)
T 1ziw_A          114 NNPFVKQKNLITLDLSHN-GLSSTKLGTQVQLENLQELLLSNNKIQAL  160 (680)
T ss_dssp             SCTTTTCTTCCEEECCSS-CCSCCCCCSSSCCTTCCEEECCSSCCCCB
T ss_pred             hhHccccCCCCEEECCCC-cccccCchhhcccccCCEEEccCCccccc
Confidence             56899999999999999 45555544488999999999999887764

>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=99.54  E-value=3.6e-14  Score=161.39  Aligned_cols=101  Identities=20%  Similarity=0.199  Sum_probs=53.9

Q ss_pred             cccccccccccc-chhhcccccCceeeecCCcccccc-hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |+|++| .++.+ |..|+++++|++|++++|.++.+| ..|+++++|++|++++| .+..+|+..++++++|++|++++|
T Consensus        31 L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~Ls~n  108 (549)
T 2z81_A           31 LDLSFN-KITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDN-HLSSLSSSWFGPLSSLKYLNLMGN  108 (549)
T ss_dssp             EECCSS-CCCEECSSTTSSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTS-CCCSCCHHHHTTCTTCCEEECTTC
T ss_pred             EECcCC-ccCccChhhhhcCCcccEEECCCCCcCccChhhccccccCCEEECCCC-ccCccCHHHhccCCCCcEEECCCC
Confidence            455555 44444 345556666666666666555544 34556666666666665 344555444556666666666655


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEee
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFR  632 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~  632 (779)
                      .+..             ...+..++.+++|+.|+++.|
T Consensus       109 ~l~~-------------~~~~~~~~~l~~L~~L~L~~n  133 (549)
T 2z81_A          109 PYQT-------------LGVTSLFPNLTNLQTLRIGNV  133 (549)
T ss_dssp             CCSS-------------SCSSCSCTTCTTCCEEEEEES
T ss_pred             cccc-------------cchhhhhhccCCccEEECCCC
Confidence            5442             112233455555666665543

>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=99.54  E-value=1.2e-13  Score=152.31  Aligned_cols=216  Identities=18%  Similarity=0.154  Sum_probs=135.4

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCCcccccchhhcc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA  557 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~  557 (779)
                      .+..+..+|.+..+.++++|++++|.+..+|..+.   .|++++| .+..+| .++++++|++|++++|.++.+|...  
T Consensus       139 ~~n~l~~lp~~~~l~~L~~L~l~~N~l~~lp~~~~~L~~L~L~~n-~l~~l~-~~~~l~~L~~L~l~~N~l~~l~~~~--  214 (454)
T 1jl5_A          139 SNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNN-QLEELP-ELQNLPFLTAIYADNNSLKKLPDLP--  214 (454)
T ss_dssp             CSSCCSSCCCCTTCTTCCEEECCSSCCSCCCCCCTTCCEEECCSS-CCSSCC-CCTTCTTCCEEECCSSCCSSCCCCC--
T ss_pred             cCCCCCCCcccCCCCCCCEEECCCCcCcccCCCcccccEEECcCC-cCCcCc-cccCCCCCCEEECCCCcCCcCCCCc--
Confidence            34455556667778889999999998888776543   4899999 888888 6899999999999999988887643  


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCC----ccCCCchhhHHhhcCCCCCCceeEEeec
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPLMRELLGLKRLNVLSWSFRS  633 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~L~~L~~L~l~~~~  633 (779)
                       .+|++|++++| .+..+|.  ++.+++|++|++++|.+.+++....+    .+.++....+.  ..+++|+.|+++.|.
T Consensus       215 -~~L~~L~l~~n-~l~~lp~--~~~l~~L~~L~l~~N~l~~l~~~~~~L~~L~l~~N~l~~l~--~~~~~L~~L~ls~N~  288 (454)
T 1jl5_A          215 -LSLESIVAGNN-ILEELPE--LQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLP--ELPQSLTFLDVSENI  288 (454)
T ss_dssp             -TTCCEEECCSS-CCSSCCC--CTTCTTCCEEECCSSCCSSCCSCCTTCCEEECCSSCCSCCC--CCCTTCCEEECCSSC
T ss_pred             -CcccEEECcCC-cCCcccc--cCCCCCCCEEECCCCcCCcccccccccCEEECCCCcccccC--cccCcCCEEECcCCc
Confidence             58899999999 6778885  88999999999999888764432111    01110000000  012456666666554


Q ss_pred             ccccccC-CCCCcccC-----cccccc-cCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCC
Q 004021          634 SLAVQKF-FKYPKLDL-----TWLVFV-QNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGP  706 (779)
Q Consensus       634 ~~~~~~~-~~L~~L~~-----~~l~~l-~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~  706 (779)
                      ...++.. ++|+.|.+     ..+..+ ++|+.|++++|.. ..++.                   .+++|+.|+++++ 
T Consensus       289 l~~l~~~~~~L~~L~l~~N~l~~i~~~~~~L~~L~Ls~N~l-~~lp~-------------------~~~~L~~L~L~~N-  347 (454)
T 1jl5_A          289 FSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKL-IELPA-------------------LPPRLERLIASFN-  347 (454)
T ss_dssp             CSEESCCCTTCCEEECCSSCCSEECCCCTTCCEEECCSSCC-SCCCC-------------------CCTTCCEEECCSS-
T ss_pred             cCcccCcCCcCCEEECcCCcCCcccCCcCcCCEEECCCCcc-ccccc-------------------cCCcCCEEECCCC-
Confidence            4433222 34444411     112222 3566666665432 22221                   2466777777663 


Q ss_pred             CCccccCCCCCCCCccEEeeeCCC
Q 004021          707 DLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       707 ~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                      .++.+|.   .+++|++|++++|+
T Consensus       348 ~l~~lp~---~l~~L~~L~L~~N~  368 (454)
T 1jl5_A          348 HLAEVPE---LPQNLKQLHVEYNP  368 (454)
T ss_dssp             CCSCCCC---CCTTCCEEECCSSC
T ss_pred             ccccccc---hhhhccEEECCCCC
Confidence            4555555   35677777776654

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.53  E-value=1.7e-12  Score=138.39  Aligned_cols=276  Identities=15%  Similarity=0.126  Sum_probs=168.6

Q ss_pred             cccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEec------------hHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQ------------TFQ  221 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~------------~i~  221 (779)
                      .+.|+||++++++|.+++..+    +++.|+|++|+|||||++++++..   .     .+|+++.            .+.
T Consensus        11 ~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~---~-----~~~~~~~~~~~~~~~~~~~~~~   78 (350)
T 2qen_A           11 REDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNER---P-----GILIDCRELYAERGHITREELI   78 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHS---S-----EEEEEHHHHHHTTTCBCHHHHH
T ss_pred             hHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHc---C-----cEEEEeecccccccCCCHHHHH
Confidence            367999999999999998764    799999999999999999998764   1     6677662            233


Q ss_pred             HHHHHHhCCC--------------c-chhhhhcchhhHHHHHHHhhCC-Ccceeehhhcccccc----------------
Q 004021          222 DDIGKRIGFS--------------E-DKKWKEKSLQDKAVDISSILSP-KKFRIDLTELGVPLQ----------------  269 (779)
Q Consensus       222 ~~i~~~l~~~--------------~-~~~~~~~~~~~~~~~l~~~L~~-kr~~~~ld~l~~~~~----------------  269 (779)
                      ..+...+...              . .......+..+....+.+..+. ++..+++|++.....                
T Consensus        79 ~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L~~~  158 (350)
T 2qen_A           79 KELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLALFAYA  158 (350)
T ss_dssp             HHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHHHHHH
Confidence            4444443320              0 0000112344455555555432 377777777643211                


Q ss_pred             -ccCCCcEEEEEeCchhhhhh-----------cC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHh
Q 004021          270 -MLNAGFKIVLKTRSAGVCDQ-----------MD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLAREC  335 (779)
Q Consensus       270 -~~~~gs~IivTTR~~~va~~-----------~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c  335 (779)
                       ....+.++|+|++...+...           .+  ...+.+.+|+.+|+.+++...+.......   -.+.+..|++.|
T Consensus       159 ~~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~---~~~~~~~i~~~t  235 (350)
T 2qen_A          159 YDSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV---PENEIEEAVELL  235 (350)
T ss_dssp             HHHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC---CHHHHHHHHHHH
T ss_pred             HHhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHh
Confidence             11257889999987543211           11  24789999999999999987654332111   146788999999


Q ss_pred             CCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcC---CccchhhhhhhccccCCCcccC
Q 004021          336 GRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSL---SMDKLRSCLLYCCLYPEDYKIP  412 (779)
Q Consensus       336 ~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L---~~~~~k~cf~~~s~fp~~~~i~  412 (779)
                      +|+|+++..++..+....+...+..   .+..          .+...+.-.+..+   ++ ..+..+..+|.   + .++
T Consensus       236 gG~P~~l~~~~~~~~~~~~~~~~~~---~~~~----------~~~~~~~~~l~~l~~~~~-~~~~~l~~la~---g-~~~  297 (350)
T 2qen_A          236 DGIPGWLVVFGVEYLRNGDFGRAMK---RTLE----------VAKGLIMGELEELRRRSP-RYVDILRAIAL---G-YNR  297 (350)
T ss_dssp             TTCHHHHHHHHHHHHHHCCHHHHHH---HHHH----------HHHHHHHHHHHHHHHHCH-HHHHHHHHHHT---T-CCS
T ss_pred             CCCHHHHHHHHHHHhccccHhHHHH---HHHH----------HHHHHHHHHHHHHHhCCh-hHHHHHHHHHh---C-CCC
Confidence            9999999998876432122222211   1110          1111111112222   66 78888888887   2 234


Q ss_pred             hHHHHHHHHHc-CCCcchhhHHHHHHHHHHcccccccCCCcEEe-chHHHHHHH
Q 004021          413 KRSLIDYWISE-GFMADFDRGCEFINDLLHACLLEEEGDDHVKM-HDMIREMSL  464 (779)
Q Consensus       413 ~~~Li~~W~a~-g~~~~~~~~~~~l~~L~~~sll~~~~~~~~~m-Hdlv~~~a~  464 (779)
                      ...+.....+. |-+ +......+++.|.+.+++...+ +.|.+ |++++++.+
T Consensus       298 ~~~l~~~~~~~~~~~-~~~~~~~~l~~L~~~gli~~~~-~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          298 WSLIRDYLAVKGTKI-PEPRLYALLENLKKMNWIVEED-NTYKIADPVVATVLR  349 (350)
T ss_dssp             HHHHHHHHHHTTCCC-CHHHHHHHHHHHHHTTSEEEET-TEEEESSHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCC-CHHHHHHHHHHHHhCCCEEecC-CEEEEecHHHHHHHc
Confidence            45554443222 112 2256778999999999998763 45665 678887753

>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=99.52  E-value=1.7e-13  Score=151.08  Aligned_cols=241  Identities=15%  Similarity=0.137  Sum_probs=161.1

Q ss_pred             cCCccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCc
Q 004021          494 WEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTH  570 (779)
Q Consensus       494 ~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~  570 (779)
                      ..+++.|++++|.+..++..+.   .|++++| .+..+| .++++++|++|++++|.++.+|..+   .+|++|++++| 
T Consensus       110 ~~~L~~L~l~~n~l~~l~~~~~~L~~L~L~~n-~l~~lp-~~~~l~~L~~L~l~~N~l~~lp~~~---~~L~~L~L~~n-  183 (454)
T 1jl5_A          110 PQSLKSLLVDNNNLKALSDLPPLLEYLGVSNN-QLEKLP-ELQNSSFLKIIDVDNNSLKKLPDLP---PSLEFIAAGNN-  183 (454)
T ss_dssp             CTTCCEEECCSSCCSCCCSCCTTCCEEECCSS-CCSSCC-CCTTCTTCCEEECCSSCCSCCCCCC---TTCCEEECCSS-
T ss_pred             cCCCcEEECCCCccCcccCCCCCCCEEECcCC-CCCCCc-ccCCCCCCCEEECCCCcCcccCCCc---ccccEEECcCC-
Confidence            3688889998888887766542   4999999 888899 6999999999999999999988654   58999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCC----ccCCCchhhHHhhcCCCCCCceeEEeecccccc-cCCCCCc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ-KFFKYPK  645 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~-~~~~L~~  645 (779)
                      .+..+|.  ++++++|++|++++|.+.++|....+    .+.++....+..++.+++|+.|+++.|....++ .+++|+.
T Consensus       184 ~l~~l~~--~~~l~~L~~L~l~~N~l~~l~~~~~~L~~L~l~~n~l~~lp~~~~l~~L~~L~l~~N~l~~l~~~~~~L~~  261 (454)
T 1jl5_A          184 QLEELPE--LQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEA  261 (454)
T ss_dssp             CCSSCCC--CTTCTTCCEEECCSSCCSSCCCCCTTCCEEECCSSCCSSCCCCTTCTTCCEEECCSSCCSSCCSCCTTCCE
T ss_pred             cCCcCcc--ccCCCCCCEEECCCCcCCcCCCCcCcccEEECcCCcCCcccccCCCCCCCEEECCCCcCCcccccccccCE
Confidence            6788884  89999999999999988875543222    111111112235778899999999887766542 2355666


Q ss_pred             ccCc-----cc-ccccCcceEEeccccccceecccccccCcccchhh--ccCCCCCC-CCccEEEccCCCCCccccCCCC
Q 004021          646 LDLT-----WL-VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEI--IGSEHNFF-TQLESLGILYGPDLKSIYPNPL  716 (779)
Q Consensus       646 L~~~-----~l-~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-~~L~~L~l~~~~~l~~l~~~~~  716 (779)
                      |.+.     .+ ..+++|+.|++++|.. ..++....  ....+.-.  ....+..+ ++|+.|++++ +.+..+|..  
T Consensus       262 L~l~~N~l~~l~~~~~~L~~L~ls~N~l-~~l~~~~~--~L~~L~l~~N~l~~i~~~~~~L~~L~Ls~-N~l~~lp~~--  335 (454)
T 1jl5_A          262 LNVRDNYLTDLPELPQSLTFLDVSENIF-SGLSELPP--NLYYLNASSNEIRSLCDLPPSLEELNVSN-NKLIELPAL--  335 (454)
T ss_dssp             EECCSSCCSCCCCCCTTCCEEECCSSCC-SEESCCCT--TCCEEECCSSCCSEECCCCTTCCEEECCS-SCCSCCCCC--
T ss_pred             EECCCCcccccCcccCcCCEEECcCCcc-CcccCcCC--cCCEEECcCCcCCcccCCcCcCCEEECCC-Ccccccccc--
Confidence            5211     01 1236788888888653 33221000  00000000  00012233 5899999988 466666653  


Q ss_pred             CCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          717 HFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       717 ~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                       +++|+.|++++| +++.+|.  ....++.+.+.++
T Consensus       336 -~~~L~~L~L~~N-~l~~lp~--~l~~L~~L~L~~N  367 (454)
T 1jl5_A          336 -PPRLERLIASFN-HLAEVPE--LPQNLKQLHVEYN  367 (454)
T ss_dssp             -CTTCCEEECCSS-CCSCCCC--CCTTCCEEECCSS
T ss_pred             -CCcCCEEECCCC-ccccccc--hhhhccEEECCCC
Confidence             689999999987 6888988  2334577777653

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.52  E-value=4e-14  Score=157.59  Aligned_cols=201  Identities=14%  Similarity=0.098  Sum_probs=149.4

Q ss_pred             cCcccccCc--cccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccch
Q 004021          481 AGVKLTEAP--KVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ  553 (779)
Q Consensus       481 ~~~~~~~~~--~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~  553 (779)
                      .+..+..++  .+..+.+++.|++++|.+...+....     .|+|++| .+..+|.    .++|++|++++|.++.+|.
T Consensus        42 s~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~l~~l~~L~~L~Ls~N-~l~~l~~----~~~L~~L~L~~N~l~~~~~  116 (487)
T 3oja_A           42 SGNPLSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLRTLDLNNN-YVQELLV----GPSIETLHAANNNISRVSC  116 (487)
T ss_dssp             CSSCCCCCCGGGGTTCTTCCEEECTTSCCEEEEECTTCTTCCEEECCSS-EEEEEEE----CTTCCEEECCSSCCCCEEE
T ss_pred             eCCcCCCCCHHHHhCCCCCCEEEeeCCCCCCCcccccCCCCCEEEecCC-cCCCCCC----CCCcCEEECcCCcCCCCCc
Confidence            344444443  35677899999999999876554322     3999999 8887764    3899999999999998875


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhc-CCCCCCceeEEee
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELL-GLKRLNVLSWSFR  632 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~L~~L~~L~l~~~  632 (779)
                      .  .+++|++|++++| .+..+++..++++++|++|++++|.+.+              ..+..+. .+++|+.|+++.|
T Consensus       117 ~--~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~--------------~~~~~l~~~l~~L~~L~Ls~N  179 (487)
T 3oja_A          117 S--RGQGKKNIYLANN-KITMLRDLDEGCRSRVQYLDLKLNEIDT--------------VNFAELAASSDTLEHLNLQYN  179 (487)
T ss_dssp             C--CCSSCEEEECCSS-CCCSGGGBCGGGGSSEEEEECTTSCCCE--------------EEGGGGGGGTTTCCEEECTTS
T ss_pred             c--ccCCCCEEECCCC-CCCCCCchhhcCCCCCCEEECCCCCCCC--------------cChHHHhhhCCcccEEecCCC
Confidence            3  5788999999999 5666655448899999999999998874              3344554 6889999999866


Q ss_pred             cccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          633 SSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       633 ~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                      ....+           +....+++|+.|+|++|. +..++.                .+..+++|+.|+|++ +.+..+|
T Consensus       180 ~l~~~-----------~~~~~l~~L~~L~Ls~N~-l~~~~~----------------~~~~l~~L~~L~Ls~-N~l~~lp  230 (487)
T 3oja_A          180 FIYDV-----------KGQVVFAKLKTLDLSSNK-LAFMGP----------------EFQSAAGVTWISLRN-NKLVLIE  230 (487)
T ss_dssp             CCCEE-----------ECCCCCTTCCEEECCSSC-CCEECG----------------GGGGGTTCSEEECTT-SCCCEEC
T ss_pred             ccccc-----------cccccCCCCCEEECCCCC-CCCCCH----------------hHcCCCCccEEEecC-CcCcccc
Confidence            54332           223357888999998865 444443                456788899999988 5677888


Q ss_pred             CCCCCCCCccEEeeeCCCCC
Q 004021          713 PNPLHFPKLKKIGVYGCPKL  732 (779)
Q Consensus       713 ~~~~~l~~L~~L~l~~c~~L  732 (779)
                      ..+..+++|+.|++++|+-.
T Consensus       231 ~~l~~l~~L~~L~l~~N~l~  250 (487)
T 3oja_A          231 KALRFSQNLEHFDLRGNGFH  250 (487)
T ss_dssp             TTCCCCTTCCEEECTTCCBC
T ss_pred             hhhccCCCCCEEEcCCCCCc
Confidence            88888889999999887644

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.51  E-value=1.1e-13  Score=165.15  Aligned_cols=135  Identities=20%  Similarity=0.242  Sum_probs=99.2

Q ss_pred             cEEEcccccccccccCcc---ccccccccccccc-chhhcccccCceeeecCC-ccccc-chhhccCccCcEeeccCCcC
Q 004021          498 KRISLMANEIESLSEIPT---LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLT-HIRGL-PQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~-~i~~l-p~~~~~L~~L~~L~l~~~~~  571 (779)
                      +.++.+++++..+|..+.   .|+|++| .+..+ |..|.++++|++|+|++| .+..+ |..|++|++|++|+|++| .
T Consensus         7 ~~~dcs~~~L~~vP~lp~~l~~LdLs~N-~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N-~   84 (844)
T 3j0a_A            7 RIAFYRFCNLTQVPQVLNTTERLLLSFN-YIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSS-K   84 (844)
T ss_dssp             EEEEESCCCSSCCCSSCTTCCEEEEESC-CCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTC-C
T ss_pred             eEEEccCCCCCCCCCCCCCcCEEECCCC-cCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCC-c
Confidence            456777888888887433   5999999 88876 789999999999999999 55566 778999999999999999 5


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCc-ccc--cCC-------ccCCCc--h-hhHHhhcCCCCCCceeEEeecc
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGV-TKE--EGN-------VLCDDA--E-PLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~-~~~--~~~-------~~~~~~--~-~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      +..++++.++++++|++|++++|.+.+. +..  +.+       .+..+.  . .....++++++|+.|+++.|..
T Consensus        85 l~~~~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i  160 (844)
T 3j0a_A           85 IYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQI  160 (844)
T ss_dssp             CCEECTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCC
T ss_pred             CcccCHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcC
Confidence            6666444499999999999999988752 221  211       111111  1 1124567777777777776654

>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=99.51  E-value=6.4e-14  Score=144.96  Aligned_cols=168  Identities=18%  Similarity=0.218  Sum_probs=96.9

Q ss_pred             ccCCccEEEcccccccccccCcccccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCC
Q 004021          493 EWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYL  572 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l  572 (779)
                      .+.+++.|++.+|.+                  ..+| .+..+++|++|++++|.++.+|. +.++++|++|++++| .+
T Consensus        44 ~l~~L~~L~l~~~~i------------------~~~~-~~~~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n-~l  102 (291)
T 1h6t_A           44 ELNSIDQIIANNSDI------------------KSVQ-GIQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDEN-KV  102 (291)
T ss_dssp             HHHTCCEEECTTSCC------------------CCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CC
T ss_pred             hcCcccEEEccCCCc------------------ccCh-hHhcCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCC-cC
Confidence            345666666665544                  4443 35566666666666666666665 666666666666666 45


Q ss_pred             CCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccc
Q 004021          573 SIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLV  652 (779)
Q Consensus       573 ~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~  652 (779)
                      ..+|.  ++.+++|++|++++|.+..                +..+..+++|+.|+++.|...         .+  +.+.
T Consensus       103 ~~~~~--l~~l~~L~~L~L~~n~i~~----------------~~~l~~l~~L~~L~l~~n~l~---------~~--~~l~  153 (291)
T 1h6t_A          103 KDLSS--LKDLKKLKSLSLEHNGISD----------------INGLVHLPQLESLYLGNNKIT---------DI--TVLS  153 (291)
T ss_dssp             CCGGG--GTTCTTCCEEECTTSCCCC----------------CGGGGGCTTCCEEECCSSCCC---------CC--GGGG
T ss_pred             CCChh--hccCCCCCEEECCCCcCCC----------------ChhhcCCCCCCEEEccCCcCC---------cc--hhhc
Confidence            55554  6666666666666665553                133555666666666644322         11  3455


Q ss_pred             cccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCC
Q 004021          653 FVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       653 ~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                      .+++|+.|++++|.. ..++                 .+..+++|+.|+++++ .++.++. +..+++|+.|++++|+
T Consensus       154 ~l~~L~~L~L~~N~l-~~~~-----------------~l~~l~~L~~L~L~~N-~i~~l~~-l~~l~~L~~L~l~~n~  211 (291)
T 1h6t_A          154 RLTKLDTLSLEDNQI-SDIV-----------------PLAGLTKLQNLYLSKN-HISDLRA-LAGLKNLDVLELFSQE  211 (291)
T ss_dssp             GCTTCSEEECCSSCC-CCCG-----------------GGTTCTTCCEEECCSS-CCCBCGG-GTTCTTCSEEEEEEEE
T ss_pred             cCCCCCEEEccCCcc-ccch-----------------hhcCCCccCEEECCCC-cCCCChh-hccCCCCCEEECcCCc
Confidence            566666666666532 2221                 2445666777776663 4555543 4566667777766653

>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=99.51  E-value=3.3e-14  Score=138.01  Aligned_cols=153  Identities=19%  Similarity=0.279  Sum_probs=119.7

Q ss_pred             hcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCc
Q 004021          532 ISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDA  611 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~  611 (779)
                      .+.+++|++|++++|.++.+| .+..+++|++|++++| .+..++.  +..+++|++|++++|.+..             
T Consensus        40 ~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~~n-~~~~~~~--l~~l~~L~~L~l~~n~l~~-------------  102 (197)
T 4ezg_A           40 EAQMNSLTYITLANINVTDLT-GIEYAHNIKDLTINNI-HATNYNP--ISGLSNLERLRIMGKDVTS-------------  102 (197)
T ss_dssp             HHHHHTCCEEEEESSCCSCCT-TGGGCTTCSEEEEESC-CCSCCGG--GTTCTTCCEEEEECTTCBG-------------
T ss_pred             hhhcCCccEEeccCCCccChH-HHhcCCCCCEEEccCC-CCCcchh--hhcCCCCCEEEeECCccCc-------------
Confidence            477889999999999999888 7899999999999999 6677664  8899999999999987763             


Q ss_pred             hhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCC
Q 004021          612 EPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEH  691 (779)
Q Consensus       612 ~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  691 (779)
                       ..+..++.+++|+.|+++.|..         ....+..+..+++|+.|++++|..+..++                 .+
T Consensus       103 -~~~~~l~~l~~L~~L~Ls~n~i---------~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-----------------~l  155 (197)
T 4ezg_A          103 -DKIPNLSGLTSLTLLDISHSAH---------DDSILTKINTLPKVNSIDLSYNGAITDIM-----------------PL  155 (197)
T ss_dssp             -GGSCCCTTCTTCCEEECCSSBC---------BGGGHHHHTTCSSCCEEECCSCTBCCCCG-----------------GG
T ss_pred             -ccChhhcCCCCCCEEEecCCcc---------CcHhHHHHhhCCCCCEEEccCCCCccccH-----------------hh
Confidence             3456678889999999885543         32234567788899999999987555542                 45


Q ss_pred             CCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCC
Q 004021          692 NFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       692 ~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                      ..+++|+.|+++++ .+..++ .+..+++|+.|++++++
T Consensus       156 ~~l~~L~~L~l~~n-~i~~~~-~l~~l~~L~~L~l~~N~  192 (197)
T 4ezg_A          156 KTLPELKSLNIQFD-GVHDYR-GIEDFPKLNQLYAFSQT  192 (197)
T ss_dssp             GGCSSCCEEECTTB-CCCCCT-TGGGCSSCCEEEECBC-
T ss_pred             cCCCCCCEEECCCC-CCcChH-HhccCCCCCEEEeeCcc
Confidence            67899999999985 566666 66788999999998865

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.50  E-value=1.1e-13  Score=157.98  Aligned_cols=212  Identities=17%  Similarity=0.143  Sum_probs=124.6

Q ss_pred             CccEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCccccc---chhhccCccCcEeeccC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL---PQELKALEKLRYLNLEY  568 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~l---p~~~~~L~~L~~L~l~~  568 (779)
                      .++.|++.+|.+..+|....    .|++++| .+...... ..+++|++|++++|.++..   |..+.++++|++|++++
T Consensus       305 ~L~~L~l~~n~~~~l~~~~l~~L~~L~l~~n-~~~~~~~~-~~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~l~~  382 (570)
T 2z63_A          305 GWQHLELVNCKFGQFPTLKLKSLKRLTFTSN-KGGNAFSE-VDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSF  382 (570)
T ss_dssp             CCSEEEEESCBCSSCCBCBCSSCCEEEEESC-BSCCBCCC-CBCTTCCEEECCSSCCBEEEEEEHHHHTCSCCCEEECCS
T ss_pred             CccEEeeccCcccccCcccccccCEEeCcCC-cccccccc-ccCCCCCEEeCcCCccCccccccccccccCccCEEECCC
Confidence            44555555554444433211    2455555 33222111 4556666666666665544   45566666666666666


Q ss_pred             CcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccC
Q 004021          569 THYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDL  648 (779)
Q Consensus       569 ~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~  648 (779)
                      | .+..+|.. +..+++|++|++++|.+..             ......+..+++|+.|+++.+.         +....+
T Consensus       383 n-~l~~~~~~-~~~l~~L~~L~l~~n~l~~-------------~~~~~~~~~l~~L~~L~l~~n~---------l~~~~~  438 (570)
T 2z63_A          383 N-GVITMSSN-FLGLEQLEHLDFQHSNLKQ-------------MSEFSVFLSLRNLIYLDISHTH---------TRVAFN  438 (570)
T ss_dssp             C-SEEEEEEE-EETCTTCCEEECTTSEEES-------------CTTSCTTTTCTTCCEEECTTSC---------CEECCT
T ss_pred             C-cccccccc-ccccCCCCEEEccCCcccc-------------ccchhhhhcCCCCCEEeCcCCc---------ccccch
Confidence            6 44555555 6666666666666665543             1111235566666666665332         222234


Q ss_pred             cccccccCcceEEeccccccc-eecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEee
Q 004021          649 TWLVFVQNLKELEIIVCTEME-EIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGV  726 (779)
Q Consensus       649 ~~l~~l~~L~~L~L~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l  726 (779)
                      ..+..+++|+.|+|++|.... .++                ..+..+++|+.|+++++ .+..+ |..+..+++|++|++
T Consensus       439 ~~~~~l~~L~~L~l~~n~l~~~~~p----------------~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l  501 (570)
T 2z63_A          439 GIFNGLSSLEVLKMAGNSFQENFLP----------------DIFTELRNLTFLDLSQC-QLEQLSPTAFNSLSSLQVLNM  501 (570)
T ss_dssp             TTTTTCTTCCEEECTTCEEGGGEEC----------------SCCTTCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEEC
T ss_pred             hhhhcCCcCcEEECcCCcCccccch----------------hhhhcccCCCEEECCCC-ccccCChhhhhcccCCCEEeC
Confidence            456778889999998876542 333                36778889999999885 45555 566778889999999


Q ss_pred             eCCCCCCCCCCC-CCCc-ccccEEEec
Q 004021          727 YGCPKLKKLPIN-SSSA-KERRVVIEG  751 (779)
Q Consensus       727 ~~c~~L~~lP~~-~~~~-~~~~l~i~~  751 (779)
                      ++| ++..+|.. +... .++.+.+.+
T Consensus       502 ~~n-~l~~~~~~~~~~l~~L~~L~l~~  527 (570)
T 2z63_A          502 ASN-QLKSVPDGIFDRLTSLQKIWLHT  527 (570)
T ss_dssp             CSS-CCSCCCTTTTTTCTTCCEEECCS
T ss_pred             CCC-cCCCCCHHHhhcccCCcEEEecC
Confidence            887 57776653 3333 347777775

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.49  E-value=7.3e-14  Score=146.66  Aligned_cols=201  Identities=14%  Similarity=0.098  Sum_probs=133.2

Q ss_pred             cCcccccCc--cccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccch
Q 004021          481 AGVKLTEAP--KVKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ  553 (779)
Q Consensus       481 ~~~~~~~~~--~~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~  553 (779)
                      .+..+..++  .+..+.+++.|++++|.+...+....     .|+|++| .+..+|    .+++|++|++++|.++.+|.
T Consensus        42 ~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~l~~L~~L~Ls~n-~l~~l~----~~~~L~~L~l~~n~l~~~~~  116 (317)
T 3o53_A           42 SGNPLSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLRTLDLNNN-YVQELL----VGPSIETLHAANNNISRVSC  116 (317)
T ss_dssp             TTSCCCCCCHHHHTTCTTCCEEECTTSCCEEEEEETTCTTCCEEECCSS-EEEEEE----ECTTCCEEECCSSCCSEEEE
T ss_pred             cCCccCcCCHHHhhCCCcCCEEECCCCcCCcchhhhhcCCCCEEECcCC-cccccc----CCCCcCEEECCCCccCCcCc
Confidence            333444443  34567788888888888766544222     3888888 777665    34788888888888887764


Q ss_pred             hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhh-cCCCCCCceeEEee
Q 004021          554 ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMREL-LGLKRLNVLSWSFR  632 (779)
Q Consensus       554 ~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~L~~L~~L~l~~~  632 (779)
                      .  .+++|++|++++| .+..+++..++.+++|++|++++|.+..              ..+..+ ..+++|+.|+++.|
T Consensus       117 ~--~~~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~--------------~~~~~~~~~l~~L~~L~L~~N  179 (317)
T 3o53_A          117 S--RGQGKKNIYLANN-KITMLRDLDEGCRSRVQYLDLKLNEIDT--------------VNFAELAASSDTLEHLNLQYN  179 (317)
T ss_dssp             C--CCSSCEEEECCSS-CCCSGGGBCTGGGSSEEEEECTTSCCCE--------------EEGGGGGGGTTTCCEEECTTS
T ss_pred             c--ccCCCCEEECCCC-CCCCccchhhhccCCCCEEECCCCCCCc--------------ccHHHHhhccCcCCEEECCCC
Confidence            3  4678888888888 5676766447788888888888887764              223333 35778888888755


Q ss_pred             cccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          633 SSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       633 ~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                      ....+           +....+++|+.|+|++|. +..++.                .+..+++|+.|++++ +.+..+|
T Consensus       180 ~l~~~-----------~~~~~l~~L~~L~Ls~N~-l~~l~~----------------~~~~l~~L~~L~L~~-N~l~~l~  230 (317)
T 3o53_A          180 FIYDV-----------KGQVVFAKLKTLDLSSNK-LAFMGP----------------EFQSAAGVTWISLRN-NKLVLIE  230 (317)
T ss_dssp             CCCEE-----------ECCCCCTTCCEEECCSSC-CCEECG----------------GGGGGTTCSEEECTT-SCCCEEC
T ss_pred             cCccc-----------ccccccccCCEEECCCCc-CCcchh----------------hhcccCcccEEECcC-Ccccchh
Confidence            43322           122236777777777754 334433                345667777777777 3666777


Q ss_pred             CCCCCCCCccEEeeeCCCCC
Q 004021          713 PNPLHFPKLKKIGVYGCPKL  732 (779)
Q Consensus       713 ~~~~~l~~L~~L~l~~c~~L  732 (779)
                      ..+..+++|+.|++++|+-.
T Consensus       231 ~~~~~l~~L~~L~l~~N~~~  250 (317)
T 3o53_A          231 KALRFSQNLEHFDLRGNGFH  250 (317)
T ss_dssp             TTCCCCTTCCEEECTTCCCB
T ss_pred             hHhhcCCCCCEEEccCCCcc
Confidence            76667777777777776543

>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=99.48  E-value=3.1e-13  Score=153.64  Aligned_cols=212  Identities=19%  Similarity=0.134  Sum_probs=149.3

Q ss_pred             CccEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~  571 (779)
                      .++.|++++|.+..+|...+    .|+|++| .++.+|.   .+++|++|+|++|.++.+|.   .+++|++|++++| .
T Consensus        41 ~l~~L~ls~n~L~~lp~~l~~~L~~L~L~~N-~l~~lp~---~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N-~  112 (622)
T 3g06_A           41 GNAVLNVGESGLTTLPDCLPAHITTLVIPDN-NLTSLPA---LPPELRTLEVSGNQLTSLPV---LPPGLLELSIFSN-P  112 (622)
T ss_dssp             CCCEEECCSSCCSCCCSCCCTTCSEEEECSC-CCSCCCC---CCTTCCEEEECSCCCSCCCC---CCTTCCEEEECSC-C
T ss_pred             CCcEEEecCCCcCccChhhCCCCcEEEecCC-CCCCCCC---cCCCCCEEEcCCCcCCcCCC---CCCCCCEEECcCC-c
Confidence            58899999999998886433    5999999 9999997   68999999999999999997   7899999999999 6


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccc-cCCCCCcccCc-
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ-KFFKYPKLDLT-  649 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~-~~~~L~~L~~~-  649 (779)
                      ++.+|.    .+++|++|++++|.+..+|.                  .+++|+.|+++.|....++ .+++|+.|.+. 
T Consensus       113 l~~l~~----~l~~L~~L~L~~N~l~~lp~------------------~l~~L~~L~Ls~N~l~~l~~~~~~L~~L~L~~  170 (622)
T 3g06_A          113 LTHLPA----LPSGLCKLWIFGNQLTSLPV------------------LPPGLQELSVSDNQLASLPALPSELCKLWAYN  170 (622)
T ss_dssp             CCCCCC----CCTTCCEEECCSSCCSCCCC------------------CCTTCCEEECCSSCCSCCCCCCTTCCEEECCS
T ss_pred             CCCCCC----CCCCcCEEECCCCCCCcCCC------------------CCCCCCEEECcCCcCCCcCCccCCCCEEECCC
Confidence            788887    56889999999998876332                  1366777777766554432 23344444110 


Q ss_pred             -cc----ccccCcceEEeccccccceeccccc--------ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCC
Q 004021          650 -WL----VFVQNLKELEIIVCTEMEEIICVDK--------LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPL  716 (779)
Q Consensus       650 -~l----~~l~~L~~L~L~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~  716 (779)
                       .+    ..+++|+.|++++|.. ..++....        ...+..+       ...+++|+.|+++++ .++.+|   .
T Consensus       171 N~l~~l~~~~~~L~~L~Ls~N~l-~~l~~~~~~L~~L~L~~N~l~~l-------~~~~~~L~~L~Ls~N-~L~~lp---~  238 (622)
T 3g06_A          171 NQLTSLPMLPSGLQELSVSDNQL-ASLPTLPSELYKLWAYNNRLTSL-------PALPSGLKELIVSGN-RLTSLP---V  238 (622)
T ss_dssp             SCCSCCCCCCTTCCEEECCSSCC-SCCCCCCTTCCEEECCSSCCSSC-------CCCCTTCCEEECCSS-CCSCCC---C
T ss_pred             CCCCCCcccCCCCcEEECCCCCC-CCCCCccchhhEEECcCCccccc-------CCCCCCCCEEEccCC-ccCcCC---C
Confidence             00    2346777777777543 33322100        0001111       123588999999984 777777   4


Q ss_pred             CCCCccEEeeeCCCCCCCCCCCCCCcccccEEEech
Q 004021          717 HFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEGL  752 (779)
Q Consensus       717 ~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~~  752 (779)
                      .+++|+.|++++| +++.+|..  ...++.+.+.++
T Consensus       239 ~l~~L~~L~Ls~N-~L~~lp~~--~~~L~~L~Ls~N  271 (622)
T 3g06_A          239 LPSELKELMVSGN-RLTSLPML--PSGLLSLSVYRN  271 (622)
T ss_dssp             CCTTCCEEECCSS-CCSCCCCC--CTTCCEEECCSS
T ss_pred             CCCcCcEEECCCC-CCCcCCcc--cccCcEEeCCCC
Confidence            6789999999997 68899983  334577777755

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.47  E-value=7.3e-14  Score=146.19  Aligned_cols=197  Identities=14%  Similarity=0.114  Sum_probs=136.0

Q ss_pred             ccccccccccc-ccchhh--cccccCceeeecCCccccc-c----hhhccCccCcEeeccCCcCCCCCchhhhcCCccCc
Q 004021          516 LLSLRRNDSLT-ELPSRI--SSLVSLHHLDLSLTHIRGL-P----QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLE  587 (779)
Q Consensus       516 lL~L~~~~~l~-~lp~~i--~~L~~L~~L~L~~~~i~~l-p----~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~  587 (779)
                      .|++++| .+. ..|..+  +++++|++|+|++|.++.. |    ..+..+++|++|++++| .+..+|+..++.+++|+
T Consensus        95 ~L~l~~n-~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~  172 (310)
T 4glp_A           95 ELTLEDL-KITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQA-HSPAFSCEQVRAFPALT  172 (310)
T ss_dssp             EEEEESC-CCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECC-SSCCCCTTSCCCCTTCC
T ss_pred             EEEeeCC-EeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCC-CcchhhHHHhccCCCCC
Confidence            3888888 665 457777  8899999999999988762 2    34567899999999999 56777765588999999


Q ss_pred             EeeeccccCCCcccccCCccCCCchhhH--HhhcCCCCCCceeEEeecccccccCCCCCccc--Cc-ccccccCcceEEe
Q 004021          588 VLRLLECGSEGVTKEEGNVLCDDAEPLM--RELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD--LT-WLVFVQNLKELEI  662 (779)
Q Consensus       588 ~L~l~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~--~~-~l~~l~~L~~L~L  662 (779)
                      +|++++|.+.+            ....+  ..++.+++|+.|+++.|..         +.+.  +. .+..+++|++|+|
T Consensus       173 ~L~Ls~N~l~~------------~~~~~~~~~~~~l~~L~~L~Ls~N~l---------~~l~~~~~~l~~~l~~L~~L~L  231 (310)
T 4glp_A          173 SLDLSDNPGLG------------ERGLMAALCPHKFPAIQNLALRNTGM---------ETPTGVCAALAAAGVQPHSLDL  231 (310)
T ss_dssp             EEECCSCTTCH------------HHHHHTTSCTTSSCCCCSCBCCSSCC---------CCHHHHHHHHHHHTCCCSSEEC
T ss_pred             EEECCCCCCcc------------chhhhHHHhhhcCCCCCEEECCCCCC---------CchHHHHHHHHhcCCCCCEEEC
Confidence            99999987653            01111  1236788999999986543         2221  11 2467789999999


Q ss_pred             ccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCc
Q 004021          663 IVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA  742 (779)
Q Consensus       663 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~  742 (779)
                      ++|......|..        +     .....+++|+.|++++ +.++.+|....  ++|+.|++++| ++..+|......
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--------A-----PRCMWSSALNSLNLSF-AGLEQVPKGLP--AKLRVLDLSSN-RLNRAPQPDELP  294 (310)
T ss_dssp             TTSCCCCCCCSC--------C-----SSCCCCTTCCCEECCS-SCCCSCCSCCC--SCCSCEECCSC-CCCSCCCTTSCC
T ss_pred             CCCCCCccchhh--------H-----HhccCcCcCCEEECCC-CCCCchhhhhc--CCCCEEECCCC-cCCCCchhhhCC
Confidence            987654432320        0     1223347999999987 46778877653  89999999887 577777643434


Q ss_pred             ccccEEEech
Q 004021          743 KERRVVIEGL  752 (779)
Q Consensus       743 ~~~~l~i~~~  752 (779)
                      .++.+.+.+.
T Consensus       295 ~L~~L~L~~N  304 (310)
T 4glp_A          295 EVDNLTLDGN  304 (310)
T ss_dssp             CCSCEECSST
T ss_pred             CccEEECcCC
Confidence            4577777654

>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=99.47  E-value=1.5e-13  Score=142.16  Aligned_cols=160  Identities=20%  Similarity=0.242  Sum_probs=95.7

Q ss_pred             EEEcCcccccCccccccCCccEEEcccccccccccCcccccccccccccccchhhcccccCceeeecCCcccccchhhcc
Q 004021          478 LVRAGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA  557 (779)
Q Consensus       478 ~~~~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~  557 (779)
                      +...+..+..++.+..+.+++.|++++|.+                  ..+|. ++++++|++|++++|.++.+|. +.+
T Consensus        51 L~l~~~~i~~~~~~~~l~~L~~L~L~~n~l------------------~~~~~-l~~l~~L~~L~l~~n~l~~~~~-l~~  110 (291)
T 1h6t_A           51 IIANNSDIKSVQGIQYLPNVTKLFLNGNKL------------------TDIKP-LANLKNLGWLFLDENKVKDLSS-LKD  110 (291)
T ss_dssp             EECTTSCCCCCTTGGGCTTCCEEECCSSCC------------------CCCGG-GTTCTTCCEEECCSSCCCCGGG-GTT
T ss_pred             EEccCCCcccChhHhcCCCCCEEEccCCcc------------------CCCcc-cccCCCCCEEECCCCcCCCChh-hcc
Confidence            334444555566666667777777766554                  44443 6666777777777776666554 666


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccc
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAV  637 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~  637 (779)
                      +++|++|++++| .+..++.  +..+++|++|++++|.+..                +..+..+++|+.|+++.|...  
T Consensus       111 l~~L~~L~L~~n-~i~~~~~--l~~l~~L~~L~l~~n~l~~----------------~~~l~~l~~L~~L~L~~N~l~--  169 (291)
T 1h6t_A          111 LKKLKSLSLEHN-GISDING--LVHLPQLESLYLGNNKITD----------------ITVLSRLTKLDTLSLEDNQIS--  169 (291)
T ss_dssp             CTTCCEEECTTS-CCCCCGG--GGGCTTCCEEECCSSCCCC----------------CGGGGGCTTCSEEECCSSCCC--
T ss_pred             CCCCCEEECCCC-cCCCChh--hcCCCCCCEEEccCCcCCc----------------chhhccCCCCCEEEccCCccc--
Confidence            777777777776 4555543  6667777777777666553                134556666777776644322  


Q ss_pred             ccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCC
Q 004021          638 QKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYG  705 (779)
Q Consensus       638 ~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~  705 (779)
                             .+.  .+..+++|+.|+|++|. +..+                 ..+..+++|+.|+++++
T Consensus       170 -------~~~--~l~~l~~L~~L~L~~N~-i~~l-----------------~~l~~l~~L~~L~l~~n  210 (291)
T 1h6t_A          170 -------DIV--PLAGLTKLQNLYLSKNH-ISDL-----------------RALAGLKNLDVLELFSQ  210 (291)
T ss_dssp             -------CCG--GGTTCTTCCEEECCSSC-CCBC-----------------GGGTTCTTCSEEEEEEE
T ss_pred             -------cch--hhcCCCccCEEECCCCc-CCCC-----------------hhhccCCCCCEEECcCC
Confidence                   221  14556677777776653 2222                 13455677777777663

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.46  E-value=1.5e-13  Score=134.66  Aligned_cols=79  Identities=32%  Similarity=0.463  Sum_probs=36.0

Q ss_pred             ccccccccccccch-hhcccccCceeeecCCcccccchh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      |++++| .+..+|. .+.++++|++|++++|.++.+|.. +.++++|++|++++| .++.+|...++++++|++|++++|
T Consensus        33 L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~N  110 (208)
T 2o6s_A           33 LDLETN-SLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTN-QLQSLPNGVFDKLTQLKELALNTN  110 (208)
T ss_dssp             EECCSS-CCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             EEcCCC-ccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCC-cCCccCHhHhcCccCCCEEEcCCC
Confidence            444444 4444432 234445555555555544444433 344455555555544 344444433344455555555444


Q ss_pred             cCC
Q 004021          595 GSE  597 (779)
Q Consensus       595 ~~~  597 (779)
                      .+.
T Consensus       111 ~l~  113 (208)
T 2o6s_A          111 QLQ  113 (208)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            443

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.46  E-value=1.3e-13  Score=135.04  Aligned_cols=176  Identities=16%  Similarity=0.164  Sum_probs=134.9

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++++++ .+..+|..+  ..+|++|++++|.++.+|.. +.++++|++|++++| .++.+|...+..+++|++|++++|.
T Consensus        12 v~c~~~-~l~~~p~~~--~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~Ls~n~   87 (208)
T 2o6s_A           12 VECYSQ-GRTSVPTGI--PAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGN-KLQSLPNGVFNKLTSLTYLNLSTNQ   87 (208)
T ss_dssp             EECCSS-CCSSCCSCC--CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EEecCC-CccCCCCCC--CCCCcEEEcCCCccCcCChhhhcccccCcEEECCCC-ccCccChhhcCCCCCcCEEECCCCc
Confidence            344555 677777655  46899999999999998875 789999999999999 6788888767899999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +..              .....+..+++|+.|+++.|.         +..+.+..+..+++|+.|+|++|. +..++.  
T Consensus        88 l~~--------------~~~~~~~~l~~L~~L~L~~N~---------l~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~--  141 (208)
T 2o6s_A           88 LQS--------------LPNGVFDKLTQLKELALNTNQ---------LQSLPDGVFDKLTQLKDLRLYQNQ-LKSVPD--  141 (208)
T ss_dssp             CCC--------------CCTTTTTTCTTCCEEECCSSC---------CCCCCTTTTTTCTTCCEEECCSSC-CSCCCT--
T ss_pred             CCc--------------cCHhHhcCccCCCEEEcCCCc---------CcccCHhHhccCCcCCEEECCCCc-cceeCH--
Confidence            875              223346788999999998553         444444557788999999999964 444443  


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCc
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSA  742 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~  742 (779)
                                   ..+..+++|+.|++++++-       .+.+++|+.|.++.+..-..+|..+...
T Consensus       142 -------------~~~~~l~~L~~L~l~~N~~-------~~~~~~l~~L~~~~n~~~g~ip~~~~~l  188 (208)
T 2o6s_A          142 -------------GVFDRLTSLQYIWLHDNPW-------DCTCPGIRYLSEWINKHSGVVRNSAGSV  188 (208)
T ss_dssp             -------------TTTTTCTTCCEEECCSCCB-------CCCTTTTHHHHHHHHHCTTTBBCTTSSB
T ss_pred             -------------HHhccCCCccEEEecCCCe-------ecCCCCHHHHHHHHHhCCceeeccCccc
Confidence                         3567889999999998632       2456889999888877666788766543

>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=99.46  E-value=4.7e-14  Score=149.59  Aligned_cols=198  Identities=17%  Similarity=0.129  Sum_probs=119.1

Q ss_pred             CCccEEEcccccccccccC----cc--cccccccccccc--cchhhcccccCceeeecCCccc-ccchhhccCccCcEee
Q 004021          495 EGAKRISLMANEIESLSEI----PT--LLSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIR-GLPQELKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~----~~--lL~L~~~~~l~~--lp~~i~~L~~L~~L~L~~~~i~-~lp~~~~~L~~L~~L~  565 (779)
                      ..++.+++.+|.+...+..    +.  .|+|++| .+..  +|..+.++++|++|++++|.++ ..|..++++++|++|+
T Consensus        70 ~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~-~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~  148 (336)
T 2ast_B           70 QGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNS-VIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLN  148 (336)
T ss_dssp             TTCSEEECTTCEECSCCCSCCCCBCCCEEECTTC-EECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEE
T ss_pred             ccceEEEcCCccccccchhhccCCCCCEEEccCC-CcCHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEEE
Confidence            5677777777666544322    11  3777777 5553  5666777777777777777665 3566677777777777


Q ss_pred             ccCCcCCC--CCchhhhcCCccCcEeeeccc-cCCCcccccCCccCCCchhhHHhhcCCC-CCCceeEEeecccccccCC
Q 004021          566 LEYTHYLS--IIPHQLISGFLKLEVLRLLEC-GSEGVTKEEGNVLCDDAEPLMRELLGLK-RLNVLSWSFRSSLAVQKFF  641 (779)
Q Consensus       566 l~~~~~l~--~lp~~~i~~L~~L~~L~l~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~L~-~L~~L~l~~~~~~~~~~~~  641 (779)
                      +++|..++  .+|.. +.++++|++|++++| .+..             ...+..+..++ +|+.|+++++..       
T Consensus       149 L~~~~~l~~~~l~~~-~~~~~~L~~L~l~~~~~l~~-------------~~~~~~~~~l~~~L~~L~l~~~~~-------  207 (336)
T 2ast_B          149 LSGCSGFSEFALQTL-LSSCSRLDELNLSWCFDFTE-------------KHVQVAVAHVSETITQLNLSGYRK-------  207 (336)
T ss_dssp             CTTCBSCCHHHHHHH-HHHCTTCCEEECCCCTTCCH-------------HHHHHHHHHSCTTCCEEECCSCGG-------
T ss_pred             CCCCCCCCHHHHHHH-HhcCCCCCEEcCCCCCCcCh-------------HHHHHHHHhcccCCCEEEeCCCcc-------
Confidence            77774444  24543 666777777777777 5542             22445566667 777777765421       


Q ss_pred             CCCcc-cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc-CCCCCCC
Q 004021          642 KYPKL-DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY-PNPLHFP  719 (779)
Q Consensus       642 ~L~~L-~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~-~~~~~l~  719 (779)
                      ++..- .+..+..+++|+.|+|++|..+.....               ..+..+++|+.|++++|..+.... ..+..++
T Consensus       208 ~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~---------------~~l~~l~~L~~L~l~~~~~~~~~~~~~l~~~~  272 (336)
T 2ast_B          208 NLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCF---------------QEFFQLNYLQHLSLSRCYDIIPETLLELGEIP  272 (336)
T ss_dssp             GSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGG---------------GGGGGCTTCCEEECTTCTTCCGGGGGGGGGCT
T ss_pred             cCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHH---------------HHHhCCCCCCEeeCCCCCCCCHHHHHHHhcCC
Confidence            00000 022345677888888888764332111               245567888888888775332211 1345678


Q ss_pred             CccEEeeeCC
Q 004021          720 KLKKIGVYGC  729 (779)
Q Consensus       720 ~L~~L~l~~c  729 (779)
                      +|++|++++|
T Consensus       273 ~L~~L~l~~~  282 (336)
T 2ast_B          273 TLKTLQVFGI  282 (336)
T ss_dssp             TCCEEECTTS
T ss_pred             CCCEEeccCc
Confidence            8888888877

>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=99.46  E-value=1.9e-13  Score=155.24  Aligned_cols=99  Identities=30%  Similarity=0.324  Sum_probs=44.6

Q ss_pred             ccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeecc
Q 004021          493 EWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLE  567 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~  567 (779)
                      .+..++.|++.+|.+..++....     .|+|++| .+..+|. +++|++|++|+|++|.++.+| .+.+|++|++|+|+
T Consensus        41 ~L~~L~~L~l~~n~i~~l~~l~~l~~L~~L~Ls~N-~l~~~~~-l~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~Ls  117 (605)
T 1m9s_A           41 ELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGN-KLTDIKP-LTNLKNLGWLFLDENKIKDLS-SLKDLKKLKSLSLE  117 (605)
T ss_dssp             HHTTCCCCBCTTCCCCCCTTGGGCTTCCEEECTTS-CCCCCGG-GGGCTTCCEEECCSSCCCCCT-TSTTCTTCCEEECT
T ss_pred             cCCCCCEEECcCCCCCCChHHccCCCCCEEEeeCC-CCCCChh-hccCCCCCEEECcCCCCCCCh-hhccCCCCCEEEec
Confidence            34455555555555544432211     1444444 4444433 444444444444444444443 34444444444444


Q ss_pred             CCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          568 YTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       568 ~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      +| .+..+|.  +..|++|+.|++++|.+.
T Consensus       118 ~N-~l~~l~~--l~~l~~L~~L~Ls~N~l~  144 (605)
T 1m9s_A          118 HN-GISDING--LVHLPQLESLYLGNNKIT  144 (605)
T ss_dssp             TS-CCCCCGG--GGGCTTCSEEECCSSCCC
T ss_pred             CC-CCCCCcc--ccCCCccCEEECCCCccC
Confidence            44 3333332  444444444444444433

>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=99.45  E-value=1.6e-13  Score=155.80  Aligned_cols=161  Identities=17%  Similarity=0.212  Sum_probs=122.9

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .+..+| .+..|++|++|+|++|.+..+|. +.+|++|++|+|++| .+..+|.  +..+++|++|++++|.+
T Consensus        48 L~l~~n-~i~~l~-~l~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N-~l~~l~~--l~~l~~L~~L~Ls~N~l  121 (605)
T 1m9s_A           48 IIANNS-DIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDEN-KIKDLSS--LKDLKKLKSLSLEHNGI  121 (605)
T ss_dssp             CBCTTC-CCCCCT-TGGGCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSS-CCCCCTT--STTCTTCCEEECTTSCC
T ss_pred             EECcCC-CCCCCh-HHccCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCC-CCCCChh--hccCCCCCEEEecCCCC
Confidence            788888 888887 58889999999999998888876 888999999999988 6777774  88899999999988877


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      ..                +..+..|++|+.|+++.|...         .+  +.+..+++|+.|+|++|... .++    
T Consensus       122 ~~----------------l~~l~~l~~L~~L~Ls~N~l~---------~l--~~l~~l~~L~~L~Ls~N~l~-~~~----  169 (605)
T 1m9s_A          122 SD----------------INGLVHLPQLESLYLGNNKIT---------DI--TVLSRLTKLDTLSLEDNQIS-DIV----  169 (605)
T ss_dssp             CC----------------CGGGGGCTTCSEEECCSSCCC---------CC--GGGGSCTTCSEEECCSSCCC-CCG----
T ss_pred             CC----------------CccccCCCccCEEECCCCccC---------Cc--hhhcccCCCCEEECcCCcCC-Cch----
Confidence            64                235777888888888855432         22  45667788888888886532 221    


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCC
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                                   .+..+++|+.|+|+++ .+..++ .+..+++|+.|++++|+
T Consensus       170 -------------~l~~l~~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~L~~N~  208 (605)
T 1m9s_A          170 -------------PLAGLTKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFSQE  208 (605)
T ss_dssp             -------------GGTTCTTCCEEECCSS-CCCBCG-GGTTCTTCSEEECCSEE
T ss_pred             -------------hhccCCCCCEEECcCC-CCCCCh-HHccCCCCCEEEccCCc
Confidence                         2567788888888874 566664 46678888888888764

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.44  E-value=2.8e-13  Score=137.84  Aligned_cols=74  Identities=24%  Similarity=0.251  Sum_probs=34.8

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |++++| .+..+| .++.+++|++|++++|.++.+|. +.++++|++|++++| .++.+|.  +.. ++|++|++++|.+
T Consensus        46 L~l~~n-~i~~l~-~l~~l~~L~~L~L~~N~i~~~~~-l~~l~~L~~L~L~~N-~l~~l~~--~~~-~~L~~L~L~~N~l  118 (263)
T 1xeu_A           46 FNGDNS-NIQSLA-GMQFFTNLKELHLSHNQISDLSP-LKDLTKLEELSVNRN-RLKNLNG--IPS-ACLSRLFLDNNEL  118 (263)
T ss_dssp             EECTTS-CCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSS-CCSCCTT--CCC-SSCCEEECCSSCC
T ss_pred             EECcCC-Ccccch-HHhhCCCCCEEECCCCccCCChh-hccCCCCCEEECCCC-ccCCcCc--ccc-CcccEEEccCCcc
Confidence            444444 444444 44444555555555554444444 444455555555544 3444443  222 4455555544444


Q ss_pred             C
Q 004021          597 E  597 (779)
Q Consensus       597 ~  597 (779)
                      .
T Consensus       119 ~  119 (263)
T 1xeu_A          119 R  119 (263)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.44  E-value=3.4e-14  Score=153.80  Aligned_cols=212  Identities=17%  Similarity=0.128  Sum_probs=126.2

Q ss_pred             ccCCccEEEccccccccc---------ccCcc--ccccccccccc----ccchhh-------cccccCceeeecCCcccc
Q 004021          493 EWEGAKRISLMANEIESL---------SEIPT--LLSLRRNDSLT----ELPSRI-------SSLVSLHHLDLSLTHIRG  550 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l---------~~~~~--lL~L~~~~~l~----~lp~~i-------~~L~~L~~L~L~~~~i~~  550 (779)
                      ..+.++.|++++|.+...         ...+.  .|+|++| .+.    .+|..+       .++++|++|+|++|.+..
T Consensus        30 ~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~~-~~~~l~~~~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~  108 (386)
T 2ca6_A           30 EDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDI-FTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGP  108 (386)
T ss_dssp             HCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSC-CTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCT
T ss_pred             cCCCccEEECCCCCCCHHHHHHHHHHHHhCCCccEEeCccc-ccCccccchhHHHHHHHHHHhhCCcccEEECCCCcCCH
Confidence            345677888877766542         11222  3777776 443    234443       677888888888887766


Q ss_pred             -----cchhhccCccCcEeeccCCcCCCC-----CchhhhcCC---------ccCcEeeeccccCCCcccccCCccCCCc
Q 004021          551 -----LPQELKALEKLRYLNLEYTHYLSI-----IPHQLISGF---------LKLEVLRLLECGSEGVTKEEGNVLCDDA  611 (779)
Q Consensus       551 -----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L---------~~L~~L~l~~~~~~~~~~~~~~~~~~~~  611 (779)
                           +|..+.++++|++|+|++|. +..     ++.. +..+         ++|++|++++|.+..          ...
T Consensus       109 ~~~~~l~~~l~~~~~L~~L~L~~n~-l~~~~~~~l~~~-l~~l~~~~~~~~~~~L~~L~L~~n~l~~----------~~~  176 (386)
T 2ca6_A          109 TAQEPLIDFLSKHTPLEHLYLHNNG-LGPQAGAKIARA-LQELAVNKKAKNAPPLRSIICGRNRLEN----------GSM  176 (386)
T ss_dssp             TTHHHHHHHHHHCTTCCEEECCSSC-CHHHHHHHHHHH-HHHHHHHHHHHTCCCCCEEECCSSCCTG----------GGH
T ss_pred             HHHHHHHHHHHhCCCCCEEECcCCC-CCHHHHHHHHHH-HHHHhhhhhcccCCCCcEEECCCCCCCc----------HHH
Confidence                 67778888888888888883 432     2222 3333         788888888877652          000


Q ss_pred             hhhHHhhcCCCCCCceeEEeeccc----------ccccCCCCCccc--------------CcccccccCcceEEeccccc
Q 004021          612 EPLMRELLGLKRLNVLSWSFRSSL----------AVQKFFKYPKLD--------------LTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       612 ~~~~~~l~~L~~L~~L~l~~~~~~----------~~~~~~~L~~L~--------------~~~l~~l~~L~~L~L~~~~~  667 (779)
                      ......+..+++|+.|+++.|...          .+..+++|+.|.              +..+..+++|+.|+|++|..
T Consensus       177 ~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~~l~~~~~L~~L~L~~n~i  256 (386)
T 2ca6_A          177 KEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLL  256 (386)
T ss_dssp             HHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTCCC
T ss_pred             HHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHHHHccCCCcCEEECCCCCC
Confidence            112245666777777777766554          233445555551              22355677788888877653


Q ss_pred             cceecccccccCcccchhhccCCC--CCCCCccEEEccCCCCCcc-----ccCCC-CCCCCccEEeeeCCC
Q 004021          668 MEEIICVDKLRDVSDISEIIGSEH--NFFTQLESLGILYGPDLKS-----IYPNP-LHFPKLKKIGVYGCP  730 (779)
Q Consensus       668 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~L~~L~l~~~~~l~~-----l~~~~-~~l~~L~~L~l~~c~  730 (779)
                      ......        .++    ..+  +.+++|+.|+|++| .+..     ++..+ ..+|+|++|++++|+
T Consensus       257 ~~~~~~--------~l~----~~l~~~~~~~L~~L~L~~n-~i~~~g~~~l~~~l~~~l~~L~~L~l~~N~  314 (386)
T 2ca6_A          257 SARGAA--------AVV----DAFSKLENIGLQTLRLQYN-EIELDAVRTLKTVIDEKMPDLLFLELNGNR  314 (386)
T ss_dssp             CHHHHH--------HHH----HHHHTCSSCCCCEEECCSS-CCBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             chhhHH--------HHH----HHHhhccCCCeEEEECcCC-cCCHHHHHHHHHHHHhcCCCceEEEccCCc
Confidence            221000        000    122  34778888888875 4444     55544 457888888888775

>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=99.44  E-value=3.4e-13  Score=133.25  Aligned_cols=144  Identities=18%  Similarity=0.262  Sum_probs=106.6

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcC
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~  571 (779)
                      +.+++.++.+..+|...+    .|+|++| .+..+|. .|.++++|++|+|++|.++.+ |..|.++++|++|+|++| .
T Consensus        14 ~~v~c~~~~l~~iP~~l~~~l~~L~l~~n-~i~~i~~~~~~~l~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N-~   91 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNLPETITEIRLEQN-TIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGN-K   91 (220)
T ss_dssp             TEEECTTSCCSSCCSSCCTTCCEEECCSS-CCCEECTTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSS-C
T ss_pred             CEEEcCCCCcCcCCCccCcCCCEEECCCC-cCCCcCHhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCC-c
Confidence            456777777777665322    4788888 7777754 678888888888888888886 667888888888888888 6


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccc
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL  651 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l  651 (779)
                      ++.+|.+.+.++++|++|++++|.+..              ..+..+..+++|+.|+++.|.         ++.+.+..+
T Consensus        92 l~~l~~~~f~~l~~L~~L~L~~N~l~~--------------~~~~~~~~l~~L~~L~L~~N~---------l~~~~~~~~  148 (220)
T 2v9t_B           92 ITELPKSLFEGLFSLQLLLLNANKINC--------------LRVDAFQDLHNLNLLSLYDNK---------LQTIAKGTF  148 (220)
T ss_dssp             CCCCCTTTTTTCTTCCEEECCSSCCCC--------------CCTTTTTTCTTCCEEECCSSC---------CSCCCTTTT
T ss_pred             CCccCHhHccCCCCCCEEECCCCCCCE--------------eCHHHcCCCCCCCEEECCCCc---------CCEECHHHH
Confidence            788888767888888888888888774              234456777888888887443         334434456


Q ss_pred             ccccCcceEEecccc
Q 004021          652 VFVQNLKELEIIVCT  666 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~  666 (779)
                      ..+++|+.|+|++|+
T Consensus       149 ~~l~~L~~L~L~~N~  163 (220)
T 2v9t_B          149 SPLRAIQTMHLAQNP  163 (220)
T ss_dssp             TTCTTCCEEECCSSC
T ss_pred             hCCCCCCEEEeCCCC
Confidence            667788888887754

>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=3.6e-13  Score=133.08  Aligned_cols=145  Identities=16%  Similarity=0.204  Sum_probs=109.5

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccch--hhcccccCceeeecCCcccccch-hhccCccCcEeeccCCc
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPS--RISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTH  570 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~--~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~  570 (779)
                      +.+++++|.+..+|....    .|+|++| .+..++.  .|.++++|++|+|++|.|+.+|. .|.++++|++|++++| 
T Consensus        14 ~~l~~s~n~l~~iP~~~~~~~~~L~L~~N-~l~~~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N-   91 (220)
T 2v70_A           14 TTVDCSNQKLNKIPEHIPQYTAELRLNNN-EFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTSN-   91 (220)
T ss_dssp             TEEECCSSCCSSCCSCCCTTCSEEECCSS-CCCEECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-
T ss_pred             CEeEeCCCCcccCccCCCCCCCEEEcCCC-cCCccCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCCC-
Confidence            578888888887775432    4888888 8887733  37888899999999988888766 6888889999999988 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTW  650 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~  650 (779)
                      .+..+|++.++.+++|++|++++|.+..              ..+..+..+++|+.|+++.|         +++.+.+..
T Consensus        92 ~l~~~~~~~~~~l~~L~~L~Ls~N~l~~--------------~~~~~~~~l~~L~~L~L~~N---------~l~~~~~~~  148 (220)
T 2v70_A           92 RLENVQHKMFKGLESLKTLMLRSNRITC--------------VGNDSFIGLSSVRLLSLYDN---------QITTVAPGA  148 (220)
T ss_dssp             CCCCCCGGGGTTCSSCCEEECTTSCCCC--------------BCTTSSTTCTTCSEEECTTS---------CCCCBCTTT
T ss_pred             ccCccCHhHhcCCcCCCEEECCCCcCCe--------------ECHhHcCCCccCCEEECCCC---------cCCEECHHH
Confidence            5777777668888999999998888775              23455677788888888743         344444556


Q ss_pred             cccccCcceEEeccccc
Q 004021          651 LVFVQNLKELEIIVCTE  667 (779)
Q Consensus       651 l~~l~~L~~L~L~~~~~  667 (779)
                      +..+++|+.|+|++|+.
T Consensus       149 ~~~l~~L~~L~L~~N~l  165 (220)
T 2v70_A          149 FDTLHSLSTLNLLANPF  165 (220)
T ss_dssp             TTTCTTCCEEECCSCCE
T ss_pred             hcCCCCCCEEEecCcCC
Confidence            67778888888887653

>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=99.42  E-value=2.1e-11  Score=130.14  Aligned_cols=275  Identities=13%  Similarity=0.134  Sum_probs=162.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech-----------HHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT-----------FQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~-----------i~~~  223 (779)
                      ..|+||+++++.|.+ +..     +++.|+|++|+|||||++++++..   ..   ..+|+.+..           +...
T Consensus        13 ~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~~---~~---~~~~~~~~~~~~~~~~~~~~~~~~   80 (357)
T 2fna_A           13 KDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINEL---NL---PYIYLDLRKFEERNYISYKDFLLE   80 (357)
T ss_dssp             GGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHHH---TC---CEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             HHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHhc---CC---CEEEEEchhhccccCCCHHHHHHH
Confidence            678999999999999 653     699999999999999999999876   22   246777621           2233


Q ss_pred             HHHHhC--------------CC----c-c--hhh-----hhcchhhHHHHHHHhhCCCcceeehhhcccccc--------
Q 004021          224 IGKRIG--------------FS----E-D--KKW-----KEKSLQDKAVDISSILSPKKFRIDLTELGVPLQ--------  269 (779)
Q Consensus       224 i~~~l~--------------~~----~-~--~~~-----~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~--------  269 (779)
                      +.+.+.              ..    . .  ...     ...........+.+.-+ ++..+++|++.....        
T Consensus        81 l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~~~~~~  159 (357)
T 2fna_A           81 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRGVNLLP  159 (357)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTTCCCHH
T ss_pred             HHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCchhHHH
Confidence            332221              00    0 0  000     01123333444433322 377777777633110        


Q ss_pred             ------ccCCCcEEEEEeCchhhhhh----------c-C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHH
Q 004021          270 ------MLNAGFKIVLKTRSAGVCDQ----------M-D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAET  330 (779)
Q Consensus       270 ------~~~~gs~IivTTR~~~va~~----------~-~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~  330 (779)
                            ....+.++|+|+|.......          . +  ...+.+.+|+.+++.+++...+....... ..   . ..
T Consensus       160 ~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~-~~---~-~~  234 (357)
T 2fna_A          160 ALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDF-KD---Y-EV  234 (357)
T ss_dssp             HHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCC-CC---H-HH
T ss_pred             HHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCC-Cc---H-HH
Confidence                  11247889999997653221          1 1  25789999999999999988654322111 11   1 88


Q ss_pred             HHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCcCCCchHHHHHHHH-HHHh--cCCccchhhhhhhccccCC
Q 004021          331 LARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSASTFSGMEENVFLRLK-FSYD--SLSMDKLRSCLLYCCLYPE  407 (779)
Q Consensus       331 I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~-~sy~--~L~~~~~k~cf~~~s~fp~  407 (779)
                      |++.|+|+|+++..++..+....+...|..   .+...      ....+...+. +.+.  .+++ ..+..+..+|.   
T Consensus       235 i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~---~~~~~------~~~~~~~~l~~~~~~~~~l~~-~~~~~l~~la~---  301 (357)
T 2fna_A          235 VYEKIGGIPGWLTYFGFIYLDNKNLDFAIN---QTLEY------AKKLILKEFENFLHGREIARK-RYLNIMRTLSK---  301 (357)
T ss_dssp             HHHHHCSCHHHHHHHHHHHHHHCCHHHHHH---HHHHH------HHHHHHHHHHHHHTTCGGGHH-HHHHHHHHHTT---
T ss_pred             HHHHhCCCHHHHHHHHHHHccccchHHHHH---HHHHH------HHHHHHHHHHHHhhccccccH-HHHHHHHHHHc---
Confidence            999999999999999877643333333322   11000      0001222222 1111  5777 78888888887   


Q ss_pred             CcccChHHHHHHHH-HcCCCcchhhHHHHHHHHHHcccccccCCCcEE-echHHHHHH
Q 004021          408 DYKIPKRSLIDYWI-SEGFMADFDRGCEFINDLLHACLLEEEGDDHVK-MHDMIREMS  463 (779)
Q Consensus       408 ~~~i~~~~Li~~W~-a~g~~~~~~~~~~~l~~L~~~sll~~~~~~~~~-mHdlv~~~a  463 (779)
                      +.  +...+..... ..|.-.+......+++.|.+.+++...+ +.|+ -|++++++.
T Consensus       302 g~--~~~~l~~~~~~~~g~~~~~~~~~~~L~~L~~~gli~~~~-~~y~f~~~~~~~~l  356 (357)
T 2fna_A          302 CG--KWSDVKRALELEEGIEISDSEIYNYLTQLTKHSWIIKEG-EKYCPSEPLISLAF  356 (357)
T ss_dssp             CB--CHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHTTSEEESS-SCEEESSHHHHHHT
T ss_pred             CC--CHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEecC-CEEEecCHHHHHhh
Confidence            22  4444433221 1231012256678899999999998764 4566 578888764

>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=99.42  E-value=4.7e-13  Score=154.92  Aligned_cols=142  Identities=20%  Similarity=0.178  Sum_probs=92.0

Q ss_pred             EEcccccccccccCc----ccccccccccccccc-hhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCC
Q 004021          500 ISLMANEIESLSEIP----TLLSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLS  573 (779)
Q Consensus       500 l~l~~~~~~~l~~~~----~lL~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~  573 (779)
                      .+.++.++..+|...    ..|||++| .|+.+| .+|.++++|++|+|++|.|+.+|+ .|.+|++|++|+|++| .++
T Consensus        36 ~~c~~~~l~~vP~~lp~~~~~LdLs~N-~i~~l~~~~f~~l~~L~~L~Ls~N~i~~i~~~~f~~L~~L~~L~Ls~N-~l~  113 (635)
T 4g8a_A           36 YQCMELNFYKIPDNLPFSTKNLDLSFN-PLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGN-PIQ  113 (635)
T ss_dssp             EECTTSCCSSCCSSSCTTCCEEECTTS-CCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTC-CCC
T ss_pred             EECCCCCcCccCCCCCcCCCEEEeeCC-CCCCCCHHHHhCCCCCCEEECCCCcCCCcChhHhcCCCCCCEEEccCC-cCC
Confidence            344444555555432    24777777 777774 467777777777777777777755 4777777777777777 567


Q ss_pred             CCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcc-cCcccc
Q 004021          574 IIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL-DLTWLV  652 (779)
Q Consensus       574 ~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L-~~~~l~  652 (779)
                      .+|++.|.+|++|++|++++|.+..+              ....+++|++|+.|+++.|.         ++.+ .+..++
T Consensus       114 ~l~~~~f~~L~~L~~L~Ls~N~l~~l--------------~~~~~~~L~~L~~L~Ls~N~---------l~~~~~~~~~~  170 (635)
T 4g8a_A          114 SLALGAFSGLSSLQKLVAVETNLASL--------------ENFPIGHLKTLKELNVAHNL---------IQSFKLPEYFS  170 (635)
T ss_dssp             EECGGGGTTCTTCCEEECTTSCCCCS--------------TTCCCTTCTTCCEEECCSSC---------CCCCCCCGGGG
T ss_pred             CCCHHHhcCCCCCCEEECCCCcCCCC--------------ChhhhhcCcccCeeccccCc---------cccCCCchhhc
Confidence            77766677777777777777776641              22236677777777777443         2222 134456


Q ss_pred             cccCcceEEecccc
Q 004021          653 FVQNLKELEIIVCT  666 (779)
Q Consensus       653 ~l~~L~~L~L~~~~  666 (779)
                      .+++|++|++++|.
T Consensus       171 ~l~~L~~L~L~~N~  184 (635)
T 4g8a_A          171 NLTNLEHLDLSSNK  184 (635)
T ss_dssp             GCTTCCEEECCSSC
T ss_pred             cchhhhhhcccCcc
Confidence            67777777777754

>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=99.42  E-value=7e-13  Score=141.18  Aligned_cols=200  Identities=15%  Similarity=0.105  Sum_probs=146.1

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEe-eeccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVL-RLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L-~l~~~  594 (779)
                      ++.+++ .++.+|..|  ..++++|+|++|+|+.+|. .|.+|++|++|+|++|..++.+|.+.+.++++|+++ .+.+|
T Consensus        14 v~C~~~-~Lt~iP~~l--~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N   90 (350)
T 4ay9_X           14 FLCQES-KVTEIPSDL--PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKAN   90 (350)
T ss_dssp             EEEEST-TCCSCCTTC--CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEET
T ss_pred             EEecCC-CCCccCcCc--CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCC
Confidence            567777 899999877  4689999999999999997 489999999999999966677888778899998865 44556


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCC----------------CCCcccCcccccc-cCc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFF----------------KYPKLDLTWLVFV-QNL  657 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~----------------~L~~L~~~~l~~l-~~L  657 (779)
                      .+..              ..+..+..+++|+.|+++.|....+....                ++..+....+..+ ..|
T Consensus        91 ~l~~--------------l~~~~f~~l~~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l  156 (350)
T 4ay9_X           91 NLLY--------------INPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFES  156 (350)
T ss_dssp             TCCE--------------ECTTSBCCCTTCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSC
T ss_pred             cccc--------------cCchhhhhccccccccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhh
Confidence            6653              33456889999999999998775542211                1222222233333 357


Q ss_pred             ceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCC
Q 004021          658 KELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLP  736 (779)
Q Consensus       658 ~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP  736 (779)
                      +.|+|++| .++.++.                .....++|+.|.+.+++.++.+|.. +..+++|+.|+++++ +++.+|
T Consensus       157 ~~L~L~~N-~i~~i~~----------------~~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N-~l~~lp  218 (350)
T 4ay9_X          157 VILWLNKN-GIQEIHN----------------SAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRT-RIHSLP  218 (350)
T ss_dssp             EEEECCSS-CCCEECT----------------TSSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTS-CCCCCC
T ss_pred             hhhccccc-cccCCCh----------------hhccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCC-CcCccC
Confidence            77777774 3455544                3334578999999988899999875 468999999999987 699999


Q ss_pred             CCCCCcccccEEEech
Q 004021          737 INSSSAKERRVVIEGL  752 (779)
Q Consensus       737 ~~~~~~~~~~l~i~~~  752 (779)
                      ...- ..++.+.+.++
T Consensus       219 ~~~~-~~L~~L~~l~~  233 (350)
T 4ay9_X          219 SYGL-ENLKKLRARST  233 (350)
T ss_dssp             SSSC-TTCCEEECTTC
T ss_pred             hhhh-ccchHhhhccC
Confidence            7542 23455555544

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.42  E-value=5.6e-13  Score=139.44  Aligned_cols=193  Identities=17%  Similarity=0.122  Sum_probs=140.3

Q ss_pred             CCccEEEcccccccccc-cC------cc--ccccccccccccc-c----hhhcccccCceeeecCCcccccc-hhhccCc
Q 004021          495 EGAKRISLMANEIESLS-EI------PT--LLSLRRNDSLTEL-P----SRISSLVSLHHLDLSLTHIRGLP-QELKALE  559 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~-~~------~~--lL~L~~~~~l~~l-p----~~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~  559 (779)
                      ..+++|++++|.+.... ..      ..  .|+|++| .+... |    ..+..+++|++|+|++|.+..+| ..+++++
T Consensus        91 ~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n-~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~  169 (310)
T 4glp_A           91 SRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNV-SWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFP  169 (310)
T ss_dssp             SCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESC-CCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCCCTTSCCCCT
T ss_pred             CceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecc-cccchhhhhHHHHhhhccCCCEEEeeCCCcchhhHHHhccCC
Confidence            46899999998876432 22      11  3899999 77652 3    34568999999999999998876 5789999


Q ss_pred             cCcEeeccCCcCCCC--Cchh-hhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHh-hcCCCCCCceeEEeeccc
Q 004021          560 KLRYLNLEYTHYLSI--IPHQ-LISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRE-LLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       560 ~L~~L~l~~~~~l~~--lp~~-~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~L~~L~~L~l~~~~~~  635 (779)
                      +|++|++++|.....  ++.. .++.+++|++|++++|.+..+            ...+.. ++.+++|++|+++.|.. 
T Consensus       170 ~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~l------------~~~~~~l~~~l~~L~~L~Ls~N~l-  236 (310)
T 4glp_A          170 ALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETP------------TGVCAALAAAGVQPHSLDLSHNSL-  236 (310)
T ss_dssp             TCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCCH------------HHHHHHHHHHTCCCSSEECTTSCC-
T ss_pred             CCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCCCCCch------------HHHHHHHHhcCCCCCEEECCCCCC-
Confidence            999999999943221  3322 146899999999999988641            122222 46789999999996553 


Q ss_pred             ccccCCCCCcccCccccc---ccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          636 AVQKFFKYPKLDLTWLVF---VQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       636 ~~~~~~~L~~L~~~~l~~---l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                              ..+.|+.+..   +++|++|+|++|.. +.++.                .+  +++|+.|++++ +.+..+|
T Consensus       237 --------~~~~p~~~~~~~~~~~L~~L~Ls~N~l-~~lp~----------------~~--~~~L~~L~Ls~-N~l~~~~  288 (310)
T 4glp_A          237 --------RATVNPSAPRCMWSSALNSLNLSFAGL-EQVPK----------------GL--PAKLRVLDLSS-NRLNRAP  288 (310)
T ss_dssp             --------CCCCCSCCSSCCCCTTCCCEECCSSCC-CSCCS----------------CC--CSCCSCEECCS-CCCCSCC
T ss_pred             --------CccchhhHHhccCcCcCCEEECCCCCC-Cchhh----------------hh--cCCCCEEECCC-CcCCCCc
Confidence                    3332333333   37999999999654 45543                22  48999999998 5777776


Q ss_pred             CCCCCCCCccEEeeeCCC
Q 004021          713 PNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       713 ~~~~~l~~L~~L~l~~c~  730 (779)
                      . ...+++|+.|++++++
T Consensus       289 ~-~~~l~~L~~L~L~~N~  305 (310)
T 4glp_A          289 Q-PDELPEVDNLTLDGNP  305 (310)
T ss_dssp             C-TTSCCCCSCEECSSTT
T ss_pred             h-hhhCCCccEEECcCCC
Confidence            5 5788999999999875

>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=99.41  E-value=6.3e-13  Score=131.28  Aligned_cols=147  Identities=18%  Similarity=0.273  Sum_probs=103.1

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      .++++++ .++.+|..+.  .+|+.|++++|.|+.+|. .|.++++|++|+|++| .+..++++.+.++++|++|++++|
T Consensus        15 ~v~c~~~-~l~~iP~~l~--~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N-~i~~~~~~~~~~l~~L~~L~Ls~N   90 (220)
T 2v9t_B           15 IVDCRGK-GLTEIPTNLP--ETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNN-QISELAPDAFQGLRSLNSLVLYGN   90 (220)
T ss_dssp             EEECTTS-CCSSCCSSCC--TTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSS-CCCEECTTTTTTCSSCCEEECCSS
T ss_pred             EEEcCCC-CcCcCCCccC--cCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCC-cCCCcCHHHhhCCcCCCEEECCCC
Confidence            3678888 8888887765  688999999999988876 6888999999999998 567664444888999999999988


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      .+..++              ...+..+++|+.|+++.|         .++.+.+..+..+++|+.|+|++|. +..++. 
T Consensus        91 ~l~~l~--------------~~~f~~l~~L~~L~L~~N---------~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~-  145 (220)
T 2v9t_B           91 KITELP--------------KSLFEGLFSLQLLLLNAN---------KINCLRVDAFQDLHNLNLLSLYDNK-LQTIAK-  145 (220)
T ss_dssp             CCCCCC--------------TTTTTTCTTCCEEECCSS---------CCCCCCTTTTTTCTTCCEEECCSSC-CSCCCT-
T ss_pred             cCCccC--------------HhHccCCCCCCEEECCCC---------CCCEeCHHHcCCCCCCCEEECCCCc-CCEECH-
Confidence            877522              223556777777777743         3333444556667777777777744 333332 


Q ss_pred             ccccCcccchhhccCCCCCCCCccEEEccCC
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESLGILYG  705 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~  705 (779)
                                    ..+..+++|+.|+|+++
T Consensus       146 --------------~~~~~l~~L~~L~L~~N  162 (220)
T 2v9t_B          146 --------------GTFSPLRAIQTMHLAQN  162 (220)
T ss_dssp             --------------TTTTTCTTCCEEECCSS
T ss_pred             --------------HHHhCCCCCCEEEeCCC
Confidence                          24556677777777663

>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=99.41  E-value=1.3e-13  Score=146.09  Aligned_cols=205  Identities=16%  Similarity=0.111  Sum_probs=147.4

Q ss_pred             cccccCCccEEEcccccccc--ccc----Ccc--ccccccccccc-ccchhhcccccCceeeecCC-cccc--cchhhcc
Q 004021          490 KVKEWEGAKRISLMANEIES--LSE----IPT--LLSLRRNDSLT-ELPSRISSLVSLHHLDLSLT-HIRG--LPQELKA  557 (779)
Q Consensus       490 ~~~~~~~lr~l~l~~~~~~~--l~~----~~~--lL~L~~~~~l~-~lp~~i~~L~~L~~L~L~~~-~i~~--lp~~~~~  557 (779)
                      ....+.++++|++++|.+..  ++.    .+.  .|+|++| .+. ..|..++++++|++|++++| .++.  +|..+.+
T Consensus        88 ~~~~~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~~-~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~  166 (336)
T 2ast_B           88 EHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGL-RLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSS  166 (336)
T ss_dssp             SCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTC-BCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHH
T ss_pred             hhccCCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcCc-ccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhc
Confidence            34567899999999998753  332    222  3999999 776 46889999999999999999 6874  7888999


Q ss_pred             CccCcEeeccCCcCCCC--CchhhhcCCc-cCcEeeecccc--CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEee
Q 004021          558 LEKLRYLNLEYTHYLSI--IPHQLISGFL-KLEVLRLLECG--SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFR  632 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~--lp~~~i~~L~-~L~~L~l~~~~--~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~  632 (779)
                      +++|++|++++|..++.  ++.. +..++ +|++|++++|.  +..             ...+..+..+++|+.|+++.+
T Consensus       167 ~~~L~~L~l~~~~~l~~~~~~~~-~~~l~~~L~~L~l~~~~~~~~~-------------~~l~~~~~~~~~L~~L~l~~~  232 (336)
T 2ast_B          167 CSRLDELNLSWCFDFTEKHVQVA-VAHVSETITQLNLSGYRKNLQK-------------SDLSTLVRRCPNLVHLDLSDS  232 (336)
T ss_dssp             CTTCCEEECCCCTTCCHHHHHHH-HHHSCTTCCEEECCSCGGGSCH-------------HHHHHHHHHCTTCSEEECTTC
T ss_pred             CCCCCEEcCCCCCCcChHHHHHH-HHhcccCCCEEEeCCCcccCCH-------------HHHHHHHhhCCCCCEEeCCCC
Confidence            99999999999955554  5664 88999 99999999984  331             345666778999999999855


Q ss_pred             cccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc
Q 004021          633 SSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       633 ~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                      ..        +..-.+..+..+++|++|+|++|..+.....               ..+..+++|+.|++++|     ++
T Consensus       233 ~~--------l~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~---------------~~l~~~~~L~~L~l~~~-----i~  284 (336)
T 2ast_B          233 VM--------LKNDCFQEFFQLNYLQHLSLSRCYDIIPETL---------------LELGEIPTLKTLQVFGI-----VP  284 (336)
T ss_dssp             TT--------CCGGGGGGGGGCTTCCEEECTTCTTCCGGGG---------------GGGGGCTTCCEEECTTS-----SC
T ss_pred             Cc--------CCHHHHHHHhCCCCCCEeeCCCCCCCCHHHH---------------HHHhcCCCCCEEeccCc-----cC
Confidence            31        2222345678889999999999863321100               24667999999999987     33


Q ss_pred             C-CCCCC-CCccEEeeeCCCCCCC-CCCC
Q 004021          713 P-NPLHF-PKLKKIGVYGCPKLKK-LPIN  738 (779)
Q Consensus       713 ~-~~~~l-~~L~~L~l~~c~~L~~-lP~~  738 (779)
                      . .+..+ .+|+.|+++ |+++.. .|..
T Consensus       285 ~~~~~~l~~~l~~L~l~-~n~l~~~~~~~  312 (336)
T 2ast_B          285 DGTLQLLKEALPHLQIN-CSHFTTIARPT  312 (336)
T ss_dssp             TTCHHHHHHHSTTSEES-CCCSCCTTCSS
T ss_pred             HHHHHHHHhhCcceEEe-cccCccccCCc
Confidence            2 12222 235556675 455665 4443

>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=99.41  E-value=7.1e-13  Score=130.91  Aligned_cols=148  Identities=16%  Similarity=0.193  Sum_probs=117.2

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccch--hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ--ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE  593 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~--~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~  593 (779)
                      .+++++| .++.+|..+.  ..+++|+|++|.++.++.  .|.++++|++|++++| .++.++++.+.++++|++|++++
T Consensus        15 ~l~~s~n-~l~~iP~~~~--~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N-~i~~i~~~~~~~l~~L~~L~Ls~   90 (220)
T 2v70_A           15 TVDCSNQ-KLNKIPEHIP--QYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNN-KITDIEEGAFEGASGVNEILLTS   90 (220)
T ss_dssp             EEECCSS-CCSSCCSCCC--TTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCS
T ss_pred             EeEeCCC-CcccCccCCC--CCCCEEEcCCCcCCccCchhhhccCCCCCEEECCCC-cCCEECHHHhCCCCCCCEEECCC
Confidence            3889999 8999998775  457899999999999853  3899999999999999 67888876699999999999999


Q ss_pred             ccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecc
Q 004021          594 CGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIIC  673 (779)
Q Consensus       594 ~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~  673 (779)
                      |.+..              ..+..+..+++|+.|+++.|         +++.+.+..+..+++|+.|+|++|.. ..++.
T Consensus        91 N~l~~--------------~~~~~~~~l~~L~~L~Ls~N---------~l~~~~~~~~~~l~~L~~L~L~~N~l-~~~~~  146 (220)
T 2v70_A           91 NRLEN--------------VQHKMFKGLESLKTLMLRSN---------RITCVGNDSFIGLSSVRLLSLYDNQI-TTVAP  146 (220)
T ss_dssp             SCCCC--------------CCGGGGTTCSSCCEEECTTS---------CCCCBCTTSSTTCTTCSEEECTTSCC-CCBCT
T ss_pred             CccCc--------------cCHhHhcCCcCCCEEECCCC---------cCCeECHhHcCCCccCCEEECCCCcC-CEECH
Confidence            98875              33445778899999998844         44455556677888999999998654 44433


Q ss_pred             cccccCcccchhhccCCCCCCCCccEEEccCCC
Q 004021          674 VDKLRDVSDISEIIGSEHNFFTQLESLGILYGP  706 (779)
Q Consensus       674 ~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~  706 (779)
                                     ..+..+++|+.|+|++++
T Consensus       147 ---------------~~~~~l~~L~~L~L~~N~  164 (220)
T 2v70_A          147 ---------------GAFDTLHSLSTLNLLANP  164 (220)
T ss_dssp             ---------------TTTTTCTTCCEEECCSCC
T ss_pred             ---------------HHhcCCCCCCEEEecCcC
Confidence                           367788899999998743

>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=99.40  E-value=1.1e-12  Score=130.55  Aligned_cols=61  Identities=25%  Similarity=0.262  Sum_probs=29.2

Q ss_pred             ccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          536 VSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       536 ~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      ++|++|+|++|.++.+ |..+.++++|++|+|++| .++.+|...+..+++|++|++++|.+.
T Consensus        40 ~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N-~l~~i~~~~~~~l~~L~~L~Ls~N~l~  101 (229)
T 3e6j_A           40 TNAQILYLHDNQITKLEPGVFDSLINLKELYLGSN-QLGALPVGVFDSLTQLTVLDLGTNQLT  101 (229)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCC
T ss_pred             CCCCEEEcCCCccCccCHHHhhCccCCcEEECCCC-CCCCcChhhcccCCCcCEEECCCCcCC
Confidence            4455555555554444 333445555555555555 344444443444555555555544443

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.39  E-value=1.5e-12  Score=146.05  Aligned_cols=184  Identities=20%  Similarity=0.165  Sum_probs=123.8

Q ss_pred             CccEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~  571 (779)
                      +++.|++.+|.+..+|....    .|+|++| .++.+|   ..+++|++|+|++|.++.+|. +.+  +|++|++++| .
T Consensus        60 ~L~~L~Ls~n~L~~lp~~l~~~L~~L~Ls~N-~l~~ip---~~l~~L~~L~Ls~N~l~~ip~-l~~--~L~~L~Ls~N-~  131 (571)
T 3cvr_A           60 QFSELQLNRLNLSSLPDNLPPQITVLEITQN-ALISLP---ELPASLEYLDACDNRLSTLPE-LPA--SLKHLDVDNN-Q  131 (571)
T ss_dssp             TCSEEECCSSCCSCCCSCCCTTCSEEECCSS-CCSCCC---CCCTTCCEEECCSSCCSCCCC-CCT--TCCEEECCSS-C
T ss_pred             CccEEEeCCCCCCccCHhHcCCCCEEECcCC-CCcccc---cccCCCCEEEccCCCCCCcch-hhc--CCCEEECCCC-c
Confidence            67788888888777765322    4888888 888888   457888888888888888887 665  8888888888 5


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccc
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL  651 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l  651 (779)
                      ++.+|.    .+++|++|++++|.+.++|               .   .+++|+.|+++.|...         .+ +. +
T Consensus       132 l~~lp~----~l~~L~~L~Ls~N~l~~lp---------------~---~l~~L~~L~Ls~N~L~---------~l-p~-l  178 (571)
T 3cvr_A          132 LTMLPE----LPALLEYINADNNQLTMLP---------------E---LPTSLEVLSVRNNQLT---------FL-PE-L  178 (571)
T ss_dssp             CSCCCC----CCTTCCEEECCSSCCSCCC---------------C---CCTTCCEEECCSSCCS---------CC-CC-C
T ss_pred             CCCCCC----cCccccEEeCCCCccCcCC---------------C---cCCCcCEEECCCCCCC---------Cc-ch-h
Confidence            677776    5788888888888776421               1   4678888888855433         22 11 3


Q ss_pred             ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCC
Q 004021          652 VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPK  731 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~  731 (779)
                      .  ++|+.|+|++|. +..++. . ..          .-....+.|+.|+|++ +.++.+|..+..+++|+.|++++|+-
T Consensus       179 ~--~~L~~L~Ls~N~-L~~lp~-~-~~----------~L~~~~~~L~~L~Ls~-N~l~~lp~~l~~l~~L~~L~L~~N~l  242 (571)
T 3cvr_A          179 P--ESLEALDVSTNL-LESLPA-V-PV----------RNHHSEETEIFFRCRE-NRITHIPENILSLDPTCTIILEDNPL  242 (571)
T ss_dssp             C--TTCCEEECCSSC-CSSCCC-C-C------------------CCEEEECCS-SCCCCCCGGGGGSCTTEEEECCSSSC
T ss_pred             h--CCCCEEECcCCC-CCchhh-H-HH----------hhhcccccceEEecCC-CcceecCHHHhcCCCCCEEEeeCCcC
Confidence            3  788888888864 334322 0 00          0011123338888887 46778888777788888888888764


Q ss_pred             CCCCC
Q 004021          732 LKKLP  736 (779)
Q Consensus       732 L~~lP  736 (779)
                      -..+|
T Consensus       243 ~~~~p  247 (571)
T 3cvr_A          243 SSRIR  247 (571)
T ss_dssp             CHHHH
T ss_pred             CCcCH
Confidence            33333

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.38  E-value=4.1e-13  Score=143.62  Aligned_cols=168  Identities=20%  Similarity=0.236  Sum_probs=124.5

Q ss_pred             ccEEEcccccccccccCcc----cccccccccccccchh-hc-ccccCceeeecCCcccccch-hhccCccCcEeeccCC
Q 004021          497 AKRISLMANEIESLSEIPT----LLSLRRNDSLTELPSR-IS-SLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYT  569 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~-i~-~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~  569 (779)
                      .+.+++.++.+..+|...+    .|+|++| .++.+|.. +. ++.+|++|+|++|.|+.+|. .|.++++|++|+|++|
T Consensus        20 ~~~l~c~~~~l~~iP~~~~~~l~~L~Ls~N-~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N   98 (361)
T 2xot_A           20 SNILSCSKQQLPNVPQSLPSYTALLDLSHN-NLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSSN   98 (361)
T ss_dssp             TTEEECCSSCCSSCCSSCCTTCSEEECCSS-CCCEECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             CCEEEeCCCCcCccCccCCCCCCEEECCCC-CCCccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECCCC
Confidence            3578888888888776433    5899999 88888655 55 89999999999999999875 5899999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLT  649 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~  649 (779)
                       .++.+|...+..+++|++|++++|.+..              ..+..+..+++|+.|+++.|..         +.+...
T Consensus        99 -~l~~~~~~~~~~l~~L~~L~L~~N~i~~--------------~~~~~~~~l~~L~~L~L~~N~l---------~~l~~~  154 (361)
T 2xot_A           99 -HLHTLDEFLFSDLQALEVLLLYNNHIVV--------------VDRNAFEDMAQLQKLYLSQNQI---------SRFPVE  154 (361)
T ss_dssp             -CCCEECTTTTTTCTTCCEEECCSSCCCE--------------ECTTTTTTCTTCCEEECCSSCC---------CSCCGG
T ss_pred             -cCCcCCHHHhCCCcCCCEEECCCCcccE--------------ECHHHhCCcccCCEEECCCCcC---------CeeCHH
Confidence             6788888768899999999999998774              3355678889999999986543         333222


Q ss_pred             cc---ccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCC--ccEEEccCC
Q 004021          650 WL---VFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQ--LESLGILYG  705 (779)
Q Consensus       650 ~l---~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--L~~L~l~~~  705 (779)
                      .+   ..+++|+.|+|++|. +..++.               ..+..+++  |+.|+|.++
T Consensus       155 ~~~~~~~l~~L~~L~L~~N~-l~~l~~---------------~~~~~l~~~~l~~l~l~~N  199 (361)
T 2xot_A          155 LIKDGNKLPKLMLLDLSSNK-LKKLPL---------------TDLQKLPAWVKNGLYLHNN  199 (361)
T ss_dssp             GTC----CTTCCEEECCSSC-CCCCCH---------------HHHHHSCHHHHTTEECCSS
T ss_pred             HhcCcccCCcCCEEECCCCC-CCccCH---------------HHhhhccHhhcceEEecCC
Confidence            33   568899999999854 444433               13344554  366777763

>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=99.38  E-value=1.3e-12  Score=126.65  Aligned_cols=142  Identities=17%  Similarity=0.245  Sum_probs=106.7

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCC-CchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI-IPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~-lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      |++++| .+..+| .+..+++|++|++++|.++.++ .+.++++|++|++++| .+.. .|.. ++++++|++|++++|.
T Consensus        49 L~l~~n-~i~~l~-~l~~l~~L~~L~l~~n~~~~~~-~l~~l~~L~~L~l~~n-~l~~~~~~~-l~~l~~L~~L~Ls~n~  123 (197)
T 4ezg_A           49 ITLANI-NVTDLT-GIEYAHNIKDLTINNIHATNYN-PISGLSNLERLRIMGK-DVTSDKIPN-LSGLTSLTLLDISHSA  123 (197)
T ss_dssp             EEEESS-CCSCCT-TGGGCTTCSEEEEESCCCSCCG-GGTTCTTCCEEEEECT-TCBGGGSCC-CTTCTTCCEEECCSSB
T ss_pred             EeccCC-CccChH-HHhcCCCCCEEEccCCCCCcch-hhhcCCCCCEEEeECC-ccCcccChh-hcCCCCCCEEEecCCc
Confidence            344455 566677 6888899999999999887775 6888999999999998 4554 5554 8899999999999988


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +..              ..+..++.+++|+.|+++.|..        +..+  +.+..+++|+.|++++|.. ..+    
T Consensus       124 i~~--------------~~~~~l~~l~~L~~L~L~~n~~--------i~~~--~~l~~l~~L~~L~l~~n~i-~~~----  174 (197)
T 4ezg_A          124 HDD--------------SILTKINTLPKVNSIDLSYNGA--------ITDI--MPLKTLPELKSLNIQFDGV-HDY----  174 (197)
T ss_dssp             CBG--------------GGHHHHTTCSSCCEEECCSCTB--------CCCC--GGGGGCSSCCEEECTTBCC-CCC----
T ss_pred             cCc--------------HhHHHHhhCCCCCEEEccCCCC--------cccc--HhhcCCCCCCEEECCCCCC-cCh----
Confidence            763              4567788899999999886540        2222  3577889999999998653 332    


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCC
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYG  705 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~  705 (779)
                                   ..+..+++|+.|+++++
T Consensus       175 -------------~~l~~l~~L~~L~l~~N  191 (197)
T 4ezg_A          175 -------------RGIEDFPKLNQLYAFSQ  191 (197)
T ss_dssp             -------------TTGGGCSSCCEEEECBC
T ss_pred             -------------HHhccCCCCCEEEeeCc
Confidence                         24567899999999874

>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=5e-13  Score=142.96  Aligned_cols=174  Identities=19%  Similarity=0.138  Sum_probs=121.1

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchh-hc-cCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LK-ALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLE  593 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~-~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~  593 (779)
                      .++++++ .++.+|..+.  .++++|+|++|.|+.+|.. +. ++++|++|+|++| .+..+|++.+.++++|++|++++
T Consensus        22 ~l~c~~~-~l~~iP~~~~--~~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N-~i~~i~~~~~~~l~~L~~L~Ls~   97 (361)
T 2xot_A           22 ILSCSKQ-QLPNVPQSLP--SYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHN-HLNFISSEAFVPVPNLRYLDLSS   97 (361)
T ss_dssp             EEECCSS-CCSSCCSSCC--TTCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCS
T ss_pred             EEEeCCC-CcCccCccCC--CCCCEEECCCCCCCccChhhhhhcccccCEEECCCC-cCCccChhhccCCCCCCEEECCC
Confidence            4788888 8999998765  4689999999999998766 44 8999999999999 67888876688999999999999


Q ss_pred             ccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecc
Q 004021          594 CGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIIC  673 (779)
Q Consensus       594 ~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~  673 (779)
                      |.+..              .....+..+++|+.|+++.|.         +..+.+..+..+++|+.|+|++|. +..++.
T Consensus        98 N~l~~--------------~~~~~~~~l~~L~~L~L~~N~---------i~~~~~~~~~~l~~L~~L~L~~N~-l~~l~~  153 (361)
T 2xot_A           98 NHLHT--------------LDEFLFSDLQALEVLLLYNNH---------IVVVDRNAFEDMAQLQKLYLSQNQ-ISRFPV  153 (361)
T ss_dssp             SCCCE--------------ECTTTTTTCTTCCEEECCSSC---------CCEECTTTTTTCTTCCEEECCSSC-CCSCCG
T ss_pred             CcCCc--------------CCHHHhCCCcCCCEEECCCCc---------ccEECHHHhCCcccCCEEECCCCc-CCeeCH
Confidence            88764              223346778888888887443         444445567777888888888854 343433


Q ss_pred             cccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-CCCCCCC--ccEEeeeCCC
Q 004021          674 VDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-NPLHFPK--LKKIGVYGCP  730 (779)
Q Consensus       674 ~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-~~~~l~~--L~~L~l~~c~  730 (779)
                      ..            +..+..+++|+.|+|++ +.+..++. .+..++.  |+.|++.++|
T Consensus       154 ~~------------~~~~~~l~~L~~L~L~~-N~l~~l~~~~~~~l~~~~l~~l~l~~N~  200 (361)
T 2xot_A          154 EL------------IKDGNKLPKLMLLDLSS-NKLKKLPLTDLQKLPAWVKNGLYLHNNP  200 (361)
T ss_dssp             GG------------TC----CTTCCEEECCS-SCCCCCCHHHHHHSCHHHHTTEECCSSC
T ss_pred             HH------------hcCcccCCcCCEEECCC-CCCCccCHHHhhhccHhhcceEEecCCC
Confidence            00            01124578888888887 46666653 2334554  3667776644

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.37  E-value=1.7e-12  Score=129.06  Aligned_cols=146  Identities=19%  Similarity=0.242  Sum_probs=117.8

Q ss_pred             CccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~  569 (779)
                      ....++.+++.+..+|....    .|+|++| .+..+ |..|.++++|++|+|++|.++.+|.. +.++++|++|+|++|
T Consensus        20 s~~~v~c~~~~l~~ip~~~~~~L~~L~Ls~n-~i~~~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N   98 (229)
T 3e6j_A           20 SGTTVDCRSKRHASVPAGIPTNAQILYLHDN-QITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTN   98 (229)
T ss_dssp             ETTEEECTTSCCSSCCSCCCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             eCCEeEccCCCcCccCCCCCCCCCEEEcCCC-ccCccCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCC
Confidence            34567888888887776433    5999999 88887 77899999999999999999999865 689999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLT  649 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~  649 (779)
                       .++.+|...+..+++|++|++++|.+..               .+..+..+++|+.|+++.|.         ++.+...
T Consensus        99 -~l~~l~~~~~~~l~~L~~L~Ls~N~l~~---------------lp~~~~~l~~L~~L~L~~N~---------l~~~~~~  153 (229)
T 3e6j_A           99 -QLTVLPSAVFDRLVHLKELFMCCNKLTE---------------LPRGIERLTHLTHLALDQNQ---------LKSIPHG  153 (229)
T ss_dssp             -CCCCCCTTTTTTCTTCCEEECCSSCCCS---------------CCTTGGGCTTCSEEECCSSC---------CCCCCTT
T ss_pred             -cCCccChhHhCcchhhCeEeccCCcccc---------------cCcccccCCCCCEEECCCCc---------CCccCHH
Confidence             6888888767899999999999998875               34556788899999988543         4444445


Q ss_pred             ccccccCcceEEeccccc
Q 004021          650 WLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       650 ~l~~l~~L~~L~L~~~~~  667 (779)
                      .+..+++|+.|+|++|+.
T Consensus       154 ~~~~l~~L~~L~l~~N~~  171 (229)
T 3e6j_A          154 AFDRLSSLTHAYLFGNPW  171 (229)
T ss_dssp             TTTTCTTCCEEECTTSCB
T ss_pred             HHhCCCCCCEEEeeCCCc
Confidence            567788899999988654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.35  E-value=1.4e-11  Score=134.37  Aligned_cols=288  Identities=12%  Similarity=0.057  Sum_probs=167.5

Q ss_pred             ccccchhhhHHHHHHHH-hcc--C--CCceEEEE--EcCCCCcHHHHHHHHHhhhcccc---CCCC-EEEEEEe------
Q 004021          155 QTIVGQEKLLPRVWRCI-TDQ--Q--KNRGIIGL--YGIGGVGKTTLLKQVNNNFCHQQ---HNFD-VVIWAAV------  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L-~~~--~--~~~~vi~I--~G~gGvGKTtLA~~v~~~~~~~~---~~F~-~~~wv~v------  217 (779)
                      ..|+||+++++++.+++ ...  .  ...+.+.|  +|++|+||||||+.+++.. ...   ..|+ .++|+..      
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  100 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRV-SEAAAKEGLTVKQAYVNAFNAPNL  100 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHH-HHHHHHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHH-HHHHhccCCceeEEEEECCCCCCH
Confidence            67999999999999998 531  1  23456666  9999999999999999876 211   1222 3567765      


Q ss_pred             chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhC--CCcceeehhhcccc-----------------cccc---C--C
Q 004021          218 QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILS--PKKFRIDLTELGVP-----------------LQML---N--A  273 (779)
Q Consensus       218 ~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~-----------------~~~~---~--~  273 (779)
                      ..++..++..++.....  ...+..+....+.+.+.  ++++.+++|++...                 +...   +  .
T Consensus       101 ~~~~~~l~~~l~~~~~~--~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~~  178 (412)
T 1w5s_A          101 YTILSLIVRQTGYPIQV--RGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVN  178 (412)
T ss_dssp             HHHHHHHHHHHTCCCCC--TTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCC
T ss_pred             HHHHHHHHHHhCCCCCC--CCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCCc
Confidence            46777888887653110  12233455566666664  56776666665221                 0001   1  3


Q ss_pred             CcEEEEEeCchhhhh-------hc-C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhC------C
Q 004021          274 GFKIVLKTRSAGVCD-------QM-D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECG------R  337 (779)
Q Consensus       274 gs~IivTTR~~~va~-------~~-~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~------g  337 (779)
                      +..||+||+...+..       .. .  ...+.+++|+.++++++|...+...... ..--.+....|++.|+      |
T Consensus       179 ~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~~~~G  257 (412)
T 1w5s_A          179 RIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRD-TVWEPRHLELISDVYGEDKGGDG  257 (412)
T ss_dssp             BEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCT-TSCCHHHHHHHHHHHCGGGTSCC
T ss_pred             eEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCC-CCCChHHHHHHHHHHHHhccCCC
Confidence            344888887655321       11 1  2338999999999999998765432211 1122567889999999      9


Q ss_pred             ChhHHHHHHHHh---c--CC---CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccC--C
Q 004021          338 LPLALKTVGRAM---K--SQ---KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYP--E  407 (779)
Q Consensus       338 lPLai~~~g~~l---~--~~---~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp--~  407 (779)
                      .|..+..+....   .  ..   -+...+.........            ...+.-++..||+ +.+.++..++.+.  .
T Consensus       258 ~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~------------~~~~~~~l~~l~~-~~~~~l~aia~l~~~~  324 (412)
T 1w5s_A          258 SARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEA------------ASIQTHELEALSI-HELIILRLIAEATLGG  324 (412)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------------------CCSSSSSCH-HHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc------------cchHHHHHHcCCH-HHHHHHHHHHHHHhcC
Confidence            997665544321   1  11   122223222221100            1223335677887 7888888888653  3


Q ss_pred             CcccChHHHHHHHH--H---cCCCc-chhhHHHHHHHHHHccccccc-----CCCcEEechHH
Q 004021          408 DYKIPKRSLIDYWI--S---EGFMA-DFDRGCEFINDLLHACLLEEE-----GDDHVKMHDMI  459 (779)
Q Consensus       408 ~~~i~~~~Li~~W~--a---~g~~~-~~~~~~~~l~~L~~~sll~~~-----~~~~~~mHdlv  459 (779)
                      +..++...+...+.  +   .|.-. .......+++.|...+++...     ..++|++|++.
T Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~~~~~~~~g~~~~~~l~  387 (412)
T 1w5s_A          325 MEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLA  387 (412)
T ss_dssp             CSSBCHHHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEECC-------CCEEEEC
T ss_pred             CCCccHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHhCCCEEeecccCCCCCceeEEEeC
Confidence            34555555554442  2   23211 124567889999999999774     23445555544

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.33  E-value=1.1e-12  Score=133.39  Aligned_cols=100  Identities=21%  Similarity=0.263  Sum_probs=52.9

Q ss_pred             ccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEee
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLN  565 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~  565 (779)
                      ...+.+++.|++.+|.+..++....     .|+|++| .+..+|. +.++++|++|++++|.++.+|....  ++|++|+
T Consensus        37 ~~~l~~L~~L~l~~n~i~~l~~l~~l~~L~~L~L~~N-~i~~~~~-l~~l~~L~~L~L~~N~l~~l~~~~~--~~L~~L~  112 (263)
T 1xeu_A           37 QKELSGVQNFNGDNSNIQSLAGMQFFTNLKELHLSHN-QISDLSP-LKDLTKLEELSVNRNRLKNLNGIPS--ACLSRLF  112 (263)
T ss_dssp             HHHHTTCSEEECTTSCCCCCTTGGGCTTCCEEECCSS-CCCCCGG-GTTCSSCCEEECCSSCCSCCTTCCC--SSCCEEE
T ss_pred             hhhcCcCcEEECcCCCcccchHHhhCCCCCEEECCCC-ccCCChh-hccCCCCCEEECCCCccCCcCcccc--CcccEEE
Confidence            3444555555555555555442211     2555555 5555554 5555555666665555555553222  5555555


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      +++| .++.+|.  ++++++|++|++++|.+.
T Consensus       113 L~~N-~l~~~~~--l~~l~~L~~L~Ls~N~i~  141 (263)
T 1xeu_A          113 LDNN-ELRDTDS--LIHLKNLEILSIRNNKLK  141 (263)
T ss_dssp             CCSS-CCSBSGG--GTTCTTCCEEECTTSCCC
T ss_pred             ccCC-ccCCChh--hcCcccccEEECCCCcCC
Confidence            5555 4455543  555555555555555544

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.29  E-value=8.6e-12  Score=139.99  Aligned_cols=170  Identities=18%  Similarity=0.171  Sum_probs=131.4

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .|+|++| .++.+|..+.  ++|++|+|++|.|+.+|   ..+++|++|++++| .++.+|.  +.+  +|++|++++|.
T Consensus        63 ~L~Ls~n-~L~~lp~~l~--~~L~~L~Ls~N~l~~ip---~~l~~L~~L~Ls~N-~l~~ip~--l~~--~L~~L~Ls~N~  131 (571)
T 3cvr_A           63 ELQLNRL-NLSSLPDNLP--PQITVLEITQNALISLP---ELPASLEYLDACDN-RLSTLPE--LPA--SLKHLDVDNNQ  131 (571)
T ss_dssp             EEECCSS-CCSCCCSCCC--TTCSEEECCSSCCSCCC---CCCTTCCEEECCSS-CCSCCCC--CCT--TCCEEECCSSC
T ss_pred             EEEeCCC-CCCccCHhHc--CCCCEEECcCCCCcccc---cccCCCCEEEccCC-CCCCcch--hhc--CCCEEECCCCc
Confidence            4899999 8999998774  89999999999999999   56899999999999 6788988  555  99999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +.++               +.   .+++|+.|+++.|...         .++ .   .+++|+.|+|++|.. ..++   
T Consensus       132 l~~l---------------p~---~l~~L~~L~Ls~N~l~---------~lp-~---~l~~L~~L~Ls~N~L-~~lp---  176 (571)
T 3cvr_A          132 LTML---------------PE---LPALLEYINADNNQLT---------MLP-E---LPTSLEVLSVRNNQL-TFLP---  176 (571)
T ss_dssp             CSCC---------------CC---CCTTCCEEECCSSCCS---------CCC-C---CCTTCCEEECCSSCC-SCCC---
T ss_pred             CCCC---------------CC---cCccccEEeCCCCccC---------cCC-C---cCCCcCEEECCCCCC-CCcc---
Confidence            8752               22   5789999999966543         221 1   468999999999754 3332   


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCc-------cEEeeeCCCCCCCCCCCCCCcc-cccE
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKL-------KKIGVYGCPKLKKLPINSSSAK-ERRV  747 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L-------~~L~l~~c~~L~~lP~~~~~~~-~~~l  747 (779)
                                    .+.  ++|+.|+|++ +.++.+|. +..  +|       +.|++++| .++.+|..+...+ ++.+
T Consensus       177 --------------~l~--~~L~~L~Ls~-N~L~~lp~-~~~--~L~~~~~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~L  235 (571)
T 3cvr_A          177 --------------ELP--ESLEALDVST-NLLESLPA-VPV--RNHHSEETEIFFRCREN-RITHIPENILSLDPTCTI  235 (571)
T ss_dssp             --------------CCC--TTCCEEECCS-SCCSSCCC-CC----------CCEEEECCSS-CCCCCCGGGGGSCTTEEE
T ss_pred             --------------hhh--CCCCEEECcC-CCCCchhh-HHH--hhhcccccceEEecCCC-cceecCHHHhcCCCCCEE
Confidence                          233  8999999998 47888887 433  77       99999987 6889998665443 3777


Q ss_pred             EEech
Q 004021          748 VIEGL  752 (779)
Q Consensus       748 ~i~~~  752 (779)
                      .+.++
T Consensus       236 ~L~~N  240 (571)
T 3cvr_A          236 ILEDN  240 (571)
T ss_dssp             ECCSS
T ss_pred             EeeCC
Confidence            77755

>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=1e-11  Score=119.67  Aligned_cols=71  Identities=24%  Similarity=0.284  Sum_probs=35.4

Q ss_pred             cccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          524 SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       524 ~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      .++.+|..+.  .+|++|++++|.++.+|..+.++++|++|++++| .++.++++.|.++++|++|++++|.+.
T Consensus        21 ~l~~ip~~~~--~~l~~L~L~~n~i~~ip~~~~~l~~L~~L~Ls~N-~i~~i~~~~f~~l~~L~~L~Ls~N~l~   91 (193)
T 2wfh_A           21 GLKVLPKGIP--RDVTELYLDGNQFTLVPKELSNYKHLTLIDLSNN-RISTLSNQSFSNMTQLLTLILSYNRLR   91 (193)
T ss_dssp             CCSSCCSCCC--TTCCEEECCSSCCCSCCGGGGGCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCC
T ss_pred             CCCcCCCCCC--CCCCEEECCCCcCchhHHHhhcccCCCEEECCCC-cCCEeCHhHccCCCCCCEEECCCCccC
Confidence            4444444332  3455555555555555555555555555555555 344444433555555555555555444

>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=99.26  E-value=6.1e-13  Score=150.16  Aligned_cols=29  Identities=24%  Similarity=0.185  Sum_probs=14.5

Q ss_pred             ccccccccccccchhhcccccCceeeecCC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLT  546 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~  546 (779)
                      |+|++| .++.+|.+|++|++|+.|++++|
T Consensus       354 L~Ls~n-~L~~Lp~~i~~l~~L~~L~l~~n  382 (567)
T 1dce_A          354 CELSVE-KSTVLQSELESCKELQELEPENK  382 (567)
T ss_dssp             CCCCHH-HHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             ccCChh-hHHhhHHHHHHHHHHHHhccccc
Confidence            444555 44455555555555555554433

>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=99.23  E-value=3e-12  Score=138.39  Aligned_cols=206  Identities=18%  Similarity=0.121  Sum_probs=141.5

Q ss_pred             cccccccccccc-----cchhhcccccCceeeecCCcccc----cchhh-------ccCccCcEeeccCCcCCCC-----
Q 004021          516 LLSLRRNDSLTE-----LPSRISSLVSLHHLDLSLTHIRG----LPQEL-------KALEKLRYLNLEYTHYLSI-----  574 (779)
Q Consensus       516 lL~L~~~~~l~~-----lp~~i~~L~~L~~L~L~~~~i~~----lp~~~-------~~L~~L~~L~l~~~~~l~~-----  574 (779)
                      .|+|++| .+..     ++..+.++++|++|+|++|.+..    +|..+       .++++|++|+|++| .+..     
T Consensus        36 ~L~L~~n-~i~~~~~~~l~~~l~~~~~L~~L~Ls~~~~~~l~~~~~~~~~~l~~~l~~~~~L~~L~Ls~n-~l~~~~~~~  113 (386)
T 2ca6_A           36 EIVLSGN-TIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDN-AFGPTAQEP  113 (386)
T ss_dssp             EEECTTS-EECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSC-CCCTTTHHH
T ss_pred             EEECCCC-CCCHHHHHHHHHHHHhCCCccEEeCcccccCccccchhHHHHHHHHHHhhCCcccEEECCCC-cCCHHHHHH
Confidence            4899999 7765     34457789999999999975553    35444       78999999999999 4554     


Q ss_pred             CchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCC---------CCCCceeEEeeccc---------c
Q 004021          575 IPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGL---------KRLNVLSWSFRSSL---------A  636 (779)
Q Consensus       575 lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L---------~~L~~L~l~~~~~~---------~  636 (779)
                      +|.. +.++++|++|++++|.+....          .......+..+         ++|+.|+++.|...         .
T Consensus       114 l~~~-l~~~~~L~~L~L~~n~l~~~~----------~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~  182 (386)
T 2ca6_A          114 LIDF-LSKHTPLEHLYLHNNGLGPQA----------GAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKT  182 (386)
T ss_dssp             HHHH-HHHCTTCCEEECCSSCCHHHH----------HHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTGGGHHHHHHH
T ss_pred             HHHH-HHhCCCCCEEECcCCCCCHHH----------HHHHHHHHHHHhhhhhcccCCCCcEEECCCCCCCcHHHHHHHHH
Confidence            6765 889999999999999875300          01222334444         89999999988764         2


Q ss_pred             cccCCCCCcccC--------------c-ccccccCcceEEecccccc----ceecccccccCcccchhhccCCCCCCCCc
Q 004021          637 VQKFFKYPKLDL--------------T-WLVFVQNLKELEIIVCTEM----EEIICVDKLRDVSDISEIIGSEHNFFTQL  697 (779)
Q Consensus       637 ~~~~~~L~~L~~--------------~-~l~~l~~L~~L~L~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~L  697 (779)
                      +..+++|+.|.+              + .+..+++|+.|+|++|...    ..++                ..+..+++|
T Consensus       183 l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~----------------~~l~~~~~L  246 (386)
T 2ca6_A          183 FQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALA----------------IALKSWPNL  246 (386)
T ss_dssp             HHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHH----------------HHGGGCTTC
T ss_pred             HHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHH----------------HHHccCCCc
Confidence            235667777711              1 5667888999999887642    2222                255678899


Q ss_pred             cEEEccCCCCCccc-----cCCC--CCCCCccEEeeeCCCCCCC-----CCCCC-C-CcccccEEEech
Q 004021          698 ESLGILYGPDLKSI-----YPNP--LHFPKLKKIGVYGCPKLKK-----LPINS-S-SAKERRVVIEGL  752 (779)
Q Consensus       698 ~~L~l~~~~~l~~l-----~~~~--~~l~~L~~L~l~~c~~L~~-----lP~~~-~-~~~~~~l~i~~~  752 (779)
                      +.|+|++|. +...     +..+  +.+++|++|++++|. +..     +|..+ . ..+++.+.+.++
T Consensus       247 ~~L~L~~n~-i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~-i~~~g~~~l~~~l~~~l~~L~~L~l~~N  313 (386)
T 2ca6_A          247 RELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGN  313 (386)
T ss_dssp             CEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTS
T ss_pred             CEEECCCCC-CchhhHHHHHHHHhhccCCCeEEEECcCCc-CCHHHHHHHHHHHHhcCCCceEEEccCC
Confidence            999999864 4432     3333  348999999999885 554     77654 2 234577777654

>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=99.22  E-value=1.2e-11  Score=116.57  Aligned_cols=128  Identities=16%  Similarity=0.114  Sum_probs=87.1

Q ss_pred             cccccccccc--ccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCC-CchhhhcCCccCcEeeecc
Q 004021          517 LSLRRNDSLT--ELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI-IPHQLISGFLKLEVLRLLE  593 (779)
Q Consensus       517 L~L~~~~~l~--~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~-lp~~~i~~L~~L~~L~l~~  593 (779)
                      |++++| .+.  .+|..+..+++|++|++++|.++.+ ..+..+++|++|++++| .+.. +|.. +..+++|++|++++
T Consensus        29 L~l~~n-~l~~~~i~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~N-~l~~~~~~~-~~~l~~L~~L~Ls~  104 (168)
T 2ell_A           29 LVLDNC-KSNDGKIEGLTAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSEN-RIFGGLDML-AEKLPNLTHLNLSG  104 (168)
T ss_dssp             EECCSC-BCBTTBCSSCCGGGGGCCEEEEESSCCCCC-SSCCCCSSCCEEEEESC-CCCSCCCHH-HHHCTTCCEEECBS
T ss_pred             EECCCC-CCChhhHHHHHHhCCCCCEEeCcCCCCCCh-hhhccCCCCCEEECcCC-cCchHHHHH-HhhCCCCCEEeccC
Confidence            444444 454  5677778888888888888888877 67888888888888888 4555 5553 66788888888888


Q ss_pred             ccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccc
Q 004021          594 CGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       594 ~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~  667 (779)
                      |.+..             ...+..+..+++|+.|+++.|....+..      .....+..+++|++|++++|..
T Consensus       105 N~l~~-------------~~~~~~l~~l~~L~~L~l~~N~l~~~~~------~~~~~~~~l~~L~~L~l~~n~~  159 (168)
T 2ell_A          105 NKLKD-------------ISTLEPLKKLECLKSLDLFNCEVTNLND------YRESVFKLLPQLTYLDGYDRED  159 (168)
T ss_dssp             SSCCS-------------SGGGGGGSSCSCCCEEECCSSGGGTSTT------HHHHHHTTCSSCCEETTEETTS
T ss_pred             CccCc-------------chhHHHHhcCCCCCEEEeeCCcCcchHH------HHHHHHHhCccCcEecCCCCCh
Confidence            87764             2233567777888888887554332110      0002456677888888877653

>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=99.21  E-value=1.9e-11  Score=117.78  Aligned_cols=122  Identities=19%  Similarity=0.186  Sum_probs=58.9

Q ss_pred             cccccccccccchhhcccccCceeeecCCcccccchh--hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          518 SLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE--LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       518 ~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~--~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      +++++ .++.+|..+..  +|++|++++|.++.+|..  ++++++|++|++++| .++.+++..++++++|++|++++|.
T Consensus        14 ~~s~~-~l~~ip~~~~~--~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N~   89 (192)
T 1w8a_A           14 DCTGR-GLKEIPRDIPL--HTTELLLNDNELGRISSDGLFGRLPHLVKLELKRN-QLTGIEPNAFEGASHIQELQLGENK   89 (192)
T ss_dssp             ECTTS-CCSSCCSCCCT--TCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             EcCCC-CcCcCccCCCC--CCCEEECCCCcCCccCCccccccCCCCCEEECCCC-CCCCcCHhHcCCcccCCEEECCCCc
Confidence            34444 44444444332  555555555555555442  555555555555555 3444432235555555555555555


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                      +..              ..+..+..+++|+.|+++.|.         ++.+.+..+..+++|++|+|++|+
T Consensus        90 l~~--------------~~~~~~~~l~~L~~L~L~~N~---------l~~~~~~~~~~l~~L~~L~L~~N~  137 (192)
T 1w8a_A           90 IKE--------------ISNKMFLGLHQLKTLNLYDNQ---------ISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCE--------------ECSSSSTTCTTCCEEECCSSC---------CCEECTTSSTTCTTCCEEECTTCC
T ss_pred             CCc--------------cCHHHhcCCCCCCEEECCCCc---------CCeeCHHHhhcCCCCCEEEeCCCC
Confidence            443              112224445555555555322         222223344555566666666544

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.21  E-value=7.2e-12  Score=134.06  Aligned_cols=212  Identities=17%  Similarity=0.174  Sum_probs=124.2

Q ss_pred             CCccEEEccccccccccc---------Cc-c--ccccccccccccc-chhhccc-----ccCceeeecCCcccccchh--
Q 004021          495 EGAKRISLMANEIESLSE---------IP-T--LLSLRRNDSLTEL-PSRISSL-----VSLHHLDLSLTHIRGLPQE--  554 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~---------~~-~--lL~L~~~~~l~~l-p~~i~~L-----~~L~~L~L~~~~i~~lp~~--  554 (779)
                      .++++|++++|.+...+.         .+ .  .|+|++| .++.. +..++.+     ++|++|+|++|.++..+..  
T Consensus        22 ~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N-~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l  100 (362)
T 3goz_A           22 HGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGN-SLGFKNSDELVQILAAIPANVTSLNLSGNFLSYKSSDEL  100 (362)
T ss_dssp             TTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSS-CGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHH
T ss_pred             CCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCC-CCCHHHHHHHHHHHhccCCCccEEECcCCcCChHHHHHH
Confidence            358888888888766542         12 2  4888888 77765 5666665     8888888888888765432  


Q ss_pred             ---hccC-ccCcEeeccCCcCCCCCchhhh----cC-CccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCC-CC
Q 004021          555 ---LKAL-EKLRYLNLEYTHYLSIIPHQLI----SG-FLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLK-RL  624 (779)
Q Consensus       555 ---~~~L-~~L~~L~l~~~~~l~~lp~~~i----~~-L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~-~L  624 (779)
                         +..+ ++|++|++++| .++..+...+    .. .++|++|++++|.+..          .........+..++ +|
T Consensus       101 ~~~l~~~~~~L~~L~Ls~N-~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~----------~~~~~l~~~l~~~~~~L  169 (362)
T 3goz_A          101 VKTLAAIPFTITVLDLGWN-DFSSKSSSEFKQAFSNLPASITSLNLRGNDLGI----------KSSDELIQILAAIPANV  169 (362)
T ss_dssp             HHHHHTSCTTCCEEECCSS-CGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGG----------SCHHHHHHHHHTSCTTC
T ss_pred             HHHHHhCCCCccEEECcCC-cCCcHHHHHHHHHHHhCCCceeEEEccCCcCCH----------HHHHHHHHHHhcCCccc
Confidence               4455 78888888888 4566555323    23 2588888888887663          11123344455555 78


Q ss_pred             CceeEEeeccccc---------ccC-CCCCcccCc--------------cccc-ccCcceEEeccccccceecccccccC
Q 004021          625 NVLSWSFRSSLAV---------QKF-FKYPKLDLT--------------WLVF-VQNLKELEIIVCTEMEEIICVDKLRD  679 (779)
Q Consensus       625 ~~L~l~~~~~~~~---------~~~-~~L~~L~~~--------------~l~~-l~~L~~L~L~~~~~~~~~~~~~~~~~  679 (779)
                      +.|+++.|.....         ..+ ++|+.|.+.              .+.. .++|+.|+|++|......+.      
T Consensus       170 ~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~------  243 (362)
T 3goz_A          170 NSLNLRGNNLASKNCAELAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCLNCLHGPSLE------  243 (362)
T ss_dssp             CEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCSSCCCCCCHH------
T ss_pred             cEeeecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcCCCCCcHHHH------
Confidence            8888876655322         122 355554111              1222 24677777776543221110      


Q ss_pred             cccchhhccCCCCCCCCccEEEccCCC-------CCccccCCCCCCCCccEEeeeCCC
Q 004021          680 VSDISEIIGSEHNFFTQLESLGILYGP-------DLKSIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       680 ~~~~~~~~~~~~~~~~~L~~L~l~~~~-------~l~~l~~~~~~l~~L~~L~l~~c~  730 (779)
                        .+.    ..+..+++|+.|+++++.       .+..++.....+++|+.|++++++
T Consensus       244 --~l~----~~~~~l~~L~~L~L~~n~l~~i~~~~~~~l~~~~~~l~~L~~LdL~~N~  295 (362)
T 3goz_A          244 --NLK----LLKDSLKHLQTVYLDYDIVKNMSKEQCKALGAAFPNIQKIILVDKNGKE  295 (362)
T ss_dssp             --HHH----HTTTTTTTCSEEEEEHHHHTTCCHHHHHHHHTTSTTCCEEEEECTTSCB
T ss_pred             --HHH----HHHhcCCCccEEEeccCCccccCHHHHHHHHHHhccCCceEEEecCCCc
Confidence              000    234556777777777643       122333445566677777777664

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.21  E-value=3e-11  Score=116.44  Aligned_cols=121  Identities=23%  Similarity=0.250  Sum_probs=101.1

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCC
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYL  572 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l  572 (779)
                      +.++++++.+..+|....    .|+|++| .+..+|..|.++++|++|+|++|.|+.++. .|.++++|++|+|++| .+
T Consensus        13 ~~l~~~~~~l~~ip~~~~~~l~~L~L~~n-~i~~ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N-~l   90 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGIPRDVTELYLDGN-QFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYN-RL   90 (193)
T ss_dssp             TEEECTTSCCSSCCSCCCTTCCEEECCSS-CCCSCCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CC
T ss_pred             CEEEcCCCCCCcCCCCCCCCCCEEECCCC-cCchhHHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCC-cc
Confidence            568888888888876433    4999999 999999999999999999999999999875 5999999999999999 68


Q ss_pred             CCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          573 SIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       573 ~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      +.+|+..+.++++|++|++++|.+..+              ....+..+++|+.|+++.|..
T Consensus        91 ~~i~~~~f~~l~~L~~L~L~~N~l~~~--------------~~~~~~~l~~L~~L~L~~N~~  138 (193)
T 2wfh_A           91 RCIPPRTFDGLKSLRLLSLHGNDISVV--------------PEGAFNDLSALSHLAIGANPL  138 (193)
T ss_dssp             CBCCTTTTTTCTTCCEEECCSSCCCBC--------------CTTTTTTCTTCCEEECCSSCE
T ss_pred             CEeCHHHhCCCCCCCEEECCCCCCCee--------------ChhhhhcCccccEEEeCCCCe
Confidence            888876699999999999999988752              223466778888888876653

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.20  E-value=1.2e-11  Score=113.92  Aligned_cols=90  Identities=19%  Similarity=0.130  Sum_probs=60.4

Q ss_pred             ccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCC-CchhhhcCCccCcEeeeccccCCCcccccCC
Q 004021          527 ELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI-IPHQLISGFLKLEVLRLLECGSEGVTKEEGN  605 (779)
Q Consensus       527 ~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~-lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~  605 (779)
                      .+|..++.+++|++|++++|.++.+ ..++++++|++|++++| .+.. +|.. ++++++|++|++++|.+..       
T Consensus        33 ~~~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~n-~i~~~~~~~-~~~l~~L~~L~ls~N~i~~-------  102 (149)
T 2je0_A           33 KLEGLTDEFEELEFLSTINVGLTSI-ANLPKLNKLKKLELSDN-RVSGGLEVL-AEKCPNLTHLNLSGNKIKD-------  102 (149)
T ss_dssp             BCCSCCTTCTTCCEEECTTSCCCCC-TTCCCCTTCCEEECCSS-CCCSCTHHH-HHHCTTCCEEECTTSCCCS-------
T ss_pred             HHHHHHhhcCCCcEEECcCCCCCCc-hhhhcCCCCCEEECCCC-cccchHHHH-hhhCCCCCEEECCCCcCCC-------
Confidence            5666667777788888877777777 56777777888888777 4555 5553 6667778888777777654       


Q ss_pred             ccCCCchhhHHhhcCCCCCCceeEEee
Q 004021          606 VLCDDAEPLMRELLGLKRLNVLSWSFR  632 (779)
Q Consensus       606 ~~~~~~~~~~~~l~~L~~L~~L~l~~~  632 (779)
                            ...+..++.+++|+.|+++.|
T Consensus       103 ------~~~~~~~~~l~~L~~L~l~~N  123 (149)
T 2je0_A          103 ------LSTIEPLKKLENLKSLDLFNC  123 (149)
T ss_dssp             ------HHHHGGGGGCTTCCEEECTTC
T ss_pred             ------hHHHHHHhhCCCCCEEeCcCC
Confidence                  223355556666666666544

>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=99.18  E-value=2.5e-11  Score=116.99  Aligned_cols=122  Identities=17%  Similarity=0.251  Sum_probs=103.2

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccchh--hcccccCceeeecCCccccc-chhhccCccCcEeeccCCc
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPSR--ISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTH  570 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~~--i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~  570 (779)
                      +.++++++.+..+|....    .|+|++| .+..+|..  |+++++|++|+|++|.++.+ |..|.++++|++|+|++| 
T Consensus        11 ~~l~~s~~~l~~ip~~~~~~l~~L~l~~n-~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N-   88 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIPLHTTELLLNDN-ELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGEN-   88 (192)
T ss_dssp             TEEECTTSCCSSCCSCCCTTCSEEECCSC-CCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSC-
T ss_pred             CEEEcCCCCcCcCccCCCCCCCEEECCCC-cCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCCC-
Confidence            678888888888876433    5999999 89888764  89999999999999999987 678999999999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      .++.+++..++++++|++|++++|.+.+              ..+..+..+++|+.|+++.|...
T Consensus        89 ~l~~~~~~~~~~l~~L~~L~L~~N~l~~--------------~~~~~~~~l~~L~~L~L~~N~l~  139 (192)
T 1w8a_A           89 KIKEISNKMFLGLHQLKTLNLYDNQISC--------------VMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             CCCEECSSSSTTCTTCCEEECCSSCCCE--------------ECTTSSTTCTTCCEEECTTCCBC
T ss_pred             cCCccCHHHhcCCCCCCEEECCCCcCCe--------------eCHHHhhcCCCCCEEEeCCCCcc
Confidence            6787777668899999999999998875              34566788999999999876543

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.15  E-value=8.3e-12  Score=145.45  Aligned_cols=114  Identities=21%  Similarity=0.079  Sum_probs=61.4

Q ss_pred             cchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCcc
Q 004021          528 LPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVL  607 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~  607 (779)
                      .|..+..+.+|++|+|++|.+..+|..+.++++|++|+|++| .++.+|.. |++|++|++|++++|.+..         
T Consensus       216 ~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~l~~L~~L~Ls~N-~l~~lp~~-~~~l~~L~~L~Ls~N~l~~---------  284 (727)
T 4b8c_D          216 PKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNGN-SLTELPAE-IKNLSNLRVLDLSHNRLTS---------  284 (727)
T ss_dssp             ------CCCCCCEEECTTSCCSCCCGGGGGCCSCSCCBCTTS-CCSCCCGG-GGGGTTCCEEECTTSCCSS---------
T ss_pred             ChhhhccCCCCcEEECCCCCCCCCChhhcCCCCCCEEEeeCC-cCcccChh-hhCCCCCCEEeCcCCcCCc---------
Confidence            355556666666666666666666666666666666666666 45566655 5666666666666665543         


Q ss_pred             CCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccccc
Q 004021          608 CDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEM  668 (779)
Q Consensus       608 ~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~  668 (779)
                            .+..++.|++|+.|+++.|.         |..+ +..++.+++|+.|+|++|...
T Consensus       285 ------lp~~~~~l~~L~~L~L~~N~---------l~~l-p~~~~~l~~L~~L~L~~N~l~  329 (727)
T 4b8c_D          285 ------LPAELGSCFQLKYFYFFDNM---------VTTL-PWEFGNLCNLQFLGVEGNPLE  329 (727)
T ss_dssp             ------CCSSGGGGTTCSEEECCSSC---------CCCC-CSSTTSCTTCCCEECTTSCCC
T ss_pred             ------cChhhcCCCCCCEEECCCCC---------CCcc-ChhhhcCCCccEEeCCCCccC
Confidence                  23345555666666665332         2222 223555666666666665443

>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=99.15  E-value=7.9e-11  Score=110.83  Aligned_cols=127  Identities=23%  Similarity=0.242  Sum_probs=105.1

Q ss_pred             CCccEEEccccccc--ccccCcc------cccccccccccccchhhcccccCceeeecCCcccc-cchhhccCccCcEee
Q 004021          495 EGAKRISLMANEIE--SLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRYLN  565 (779)
Q Consensus       495 ~~lr~l~l~~~~~~--~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~-lp~~~~~L~~L~~L~  565 (779)
                      ..++.|++++|.+.  .+|....      .|+|++| .+..+ ..++.+++|++|++++|.++. +|..+.++++|++|+
T Consensus        24 ~~L~~L~l~~n~l~~~~i~~~~~~l~~L~~L~l~~n-~l~~~-~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~  101 (168)
T 2ell_A           24 AAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINV-GLISV-SNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLN  101 (168)
T ss_dssp             TSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESS-CCCCC-SSCCCCSSCCEEEEESCCCCSCCCHHHHHCTTCCEEE
T ss_pred             ccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCC-CCCCh-hhhccCCCCCEEECcCCcCchHHHHHHhhCCCCCEEe
Confidence            58999999999988  7766522      3999999 88888 789999999999999999998 888888899999999


Q ss_pred             ccCCcCCCCCch-hhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc
Q 004021          566 LEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       566 l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      +++| .++.+|. ..+..+++|++|++++|.+...+           ......+..+++|+.|+++.+...
T Consensus       102 Ls~N-~l~~~~~~~~l~~l~~L~~L~l~~N~l~~~~-----------~~~~~~~~~l~~L~~L~l~~n~~~  160 (168)
T 2ell_A          102 LSGN-KLKDISTLEPLKKLECLKSLDLFNCEVTNLN-----------DYRESVFKLLPQLTYLDGYDREDQ  160 (168)
T ss_dssp             CBSS-SCCSSGGGGGGSSCSCCCEEECCSSGGGTST-----------THHHHHHTTCSSCCEETTEETTSC
T ss_pred             ccCC-ccCcchhHHHHhcCCCCCEEEeeCCcCcchH-----------HHHHHHHHhCccCcEecCCCCChh
Confidence            9999 6788772 23899999999999999887511           112246888999999999977654

>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=99.13  E-value=4.7e-11  Score=113.30  Aligned_cols=134  Identities=17%  Similarity=0.176  Sum_probs=65.1

Q ss_pred             ccCCccEEEcccccccccccCcccccccccccccccchhhcccc-cCceeeecCCcccccchhhccCccCcEeeccCCcC
Q 004021          493 EWEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLV-SLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHY  571 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~-~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~  571 (779)
                      ...+++.|++.+|.+..++.                   +..+. +|++|++++|.++.+ ..++++++|++|++++| .
T Consensus        17 ~~~~L~~L~l~~n~l~~i~~-------------------~~~~~~~L~~L~Ls~N~l~~~-~~l~~l~~L~~L~Ls~N-~   75 (176)
T 1a9n_A           17 NAVRDRELDLRGYKIPVIEN-------------------LGATLDQFDAIDFSDNEIRKL-DGFPLLRRLKTLLVNNN-R   75 (176)
T ss_dssp             CTTSCEEEECTTSCCCSCCC-------------------GGGGTTCCSEEECCSSCCCEE-CCCCCCSSCCEEECCSS-C
T ss_pred             CcCCceEEEeeCCCCchhHH-------------------hhhcCCCCCEEECCCCCCCcc-cccccCCCCCEEECCCC-c
Confidence            34567777777666554432                   22333 555555555555554 34555555555555555 3


Q ss_pred             CCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccc
Q 004021          572 LSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWL  651 (779)
Q Consensus       572 l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l  651 (779)
                      +..+|++.++.+++|++|++++|.+..             ...+..+..+++|+.|++++|....++..      ....+
T Consensus        76 l~~~~~~~~~~l~~L~~L~L~~N~i~~-------------~~~~~~l~~l~~L~~L~l~~N~i~~~~~~------~~~~~  136 (176)
T 1a9n_A           76 ICRIGEGLDQALPDLTELILTNNSLVE-------------LGDLDPLASLKSLTYLCILRNPVTNKKHY------RLYVI  136 (176)
T ss_dssp             CCEECSCHHHHCTTCCEEECCSCCCCC-------------GGGGGGGGGCTTCCEEECCSSGGGGSTTH------HHHHH
T ss_pred             ccccCcchhhcCCCCCEEECCCCcCCc-------------chhhHhhhcCCCCCEEEecCCCCCCcHhH------HHHHH
Confidence            445554423555555555555554432             11112344555555555555544432110      00113


Q ss_pred             ccccCcceEEecccc
Q 004021          652 VFVQNLKELEIIVCT  666 (779)
Q Consensus       652 ~~l~~L~~L~L~~~~  666 (779)
                      ..+++|+.|+++.|.
T Consensus       137 ~~l~~L~~Ld~~~n~  151 (176)
T 1a9n_A          137 YKVPQVRVLDFQKVK  151 (176)
T ss_dssp             HHCTTCSEETTEECC
T ss_pred             HHCCccceeCCCcCC
Confidence            455666666666544

>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=99.13  E-value=4.2e-09  Score=113.47  Aligned_cols=277  Identities=14%  Similarity=0.056  Sum_probs=163.9

Q ss_pred             ccccchhhhHHHHHHHHhc--cCCCceEEEEEcCCCCcHHHHHHHHHhhhccc---cCC--CCEEEEEEe-------chH
Q 004021          155 QTIVGQEKLLPRVWRCITD--QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ---QHN--FDVVIWAAV-------QTF  220 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~~~--F~~~~wv~v-------~~i  220 (779)
                      ..++||+++++++.+++..  .....+.+.|+|++|+||||||+.+++.....   ...  ....+|++.       ..+
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            6789999999999988865  23356789999999999999999999875211   011  335667765       234


Q ss_pred             HHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhcccc------------ccccCCCcEEEEEeCchhh--
Q 004021          221 QDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP------------LQMLNAGFKIVLKTRSAGV--  286 (779)
Q Consensus       221 ~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~------------~~~~~~gs~IivTTR~~~v--  286 (779)
                      ...++..+... .......+.......+.+.+..++..+.+|++...            +.....+..||+||+....  
T Consensus       100 ~~~l~~~l~~~-~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~~~~  178 (384)
T 2qby_B          100 LSSLAGKLTGF-SVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDINVRD  178 (384)
T ss_dssp             HHHHHHHHHCS-CCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTTTTT
T ss_pred             HHHHHHHhcCC-CCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCchHh
Confidence            55666665211 11112233455667777888777755555554211            1111157889999987532  


Q ss_pred             --hhhc--C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhC---CChh-HHHHHHHH--hcC---C
Q 004021          287 --CDQM--D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECG---RLPL-ALKTVGRA--MKS---Q  352 (779)
Q Consensus       287 --a~~~--~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~---glPL-ai~~~g~~--l~~---~  352 (779)
                        ....  . ...+.+++++.++..++|...+.... ....--.+....|++.|+   |.|. |+..+-..  +..   .
T Consensus       179 ~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~-~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~~~~  257 (384)
T 2qby_B          179 YMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGL-IKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASGGGI  257 (384)
T ss_dssp             TSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTS-CTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTSSSC
T ss_pred             hhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhc-ccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcCCCc
Confidence              1111  1 24889999999999999998865311 001111456778888888   8876 44433322  221   1


Q ss_pred             CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccCCCcccChHHHHHHHHHcCCCc-chhh
Q 004021          353 KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPEDYKIPKRSLIDYWISEGFMA-DFDR  431 (779)
Q Consensus       353 ~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~a~g~~~-~~~~  431 (779)
                      -+.+.+..+++...             ...+.-++..|++ +.+..+..++....+..+. .......-..|... ....
T Consensus       258 i~~~~v~~~~~~~~-------------~~~~~~~~~~l~~-~~~~~l~al~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~  322 (384)
T 2qby_B          258 IRKEHVDKAIVDYE-------------QERLIEAVKALPF-HYKLALRSLIESEDVMSAH-KMYTDLCNKFKQKPLSYRR  322 (384)
T ss_dssp             CCHHHHHHHHHHHH-------------HHHHHHHHHSSCH-HHHHHHHHHHTCCBHHHHH-HHHHHHHHHTTCCCCCHHH
T ss_pred             cCHHHHHHHHHHHh-------------cchHHHHHHcCCH-HHHHHHHHHHHhcccChHH-HHHHHHHHHcCCCCCCHHH
Confidence            34556665554321             2345667788987 6666666565511101111 11112222233111 2256


Q ss_pred             HHHHHHHHHHccccccc
Q 004021          432 GCEFINDLLHACLLEEE  448 (779)
Q Consensus       432 ~~~~l~~L~~~sll~~~  448 (779)
                      ..+++..|...++++..
T Consensus       323 ~~~~l~~L~~~gli~~~  339 (384)
T 2qby_B          323 FSDIISELDMFGIVKIR  339 (384)
T ss_dssp             HHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhCCCEEEE
Confidence            77889999999999874

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.11  E-value=3.6e-11  Score=128.61  Aligned_cols=190  Identities=15%  Similarity=0.099  Sum_probs=115.7

Q ss_pred             cccccccccccccc-----hhhcccc-cCceeeecCCccccc-chhhccC-----ccCcEeeccCCcCCCCCchhhh---
Q 004021          516 LLSLRRNDSLTELP-----SRISSLV-SLHHLDLSLTHIRGL-PQELKAL-----EKLRYLNLEYTHYLSIIPHQLI---  580 (779)
Q Consensus       516 lL~L~~~~~l~~lp-----~~i~~L~-~L~~L~L~~~~i~~l-p~~~~~L-----~~L~~L~l~~~~~l~~lp~~~i---  580 (779)
                      .|+|++| .++..+     ..+.+++ +|++|+|++|.++.. +..+..+     ++|++|++++| .++..+...+   
T Consensus        26 ~L~Ls~n-~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n-~l~~~~~~~l~~~  103 (362)
T 3goz_A           26 SLDLSLN-NLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGN-FLSYKSSDELVKT  103 (362)
T ss_dssp             EEECTTS-CGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSS-CGGGSCHHHHHHH
T ss_pred             EEEccCC-CCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCC-cCChHHHHHHHHH
Confidence            4899999 888775     5677888 899999999988875 4556554     89999999999 4565544323   


Q ss_pred             -cCC-ccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCC-CCCCceeEEeeccccc---------ccC-CCCCccc
Q 004021          581 -SGF-LKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGL-KRLNVLSWSFRSSLAV---------QKF-FKYPKLD  647 (779)
Q Consensus       581 -~~L-~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L-~~L~~L~l~~~~~~~~---------~~~-~~L~~L~  647 (779)
                       ..+ ++|++|++++|.+...+          .......+..+ ++|++|+++.|.....         ..+ ++|+.|.
T Consensus       104 l~~~~~~L~~L~Ls~N~l~~~~----------~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~  173 (362)
T 3goz_A          104 LAAIPFTITVLDLGWNDFSSKS----------SSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQILAAIPANVNSLN  173 (362)
T ss_dssp             HHTSCTTCCEEECCSSCGGGSC----------HHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEE
T ss_pred             HHhCCCCccEEECcCCcCCcHH----------HHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHHHhcCCccccEee
Confidence             344 89999999999876411          12233445554 6899999987765421         122 2566651


Q ss_pred             Cc--------------ccccc-cCcceEEeccccccceecccccccCcccchhhccCCCCC-CCCccEEEccCCCCCccc
Q 004021          648 LT--------------WLVFV-QNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNF-FTQLESLGILYGPDLKSI  711 (779)
Q Consensus       648 ~~--------------~l~~l-~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~L~~L~l~~~~~l~~l  711 (779)
                      +.              .+..+ ++|+.|+|++|........        .++    ..+.. .++|+.|+|+++ .+...
T Consensus       174 Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~--------~l~----~~l~~~~~~L~~L~Ls~N-~l~~~  240 (362)
T 3goz_A          174 LRGNNLASKNCAELAKFLASIPASVTSLDLSANLLGLKSYA--------ELA----YIFSSIPNHVVSLNLCLN-CLHGP  240 (362)
T ss_dssp             CTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHH--------HHH----HHHHHSCTTCCEEECCSS-CCCCC
T ss_pred             ecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCCCChhHHH--------HHH----HHHhcCCCCceEEECcCC-CCCcH
Confidence            11              11223 3677777776543221000        000    12222 347777777764 44433


Q ss_pred             cC-----CCCCCCCccEEeeeCCC
Q 004021          712 YP-----NPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       712 ~~-----~~~~l~~L~~L~l~~c~  730 (779)
                      +.     ....+++|+.|++++|.
T Consensus       241 ~~~~l~~~~~~l~~L~~L~L~~n~  264 (362)
T 3goz_A          241 SLENLKLLKDSLKHLQTVYLDYDI  264 (362)
T ss_dssp             CHHHHHHTTTTTTTCSEEEEEHHH
T ss_pred             HHHHHHHHHhcCCCccEEEeccCC
Confidence            22     33456777777777764

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.11  E-value=8e-11  Score=137.18  Aligned_cols=127  Identities=20%  Similarity=0.168  Sum_probs=102.6

Q ss_pred             cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          516 LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       516 lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .|+|++| .+..+|..+++|++|++|+|++|.|+.+|..|++|++|++|+|++| .++.+|.. |++|++|++|++++|.
T Consensus       228 ~L~Ls~n-~l~~l~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp~~-~~~l~~L~~L~L~~N~  304 (727)
T 4b8c_D          228 ALDLSNL-QIFNISANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHN-RLTSLPAE-LGSCFQLKYFYFFDNM  304 (727)
T ss_dssp             EEECTTS-CCSCCCGGGGGCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTS-CCSSCCSS-GGGGTTCSEEECCSSC
T ss_pred             EEECCCC-CCCCCChhhcCCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCC-cCCccChh-hcCCCCCCEEECCCCC
Confidence            3999999 8999999999999999999999999999999999999999999999 67899997 9999999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCccccccc-CcceEEeccccccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQ-NLKELEIIVCTEME  669 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~-~L~~L~L~~~~~~~  669 (779)
                      +..               .+..++.|++|+.|+|+.|.         |....+..+..+. .+..|+|++|....
T Consensus       305 l~~---------------lp~~~~~l~~L~~L~L~~N~---------l~~~~p~~~~~~~~~~~~l~l~~N~l~~  355 (727)
T 4b8c_D          305 VTT---------------LPWEFGNLCNLQFLGVEGNP---------LEKQFLKILTEKSVTGLIFYLRDNRPEI  355 (727)
T ss_dssp             CCC---------------CCSSTTSCTTCCCEECTTSC---------CCSHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCc---------------cChhhhcCCCccEEeCCCCc---------cCCCChHHHhhcchhhhHHhhccCcccC
Confidence            764               45568899999999998554         3333333333321 12346677765433

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.10  E-value=2.4e-10  Score=108.49  Aligned_cols=117  Identities=20%  Similarity=0.253  Sum_probs=59.8

Q ss_pred             cccccchhhcccccCceeeecCCcccccchh-hccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccc
Q 004021          524 SLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKE  602 (779)
Q Consensus       524 ~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~  602 (779)
                      .+..+|..+.  .+|++|++++|.++.+|.. ++++++|++|++++| .++.+|...++.+++|++|++++|.+..    
T Consensus        18 ~l~~~p~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~N~l~~----   90 (177)
T 2o6r_A           18 GLTSVPTGIP--SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQN-QIQSLPDGVFDKLTKLTILYLHENKLQS----   90 (177)
T ss_dssp             CCSSCCTTCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCC----
T ss_pred             CCccCCCCCC--CCCcEEEeCCCcccEeCHHHhcCcccccEEECCCC-cceEeChhHccCCCccCEEECCCCCccc----
Confidence            4444443332  4566666666666555543 455666666666665 4555555444556666666666655543    


Q ss_pred             cCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          603 EGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       603 ~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                                .....+..+++|+.|+++.|.         ++.+.+..+..+++|++|+|++|+
T Consensus        91 ----------~~~~~~~~l~~L~~L~l~~N~---------l~~~~~~~~~~l~~L~~L~l~~N~  135 (177)
T 2o6r_A           91 ----------LPNGVFDKLTQLKELALDTNQ---------LKSVPDGIFDRLTSLQKIWLHTNP  135 (177)
T ss_dssp             ----------CCTTTTTTCTTCCEEECCSSC---------CSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             ----------cCHHHhhCCcccCEEECcCCc---------ceEeCHHHhcCCcccCEEEecCCC
Confidence                      111223445555555555332         222222234455666666666654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.09  E-value=6.4e-09  Score=112.11  Aligned_cols=275  Identities=15%  Similarity=0.124  Sum_probs=161.8

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhcccc---CCCCEEEEEEe------chHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ---HNFDVVIWAAV------QTFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~~F~~~~wv~v------~~i~~~  223 (779)
                      ..++||+++++++.+++...  ....+.+.|+|++|+||||||+.+++......   +.-...+|++.      ..+...
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            67899999999999998653  33567899999999999999999998762110   10123456665      356777


Q ss_pred             HHHHhCCCcchhhhhcchhhHHHHHHHhhC--CCcceeehhhcccc-------------cccc-----CCCcEEEEEeCc
Q 004021          224 IGKRIGFSEDKKWKEKSLQDKAVDISSILS--PKKFRIDLTELGVP-------------LQML-----NAGFKIVLKTRS  283 (779)
Q Consensus       224 i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~-------------~~~~-----~~gs~IivTTR~  283 (779)
                      ++..++....  ....+..+....+.+.+.  +++..+.+|++...             +...     ..+..+|.||+.
T Consensus        99 l~~~l~~~~~--~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t~~  176 (387)
T 2v1u_A           99 IAEAVGVRVP--FTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNS  176 (387)
T ss_dssp             HHHHHSCCCC--SSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEECSC
T ss_pred             HHHHhCCCCC--CCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEECC
Confidence            8887765311  122234455566666664  33455555554221             1111     345678888876


Q ss_pred             hhh--------hhhcCCceeEccCCChHHHHHHHHHHhhc--cCCCCCCChHHHHHHHHHHhC---CChhH-HHHHHHHh
Q 004021          284 AGV--------CDQMDSKNLEVYSLAHDEAWKLFQEMIER--STLDSHTSIPELAETLARECG---RLPLA-LKTVGRAM  349 (779)
Q Consensus       284 ~~v--------a~~~~~~~~~l~~L~~~~a~~Lf~~~a~~--~~~~~~~~l~~~~~~I~~~c~---glPLa-i~~~g~~l  349 (779)
                      ...        ...++...+.+++++.++..+++...+..  .....+   .+....|++.++   |.|-. +..+....
T Consensus       177 ~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~G~~r~~~~~l~~a~  253 (387)
T 2v1u_A          177 LGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLD---PDVVPLCAALAAREHGDARRALDLLRVAG  253 (387)
T ss_dssp             STTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBC---SSHHHHHHHHHHSSSCCHHHHHHHHHHHH
T ss_pred             CchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCC---HHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            532        11122247899999999999999988653  111122   345677888888   99943 33332221


Q ss_pred             --c---C--CCChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhcc-ccCCCcccChHHHHHHH-
Q 004021          350 --K---S--QKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCC-LYPEDYKIPKRSLIDYW-  420 (779)
Q Consensus       350 --~---~--~~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s-~fp~~~~i~~~~Li~~W-  420 (779)
                        .   +  .-+.+.+..+++...             ...+.-++..+++ +.+..+..++ ++.....+....+.+.. 
T Consensus       254 ~~a~~~~~~~i~~~~v~~a~~~~~-------------~~~~~~~~~~l~~-~~~~~l~a~~~~~~~~~~~~~~~~~~~~~  319 (387)
T 2v1u_A          254 EIAERRREERVRREHVYSARAEIE-------------RDRVSEVVRTLPL-HAKLVLLSIMMLEDGGRPASTGEIYERYK  319 (387)
T ss_dssp             HHHHHTTCSCBCHHHHHHHHHHHH-------------HHHHHHHHHSSCH-HHHHHHHHHHHHSSSSCCEEHHHHHHHHH
T ss_pred             HHHHHcCCCCcCHHHHHHHHHHHh-------------hchHHHHHHcCCH-HHHHHHHHHHHHhcCCCCCcHHHHHHHHH
Confidence              1   1  124455555444321             2235557788987 6666555554 34322344444333332 


Q ss_pred             ---HHcCCCc-chhhHHHHHHHHHHccccccc
Q 004021          421 ---ISEGFMA-DFDRGCEFINDLLHACLLEEE  448 (779)
Q Consensus       421 ---~a~g~~~-~~~~~~~~l~~L~~~sll~~~  448 (779)
                         -..|... .......+++.|...++++..
T Consensus       320 ~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~  351 (387)
T 2v1u_A          320 ELTSTLGLEHVTLRRVSGIISELDMLGIVKSR  351 (387)
T ss_dssp             HHHHHTTCCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence               2223211 125677889999999999874

>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=99.09  E-value=1.1e-10  Score=131.63  Aligned_cols=100  Identities=28%  Similarity=0.341  Sum_probs=68.4

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .++.+|. |++|++|++|+|++|.++.+|..+++|++|++|+|++| .++.+| . +++|++|++|++++|.+
T Consensus       446 L~Ls~n-~l~~lp~-~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N-~l~~lp-~-l~~l~~L~~L~Ls~N~l  520 (567)
T 1dce_A          446 LHLAHK-DLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDN-ALENVD-G-VANLPRLQELLLCNNRL  520 (567)
T ss_dssp             EECTTS-CCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSS-CCCCCG-G-GTTCSSCCEEECCSSCC
T ss_pred             EEecCC-CCCCCcC-ccccccCcEeecCcccccccchhhhcCCCCCEEECCCC-CCCCCc-c-cCCCCCCcEEECCCCCC
Confidence            555666 6666765 77777777777777777777777777777777777777 566677 4 77777777777777766


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      .+             ...+..++.|++|+.|++++|..
T Consensus       521 ~~-------------~~~p~~l~~l~~L~~L~L~~N~l  545 (567)
T 1dce_A          521 QQ-------------SAAIQPLVSCPRLVLLNLQGNSL  545 (567)
T ss_dssp             CS-------------SSTTGGGGGCTTCCEEECTTSGG
T ss_pred             CC-------------CCCcHHHhcCCCCCEEEecCCcC
Confidence            64             11145566666666666665443

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.09  E-value=7e-11  Score=108.69  Aligned_cols=132  Identities=20%  Similarity=0.163  Sum_probs=100.6

Q ss_pred             ccccCceeeecCCccc--ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCc
Q 004021          534 SLVSLHHLDLSLTHIR--GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDA  611 (779)
Q Consensus       534 ~L~~L~~L~L~~~~i~--~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~  611 (779)
                      ..++|+.|++++|.++  .+|..+..+++|++|++++| .+..+ .. ++.+++|++|++++|.+..             
T Consensus        15 ~~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n-~l~~~-~~-~~~l~~L~~L~Ls~n~i~~-------------   78 (149)
T 2je0_A           15 TPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINV-GLTSI-AN-LPKLNKLKKLELSDNRVSG-------------   78 (149)
T ss_dssp             CGGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTS-CCCCC-TT-CCCCTTCCEEECCSSCCCS-------------
T ss_pred             CCccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCC-CCCCc-hh-hhcCCCCCEEECCCCcccc-------------
Confidence            4588999999999998  89998999999999999999 67777 43 8999999999999998874             


Q ss_pred             hhhHHhhcCCCCCCceeEEeecccccccCCCCCcc-cCcccccccCcceEEeccccccceecccccccCcccchhhccCC
Q 004021          612 EPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL-DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSE  690 (779)
Q Consensus       612 ~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L-~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~  690 (779)
                       ..+..++.+++|+.|+++.|..         ..+ .+..+..+++|++|++++|... .++..            ....
T Consensus        79 -~~~~~~~~l~~L~~L~ls~N~i---------~~~~~~~~~~~l~~L~~L~l~~N~l~-~~~~~------------~~~~  135 (149)
T 2je0_A           79 -GLEVLAEKCPNLTHLNLSGNKI---------KDLSTIEPLKKLENLKSLDLFNCEVT-NLNDY------------RENV  135 (149)
T ss_dssp             -CTHHHHHHCTTCCEEECTTSCC---------CSHHHHGGGGGCTTCCEEECTTCGGG-GSTTH------------HHHH
T ss_pred             -hHHHHhhhCCCCCEEECCCCcC---------CChHHHHHHhhCCCCCEEeCcCCccc-chHHH------------HHHH
Confidence             2455566789999999985543         333 2356788899999999997543 22210            0013


Q ss_pred             CCCCCCccEEEccC
Q 004021          691 HNFFTQLESLGILY  704 (779)
Q Consensus       691 ~~~~~~L~~L~l~~  704 (779)
                      +..+++|+.|++++
T Consensus       136 ~~~l~~L~~L~l~d  149 (149)
T 2je0_A          136 FKLLPQLTYLDGYD  149 (149)
T ss_dssp             HHHCTTCCEETTBC
T ss_pred             HHHCCCcccccCCC
Confidence            56788898888763

>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=99.08  E-value=9.1e-11  Score=111.32  Aligned_cols=139  Identities=14%  Similarity=0.014  Sum_probs=103.2

Q ss_pred             hhcccccCceeeecCCcccccchhhccCc-cCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCC
Q 004021          531 RISSLVSLHHLDLSLTHIRGLPQELKALE-KLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCD  609 (779)
Q Consensus       531 ~i~~L~~L~~L~L~~~~i~~lp~~~~~L~-~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~  609 (779)
                      .+.++.+|++|++++|.++.+|. +..+. +|++|++++| .++.++ . ++.+++|++|++++|.+..++         
T Consensus        14 ~~~~~~~L~~L~l~~n~l~~i~~-~~~~~~~L~~L~Ls~N-~l~~~~-~-l~~l~~L~~L~Ls~N~l~~~~---------   80 (176)
T 1a9n_A           14 QYTNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSDN-EIRKLD-G-FPLLRRLKTLLVNNNRICRIG---------   80 (176)
T ss_dssp             EEECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCSS-CCCEEC-C-CCCCSSCCEEECCSSCCCEEC---------
T ss_pred             hcCCcCCceEEEeeCCCCchhHH-hhhcCCCCCEEECCCC-CCCccc-c-cccCCCCCEEECCCCcccccC---------
Confidence            46678899999999999999875 55555 9999999999 677774 3 899999999999999887521         


Q ss_pred             CchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccC
Q 004021          610 DAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGS  689 (779)
Q Consensus       610 ~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~  689 (779)
                           +..+..+++|+.|+++.|....++.        ...+..+++|+.|++++|+.. .++..    .   .     .
T Consensus        81 -----~~~~~~l~~L~~L~L~~N~i~~~~~--------~~~l~~l~~L~~L~l~~N~i~-~~~~~----~---~-----~  134 (176)
T 1a9n_A           81 -----EGLDQALPDLTELILTNNSLVELGD--------LDPLASLKSLTYLCILRNPVT-NKKHY----R---L-----Y  134 (176)
T ss_dssp             -----SCHHHHCTTCCEEECCSCCCCCGGG--------GGGGGGCTTCCEEECCSSGGG-GSTTH----H---H-----H
T ss_pred             -----cchhhcCCCCCEEECCCCcCCcchh--------hHhhhcCCCCCEEEecCCCCC-CcHhH----H---H-----H
Confidence                 1224678899999999665432211        135778899999999997653 33320    0   0     1


Q ss_pred             CCCCCCCccEEEccCCCCC
Q 004021          690 EHNFFTQLESLGILYGPDL  708 (779)
Q Consensus       690 ~~~~~~~L~~L~l~~~~~l  708 (779)
                      .+..+|+|+.|+++++..-
T Consensus       135 ~~~~l~~L~~Ld~~~n~~~  153 (176)
T 1a9n_A          135 VIYKVPQVRVLDFQKVKLK  153 (176)
T ss_dssp             HHHHCTTCSEETTEECCHH
T ss_pred             HHHHCCccceeCCCcCCHH
Confidence            3678899999999987654

>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=99.06  E-value=1.5e-11  Score=136.36  Aligned_cols=38  Identities=16%  Similarity=0.061  Sum_probs=19.2

Q ss_pred             CCCCCccEEEccCCCCCcccc-----CC-CCCCCCccEEeeeCCC
Q 004021          692 NFFTQLESLGILYGPDLKSIY-----PN-PLHFPKLKKIGVYGCP  730 (779)
Q Consensus       692 ~~~~~L~~L~l~~~~~l~~l~-----~~-~~~l~~L~~L~l~~c~  730 (779)
                      ..+++|++|+++++ .+....     .. ....++|++|++++|.
T Consensus       281 ~~~~~L~~L~Ls~n-~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~  324 (461)
T 1z7x_W          281 RAKESLKELSLAGN-ELGDEGARLLCETLLEPGCQLESLWVKSCS  324 (461)
T ss_dssp             HHCTTCCEEECTTC-CCHHHHHHHHHHHHTSTTCCCCEEECTTSC
T ss_pred             hhCCCcceEECCCC-CCchHHHHHHHHHhccCCccceeeEcCCCC
Confidence            34566666666653 332211     11 1123567777777764

>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=99.06  E-value=1.4e-08  Score=109.35  Aligned_cols=276  Identities=12%  Similarity=0.100  Sum_probs=157.9

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCC-CCEEEEEEe------chHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHN-FDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~-F~~~~wv~v------~~i~~~i~  225 (779)
                      ..|+||+++++.+.+++...  ....+.+.|+|++|+||||||+.+++.. ..... -...+|+..      ..+...++
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~-~~~~~~~~~~~~i~~~~~~~~~~~~~~i~   98 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKL-HKKFLGKFKHVYINTRQIDTPYRVLADLL   98 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHH-HHHTCSSCEEEEEEHHHHCSHHHHHHHHT
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHH-HHHhcCCceEEEEECCCCCCHHHHHHHHH
Confidence            67999999999999998752  3356789999999999999999999876 21110 224566665      34566666


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCC--Ccceeehhhccccc--------------cc--cCCCcEEEEEeCchhhh
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSP--KKFRIDLTELGVPL--------------QM--LNAGFKIVLKTRSAGVC  287 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l~~~~--------------~~--~~~gs~IivTTR~~~va  287 (779)
                      ..++....  ....+..+....+.+.+..  ++..+.+|++....              ..  ...+..+|+||+.....
T Consensus        99 ~~l~~~~~--~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~~  176 (386)
T 2qby_A           99 ESLDVKVP--FTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFV  176 (386)
T ss_dssp             TTTSCCCC--SSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGGG
T ss_pred             HHhCCCCC--CCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCChH
Confidence            66654311  0122334445555555543  35566666542211              00  23356678888876432


Q ss_pred             hhcC--------CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhC---CChhHHHHH-HHHh--c---
Q 004021          288 DQMD--------SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECG---RLPLALKTV-GRAM--K---  350 (779)
Q Consensus       288 ~~~~--------~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~---glPLai~~~-g~~l--~---  350 (779)
                      ..+.        ...+.+++++.++..+++...+.... ....--.+....|++.++   |.|..+..+ ....  .   
T Consensus       177 ~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~  255 (386)
T 2qby_A          177 DLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAF-KPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERM  255 (386)
T ss_dssp             GGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHB-CSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHT
T ss_pred             hhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhc-cCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhc
Confidence            2221        25789999999999999998764321 111222566778888887   998844432 2221  1   


Q ss_pred             C--CCChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccCC-C-cccChHHHHHHH----HH
Q 004021          351 S--QKKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYPE-D-YKIPKRSLIDYW----IS  422 (779)
Q Consensus       351 ~--~~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp~-~-~~i~~~~Li~~W----~a  422 (779)
                      .  .-+.+....++...             ....+.-++..+|+ ..+..+..++...+ + ..+....+.+..    -.
T Consensus       256 ~~~~i~~~~v~~a~~~~-------------~~~~~~~~~~~l~~-~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~  321 (386)
T 2qby_A          256 KDTKVKEEYVYMAKEEI-------------ERDRVRDIILTLPF-HSKLVLMAVVSISSEENVVSTTGAVYETYLNICKK  321 (386)
T ss_dssp             TCSSCCHHHHHHHHHHH-------------HHHHHHHHHHTSCH-HHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHH
T ss_pred             CCCccCHHHHHHHHHHH-------------hhchHHHHHHcCCH-HHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHh
Confidence            1  12344444433322             12345556778887 66665555553211 1 123333332221    12


Q ss_pred             cCCCc-chhhHHHHHHHHHHccccccc
Q 004021          423 EGFMA-DFDRGCEFINDLLHACLLEEE  448 (779)
Q Consensus       423 ~g~~~-~~~~~~~~l~~L~~~sll~~~  448 (779)
                      .|.-. .......+++.|...+++...
T Consensus       322 ~g~~~~~~~~~~~~l~~L~~~gli~~~  348 (386)
T 2qby_A          322 LGVEAVTQRRVSDIINELDMVGILTAK  348 (386)
T ss_dssp             HTCCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             cCCCCCCHHHHHHHHHHHHhCCCEEEE
Confidence            23211 114567889999999999763

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.02  E-value=6.2e-10  Score=105.61  Aligned_cols=122  Identities=24%  Similarity=0.254  Sum_probs=96.1

Q ss_pred             ccEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCcccccchh-hccCccCcEeeccCCc
Q 004021          497 AKRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTH  570 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~  570 (779)
                      .+.+++.++.+..+|....    .|++++| .+..+|. .++++++|++|++++|.++.+|.. +.++++|++|++++| 
T Consensus         9 ~~~l~~~~~~l~~~p~~~~~~l~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N-   86 (177)
T 2o6r_A            9 GTEIRCNSKGLTSVPTGIPSSATRLELESN-KLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHEN-   86 (177)
T ss_dssp             TTEEECCSSCCSSCCTTCCTTCSEEECCSS-CCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-
T ss_pred             CCEEEecCCCCccCCCCCCCCCcEEEeCCC-cccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCCC-
Confidence            4567777777777664322    4888888 7888765 468899999999999999998765 689999999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      .++.+|...+..+++|++|++++|.+..+              ....+..+++|+.|+++.|..
T Consensus        87 ~l~~~~~~~~~~l~~L~~L~l~~N~l~~~--------------~~~~~~~l~~L~~L~l~~N~~  136 (177)
T 2o6r_A           87 KLQSLPNGVFDKLTQLKELALDTNQLKSV--------------PDGIFDRLTSLQKIWLHTNPW  136 (177)
T ss_dssp             CCCCCCTTTTTTCTTCCEEECCSSCCSCC--------------CTTTTTTCTTCCEEECCSSCB
T ss_pred             CccccCHHHhhCCcccCEEECcCCcceEe--------------CHHHhcCCcccCEEEecCCCe
Confidence            67888887678999999999999988752              223356788999999987653

>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=99.02  E-value=2.9e-11  Score=134.05  Aligned_cols=183  Identities=19%  Similarity=0.062  Sum_probs=95.4

Q ss_pred             ccccccccccc-----cchhhcccccCceeeecCCccccc-----chh-hccCccCcEeeccCCcCCCC-----Cchhhh
Q 004021          517 LSLRRNDSLTE-----LPSRISSLVSLHHLDLSLTHIRGL-----PQE-LKALEKLRYLNLEYTHYLSI-----IPHQLI  580 (779)
Q Consensus       517 L~L~~~~~l~~-----lp~~i~~L~~L~~L~L~~~~i~~l-----p~~-~~~L~~L~~L~l~~~~~l~~-----lp~~~i  580 (779)
                      |+|++| .++.     +|..+..+++|++|++++|.+...     ++. +..+++|++|++++| .++.     +|.. +
T Consensus       204 L~L~~n-~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~n-~l~~~~~~~l~~~-l  280 (461)
T 1z7x_W          204 LKLESC-GVTSDNCRDLCGIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWEC-GITAKGCGDLCRV-L  280 (461)
T ss_dssp             EECTTS-CCBTTHHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTS-CCCHHHHHHHHHH-H
T ss_pred             EEccCC-CCcHHHHHHHHHHHHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcCC-CCCHHHHHHHHHH-H
Confidence            555555 4443     355555556666666666554432     111 224556666666665 3443     4443 5


Q ss_pred             cCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhc-CCCCCCceeEEeecccccccCCCCCcccCcccccccCcce
Q 004021          581 SGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELL-GLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKE  659 (779)
Q Consensus       581 ~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~  659 (779)
                      .++++|++|++++|.+....          .......+. ..++|+.|+++.|.......    .. .+.++..+++|+.
T Consensus       281 ~~~~~L~~L~Ls~n~i~~~~----------~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~----~~-l~~~l~~~~~L~~  345 (461)
T 1z7x_W          281 RAKESLKELSLAGNELGDEG----------ARLLCETLLEPGCQLESLWVKSCSFTAACC----SH-FSSVLAQNRFLLE  345 (461)
T ss_dssp             HHCTTCCEEECTTCCCHHHH----------HHHHHHHHTSTTCCCCEEECTTSCCBGGGH----HH-HHHHHHHCSSCCE
T ss_pred             hhCCCcceEECCCCCCchHH----------HHHHHHHhccCCccceeeEcCCCCCchHHH----HH-HHHHHhhCCCccE
Confidence            55566666666655443200          000111111 22455666555433211000    00 1234566789999


Q ss_pred             EEeccccccceecccccccCcccchhhccCCC-CCCCCccEEEccCCCCCc-----cccCCCCCCCCccEEeeeCCC
Q 004021          660 LEIIVCTEMEEIICVDKLRDVSDISEIIGSEH-NFFTQLESLGILYGPDLK-----SIYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       660 L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~L~~L~l~~~~~l~-----~l~~~~~~l~~L~~L~l~~c~  730 (779)
                      |+|++|......+.        .+.    ..+ ...++|+.|++++| .+.     .++..+..+++|++|++++|+
T Consensus       346 L~Ls~n~i~~~~~~--------~l~----~~l~~~~~~L~~L~L~~n-~i~~~~~~~l~~~l~~~~~L~~L~l~~N~  409 (461)
T 1z7x_W          346 LQISNNRLEDAGVR--------ELC----QGLGQPGSVLRVLWLADC-DVSDSSCSSLAATLLANHSLRELDLSNNC  409 (461)
T ss_dssp             EECCSSBCHHHHHH--------HHH----HHHTSTTCCCCEEECTTS-CCCHHHHHHHHHHHHHCCCCCEEECCSSS
T ss_pred             EEccCCccccccHH--------HHH----HHHcCCCCceEEEECCCC-CCChhhHHHHHHHHHhCCCccEEECCCCC
Confidence            99998743221111        000    111 13679999999986 455     566666678999999999985

>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=99.01  E-value=1e-11  Score=120.47  Aligned_cols=119  Identities=22%  Similarity=0.212  Sum_probs=92.9

Q ss_pred             cccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCccccc
Q 004021          524 SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEE  603 (779)
Q Consensus       524 ~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~  603 (779)
                      .++.+|..++++++|++|++++|.++.+| .+.++++|++|++++| .+..+|.. +..+++|++|++++|.+..     
T Consensus        36 ~l~~l~~~~~~l~~L~~L~ls~n~l~~l~-~~~~l~~L~~L~l~~n-~l~~l~~~-~~~~~~L~~L~L~~N~l~~-----  107 (198)
T 1ds9_A           36 PIEKMDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRN-LIKKIENL-DAVADTLEELWISYNQIAS-----  107 (198)
T ss_dssp             TCCCCHHHHHHTTTCSEEECSEEEESCCC-CHHHHTTCCEEEEEEE-EECSCSSH-HHHHHHCSEEEEEEEECCC-----
T ss_pred             cHhhhhHHHhcCCCCCEEECCCCCCcccc-ccccCCCCCEEECCCC-Ccccccch-hhcCCcCCEEECcCCcCCc-----
Confidence            56677778999999999999999999988 8899999999999999 67888875 7788999999999988774     


Q ss_pred             CCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccc
Q 004021          604 GNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEME  669 (779)
Q Consensus       604 ~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~  669 (779)
                                . ..+..+++|+.|+++.|....+..        +..+..+++|++|++++|+...
T Consensus       108 ----------l-~~~~~l~~L~~L~l~~N~i~~~~~--------~~~l~~l~~L~~L~l~~N~l~~  154 (198)
T 1ds9_A          108 ----------L-SGIEKLVNLRVLYMSNNKITNWGE--------IDKLAALDKLEDLLLAGNPLYN  154 (198)
T ss_dssp             ----------H-HHHHHHHHSSEEEESEEECCCHHH--------HHHHTTTTTCSEEEECSCHHHH
T ss_pred             ----------C-CccccCCCCCEEECCCCcCCchhH--------HHHHhcCCCCCEEEecCCcccc
Confidence                      2 256677888888888765432211        1346677888889988875433

>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=98.99  E-value=5.4e-10  Score=105.15  Aligned_cols=76  Identities=24%  Similarity=0.348  Sum_probs=36.9

Q ss_pred             cccccccccccchhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          518 SLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       518 ~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      ++++| .++.+|..+.  .+|++|+|++|.|+.+ |..|.++++|++|+|++| .++.+|++.+.++++|++|++++|.+
T Consensus        15 ~~s~n-~l~~ip~~~~--~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~f~~l~~L~~L~L~~N~l   90 (170)
T 3g39_A           15 DCSGK-SLASVPTGIP--TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNN-QLTVLPAGVFDKLTQLTQLSLNDNQL   90 (170)
T ss_dssp             ECTTS-CCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCC
T ss_pred             EeCCC-CcCccCccCC--CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCC-CcCccChhhccCCCCCCEEECCCCcc
Confidence            33344 4444444332  4455555555555554 333455555555555555 34455544344555555555555544


Q ss_pred             C
Q 004021          597 E  597 (779)
Q Consensus       597 ~  597 (779)
                      .
T Consensus        91 ~   91 (170)
T 3g39_A           91 K   91 (170)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.98  E-value=5.7e-10  Score=105.36  Aligned_cols=78  Identities=22%  Similarity=0.295  Sum_probs=44.1

Q ss_pred             ccccccccccccchhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++++++ .++.+|..+.  .+|++|+|++|.|+.+ |..|.++++|++|+|++| .++.+|.+.+.++++|++|++++|.
T Consensus        17 l~~~~n-~l~~iP~~~~--~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N-~l~~i~~~~~~~l~~L~~L~L~~N~   92 (174)
T 2r9u_A           17 VNCQNI-RLASVPAGIP--TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSN-KLTAIPTGVFDKLTQLTQLDLNDNH   92 (174)
T ss_dssp             EECCSS-CCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EEeCCC-CCCccCCCcC--CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCC-CCCccChhHhCCcchhhEEECCCCc
Confidence            444555 5555555443  5566666666666555 334556666666666666 4555555544566666666666665


Q ss_pred             CCC
Q 004021          596 SEG  598 (779)
Q Consensus       596 ~~~  598 (779)
                      +..
T Consensus        93 l~~   95 (174)
T 2r9u_A           93 LKS   95 (174)
T ss_dssp             CCC
T ss_pred             cce
Confidence            543

>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=98.97  E-value=1.2e-09  Score=102.80  Aligned_cols=101  Identities=24%  Similarity=0.320  Sum_probs=88.6

Q ss_pred             CccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCcEeeccCC
Q 004021          496 GAKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYT  569 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~  569 (779)
                      ..+.+++++|.+..+|....    .|+|++| .+..+ |..|.++++|++|+|++|.|+.+|.. |.++++|++|+|++|
T Consensus        10 ~~~~l~~s~n~l~~ip~~~~~~l~~L~L~~N-~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N   88 (170)
T 3g39_A           10 SGTTVDCSGKSLASVPTGIPTTTQVLYLYDN-QITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDN   88 (170)
T ss_dssp             ETTEEECTTSCCSSCCSCCCTTCSEEECCSS-CCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CCCEEEeCCCCcCccCccCCCCCcEEEcCCC-cCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCC
Confidence            34678999999988876433    5999999 99988 67799999999999999999999876 589999999999999


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                       .++.+|++.+.++++|++|++++|.+..
T Consensus        89 -~l~~~~~~~~~~l~~L~~L~L~~N~~~c  116 (170)
T 3g39_A           89 -QLKSIPRGAFDNLKSLTHIWLLNNPWDC  116 (170)
T ss_dssp             -CCCCCCTTTTTTCTTCCEEECCSSCBCT
T ss_pred             -ccCEeCHHHhcCCCCCCEEEeCCCCCCC
Confidence             6888998778999999999999998764

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.96  E-value=2.8e-08  Score=107.16  Aligned_cols=274  Identities=10%  Similarity=0.041  Sum_probs=162.0

Q ss_pred             ccccchhhhHHHHHHHHhc----cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCC-CCEEEEEEe------chHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHN-FDVVIWAAV------QTFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~-F~~~~wv~v------~~i~~~  223 (779)
                      +.++||+.+++++.+++..    ..+..+.+.|+|.+|+||||||+.+++..   ... -..++|+..      ..+...
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~---~~~~~~~~~~i~~~~~~~~~~~~~~   93 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY---KDKTTARFVYINGFIYRNFTAIIGE   93 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH---TTSCCCEEEEEETTTCCSHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHH---hhhcCeeEEEEeCccCCCHHHHHHH
Confidence            5689999999999999876    22223489999999999999999999887   222 124566664      356777


Q ss_pred             HHHHhCCCcchhhhhcchhhHHHHHHHhhC--CCcceeehhhcccc-----------ccc-cC---CCcEEEEEeCchhh
Q 004021          224 IGKRIGFSEDKKWKEKSLQDKAVDISSILS--PKKFRIDLTELGVP-----------LQM-LN---AGFKIVLKTRSAGV  286 (779)
Q Consensus       224 i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~~~~ld~l~~~-----------~~~-~~---~gs~IivTTR~~~v  286 (779)
                      ++..++....  ....+.......+...+.  +++..+.+|++...           +.. ..   .+..||+||+....
T Consensus        94 l~~~l~~~~~--~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~  171 (389)
T 1fnn_A           94 IARSLNIPFP--RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAV  171 (389)
T ss_dssp             HHHHTTCCCC--SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHH
T ss_pred             HHHHhCccCC--CCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchH
Confidence            7777764311  012233444555555553  44555666654221           100 11   46778888887643


Q ss_pred             hhhc--------CCceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHh---------CCChhHHHHHHHH-
Q 004021          287 CDQM--------DSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLAREC---------GRLPLALKTVGRA-  348 (779)
Q Consensus       287 a~~~--------~~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c---------~glPLai~~~g~~-  348 (779)
                      ....        ....+.+++++.++..+++...+..... ...--.+....|++.+         +|.|..+..+... 
T Consensus       172 ~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a  250 (389)
T 1fnn_A          172 LNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLA-EGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRS  250 (389)
T ss_dssp             HHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBC-TTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHH
T ss_pred             HHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHH
Confidence            3222        1236999999999999999988754210 1112256788999999         7887554433322 


Q ss_pred             h--c---CC--CChhHHHHHHHHHhcccCcCCCchHHHHHHHHHHHhcCCccchhhhhhhccccC---CCcccChHHHHH
Q 004021          349 M--K---SQ--KKVGDRERAIEKMRTSASTFSGMEENVFLRLKFSYDSLSMDKLRSCLLYCCLYP---EDYKIPKRSLID  418 (779)
Q Consensus       349 l--~---~~--~~~~~w~~~~~~l~~~~~~~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~s~fp---~~~~i~~~~Li~  418 (779)
                      .  .   ..  -+.+....+......             ..+.-.+..|+. +.+.++..++.+.   .+..+....+..
T Consensus       251 ~~~a~~~~~~~i~~~~v~~~~~~~~~-------------~~~~~~l~~l~~-~~~~~L~~l~~~~~~~~~~~~~~~~i~~  316 (389)
T 1fnn_A          251 AYAAQQNGRKHIAPEDVRKSSKEVLF-------------GISEEVLIGLPL-HEKLFLLAIVRSLKISHTPYITFGDAEE  316 (389)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHSC-------------CCCHHHHHHSCH-HHHHHHHHHHHHHHHHCSSCEEHHHHHH
T ss_pred             HHHHHHhCCCCcCHHHHHHHHHHHhh-------------hhHHHHHHcCCH-HHHHHHHHHHHHHhhccCCCccHHHHHH
Confidence            1  1   11  122222222222111             112234566777 6777776666543   221455566655


Q ss_pred             HHHH----cCCCc-chhhHHHHHHHHHHccccccc
Q 004021          419 YWIS----EGFMA-DFDRGCEFINDLLHACLLEEE  448 (779)
Q Consensus       419 ~W~a----~g~~~-~~~~~~~~l~~L~~~sll~~~  448 (779)
                      .+..    .|... .......++.+|...+++...
T Consensus       317 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~~gli~~~  351 (389)
T 1fnn_A          317 SYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETR  351 (389)
T ss_dssp             HHHHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEEE
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEe
Confidence            4433    23222 125677889999999999874

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.95  E-value=1.4e-09  Score=102.59  Aligned_cols=100  Identities=21%  Similarity=0.282  Sum_probs=87.8

Q ss_pred             ccEEEcccccccccccCcc----ccccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCcEeeccCCc
Q 004021          497 AKRISLMANEIESLSEIPT----LLSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTH  570 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~  570 (779)
                      .+.+++++|.+..+|....    .|+|++| .+..+ |..|.++++|++|+|++|.|+.+|.. |.++++|++|+|++| 
T Consensus        14 ~~~l~~~~n~l~~iP~~~~~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N-   91 (174)
T 2r9u_A           14 QTLVNCQNIRLASVPAGIPTDKQRLWLNNN-QITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDN-   91 (174)
T ss_dssp             SSEEECCSSCCSSCCSCCCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-
T ss_pred             CcEEEeCCCCCCccCCCcCCCCcEEEeCCC-CccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCC-
Confidence            3678888888888876433    5999999 88888 66899999999999999999999886 589999999999999 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      .++.+|++.+..+++|++|++++|.+..
T Consensus        92 ~l~~l~~~~~~~l~~L~~L~L~~N~~~c  119 (174)
T 2r9u_A           92 HLKSIPRGAFDNLKSLTHIYLYNNPWDC  119 (174)
T ss_dssp             CCCCCCTTTTTTCTTCSEEECCSSCBCT
T ss_pred             ccceeCHHHhccccCCCEEEeCCCCccc
Confidence            7889998778999999999999998775

>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=98.95  E-value=4.2e-10  Score=128.92  Aligned_cols=61  Identities=10%  Similarity=-0.002  Sum_probs=34.8

Q ss_pred             CCCCCccEEEccCCCC-Cccc-cC-CCCCCCCccEEeeeCCCCCCC--CCCCCC-CcccccEEEechH
Q 004021          692 NFFTQLESLGILYGPD-LKSI-YP-NPLHFPKLKKIGVYGCPKLKK--LPINSS-SAKERRVVIEGLK  753 (779)
Q Consensus       692 ~~~~~L~~L~l~~~~~-l~~l-~~-~~~~l~~L~~L~l~~c~~L~~--lP~~~~-~~~~~~l~i~~~~  753 (779)
                      .++++|+.|++++|++ +..- .. ....+++|++|++++|. +..  +|..+. ..+++.+.|++|+
T Consensus       433 ~~~~~L~~L~L~~~~~~l~~~~~~~~~~~~~~L~~L~L~~n~-l~~~~~~~~~~~~~~L~~L~l~~n~  499 (592)
T 3ogk_B          433 IGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVG-ESDEGLMEFSRGCPNLQKLEMRGCC  499 (592)
T ss_dssp             HHCTTCCEEEEECCGGGCCHHHHHHHHHSCTTCCEEEECSCC-SSHHHHHHHHTCCTTCCEEEEESCC
T ss_pred             HhCCCCCEEEEecCCCCccHHHHHHHHHhCccceEeeccCCC-CCHHHHHHHHhcCcccCeeeccCCC
Confidence            4577888888876543 2111 11 11247888999988875 432  232222 2345888888774

>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=98.94  E-value=2.1e-10  Score=131.47  Aligned_cols=118  Identities=11%  Similarity=0.077  Sum_probs=57.1

Q ss_pred             hcccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCC-----CCchhhhcCCccCcEeeeccccCCCccc
Q 004021          532 ISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLS-----IIPHQLISGFLKLEVLRLLECGSEGVTK  601 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~-----~lp~~~i~~L~~L~~L~l~~~~~~~~~~  601 (779)
                      +.++++|++|+|++|.+..     ++..+.++++|++|++++|. +.     .++.- +.++++|++|++.+|.+.+   
T Consensus       160 ~~~~~~L~~L~L~~~~~~~~~~~~l~~~~~~~~~L~~L~L~~n~-~~~~~~~~l~~~-~~~~~~L~~L~L~~~~~~~---  234 (592)
T 3ogk_B          160 VTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYMTE-FAKISPKDLETI-ARNCRSLVSVKVGDFEILE---  234 (592)
T ss_dssp             HHHCTTCSEEECTTCEEECCCSHHHHHHHHHCCCCCEEECTTCC-CSSCCHHHHHHH-HHHCTTCCEEECSSCBGGG---
T ss_pred             HhhCCCCCEEECccccccCcchhHHHHHHhcCCCccEEEeeccC-CCccCHHHHHHH-HhhCCCCcEEeccCccHHH---
Confidence            3455666666666665432     22334455666666666552 22     22221 3455666666666554432   


Q ss_pred             ccCCccCCCchhhHHhhcCCCCCCceeEEeecc--------cccccCCCCCcc---------cCcccccccCcceEEecc
Q 004021          602 EEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS--------LAVQKFFKYPKL---------DLTWLVFVQNLKELEIIV  664 (779)
Q Consensus       602 ~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~--------~~~~~~~~L~~L---------~~~~l~~l~~L~~L~L~~  664 (779)
                                  .+..+..+++|+.|+++....        ..+..+++|+.|         .+..+..+++|++|+|++
T Consensus       235 ------------l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~  302 (592)
T 3ogk_B          235 ------------LVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLY  302 (592)
T ss_dssp             ------------GHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGGGGCCEEEETT
T ss_pred             ------------HHHHHhhhhHHHhhcccccccccchHHHHHHhhccccccccCccccchhHHHHHHhhcCCCcEEecCC
Confidence                        233444455555555542111        112233333333         122344566777777777


Q ss_pred             cc
Q 004021          665 CT  666 (779)
Q Consensus       665 ~~  666 (779)
                      |.
T Consensus       303 ~~  304 (592)
T 3ogk_B          303 AL  304 (592)
T ss_dssp             CC
T ss_pred             Cc
Confidence            65

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.87  E-value=2.4e-10  Score=110.65  Aligned_cols=127  Identities=19%  Similarity=0.211  Sum_probs=97.2

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .+..+| .+.++++|++|++++|.++.+|..+..+++|++|++++| .++.+|.  ++.+++|++|++++|.+
T Consensus        53 L~ls~n-~l~~l~-~~~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~~L~L~~N-~l~~l~~--~~~l~~L~~L~l~~N~i  127 (198)
T 1ds9_A           53 LALSTN-NIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYN-QIASLSG--IEKLVNLRVLYMSNNKI  127 (198)
T ss_dssp             EECSEE-EESCCC-CHHHHTTCCEEEEEEEEECSCSSHHHHHHHCSEEEEEEE-ECCCHHH--HHHHHHSSEEEESEEEC
T ss_pred             EECCCC-CCcccc-ccccCCCCCEEECCCCCcccccchhhcCCcCCEEECcCC-cCCcCCc--cccCCCCCEEECCCCcC
Confidence            788888 888888 899999999999999999999998888999999999999 6788874  88999999999999988


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCC-CCCcccCcccccccCcceEE
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFF-KYPKLDLTWLVFVQNLKELE  661 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~-~L~~L~~~~l~~l~~L~~L~  661 (779)
                      ..             ...+..+..+++|+.|+++.|.......-. .........+..+++|+.|+
T Consensus       128 ~~-------------~~~~~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~~~~~~~~l~~L~~Ld  180 (198)
T 1ds9_A          128 TN-------------WGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLD  180 (198)
T ss_dssp             CC-------------HHHHHHHTTTTTCSEEEECSCHHHHHHHTTTTHHHHHHHHHHHCSSCSEEC
T ss_pred             Cc-------------hhHHHHHhcCCCCCEEEecCCccccccccccchHHHHHHHHHhCCCcEEEC
Confidence            74             233457888999999999877653321100 00001112356788888886

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.86  E-value=2e-08  Score=100.42  Aligned_cols=187  Identities=12%  Similarity=0.121  Sum_probs=108.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCc-
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSE-  232 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~-  232 (779)
                      ..++||+..++.+..++..+. ..+.+.|+|.+|+||||||+.+++.. .....+..  +.+. ......+........ 
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   98 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGL-NCETGITA--TPCGVCDNCREIEQGRFVDLI   98 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHH-HCTTCSCS--SCCSCSHHHHHHHTTCCSSEE
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHh-cCCCCCCC--CCCcccHHHHHHhccCCcceE
Confidence            468999999999999998753 23588999999999999999999876 22111100  0000 000111111000000 


Q ss_pred             chhhhhcchhhHHHHHHHhh-----CCCcceeehhhcccc-----------ccccCCCcEEEEEeCchh-hhhhc-C-Cc
Q 004021          233 DKKWKEKSLQDKAVDISSIL-----SPKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSAG-VCDQM-D-SK  293 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L-----~~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~~-va~~~-~-~~  293 (779)
                      ...............+.+.+     .+++..+.+|++...           +.....+..+|+||+... +.... . ..
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l~~r~~  178 (250)
T 1njg_A           99 EIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL  178 (250)
T ss_dssp             EEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             EecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHHHHHhh
Confidence            00000001111122222322     233455556655221           122245778888887643 22211 2 46


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRA  348 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~  348 (779)
                      .+.+++++.++..+++...+.......+   .+....|++.|+|.|..+..+...
T Consensus       179 ~i~l~~l~~~e~~~~l~~~~~~~~~~~~---~~~~~~l~~~~~G~~~~~~~~~~~  230 (250)
T 1njg_A          179 QFHLKALDVEQIRHQLEHILNEEHIAHE---PRALQLLARAAEGSLRDALSLTDQ  230 (250)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHTTCCBC---HHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hccCCCCCHHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHcCCCHHHHHHHHHH
Confidence            7899999999999999988765432211   467889999999999998876654

>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=98.84  E-value=4.8e-10  Score=128.55  Aligned_cols=76  Identities=21%  Similarity=0.278  Sum_probs=34.1

Q ss_pred             ccccccccccc--cchhhcccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCCCCchh----hhcCCcc
Q 004021          517 LSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLSIIPHQ----LISGFLK  585 (779)
Q Consensus       517 L~L~~~~~l~~--lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~lp~~----~i~~L~~  585 (779)
                      |+|++|..++.  ++..+.++++|++|+|++|.++.     ++.....+++|++|++++|.  ..++..    ++.++++
T Consensus       135 L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~~~~~L~~L~l~~~~--~~~~~~~l~~l~~~~~~  212 (594)
T 2p1m_B          135 LVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDTYTSLVSLNISCLA--SEVSFSALERLVTRCPN  212 (594)
T ss_dssp             EEEESCEEEEHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCTTCCCCCEEECTTCC--SCCCHHHHHHHHHHCTT
T ss_pred             EeCCCcCCCCHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhhcCCcCcEEEecccC--CcCCHHHHHHHHHhCCC
Confidence            45554433332  33333455556666665554432     22222344555555555552  122211    1233455


Q ss_pred             CcEeeeccc
Q 004021          586 LEVLRLLEC  594 (779)
Q Consensus       586 L~~L~l~~~  594 (779)
                      |++|++.+|
T Consensus       213 L~~L~L~~~  221 (594)
T 2p1m_B          213 LKSLKLNRA  221 (594)
T ss_dssp             CCEEECCTT
T ss_pred             CcEEecCCC
Confidence            555555555

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=98.74  E-value=6.6e-08  Score=101.61  Aligned_cols=211  Identities=12%  Similarity=0.048  Sum_probs=136.1

Q ss_pred             cCCccEEEcccccccc--cccC----cccccccccccccccc-hhhcc--------cccCceeeecCCcccccchh-hcc
Q 004021          494 WEGAKRISLMANEIES--LSEI----PTLLSLRRNDSLTELP-SRISS--------LVSLHHLDLSLTHIRGLPQE-LKA  557 (779)
Q Consensus       494 ~~~lr~l~l~~~~~~~--l~~~----~~lL~L~~~~~l~~lp-~~i~~--------L~~L~~L~L~~~~i~~lp~~-~~~  557 (779)
                      +.+++.|+|++|.+..  ....    ..++.+..+    .+| ..|.+        +.+|+.|+|.+ .++.++.. |.+
T Consensus        48 l~~L~~LdLs~n~i~~~~~~~~~~~~~~~~~~~~~----~I~~~aF~~~~~~~~~g~~~L~~l~L~~-~i~~I~~~aF~~  122 (329)
T 3sb4_A           48 FPSLKVLDISNAEIKMYSGKAGTYPNGKFYIYMAN----FVPAYAFSNVVNGVTKGKQTLEKVILSE-KIKNIEDAAFKG  122 (329)
T ss_dssp             CTTCCEEEEEEEEECCEEESSSSSGGGCCEEECTT----EECTTTTEEEETTEEEECTTCCC-CBCT-TCCEECTTTTTT
T ss_pred             hccCeEEecCcceeEEecCcccccccccccccccc----ccCHHHhcccccccccccCCCcEEECCc-cccchhHHHhhc
Confidence            4678899999888872  2211    012333333    343 34667        99999999998 88888764 899


Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC----CCcccccC-C--c------------------------
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS----EGVTKEEG-N--V------------------------  606 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~----~~~~~~~~-~--~------------------------  606 (779)
                      |++|+.|++.+| .+..+++..|..+.++..+.......    ..+....+ +  .                        
T Consensus       123 ~~~L~~l~l~~n-~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~~L~~~i~~~~~~~l~~~~~~~~~~~  201 (329)
T 3sb4_A          123 CDNLKICQIRKK-TAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGEPLETTIQVGAMGKLEDEIMKAGLQP  201 (329)
T ss_dssp             CTTCCEEEBCCS-SCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESCCCEEEEEECTTCCHHHHHHHTTCCG
T ss_pred             CcccceEEcCCC-CccccchhhhcCCCceEEecCcchhhhhccccccccccccccccceeEEecCCCcHHHHHhhcccCc
Confidence            999999999998 56778887788877777776544110    00000000 0  0                        


Q ss_pred             -------c-CCCchhhHHhhc-CCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccc
Q 004021          607 -------L-CDDAEPLMRELL-GLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKL  677 (779)
Q Consensus       607 -------~-~~~~~~~~~~l~-~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~  677 (779)
                             . ..........+. .+++|+.|+++.+         +++.+....+..+++|+.|+|..+  +..+..    
T Consensus       202 ~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n---------~i~~I~~~aF~~~~~L~~l~l~~n--i~~I~~----  266 (329)
T 3sb4_A          202 RDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKT---------NATTIPDFTFAQKKYLLKIKLPHN--LKTIGQ----  266 (329)
T ss_dssp             GGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTB---------CCCEECTTTTTTCTTCCEEECCTT--CCEECT----
T ss_pred             cccceEEEeeeecHHHHHHHHHhcCCCeEEECCCC---------CcceecHhhhhCCCCCCEEECCcc--cceehH----
Confidence                   0 000000111111 2688999988733         355555566788889999999874  666665    


Q ss_pred             cCcccchhhccCCCCCCCCcc-EEEccCCCCCccccC-CCCCCCCccEEeeeCCCCCCCCCCCC
Q 004021          678 RDVSDISEIIGSEHNFFTQLE-SLGILYGPDLKSIYP-NPLHFPKLKKIGVYGCPKLKKLPINS  739 (779)
Q Consensus       678 ~~~~~~~~~~~~~~~~~~~L~-~L~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~~L~~lP~~~  739 (779)
                                 ..+.++++|+ .|.+.+  +++.++. .+..+++|+.|++.+ .+++.++...
T Consensus       267 -----------~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~L~~l~l~~-n~i~~I~~~a  316 (329)
T 3sb4_A          267 -----------RVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDNLRYVLATG-DKITTLGDEL  316 (329)
T ss_dssp             -----------TTTTTCTTCCEEEEECT--TCCEECTTTTTTCTTEEEEEECS-SCCCEECTTT
T ss_pred             -----------HHhhCChhccEEEEEcc--cceEEchhhhhCCccCCEEEeCC-CccCccchhh
Confidence                       5778889998 999986  6777765 455788999999865 3577777643

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.70  E-value=2.3e-07  Score=91.20  Aligned_cols=167  Identities=15%  Similarity=0.153  Sum_probs=101.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|+++.++.+.+++...  ..+.+.|+|.+|+|||++|+.+++.. .. ..+. ..+.+....              
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~l~~~~-~~-~~~~~~~~~~~~~~--------------   78 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERK--NIPHLLFSGPPGTGKTATAIALARDL-FG-ENWRDNFIEMNASD--------------   78 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT--CCCCEEEECSTTSSHHHHHHHHHHHH-HG-GGGGGGEEEEETTC--------------
T ss_pred             HHHcCcHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHH-hc-cccccceEEecccc--------------
Confidence            46899999999999999876  33448999999999999999999875 11 1111 122222100              


Q ss_pred             hhhhhcchhhHHHHHHHhh------CCCcceeehhhcccc-----------ccccCCCcEEEEEeCchhh-hhhc-C-Cc
Q 004021          234 KKWKEKSLQDKAVDISSIL------SPKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSAGV-CDQM-D-SK  293 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L------~~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~~v-a~~~-~-~~  293 (779)
                          ..........+....      .+++..+.+|++...           +.....+.++|+||+...- .... . ..
T Consensus        79 ----~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~  154 (226)
T 2chg_A           79 ----ERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCA  154 (226)
T ss_dssp             ----TTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             ----ccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCc
Confidence                000111111122221      123334444444221           1223456788988886432 1111 2 34


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      .+.+.+++.++..+++.+.+.......+   .+....|++.++|.|..+..+.
T Consensus       155 ~i~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~~l~~~~~g~~r~l~~~l  204 (226)
T 2chg_A          155 VFRFKPVPKEAMKKRLLEICEKEGVKIT---EDGLEALIYISGGDFRKAINAL  204 (226)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHHTTCHHHHHHHH
T ss_pred             eeecCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHH
Confidence            7899999999999999988765432211   4677889999999998655443

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=98.69  E-value=9.1e-08  Score=100.53  Aligned_cols=169  Identities=12%  Similarity=0.047  Sum_probs=99.7

Q ss_pred             CccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccC------CCchhh--------HHhhcCCCC
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLC------DDAEPL--------MRELLGLKR  623 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~------~~~~~~--------~~~l~~L~~  623 (779)
                      +++|+.|++.+  .++.++.+.|.++++|+.|++..|.+..++...+....      ......        ...+..+.+
T Consensus       100 ~~~L~~l~L~~--~i~~I~~~aF~~~~~L~~l~l~~n~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~~  177 (329)
T 3sb4_A          100 KQTLEKVILSE--KIKNIEDAAFKGCDNLKICQIRKKTAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGEP  177 (329)
T ss_dssp             CTTCCC-CBCT--TCCEECTTTTTTCTTCCEEEBCCSSCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESCC
T ss_pred             cCCCcEEECCc--cccchhHHHhhcCcccceEEcCCCCccccchhhhcCCCceEEecCcchhhhhccccccccccccccc
Confidence            99999999998  47889998899999999999999877654433322100      000000        000111111


Q ss_pred             CC-ceeEEeeccccc--------ccCCCCCcccC---------ccc-ccccCcceEEeccccccceecccccccCcccch
Q 004021          624 LN-VLSWSFRSSLAV--------QKFFKYPKLDL---------TWL-VFVQNLKELEIIVCTEMEEIICVDKLRDVSDIS  684 (779)
Q Consensus       624 L~-~L~l~~~~~~~~--------~~~~~L~~L~~---------~~l-~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~  684 (779)
                      |+ .+.+..  ...+        ....++..+..         ..+ ..+++|+.|+|++|+ +..++.           
T Consensus       178 L~~~i~~~~--~~~l~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n~-i~~I~~-----------  243 (329)
T 3sb4_A          178 LETTIQVGA--MGKLEDEIMKAGLQPRDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKTN-ATTIPD-----------  243 (329)
T ss_dssp             CEEEEEECT--TCCHHHHHHHTTCCGGGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTBC-CCEECT-----------
T ss_pred             cceeEEecC--CCcHHHHHhhcccCccccceEEEeeeecHHHHHHHHHhcCCCeEEECCCCC-cceecH-----------
Confidence            11 011100  0000        00111111100         001 137899999999854 677766           


Q ss_pred             hhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCcc-EEeeeCCCCCCCCCCCC-CCc-ccccEEEe
Q 004021          685 EIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLK-KIGVYGCPKLKKLPINS-SSA-KERRVVIE  750 (779)
Q Consensus       685 ~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~-~L~l~~c~~L~~lP~~~-~~~-~~~~l~i~  750 (779)
                          ..+.++++|+.|.|.+  +++.++.. +..+++|+ .+.+.+  +++.++... ..+ .++.+.+.
T Consensus       244 ----~aF~~~~~L~~l~l~~--ni~~I~~~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~L~~l~l~  305 (329)
T 3sb4_A          244 ----FTFAQKKYLLKIKLPH--NLKTIGQRVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDNLRYVLAT  305 (329)
T ss_dssp             ----TTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCEEEEECT--TCCEECTTTTTTCTTEEEEEEC
T ss_pred             ----hhhhCCCCCCEEECCc--ccceehHHHhhCChhccEEEEEcc--cceEEchhhhhCCccCCEEEeC
Confidence                5788999999999987  48888774 45788999 999987  688887543 222 33656553

>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=98.65  E-value=3.3e-09  Score=121.48  Aligned_cols=37  Identities=14%  Similarity=-0.055  Sum_probs=22.6

Q ss_pred             CCCCCccEEEccCCCCCcccc-CCCC-CCCCccEEeeeCCC
Q 004021          692 NFFTQLESLGILYGPDLKSIY-PNPL-HFPKLKKIGVYGCP  730 (779)
Q Consensus       692 ~~~~~L~~L~l~~~~~l~~l~-~~~~-~l~~L~~L~l~~c~  730 (779)
                      ..+++|+.|++++  .+.... ..+. .+++|+.|++++|.
T Consensus       429 ~~~~~L~~L~L~~--~l~~~~~~~l~~~~~~L~~L~L~~~~  467 (594)
T 2p1m_B          429 EHCKDLRRLSLSG--LLTDKVFEYIGTYAKKMEMLSVAFAG  467 (594)
T ss_dssp             HHCTTCCEEECCS--SCCHHHHHHHHHHCTTCCEEEEESCC
T ss_pred             hhCCCccEEeecC--cccHHHHHHHHHhchhccEeeccCCC
Confidence            4567788887755  332211 1122 37889999998875

>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=98.60  E-value=4e-07  Score=95.37  Aligned_cols=185  Identities=14%  Similarity=0.123  Sum_probs=106.0

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech--HHHHHHHHhC
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT--FQDDIGKRIG  229 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~--i~~~i~~~l~  229 (779)
                      ..++|++..++.+.+++...   ......|.|+|.+|+|||++|+++++..   ...|   .++....  -..++...+.
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~---~~~~---~~~~~~~~~~~~~l~~~l~   85 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL---GVNL---RVTSGPAIEKPGDLAAILA   85 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH---TCCE---EEECTTTCCSHHHHHHHHT
T ss_pred             HHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh---CCCE---EEEeccccCChHHHHHHHH
Confidence            56899999999988887631   2244678899999999999999999876   2222   3343311  1122222222


Q ss_pred             C----Ccc---hhhhhcchhhHHHHHHHhhCCCcceeehhhcccc--ccccCCCcEEEEEeCchh-hhhhc-C--CceeE
Q 004021          230 F----SED---KKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP--LQMLNAGFKIVLKTRSAG-VCDQM-D--SKNLE  296 (779)
Q Consensus       230 ~----~~~---~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~--~~~~~~gs~IivTTR~~~-va~~~-~--~~~~~  296 (779)
                      .    ...   +..+..+ ......+...+.+..+..+...-...  ......+..+|.||.... +...+ .  ...+.
T Consensus        86 ~~~~~~~~l~lDEi~~l~-~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~  164 (324)
T 1hqc_A           86 NSLEEGDILFIDEIHRLS-RQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEH  164 (324)
T ss_dssp             TTCCTTCEEEETTTTSCC-HHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEE
T ss_pred             HhccCCCEEEEECCcccc-cchHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEe
Confidence            1    100   0001111 22344455555554443322211000  001113456777776532 21111 1  35789


Q ss_pred             ccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHh
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAM  349 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l  349 (779)
                      +.+++.++...++.+.+.......   -.+....+++.|+|.|-.+..+...+
T Consensus       165 l~~~~~~e~~~~l~~~~~~~~~~~---~~~~~~~l~~~~~G~~r~l~~~l~~~  214 (324)
T 1hqc_A          165 LEYYTPEELAQGVMRDARLLGVRI---TEEAALEIGRRSRGTMRVAKRLFRRV  214 (324)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCCC---CHHHHHHHHHHSCSCHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            999999999999988876543222   25678899999999998887665543

>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=98.60  E-value=4.3e-08  Score=103.89  Aligned_cols=97  Identities=20%  Similarity=0.290  Sum_probs=62.7

Q ss_pred             EEEcccc-cccccccCcc-----cccccc-cccccccc-hhhcccccCceeeecCCcccccch-hhccCccCcEeeccCC
Q 004021          499 RISLMAN-EIESLSEIPT-----LLSLRR-NDSLTELP-SRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYT  569 (779)
Q Consensus       499 ~l~l~~~-~~~~l~~~~~-----lL~L~~-~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~  569 (779)
                      .++++++ .+..+|....     .|+|++ | .+..+| ..|++|.+|++|+|++|.|+.+|+ .|.+|++|++|+|++|
T Consensus        12 ~v~~~~~n~l~~ip~l~~~~~L~~L~l~~~n-~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N   90 (347)
T 2ifg_A           12 GLRCTRDGALDSLHHLPGAENLTELYIENQQ-HLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFN   90 (347)
T ss_dssp             CEECCSSCCCTTTTTSCSCSCCSEEECCSCS-SCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSS
T ss_pred             EEEcCCCCCCCccCCCCCCCCeeEEEccCCC-CCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCC
Confidence            4566665 5666655222     277775 6 677665 457777777777777777777654 4677777777777777


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                       .+..+|++.+..+. |++|++.+|.+..
T Consensus        91 -~l~~~~~~~~~~~~-L~~l~l~~N~~~c  117 (347)
T 2ifg_A           91 -ALESLSWKTVQGLS-LQELVLSGNPLHC  117 (347)
T ss_dssp             -CCSCCCSTTTCSCC-CCEEECCSSCCCC
T ss_pred             -ccceeCHHHcccCC-ceEEEeeCCCccC
Confidence             56677766444444 7777777776553

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.46  E-value=9.7e-07  Score=92.30  Aligned_cols=170  Identities=14%  Similarity=0.194  Sum_probs=101.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|++..++.+.+++..+  ..+.+.|+|++|+||||+|+.+++.. .. ..+. ..+++....             .
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l-~~-~~~~~~~~~~~~~~-------------~   83 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDG--NMPHMIISGMPGIGKTTSVHCLAHEL-LG-RSYADGVLELNASD-------------D   83 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC--CCCCEEEECSTTSSHHHHHHHHHHHH-HG-GGHHHHEEEECTTS-------------C
T ss_pred             HHHHCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHh-cC-CcccCCEEEecCcc-------------c
Confidence            56899999999999999876  33348999999999999999999875 11 1111 122222110             0


Q ss_pred             hhhhhcchhhHHHHHHH---hh-CCCcceeehhhcccc-----------ccccCCCcEEEEEeCchh-hhhhc-C-Ccee
Q 004021          234 KKWKEKSLQDKAVDISS---IL-SPKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSAG-VCDQM-D-SKNL  295 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~---~L-~~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~~-va~~~-~-~~~~  295 (779)
                        .......+....+..   .+ .+++..+.+|++...           +.....++.+|+||+... +.... . ...+
T Consensus        84 --~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~~i  161 (323)
T 1sxj_B           84 --RGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCAIL  161 (323)
T ss_dssp             --CSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEE
T ss_pred             --cChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhceEE
Confidence              000011111111110   11 233445555554221           122245678888887633 22222 2 4588


Q ss_pred             EccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH-HHHHH
Q 004021          296 EVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA-LKTVG  346 (779)
Q Consensus       296 ~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa-i~~~g  346 (779)
                      .+.+++.++..+++...+...+...+   .+....|++.|+|.|.. +..+.
T Consensus       162 ~~~~~~~~~~~~~l~~~~~~~~~~~~---~~~~~~l~~~~~G~~r~a~~~l~  210 (323)
T 1sxj_B          162 RYSKLSDEDVLKRLLQIIKLEDVKYT---NDGLEAIIFTAEGDMRQAINNLQ  210 (323)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             eecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHHHH
Confidence            99999999999999988764432211   46778999999999954 44443

>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=98.43  E-value=2.6e-07  Score=97.86  Aligned_cols=102  Identities=23%  Similarity=0.256  Sum_probs=81.8

Q ss_pred             ccccccccccccchhhcccccCceeeecC-Ccccccc-hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSL-THIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~-~~i~~lp-~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      ++++++..+..+|. |..+.+|++|+|++ |.++.+| ..|++|++|++|+|++| .++.+|++.|++|++|++|+|++|
T Consensus        13 v~~~~~n~l~~ip~-l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l~~N   90 (347)
T 2ifg_A           13 LRCTRDGALDSLHH-LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRLNLSFN   90 (347)
T ss_dssp             EECCSSCCCTTTTT-SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEEECCSS
T ss_pred             EEcCCCCCCCccCC-CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCC-ccceeCHHHhcCCcCCCEEeCCCC
Confidence            46666436888999 99999999999996 9999988 46999999999999999 688888776899999999999999


Q ss_pred             cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccc
Q 004021          595 GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       595 ~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                      .+..++.              ..+..++ |+.|++..|...
T Consensus        91 ~l~~~~~--------------~~~~~~~-L~~l~l~~N~~~  116 (347)
T 2ifg_A           91 ALESLSW--------------KTVQGLS-LQELVLSGNPLH  116 (347)
T ss_dssp             CCSCCCS--------------TTTCSCC-CCEEECCSSCCC
T ss_pred             ccceeCH--------------HHcccCC-ceEEEeeCCCcc
Confidence            8886332              2233344 888888866543

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.37  E-value=5.8e-06  Score=88.83  Aligned_cols=187  Identities=17%  Similarity=0.044  Sum_probs=109.5

Q ss_pred             ccccc-chhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccc
Q 004021          524 SLTEL-PSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKE  602 (779)
Q Consensus       524 ~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~  602 (779)
                      .+..+ +..|.++.+|+.+++.+|.++.+|...-...+|+.+.+..+  ++.++...|.++++|+.+.+..+ +..++..
T Consensus       167 ~l~~I~~~aF~~c~~L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp~~--l~~I~~~aF~~~~~L~~l~l~~~-l~~I~~~  243 (401)
T 4fdw_A          167 TLEQLKEDIFYYCYNLKKADLSKTKITKLPASTFVYAGIEEVLLPVT--LKEIGSQAFLKTSQLKTIEIPEN-VSTIGQE  243 (401)
T ss_dssp             TCCEECSSTTTTCTTCCEEECTTSCCSEECTTTTTTCCCSEEECCTT--CCEECTTTTTTCTTCCCEECCTT-CCEECTT
T ss_pred             CccEehHHHhhCcccCCeeecCCCcceEechhhEeecccCEEEeCCc--hheehhhHhhCCCCCCEEecCCC-ccCcccc
Confidence            35555 34677888899999988888888776544688888888754  77888877888888888888753 2221111


Q ss_pred             cCCc-------cCCC-chhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccc
Q 004021          603 EGNV-------LCDD-AEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICV  674 (779)
Q Consensus       603 ~~~~-------~~~~-~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~  674 (779)
                      .+..       +++. .......+.++++|+.+.+..+...    -..+..+....+..+++|+.+.|..  .+..+.. 
T Consensus       244 aF~~~~L~~i~lp~~i~~I~~~aF~~c~~L~~l~l~~~~~~----~~~~~~I~~~aF~~c~~L~~l~l~~--~i~~I~~-  316 (401)
T 4fdw_A          244 AFRESGITTVKLPNGVTNIASRAFYYCPELAEVTTYGSTFN----DDPEAMIHPYCLEGCPKLARFEIPE--SIRILGQ-  316 (401)
T ss_dssp             TTTTCCCSEEEEETTCCEECTTTTTTCTTCCEEEEESSCCC----CCTTCEECTTTTTTCTTCCEECCCT--TCCEECT-
T ss_pred             ccccCCccEEEeCCCccEEChhHhhCCCCCCEEEeCCcccc----CCcccEECHHHhhCCccCCeEEeCC--ceEEEhh-
Confidence            1100       0000 0001112333334444433321110    0011122334456677777777763  3555544 


Q ss_pred             ccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCC-CCCCCccEEeeeCCCCCCCCCCC
Q 004021          675 DKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNP-LHFPKLKKIGVYGCPKLKKLPIN  738 (779)
Q Consensus       675 ~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~-~~l~~L~~L~l~~c~~L~~lP~~  738 (779)
                                    ..+.++++|+.+.|.+  +++.+.... ..+ +|+.|.+.++ .+..++..
T Consensus       317 --------------~aF~~c~~L~~l~lp~--~l~~I~~~aF~~~-~L~~l~l~~n-~~~~l~~~  363 (401)
T 4fdw_A          317 --------------GLLGGNRKVTQLTIPA--NVTQINFSAFNNT-GIKEVKVEGT-TPPQVFEK  363 (401)
T ss_dssp             --------------TTTTTCCSCCEEEECT--TCCEECTTSSSSS-CCCEEEECCS-SCCBCCCS
T ss_pred             --------------hhhcCCCCccEEEECc--cccEEcHHhCCCC-CCCEEEEcCC-CCcccccc
Confidence                          4677888999999864  577776643 356 8999999875 45555543

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.34  E-value=2.8e-07  Score=97.31  Aligned_cols=171  Identities=18%  Similarity=0.095  Sum_probs=110.0

Q ss_pred             ccchhhcccccCceeeecCCcc----------cccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          527 ELPSRISSLVSLHHLDLSLTHI----------RGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       527 ~lp~~i~~L~~L~~L~L~~~~i----------~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      .++.++.++++|+.|.+.....          ..++..+..+++|+.|+|++|..+ .+|.  + .+++|++|++..|.+
T Consensus       130 ~L~~s~~~l~~L~~L~l~~~~~e~~~is~~~~~~L~~ll~~~P~L~~L~L~g~~~l-~l~~--~-~~~~L~~L~L~~~~l  205 (362)
T 2ra8_A          130 GIVENKEKFAHFEGLFWGDIDFEEQEISWIEQVDLSPVLDAMPLLNNLKIKGTNNL-SIGK--K-PRPNLKSLEIISGGL  205 (362)
T ss_dssp             HHHTTHHHHTTCSEEEECCCCTTTCCGGGCBCCBCHHHHHTCTTCCEEEEECCBTC-BCCS--C-BCTTCSEEEEECSBC
T ss_pred             HHHHhhhhcchhhheeecCcchhhcccccccccCHHHHHhcCCCCcEEEEeCCCCc-eecc--c-cCCCCcEEEEecCCC
Confidence            4566677888999998865422          135566788899999999988433 4555  4 388999999998876


Q ss_pred             CCcccccCCccCCCchhhHHhhc--CCCCCCceeEEeecccccccCCCCCcccC-cccccccCcceEEeccccccceecc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELL--GLKRLNVLSWSFRSSLAVQKFFKYPKLDL-TWLVFVQNLKELEIIVCTEMEEIIC  673 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~--~L~~L~~L~l~~~~~~~~~~~~~L~~L~~-~~l~~l~~L~~L~L~~~~~~~~~~~  673 (779)
                      ..              .....+.  .+++|+.|+|+.+.... .....++.+.. .....+|+|++|.|++|........
T Consensus       206 ~~--------------~~l~~l~~~~lp~L~~L~L~~~~~~~-~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~  270 (362)
T 2ra8_A          206 PD--------------SVVEDILGSDLPNLEKLVLYVGVEDY-GFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVE  270 (362)
T ss_dssp             CH--------------HHHHHHHHSBCTTCCEEEEECBCGGG-TCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHH
T ss_pred             Ch--------------HHHHHHHHccCCCCcEEEEecccccc-ccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHH
Confidence            52              4444554  78999999987421110 00111111110 0113579999999998765432211


Q ss_pred             cccccCcccchhhccCCCCCCCCccEEEccCCCCCcc-----ccCCCCCCCCccEEeeeCCC
Q 004021          674 VDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS-----IYPNPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       674 ~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~-----l~~~~~~l~~L~~L~l~~c~  730 (779)
                              .+     .....+|+|++|+|+. +.+..     +...+..+++|+.|++++|.
T Consensus       271 --------~l-----a~a~~~~~L~~LdLs~-n~L~d~G~~~L~~~L~~l~~L~~L~L~~n~  318 (362)
T 2ra8_A          271 --------MF-----LESDILPQLETMDISA-GVLTDEGARLLLDHVDKIKHLKFINMKYNY  318 (362)
T ss_dssp             --------HH-----HHCSSGGGCSEEECCS-SCCBHHHHHHHHTTHHHHTTCSEEECCSBB
T ss_pred             --------HH-----HhCccCCCCCEEECCC-CCCChHHHHHHHhhcccCCcceEEECCCCc
Confidence                    00     1224689999999986 56655     34444578999999999884

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.25  E-value=3e-05  Score=83.26  Aligned_cols=179  Identities=13%  Similarity=0.088  Sum_probs=123.4

Q ss_pred             ccccCCccEEEcccccccccccCcc----c--cccccccccccc-chhhcccccCceeeecCCcccccchh-hccCccCc
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT----L--LSLRRNDSLTEL-PSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLR  562 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~----l--L~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~  562 (779)
                      ...+.+++.+.+.+|.+..++....    |  +.|.+  .+..+ +..|.++.+|+.+++..+ ++.++.. |.+ .+|+
T Consensus       176 F~~c~~L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp~--~l~~I~~~aF~~~~~L~~l~l~~~-l~~I~~~aF~~-~~L~  251 (401)
T 4fdw_A          176 FYYCYNLKKADLSKTKITKLPASTFVYAGIEEVLLPV--TLKEIGSQAFLKTSQLKTIEIPEN-VSTIGQEAFRE-SGIT  251 (401)
T ss_dssp             TTTCTTCCEEECTTSCCSEECTTTTTTCCCSEEECCT--TCCEECTTTTTTCTTCCCEECCTT-CCEECTTTTTT-CCCS
T ss_pred             hhCcccCCeeecCCCcceEechhhEeecccCEEEeCC--chheehhhHhhCCCCCCEEecCCC-ccCcccccccc-CCcc
Confidence            3456778888888887777766533    1  44443  35555 345778888999988764 6666554 555 7889


Q ss_pred             EeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCC
Q 004021          563 YLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFK  642 (779)
Q Consensus       563 ~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~  642 (779)
                      .+.+.++  +..++...|.++++|+.+.+.++.....+         ........+.++++|+.+.+.          .+
T Consensus       252 ~i~lp~~--i~~I~~~aF~~c~~L~~l~l~~~~~~~~~---------~~~I~~~aF~~c~~L~~l~l~----------~~  310 (401)
T 4fdw_A          252 TVKLPNG--VTNIASRAFYYCPELAEVTTYGSTFNDDP---------EAMIHPYCLEGCPKLARFEIP----------ES  310 (401)
T ss_dssp             EEEEETT--CCEECTTTTTTCTTCCEEEEESSCCCCCT---------TCEECTTTTTTCTTCCEECCC----------TT
T ss_pred             EEEeCCC--ccEEChhHhhCCCCCCEEEeCCccccCCc---------ccEECHHHhhCCccCCeEEeC----------Cc
Confidence            9988554  77888877889999999999877543100         001233457788888888774          34


Q ss_pred             CCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC
Q 004021          643 YPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP  713 (779)
Q Consensus       643 L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~  713 (779)
                      ++.+....+..+++|+.|.|..+  +..+..               ..+.++ +|+.+.+.+. .+..++.
T Consensus       311 i~~I~~~aF~~c~~L~~l~lp~~--l~~I~~---------------~aF~~~-~L~~l~l~~n-~~~~l~~  362 (401)
T 4fdw_A          311 IRILGQGLLGGNRKVTQLTIPAN--VTQINF---------------SAFNNT-GIKEVKVEGT-TPPQVFE  362 (401)
T ss_dssp             CCEECTTTTTTCCSCCEEEECTT--CCEECT---------------TSSSSS-CCCEEEECCS-SCCBCCC
T ss_pred             eEEEhhhhhcCCCCccEEEECcc--ccEEcH---------------HhCCCC-CCCEEEEcCC-CCccccc
Confidence            66666677888999999999653  666654               477788 9999999974 4444443

>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=98.24  E-value=7.5e-06  Score=85.63  Aligned_cols=172  Identities=15%  Similarity=0.177  Sum_probs=101.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC-CEEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF-DVVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F-~~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|++..++.+.+++..+  ..+.+.|+|.+|+||||+|+.+++.. .. ..+ ...+.+......            
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~la~~l~~~l-~~-~~~~~~~~~~~~~~~~------------   88 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALAREL-FG-ENWRHNFLELNASDER------------   88 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHH-HG-GGHHHHEEEEETTCHH------------
T ss_pred             HHhhCCHHHHHHHHHHHHcC--CCCeEEEECcCCCCHHHHHHHHHHHh-cC-CcccCceEEeeccccC------------
Confidence            45899999999999999876  44458999999999999999999875 11 111 112222221100            


Q ss_pred             hhhhhcchhhHHHHHHHh--hC-CCcceeehhhcccc-----------ccccCCCcEEEEEeCchh-hhhhcC--CceeE
Q 004021          234 KKWKEKSLQDKAVDISSI--LS-PKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSAG-VCDQMD--SKNLE  296 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~--L~-~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~~-va~~~~--~~~~~  296 (779)
                         ......+........  +. +++..+.+|++...           +.....++++|+||+... +.....  ...+.
T Consensus        89 ---~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~~~  165 (327)
T 1iqp_A           89 ---GINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFR  165 (327)
T ss_dssp             ---HHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEE
T ss_pred             ---chHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhhCcEEE
Confidence               000000011111100  11 23334444443211           122345678888887643 222211  34789


Q ss_pred             ccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHH
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRA  348 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~  348 (779)
                      +.+++.++...++...+.......+   .+....|++.++|.|..+..+...
T Consensus       166 ~~~l~~~~~~~~l~~~~~~~~~~~~---~~~~~~l~~~~~g~~r~~~~~l~~  214 (327)
T 1iqp_A          166 FRPLRDEDIAKRLRYIAENEGLELT---EEGLQAILYIAEGDMRRAINILQA  214 (327)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTTCEEC---HHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHCCCCHHHHHHHHHH
Confidence            9999999999999888764432211   467788999999999876654443

>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=98.13  E-value=1.8e-05  Score=78.47  Aligned_cols=161  Identities=11%  Similarity=0.075  Sum_probs=90.7

Q ss_pred             ccccchh---hhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQE---KLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~---~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      ..|+|.+   ..++.+..++..+  ..+.+.|+|.+|+||||||+.+++.. .  .....+.|+....+...+...+.. 
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~-  101 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACARA-N--ELERRSFYIPLGIHASISTALLEG-  101 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHHH-H--HTTCCEEEEEGGGGGGSCGGGGTT-
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHH-H--HcCCeEEEEEHHHHHHHHHHHHHh-
Confidence            4567633   4455555555543  45788999999999999999999877 2  223345666663322211111100 


Q ss_pred             cchhhhhcchhhHHHHHHHhhCCCcceeehhhcccc-------------ccc-cCCCc-EEEEEeCchh---------hh
Q 004021          232 EDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVP-------------LQM-LNAGF-KIVLKTRSAG---------VC  287 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~-------------~~~-~~~gs-~IivTTR~~~---------va  287 (779)
                                          +. +...+.+|++...             +.. ...+. ++|+||+...         +.
T Consensus       102 --------------------~~-~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~  160 (242)
T 3bos_A          102 --------------------LE-QFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLV  160 (242)
T ss_dssp             --------------------GG-GSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCCHHHH
T ss_pred             --------------------cc-CCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhhhhhh
Confidence                                00 0112222222110             000 01222 4788776422         11


Q ss_pred             hhcC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          288 DQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       288 ~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      ..+. ...+.+++++.++..+++...+.......   -.+....|++.++|.+-.+..+
T Consensus       161 ~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~---~~~~~~~l~~~~~g~~r~l~~~  216 (242)
T 3bos_A          161 SRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQL---PEDVGRFLLNRMARDLRTLFDV  216 (242)
T ss_dssp             HHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCC---CHHHHHHHHHHTTTCHHHHHHH
T ss_pred             hHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHccCCHHHHHHH
Confidence            1121 36889999999999999998876433222   2567788999999988766544

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.11  E-value=2.2e-07  Score=98.86  Aligned_cols=115  Identities=18%  Similarity=0.113  Sum_probs=51.6

Q ss_pred             ccCceeeecCCcccc--cchhhccCccCcEeeccCCcCCCCCchhhh-----cCCccCcEeeeccccCCCcccccCCccC
Q 004021          536 VSLHHLDLSLTHIRG--LPQELKALEKLRYLNLEYTHYLSIIPHQLI-----SGFLKLEVLRLLECGSEGVTKEEGNVLC  608 (779)
Q Consensus       536 ~~L~~L~L~~~~i~~--lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i-----~~L~~L~~L~l~~~~~~~~~~~~~~~~~  608 (779)
                      .+|++|+|++|.++.  +..-...+++|++|+|++| .++......+     ...++|++|++++|.+...         
T Consensus       101 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n-~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~---------  170 (372)
T 3un9_A          101 HALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLN-SLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAA---------  170 (372)
T ss_dssp             SCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSS-CCCHHHHHHHHHHHHSTTCCCCEEECCSSCCHHH---------
T ss_pred             CCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCC-CCCHHHHHHHHHHHHhcCCccceeeCCCCCCChH---------
Confidence            456666666665543  1111233455666666666 3332221111     2345566666666654320         


Q ss_pred             CCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          609 DDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       609 ~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                       ........+..+++|++|+++.|.....+.    .. ....+...++|+.|+|++|.
T Consensus       171 -~~~~l~~~L~~~~~L~~L~Ls~N~l~~~g~----~~-L~~~L~~~~~L~~L~Ls~N~  222 (372)
T 3un9_A          171 -GVAVLMEGLAGNTSVTHLSLLHTGLGDEGL----EL-LAAQLDRNRQLQELNVAYNG  222 (372)
T ss_dssp             -HHHHHHHHHHTCSSCCEEECTTSSCHHHHH----HH-HHHHGGGCSCCCEEECCSSC
T ss_pred             -HHHHHHHHHhcCCCcCEEeCCCCCCCcHHH----HH-HHHHHhcCCCcCeEECCCCC
Confidence             001223334555666666665443221000    00 01223344566777776654

>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=98.10  E-value=6e-05  Score=81.87  Aligned_cols=172  Identities=14%  Similarity=0.164  Sum_probs=99.6

Q ss_pred             ccc-chhhh--HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCc
Q 004021          156 TIV-GQEKL--LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       156 ~~v-Gr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~  232 (779)
                      .|+ |....  ...+........ ....+.|+|.+|+||||||+.+++... ....-..+++++...+..++...+... 
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~-~~~~lll~Gp~G~GKTtLa~aia~~l~-~~~~~~~v~~v~~~~~~~~~~~~~~~~-  182 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPG-RYNPLFIYGGVGLGKTHLLQSIGNYVV-QNEPDLRVMYITSEKFLNDLVDSMKEG-  182 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTT-SSCCEEEECSSSSSHHHHHHHHHHHHH-HHCCSSCEEEEEHHHHHHHHHHHHHTT-
T ss_pred             hcCCCCchHHHHHHHHHHHhCCC-CCCeEEEECCCCCCHHHHHHHHHHHHH-HhCCCCeEEEeeHHHHHHHHHHHHHcc-
Confidence            444 65433  333333333332 267889999999999999999998762 111112345666655555555444321 


Q ss_pred             chhhhhcchhhHHHHHHHhhCCCcceeehhhccccc----------c----ccCCCcEEEEEeCch---------hhhhh
Q 004021          233 DKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPL----------Q----MLNAGFKIVLKTRSA---------GVCDQ  289 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~----------~----~~~~gs~IivTTR~~---------~va~~  289 (779)
                             .    ...+...+..+...+.+|++....          .    ....|..||+||.+.         .+...
T Consensus       183 -------~----~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR  251 (440)
T 2z4s_A          183 -------K----LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSR  251 (440)
T ss_dssp             -------C----HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHH
T ss_pred             -------c----HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhh
Confidence                   0    112333333233344445442111          0    024577899999862         12222


Q ss_pred             cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          290 MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       290 ~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      +. ...+.+++++.++-.+++.+.+.......+   .+....|++.++|.+-.+..
T Consensus       252 ~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~---~e~l~~la~~~~gn~R~l~~  304 (440)
T 2z4s_A          252 FQMGLVAKLEPPDEETRKSIARKMLEIEHGELP---EEVLNFVAENVDDNLRRLRG  304 (440)
T ss_dssp             HHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCC---TTHHHHHHHHCCSCHHHHHH
T ss_pred             ccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhcCCCHHHHHH
Confidence            32 357899999999999999988765432223   34567888999998865543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.10  E-value=3.6e-05  Score=78.83  Aligned_cols=158  Identities=9%  Similarity=0.046  Sum_probs=93.7

Q ss_pred             ccccchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhhccccC--CCCE--EEEEEe------chHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH--NFDV--VIWAAV------QTFQD  222 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~--~F~~--~~wv~v------~~i~~  222 (779)
                      ..+.||++++++|...|...  .+..+.+-|+|.+|+|||++|+.|++.......  ....  .+.++.      ..+..
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            34799999999999888753  346778899999999999999999988722111  1112  334443      46788


Q ss_pred             HHHHHhCCCcchhhhhcchhhHHHHHHHhh---CCCcceeehhhcccc---------ccc-cCCCcE--EEEEeCchhh-
Q 004021          223 DIGKRIGFSEDKKWKEKSLQDKAVDISSIL---SPKKFRIDLTELGVP---------LQM-LNAGFK--IVLKTRSAGV-  286 (779)
Q Consensus       223 ~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L---~~kr~~~~ld~l~~~---------~~~-~~~gs~--IivTTR~~~v-  286 (779)
                      .|++++... ..  ......+....+...+   +++.+.+.+|++...         +.+ ...+++  ||.++...+. 
T Consensus       100 ~I~~~L~g~-~~--~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~  176 (318)
T 3te6_A          100 KIWFAISKE-NL--CGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTI  176 (318)
T ss_dssp             HHHHHHSCC-C----CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCC
T ss_pred             HHHHHhcCC-CC--CchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccc
Confidence            888888543 10  1111122223333333   334455555554221         110 013333  3344544322 


Q ss_pred             --------hhhcCCceeEccCCChHHHHHHHHHHhhc
Q 004021          287 --------CDQMDSKNLEVYSLAHDEAWKLFQEMIER  315 (779)
Q Consensus       287 --------a~~~~~~~~~l~~L~~~~a~~Lf~~~a~~  315 (779)
                              ...++...+.+++++.+|-.+++.+++..
T Consensus       177 ~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          177 REQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             HHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             hhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence                    12222357899999999999999988754

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.07  E-value=9.1e-07  Score=94.16  Aligned_cols=155  Identities=14%  Similarity=0.113  Sum_probs=101.8

Q ss_pred             CCccEEEcccccccccc---------cC-cc--ccccccccccccc--chhhcccccCceeeecCCccccc-----chhh
Q 004021          495 EGAKRISLMANEIESLS---------EI-PT--LLSLRRNDSLTEL--PSRISSLVSLHHLDLSLTHIRGL-----PQEL  555 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~---------~~-~~--lL~L~~~~~l~~l--p~~i~~L~~L~~L~L~~~~i~~l-----p~~~  555 (779)
                      ..++.|++++|.+....         .. ..  -|+|++| .++..  ..-...+.+|++|+|++|.++..     ...+
T Consensus        72 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n-~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L  150 (372)
T 3un9_A           72 SSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASC-QLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLL  150 (372)
T ss_dssp             TTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTC-CCCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHH
T ss_pred             hhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCC-CCCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHH
Confidence            46788888888775421         11 12  4889998 77542  22234577899999999988653     2223


Q ss_pred             -ccCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeE
Q 004021          556 -KALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSW  629 (779)
Q Consensus       556 -~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l  629 (779)
                       ...++|++|+|++| .++.     ++.. +..+++|++|++++|.+...          ........+...++|+.|++
T Consensus       151 ~~~~~~L~~L~Ls~n-~l~~~~~~~l~~~-L~~~~~L~~L~Ls~N~l~~~----------g~~~L~~~L~~~~~L~~L~L  218 (372)
T 3un9_A          151 LHDQCQITTLRLSNN-PLTAAGVAVLMEG-LAGNTSVTHLSLLHTGLGDE----------GLELLAAQLDRNRQLQELNV  218 (372)
T ss_dssp             HSTTCCCCEEECCSS-CCHHHHHHHHHHH-HHTCSSCCEEECTTSSCHHH----------HHHHHHHHGGGCSCCCEEEC
T ss_pred             HhcCCccceeeCCCC-CCChHHHHHHHHH-HhcCCCcCEEeCCCCCCCcH----------HHHHHHHHHhcCCCcCeEEC
Confidence             34678999999999 4543     4443 57889999999999987630          01223556778889999999


Q ss_pred             EeecccccccCCCCCcccCcccccccCcceEEeccccc
Q 004021          630 SFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       630 ~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~  667 (779)
                      +.|.....+.    .. ....+...++|++|+|++|..
T Consensus       219 s~N~i~~~g~----~~-l~~~L~~~~~L~~L~Ls~N~i  251 (372)
T 3un9_A          219 AYNGAGDTAA----LA-LARAAREHPSLELLHLYFNEL  251 (372)
T ss_dssp             CSSCCCHHHH----HH-HHHHHHHCSSCCEEECTTSSC
T ss_pred             CCCCCCHHHH----HH-HHHHHHhCCCCCEEeccCCCC
Confidence            9665432100    00 012344568899999999753

>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=98.03  E-value=6.6e-05  Score=80.01  Aligned_cols=185  Identities=14%  Similarity=0.150  Sum_probs=101.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCc-c
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSE-D  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~-~  233 (779)
                      ..++|++..++.+.+.+..+. ....+.|+|.+|+||||+|+.+++.. .....+.... .........+...-.... .
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~l-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   92 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGL-NCETGITATP-CGVCDNCREIEQGRFVDLIE   92 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHHH-SCTTCSCSSC-CSSSHHHHHHHTSCCSSCEE
T ss_pred             hhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHHh-CCCCCCCCCC-CcccHHHHHHhccCCCceEE
Confidence            458999999999999997652 23578899999999999999998876 2111110000 000001111111000000 0


Q ss_pred             -hhhhhcchhhHHHHHHHhhC-----CCcceeehhhcccc-----------ccccCCCcEEEEEeCchh-hhhhc-C-Cc
Q 004021          234 -KKWKEKSLQDKAVDISSILS-----PKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSAG-VCDQM-D-SK  293 (779)
Q Consensus       234 -~~~~~~~~~~~~~~l~~~L~-----~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~~-va~~~-~-~~  293 (779)
                       ........++ ...+.+.+.     +++..+.+|++...           +.....+..+|++|.... +.... . ..
T Consensus        93 ~~~~~~~~~~~-~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~~~l~sr~~  171 (373)
T 1jr3_A           93 IDAASRTKVED-TRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL  171 (373)
T ss_dssp             EETTCSCCSSC-HHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSCHHHHTTSE
T ss_pred             ecccccCCHHH-HHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCcHHHHhhee
Confidence             0000001111 222333332     22334444443211           112234566777776432 22222 2 46


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      .+.+.+++.++...++.+.+...+...+   .+....|++.++|.|..+..+.
T Consensus       172 ~i~~~~l~~~~~~~~l~~~~~~~~~~~~---~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          172 QFHLKALDVEQIRHQLEHILNEEHIAHE---PRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHSSSCHHHHHHHH
T ss_pred             EeeCCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHCCCCHHHHHHHH
Confidence            7899999999999999887754432211   4667889999999998876554

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.99  E-value=2.5e-05  Score=74.35  Aligned_cols=46  Identities=20%  Similarity=0.424  Sum_probs=40.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++.+.+...  ..+.+.|+|.+|+|||+||+.+++..
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~l~~~~~~~~   67 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcC--CCCceEEECCCCCCHHHHHHHHHHHH
Confidence            45899999999999999775  45678899999999999999999876

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=97.91  E-value=9.2e-05  Score=76.90  Aligned_cols=169  Identities=14%  Similarity=0.171  Sum_probs=98.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|++..++.+.+++..+  ..+.+.++|.+|+|||++|+.+++.. . ...+. ..+.++...             .
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKt~la~~l~~~l-~-~~~~~~~~~~~~~~~-------------~   79 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERK--NIPHLLFSGPPGTGKTATAIALARDL-F-GENWRDNFIEMNASD-------------E   79 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTT--CCCCEEEESSSSSSHHHHHHHHHHHH-H-TTCHHHHCEEEETTS-------------T
T ss_pred             HHHhCCHHHHHHHHHHHhCC--CCCeEEEECcCCcCHHHHHHHHHHHh-c-CCcccCCeEEEeCcc-------------c
Confidence            45899999999999988775  33448999999999999999998875 1 11111 111122110             0


Q ss_pred             hhhhhcchhhHHHHHHHh--hC-CCcceeehhhcc-----------ccccccCCCcEEEEEeCchh-hhhhc-C-CceeE
Q 004021          234 KKWKEKSLQDKAVDISSI--LS-PKKFRIDLTELG-----------VPLQMLNAGFKIVLKTRSAG-VCDQM-D-SKNLE  296 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~--L~-~kr~~~~ld~l~-----------~~~~~~~~gs~IivTTR~~~-va~~~-~-~~~~~  296 (779)
                        .......+........  +. +++..+.+|++.           ..+.....++.+|+||.... +.... . ...+.
T Consensus        80 --~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr~~~i~  157 (319)
T 2chq_A           80 --RGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVFR  157 (319)
T ss_dssp             --TCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTTCEEEE
T ss_pred             --cChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhhCeEEE
Confidence              0001111111111111  11 223334444431           11222235677888876543 22222 2 45789


Q ss_pred             ccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      +.+++.++...++...+...+...+   .+....|++.++|.+..+...
T Consensus       158 ~~~~~~~~~~~~l~~~~~~~~~~i~---~~~l~~l~~~~~G~~r~~~~~  203 (319)
T 2chq_A          158 FKPVPKEAMKKRLLEICEKEGVKIT---EDGLEALIYISGGDFRKAINA  203 (319)
T ss_dssp             CCCCCHHHHHHHHHHHHHTTCCCBC---HHHHHHHHHTTTTCHHHHHHH
T ss_pred             ecCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHHHH
Confidence            9999999999999888765432211   466788899999998765543

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.88  E-value=0.00019  Score=75.25  Aligned_cols=181  Identities=14%  Similarity=0.106  Sum_probs=102.7

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~  226 (779)
                      ..++|++..++++..++...   ......|.|+|.+|+|||++|+.+++..   ...|   +.++.     ..-...++.
T Consensus        29 ~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~---~~~~---~~~~~~~~~~~~~~~~~~~  102 (338)
T 3pfi_A           29 DGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM---SANI---KTTAAPMIEKSGDLAAILT  102 (338)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT---TCCE---EEEEGGGCCSHHHHHHHHH
T ss_pred             HHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCe---EEecchhccchhHHHHHHH
Confidence            56899999999999888653   2345678999999999999999998876   2332   22222     112222222


Q ss_pred             HhCCCcc---hhhhhcchhhHHHHHHHhhCCCcceeehhhcc--ccccccCCCcEEEEEeCchhh-hhh-cC--CceeEc
Q 004021          227 RIGFSED---KKWKEKSLQDKAVDISSILSPKKFRIDLTELG--VPLQMLNAGFKIVLKTRSAGV-CDQ-MD--SKNLEV  297 (779)
Q Consensus       227 ~l~~~~~---~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~--~~~~~~~~gs~IivTTR~~~v-a~~-~~--~~~~~l  297 (779)
                      .......   +..+.. ....+..+...+++.++..+...-.  .......++..+|.||..... ... ..  ...+.+
T Consensus       103 ~~~~~~vl~lDEi~~l-~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l  181 (338)
T 3pfi_A          103 NLSEGDILFIDEIHRL-SPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRL  181 (338)
T ss_dssp             TCCTTCEEEEETGGGC-CHHHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEEC
T ss_pred             hccCCCEEEEechhhc-CHHHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeC
Confidence            2211100   000111 1344555666666655432221100  001111124567766665332 111 11  367899


Q ss_pred             cCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          298 YSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       298 ~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .+++.++...++.+.+.......   -.+....|++.+.|.|-.+..+
T Consensus       182 ~~~~~~e~~~il~~~~~~~~~~~---~~~~~~~l~~~~~G~~r~l~~~  226 (338)
T 3pfi_A          182 EFYKDSELALILQKAALKLNKTC---EEKAALEIAKRSRSTPRIALRL  226 (338)
T ss_dssp             CCCCHHHHHHHHHHHHHHTTCEE---CHHHHHHHHHTTTTCHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHHCcCHHHHHHH
Confidence            99999999999988876533111   2567788899999999655543

>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=97.85  E-value=0.00015  Score=80.62  Aligned_cols=176  Identities=14%  Similarity=0.123  Sum_probs=99.5

Q ss_pred             ccccchhhhHHHHHHHHhcc---------------CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe--
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---------------QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV--  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v--  217 (779)
                      ..++|++..++++.+++...               .+..+.+.|+|.+|+||||+|+.+++..     .+. ++.++.  
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l-----~~~-~i~in~s~  112 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL-----GYD-ILEQNASD  112 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT-----TCE-EEEECTTS
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc-----CCC-EEEEeCCC
Confidence            56899999999999999751               0134789999999999999999999876     122 223333  


Q ss_pred             ---chHHHHHHHHhCCCcchhhhhcchhhHHHHHHH--hhCCCcceeehhhccccccc------------cCCCcEEEEE
Q 004021          218 ---QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISS--ILSPKKFRIDLTELGVPLQM------------LNAGFKIVLK  280 (779)
Q Consensus       218 ---~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~--~L~~kr~~~~ld~l~~~~~~------------~~~gs~IivT  280 (779)
                         ..+....+......       .+.........+  ...+++..+.+|++......            ...+..||++
T Consensus       113 ~~~~~~~~~~i~~~~~~-------~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~~~~iIli  185 (516)
T 1sxj_A          113 VRSKTLLNAGVKNALDN-------MSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILI  185 (516)
T ss_dssp             CCCHHHHHHTGGGGTTB-------CCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEE
T ss_pred             cchHHHHHHHHHHHhcc-------ccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHhcCCCEEEE
Confidence               11222222111100       000000000000  01233445555555322110            1134456666


Q ss_pred             eCchh---hhhhcC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHH
Q 004021          281 TRSAG---VCDQMD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVG  346 (779)
Q Consensus       281 TR~~~---va~~~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g  346 (779)
                      +....   +..... ...+.+++++.++..+.+...+.......+   .+....|++.++| ++-++..+.
T Consensus       186 ~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~---~~~l~~la~~s~GdiR~~i~~L~  253 (516)
T 1sxj_A          186 CNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD---PNVIDRLIQTTRGDIRQVINLLS  253 (516)
T ss_dssp             ESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC---TTHHHHHHHHTTTCHHHHHHHHT
T ss_pred             EcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCcHHHHHHHHH
Confidence            65432   222222 567899999999999999887765443333   3457789999999 555555543

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.78  E-value=2.2e-05  Score=72.57  Aligned_cols=68  Identities=16%  Similarity=0.280  Sum_probs=36.5

Q ss_pred             cchhhcccccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCCchhhhcCC----ccCcEeeecccc
Q 004021          528 LPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGF----LKLEVLRLLECG  595 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L----~~L~~L~l~~~~  595 (779)
                      +|.....-.+|+.||+++|.|+.. -..+..+++|++|+|++|..++.---..++.+    ++|++|++++|.
T Consensus        53 LP~~~~~~~~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~  125 (176)
T 3e4g_A           53 LPTGPLDKYKIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCG  125 (176)
T ss_dssp             SCCCSTTCCCEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCT
T ss_pred             CCcccCCCceEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCC
Confidence            454332335677888887766542 12356677777777777754432111113333    246666666654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.77  E-value=0.00011  Score=75.08  Aligned_cols=48  Identities=31%  Similarity=0.333  Sum_probs=39.7

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.+++|.+.+...           -...+-+.|+|.+|+|||+||+++++..
T Consensus        17 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~   75 (285)
T 3h4m_A           17 EDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET   75 (285)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            56899999999998887531           1245678999999999999999999876

>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=97.76  E-value=0.0007  Score=70.40  Aligned_cols=157  Identities=15%  Similarity=0.221  Sum_probs=87.6

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcchhhhhcchhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDKKWKEKSLQD  243 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~~~~~~~~~~  243 (779)
                      ...+...+..+......+.|+|.+|+||||||+.+++.. ... . ..+++++...+...+...+...        ..  
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~-~~~-~-~~~~~i~~~~~~~~~~~~~~~~--------~~--   89 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEA-KKR-G-YRVIYSSADDFAQAMVEHLKKG--------TI--   89 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHH-HHT-T-CCEEEEEHHHHHHHHHHHHHHT--------CH--
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHH-HHC-C-CEEEEEEHHHHHHHHHHHHHcC--------cH--
Confidence            344444444433245678999999999999999999876 211 2 2345666555544444333211        01  


Q ss_pred             HHHHHHHhhCCCcceeehhhcccc-------------cc-ccCCCcEEEEEeCchh---------hhhhcC-CceeEccC
Q 004021          244 KAVDISSILSPKKFRIDLTELGVP-------------LQ-MLNAGFKIVLKTRSAG---------VCDQMD-SKNLEVYS  299 (779)
Q Consensus       244 ~~~~l~~~L~~kr~~~~ld~l~~~-------------~~-~~~~gs~IivTTR~~~---------va~~~~-~~~~~l~~  299 (779)
                        ..+...+.+ ...+.+|++...             +. ....|..||+||....         +...+. ...+.+++
T Consensus        90 --~~~~~~~~~-~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~  166 (324)
T 1l8q_A           90 --NEFRNMYKS-VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL  166 (324)
T ss_dssp             --HHHHHHHHT-CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC
T ss_pred             --HHHHHHhcC-CCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC
Confidence              111222222 223334443211             00 0134667888886421         122222 35789999


Q ss_pred             CChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH
Q 004021          300 LAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA  341 (779)
Q Consensus       300 L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa  341 (779)
                       +.++-.+++...+.......+   .+....|++.+ |.+-.
T Consensus       167 -~~~e~~~il~~~~~~~~~~l~---~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          167 -DNKTRFKIIKEKLKEFNLELR---KEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             -CHHHHHHHHHHHHHHTTCCCC---HHHHHHHHHHC-SSHHH
T ss_pred             -CHHHHHHHHHHHHHhcCCCCC---HHHHHHHHHhC-CCHHH
Confidence             999999999988765432222   56678888888 76543

>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=97.73  E-value=1.5e-05  Score=79.62  Aligned_cols=78  Identities=21%  Similarity=0.155  Sum_probs=56.0

Q ss_pred             ccccccccccccchh----hcccccCceeeecCCcccccc---hhhccCccCcEeeccCCcCCCCCchhhhcCCc--cCc
Q 004021          517 LSLRRNDSLTELPSR----ISSLVSLHHLDLSLTHIRGLP---QELKALEKLRYLNLEYTHYLSIIPHQLISGFL--KLE  587 (779)
Q Consensus       517 L~L~~~~~l~~lp~~----i~~L~~L~~L~L~~~~i~~lp---~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~--~L~  587 (779)
                      ++++.| ....++..    ..++++|+.|+|++|.|+.++   ..+.++++|++|+|++| .+..+..  +..+.  +|+
T Consensus       148 l~l~~N-~~~~~~~~l~i~~~~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N-~i~~~~~--l~~l~~l~L~  223 (267)
T 3rw6_A          148 IDVVLN-RRSCMAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGN-ELKSERE--LDKIKGLKLE  223 (267)
T ss_dssp             CCCCTT-SHHHHHHHHHHHHHHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTS-CCCSGGG--GGGGTTSCCS
T ss_pred             ccccCC-HHHHHHHHHHHHHhhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCC-ccCCchh--hhhcccCCcc
Confidence            445555 44444432    256889999999999887654   56778999999999999 5676633  55555  899


Q ss_pred             EeeeccccCCC
Q 004021          588 VLRLLECGSEG  598 (779)
Q Consensus       588 ~L~l~~~~~~~  598 (779)
                      +|++.+|.+.+
T Consensus       224 ~L~L~~Npl~~  234 (267)
T 3rw6_A          224 ELWLDGNSLCD  234 (267)
T ss_dssp             EEECTTSTTGG
T ss_pred             eEEccCCcCcc
Confidence            99999988763

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.70  E-value=4e-05  Score=70.83  Aligned_cols=80  Identities=11%  Similarity=0.091  Sum_probs=53.3

Q ss_pred             cccccccccccc-chhhcccccCceeeecCC-ccccc-chhhccC----ccCcEeeccCCcCCCCCchhhhcCCccCcEe
Q 004021          517 LSLRRNDSLTEL-PSRISSLVSLHHLDLSLT-HIRGL-PQELKAL----EKLRYLNLEYTHYLSIIPHQLISGFLKLEVL  589 (779)
Q Consensus       517 L~L~~~~~l~~l-p~~i~~L~~L~~L~L~~~-~i~~l-p~~~~~L----~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L  589 (779)
                      |||++| .++.. -..+.++++|++|+|++| .|+.- -..+..+    ++|++|+|++|..++.---..+.++++|++|
T Consensus        66 LDLs~~-~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~L~~L  144 (176)
T 3e4g_A           66 IDATDS-CIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRNLKYL  144 (176)
T ss_dssp             EEEESC-CCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTTCCEE
T ss_pred             EeCcCC-CccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCCCCEE
Confidence            888888 56643 345678888888888888 46541 1234443    4688888888866554221226678888888


Q ss_pred             eeccccCC
Q 004021          590 RLLECGSE  597 (779)
Q Consensus       590 ~l~~~~~~  597 (779)
                      ++++|...
T Consensus       145 ~L~~c~~I  152 (176)
T 3e4g_A          145 FLSDLPGV  152 (176)
T ss_dssp             EEESCTTC
T ss_pred             ECCCCCCC
Confidence            88887643

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.67  E-value=0.00029  Score=74.26  Aligned_cols=177  Identities=12%  Similarity=0.092  Sum_probs=96.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc-cCCCCEEEEEEech-----HHHHHHHHh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ-QHNFDVVIWAAVQT-----FQDDIGKRI  228 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~-~~~F~~~~wv~v~~-----i~~~i~~~l  228 (779)
                      ..++|+++.++.+..++..+  ..+.+.|+|.+|+||||+|+.+++..... ...+. ...+...+     ...+....+
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~--~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  113 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSA--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSR-ILELNASDERGISIVREKVKNF  113 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCT--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTS-EEEECSSSCCCHHHHTTHHHHH
T ss_pred             HHhhCCHHHHHHHHHHHhcC--CCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccc-eEEEccccccchHHHHHHHHHH
Confidence            46899999999999998776  33338999999999999999998875100 01111 11222210     111111100


Q ss_pred             CCCcchhhhhcchhhHHHHHHHhhC-CCcceeehhhcccc-----------ccccCCCcEEEEEeCch-hhhhhcC--Cc
Q 004021          229 GFSEDKKWKEKSLQDKAVDISSILS-PKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSA-GVCDQMD--SK  293 (779)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~l~~~L~-~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~-~va~~~~--~~  293 (779)
                      ... .   .......    ...... +++-.+.+|++...           +.......++|++|... .+.....  ..
T Consensus       114 ~~~-~---~~~~~~~----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~  185 (353)
T 1sxj_D          114 ARL-T---VSKPSKH----DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCS  185 (353)
T ss_dssp             HHS-C---CCCCCTT----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSE
T ss_pred             hhh-c---ccccchh----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCc
Confidence            000 0   0000000    000001 11113334443211           11223456777777543 2322222  45


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      .+.+.+++.++....+...+.......+   ++....|++.++|.|-.+..+
T Consensus       186 ~i~~~~~~~~~~~~~l~~~~~~~~~~i~---~~~l~~l~~~~~G~~r~~~~~  234 (353)
T 1sxj_D          186 KFRFKALDASNAIDRLRFISEQENVKCD---DGVLERILDISAGDLRRGITL  234 (353)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCCC---HHHHHHHHHHTSSCHHHHHHH
T ss_pred             eEEeCCCCHHHHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCCHHHHHHH
Confidence            7899999999999999887754432222   567889999999998865543

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.65  E-value=0.00094  Score=69.30  Aligned_cols=170  Identities=14%  Similarity=0.070  Sum_probs=93.5

Q ss_pred             ccccchhhhHHHHHHHHhc----------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      ..++|.+..++.|.+.+.-          .....+-|.++|.+|+|||+||+++++..   ...|   +.++...+..  
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~~---~~v~~~~l~~--   89 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTF---FSVSSSDLVS--   89 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH---TCEE---EEEEHHHHHT--
T ss_pred             HHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH---CCCE---EEEchHHHhh--
Confidence            5689999999999988731          11234578999999999999999999876   2222   2233222211  


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhccccc-------------------------cccCCCcEEE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVPL-------------------------QMLNAGFKIV  278 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~~-------------------------~~~~~gs~Ii  278 (779)
                        ..        .. ..+.....+.... ..+...+.+|++....                         .....+..||
T Consensus        90 --~~--------~g-~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi  158 (322)
T 3eie_A           90 --KW--------MG-ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVL  158 (322)
T ss_dssp             --TT--------GG-GHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCCCEEEE
T ss_pred             --cc--------cc-hHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCCceEEE
Confidence              00        00 0111111111111 1222233333332111                         0122345666


Q ss_pred             EEeCchhhh-hhc--C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHH
Q 004021          279 LKTRSAGVC-DQM--D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVG  346 (779)
Q Consensus       279 vTTR~~~va-~~~--~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g  346 (779)
                      .||...... ..+  . ...+.++..+.++-.++|...+.......   -......|++.+.| .+-.|..+.
T Consensus       159 ~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~---~~~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          159 GATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVL---TKEDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             EEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCC---CHHHHHHHHHTTTTCCHHHHHHHH
T ss_pred             EecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            677753321 111  1 45678888999999999998876533111   14556788888887 454555443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.56  E-value=0.0012  Score=69.65  Aligned_cols=171  Identities=12%  Similarity=0.071  Sum_probs=92.7

Q ss_pred             ccccchhhhHHHHHHHHhc----------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      ..++|.+..++.|.+.+..          .....+-|.|+|.+|+|||+||+++++..   ...   .+.++...+... 
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~---~~~i~~~~l~~~-  156 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS---GAT---FFSISASSLTSK-  156 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT---TCE---EEEEEGGGGCCS-
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc---CCe---EEEEehHHhhcc-
Confidence            4689999999999888753          11245678999999999999999998875   222   233333211100 


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhcccc----------------------cc----ccCCCcEE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVP----------------------LQ----MLNAGFKI  277 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~----------------------~~----~~~~gs~I  277 (779)
                            .     .. ........+.... ..+...+.+|++...                      +.    ....+..|
T Consensus       157 ------~-----~g-~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~v  224 (357)
T 3d8b_A          157 ------W-----VG-EGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILV  224 (357)
T ss_dssp             ------S-----TT-HHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCCEEE
T ss_pred             ------c-----cc-hHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCCEEE
Confidence                  0     00 0001111111111 112222223322100                      00    01234456


Q ss_pred             EEEeCchh-hhhhc--C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHHH
Q 004021          278 VLKTRSAG-VCDQM--D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVGR  347 (779)
Q Consensus       278 ivTTR~~~-va~~~--~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g~  347 (779)
                      |.||.... +....  . ...+.+...+.++..+++...+.......   -.+....|++.+.| .+-.+..+..
T Consensus       225 I~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l---~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          225 VGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCL---SEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             EEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCC---CHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCc---cHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            66776532 21111  1 35678888999999999888775432111   14567889999988 5666665543

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.55  E-value=9.2e-05  Score=77.95  Aligned_cols=173  Identities=13%  Similarity=0.040  Sum_probs=96.6

Q ss_pred             cCCccEEEcccccccccccCcccccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCC
Q 004021          494 WEGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLS  573 (779)
Q Consensus       494 ~~~lr~l~l~~~~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~  573 (779)
                      +++++.|.+.......       .+++.+ ....++..+..+++|+.|+|++|.-..+|. +. +++|++|++..|. +.
T Consensus       138 l~~L~~L~l~~~~~e~-------~~is~~-~~~~L~~ll~~~P~L~~L~L~g~~~l~l~~-~~-~~~L~~L~L~~~~-l~  206 (362)
T 2ra8_A          138 FAHFEGLFWGDIDFEE-------QEISWI-EQVDLSPVLDAMPLLNNLKIKGTNNLSIGK-KP-RPNLKSLEIISGG-LP  206 (362)
T ss_dssp             HTTCSEEEECCCCTTT-------CCGGGC-BCCBCHHHHHTCTTCCEEEEECCBTCBCCS-CB-CTTCSEEEEECSB-CC
T ss_pred             cchhhheeecCcchhh-------cccccc-cccCHHHHHhcCCCCcEEEEeCCCCceecc-cc-CCCCcEEEEecCC-CC
Confidence            4578888775432211       112222 233466667788999999999884234554 43 8899999998873 32


Q ss_pred             CCchhhh--cCCccCcEeeecccc--CCCcccccCCccCCCch-hhHHhh--cCCCCCCceeEEeecccccccCCCCCcc
Q 004021          574 IIPHQLI--SGFLKLEVLRLLECG--SEGVTKEEGNVLCDDAE-PLMREL--LGLKRLNVLSWSFRSSLAVQKFFKYPKL  646 (779)
Q Consensus       574 ~lp~~~i--~~L~~L~~L~l~~~~--~~~~~~~~~~~~~~~~~-~~~~~l--~~L~~L~~L~l~~~~~~~~~~~~~L~~L  646 (779)
                      .-.-..+  ..+++|++|+++.+.  ..+          +... .....+  ..+++|+.|++..+.......    ..+
T Consensus       207 ~~~l~~l~~~~lp~L~~L~L~~~~~~~~~----------~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~----~~l  272 (362)
T 2ra8_A          207 DSVVEDILGSDLPNLEKLVLYVGVEDYGF----------DGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVV----EMF  272 (362)
T ss_dssp             HHHHHHHHHSBCTTCCEEEEECBCGGGTC----------CSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHH----HHH
T ss_pred             hHHHHHHHHccCCCCcEEEEecccccccc----------chhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHH----HHH
Confidence            1111113  378999999986421  111          0000 011112  357899999998654321000    000


Q ss_pred             cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCC
Q 004021          647 DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYG  705 (779)
Q Consensus       647 ~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~  705 (779)
                        .....+|+|++|+|+.|. ++..-.       ..+.    ..+..+++|+.|+|++|
T Consensus       273 --a~a~~~~~L~~LdLs~n~-L~d~G~-------~~L~----~~L~~l~~L~~L~L~~n  317 (362)
T 2ra8_A          273 --LESDILPQLETMDISAGV-LTDEGA-------RLLL----DHVDKIKHLKFINMKYN  317 (362)
T ss_dssp             --HHCSSGGGCSEEECCSSC-CBHHHH-------HHHH----TTHHHHTTCSEEECCSB
T ss_pred             --HhCccCCCCCEEECCCCC-CChHHH-------HHHH----hhcccCCcceEEECCCC
Confidence              001247899999998754 332100       0000    23356899999999875

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.53  E-value=0.00029  Score=76.39  Aligned_cols=167  Identities=16%  Similarity=0.153  Sum_probs=93.8

Q ss_pred             ccccchhhhH---HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLL---PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~---~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      ..++|.+..+   ..+...+..+  ..+.+.|+|.+|+||||||+.+++..   ...|.   -++...          . 
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~--~~~~vLL~GppGtGKTtlAr~ia~~~---~~~f~---~l~a~~----------~-   86 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAG--HLHSMILWGPPGTGKTTLAEVIARYA---NADVE---RISAVT----------S-   86 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHT--CCCEEEEECSTTSSHHHHHHHHHHHT---TCEEE---EEETTT----------C-
T ss_pred             HHhCCcHHHHhchHHHHHHHHcC--CCcEEEEECCCCCcHHHHHHHHHHHh---CCCeE---EEEecc----------C-
Confidence            4589998888   7777888777  55789999999999999999999876   23331   111100          0 


Q ss_pred             cchhhhhcchhhHHHHHHHh-hCCCcceeehhhcccc--------ccccCCCc-EEEE-EeCchh--hhhh-cC-CceeE
Q 004021          232 EDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELGVP--------LQMLNAGF-KIVL-KTRSAG--VCDQ-MD-SKNLE  296 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~~~--------~~~~~~gs-~Iiv-TTR~~~--va~~-~~-~~~~~  296 (779)
                           ...+........... ..+++..+.+|++...        ++.-..|. .+|. ||.+..  +... .. ...+.
T Consensus        87 -----~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~~~v~lI~att~n~~~~l~~aL~sR~~v~~  161 (447)
T 3pvs_A           87 -----GVKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIEDGTITFIGATTENPSFELNSALLSRARVYL  161 (447)
T ss_dssp             -----CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC------CCHHHHHTTSCEEEEEESSCGGGSSCHHHHTTEEEEE
T ss_pred             -----CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhcCceEEEecCCCCcccccCHHHhCceeEEe
Confidence                 000011111111111 1233444555554221        11111222 3333 555532  2111 12 45788


Q ss_pred             ccCCChHHHHHHHHHHhhccCCC----CCCChHHHHHHHHHHhCCChhHHHHH
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLD----SHTSIPELAETLARECGRLPLALKTV  345 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~----~~~~l~~~~~~I~~~c~glPLai~~~  345 (779)
                      +++++.++-..++.+.+......    ...--.+....|++.++|.+-.+..+
T Consensus       162 l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~  214 (447)
T 3pvs_A          162 LKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNT  214 (447)
T ss_dssp             CCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHH
T ss_pred             eCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHH
Confidence            99999999999999887542100    01112567788889999988765543

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.52  E-value=2.4e-05  Score=74.19  Aligned_cols=68  Identities=18%  Similarity=0.183  Sum_probs=32.3

Q ss_pred             cchhhcccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeee--cccc
Q 004021          528 LPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRL--LECG  595 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l--~~~~  595 (779)
                      +...+...++|++|+|++|.|..     +...+...++|++|+|++| .++.     +... +...++|++|++  .+|.
T Consensus        57 l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N-~i~~~g~~~l~~~-L~~n~~L~~L~L~~~~N~  134 (185)
T 1io0_A           57 CAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESN-FISGSGILALVEA-LQSNTSLIELRIDNQSQP  134 (185)
T ss_dssp             HHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSS-CCCHHHHHHHHHG-GGGCSSCCEEECCCCSSC
T ss_pred             HHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCC-cCCHHHHHHHHHH-HHhCCCceEEEecCCCCC
Confidence            33344444555555555555432     3333444455555555555 2332     2222 444455555555  4444


Q ss_pred             CC
Q 004021          596 SE  597 (779)
Q Consensus       596 ~~  597 (779)
                      +.
T Consensus       135 i~  136 (185)
T 1io0_A          135 LG  136 (185)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.51  E-value=0.0019  Score=66.20  Aligned_cols=169  Identities=14%  Similarity=0.085  Sum_probs=91.0

Q ss_pred             ccccchhhhHHHHHHHHhcc----------CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      ..++|.+..++.+.+.+...          ....+.+.|+|.+|+||||+|+++++..   ...|   +.++...+.   
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~---~~~~---~~i~~~~l~---   91 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATEC---SATF---LNISAASLT---   91 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHT---TCEE---EEEESTTTS---
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCe---EEeeHHHHh---
Confidence            56899999999998887431          1134688999999999999999999876   2222   223321110   


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHh-hCCCcceeehhhccccc-------------------------cc--cCCCcE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSI-LSPKKFRIDLTELGVPL-------------------------QM--LNAGFK  276 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~-L~~kr~~~~ld~l~~~~-------------------------~~--~~~gs~  276 (779)
                           ..     ...........+... ...+...+.+|++....                         +.  .+.+..
T Consensus        92 -----~~-----~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~  161 (297)
T 3b9p_A           92 -----SK-----YVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIV  161 (297)
T ss_dssp             -----SS-----SCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEE
T ss_pred             -----hc-----ccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEE
Confidence                 00     000011111111111 11222233333331110                         00  113345


Q ss_pred             EEEEeCchhh-----hhhcCCceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHHHH
Q 004021          277 IVLKTRSAGV-----CDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKTVG  346 (779)
Q Consensus       277 IivTTR~~~v-----a~~~~~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~~g  346 (779)
                      ||.||.....     ...+ ...+.+...+.++-..++...+.......   -.+....|++.+.|.+- ++..+.
T Consensus       162 vi~~tn~~~~l~~~l~~R~-~~~i~~~~p~~~~r~~il~~~~~~~~~~~---~~~~~~~la~~~~g~~~~~l~~l~  233 (297)
T 3b9p_A          162 VLAATNRPQELDEAALRRF-TKRVYVSLPDEQTRELLLNRLLQKQGSPL---DTEALRRLAKITDGYSGSDLTALA  233 (297)
T ss_dssp             EEEEESCGGGBCHHHHHHC-CEEEECCCCCHHHHHHHHHHHHGGGSCCS---CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             EEeecCChhhCCHHHHhhC-CeEEEeCCcCHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            6777775432     2222 35677777888888888887765433111   14567889999988775 554443

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.50  E-value=0.002  Score=64.57  Aligned_cols=48  Identities=25%  Similarity=0.241  Sum_probs=36.8

Q ss_pred             ccccchhhhHHHHHHHHh---ccC-------CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQQ-------KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.+..++.+.+.+.   ...       ...+-|.|+|.+|+|||++|+++++..
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~   63 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA   63 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            458999988877766543   211       234568899999999999999999876

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.49  E-value=0.00057  Score=70.53  Aligned_cols=47  Identities=17%  Similarity=0.229  Sum_probs=37.3

Q ss_pred             cccchhhhHHHHHHHHhcc-------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQ-------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~-------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.+..++.+.+.+...             ......+.|+|.+|+|||++|+.+++..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l   91 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLL   91 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHH
Confidence            5899999888888765421             2244578999999999999999998876

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.45  E-value=0.0021  Score=68.02  Aligned_cols=48  Identities=23%  Similarity=0.262  Sum_probs=38.1

Q ss_pred             ccccchhhhHHH---HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPR---VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|+|++..++.   +.+.+..+....+.+.|+|.+|+|||++|+.+++..
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l   94 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQAL   94 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            568999988766   455555553334689999999999999999999987

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.43  E-value=0.0039  Score=64.49  Aligned_cols=172  Identities=15%  Similarity=0.129  Sum_probs=91.7

Q ss_pred             ccccchhhhHHHHHHHHhc----------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      .+++|.++.++.|.+.+.-          .....+-|.++|.+|+|||+||+++++.. . ..   ..+.++...+..  
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~-~-~~---~~~~i~~~~l~~--   84 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA-N-NS---TFFSISSSDLVS--   84 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT-T-SC---EEEEEECCSSCC--
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc-C-CC---cEEEEEhHHHHh--
Confidence            5689999998888887632          11234678999999999999999999875 1 11   122222221100  


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhcccccc-------------------------ccCCCcEEE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVPLQ-------------------------MLNAGFKIV  278 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~~~-------------------------~~~~gs~Ii  278 (779)
                            .    +.... +.....+.... ..++..+.+|++....+                         ....+..||
T Consensus        85 ------~----~~g~~-~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~v~vI  153 (322)
T 1xwi_A           85 ------K----WLGES-EKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVL  153 (322)
T ss_dssp             ------S----SCCSC-HHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTTEEEE
T ss_pred             ------h----hhhHH-HHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCCEEEE
Confidence                  0    00000 11111111111 12222333333311100                         012344566


Q ss_pred             EEeCchhhh-hhc--C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCC-hhHHHHHHH
Q 004021          279 LKTRSAGVC-DQM--D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRL-PLALKTVGR  347 (779)
Q Consensus       279 vTTR~~~va-~~~--~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~gl-PLai~~~g~  347 (779)
                      .||...... ..+  . ...+.++..+.++-.+++...+.......   -......|++.+.|. +-.|..+..
T Consensus       154 ~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l---~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          154 GATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSL---TEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             EEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCC---CHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             EecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC---CHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            677653221 111  2 46778888899999999988775432111   145678888998886 544555443

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.42  E-value=0.0026  Score=66.81  Aligned_cols=169  Identities=14%  Similarity=0.073  Sum_probs=91.4

Q ss_pred             ccccchhhhHHHHHHHHhcc----------CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      .+++|.+..++.|.+.+...          ....+-|.|+|.+|+|||+||+++++..   ...|   +.+....+..  
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~---~~~~---~~v~~~~l~~--  122 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTF---FSVSSSDLVS--  122 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH---TCEE---EEEEHHHHHS--
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh---CCCE---EEeeHHHHhh--
Confidence            56899999999998877321          1123458899999999999999999987   2222   2233222211  


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhcccccc-------------------------ccCCCcEEE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVPLQ-------------------------MLNAGFKIV  278 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~~~-------------------------~~~~gs~Ii  278 (779)
                        ...        ... +.....+.... ..+...+.+|++....+                         ....+..||
T Consensus       123 --~~~--------g~~-~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vI  191 (355)
T 2qp9_X          123 --KWM--------GES-EKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVL  191 (355)
T ss_dssp             --CC-----------C-HHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CCEEEE
T ss_pred             --hhc--------chH-HHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCCeEEE
Confidence              000        000 11111111111 12233333333221110                         112345566


Q ss_pred             EEeCchhh-----hhhcCCceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHH
Q 004021          279 LKTRSAGV-----CDQMDSKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVG  346 (779)
Q Consensus       279 vTTR~~~v-----a~~~~~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g  346 (779)
                      .||.....     ...+ ...+.+...+.++-.+++...+.......   -......|++.+.| .+-.|..+.
T Consensus       192 ~atn~~~~ld~al~rRf-~~~i~i~~P~~~~r~~il~~~l~~~~~~~---~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          192 GATNIPWQLDSAIRRRF-ERRIYIPLPDLAARTTMFEINVGDTPSVL---TKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             EEESCGGGSCHHHHHTC-CEEEECCCCCHHHHHHHHHHHHTTSCBCC---CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             eecCCcccCCHHHHccc-CEEEEeCCcCHHHHHHHHHHHHhhCCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            67765422     2211 46778888999999999988775433111   14556788899988 554555443

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.41  E-value=0.0052  Score=61.90  Aligned_cols=48  Identities=19%  Similarity=0.141  Sum_probs=35.7

Q ss_pred             ccccchhhhHHHHHHH-------Hhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRC-------ITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~-------L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|....++++...       +... ....+-+.|+|.+|+|||+||+++++..
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            4567887776666663       3221 3356788999999999999999999875

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.40  E-value=0.00053  Score=72.34  Aligned_cols=185  Identities=10%  Similarity=0.099  Sum_probs=94.1

Q ss_pred             ccccchhhhHHHHHHHH-hccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-C--CCCEEEEEEechHHHHHHH----
Q 004021          155 QTIVGQEKLLPRVWRCI-TDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-H--NFDVVIWAAVQTFQDDIGK----  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L-~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~--~F~~~~wv~v~~i~~~i~~----  226 (779)
                      ..++|.+..++.+.+++ ..+  ..+.+.|+|..|+||||+|+.+++...... +  .+++..|.........+..    
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~--~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~~   91 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPR--DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSP   91 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT--CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEECS
T ss_pred             HHhcCCHHHHHHHHHHHhhCC--CCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeeccc
Confidence            45899999999998888 544  223389999999999999999988531100 1  1111101000000000000    


Q ss_pred             ---HhCCCcchhhhhcchhhHHHHHHHhh--------------CCCcceeehhhccc-----------cccccCCCcEEE
Q 004021          227 ---RIGFSEDKKWKEKSLQDKAVDISSIL--------------SPKKFRIDLTELGV-----------PLQMLNAGFKIV  278 (779)
Q Consensus       227 ---~l~~~~~~~~~~~~~~~~~~~l~~~L--------------~~kr~~~~ld~l~~-----------~~~~~~~gs~Ii  278 (779)
                         .+... .  ............+....              .+++-.+.+|++..           .+.....+..+|
T Consensus        92 ~~~~~~~~-~--~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~~~~~~~I  168 (354)
T 1sxj_E           92 YHLEITPS-D--MGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLI  168 (354)
T ss_dssp             SEEEECCC-------CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEE
T ss_pred             ceEEecHh-h--cCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccCHHHHHHHHHHHHhhcCCCEEE
Confidence               00000 0  00000000111111111              11222344444322           111123467788


Q ss_pred             EEeCch-hhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHH
Q 004021          279 LKTRSA-GVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVG  346 (779)
Q Consensus       279 vTTR~~-~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g  346 (779)
                      +||.+. .+.....  ...+.+.+++.++..+.+.+.+...+...+.  ++....|++.++|.+-.+..+.
T Consensus       169 l~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          169 MVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLET--KDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             EEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECC--SHHHHHHHHHHTTCHHHHHHHH
T ss_pred             EEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCc--HHHHHHHHHHcCCCHHHHHHHH
Confidence            887763 3322222  4678999999999999999887654322110  3567889999999887665443

>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=97.38  E-value=0.0065  Score=63.23  Aligned_cols=174  Identities=16%  Similarity=0.169  Sum_probs=89.1

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i~  225 (779)
                      ..++|.+..++.+...+..+   ......+.++|.+|+||||||+.+++..   ...|.   ..+-      .++ ..+.
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l---~~~~~---~~sg~~~~~~~~l-~~~~   97 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL---QTNIH---VTSGPVLVKQGDM-AAIL   97 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH---TCCEE---EEETTTCCSHHHH-HHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHh---CCCEE---EEechHhcCHHHH-HHHH
Confidence            45789888777777666542   2345679999999999999999999876   22221   1111      111 1222


Q ss_pred             HHhCCCc----chhhhhcchhhHHHHHHHhhCCCcceeeh------hhccccccccCCCcEE-EEEeCchhhhhhcC---
Q 004021          226 KRIGFSE----DKKWKEKSLQDKAVDISSILSPKKFRIDL------TELGVPLQMLNAGFKI-VLKTRSAGVCDQMD---  291 (779)
Q Consensus       226 ~~l~~~~----~~~~~~~~~~~~~~~l~~~L~~kr~~~~l------d~l~~~~~~~~~gs~I-ivTTR~~~va~~~~---  291 (779)
                      ..+....    ++ ..... ....+.+...+......+..      ..+...+    +...+ -.|++...+.....   
T Consensus        98 ~~~~~~~v~~iDE-~~~l~-~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l----~~~~li~at~~~~~Ls~~l~sR~  171 (334)
T 1in4_A           98 TSLERGDVLFIDE-IHRLN-KAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDI----QPFTLVGATTRSGLLSSPLRSRF  171 (334)
T ss_dssp             HHCCTTCEEEEET-GGGCC-HHHHHHHHHHHHTSCCCC-------------------CCCEEEEEESCGGGSCHHHHTTC
T ss_pred             HHccCCCEEEEcc-hhhcC-HHHHHHHHHHHHhcccceeeccCcccccccccC----CCeEEEEecCCcccCCHHHHHhc
Confidence            2221100    00 00000 01122222222211110000      0000000    11122 23555443322222   


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ...+.+++.+.++-.+++.+.+......   --.+.+..|+++++|.|-.+..
T Consensus       172 ~l~~~Ld~~~~~~l~~iL~~~~~~~~~~---~~~~~~~~ia~~~~G~~R~a~~  221 (334)
T 1in4_A          172 GIILELDFYTVKELKEIIKRAASLMDVE---IEDAAAEMIAKRSRGTPRIAIR  221 (334)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHHTTCC---BCHHHHHHHHHTSTTCHHHHHH
T ss_pred             CceeeCCCCCHHHHHHHHHHHHHHcCCC---cCHHHHHHHHHhcCCChHHHHH
Confidence            2357899999999999999887543321   1256789999999999975543

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=97.37  E-value=0.0032  Score=64.53  Aligned_cols=48  Identities=25%  Similarity=0.295  Sum_probs=39.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++.+.+...           -...+.|.|+|.+|+|||+||+++++..
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~   73 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC   73 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh
Confidence            46899999988888876531           1245678999999999999999999876

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.34  E-value=0.00014  Score=68.74  Aligned_cols=46  Identities=20%  Similarity=0.387  Sum_probs=40.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.+++.+.+.+...  ..+.+.|+|.+|+|||+||+.+++..
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~--~~~~vll~G~~G~GKT~la~~~~~~~   67 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRR--TKNNPILLGDPGVGKTAIVEGLAIKI   67 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS--SSCEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCC--CCCceEEECCCCCCHHHHHHHHHHHH
Confidence            45899999999999999775  45677899999999999999998876

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.33  E-value=0.0028  Score=65.78  Aligned_cols=47  Identities=17%  Similarity=0.027  Sum_probs=39.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+++..+. ...++-+.|.+|+|||++|+++++..
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~~l   72 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCHDV   72 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHHHT
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHHHh
Confidence            568999999999999998652 33677888889999999999998876

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.30  E-value=8e-05  Score=70.50  Aligned_cols=122  Identities=13%  Similarity=0.007  Sum_probs=81.7

Q ss_pred             cchhhcccccCceeeecCC-cccc-----cchhhccCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeeeccccC
Q 004021          528 LPSRISSLVSLHHLDLSLT-HIRG-----LPQELKALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~-~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      +...+...++|++|+|++| .+..     +...+...++|++|+|++| .+..     +... +...++|++|++++|.+
T Consensus        28 l~~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n-~i~~~g~~~l~~~-L~~n~~L~~L~L~~N~i  105 (185)
T 1io0_A           28 LKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGT-RSNDPVAFALAEM-LKVNNTLKSLNVESNFI  105 (185)
T ss_dssp             HHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTS-CCCHHHHHHHHHH-HHHCSSCCEEECCSSCC
T ss_pred             HHHHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCC-CCChHHHHHHHHH-HHhCCCcCEEECcCCcC
Confidence            3445677899999999999 7754     5667788899999999999 4443     3333 56668899999999987


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeE--EeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSW--SFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l--~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                      ..          .........+...++|++|++  +.|....-..    ..+ ...+...++|++|+|++|.
T Consensus       106 ~~----------~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~g~----~~l-~~~L~~n~~L~~L~L~~n~  162 (185)
T 1io0_A          106 SG----------SGILALVEALQSNTSLIELRIDNQSQPLGNNVE----MEI-ANMLEKNTTLLKFGYHFTQ  162 (185)
T ss_dssp             CH----------HHHHHHHHGGGGCSSCCEEECCCCSSCCCHHHH----HHH-HHHHHHCSSCCEEECCCSS
T ss_pred             CH----------HHHHHHHHHHHhCCCceEEEecCCCCCCCHHHH----HHH-HHHHHhCCCcCEEeccCCC
Confidence            63          101234566777788999998  5444321100    000 1123455788888888764

>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=97.30  E-value=0.00023  Score=70.99  Aligned_cols=82  Identities=22%  Similarity=0.225  Sum_probs=60.9

Q ss_pred             CCccEEEcccccccccccCcccccccccccccccchhhcccccCceeeecCCcccccchhhccCc--cCcEeeccCCcCC
Q 004021          495 EGAKRISLMANEIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALE--KLRYLNLEYTHYL  572 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~--~L~~L~l~~~~~l  572 (779)
                      ..++.|+|++|.+..+               ..+|..+..+++|++|+|++|.|+.+ ..+..+.  +|++|+|++|...
T Consensus       170 ~~L~~L~Ls~N~l~~l---------------~~l~~~~~~l~~L~~L~Ls~N~i~~~-~~l~~l~~l~L~~L~L~~Npl~  233 (267)
T 3rw6_A          170 PELLSLNLSNNRLYRL---------------DDMSSIVQKAPNLKILNLSGNELKSE-RELDKIKGLKLEELWLDGNSLC  233 (267)
T ss_dssp             TTCCEEECTTSCCCCC---------------GGGTTHHHHSTTCCEEECTTSCCCSG-GGGGGGTTSCCSEEECTTSTTG
T ss_pred             CCCCEEECCCCCCCCC---------------ccchhHHhhCCCCCEEECCCCccCCc-hhhhhcccCCcceEEccCCcCc
Confidence            4678888887776443               33567788999999999999999987 3456565  9999999999644


Q ss_pred             CCCch------hhhcCCccCcEeeec
Q 004021          573 SIIPH------QLISGFLKLEVLRLL  592 (779)
Q Consensus       573 ~~lp~------~~i~~L~~L~~L~l~  592 (779)
                      ..+|.      .++..+++|+.|+-.
T Consensus       234 ~~~~~~~~y~~~il~~~P~L~~LDg~  259 (267)
T 3rw6_A          234 DTFRDQSTYISAIRERFPKLLRLDGH  259 (267)
T ss_dssp             GGCSSHHHHHHHHHHHCTTCCEESSC
T ss_pred             cccCcchhHHHHHHHHCcccCeECCc
Confidence            44552      246778888888643

>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=97.27  E-value=0.0051  Score=66.72  Aligned_cols=171  Identities=16%  Similarity=0.109  Sum_probs=90.3

Q ss_pred             ccccchhhhHHHHHHHHhc----------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      .+++|.+..++.|.+.+..          .....+-|.++|++|+|||+||+++++.. . ..   ..+.++...+....
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~-~-~~---~~~~v~~~~l~~~~  208 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA-N-NS---TFFSISSSDLVSKW  208 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC-C-SS---EEEEECCC------
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc-C-CC---CEEEEeHHHHHhhh
Confidence            5689999999999887731          11234678999999999999999999875 1 11   11222222222111


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhh-CCCcceeehhhcccc----------------------cc---ccCCCcEEE
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSIL-SPKKFRIDLTELGVP----------------------LQ---MLNAGFKIV  278 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~~~~ld~l~~~----------------------~~---~~~~gs~Ii  278 (779)
                      .   +..      ....    ..+.... ..+...+.+|++...                      +.   ....+..||
T Consensus       209 ~---g~~------~~~~----~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~v~vI  275 (444)
T 2zan_A          209 L---GES------EKLV----KNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVL  275 (444)
T ss_dssp             ------C------CCTH----HHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSSCEEE
T ss_pred             c---chH------HHHH----HHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCCEEEE
Confidence            0   000      0001    1111111 122223333333211                      00   012455677


Q ss_pred             EEeCchhhh-hh-c-C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCC-ChhHHHHHH
Q 004021          279 LKTRSAGVC-DQ-M-D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGR-LPLALKTVG  346 (779)
Q Consensus       279 vTTR~~~va-~~-~-~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~g-lPLai~~~g  346 (779)
                      .||...... .. . . ...+.++..+.++-..+|...+.......   -......|++.+.| .+-.|..+.
T Consensus       276 ~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l---~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          276 GATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL---TEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             EEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC---CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             ecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC---CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            777654321 11 1 1 35678888888888888888765432111   13556788899988 454555443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.25  E-value=0.0047  Score=65.88  Aligned_cols=48  Identities=25%  Similarity=0.240  Sum_probs=39.1

Q ss_pred             ccccchhhhHHHHHHHHhcc----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.|.+++...          ....+-|.|+|.+|+|||+||+++++..
T Consensus       115 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~  172 (389)
T 3vfd_A          115 DDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES  172 (389)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence            56899999999999887321          1134678999999999999999998875

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.25  E-value=0.0044  Score=65.04  Aligned_cols=48  Identities=25%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||.||+++++..
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~  206 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHT  206 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhh
Confidence            4578899888888776532           12234668899999999999999999987

>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=97.06  E-value=0.005  Score=64.32  Aligned_cols=164  Identities=13%  Similarity=0.182  Sum_probs=90.3

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCC-EEEEEEechHHHHHHHHhCCCcc
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFD-VVIWAAVQTFQDDIGKRIGFSED  233 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~-~~~wv~v~~i~~~i~~~l~~~~~  233 (779)
                      ..++|.+..++.+...+..+  ..+.+.++|.+|+||||+|+.+++.. . ...+. .+.-++.             .  
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g--~~~~~ll~Gp~G~GKTtla~~la~~l-~-~~~~~~~~~~~~~-------------~--   85 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVALAREI-Y-GKNYSNMVLELNA-------------S--   85 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHHHHHH-H-TTSHHHHEEEECT-------------T--
T ss_pred             HHhcCcHHHHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHH-c-CCCccceEEEEcC-------------c--
Confidence            45789998889888888776  44348999999999999999999875 1 11111 0111111             0  


Q ss_pred             hhhhhcchhhHHHHHHHhh------CCCcceeehhhccc-----------cccccCCCcEEEEEeCch-hhhhhcC--Cc
Q 004021          234 KKWKEKSLQDKAVDISSIL------SPKKFRIDLTELGV-----------PLQMLNAGFKIVLKTRSA-GVCDQMD--SK  293 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L------~~kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~~-~va~~~~--~~  293 (779)
                         .....+.....+....      .+.+-...+|++..           .+......+++|++|... .+.....  ..
T Consensus        86 ---~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~~  162 (340)
T 1sxj_C           86 ---DDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCT  162 (340)
T ss_dssp             ---SCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             ---ccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhce
Confidence               0000111111111111      11112333343311           111122455677776543 2222221  35


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALK  343 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~  343 (779)
                      .+.+.+++.++..+.+.+.+......-+   .+....|++.++|-+--+.
T Consensus       163 ~~~~~~l~~~~~~~~l~~~~~~~~~~i~---~~~~~~i~~~s~G~~r~~~  209 (340)
T 1sxj_C          163 RFRFQPLPQEAIERRIANVLVHEKLKLS---PNAEKALIELSNGDMRRVL  209 (340)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCCBC---HHHHHHHHHHHTTCHHHHH
T ss_pred             eEeccCCCHHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHcCCCHHHHH
Confidence            7889999999998888877643332111   4567889999999876433

>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=97.05  E-value=0.0053  Score=67.09  Aligned_cols=48  Identities=31%  Similarity=0.328  Sum_probs=38.9

Q ss_pred             ccccchhhhHHHHHHHHhcc-----------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-----------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..+++|.+.+...           ....+-|.|+|.+|+|||++|+++++..
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~  262 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET  262 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh
Confidence            35899999999998887532           2345568899999999999999998865

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.99  E-value=0.00062  Score=61.37  Aligned_cols=47  Identities=17%  Similarity=0.285  Sum_probs=36.8

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|+...++++.+.+..-.....-|-|+|.+|+|||++|+.+++..
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~   48 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC
Confidence            47899999999998886532233456799999999999999998865

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=96.97  E-value=0.015  Score=57.83  Aligned_cols=48  Identities=21%  Similarity=0.230  Sum_probs=35.7

Q ss_pred             ccccchhhhHHHHHHHHh---cc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.+..++++.+.+.   ..       ....+-|.|+|.+|+||||||+.+++..
T Consensus        12 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   69 (257)
T 1lv7_A           12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (257)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc
Confidence            568999988877766542   21       0123458899999999999999999876

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.94  E-value=0.0089  Score=63.72  Aligned_cols=48  Identities=21%  Similarity=0.236  Sum_probs=38.6

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||.||+++++..
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~  239 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQT  239 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHh
Confidence            4678999999888876532           12345678899999999999999999987

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.92  E-value=0.0047  Score=65.77  Aligned_cols=48  Identities=23%  Similarity=0.247  Sum_probs=38.2

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||.||+++++..
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~  267 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRT  267 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhcc
Confidence            3578999888888776531           12356778899999999999999999987

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.91  E-value=0.0085  Score=63.95  Aligned_cols=48  Identities=29%  Similarity=0.288  Sum_probs=38.3

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-..++=|-++|++|.|||+||+++++..
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~  239 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATI  239 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            4578899888888776642           12345678899999999999999999987

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.76  E-value=0.0081  Score=63.31  Aligned_cols=48  Identities=31%  Similarity=0.324  Sum_probs=38.1

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||.||+++++..
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~  240 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT  240 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHH
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHh
Confidence            4568899888888776532           12345678999999999999999999987

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.70  E-value=0.003  Score=60.46  Aligned_cols=62  Identities=21%  Similarity=0.193  Sum_probs=42.1

Q ss_pred             hhHHHHHHHHhccCCC--ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          162 KLLPRVWRCITDQQKN--RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       162 ~~~~~l~~~L~~~~~~--~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      ..++.+.+++......  .+.+.|+|.+|+|||+||+++++..   ......++|+++..+...+..
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~---~~~~~~~~~~~~~~~~~~~~~   99 (202)
T 2w58_A           36 KAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANEL---AKRNVSSLIVYVPELFRELKH   99 (202)
T ss_dssp             HHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHH---HTTTCCEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHH---HHcCCeEEEEEhHHHHHHHHH
Confidence            3445555665543222  2688999999999999999999887   233345677777666655544

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.69  E-value=0.0075  Score=64.24  Aligned_cols=48  Identities=25%  Similarity=0.277  Sum_probs=38.6

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||+||+++++..
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~  230 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANST  230 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            4678999999888876642           12345668899999999999999999987

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=96.68  E-value=0.026  Score=61.19  Aligned_cols=48  Identities=25%  Similarity=0.306  Sum_probs=35.8

Q ss_pred             ccccchhhhHHHHHHHHh---cc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++.+.+.   ..       -...+-|.|+|.+|+|||+||+++++..
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~   73 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA   73 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            568999988777766543   21       1123447899999999999999999876

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=96.57  E-value=0.013  Score=62.52  Aligned_cols=61  Identities=8%  Similarity=0.112  Sum_probs=33.6

Q ss_pred             hhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccc
Q 004021          531 RISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLEC  594 (779)
Q Consensus       531 ~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~  594 (779)
                      .+.++..|+.+.+..+. ..+........+|+.+.+..+  +..++...+..+.+|+.+.+..+
T Consensus       203 ~F~~~~~L~~i~~~~~~-~~i~~~~~~~~~l~~i~ip~~--~~~i~~~~f~~~~~l~~~~~~~~  263 (394)
T 4fs7_A          203 CFAECILLENMEFPNSL-YYLGDFALSKTGVKNIIIPDS--FTELGKSVFYGCTDLESISIQNN  263 (394)
T ss_dssp             TTTTCTTCCBCCCCTTC-CEECTTTTTTCCCCEEEECTT--CCEECSSTTTTCSSCCEEEECCT
T ss_pred             hhccccccceeecCCCc-eEeehhhcccCCCceEEECCC--ceecccccccccccceeEEcCCC
Confidence            45666777777665542 222333334456666666543  34555544566666776666543

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.56  E-value=0.038  Score=57.33  Aligned_cols=170  Identities=11%  Similarity=0.035  Sum_probs=87.4

Q ss_pred             hhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEEEe-chHHHHHHHHhCC-----Ccc
Q 004021          161 EKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAV-QTFQDDIGKRIGF-----SED  233 (779)
Q Consensus       161 ~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv~v-~~i~~~i~~~l~~-----~~~  233 (779)
                      ++..+.+.+.+..+. -...+-++|..|+|||++|+.+++...... ..+..    +- -.....+...-..     ...
T Consensus         8 ~~~~~~l~~~i~~~~-~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~----c~~c~~c~~~~~~~~~d~~~~~~~   82 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKS----CGHCRGCQLMQAGTHPDYYTLAPE   82 (334)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBC----CSCSHHHHHHHHTCCTTEEEECCC
T ss_pred             HHHHHHHHHHHHcCC-cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCC----CCCCHHHHHHhcCCCCCEEEEecc
Confidence            455667777776552 345789999999999999999988752111 00000    00 0011111110000     000


Q ss_pred             hhhhhcchhhHHHHHHHhhCC-----Ccceeehhhccc-----------cccccCCCcEEEEEeCch-hhhhhcC--Cce
Q 004021          234 KKWKEKSLQDKAVDISSILSP-----KKFRIDLTELGV-----------PLQMLNAGFKIVLKTRSA-GVCDQMD--SKN  294 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L~~-----kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~~-~va~~~~--~~~  294 (779)
                      ........++ ...+.+.+..     ++-...+|++..           .+.....++.+|++|.+. .+.....  ...
T Consensus        83 ~~~~~~~i~~-ir~l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~ti~SRc~~  161 (334)
T 1a5t_A           83 KGKNTLGVDA-VREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRL  161 (334)
T ss_dssp             TTCSSBCHHH-HHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEE
T ss_pred             ccCCCCCHHH-HHHHHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHhhccee
Confidence            0000111111 2223333322     122333333211           111122456667666654 3433332  568


Q ss_pred             eEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          295 LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       295 ~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      +.+.+++.++..+.+.+..   .  .   -.+....+++.++|.|..+..
T Consensus       162 ~~~~~~~~~~~~~~L~~~~---~--~---~~~~~~~l~~~s~G~~r~a~~  203 (334)
T 1a5t_A          162 HYLAPPPEQYAVTWLSREV---T--M---SQDALLAALRLSAGSPGAALA  203 (334)
T ss_dssp             EECCCCCHHHHHHHHHHHC---C--C---CHHHHHHHHHHTTTCHHHHHH
T ss_pred             eeCCCCCHHHHHHHHHHhc---C--C---CHHHHHHHHHHcCCCHHHHHH
Confidence            8999999999999888775   1  1   145668899999999976654

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.53  E-value=0.021  Score=65.71  Aligned_cols=48  Identities=31%  Similarity=0.358  Sum_probs=37.6

Q ss_pred             ccccchhhhHHHHHHHHh----cc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT----DQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~----~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+.    ..       -..++=|-++|++|+|||+||+++++..
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el  262 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET  262 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            356888888888877653    21       1245678999999999999999999987

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.38  E-value=0.0024  Score=69.81  Aligned_cols=46  Identities=24%  Similarity=0.434  Sum_probs=39.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.+++.+.+.|...  ...-+.++|.+|+|||++|+.+++..
T Consensus       180 d~iiGr~~~i~~l~~~l~r~--~~~~~LL~G~pG~GKT~la~~la~~l  225 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQI  225 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhcc--CCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            35899999999999999765  33456799999999999999999876

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.29  E-value=0.00095  Score=59.97  Aligned_cols=48  Identities=17%  Similarity=0.133  Sum_probs=34.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.++|++..++++.+.+..-.....-|-|+|.+|+|||++|+.+++..
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG   51 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            357999999998888876421123447799999999999999997765

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=96.12  E-value=0.19  Score=53.32  Aligned_cols=68  Identities=18%  Similarity=0.284  Sum_probs=43.7

Q ss_pred             CCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCCCCC-CC-cccccEEEechHhhhhhCc
Q 004021          689 SEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLPINS-SS-AKERRVVIEGLKEWWEELQ  760 (779)
Q Consensus       689 ~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP~~~-~~-~~~~~l~i~~~~~~~~~l~  760 (779)
                      ..+.++++|+.+.|..  +++.+... +..+.+|+.+.|..  +++.++... .. .+++.+.+.+...-|+...
T Consensus       305 ~aF~~c~~L~~i~lp~--~v~~I~~~aF~~C~~L~~i~ip~--sv~~I~~~aF~~C~~L~~i~~~~~~~~~~~~~  375 (394)
T 4gt6_A          305 SVFAGCISLKSIDIPE--GITQILDDAFAGCEQLERIAIPS--SVTKIPESAFSNCTALNNIEYSGSRSQWNAIS  375 (394)
T ss_dssp             TTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCEEEECT--TCCBCCGGGGTTCTTCCEEEESSCHHHHHTCB
T ss_pred             eeecCCCCcCEEEeCC--cccEehHhHhhCCCCCCEEEECc--ccCEEhHhHhhCCCCCCEEEECCceeehhhhh
Confidence            4667788888888864  56777653 34678888888853  466676542 22 3457777777665555443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.09  E-value=0.03  Score=65.29  Aligned_cols=48  Identities=23%  Similarity=0.431  Sum_probs=38.9

Q ss_pred             ccccchhhhHHHHHHHHhccC-------CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQ-------KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~-------~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+.+....       .....+.++|.+|+|||++|+++++..
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l  545 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESI  545 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            568999999999888886421       122379999999999999999999876

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.89  E-value=0.0085  Score=57.17  Aligned_cols=44  Identities=23%  Similarity=0.352  Sum_probs=35.0

Q ss_pred             chhhhHHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          159 GQEKLLPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|++.++++.+.+... .....+|+|.|..|+||||+++.+....
T Consensus         2 ~~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A            2 ELRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             CHHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3566778888877653 2355799999999999999999998765

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.87  E-value=0.0062  Score=58.51  Aligned_cols=40  Identities=28%  Similarity=0.414  Sum_probs=30.5

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -+++|.+.+........+|+|+|..|+|||||++.+....
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~   46 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAAL   46 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4455555554333356799999999999999999998876

>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=95.84  E-value=0.0058  Score=61.25  Aligned_cols=48  Identities=13%  Similarity=0.190  Sum_probs=35.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..+.++.+.+..-.....-|.|+|.+|+|||++|+.+++..
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~   53 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLS   53 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTS
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhc
Confidence            347999999998888776522233567799999999999999999876

>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=95.84  E-value=0.0048  Score=63.41  Aligned_cols=48  Identities=25%  Similarity=0.307  Sum_probs=38.9

Q ss_pred             ccccchhhhHHHHHHHHhcc------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|++..++.+...+...            .....-+.++|.+|+|||++|+.+++..
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            56899999999998887641            1134567899999999999999999876

>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=95.77  E-value=0.0063  Score=56.91  Aligned_cols=66  Identities=14%  Similarity=0.133  Sum_probs=41.0

Q ss_pred             hhhhHHHHHHHHhccC-CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHH
Q 004021          160 QEKLLPRVWRCITDQQ-KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKR  227 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~-~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~  227 (779)
                      .+..++.+.+++..-. .....+.|+|.+|+||||||+.+++.. .....+ .++++++.++...+...
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~-~~~~g~-~~~~~~~~~~~~~~~~~   85 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAI-YEKKGI-RGYFFDTKDLIFRLKHL   85 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHH-HHHSCC-CCCEEEHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHH-HHHcCC-eEEEEEHHHHHHHHHHH
Confidence            4444555555554321 134789999999999999999999877 211222 24456665555555443

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=95.71  E-value=0.029  Score=59.79  Aligned_cols=147  Identities=14%  Similarity=0.048  Sum_probs=86.3

Q ss_pred             hcccccCceeeecCCcccccc-hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCC
Q 004021          532 ISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDD  610 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~  610 (779)
                      .....+|+.+.+..+ ++.++ ..+..+.+|+.+.+..+  +..++...+..+.+|+.+......+..            
T Consensus       226 ~~~~~~l~~i~ip~~-~~~i~~~~f~~~~~l~~~~~~~~--~~~i~~~~F~~~~~l~~~~~~~~~i~~------------  290 (394)
T 4fs7_A          226 ALSKTGVKNIIIPDS-FTELGKSVFYGCTDLESISIQNN--KLRIGGSLFYNCSGLKKVIYGSVIVPE------------  290 (394)
T ss_dssp             TTTTCCCCEEEECTT-CCEECSSTTTTCSSCCEEEECCT--TCEECSCTTTTCTTCCEEEECSSEECT------------
T ss_pred             hcccCCCceEEECCC-ceecccccccccccceeEEcCCC--cceeeccccccccccceeccCceeecc------------
Confidence            334466777776543 33332 34667788888888765  345555557777777777665443221            


Q ss_pred             chhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCC
Q 004021          611 AEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSE  690 (779)
Q Consensus       611 ~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~  690 (779)
                           ..+..+.+|+.+.+.          .+++.+....+..+.+|+.++|..  .++.+..               ..
T Consensus       291 -----~~F~~~~~L~~i~l~----------~~i~~I~~~aF~~c~~L~~i~lp~--~v~~I~~---------------~a  338 (394)
T 4fs7_A          291 -----KTFYGCSSLTEVKLL----------DSVKFIGEEAFESCTSLVSIDLPY--LVEEIGK---------------RS  338 (394)
T ss_dssp             -----TTTTTCTTCCEEEEC----------TTCCEECTTTTTTCTTCCEECCCT--TCCEECT---------------TT
T ss_pred             -----ccccccccccccccc----------cccceechhhhcCCCCCCEEEeCC--cccEEhH---------------Hh
Confidence                 124456667766653          334444445566667777777643  2444433               45


Q ss_pred             CCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeee
Q 004021          691 HNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVY  727 (779)
Q Consensus       691 ~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~  727 (779)
                      +.++++|+.+.|..  +++.+... +..+++|+.+.+.
T Consensus       339 F~~c~~L~~i~lp~--~l~~I~~~aF~~C~~L~~i~lp  374 (394)
T 4fs7_A          339 FRGCTSLSNINFPL--SLRKIGANAFQGCINLKKVELP  374 (394)
T ss_dssp             TTTCTTCCEECCCT--TCCEECTTTBTTCTTCCEEEEE
T ss_pred             ccCCCCCCEEEECc--cccEehHHHhhCCCCCCEEEEC
Confidence            66777777777753  36666543 3356677777764

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.68  E-value=0.0087  Score=61.25  Aligned_cols=48  Identities=13%  Similarity=0.216  Sum_probs=38.5

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|+...+.++.+.+..-.....-|-|+|.+|+|||++|+.+++..
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            458999999999998886632234557799999999999999999865

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=95.63  E-value=0.012  Score=51.64  Aligned_cols=55  Identities=18%  Similarity=0.172  Sum_probs=36.3

Q ss_pred             eeeecCCccc--ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          540 HLDLSLTHIR--GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       540 ~L~L~~~~i~--~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      .++.++++++  .+|..+.  .+|++|+|++| .++.+|.+.+..+.+|++|++.+|...
T Consensus        12 ~v~Cs~~~L~~~~vP~~lp--~~l~~L~Ls~N-~l~~l~~~~f~~l~~L~~L~L~~NP~~   68 (130)
T 3rfe_A           12 LVDCGRRGLTWASLPTAFP--VDTTELVLTGN-NLTALPPGLLDALPALRTAHLGANPWR   68 (130)
T ss_dssp             EEECCSSCCCTTTSCSCCC--TTCSEEECTTS-CCSSCCTTTGGGCTTCCEEECCSSCCB
T ss_pred             EEEeCCCCCccccCCCCCC--cCCCEEECCCC-cCCccChhhhhhccccCEEEecCCCee
Confidence            5566666666  6665432  35777777777 567777776677777777777776554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.59  E-value=0.0083  Score=70.05  Aligned_cols=46  Identities=24%  Similarity=0.434  Sum_probs=39.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++.+.|...  ...-+.++|.+|+|||++|+.+++..
T Consensus       180 d~iiG~~~~i~~l~~~l~~~--~~~~vLL~G~pGtGKT~la~~la~~l  225 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRR--TKNNPVLIGEPGVGKTAIAEGLAQQI  225 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS--SSCEEEEESCTTTTTHHHHHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCC--CCCCeEEECCCCCCHHHHHHHHHHHH
Confidence            35899999999999999765  33457899999999999999999875

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.55  E-value=0.18  Score=54.93  Aligned_cols=48  Identities=23%  Similarity=0.294  Sum_probs=35.2

Q ss_pred             ccccchhhhHHHHHHHHh---ccC-------CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQQ-------KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.+.++.+...   ...       .-.+=|.|+|.+|+||||||+++++..
T Consensus        31 ~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~   88 (499)
T 2dhr_A           31 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   88 (499)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT
T ss_pred             HHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            568999887777666542   210       112338999999999999999999876

>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=95.55  E-value=0.0071  Score=71.54  Aligned_cols=46  Identities=22%  Similarity=0.432  Sum_probs=39.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+++++++++.|...  ...-+.++|.+|+||||+|+.+++..
T Consensus       170 d~viGr~~~i~~l~~~l~~~--~~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRR--TKNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCS--SCCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHhcC--CCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            45799999999999999765  34456899999999999999999876

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.55  E-value=0.012  Score=60.99  Aligned_cols=44  Identities=27%  Similarity=0.430  Sum_probs=38.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++|+++.++.+...+..+    .-+.++|.+|+|||+||+.+++..
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~----~~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTG----GHILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT----CCEEEESCCCHHHHHHHHHHHHHT
T ss_pred             cceeCcHHHHHHHHHHHHcC----CeEEEECCCCCcHHHHHHHHHHHh
Confidence            55899999999998888765    357899999999999999998866

>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=95.31  E-value=0.013  Score=68.44  Aligned_cols=46  Identities=26%  Similarity=0.401  Sum_probs=39.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++||+.+++++.+.|...  ...-+.|+|.+|+|||++|+.+++..
T Consensus       186 d~~iGr~~~i~~l~~~l~~~--~~~~vlL~G~~GtGKT~la~~la~~l  231 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRI  231 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhcc--CCCCeEEEcCCCCCHHHHHHHHHHHH
Confidence            45799999999999999866  44557899999999999999999876

>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=95.25  E-value=0.0092  Score=59.86  Aligned_cols=48  Identities=27%  Similarity=0.236  Sum_probs=36.5

Q ss_pred             ccccchhhhHHHHHHHHhc----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+.+.+..          +....+-+.|+|.+|+|||+||+++++..
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            5689999888888776541          11122347799999999999999999876

>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=95.24  E-value=0.014  Score=61.40  Aligned_cols=48  Identities=23%  Similarity=0.278  Sum_probs=37.8

Q ss_pred             ccccchhhhHHHHHHHHhc-------------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-------------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-------------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+..             .......|.++|.+|+|||++|+++++..
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            3479999999998888731             11134578899999999999999999876

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=95.23  E-value=0.011  Score=60.85  Aligned_cols=48  Identities=29%  Similarity=0.436  Sum_probs=39.1

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+...       ......+.++|.+|+|||++|+.+++..
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            45789999999988888653       1123589999999999999999999876

>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=95.22  E-value=0.019  Score=58.03  Aligned_cols=28  Identities=29%  Similarity=0.243  Sum_probs=24.5

Q ss_pred             CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          175 QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       175 ~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .....+|+|+|..|+||||||+.+....
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l   55 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHL   55 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3466799999999999999999988776

>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=95.20  E-value=0.01  Score=55.20  Aligned_cols=24  Identities=21%  Similarity=0.347  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|++|+||||+|+.+.+..
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            589999999999999999998876

>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=95.14  E-value=0.011  Score=54.51  Aligned_cols=24  Identities=21%  Similarity=0.206  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|++|+||||+|+.+....
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            478999999999999999998876

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=95.14  E-value=0.13  Score=52.21  Aligned_cols=133  Identities=17%  Similarity=0.065  Sum_probs=72.3

Q ss_pred             chhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc-CCCCEEEEEEec------hHHHHHHHHhCCC
Q 004021          159 GQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ-HNFDVVIWAAVQ------TFQDDIGKRIGFS  231 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~-~~F~~~~wv~v~------~i~~~i~~~l~~~  231 (779)
                      |-++.++.+.+.+..+  +.+..-++|.+|+||||+|+.+++...... .+.+. .++...      +..+++.+.+...
T Consensus         1 g~~~~~~~L~~~i~~~--~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~-~~l~~~~~~~~id~ir~li~~~~~~   77 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS--EGISILINGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDIRTIKDFLNYS   77 (305)
T ss_dssp             ---CHHHHHHHHHHTC--SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHHHHHHHHHTSC
T ss_pred             ChHHHHHHHHHHHHCC--CCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCE-EEEcCCcCCCCHHHHHHHHHHHhhc
Confidence            4456677788887776  367899999999999999999987531011 23443 333321      0112222222111


Q ss_pred             cchhhhhcchhhHHHHHHHhhCCCcceeehhhcc-----------ccccccCCCcEEEEEeCc-hhhhhhcCCceeEccC
Q 004021          232 EDKKWKEKSLQDKAVDISSILSPKKFRIDLTELG-----------VPLQMLNAGFKIVLKTRS-AGVCDQMDSKNLEVYS  299 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~-----------~~~~~~~~gs~IivTTR~-~~va~~~~~~~~~l~~  299 (779)
                      +.                   .+++-...+|++.           ..+....+.+.+|++|.+ ..+...+..+.+++.+
T Consensus        78 p~-------------------~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR~~~f~~  138 (305)
T 2gno_A           78 PE-------------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVV  138 (305)
T ss_dssp             CS-------------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             cc-------------------cCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHceeEeCCC
Confidence            00                   0111122222221           111122345666666644 3454444433899999


Q ss_pred             CChHHHHHHHHHHh
Q 004021          300 LAHDEAWKLFQEMI  313 (779)
Q Consensus       300 L~~~~a~~Lf~~~a  313 (779)
                      +++++..+.+.+.+
T Consensus       139 l~~~~i~~~L~~~~  152 (305)
T 2gno_A          139 NVPKEFRDLVKEKI  152 (305)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999988776

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.11  E-value=0.014  Score=63.84  Aligned_cols=44  Identities=11%  Similarity=0.187  Sum_probs=38.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++|+++.++.+...+..+    .-|.++|.+|+|||+||+.+++..
T Consensus        22 ~~ivGq~~~i~~l~~al~~~----~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSG----ESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHT----CEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             hhhHHHHHHHHHHHHHHhcC----CeeEeecCchHHHHHHHHHHHHHH
Confidence            45899999999988888766    468899999999999999998866

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=95.07  E-value=0.02  Score=62.27  Aligned_cols=48  Identities=25%  Similarity=0.278  Sum_probs=37.3

Q ss_pred             ccccchhhhHHHHHHH---HhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRC---ITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~---L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+..+   +..+....+-+.++|++|+|||++|+++++..
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHh
Confidence            5689999887765544   44443334578899999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.05  E-value=0.013  Score=55.70  Aligned_cols=25  Identities=40%  Similarity=0.307  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|+|++|+||||+|+.++...
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            4689999999999999999999876

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.04  E-value=0.025  Score=58.22  Aligned_cols=45  Identities=24%  Similarity=0.344  Sum_probs=33.9

Q ss_pred             cchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          158 VGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |+.+.-.+++++.+...  .+....|.|+|++|+||||+++.++...
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHh
Confidence            45566667777776532  3356679999999999999999998766

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=95.02  E-value=0.019  Score=50.23  Aligned_cols=51  Identities=31%  Similarity=0.415  Sum_probs=39.0

Q ss_pred             cccccccccc--ccchhhcccccCceeeecCCcccccchh-hccCccCcEeeccCCc
Q 004021          517 LSLRRNDSLT--ELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTH  570 (779)
Q Consensus       517 L~L~~~~~l~--~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~  570 (779)
                      ++.+++ .++  .+|..+.  .+|++|+|++|.|+.+|.. |..+++|++|+|++|.
T Consensus        13 v~Cs~~-~L~~~~vP~~lp--~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~NP   66 (130)
T 3rfe_A           13 VDCGRR-GLTWASLPTAFP--VDTTELVLTGNNLTALPPGLLDALPALRTAHLGANP   66 (130)
T ss_dssp             EECCSS-CCCTTTSCSCCC--TTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSC
T ss_pred             EEeCCC-CCccccCCCCCC--cCCCEEECCCCcCCccChhhhhhccccCEEEecCCC
Confidence            455555 666  6775442  4689999999999998775 6788999999999884

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=94.98  E-value=0.032  Score=57.02  Aligned_cols=65  Identities=15%  Similarity=0.236  Sum_probs=41.9

Q ss_pred             hhhhHHHHHHHHhccCC-CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          160 QEKLLPRVWRCITDQQK-NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~-~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      +...++.+.+++..... ...-+.|+|.+|+|||+||+++++.. .. ..-..+.++++..+...+..
T Consensus       133 ~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~-~~-~~g~~v~~~~~~~l~~~l~~  198 (308)
T 2qgz_A          133 RMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHEL-SE-KKGVSTTLLHFPSFAIDVKN  198 (308)
T ss_dssp             HHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHH-HH-HSCCCEEEEEHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHH-HH-hcCCcEEEEEHHHHHHHHHH
Confidence            34445555566655321 24678899999999999999999987 20 12234556666666555543

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=94.96  E-value=0.012  Score=54.42  Aligned_cols=20  Identities=30%  Similarity=0.517  Sum_probs=18.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQV  198 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v  198 (779)
                      .+|.|.|++|+||||+|+.+
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            47999999999999999999

>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=94.93  E-value=0.025  Score=55.67  Aligned_cols=44  Identities=23%  Similarity=0.191  Sum_probs=31.2

Q ss_pred             chhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          159 GQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +....+.++............+|.|.|++|+||||+|+.+.+..
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           10 STIDLLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CHHHHHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            33344445554444433356789999999999999999998765

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=94.90  E-value=0.015  Score=54.78  Aligned_cols=25  Identities=32%  Similarity=0.364  Sum_probs=22.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|+|++|+|||||++.+....
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~~   33 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANLP   33 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhcc
Confidence            4689999999999999999997753

>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=94.87  E-value=0.06  Score=59.83  Aligned_cols=48  Identities=29%  Similarity=0.412  Sum_probs=36.9

Q ss_pred             ccccchhhhHHHHHHHHhc----cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD----QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++..+.+.+.+.-    .......+.++|.+|+||||||+.++...
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            4578888877777665432    12245689999999999999999999876

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=94.86  E-value=0.055  Score=57.60  Aligned_cols=58  Identities=10%  Similarity=0.240  Sum_probs=31.1

Q ss_pred             hcccccCceeeecCCccccc-chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeec
Q 004021          532 ISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL  592 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~  592 (779)
                      |.++.+|+.+.+..+. ..+ ...+.++.+|+.+.+...  +..++...|.++.+|+.+.+.
T Consensus       261 F~~c~~L~~i~lp~~~-~~I~~~aF~~c~~L~~i~l~~~--i~~I~~~aF~~c~~L~~i~lp  319 (394)
T 4gt6_A          261 FDSCAYLASVKMPDSV-VSIGTGAFMNCPALQDIEFSSR--ITELPESVFAGCISLKSIDIP  319 (394)
T ss_dssp             TTTCSSCCEEECCTTC-CEECTTTTTTCTTCCEEECCTT--CCEECTTTTTTCTTCCEEECC
T ss_pred             eeecccccEEeccccc-ceecCcccccccccccccCCCc--ccccCceeecCCCCcCEEEeC
Confidence            4455556666554432 222 223555666666666432  455665556666666666654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.84  E-value=0.016  Score=53.98  Aligned_cols=22  Identities=32%  Similarity=0.354  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      .+|.|.|++|+||||+|+.+..
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            5799999999999999999987

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=94.80  E-value=0.024  Score=56.90  Aligned_cols=48  Identities=27%  Similarity=0.193  Sum_probs=34.1

Q ss_pred             ccccchhhhHHHHHHHHhcc----------C-CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ----------Q-KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~----------~-~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|.++.+++|.+.+...          . .-.+=+.++|.+|+||||||+.++...
T Consensus        10 ~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~   68 (274)
T 2x8a_A           10 ADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANES   68 (274)
T ss_dssp             --CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHc
Confidence            45788888888887754210          0 111229999999999999999999876

>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=94.79  E-value=0.18  Score=53.14  Aligned_cols=35  Identities=9%  Similarity=0.169  Sum_probs=14.9

Q ss_pred             ccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeec
Q 004021          556 KALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLL  592 (779)
Q Consensus       556 ~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~  592 (779)
                      ....+|+.+.+..+  +..++...+..+.+|+.+.+.
T Consensus       214 ~~~~~l~~i~~~~~--~~~i~~~~f~~~~~L~~i~lp  248 (379)
T 4h09_A          214 SYGKNLKKITITSG--VTTLGDGAFYGMKALDEIAIP  248 (379)
T ss_dssp             TTCSSCSEEECCTT--CCEECTTTTTTCSSCCEEEEC
T ss_pred             ccccccceeeeccc--eeEEccccccCCccceEEEcC
Confidence            33444444444332  333333334444445544443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.78  E-value=0.016  Score=54.22  Aligned_cols=25  Identities=32%  Similarity=0.280  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|.|+|+.|+||||+|+.++...
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            4678999999999999999998876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.70  E-value=0.015  Score=53.83  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|+|+.|+||||+++.++...
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            579999999999999999998875

>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=94.64  E-value=0.02  Score=53.95  Aligned_cols=26  Identities=27%  Similarity=0.360  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.+....
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999998866

>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=94.64  E-value=0.021  Score=54.32  Aligned_cols=26  Identities=31%  Similarity=0.461  Sum_probs=23.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+||||+|+.+....
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~l   49 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQML   49 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45899999999999999999998876

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.54  E-value=0.035  Score=53.85  Aligned_cols=39  Identities=21%  Similarity=0.356  Sum_probs=29.2

Q ss_pred             hhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          162 KLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       162 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+.+.+.+...  ...+|+|+|.+|+|||||+..+....
T Consensus        24 ~~a~~~r~~~~~~--~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           24 RLADKNRKLLNKH--GVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHHHHHT--TCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3344444444433  57899999999999999999998765

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.53  E-value=0.33  Score=51.92  Aligned_cols=26  Identities=23%  Similarity=0.424  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|+|.||+||||+|..++...
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l  124 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFL  124 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            56899999999999999999998877

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.53  E-value=0.019  Score=54.64  Aligned_cols=25  Identities=24%  Similarity=0.477  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|+.|+||||+|+.+....
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            4689999999999999999998875

>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=94.52  E-value=0.019  Score=53.47  Aligned_cols=25  Identities=44%  Similarity=0.391  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.|.|++|+||||+|+.+....
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            4678999999999999999998776

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.51  E-value=0.02  Score=53.91  Aligned_cols=24  Identities=42%  Similarity=0.526  Sum_probs=22.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|++|+||||+|+.+....
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l   25 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999999877

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.51  E-value=0.022  Score=54.21  Aligned_cols=26  Identities=27%  Similarity=0.422  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+|||||++.++...
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            45799999999999999999998765

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.51  E-value=0.034  Score=56.24  Aligned_cols=26  Identities=27%  Similarity=0.239  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.+....
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998765

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.51  E-value=0.021  Score=53.61  Aligned_cols=26  Identities=27%  Similarity=0.433  Sum_probs=23.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.++...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l   37 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLL   37 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            45789999999999999999999876

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.48  E-value=0.021  Score=53.31  Aligned_cols=25  Identities=24%  Similarity=0.420  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++++|+|+.|+|||||++.+....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3689999999999999999998765

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=94.46  E-value=0.028  Score=55.77  Aligned_cols=48  Identities=23%  Similarity=0.286  Sum_probs=33.6

Q ss_pred             ccccchhhhHHHHHHHHh---cc------C-CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT---DQ------Q-KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~---~~------~-~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.+.++.+...   ..      . .-.+=+.|+|.+|+||||||+.+++..
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh
Confidence            467898877666655432   11      0 011238999999999999999999876

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.44  E-value=0.014  Score=52.46  Aligned_cols=26  Identities=27%  Similarity=0.379  Sum_probs=23.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....+.|+|..|+|||||++.+++..
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~   60 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQA   60 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999877

>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=94.44  E-value=0.031  Score=59.11  Aligned_cols=48  Identities=21%  Similarity=0.297  Sum_probs=36.6

Q ss_pred             ccccchhhhHHHHHHHHhc----------------------------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD----------------------------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----------------------------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.|...+..                            .......+.++|.+|+|||++|+.+++..
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            4578998888888877621                            01123468899999999999999999876

>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=94.41  E-value=0.16  Score=53.61  Aligned_cols=136  Identities=11%  Similarity=0.078  Sum_probs=81.5

Q ss_pred             hhcccccCceeeecCCcccccc-hhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCC
Q 004021          531 RISSLVSLHHLDLSLTHIRGLP-QELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCD  609 (779)
Q Consensus       531 ~i~~L~~L~~L~L~~~~i~~lp-~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~  609 (779)
                      .+....+|+.+.+..+ +..++ ..+.++.+|+.+.+..+  ++.++...+.++.+|+.+.+..+ +..           
T Consensus       212 ~f~~~~~l~~i~~~~~-~~~i~~~~f~~~~~L~~i~lp~~--v~~I~~~aF~~~~~l~~i~l~~~-i~~-----------  276 (379)
T 4h09_A          212 GFSYGKNLKKITITSG-VTTLGDGAFYGMKALDEIAIPKN--VTSIGSFLLQNCTALKTLNFYAK-VKT-----------  276 (379)
T ss_dssp             TTTTCSSCSEEECCTT-CCEECTTTTTTCSSCCEEEECTT--CCEECTTTTTTCTTCCEEEECCC-CSE-----------
T ss_pred             ccccccccceeeeccc-eeEEccccccCCccceEEEcCCC--ccEeCccccceeehhcccccccc-cee-----------
Confidence            4455667777766544 33433 34667788888888765  56777666777888888877543 111           


Q ss_pred             CchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccC
Q 004021          610 DAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGS  689 (779)
Q Consensus       610 ~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~  689 (779)
                         .....+..+++|+.+.+.         -+.++.+....+.++.+|+.+.|..  .++.+..               .
T Consensus       277 ---i~~~aF~~c~~L~~i~l~---------~~~i~~I~~~aF~~c~~L~~i~lp~--~l~~I~~---------------~  327 (379)
T 4h09_A          277 ---VPYLLCSGCSNLTKVVMD---------NSAIETLEPRVFMDCVKLSSVTLPT--ALKTIQV---------------Y  327 (379)
T ss_dssp             ---ECTTTTTTCTTCCEEEEC---------CTTCCEECTTTTTTCTTCCEEECCT--TCCEECT---------------T
T ss_pred             ---cccccccccccccccccc---------ccccceehhhhhcCCCCCCEEEcCc--cccEEHH---------------H
Confidence               122335566777777664         2234444445566677777777753  2455543               4


Q ss_pred             CCCCCCCccEEEccCCCCCcccc
Q 004021          690 EHNFFTQLESLGILYGPDLKSIY  712 (779)
Q Consensus       690 ~~~~~~~L~~L~l~~~~~l~~l~  712 (779)
                      .+.++++|+.+.+..  +++.+.
T Consensus       328 aF~~C~~L~~i~ip~--~v~~I~  348 (379)
T 4h09_A          328 AFKNCKALSTISYPK--SITLIE  348 (379)
T ss_dssp             TTTTCTTCCCCCCCT--TCCEEC
T ss_pred             HhhCCCCCCEEEECC--ccCEEc
Confidence            666777777777643  355553

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=94.41  E-value=0.022  Score=58.30  Aligned_cols=26  Identities=31%  Similarity=0.692  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+||+|.|-|||||||.|..++...
T Consensus        47 ~aKVIAIaGKGGVGKTTtavNLA~aL   72 (314)
T 3fwy_A           47 GAKVFAVYGKGGIGKSTTSSNLSAAF   72 (314)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CceEEEEECCCccCHHHHHHHHHHHH
Confidence            56899999999999999998887766

>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=94.40  E-value=0.027  Score=52.13  Aligned_cols=26  Identities=27%  Similarity=0.542  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+||||+|+.+....
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            34689999999999999999998764

>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=94.39  E-value=0.023  Score=53.48  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=31.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKR  227 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~  227 (779)
                      .+|.|.|++|+||||+|+.+.... .. ...+ ..+++..++...++..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l-~~-~g~~-~~~i~~~~~~r~~~~~   49 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNL-RK-EGVN-YKMVSFGSVMFEVAKE   49 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH-HT-TTCC-CEEEEHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH-Hh-cCcc-eEEEehHHHHHHHHhc
Confidence            589999999999999999999876 21 1111 2344555555555543

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=94.32  E-value=0.044  Score=55.18  Aligned_cols=48  Identities=23%  Similarity=0.239  Sum_probs=34.3

Q ss_pred             ccccchhhhHHHHHHHHhc---c------C-CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD---Q------Q-KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---~------~-~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.++++.+....   .      . .-.+=+.|+|.+|+||||||+.+++..
T Consensus        40 ~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           40 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             GGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc
Confidence            5688988777666654421   1      0 011228999999999999999999876

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.31  E-value=0.025  Score=52.03  Aligned_cols=26  Identities=23%  Similarity=0.367  Sum_probs=22.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+|+.+....
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.30  E-value=0.024  Score=56.18  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|+.|+||||||+.++...
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            478999999999999999998876

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.30  E-value=0.036  Score=53.50  Aligned_cols=42  Identities=17%  Similarity=0.322  Sum_probs=31.9

Q ss_pred             chhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          159 GQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       159 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++..+.+.+.+...  ..++|+|+|.+|+|||||+..+....
T Consensus        13 ~~~~~~~~~~~~~~~~--~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           13 ENKRLAEKNREALRES--GTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             HHHHHHHHHHHHHHHH--TCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             hcHHHHHHHHHhhccc--CceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3445555555555444  67899999999999999999988765

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.30  E-value=0.021  Score=53.01  Aligned_cols=24  Identities=29%  Similarity=0.465  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.|.|++|+||||+|+.++...
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            368999999999999999998876

>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=94.28  E-value=0.027  Score=52.69  Aligned_cols=25  Identities=24%  Similarity=0.308  Sum_probs=22.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ....|.|+|+.|+||||+|+.+...
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999999876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.23  E-value=0.044  Score=56.00  Aligned_cols=45  Identities=24%  Similarity=0.232  Sum_probs=33.0

Q ss_pred             cchhhhHHHHHHHHhcc--CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          158 VGQEKLLPRVWRCITDQ--QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|-...+..+...+...  .....+|+|.|..|+||||||+.+....
T Consensus        70 ~~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~ll  116 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKALL  116 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hcchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            55555555555555443  3456699999999999999999998765

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.23  E-value=0.027  Score=53.20  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.+....
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998866

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.21  E-value=0.025  Score=53.78  Aligned_cols=23  Identities=26%  Similarity=0.625  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+|.|+.|+||||+|+.+.+..
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            68999999999999999999876

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=94.21  E-value=0.03  Score=53.32  Aligned_cols=26  Identities=23%  Similarity=0.367  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+|+.+++..
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            45789999999999999999998765

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.21  E-value=0.027  Score=53.08  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998765

>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=94.18  E-value=0.029  Score=53.73  Aligned_cols=26  Identities=35%  Similarity=0.337  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+|||||++.+....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            45799999999999999999998765

>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=94.15  E-value=0.03  Score=53.26  Aligned_cols=25  Identities=32%  Similarity=0.375  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ...+|+|.|+.|+||||+|+.+...
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHC
Confidence            5679999999999999999998763

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.14  E-value=0.023  Score=54.20  Aligned_cols=26  Identities=38%  Similarity=0.524  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|+|++|+||||+++.+....
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            45789999999999999999998765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=94.13  E-value=0.032  Score=56.70  Aligned_cols=26  Identities=27%  Similarity=0.354  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.+.++|++|+|||+||+++++..
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l   60 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKM   60 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45688899999999999999999987

>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=94.10  E-value=0.022  Score=53.28  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|++|+||||+|+.+....
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            468999999999999999998876

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=94.08  E-value=0.08  Score=54.92  Aligned_cols=98  Identities=11%  Similarity=0.094  Sum_probs=53.0

Q ss_pred             HHHHHHh-ccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEec-hHHHHHHHHhCCCcchh--hhhcch
Q 004021          166 RVWRCIT-DQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQ-TFQDDIGKRIGFSEDKK--WKEKSL  241 (779)
Q Consensus       166 ~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~-~i~~~i~~~l~~~~~~~--~~~~~~  241 (779)
                      .|-..|. .+=..-.++.|.|.+|+||||||.+++... .  ..=..++|++.. ......++.++......  ....+.
T Consensus        48 ~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~-~--~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~  124 (356)
T 3hr8_A           48 AIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEA-Q--KMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHG  124 (356)
T ss_dssp             HHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHH-H--HTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSH
T ss_pred             HHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHH-H--hcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCH
Confidence            3444454 221234799999999999999999998876 2  111346788872 12222556666542110  112334


Q ss_pred             hhHHHHHHHhhCCCcc-eeehhhccc
Q 004021          242 QDKAVDISSILSPKKF-RIDLTELGV  266 (779)
Q Consensus       242 ~~~~~~l~~~L~~kr~-~~~ld~l~~  266 (779)
                      ++....+...++..+. .+++|.+..
T Consensus       125 e~~l~~~~~l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          125 EQALEIVDELVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             HHHHHHHHHHHHTSCCSEEEEECTTT
T ss_pred             HHHHHHHHHHhhhcCCCeEEehHhhh
Confidence            4444444444432222 444555443

>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=94.07  E-value=0.029  Score=52.69  Aligned_cols=22  Identities=32%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      .+++|+|+.|+|||||++.+..
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            5789999999999999999976

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.07  E-value=0.031  Score=53.24  Aligned_cols=25  Identities=20%  Similarity=0.391  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++|+|+.|+|||||++.+....
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3689999999999999999998754

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.04  E-value=0.036  Score=54.94  Aligned_cols=40  Identities=35%  Similarity=0.395  Sum_probs=28.9

Q ss_pred             hHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++...+..+   .....+|.|+|++|+||||+|+.+....
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           14 ALARNLRSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             HHHHHHHHHHTTCCCCSSCEEEEEESCGGGTTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHccCCcccCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            334444444432   2345789999999999999999998876

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.01  E-value=0.033  Score=53.15  Aligned_cols=25  Identities=36%  Similarity=0.393  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|+|+.|+||||+++.+....
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998765

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=93.99  E-value=0.032  Score=53.33  Aligned_cols=26  Identities=38%  Similarity=0.602  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+||||+|+.+....
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            45799999999999999999987654

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=93.99  E-value=0.036  Score=53.23  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=24.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|.|++|+||||.|+.++..+
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            56899999999999999999998876

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.98  E-value=0.19  Score=50.71  Aligned_cols=88  Identities=11%  Similarity=0.087  Sum_probs=50.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchhh--hhcchhhH-HHHHHHh--hC
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKKW--KEKSLQDK-AVDISSI--LS  253 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~~--~~~~~~~~-~~~l~~~--L~  253 (779)
                      ++-|.|.+|+||||||.+++... .....=..++||+. ..+....+++++.+.+.-.  ...+.++. ...+...  ++
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~-~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~  108 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSY-MRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIE  108 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH-HHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH-HhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhh
Confidence            78999999999999999887766 21111246889988 2233345777776522111  12334444 3222222  34


Q ss_pred             CCcc-eeehhhccccc
Q 004021          254 PKKF-RIDLTELGVPL  268 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~~  268 (779)
                      ..++ ++++|.+...+
T Consensus       109 ~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A          109 RGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             TTCCEEEEEECSTTCB
T ss_pred             ccCceEEEEecccccc
Confidence            3333 66777765554

>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=93.92  E-value=0.042  Score=58.64  Aligned_cols=48  Identities=25%  Similarity=0.307  Sum_probs=37.8

Q ss_pred             ccccchhhhHHHHHHHHhcc------------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ------------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+...+...            ....+-|.++|++|+||||+|+.++...
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            56899999888887776331            1124568899999999999999999876

>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=93.92  E-value=0.037  Score=52.60  Aligned_cols=26  Identities=23%  Similarity=0.268  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|++|+||||+|+.+....
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34589999999999999999998876

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=93.92  E-value=0.035  Score=51.91  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998765

>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=93.91  E-value=0.033  Score=55.42  Aligned_cols=25  Identities=36%  Similarity=0.473  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L   28 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKIL   28 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998874

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=93.90  E-value=0.03  Score=53.36  Aligned_cols=22  Identities=36%  Similarity=0.475  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      .+|+|.|+.|+||||+++.+..
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            4799999999999999999977

>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=93.89  E-value=0.028  Score=51.91  Aligned_cols=24  Identities=25%  Similarity=0.335  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|.|++|+||||+|+.+....
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            468999999999999999998876

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.88  E-value=0.036  Score=53.12  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999999877

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.88  E-value=0.032  Score=52.84  Aligned_cols=25  Identities=28%  Similarity=0.333  Sum_probs=22.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|++|+||||+|+.+....
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999998876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=93.88  E-value=0.034  Score=53.35  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+|||||++.+....
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            44699999999999999999998865

>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=93.85  E-value=0.037  Score=50.66  Aligned_cols=26  Identities=23%  Similarity=0.238  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++++|+|..|+|||||+..+....
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l   28 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAA   28 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhh
Confidence            46799999999999999999998876

>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=93.85  E-value=0.032  Score=54.13  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|+|+.|+||||+|+.+....
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            589999999999999999998765

>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=93.74  E-value=0.1  Score=54.57  Aligned_cols=40  Identities=20%  Similarity=0.366  Sum_probs=31.1

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++.+.+....+...+|+|+|.+|+|||||+..+....
T Consensus        64 ~~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           64 QAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             HHHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            3455566665444577899999999999999999988765

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=93.74  E-value=0.036  Score=51.47  Aligned_cols=23  Identities=43%  Similarity=0.580  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|+|..|+|||||++.++...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998776

>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=93.74  E-value=0.037  Score=54.55  Aligned_cols=25  Identities=28%  Similarity=0.355  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|+|+.|+|||||++.++...
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4799999999999999999998765

>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=93.73  E-value=0.038  Score=53.39  Aligned_cols=26  Identities=27%  Similarity=0.317  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|.|.|++|+||||+|+.++...
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34689999999999999999998876

>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=93.72  E-value=0.043  Score=51.59  Aligned_cols=26  Identities=23%  Similarity=0.360  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|++|+||||+|+.+....
T Consensus         5 ~~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            5 KPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.71  E-value=0.038  Score=50.70  Aligned_cols=23  Identities=26%  Similarity=0.257  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|+.|+||||+|+.+....
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            58999999999999999998876

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=93.65  E-value=0.026  Score=52.67  Aligned_cols=25  Identities=32%  Similarity=0.384  Sum_probs=18.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998765

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.65  E-value=0.032  Score=51.49  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=20.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      ..+++|+|..|+|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            46999999999999999998553

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=93.64  E-value=0.038  Score=52.76  Aligned_cols=22  Identities=41%  Similarity=0.507  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      .+|+|.|+.|+||||+++.+..
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            4799999999999999999965

>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=93.62  E-value=0.041  Score=54.45  Aligned_cols=26  Identities=19%  Similarity=0.301  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+|+.+....
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999998865

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.62  E-value=0.18  Score=53.64  Aligned_cols=26  Identities=35%  Similarity=0.353  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.++|.+|+||||++..++...
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l  121 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFY  121 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999999998777

>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=93.60  E-value=0.17  Score=53.90  Aligned_cols=26  Identities=35%  Similarity=0.538  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.++|.+|+||||++..++...
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l  124 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYF  124 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHH
Confidence            46899999999999999999998877

>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=93.59  E-value=0.032  Score=58.27  Aligned_cols=46  Identities=26%  Similarity=0.383  Sum_probs=34.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+...  ...-|-|+|.+|+|||++|+.+++..
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~--~~~~vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             hhccChHHHHHHHHHHhhCC--CCceEEEECCCCccHHHHHHHHHHhC
Confidence            45899988666654444432  22338899999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.52  E-value=0.042  Score=51.77  Aligned_cols=23  Identities=39%  Similarity=0.602  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +|+|.|+.|+||||+|+.+....
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            68999999999999999998865

>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=93.50  E-value=0.045  Score=52.54  Aligned_cols=25  Identities=24%  Similarity=0.397  Sum_probs=23.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|+.|+||||+|+.+....
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999876

>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=93.48  E-value=0.043  Score=51.66  Aligned_cols=26  Identities=31%  Similarity=0.567  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+|+.+....
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHhc
Confidence            45799999999999999999998764

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.46  E-value=0.16  Score=51.49  Aligned_cols=37  Identities=24%  Similarity=0.207  Sum_probs=27.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+|+++|.+|+||||++..++... ...  -..+.++..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~-~~~--g~~v~l~~~  134 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFY-KKK--GFKVGLVGA  134 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHH-HHT--TCCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH-HHC--CCeEEEEec
Confidence            5799999999999999999998776 222  123555555

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=93.43  E-value=0.045  Score=52.44  Aligned_cols=25  Identities=24%  Similarity=0.258  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|+.|+||||+|+.+....
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999998876

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=93.39  E-value=0.038  Score=51.58  Aligned_cols=24  Identities=38%  Similarity=0.555  Sum_probs=21.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.|+|+.|+|||||++.+..+.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            457899999999999999998765

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.37  E-value=0.042  Score=53.39  Aligned_cols=25  Identities=24%  Similarity=0.323  Sum_probs=22.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|.|.|++|+||||+|+.+....
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998765

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=93.34  E-value=0.14  Score=53.12  Aligned_cols=88  Identities=14%  Similarity=0.185  Sum_probs=48.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech-HHHHHHHHhCCCcchh--hhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT-FQDDIGKRIGFSEDKK--WKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~-i~~~i~~~l~~~~~~~--~~~~~~~~~~~~l~~~L~  253 (779)
                      .-+++.|.|.+|+||||||.+++....   ..=..++|++... .-...++.++.....-  ....+.++....+....+
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~---~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~  136 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQ---AAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVR  136 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH---HTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---hCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            447999999999999999999987652   1224578888821 1122355555431110  012233444444444444


Q ss_pred             CCcc-eeehhhcccc
Q 004021          254 PKKF-RIDLTELGVP  267 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~  267 (779)
                      ..++ ++++|.+...
T Consensus       137 ~~~~~lIVIDsl~~l  151 (349)
T 2zr9_A          137 SGALDIIVIDSVAAL  151 (349)
T ss_dssp             TTCCSEEEEECGGGC
T ss_pred             cCCCCEEEEcChHhh
Confidence            3333 5555655433

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=93.34  E-value=0.038  Score=52.46  Aligned_cols=25  Identities=36%  Similarity=0.470  Sum_probs=21.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++++|+|+.|+|||||++.+....
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3689999999999999999998765

>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=93.34  E-value=0.049  Score=51.29  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|+|+|+.|+|||||++.+....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            45789999999999999999998765

>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=93.31  E-value=0.05  Score=55.61  Aligned_cols=26  Identities=31%  Similarity=0.322  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+|||||++.+..-.
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~gll  114 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQALL  114 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHhhc
Confidence            56799999999999999999998866

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=93.27  E-value=0.17  Score=52.03  Aligned_cols=55  Identities=20%  Similarity=0.309  Sum_probs=36.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhcccc---CCCCEEEEEEec-----hHHHHHHHHhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ---HNFDVVIWAAVQ-----TFQDDIGKRIGFS  231 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~---~~F~~~~wv~v~-----~i~~~i~~~l~~~  231 (779)
                      ...++.|+|.+|+||||||..++.......   ..-..++|++..     .-+..+++.++.+
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~g~~  168 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLD  168 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHTTCC
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHhCCC
Confidence            346999999999999999999887641110   002478899882     2233455555543

>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=93.25  E-value=0.074  Score=54.64  Aligned_cols=26  Identities=31%  Similarity=0.451  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+++|+|..|+||||+++.++...
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            56899999999999999999998776

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.21  E-value=0.053  Score=53.66  Aligned_cols=26  Identities=31%  Similarity=0.425  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|+.|+||||+++.++...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhc
Confidence            34699999999999999999998765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.20  E-value=0.049  Score=52.38  Aligned_cols=23  Identities=35%  Similarity=0.517  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=93.20  E-value=0.23  Score=51.52  Aligned_cols=64  Identities=16%  Similarity=0.129  Sum_probs=40.1

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccC----CCCEEEEEEech-----HHHHHHHHhCCC
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH----NFDVVIWAAVQT-----FQDDIGKRIGFS  231 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----~F~~~~wv~v~~-----i~~~i~~~l~~~  231 (779)
                      |-..|..+=....++.|+|.+|+||||||..++... ....    .-..++|++...     -+..++..++..
T Consensus       111 LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~-~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~g~~  183 (343)
T 1v5w_A          111 FDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTA-QLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVD  183 (343)
T ss_dssp             HHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHT-TSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHTTCC
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHH-hcccccCCCCCeEEEEECCCCCCHHHHHHHHHHcCCC
Confidence            333443332245799999999999999999988764 1111    234788998822     233455555543

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.16  E-value=0.045  Score=52.96  Aligned_cols=26  Identities=15%  Similarity=0.220  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|.|.|++|+||||+|+.++...
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34679999999999999999998876

>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=93.13  E-value=0.057  Score=51.33  Aligned_cols=25  Identities=24%  Similarity=0.327  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|+.|+||||+|+.+....
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998765

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.13  E-value=0.057  Score=53.18  Aligned_cols=26  Identities=23%  Similarity=0.330  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|..|+|||||++.+....
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            34799999999999999999998754

>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=93.09  E-value=0.056  Score=54.97  Aligned_cols=26  Identities=27%  Similarity=0.578  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+|||||++.++...
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            45799999999999999999998776

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.09  E-value=0.098  Score=59.06  Aligned_cols=44  Identities=20%  Similarity=0.314  Sum_probs=38.0

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+..+    ..+.|+|.+|+||||||+.++...
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhccC
Confidence            45799998888888777766    588999999999999999999876

>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=93.03  E-value=0.065  Score=48.59  Aligned_cols=26  Identities=31%  Similarity=0.321  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||++.++.-.
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            44799999999999999999998764

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=93.01  E-value=0.053  Score=52.15  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+|.|++|+||||+|+.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998765

>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=93.00  E-value=0.062  Score=51.47  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|.|+.|+||||+|+.+....
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~l   49 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQL   49 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            34789999999999999999998876

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=92.99  E-value=0.18  Score=52.68  Aligned_cols=88  Identities=11%  Similarity=0.126  Sum_probs=50.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEech-HHHHHHHHhCCCcchh--hhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQT-FQDDIGKRIGFSEDKK--WKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~-i~~~i~~~l~~~~~~~--~~~~~~~~~~~~l~~~L~  253 (779)
                      ...++.|.|.+|+||||||.+++....   ..-..++|++... .-...+..++.+...-  ....+.++....+....+
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~---~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~  149 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQ---KAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  149 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH---HTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHH---HCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHh
Confidence            346899999999999999999887652   1223688998821 1112345555431110  012334555555555554


Q ss_pred             CCcc-eeehhhcccc
Q 004021          254 PKKF-RIDLTELGVP  267 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~  267 (779)
                      ...+ ++++|.+...
T Consensus       150 ~~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          150 SGAIDVVVVDSVAAL  164 (366)
T ss_dssp             TTCCSEEEEECTTTC
T ss_pred             cCCCCEEEEeChHHh
Confidence            4444 5556665443

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.99  E-value=0.11  Score=53.24  Aligned_cols=26  Identities=38%  Similarity=0.593  Sum_probs=23.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+||||++..++...
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l  129 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYY  129 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999998876

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=92.94  E-value=0.06  Score=51.41  Aligned_cols=25  Identities=24%  Similarity=0.445  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||++.+..-.
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            4799999999999999999998765

>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=92.93  E-value=0.031  Score=53.67  Aligned_cols=24  Identities=33%  Similarity=0.706  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|.|..|+||||+|+.+....
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~~l   24 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSGAF   24 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            378999999999999999998876

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=92.89  E-value=0.27  Score=45.88  Aligned_cols=103  Identities=17%  Similarity=0.093  Sum_probs=56.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-ch----HHHHHHHHhCC---------Ccch---hhhhcch
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QT----FQDDIGKRIGF---------SEDK---KWKEKSL  241 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~----i~~~i~~~l~~---------~~~~---~~~~~~~  241 (779)
                      ..|-|++-.|.||||.|-..+-+..  ...+ .+.++.. +.    =-..+++.+..         ....   .......
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~--g~G~-rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a  105 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAV--GHGK-NVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAAC  105 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHH--HTTC-CEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH--HCCC-eEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHH
Confidence            4666777777999999988877662  2223 3444433 11    11234444420         0000   0011122


Q ss_pred             hhHHHHHHHhhCCCcc-eeehhhcccc--------------ccccCCCcEEEEEeCch
Q 004021          242 QDKAVDISSILSPKKF-RIDLTELGVP--------------LQMLNAGFKIVLKTRSA  284 (779)
Q Consensus       242 ~~~~~~l~~~L~~kr~-~~~ld~l~~~--------------~~~~~~gs~IivTTR~~  284 (779)
                      .......++.+.+.+| ++++|++...              +........||+|+|..
T Consensus       106 ~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          106 MAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            3445567777877888 6667776322              22334677899999984

>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=92.88  E-value=0.12  Score=50.43  Aligned_cols=40  Identities=13%  Similarity=0.160  Sum_probs=29.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccC----CCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH----NFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----~F~~~~wv~v  217 (779)
                      .-.++.|+|.+|+|||||+..++... ....    .-..++|++.
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~-~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTC-QLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT-TSCGGGTCCSSEEEEEES
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH-hCchhcCCCCCeEEEEEC
Confidence            34699999999999999999998753 1111    2357888876

>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=92.88  E-value=0.065  Score=49.74  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+++.+....
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l   29 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYL   29 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999998865

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=92.86  E-value=0.089  Score=49.40  Aligned_cols=38  Identities=11%  Similarity=0.111  Sum_probs=28.1

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+..++.+- +....+.|+|++|+||||+|.++++..
T Consensus        45 ~~~l~~~~~~i-Pkkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           45 LGALKSFLKGT-PKKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             HHHHHHHHHTC-TTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            45555555432 233579999999999999999998876

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=92.78  E-value=0.064  Score=53.99  Aligned_cols=23  Identities=30%  Similarity=0.644  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVN  199 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~  199 (779)
                      ...+|+|.|+.|+||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45789999999999999999997

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=92.76  E-value=0.054  Score=52.22  Aligned_cols=25  Identities=40%  Similarity=0.539  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++|+|..|+|||||++.+....
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4689999999999999999998754

>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=92.75  E-value=0.07  Score=51.37  Aligned_cols=23  Identities=35%  Similarity=0.445  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999865

>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=92.69  E-value=0.069  Score=54.11  Aligned_cols=26  Identities=35%  Similarity=0.432  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+||||++..++...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l  129 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAIS  129 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999998776

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=92.66  E-value=0.055  Score=53.28  Aligned_cols=24  Identities=33%  Similarity=0.387  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|+|+.|+||||+++.++...
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            689999999999999999999876

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.51  E-value=0.081  Score=50.48  Aligned_cols=23  Identities=30%  Similarity=0.213  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .+++|+|..|+|||||++.++.-
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            68999999999999999998764

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=92.49  E-value=0.075  Score=51.18  Aligned_cols=26  Identities=15%  Similarity=0.252  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+++|+|+.|+|||||.+.+....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccC
Confidence            34799999999999999999998765

>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=92.45  E-value=0.13  Score=52.58  Aligned_cols=26  Identities=27%  Similarity=0.263  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+|||||++.+....
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~~l  104 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQALL  104 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999999999998765

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=92.40  E-value=0.074  Score=50.64  Aligned_cols=24  Identities=25%  Similarity=0.537  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|+.|+||||+|+.+....
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            3 GIVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            389999999999999999998876

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.38  E-value=0.12  Score=50.59  Aligned_cols=25  Identities=24%  Similarity=0.352  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      . .+++|+|..|+|||||.+.++.-.
T Consensus        24 ~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           24 R-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             S-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             C-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            5 799999999999999999998765

>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=92.38  E-value=0.1  Score=50.05  Aligned_cols=35  Identities=26%  Similarity=0.217  Sum_probs=27.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...++.|+|.+|+||||||..++. . .    -..++|++.
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-~-~----~~~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-L-S----GKKVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-H-H----CSEEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-H-c----CCcEEEEEC
Confidence            446999999999999999999987 3 1    135677765

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=92.36  E-value=0.072  Score=51.30  Aligned_cols=24  Identities=25%  Similarity=0.343  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|.|.|++|+||||+|+.++...
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            578999999999999999998876

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=92.35  E-value=0.077  Score=51.45  Aligned_cols=25  Identities=16%  Similarity=0.400  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|++|+||||+|+.+....
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999998876

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.32  E-value=0.077  Score=54.41  Aligned_cols=24  Identities=33%  Similarity=0.387  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|.|+.|+||||||..++...
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHc
Confidence            589999999999999999998876

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=92.30  E-value=0.086  Score=51.40  Aligned_cols=25  Identities=32%  Similarity=0.331  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|.|.|+.|+||||+|+.++...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999998876

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.27  E-value=0.081  Score=50.38  Aligned_cols=37  Identities=19%  Similarity=0.278  Sum_probs=27.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHH
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDI  224 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i  224 (779)
                      +|.|.|++|+||||.|+.++.++     .   ...++..+++++-
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~-----g---~~~istGdllR~~   38 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK-----G---FVHISTGDILREA   38 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH-----C---CEEEEHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-----C---CeEEcHHHHHHHH
Confidence            57899999999999999998876     1   2345555555543

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=92.27  E-value=0.066  Score=50.22  Aligned_cols=24  Identities=38%  Similarity=0.481  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|+|..|+|||||++.++...
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhc
Confidence            368999999999999999998876

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.27  E-value=0.078  Score=51.31  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998876

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.24  E-value=0.45  Score=48.83  Aligned_cols=47  Identities=11%  Similarity=0.019  Sum_probs=34.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGK  226 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~  226 (779)
                      .-.++.|.|.+|+||||||..++.....   .=..++|++.    .++...++.
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSlEms~~ql~~Rlls   95 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSLEMSAEQLALRALS   95 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEESSSCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCCCCHHHHHHHHHH
Confidence            3468999999999999999999887622   2246788888    444444443

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.22  E-value=0.26  Score=50.36  Aligned_cols=47  Identities=17%  Similarity=0.192  Sum_probs=34.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe----chHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV----QTFQDDIGK  226 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v----~~i~~~i~~  226 (779)
                      .-.++.|.|.+|+||||||..++... ..+.  ..++|++.    .++...+..
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~-a~~g--~~vl~~slE~s~~~l~~R~~~  117 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNM-SDND--DVVNLHSLEMGKKENIKRLIV  117 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHH-HTTT--CEEEEEESSSCHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHH-HHcC--CeEEEEECCCCHHHHHHHHHH
Confidence            44799999999999999999998766 2222  67889988    344444443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=92.21  E-value=0.084  Score=53.62  Aligned_cols=26  Identities=31%  Similarity=0.529  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+++|+|..|+||||+++.++...
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34799999999999999999998876

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=92.21  E-value=0.078  Score=50.92  Aligned_cols=23  Identities=26%  Similarity=0.250  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.+....
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999998866

>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=92.17  E-value=0.089  Score=51.00  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.++...
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34799999999999999999998743

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=92.14  E-value=0.88  Score=49.00  Aligned_cols=39  Identities=13%  Similarity=-0.026  Sum_probs=29.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...++.|.|.+|+||||||..++.... . ..=..++|++.
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a-~-~~g~~vl~~sl  237 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAA-L-KEGVGVGIYSL  237 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHH-H-TTCCCEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH-H-hCCCeEEEEEC
Confidence            446999999999999999999988762 1 11235788887

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=92.12  E-value=0.16  Score=53.26  Aligned_cols=38  Identities=18%  Similarity=0.135  Sum_probs=27.7

Q ss_pred             HHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          165 PRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       165 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+.+-+.-+-....+++|+|++|+|||||++.++...
T Consensus       156 ~~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          156 YDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             HHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            33444443332355799999999999999999998754

>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=92.06  E-value=0.099  Score=48.21  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++++|+|..|+|||||+..+....
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999998765

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=92.03  E-value=0.094  Score=53.29  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+||||++..++...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l  128 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMF  128 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHH
Confidence            45799999999999999999998876

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=92.01  E-value=0.12  Score=50.32  Aligned_cols=26  Identities=23%  Similarity=0.385  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.+..-.
T Consensus        30 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           30 EGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            34699999999999999999997654

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=91.98  E-value=0.053  Score=49.93  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++++|+|..|+|||||++.+....
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~   26 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPIL   26 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            689999999999999999998776

>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=91.93  E-value=1  Score=53.09  Aligned_cols=48  Identities=29%  Similarity=0.436  Sum_probs=38.5

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+...       ......+.|+|.+|+|||++|+.+++..
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            45799999999888887542       1123578999999999999999998876

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=91.87  E-value=0.1  Score=53.36  Aligned_cols=26  Identities=27%  Similarity=0.497  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|+|+.|+||||||..++...
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHC
Confidence            34699999999999999999998765

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=91.86  E-value=0.091  Score=53.48  Aligned_cols=25  Identities=28%  Similarity=0.291  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.|+|+.|+||||||+.++...
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3589999999999999999998876

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.79  E-value=0.15  Score=50.03  Aligned_cols=37  Identities=30%  Similarity=0.233  Sum_probs=28.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      -.++.|.|.+|+||||||..++.....   .=..++|++.
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~---~~~~v~~~~~   59 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLK---MGEPGIYVAL   59 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHH---TTCCEEEEES
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEEc
Confidence            468999999999999999888765521   1235777776

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=91.71  E-value=0.11  Score=51.53  Aligned_cols=26  Identities=31%  Similarity=0.415  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++.+.|.||+||||++..++...
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l   38 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYL   38 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHH
Confidence            45788999999999999999998766

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=91.66  E-value=0.12  Score=49.94  Aligned_cols=25  Identities=28%  Similarity=0.349  Sum_probs=22.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3689999999999999999997654

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.64  E-value=0.066  Score=52.14  Aligned_cols=25  Identities=28%  Similarity=0.279  Sum_probs=16.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHH-hhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVN-NNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~-~~~  202 (779)
                      ..+++|+|..|+|||||++.+. ...
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3689999999999999999998 544

>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=91.62  E-value=0.12  Score=51.51  Aligned_cols=25  Identities=32%  Similarity=0.561  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||++.+..-.
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcCC
Confidence            4689999999999999999997754

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=91.59  E-value=0.11  Score=52.24  Aligned_cols=25  Identities=20%  Similarity=0.336  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.|.|+.|+||||||..++...
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~~   27 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKRL   27 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHhC
Confidence            3689999999999999999998765

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=91.58  E-value=0.12  Score=50.55  Aligned_cols=26  Identities=27%  Similarity=0.400  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+++.+....
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            55689999999999999999998765

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=91.56  E-value=0.14  Score=50.77  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   56 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINFLE   56 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34699999999999999999997754

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=91.47  E-value=0.11  Score=52.57  Aligned_cols=24  Identities=29%  Similarity=0.547  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .+++.|+|++|+|||+||.+++..
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~  146 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA  146 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            357789999999999999999875

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=91.41  E-value=0.11  Score=53.83  Aligned_cols=26  Identities=31%  Similarity=0.529  Sum_probs=23.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+++|+|..|+||||+++.++...
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            35799999999999999999998876

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=91.38  E-value=0.11  Score=55.68  Aligned_cols=26  Identities=23%  Similarity=0.368  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.|+|++|+||||+|+.++.+.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            56799999999999999999987765

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=91.31  E-value=0.16  Score=50.40  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~Gl~   74 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNLLE   74 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHcCC
Confidence            34699999999999999999997754

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=91.26  E-value=0.14  Score=51.55  Aligned_cols=26  Identities=27%  Similarity=0.215  Sum_probs=23.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|.|+.|+||||||..++...
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhC
Confidence            45789999999999999999998765

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=91.26  E-value=0.11  Score=50.04  Aligned_cols=104  Identities=16%  Similarity=0.041  Sum_probs=54.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~  253 (779)
                      .-.++.|+|..|+||||++..+.++. .. .... ++.+..   .+-...++..++.. .+........+....+.+.+.
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~-~~-~g~k-Vli~~~~~d~r~~~~i~srlG~~-~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRL-EY-ADVK-YLVFKPKIDTRSIRNIQSRTGTS-LPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHH-HH-TTCC-EEEEEECCCGGGCSSCCCCCCCS-SCCEEESSTHHHHHHHHSTTS
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHH-Hh-cCCE-EEEEEeccCchHHHHHHHhcCCC-ccccccCCHHHHHHHHHHHhh
Confidence            34789999999999999999888877 22 2223 333433   11112344444432 111112233444555555555


Q ss_pred             CCcc-eeehhhcccc-------cc-ccCCCcEEEEEeCch
Q 004021          254 PKKF-RIDLTELGVP-------LQ-MLNAGFKIVLKTRSA  284 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~-------~~-~~~~gs~IivTTR~~  284 (779)
                      +.++ .+.+|++...       +. -...|-.||+|-+..
T Consensus        87 ~~~~dvViIDEaQ~l~~~~ve~l~~L~~~gi~Vil~Gl~~  126 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDK  126 (223)
T ss_dssp             CTTCCEEEECSGGGSCTHHHHHHHHHHHTTCEEEEECCSB
T ss_pred             CCCCCEEEEecCccCcHHHHHHHHHHHhCCCeEEEEeccc
Confidence            5555 4455554211       00 012467788887743

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=91.18  E-value=0.066  Score=54.12  Aligned_cols=26  Identities=27%  Similarity=0.491  Sum_probs=20.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|..|+||||+|+.+....
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~l   29 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIF   29 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHH
Confidence            45689999999999999999998765

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=91.17  E-value=0.37  Score=49.49  Aligned_cols=25  Identities=28%  Similarity=0.460  Sum_probs=22.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .-.++.|.|.+|+||||||..++..
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4479999999999999999998865

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=91.16  E-value=0.15  Score=49.85  Aligned_cols=25  Identities=36%  Similarity=0.506  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3689999999999999999997754

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=91.14  E-value=0.15  Score=50.06  Aligned_cols=25  Identities=36%  Similarity=0.640  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3689999999999999999997765

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=91.14  E-value=0.12  Score=52.65  Aligned_cols=23  Identities=30%  Similarity=0.351  Sum_probs=21.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .+|.|.|++|+||||+|+.+...
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            57999999999999999999874

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=91.08  E-value=0.13  Score=49.17  Aligned_cols=25  Identities=36%  Similarity=0.680  Sum_probs=22.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3689999999999999999997754

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=91.08  E-value=0.16  Score=49.30  Aligned_cols=25  Identities=28%  Similarity=0.504  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||.+.++.-.
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4689999999999999999998765

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.05  E-value=0.17  Score=50.43  Aligned_cols=26  Identities=27%  Similarity=0.433  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.++.-.
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34699999999999999999998765

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.05  E-value=0.19  Score=48.05  Aligned_cols=23  Identities=30%  Similarity=0.213  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.+.|.||+||||+|..++...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l   30 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQ   30 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH
Confidence            47788999999999999998876

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=91.04  E-value=0.11  Score=50.61  Aligned_cols=26  Identities=23%  Similarity=0.478  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.++.-.
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34699999999999999999997754

>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=90.97  E-value=0.18  Score=49.80  Aligned_cols=26  Identities=38%  Similarity=0.589  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            34699999999999999999997754

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=90.94  E-value=0.12  Score=48.36  Aligned_cols=25  Identities=36%  Similarity=0.388  Sum_probs=21.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.|+|+|..|+|||||.+.+....
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            4578999999999999999988754

>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=90.93  E-value=0.16  Score=50.23  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3699999999999999999997755

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=90.91  E-value=0.16  Score=49.37  Aligned_cols=26  Identities=31%  Similarity=0.482  Sum_probs=23.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|.|+.|+||||+++.+....
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l   50 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRL   50 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999999987

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=90.88  E-value=1.1  Score=48.28  Aligned_cols=39  Identities=18%  Similarity=0.202  Sum_probs=29.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...++.|.|.+|+||||||..++.... .. .=..++|++.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~-~~-~g~~Vl~~s~  240 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVA-TK-TNENVAIFSL  240 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHH-HH-SSCCEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHH-Hh-CCCcEEEEEC
Confidence            346999999999999999999988762 11 1125777777

>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=90.87  E-value=0.16  Score=59.27  Aligned_cols=48  Identities=27%  Similarity=0.357  Sum_probs=38.4

Q ss_pred             ccccchhhhHHHHHHHHhcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+..++.+...+...       ......+.++|.+|+|||++|+.+++..
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l  512 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL  512 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh
Confidence            56799999998888877532       1233478999999999999999998876

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=90.87  E-value=0.22  Score=46.58  Aligned_cols=26  Identities=27%  Similarity=0.280  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|+|+|.+|+|||||...+....
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            44589999999999999999987654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=90.83  E-value=0.069  Score=59.91  Aligned_cols=49  Identities=16%  Similarity=0.121  Sum_probs=35.6

Q ss_pred             cccccchhhhHHHHHHHHhccCC---------CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQK---------NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~---------~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.++|.+..+..+.-.+..+..         .-.-|-++|.+|+|||+||+.+++..
T Consensus       294 ~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          294 APSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             SSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTC
T ss_pred             cchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhC
Confidence            36789999877776655554410         00147899999999999999998765

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=90.82  E-value=0.13  Score=50.71  Aligned_cols=24  Identities=33%  Similarity=0.464  Sum_probs=21.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -.+++|+|..|+|||||.+.++.-
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            368999999999999999999874

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=90.82  E-value=0.42  Score=50.76  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|+|.+|+||||++..++...
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l  122 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYY  122 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999999998877

>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=90.79  E-value=0.15  Score=54.99  Aligned_cols=26  Identities=35%  Similarity=0.569  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|..|+|||||++.++...
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHh
Confidence            45799999999999999999998776

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=90.73  E-value=0.13  Score=49.77  Aligned_cols=25  Identities=28%  Similarity=0.183  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|.|.+|+|||||++.++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999998665

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=90.65  E-value=0.16  Score=45.78  Aligned_cols=24  Identities=21%  Similarity=0.317  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-|.|+|.+|+|||||+..+.+..
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999987653

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=90.62  E-value=0.2  Score=49.84  Aligned_cols=26  Identities=31%  Similarity=0.350  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        32 ~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34699999999999999999997654

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=90.61  E-value=0.27  Score=48.40  Aligned_cols=36  Identities=22%  Similarity=0.308  Sum_probs=27.2

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -+..++....+...-|.++|++|.|||.+|.++++.
T Consensus        92 ~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A           92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhh
Confidence            355555543234457999999999999999999985

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=90.60  E-value=0.15  Score=50.72  Aligned_cols=25  Identities=24%  Similarity=0.385  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .-.+++|+|..|+|||||.+.++.-
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999875

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=90.58  E-value=0.15  Score=51.56  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=22.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++|+|.+|+||||++..++...
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~  122 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYY  122 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4799999999999999999998876

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=90.57  E-value=0.19  Score=52.29  Aligned_cols=38  Identities=26%  Similarity=0.241  Sum_probs=29.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..+++.|.|.+|+||||||.+++....   ..-..++|++.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~---~~g~~vlyid~   99 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQ---REGKTCAFIDA   99 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHH---HTTCCEEEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH---HCCCeEEEEeC
Confidence            446999999999999999999887652   12235788887

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=90.57  E-value=0.15  Score=54.13  Aligned_cols=36  Identities=11%  Similarity=0.241  Sum_probs=26.9

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ++.+.|........+++|+|..|+|||||.+.+...
T Consensus        57 ~i~~~L~~~~~~~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           57 AISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             HHHHHHHHHHHCCEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             hhhhhhhhcccCCeEEEEECCCCCcHHHHHHHHhCC
Confidence            344444433234579999999999999999999874

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=90.54  E-value=0.14  Score=46.54  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999998764

>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=90.52  E-value=0.12  Score=51.42  Aligned_cols=25  Identities=28%  Similarity=0.583  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||++.+..-.
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            4699999999999999999998754

>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=90.50  E-value=0.14  Score=50.22  Aligned_cols=26  Identities=27%  Similarity=0.487  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34699999999999999999998754

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=90.49  E-value=0.16  Score=51.44  Aligned_cols=26  Identities=15%  Similarity=0.303  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||++.+..-.
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            45799999999999999999998754

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.44  E-value=0.23  Score=49.51  Aligned_cols=36  Identities=19%  Similarity=0.455  Sum_probs=26.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++|+|.|-||+||||+|..++.... . ... .++-|..
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la-~-~G~-~VlliD~   37 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLH-A-MGK-TIMVVGC   37 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHH-T-TTC-CEEEEEE
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHH-H-CCC-cEEEEcC
Confidence            5788899999999999999988772 1 222 3555555

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=90.39  E-value=0.19  Score=50.31  Aligned_cols=25  Identities=44%  Similarity=0.543  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            4689999999999999999998755

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.35  E-value=0.16  Score=49.71  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|+|.|..|+||||+++.++...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHc
Confidence            3689999999999999999998876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=90.33  E-value=0.24  Score=53.96  Aligned_cols=26  Identities=27%  Similarity=0.496  Sum_probs=22.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|+|+|.+|+||||++..++...
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l  125 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYY  125 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46799999999999999999998776

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=90.27  E-value=0.16  Score=47.87  Aligned_cols=25  Identities=36%  Similarity=0.388  Sum_probs=21.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|+|+|.+|+|||||.+.+....
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcCC
Confidence            3568999999999999999998753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=90.25  E-value=0.18  Score=49.90  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.+....
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhC
Confidence            44799999999999999999988765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=90.25  E-value=0.15  Score=50.62  Aligned_cols=26  Identities=27%  Similarity=0.374  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            34699999999999999999998765

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=90.14  E-value=0.12  Score=47.99  Aligned_cols=22  Identities=41%  Similarity=0.533  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|+|+|.+|+|||||...+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5889999999999999998764

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=90.12  E-value=0.15  Score=51.23  Aligned_cols=25  Identities=28%  Similarity=0.375  Sum_probs=22.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.++.|+|.+|+||||||..++...
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4799999999999999999988754

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=90.09  E-value=0.16  Score=47.40  Aligned_cols=25  Identities=20%  Similarity=0.090  Sum_probs=22.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -+.|.|.|..|+||||||.++..+.
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            3678999999999999999998765

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=90.04  E-value=0.32  Score=50.38  Aligned_cols=27  Identities=30%  Similarity=0.423  Sum_probs=23.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....+|+|+|.+|+|||||+..+....
T Consensus        54 ~~~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           54 GNTLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            367899999999999999999987655

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=90.04  E-value=0.14  Score=50.33  Aligned_cols=25  Identities=36%  Similarity=0.505  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3689999999999999999998765

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=89.99  E-value=0.11  Score=55.53  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|+|+|.+|+||||+|..++...
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~l  123 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARYI  123 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35799999999999999999988776

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=89.95  E-value=0.16  Score=45.77  Aligned_cols=23  Identities=39%  Similarity=0.567  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|.+|+|||||+..+....
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            48899999999999999987653

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=89.90  E-value=0.17  Score=51.12  Aligned_cols=24  Identities=29%  Similarity=0.588  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|-||+||||+|..++...
T Consensus         3 kvIavs~KGGvGKTT~a~nLA~~L   26 (289)
T 2afh_E            3 RQCAIYGKGGIGKSTTTQNLVAAL   26 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEeCCCcCcHHHHHHHHHHHH
Confidence            688889999999999999998877

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=89.88  E-value=0.13  Score=49.89  Aligned_cols=25  Identities=28%  Similarity=0.254  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ...+|+|.|..|+||||+++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            4579999999999999999988664

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=89.86  E-value=0.2  Score=54.50  Aligned_cols=45  Identities=13%  Similarity=0.014  Sum_probs=30.9

Q ss_pred             cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          158 VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.+-.+.+.+..........+|.+.|+.|+||||+|++++...
T Consensus       375 f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L  419 (511)
T 1g8f_A          375 FSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTF  419 (511)
T ss_dssp             TSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             ccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHH
Confidence            344444444444432212244789999999999999999999988

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=89.86  E-value=0.31  Score=50.34  Aligned_cols=36  Identities=22%  Similarity=0.391  Sum_probs=26.9

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +++-+.-.-....+++|+|.+|+|||||...+....
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            444443222356899999999999999999998654

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=89.80  E-value=0.18  Score=51.08  Aligned_cols=26  Identities=23%  Similarity=0.374  Sum_probs=23.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|.|.+|+|||||++.++...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34699999999999999999998776

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=89.77  E-value=0.15  Score=50.32  Aligned_cols=25  Identities=32%  Similarity=0.493  Sum_probs=22.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3689999999999999999987654

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=89.72  E-value=0.18  Score=45.71  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .--|.|+|.+|+|||||+..+.+..
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            3468899999999999999987653

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=89.71  E-value=0.21  Score=46.39  Aligned_cols=24  Identities=29%  Similarity=0.414  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ...|+|+|.+|+|||||...+...
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            357999999999999999999874

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=89.71  E-value=0.18  Score=47.05  Aligned_cols=24  Identities=38%  Similarity=0.488  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.|+|+|.+|+|||||+..+....
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468899999999999999998653

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=89.69  E-value=0.19  Score=48.46  Aligned_cols=24  Identities=29%  Similarity=0.369  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.++|.|++|+||||+|+.+....
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998876

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=89.57  E-value=0.21  Score=50.70  Aligned_cols=26  Identities=27%  Similarity=0.469  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||++.+..-.
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHHcCC
Confidence            34799999999999999999997654

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=89.42  E-value=0.25  Score=45.29  Aligned_cols=26  Identities=27%  Similarity=0.386  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|+|+|.+|+|||||...+.+..
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~~   32 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHSK   32 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            45689999999999999999987643

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=89.39  E-value=0.65  Score=49.00  Aligned_cols=52  Identities=12%  Similarity=0.079  Sum_probs=32.6

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccc---cCCCCEEEEEEe
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ---QHNFDVVIWAAV  217 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~~~F~~~~wv~v  217 (779)
                      .|-+.|..+=..-.++.|+|.+|+|||||+..++-.....   ...-..++|++.
T Consensus       166 ~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~  220 (400)
T 3lda_A          166 NLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDT  220 (400)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             hHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeC
Confidence            3444443332234799999999999999999775332010   112356888877

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=89.36  E-value=0.2  Score=52.44  Aligned_cols=24  Identities=38%  Similarity=0.584  Sum_probs=22.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|+.|+||||||..++...
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            589999999999999999998876

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=89.28  E-value=0.38  Score=47.69  Aligned_cols=39  Identities=21%  Similarity=0.340  Sum_probs=28.5

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++.+.+.........|+|+|.+|+|||||...+....
T Consensus        22 l~~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           22 LIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             HHHHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            344444555443355678999999999999999988654

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=89.27  E-value=0.26  Score=45.56  Aligned_cols=25  Identities=44%  Similarity=0.547  Sum_probs=21.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ....|+|+|.+|+|||||...+.+.
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999988654

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=89.16  E-value=0.21  Score=45.14  Aligned_cols=24  Identities=33%  Similarity=0.393  Sum_probs=20.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-|+|+|.+|+|||||...+.+..
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            468999999999999999987653

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=89.14  E-value=0.19  Score=45.90  Aligned_cols=25  Identities=32%  Similarity=0.267  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .--|+|+|.+|+|||||...+....
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~~   28 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGKQ   28 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC-
T ss_pred             EEEEEEECCCCccHHHHHHHHhcCC
Confidence            3568999999999999999987643

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=89.07  E-value=0.25  Score=47.24  Aligned_cols=26  Identities=27%  Similarity=0.280  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|.|+|.+|+|||||+..+.+..
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45688999999999999999988754

>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=89.01  E-value=0.15  Score=47.86  Aligned_cols=114  Identities=15%  Similarity=0.120  Sum_probs=0.0

Q ss_pred             CCccEEEcccc-cccccccCcccccccccccccccchhhcccccCceeeecCCcccc-----cchhhccCccCcEeeccC
Q 004021          495 EGAKRISLMAN-EIESLSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEY  568 (779)
Q Consensus       495 ~~lr~l~l~~~-~~~~l~~~~~lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~  568 (779)
                      ..++.|+++++ .|..-             ....+-+.+..=++|+.|+|++|.|..     +-..+..=+.|++|+|++
T Consensus        41 ~~L~~L~L~~nn~igd~-------------ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~  107 (197)
T 1pgv_A           41 TDLKEVNINNMKRVSKE-------------RIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVES  107 (197)
T ss_dssp             SSCCEEECTTCCSSCHH-------------HHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCS
T ss_pred             CCccEEECCCCCCCCHH-------------HHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCC


Q ss_pred             CcCCC-----CCchhhhcCCccCcEeeeccc---cCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeec
Q 004021          569 THYLS-----IIPHQLISGFLKLEVLRLLEC---GSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRS  633 (779)
Q Consensus       569 ~~~l~-----~lp~~~i~~L~~L~~L~l~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~  633 (779)
                      | .++     .+-.. +..-+.|++|++++|   .+..          .........|..-+.|+.|+++.+.
T Consensus       108 N-~Ig~~Ga~ala~a-L~~N~tL~~L~L~n~~~~~ig~----------~g~~~ia~aL~~N~tL~~L~l~~~~  168 (197)
T 1pgv_A          108 N-FLTPELLARLLRS-TLVTQSIVEFKADNQRQSVLGN----------QVEMDMMMAIEENESLLRVGISFAS  168 (197)
T ss_dssp             S-BCCHHHHHHHHHH-TTTTCCCSEEECCCCSSCCCCH----------HHHHHHHHHHHHCSSCCEEECCCCC
T ss_pred             C-cCCHHHHHHHHHH-HhhCCceeEEECCCCcCcCcCH----------HHHHHHHHHHHhCCCcCeEeccCCC

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=88.98  E-value=0.21  Score=45.90  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999865

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=88.94  E-value=0.24  Score=54.41  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.++|++|.||||+|+.++...
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L   59 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYL   59 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            45789999999999999999998876

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=88.91  E-value=0.19  Score=49.81  Aligned_cols=23  Identities=35%  Similarity=0.511  Sum_probs=20.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .+++|+|..|+|||||.+.++.-
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            58999999999999999998653

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=88.87  E-value=0.23  Score=44.96  Aligned_cols=24  Identities=33%  Similarity=0.448  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      --|+|+|.+|+|||||...+.+..
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~~   27 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            358899999999999999987643

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=88.86  E-value=20  Score=36.91  Aligned_cols=26  Identities=31%  Similarity=0.351  Sum_probs=22.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|+|+|.+|+|||||...+....
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            55789999999999999999987643

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=88.84  E-value=0.14  Score=50.84  Aligned_cols=26  Identities=19%  Similarity=0.195  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|+|.|..|+||||+|+.+.+..
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l   48 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLC   48 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhc
Confidence            45799999999999999999987765

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=88.78  E-value=0.23  Score=45.12  Aligned_cols=24  Identities=38%  Similarity=0.361  Sum_probs=20.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      --|+|+|.+|+|||||...+.+..
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468999999999999999987653

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=88.76  E-value=0.22  Score=46.19  Aligned_cols=25  Identities=28%  Similarity=0.324  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .--|+|+|.+|+|||||+..+.+..
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcCC
Confidence            4568899999999999999987653

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=88.75  E-value=0.43  Score=47.50  Aligned_cols=40  Identities=23%  Similarity=0.307  Sum_probs=28.4

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.++.+.+.........|.++|.+|+|||||...+....
T Consensus        24 ~l~~~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~~~   63 (270)
T 1h65_A           24 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   63 (270)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            3344444444443345688999999999999999988654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=88.75  E-value=0.23  Score=49.54  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|+|..|+|||||.+.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998765

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=88.73  E-value=0.23  Score=46.43  Aligned_cols=24  Identities=42%  Similarity=0.365  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      --|.|+|.+|+|||||.+.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            468999999999999998776654

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=88.66  E-value=0.45  Score=51.55  Aligned_cols=40  Identities=25%  Similarity=0.384  Sum_probs=29.8

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+.++.+.+.+..++   +.+.|.|.+|+||||++..+....
T Consensus        30 Q~~av~~~~~~i~~~~---~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           30 QKNAFNIVMKAIKEKK---HHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             HHHHHHHHHHHHHSSS---CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCC---CEEEEEeCCCCCHHHHHHHHHHHH
Confidence            3444455555555542   389999999999999999998877

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=88.63  E-value=0.27  Score=45.95  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ....|+|+|.+|+|||||...+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999998764

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=88.62  E-value=0.24  Score=44.88  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|+|.+|+|||||...+.+..
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            57899999999999999987654

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=88.62  E-value=0.24  Score=44.95  Aligned_cols=24  Identities=25%  Similarity=0.347  Sum_probs=20.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      --|+|+|.+|+|||||...+.+..
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            368999999999999999987654

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=88.59  E-value=0.23  Score=45.12  Aligned_cols=23  Identities=35%  Similarity=0.333  Sum_probs=19.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      --|+|+|.+|+|||||...+...
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~~   25 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGGL   25 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhc
Confidence            35889999999999999988643

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=88.58  E-value=0.24  Score=46.05  Aligned_cols=24  Identities=21%  Similarity=0.289  Sum_probs=20.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .--|+|+|.+|+|||||+..+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            357899999999999999877654

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=88.58  E-value=0.24  Score=45.03  Aligned_cols=23  Identities=30%  Similarity=0.632  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      --|+|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45889999999999999998764

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=88.58  E-value=0.24  Score=44.66  Aligned_cols=24  Identities=33%  Similarity=0.405  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      --|+|+|.+|+|||||...+.+..
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999998887543

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=88.57  E-value=0.26  Score=46.67  Aligned_cols=26  Identities=35%  Similarity=0.289  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..-.|+|+|.+|+|||||...+.+..
T Consensus        29 ~~~ki~vvG~~~~GKSsLi~~l~~~~   54 (204)
T 4gzl_A           29 QAIKCVVVGDGAVGKTCLLISYTTNA   54 (204)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             CeEEEEEECcCCCCHHHHHHHHHhCC
Confidence            34578899999999999998887653

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=88.57  E-value=0.22  Score=47.85  Aligned_cols=24  Identities=33%  Similarity=0.425  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|+|.|+.|+||||+|+.+....
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            479999999999999999998765

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=88.55  E-value=0.25  Score=44.55  Aligned_cols=22  Identities=32%  Similarity=0.433  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |+|+|.+|+|||||...+.+..
T Consensus         3 i~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            7899999999999999987643

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=88.54  E-value=0.27  Score=45.80  Aligned_cols=24  Identities=25%  Similarity=0.133  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+|..|+||||++..++++.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~   27 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIY   27 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            578899999999999997776655

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=88.53  E-value=0.29  Score=50.81  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.++.|+|.+|+|||||+..++...
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45799999999999999999998764

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=88.51  E-value=0.27  Score=50.90  Aligned_cols=26  Identities=38%  Similarity=0.370  Sum_probs=23.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++.+.|.||+||||+|..++...
T Consensus        17 ~~~i~~~~gkGGvGKTt~a~~lA~~l   42 (348)
T 3io3_A           17 SLKWIFVGGKGGVGKTTTSSSVAVQL   42 (348)
T ss_dssp             TCSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHHH
Confidence            56899999999999999999988776

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=88.43  E-value=0.28  Score=46.45  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=23.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|+|.|+.|+||||+|+.++...
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999999987

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=88.38  E-value=0.23  Score=49.98  Aligned_cols=26  Identities=27%  Similarity=0.488  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            34699999999999999999997654

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=88.36  E-value=0.22  Score=51.10  Aligned_cols=26  Identities=38%  Similarity=0.465  Sum_probs=23.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++++|+|+.|+|||||.+.+....
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhhc
Confidence            56899999999999999999998653

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=88.34  E-value=0.27  Score=45.06  Aligned_cols=25  Identities=28%  Similarity=0.266  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .--|+|+|.+|+|||||...+.+..
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~~   30 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQET   30 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhCc
Confidence            3468999999999999999987643

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=88.34  E-value=0.47  Score=45.25  Aligned_cols=25  Identities=24%  Similarity=0.280  Sum_probs=22.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.|-|+.|+||||+++.+....
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l   30 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERL   30 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999887

---

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	779
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	6e-24
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	2e-06
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	7e-06
d1ogqa_	313	c.10.2.8 (A:) Polygalacturonase inhibiting protein	6e-05
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	5e-04
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	0.002
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	0.002
d2astb2	284	c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p1	0.002
d1p9ag_	266	c.10.2.7 (G:) von Willebrand factor binding domain	0.002

>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 =  100 bits (249), Expect = 6e-24
 Identities = 37/269 (13%), Positives = 84/269 (31%), Gaps = 30/269 (11%)

Query: 151 LPLEQTIVGQEKLLPRVWRCITDQQKN-RGIIGLYGIGGVGKTTLLKQV-NNNFCHQQHN 208
           +P + T   +E  + RV + + +        + L+G  G GK+ +  Q  + +      N
Sbjct: 16  VPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGIN 75

Query: 209 FDVVIWAAVQTFQDD-------------IGKRIGFSEDKKWKEKSLQDKAVDISSILSPK 255
           +D ++W                        +    +        S+  K +  ++++   
Sbjct: 76  YDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRP 135

Query: 256 KFRI---DLTELGVPLQMLNAGFKIVLKTRSAGVCDQMDSKN--LEVYSLAHDEAWKLFQ 310
                  D+ +            + ++ TR   + +        +EV SL  DE +   +
Sbjct: 136 NTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLE 195

Query: 311 EMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSAS 370
                  +       ++           P  L    ++ +  K      +   K+ +   
Sbjct: 196 AYGMPMPVGEK--EEDVLNKTIELSSGNPATLMMFFKSCEP-KTFEKMAQLNNKLESR-- 250

Query: 371 TFSGMEENVFLRLKFSYDSLSMDKLRSCL 399
                   V     +SY SL+M  L+ C+
Sbjct: 251 ----GLVGVECITPYSYKSLAMA-LQRCV 274

>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 = 48.8 bits (115), Expect = 2e-06
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 498 KRISLMANEIESLSEIPTLLSLRR----NDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ 553
             ++L  N I  +S + +L  L+R    N+ ++++ S +++L +++ L      I  L  
Sbjct: 310 TYLTLYFNNISDISPVSSLTKLQRLFFANNKVSDVSS-LANLTNINWLSAGHNQISDLT- 367

Query: 554 ELKALEKLRYLNLEY 568
            L  L ++  L L  
Sbjct: 368 PLANLTRITQLGLND 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 = 46.5 bits (109), Expect = 7e-06
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 515 TLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSI 574
           T L+L  N +++++   +SSL  L  L  +   +  +   L  L  + +L+  +     +
Sbjct: 310 TYLTLYFN-NISDISP-VSSLTKLQRLFFANNKVSDVS-SLANLTNINWLSAGHNQISDL 366

Query: 575 IPHQLISGFLKLEVLRL 591
            P   ++   ++  L L
Sbjct: 367 TP---LANLTRITQLGL 380

>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 = 43.6 bits (101), Expect = 6e-05
 Identities = 14/58 (24%), Positives = 23/58 (39%)

Query: 519 LRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIP 576
           LR N     LP  ++ L  LH L++S  ++ G   +   L++           L   P
Sbjct: 251 LRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYANNKCLCGSP 308

>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 = 40.4 bits (93), Expect = 5e-04
 Identities = 20/78 (25%), Positives = 29/78 (37%), Gaps = 10/78 (12%)

Query: 509 SLSEIP-------TLLSLRRNDSLTELPSR-ISSLVSLHHLDLSLTHIRGL-PQELKALE 559
            L ++P        LL L+ N  +TE+      +L +LH L L    I  + P     L 
Sbjct: 21  GLEKVPKDLPPDTALLDLQNN-KITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLV 79

Query: 560 KLRYLNLEYTHYLSIIPH 577
           KL  L L       +   
Sbjct: 80  KLERLYLSKNQLKELPEK 97

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]} Length = 353

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

 Score = 39.0 bits (89), Expect = 0.002
 Identities = 18/93 (19%), Positives = 28/93 (30%), Gaps = 11/93 (11%)

Query: 492 KEWEGAKRISLMANEIESLSEIP-------TLLSLRRNDSLTELPSRISSLVSLHHLDLS 544
            EWE             ++S +          L L     L+ LP        L  L  S
Sbjct: 11  SEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLG-LSSLPE---LPPHLESLVAS 66

Query: 545 LTHIRGLPQELKALEKLRYLNLEYTHYLSIIPH 577
              +  LP+  ++L+ L   N        + P 
Sbjct: 67  CNSLTELPELPQSLKSLLVDNNNLKALSDLPPL 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 = 38.7 bits (88), Expect = 0.002
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 12/75 (16%)

Query: 517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIP 576
           L++  N  L ELP+       L  L  S  H+  +P+  +    L+ L++EY   L   P
Sbjct: 289 LNVSNN-KLIELPA---LPPRLERLIASFNHLAEVPELPQ---NLKQLHVEYNP-LREFP 340

Query: 577 HQLISGFLKLEVLRL 591
               S    +E LR+
Sbjct: 341 DIPES----VEDLRM 351

>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 = 38.5 bits (88), Expect = 0.002
 Identities = 45/244 (18%), Positives = 78/244 (31%), Gaps = 17/244 (6%)

Query: 510 LSEIPTLLSLRRNDSLTELPSRISSLVSLHHLDLSLTHI--RGLPQELKALEKLRYLNLE 567
           LS+        R+     L    S    + H+DLS + I    L   L    KL+ L+LE
Sbjct: 21  LSQGVIAFRCPRSFMDQPLAEHFSPF-RVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLE 79

Query: 568 YTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVL 627
                  I +  ++    L  L L  C                 + L+     L  LN+ 
Sbjct: 80  GLRLSDPIVNT-LAKNSNLVRLNLSGC---------SGFSEFALQTLLSSCSRLDELNLS 129

Query: 628 SWSFRSSLAVQKFFKYPKLDLTWLV---FVQNLKELEIIVCTEMEEIICVDKLRDVSDIS 684
                +   VQ    +    +T L    + +NL++ ++         +    L D   + 
Sbjct: 130 WCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLK 189

Query: 685 EIIGSEHNFFTQLESLGILYGPDLKSIYPNPL-HFPKLKKIGVYGCPKLKKLPINSSSAK 743
                E      L+ L +    D+       L   P LK + V+G      L +   +  
Sbjct: 190 NDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALP 249

Query: 744 ERRV 747
             ++
Sbjct: 250 HLQI 253

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 266

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]

 Score = 38.5 bits (88), Expect = 0.002
 Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 4/65 (6%)

Query: 509 SLSEIPTLLSLR-RNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNL 566
            +S++ + L +     +LT LP  +        L LS   +       L    +L  LNL
Sbjct: 5   EVSKVASHLEVNCDKRNLTALPPDLPK--DTTILHLSENLLYTFSLATLMPYTRLTQLNL 62

Query: 567 EYTHY 571
           +    
Sbjct: 63  DRAEL 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	779
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.68
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.62
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.61
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.55
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.5
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.5
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.49
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.48
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.48
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.47
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.45
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.45
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.45
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.44
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.41
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.41
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.4
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.38
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.36
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.32
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.25
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.23
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.21
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.13
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.12
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.1
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.07
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.05
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.01
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.93
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.88
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.59
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.58
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.45
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.17
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	98.14
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.12
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.11
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.06
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.01
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.01
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.97
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.96
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.95
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.95
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.94
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.93
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.89
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.88
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.79
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.63
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.46
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.43
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.43
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.39
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.31
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.28
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.09
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.52
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.51
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	96.46
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.43
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.38
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.37
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.32
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.31
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.2
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.09
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.04
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.98
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.93
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.92
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.91
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.87
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.86
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.85
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.84
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.82
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.82
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.75
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.7
d1ls1a2	207	GTPase domain of the signal sequence recognition p	95.7
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.68
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.67
d1okkd2	207	GTPase domain of the signal recognition particle r	95.65
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.62
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	95.6
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.58
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.46
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	95.43
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.39
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.36
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.27
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.17
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.05
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.02
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	95.0
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.98
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.95
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.91
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.91
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.87
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.86
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.84
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	94.74
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.74
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	94.67
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.67
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	94.58
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.58
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.57
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.52
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.52
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.48
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.46
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.37
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.34
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.94
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	93.93
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	93.87
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	93.86
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	93.78
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	93.78
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	93.75
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.75
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.74
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	93.73
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	93.69
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.6
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	93.54
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.39
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	93.39
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	93.37
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.29
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.19
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	92.95
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	92.95
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.5
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	92.44
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.41
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.02
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	91.88
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.85
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	91.76
d1g2912	240	Maltose transport protein MalK, N-terminal domain	91.73
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	91.73
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	91.72
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	91.7
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	91.65
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.63
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.61
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	91.6
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.53
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	91.44
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	91.41
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.39
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.3
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	91.28
d2awna2	232	Maltose transport protein MalK, N-terminal domain	91.26
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.19
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.18
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	91.04
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	90.92
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	90.92
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	90.79
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	90.71
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	90.67
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.66
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	90.63
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	90.59
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	90.53
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	90.52
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.46
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	90.46
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.39
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	90.24
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	90.05
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	90.02
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	89.99
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	89.98
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	89.96
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	89.89
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	89.87
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	89.75
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	89.73
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	89.68
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	89.61
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	89.61
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	89.55
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	89.46
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	89.41
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	89.34
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	89.29
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	89.29
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	89.28
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	89.24
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	89.23
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	89.22
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	89.09
d1nrjb_	209	Signal recognition particle receptor beta-subunit	89.06
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	89.05
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	89.05
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.0
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	88.94
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	88.89
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	88.88
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	88.83
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	88.82
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	88.71
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	88.64
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	88.63
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.46
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	88.42
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	88.41
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	88.4
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	88.33
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	88.31
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	88.23
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	88.19
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	88.16
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	87.99
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	87.82
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	87.77
d2fh5b1	207	Signal recognition particle receptor beta-subunit	87.77
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	87.73
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	87.71
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	87.71
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	87.7
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	87.58
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	87.33
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	87.31
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	87.24
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	87.12
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	87.05
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	86.93
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	86.73
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	86.61
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	86.59
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	86.54
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	86.3
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	86.27
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	86.2
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.11
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	86.04
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	86.02
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	85.82
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	85.55
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	85.33
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.08
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	84.95
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	84.75
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	84.54
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	84.05
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	83.59
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	82.94
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	82.53
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	82.24
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	81.29
d1xpua3	289	Transcription termination factor Rho, ATPase domai	80.53
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	80.09

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=3e-37  Score=313.99  Aligned_cols=241  Identities=16%  Similarity=0.141  Sum_probs=187.5

Q ss_pred             cccccccchhhhHHHHHHHHhc-cCCCceEEEEEcCCCCcHHHHHHHHHhhhc-cccCCCCEEEEEEe------chHHHH
Q 004021          152 PLEQTIVGQEKLLPRVWRCITD-QQKNRGIIGLYGIGGVGKTTLLKQVNNNFC-HQQHNFDVVIWAAV------QTFQDD  223 (779)
Q Consensus       152 ~~~~~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~-~~~~~F~~~~wv~v------~~i~~~  223 (779)
                      |..+.++||+.++++|+++|.. .+.+.++|+|+||||+||||||+++|++.. .++.+|++++||++      ..+...
T Consensus        17 p~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~   96 (277)
T d2a5yb3          17 PKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLF   96 (277)
T ss_dssp             BCCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHH
T ss_pred             CCCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHH
Confidence            3456789999999999999975 345678999999999999999999998751 25678999999998      223333


Q ss_pred             H---HHHhCCCcchh----hhhcchhhHHHHHHHhhCCCcceeehhhcccccc---ccCCCcEEEEEeCchhhhhhcC--
Q 004021          224 I---GKRIGFSEDKK----WKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQ---MLNAGFKIVLKTRSAGVCDQMD--  291 (779)
Q Consensus       224 i---~~~l~~~~~~~----~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~---~~~~gs~IivTTR~~~va~~~~--  291 (779)
                      +   +..++......    ............+.+.+.++|+++++|+++....   ....||+||||||+..|+..+.  
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~~~srilvTTR~~~v~~~~~~~  176 (277)
T d2a5yb3          97 TDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQT  176 (277)
T ss_dssp             HHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEESBGGGGGGCCSC
T ss_pred             HHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcccCceEEEEeehHHHHHhcCCC
Confidence            3   33333221110    0112233345567888999999999999976532   2347999999999999998876  


Q ss_pred             CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHHHHHHhcCCCChhHHHHHHHHHhcccCc
Q 004021          292 SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKTVGRAMKSQKKVGDRERAIEKMRTSAST  371 (779)
Q Consensus       292 ~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~~g~~l~~~~~~~~w~~~~~~l~~~~~~  371 (779)
                      ...|+|++|+.+|||+||.++++...  ..+..++++++|+++|+|+||||+++|+.|+. ++.++|.+..+.|.+... 
T Consensus       177 ~~~~~l~~L~~~ea~~Lf~~~~~~~~--~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~-k~~~~~~~~~~~L~~~~~-  252 (277)
T d2a5yb3         177 CEFIEVTSLEIDECYDFLEAYGMPMP--VGEKEEDVLNKTIELSSGNPATLMMFFKSCEP-KTFEKMAQLNNKLESRGL-  252 (277)
T ss_dssp             EEEEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCS-SSHHHHHHHHHHHHHHCS-
T ss_pred             CceEECCCCCHHHHHHHHHHHhCCcc--CchhhHHHHHHHHHHhCCCHHHHHHHHHHhcc-CCHHHHHHHHHHHhcCcH-
Confidence            36799999999999999999887654  34456889999999999999999999999976 678899988888876432 


Q ss_pred             CCCchHHHHHHHHHHHhcCCccchhhhhhhc
Q 004021          372 FSGMEENVFLRLKFSYDSLSMDKLRSCLLYC  402 (779)
Q Consensus       372 ~~~~~~~i~~~l~~sy~~L~~~~~k~cf~~~  402 (779)
                           .++..++.+||++||+ ++|.||.++
T Consensus       253 -----~~v~~il~~sY~~L~~-~lk~c~~~l  277 (277)
T d2a5yb3         253 -----VGVECITPYSYKSLAM-ALQRCVEVL  277 (277)
T ss_dssp             -----STTCCCSSSSSSSHHH-HHHHHHHTS
T ss_pred             -----HHHHHHHHHHHhcccH-HHHHHHHhC
Confidence                 2677889999999999 999999874

>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=160.32  Aligned_cols=192  Identities=19%  Similarity=0.136  Sum_probs=145.6

Q ss_pred             CCccEEEcccccccccccCcc----cccccccccccccc-hhhcccccCceeeecCCcccccchhhccCccCcEeeccCC
Q 004021          495 EGAKRISLMANEIESLSEIPT----LLSLRRNDSLTELP-SRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYT  569 (779)
Q Consensus       495 ~~lr~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp-~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~  569 (779)
                      .....++.++++++.+|...+    .|+|++| .++.+| ..|.++++|++|+|++|.|+.+|. ++.+++|++|++++|
T Consensus        10 ~~~~~v~C~~~~L~~iP~~lp~~l~~L~Ls~N-~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~~-~~~l~~L~~L~Ls~N   87 (266)
T d1p9ag_          10 ASHLEVNCDKRNLTALPPDLPKDTTILHLSEN-LLYTFSLATLMPYTRLTQLNLDRAELTKLQV-DGTLPVLGTLDLSHN   87 (266)
T ss_dssp             TTCCEEECTTSCCSSCCSCCCTTCCEEECTTS-CCSEEEGGGGTTCTTCCEEECTTSCCCEEEC-CSCCTTCCEEECCSS
T ss_pred             CCCeEEEccCCCCCeeCcCcCcCCCEEECcCC-cCCCcCHHHhhcccccccccccccccccccc-ccccccccccccccc
Confidence            455567777888877765322    5888988 888886 468889999999999999888874 578899999999998


Q ss_pred             cCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCc
Q 004021          570 HYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLT  649 (779)
Q Consensus       570 ~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~  649 (779)
                       .+..+|.. +..+++|+.|++++|.+..              .....+..+.+++.|.++.+         .++.+.+.
T Consensus        88 -~l~~~~~~-~~~l~~L~~L~l~~~~~~~--------------~~~~~~~~l~~l~~L~l~~n---------~l~~l~~~  142 (266)
T d1p9ag_          88 -QLQSLPLL-GQTLPALTVLDVSFNRLTS--------------LPLGALRGLGELQELYLKGN---------ELKTLPPG  142 (266)
T ss_dssp             -CCSSCCCC-TTTCTTCCEEECCSSCCCC--------------CCSSTTTTCTTCCEEECTTS---------CCCCCCTT
T ss_pred             -cccccccc-cccccccccccccccccce--------------eecccccccccccccccccc---------ccceeccc
Confidence             57777775 8889999999998887664              22334556778888887633         44445455


Q ss_pred             ccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCC
Q 004021          650 WLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGC  729 (779)
Q Consensus       650 ~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c  729 (779)
                      .+..+++|+.|++++|. +..++.               ..+..+++|++|+|++ +.++++|.++..+++|+.|+++++
T Consensus       143 ~~~~l~~l~~l~l~~N~-l~~~~~---------------~~~~~l~~L~~L~Ls~-N~L~~lp~~~~~~~~L~~L~L~~N  205 (266)
T d1p9ag_         143 LLTPTPKLEKLSLANNN-LTELPA---------------GLLNGLENLDTLLLQE-NSLYTIPKGFFGSHLLPFAFLHGN  205 (266)
T ss_dssp             TTTTCTTCCEEECTTSC-CSCCCT---------------TTTTTCTTCCEEECCS-SCCCCCCTTTTTTCCCSEEECCSC
T ss_pred             cccccccchhccccccc-ccccCc---------------cccccccccceeeccc-CCCcccChhHCCCCCCCEEEecCC
Confidence            66778889999998864 444443               3567889999999988 468888888888899999999887


Q ss_pred             C
Q 004021          730 P  730 (779)
Q Consensus       730 ~  730 (779)
                      |
T Consensus       206 p  206 (266)
T d1p9ag_         206 P  206 (266)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.62  E-value=3.4e-15  Score=153.51  Aligned_cols=234  Identities=19%  Similarity=0.156  Sum_probs=156.4

Q ss_pred             ccEEEcccccccccccCc----ccccccccccccccch-hhcccccCceeeecCCccccc-chhhccCccCcEeeccCCc
Q 004021          497 AKRISLMANEIESLSEIP----TLLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-PQELKALEKLRYLNLEYTH  570 (779)
Q Consensus       497 lr~l~l~~~~~~~l~~~~----~lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~L~l~~~~  570 (779)
                      .+.++..++.++.+|...    ..|+|++| .++.+|+ .|.++++|++|++++|.+..+ |..|.++++|++|++++| 
T Consensus        12 ~~~~~C~~~~L~~lP~~l~~~l~~L~Ls~N-~i~~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n-   89 (305)
T d1xkua_          12 LRVVQCSDLGLEKVPKDLPPDTALLDLQNN-KITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKN-   89 (305)
T ss_dssp             TTEEECTTSCCCSCCCSCCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSS-
T ss_pred             CCEEEecCCCCCccCCCCCCCCCEEECcCC-cCCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccCC-
Confidence            344555555565555432    24777777 7777765 577778888888888877776 445777888888888877 


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCCcccccCC--------cc----CCCchhhHHhhcCCCCCCceeEEeeccccc-
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGN--------VL----CDDAEPLMRELLGLKRLNVLSWSFRSSLAV-  637 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~--------~~----~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~-  637 (779)
                      .++.+|..   ....|..|.+..|.+..++.....        ..    ..........+..+++|+.++++.+....+ 
T Consensus        90 ~l~~l~~~---~~~~l~~L~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~  166 (305)
T d1xkua_          90 QLKELPEK---MPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIP  166 (305)
T ss_dssp             CCSBCCSS---CCTTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCC
T ss_pred             ccCcCccc---hhhhhhhhhccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccC
Confidence            56777764   234667777777666554322111        00    000122334567788889888887766444 


Q ss_pred             -ccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCC
Q 004021          638 -QKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGP  706 (779)
Q Consensus       638 -~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~  706 (779)
                       ..+++|+.|          .+..+..+++++.|++++|. +..++.               ..+.++++|++|+|+++ 
T Consensus       167 ~~~~~~L~~L~l~~n~~~~~~~~~~~~~~~l~~L~~s~n~-l~~~~~---------------~~~~~l~~L~~L~L~~N-  229 (305)
T d1xkua_         167 QGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNS-ISAVDN---------------GSLANTPHLRELHLNNN-  229 (305)
T ss_dssp             SSCCTTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSC-CCEECT---------------TTGGGSTTCCEEECCSS-
T ss_pred             cccCCccCEEECCCCcCCCCChhHhhcccccccccccccc-cccccc---------------ccccccccceeeecccc-
Confidence             235566666          33456677888888888854 444433               36678999999999995 


Q ss_pred             CCccccCCCCCCCCccEEeeeCCCCCCCCCCCC--------CCcccccEEEechH
Q 004021          707 DLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINS--------SSAKERRVVIEGLK  753 (779)
Q Consensus       707 ~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~--------~~~~~~~l~i~~~~  753 (779)
                      .++.+|..+..+++|++|++++| +|+.||...        ...+++.+.+.+.+
T Consensus       230 ~L~~lp~~l~~l~~L~~L~Ls~N-~i~~i~~~~f~~~~~~~~~~~L~~L~L~~N~  283 (305)
T d1xkua_         230 KLVKVPGGLADHKYIQVVYLHNN-NISAIGSNDFCPPGYNTKKASYSGVSLFSNP  283 (305)
T ss_dssp             CCSSCCTTTTTCSSCCEEECCSS-CCCCCCTTSSSCSSCCTTSCCCSEEECCSSS
T ss_pred             cccccccccccccCCCEEECCCC-ccCccChhhccCcchhcccCCCCEEECCCCc
Confidence            78999988889999999999997 699987532        12344778887765

>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=99.61  E-value=1.8e-15  Score=152.11  Aligned_cols=188  Identities=20%  Similarity=0.150  Sum_probs=151.4

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      .+.+++ .++.+|+.|.  ++|++|+|++|.|+.+|. .|.++++|++|+|++| .++.+|.  ++.+++|++|++++|.
T Consensus        15 v~C~~~-~L~~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N-~l~~l~~--~~~l~~L~~L~Ls~N~   88 (266)
T d1p9ag_          15 VNCDKR-NLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRA-ELTKLQV--DGTLPVLGTLDLSHNQ   88 (266)
T ss_dssp             EECTTS-CCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTS-CCCEEEC--CSCCTTCCEEECCSSC
T ss_pred             EEccCC-CCCeeCcCcC--cCCCEEECcCCcCCCcCHHHhhccccccccccccc-ccccccc--cccccccccccccccc
Confidence            477788 8999998775  689999999999999985 5899999999999999 7888886  6899999999999998


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVD  675 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~  675 (779)
                      +..               .+..+..+++|+.|+++.+.         +..+....+..+++|+.|++++|. +..++.  
T Consensus        89 l~~---------------~~~~~~~l~~L~~L~l~~~~---------~~~~~~~~~~~l~~l~~L~l~~n~-l~~l~~--  141 (266)
T d1p9ag_          89 LQS---------------LPLLGQTLPALTVLDVSFNR---------LTSLPLGALRGLGELQELYLKGNE-LKTLPP--  141 (266)
T ss_dssp             CSS---------------CCCCTTTCTTCCEEECCSSC---------CCCCCSSTTTTCTTCCEEECTTSC-CCCCCT--
T ss_pred             ccc---------------cccccccccccccccccccc---------cceeeccccccccccccccccccc-cceecc--
Confidence            775               34456788999999998543         333444556778899999999864 445544  


Q ss_pred             cccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCCCCCCCcc-cccEEEech
Q 004021          676 KLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLPINSSSAK-ERRVVIEGL  752 (779)
Q Consensus       676 ~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP~~~~~~~-~~~l~i~~~  752 (779)
                                   ..+..+++|+.|++++ +++..++.. +..+++|++|++++| .|+.||.++...+ ++.+.+.|.
T Consensus       142 -------------~~~~~l~~l~~l~l~~-N~l~~~~~~~~~~l~~L~~L~Ls~N-~L~~lp~~~~~~~~L~~L~L~~N  205 (266)
T d1p9ag_         142 -------------GLLTPTPKLEKLSLAN-NNLTELPAGLLNGLENLDTLLLQEN-SLYTIPKGFFGSHLLPFAFLHGN  205 (266)
T ss_dssp             -------------TTTTTCTTCCEEECTT-SCCSCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCCCSEEECCSC
T ss_pred             -------------ccccccccchhccccc-ccccccCccccccccccceeecccC-CCcccChhHCCCCCCCEEEecCC
Confidence                         3667899999999998 577777764 568999999999997 5999998766544 488888753

>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=99.55  E-value=2.5e-15  Score=155.11  Aligned_cols=221  Identities=14%  Similarity=0.167  Sum_probs=136.8

Q ss_pred             CccEEEcccccccc---cccCcc------cccccc-ccccc-ccchhhcccccCceeeecCCccccc-chhhccCccCcE
Q 004021          496 GAKRISLMANEIES---LSEIPT------LLSLRR-NDSLT-ELPSRISSLVSLHHLDLSLTHIRGL-PQELKALEKLRY  563 (779)
Q Consensus       496 ~lr~l~l~~~~~~~---l~~~~~------lL~L~~-~~~l~-~lp~~i~~L~~L~~L~L~~~~i~~l-p~~~~~L~~L~~  563 (779)
                      +++.|++.++.+..   +|....      .|+|++ | .+. .+|.+|++|++|++|+|++|++..+ |..+.++.+|++
T Consensus        51 ~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N-~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~  129 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGIN-NLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEET-TEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             EEEEEECCCCCCCCCCCCChHHhcCcccccccccccc-ccccccccccccccccchhhhccccccccccccccchhhhcc
Confidence            57778888877653   333221      377876 4 444 6788888888888888888887764 445777888888


Q ss_pred             eeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCC-CceeEEeecccc-----c
Q 004021          564 LNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRL-NVLSWSFRSSLA-----V  637 (779)
Q Consensus       564 L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L-~~L~l~~~~~~~-----~  637 (779)
                      +++++|.....+|.. ++++++|+++++++|.+.+              ..+..+..+.++ +.+.++.+....     +
T Consensus       130 l~l~~N~~~~~~p~~-l~~l~~L~~l~l~~n~l~~--------------~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~  194 (313)
T d1ogqa_         130 LDFSYNALSGTLPPS-ISSLPNLVGITFDGNRISG--------------AIPDSYGSFSKLFTSMTISRNRLTGKIPPTF  194 (313)
T ss_dssp             EECCSSEEESCCCGG-GGGCTTCCEEECCSSCCEE--------------ECCGGGGCCCTTCCEEECCSSEEEEECCGGG
T ss_pred             cccccccccccCchh-hccCcccceeecccccccc--------------ccccccccccccccccccccccccccccccc
Confidence            888888666777776 7888888888888877653              234444455444 444444333211     1


Q ss_pred             ccCCCCCcc----------cCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCC
Q 004021          638 QKFFKYPKL----------DLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPD  707 (779)
Q Consensus       638 ~~~~~L~~L----------~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~  707 (779)
                      ..+..+ .+          .+..+..+++|+.|++++|.....+                 ..++.+++|+.|+++++.-
T Consensus       195 ~~l~~~-~l~l~~~~~~~~~~~~~~~~~~l~~l~~~~~~l~~~~-----------------~~~~~~~~L~~L~Ls~N~l  256 (313)
T d1ogqa_         195 ANLNLA-FVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDL-----------------GKVGLSKNLNGLDLRNNRI  256 (313)
T ss_dssp             GGCCCS-EEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCBG-----------------GGCCCCTTCCEEECCSSCC
T ss_pred             cccccc-ccccccccccccccccccccccccccccccccccccc-----------------cccccccccccccCccCee
Confidence            111111 11          2334456677777777775543322                 2455677888888887433


Q ss_pred             CccccCCCCCCCCccEEeeeCCCCCC-CCCCCCCCcccccEEEec
Q 004021          708 LKSIYPNPLHFPKLKKIGVYGCPKLK-KLPINSSSAKERRVVIEG  751 (779)
Q Consensus       708 l~~l~~~~~~l~~L~~L~l~~c~~L~-~lP~~~~~~~~~~l~i~~  751 (779)
                      ...+|..++.+++|++|++++|. |. .+|.......++.+.+.+
T Consensus       257 ~g~iP~~l~~L~~L~~L~Ls~N~-l~g~iP~~~~L~~L~~l~l~~  300 (313)
T d1ogqa_         257 YGTLPQGLTQLKFLHSLNVSFNN-LCGEIPQGGNLQRFDVSAYAN  300 (313)
T ss_dssp             EECCCGGGGGCTTCCEEECCSSE-EEEECCCSTTGGGSCGGGTCS
T ss_pred             cccCChHHhCCCCCCEEECcCCc-ccccCCCcccCCCCCHHHhCC
Confidence            33677777788888888888764 44 677543333334444433

>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=99.50  E-value=1.4e-13  Score=146.09  Aligned_cols=59  Identities=7%  Similarity=0.081  Sum_probs=40.3

Q ss_pred             CCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEec
Q 004021          690 EHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIEG  751 (779)
Q Consensus       690 ~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~~  751 (779)
                      .+..+++|++|++++| .++.++ .+..+++|++|++++| +++.+|.......++.+.|++
T Consensus       324 ~l~~l~~L~~L~L~~n-~l~~l~-~l~~l~~L~~L~l~~N-~l~~l~~l~~l~~L~~L~L~~  382 (384)
T d2omza2         324 PVSSLTKLQRLFFANN-KVSDVS-SLANLTNINWLSAGHN-QISDLTPLANLTRITQLGLND  382 (384)
T ss_dssp             GGGGCTTCCEEECCSS-CCCCCG-GGGGCTTCCEEECCSS-CCCBCGGGTTCTTCSEEECCC
T ss_pred             ccccCCCCCEEECCCC-CCCCCh-hHcCCCCCCEEECCCC-cCCCChhhccCCCCCEeeCCC
Confidence            3567888888888885 667665 3667888888888776 577776533333446666653

>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=99.50  E-value=7.9e-14  Score=141.46  Aligned_cols=208  Identities=15%  Similarity=0.128  Sum_probs=129.2

Q ss_pred             EcccccccccccCc----ccccccccccccccch-hhcccccCceeeecCCcccccchh-hccCccCcEeeccCCcCCCC
Q 004021          501 SLMANEIESLSEIP----TLLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGLPQE-LKALEKLRYLNLEYTHYLSI  574 (779)
Q Consensus       501 ~l~~~~~~~l~~~~----~lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L~~L~l~~~~~l~~  574 (779)
                      ..+++.++.+|...    ..|+|++| .++.+|. .|.++++|++|++++|.+..++.. +..+..++.+....+..+..
T Consensus        17 ~c~~~~L~~iP~~ip~~~~~L~Ls~N-~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~   95 (284)
T d1ozna_          17 SCPQQGLQAVPVGIPAASQRIFLHGN-RISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRS   95 (284)
T ss_dssp             ECCSSCCSSCCTTCCTTCSEEECTTS-CCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCC
T ss_pred             EcCCCCCCccCCCCCCCCCEEECcCC-cCCCCCHHHhhcccccccccccccccccccccccccccccccccccccccccc
Confidence            34444455554322    24777777 7777764 578888888888888888776544 56677788877766667777


Q ss_pred             CchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccc
Q 004021          575 IPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFV  654 (779)
Q Consensus       575 lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l  654 (779)
                      +++..+.++++|++|++.+|....              .....+..+++|+.++++.+         +++.+.+..+..+
T Consensus        96 l~~~~~~~l~~L~~L~l~~n~~~~--------------~~~~~~~~~~~L~~l~l~~N---------~l~~i~~~~f~~~  152 (284)
T d1ozna_          96 VDPATFHGLGRLHTLHLDRCGLQE--------------LGPGLFRGLAALQYLYLQDN---------ALQALPDDTFRDL  152 (284)
T ss_dssp             CCTTTTTTCTTCCEEECTTSCCCC--------------CCTTTTTTCTTCCEEECCSS---------CCCCCCTTTTTTC
T ss_pred             ccchhhcccccCCEEecCCccccc--------------ccccccchhcccchhhhccc---------cccccChhHhccc
Confidence            766667888888888888877653              22334555667777777633         3344434445566


Q ss_pred             cCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccc-cCCCCCCCCccEEeeeCCCCCC
Q 004021          655 QNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSI-YPNPLHFPKLKKIGVYGCPKLK  733 (779)
Q Consensus       655 ~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l-~~~~~~l~~L~~L~l~~c~~L~  733 (779)
                      ++|+.|++++|. +..++.               ..+.++++|+.|.+.++ .+..+ +..+..+++|++|+++++. +.
T Consensus       153 ~~L~~L~l~~N~-l~~l~~---------------~~f~~l~~L~~l~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N~-i~  214 (284)
T d1ozna_         153 GNLTHLFLHGNR-ISSVPE---------------RAFRGLHSLDRLLLHQN-RVAHVHPHAFRDLGRLMTLYLFANN-LS  214 (284)
T ss_dssp             TTCCEEECCSSC-CCEECT---------------TTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSC-CS
T ss_pred             cchhhcccccCc-ccccch---------------hhhccccccchhhhhhc-cccccChhHhhhhhhcccccccccc-cc
Confidence            677777777653 444444               35566777777777764 34344 4455667777777777653 55


Q ss_pred             CCCCC-CC-CcccccEEEe
Q 004021          734 KLPIN-SS-SAKERRVVIE  750 (779)
Q Consensus       734 ~lP~~-~~-~~~~~~l~i~  750 (779)
                      .+|.. +. ...++.+.+.
T Consensus       215 ~~~~~~~~~~~~L~~L~l~  233 (284)
T d1ozna_         215 ALPTEALAPLRALQYLRLN  233 (284)
T ss_dssp             CCCHHHHTTCTTCCEEECC
T ss_pred             cccccccccccccCEEEec
Confidence            55532 21 2223555554

>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=99.49  E-value=6e-14  Score=137.20  Aligned_cols=180  Identities=21%  Similarity=0.256  Sum_probs=115.6

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |++++| .++.++ .+.+|++|++|++++|.+..+++ +.++++|++|++++| .++.++.  +.++++|+.+.+.++..
T Consensus        46 L~l~~~-~i~~l~-~l~~l~~L~~L~ls~n~i~~~~~-l~~l~~l~~l~~~~n-~~~~i~~--l~~l~~L~~l~l~~~~~  119 (227)
T d1h6ua2          46 LSAFGT-GVTTIE-GVQYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGN-PLKNVSA--IAGLQSIKTLDLTSTQI  119 (227)
T ss_dssp             EECTTS-CCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSC-CCSCCGG--GTTCTTCCEEECTTSCC
T ss_pred             EECCCC-CCCcch-hHhcCCCCcEeecCCceeecccc-ccccccccccccccc-ccccccc--ccccccccccccccccc
Confidence            667777 666663 56777777777777777766653 667777777777766 4566654  66777777777766654


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      ..                ...+...+.+..+.++.+.         +.  ....+...++|+.|++++|... ..     
T Consensus       120 ~~----------------~~~~~~~~~~~~l~~~~~~---------~~--~~~~~~~~~~L~~L~l~~n~~~-~~-----  166 (227)
T d1h6ua2         120 TD----------------VTPLAGLSNLQVLYLDLNQ---------IT--NISPLAGLTNLQYLSIGNAQVS-DL-----  166 (227)
T ss_dssp             CC----------------CGGGTTCTTCCEEECCSSC---------CC--CCGGGGGCTTCCEEECCSSCCC-CC-----
T ss_pred             cc----------------cchhccccchhhhhchhhh---------hc--hhhhhccccccccccccccccc-cc-----
Confidence            42                1223344555555544221         11  1233566788889988876432 21     


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCCCCCCCCcccccEEEe
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKLPINSSSAKERRVVIE  750 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~lP~~~~~~~~~~l~i~  750 (779)
                                  ..+..+++|+.|+++++ .++.++. ...+++|++|++++| +++++|.......++.+.++
T Consensus       167 ------------~~l~~l~~L~~L~Ls~n-~l~~l~~-l~~l~~L~~L~Ls~N-~lt~i~~l~~l~~L~~L~ls  225 (227)
T d1h6ua2         167 ------------TPLANLSKLTTLKADDN-KISDISP-LASLPNLIEVHLKNN-QISDVSPLANTSNLFIVTLT  225 (227)
T ss_dssp             ------------GGGTTCTTCCEEECCSS-CCCCCGG-GGGCTTCCEEECTTS-CCCBCGGGTTCTTCCEEEEE
T ss_pred             ------------hhhcccccceecccCCC-ccCCChh-hcCCCCCCEEECcCC-cCCCCcccccCCCCCEEEee
Confidence                        24567889999999885 6777654 567899999999988 58888753333344766664

>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=99.48  E-value=9.3e-14  Score=133.79  Aligned_cols=159  Identities=18%  Similarity=0.224  Sum_probs=114.2

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |++++| .++.++ .+..+++|++|++++|.++.++. ++++++|++|++++| .++.+|.  +..+++|+.|++.+|..
T Consensus        51 L~l~~~-~i~~l~-~l~~l~~L~~L~L~~n~i~~l~~-~~~l~~L~~L~l~~n-~i~~l~~--l~~l~~L~~L~l~~~~~  124 (210)
T d1h6ta2          51 IIANNS-DIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDEN-KVKDLSS--LKDLKKLKSLSLEHNGI  124 (210)
T ss_dssp             EECTTS-CCCCCT-TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCGGG--GTTCTTCCEEECTTSCC
T ss_pred             EECcCC-CCCCch-hHhhCCCCCEEeCCCccccCccc-cccCccccccccccc-ccccccc--ccccccccccccccccc
Confidence            344444 555554 47778888899998888888874 688888999998888 6778875  78888888888888765


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceeccccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDK  676 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  676 (779)
                      ..                +..+..+++|+.+.++.+..         .  .+..+..+++|+.+++++|.. ..+     
T Consensus       125 ~~----------------~~~l~~l~~l~~l~~~~n~l---------~--~~~~~~~l~~L~~l~l~~n~l-~~i-----  171 (210)
T d1h6ta2         125 SD----------------INGLVHLPQLESLYLGNNKI---------T--DITVLSRLTKLDTLSLEDNQI-SDI-----  171 (210)
T ss_dssp             CC----------------CGGGGGCTTCCEEECCSSCC---------C--CCGGGGGCTTCSEEECCSSCC-CCC-----
T ss_pred             cc----------------cccccccccccccccccccc---------c--ccccccccccccccccccccc-ccc-----
Confidence            53                23466777888777764432         2  234566778888888888643 333     


Q ss_pred             ccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeC
Q 004021          677 LRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYG  728 (779)
Q Consensus       677 ~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~  728 (779)
                                  ..+..+++|+.|+++++ .++.++ .+..+++|++|++++
T Consensus       172 ------------~~l~~l~~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         172 ------------VPLAGLTKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFS  209 (210)
T ss_dssp             ------------GGGTTCTTCCEEECCSS-CCCBCG-GGTTCTTCSEEEEEE
T ss_pred             ------------ccccCCCCCCEEECCCC-CCCCCh-hhcCCCCCCEEEccC
Confidence                        13567888999998875 677776 366788888888864

>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=99.48  E-value=2.9e-14  Score=147.06  Aligned_cols=202  Identities=15%  Similarity=0.098  Sum_probs=144.0

Q ss_pred             cccccccccc---ccchhhcccccCceeeecC-Cccc-ccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeee
Q 004021          517 LSLRRNDSLT---ELPSRISSLVSLHHLDLSL-THIR-GLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRL  591 (779)
Q Consensus       517 L~L~~~~~l~---~lp~~i~~L~~L~~L~L~~-~~i~-~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l  591 (779)
                      |+|+++ .+.   .+|.+|++|++|++|+|++ |.+. .+|..|++|++|++|+|++|. +..++...+..+.+|+++++
T Consensus        55 L~L~~~-~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~-l~~~~~~~~~~~~~L~~l~l  132 (313)
T d1ogqa_          55 LDLSGL-NLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTN-VSGAIPDFLSQIKTLVTLDF  132 (313)
T ss_dssp             EEEECC-CCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEEC-CEEECCGGGGGCTTCCEEEC
T ss_pred             EECCCC-CCCCCCCCChHHhcCccccccccccccccccccccccccccccchhhhcccc-ccccccccccchhhhccccc
Confidence            899998 666   5899999999999999987 6776 699999999999999999994 55555445889999999999


Q ss_pred             ccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc-----cccCCCC-Ccc----------cCccccccc
Q 004021          592 LECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA-----VQKFFKY-PKL----------DLTWLVFVQ  655 (779)
Q Consensus       592 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~-----~~~~~~L-~~L----------~~~~l~~l~  655 (779)
                      ..|....              ..+..++.+++|+.++++.+....     +..+.++ +.+          .+..+..+.
T Consensus       133 ~~N~~~~--------------~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~  198 (313)
T d1ogqa_         133 SYNALSG--------------TLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLN  198 (313)
T ss_dssp             CSSEEES--------------CCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCC
T ss_pred             ccccccc--------------cCchhhccCcccceeeccccccccccccccccccccccccccccccccccccccccccc
Confidence            9987664              456778899999999998765431     1222222 111          122222222


Q ss_pred             CcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCCCCCCCC
Q 004021          656 NLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGCPKLKKL  735 (779)
Q Consensus       656 ~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c~~L~~l  735 (779)
                       +..++++.+.....++                .....+++|+.|++.++. +...+...+.+++|+.|++++|.--..+
T Consensus       199 -~~~l~l~~~~~~~~~~----------------~~~~~~~~l~~l~~~~~~-l~~~~~~~~~~~~L~~L~Ls~N~l~g~i  260 (313)
T d1ogqa_         199 -LAFVDLSRNMLEGDAS----------------VLFGSDKNTQKIHLAKNS-LAFDLGKVGLSKNLNGLDLRNNRIYGTL  260 (313)
T ss_dssp             -CSEEECCSSEEEECCG----------------GGCCTTSCCSEEECCSSE-ECCBGGGCCCCTTCCEEECCSSCCEECC
T ss_pred             -cccccccccccccccc----------------cccccccccccccccccc-ccccccccccccccccccCccCeecccC
Confidence             2234444433322222                356788999999999864 4544556778999999999998644489


Q ss_pred             CCCCCCccc-ccEEEech
Q 004021          736 PINSSSAKE-RRVVIEGL  752 (779)
Q Consensus       736 P~~~~~~~~-~~l~i~~~  752 (779)
                      |..+...+. +.+.++++
T Consensus       261 P~~l~~L~~L~~L~Ls~N  278 (313)
T d1ogqa_         261 PQGLTQLKFLHSLNVSFN  278 (313)
T ss_dssp             CGGGGGCTTCCEEECCSS
T ss_pred             ChHHhCCCCCCEEECcCC
Confidence            987765543 77777643

>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=99.47  E-value=3.6e-13  Score=138.09  Aligned_cols=214  Identities=18%  Similarity=0.184  Sum_probs=145.4

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++-++. .++.+|..|.  +++++|+|++|+|+.+|+ .|.++++|++|++++| .+..+++..|.++++|++|++.+|.
T Consensus        15 ~~C~~~-~L~~lP~~l~--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n-~~~~i~~~~f~~l~~L~~L~l~~n~   90 (305)
T d1xkua_          15 VQCSDL-GLEKVPKDLP--PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINN-KISKISPGAFAPLVKLERLYLSKNQ   90 (305)
T ss_dssp             EECTTS-CCCSCCCSCC--TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSSC
T ss_pred             EEecCC-CCCccCCCCC--CCCCEEECcCCcCCCcChhHhhccccccccccccc-cccccchhhhhCCCccCEecccCCc
Confidence            566666 7999998774  689999999999999987 5999999999999999 5677766569999999999999999


Q ss_pred             CCCcccccCCcc-----C--CCchhhHHhhcCCCCCCceeEEeeccc-------ccccCCCCCcccC-----cc--cccc
Q 004021          596 SEGVTKEEGNVL-----C--DDAEPLMRELLGLKRLNVLSWSFRSSL-------AVQKFFKYPKLDL-----TW--LVFV  654 (779)
Q Consensus       596 ~~~~~~~~~~~~-----~--~~~~~~~~~l~~L~~L~~L~l~~~~~~-------~~~~~~~L~~L~~-----~~--l~~l  654 (779)
                      +..++......+     .  .........+.....+..+....+...       .+..+++|+.+..     ..  ...+
T Consensus        91 l~~l~~~~~~~l~~L~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~  170 (305)
T d1xkua_          91 LKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLP  170 (305)
T ss_dssp             CSBCCSSCCTTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCC
T ss_pred             cCcCccchhhhhhhhhccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccC
Confidence            887665443210     0  001112222334444444444433221       1233344444411     00  1234


Q ss_pred             cCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccC-CCCCCCCccEEeeeCCCCCC
Q 004021          655 QNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYP-NPLHFPKLKKIGVYGCPKLK  733 (779)
Q Consensus       655 ~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~-~~~~l~~L~~L~l~~c~~L~  733 (779)
                      ++|+.|++++|......+                ..+..++.++.|.++++ .+..++. .+..+++|++|++++| +++
T Consensus       171 ~~L~~L~l~~n~~~~~~~----------------~~~~~~~~l~~L~~s~n-~l~~~~~~~~~~l~~L~~L~L~~N-~L~  232 (305)
T d1xkua_         171 PSLTELHLDGNKITKVDA----------------ASLKGLNNLAKLGLSFN-SISAVDNGSLANTPHLRELHLNNN-KLV  232 (305)
T ss_dssp             TTCSEEECTTSCCCEECT----------------GGGTTCTTCCEEECCSS-CCCEECTTTGGGSTTCCEEECCSS-CCS
T ss_pred             CccCEEECCCCcCCCCCh----------------hHhhccccccccccccc-cccccccccccccccceeeecccc-ccc
Confidence            667777777654433322                35678899999999985 6777754 4567899999999998 799


Q ss_pred             CCCCCCCCc-ccccEEEech
Q 004021          734 KLPINSSSA-KERRVVIEGL  752 (779)
Q Consensus       734 ~lP~~~~~~-~~~~l~i~~~  752 (779)
                      ++|.++... .++.+.++++
T Consensus       233 ~lp~~l~~l~~L~~L~Ls~N  252 (305)
T d1xkua_         233 KVPGGLADHKYIQVVYLHNN  252 (305)
T ss_dssp             SCCTTTTTCSSCCEEECCSS
T ss_pred             ccccccccccCCCEEECCCC
Confidence            999877654 4488888765

>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=99.45  E-value=4.5e-13  Score=135.79  Aligned_cols=207  Identities=19%  Similarity=0.203  Sum_probs=159.0

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccCcc-------ccccccccccccc-chhhcccccCceeeecC-Cccccc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT-------LLSLRRNDSLTEL-PSRISSLVSLHHLDLSL-THIRGL  551 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~-------lL~L~~~~~l~~l-p~~i~~L~~L~~L~L~~-~~i~~l  551 (779)
                      .+..+..+|.. -...++.|++++|.++.++....       .|++++| .+..+ +..+.++..++.+.... +.++.+
T Consensus        19 ~~~~L~~iP~~-ip~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n-~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l   96 (284)
T d1ozna_          19 PQQGLQAVPVG-IPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSN-VLARIDAAAFTGLALLEQLDLSDNAQLRSV   96 (284)
T ss_dssp             CSSCCSSCCTT-CCTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSCTTCCCC
T ss_pred             CCCCCCccCCC-CCCCCCEEECcCCcCCCCCHHHhhccccccccccccc-cccccccccccccccccccccccccccccc
Confidence            34445555542 23578999999999998876422       4999999 88877 44567888999988764 477777


Q ss_pred             -chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEE
Q 004021          552 -PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       552 -p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                       |..+.++++|++|++++| .+..++...+..+.+|+.+++.+|.+..+              ....+..+++|+.|+++
T Consensus        97 ~~~~~~~l~~L~~L~l~~n-~~~~~~~~~~~~~~~L~~l~l~~N~l~~i--------------~~~~f~~~~~L~~L~l~  161 (284)
T d1ozna_          97 DPATFHGLGRLHTLHLDRC-GLQELGPGLFRGLAALQYLYLQDNALQAL--------------PDDTFRDLGNLTHLFLH  161 (284)
T ss_dssp             CTTTTTTCTTCCEEECTTS-CCCCCCTTTTTTCTTCCEEECCSSCCCCC--------------CTTTTTTCTTCCEEECC
T ss_pred             cchhhcccccCCEEecCCc-ccccccccccchhcccchhhhcccccccc--------------ChhHhccccchhhcccc
Confidence             556899999999999999 55666666588899999999999988752              23446778899999998


Q ss_pred             eecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcc
Q 004021          631 FRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKS  710 (779)
Q Consensus       631 ~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~  710 (779)
                      .+         +++.+.+..+..+++|+.|++++|... .+..               ..+..+++|+.|++++ +.+..
T Consensus       162 ~N---------~l~~l~~~~f~~l~~L~~l~l~~N~l~-~i~~---------------~~f~~l~~L~~L~l~~-N~i~~  215 (284)
T d1ozna_         162 GN---------RISSVPERAFRGLHSLDRLLLHQNRVA-HVHP---------------HAFRDLGRLMTLYLFA-NNLSA  215 (284)
T ss_dssp             SS---------CCCEECTTTTTTCTTCCEEECCSSCCC-EECT---------------TTTTTCTTCCEEECCS-SCCSC
T ss_pred             cC---------cccccchhhhccccccchhhhhhcccc-ccCh---------------hHhhhhhhcccccccc-ccccc
Confidence            44         455666677888999999999997654 4433               4788899999999998 45666


Q ss_pred             ccC-CCCCCCCccEEeeeCCC
Q 004021          711 IYP-NPLHFPKLKKIGVYGCP  730 (779)
Q Consensus       711 l~~-~~~~l~~L~~L~l~~c~  730 (779)
                      ++. .+..+++|++|+++++|
T Consensus       216 ~~~~~~~~~~~L~~L~l~~N~  236 (284)
T d1ozna_         216 LPTEALAPLRALQYLRLNDNP  236 (284)
T ss_dssp             CCHHHHTTCTTCCEEECCSSC
T ss_pred             ccccccccccccCEEEecCCC
Confidence            654 56689999999999865

>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=99.45  E-value=2.8e-13  Score=132.30  Aligned_cols=185  Identities=19%  Similarity=0.279  Sum_probs=145.8

Q ss_pred             ccccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEee
Q 004021          491 VKEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLN  565 (779)
Q Consensus       491 ~~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~  565 (779)
                      ...+.+++.|++.+|.++.++....     .|++++| .+..++ .+.++.+|++|++++|.++.++ .+.++++|++|+
T Consensus        37 ~~~l~~L~~L~l~~~~i~~l~~l~~l~~L~~L~ls~n-~i~~~~-~l~~l~~l~~l~~~~n~~~~i~-~l~~l~~L~~l~  113 (227)
T d1h6ua2          37 QADLDGITTLSAFGTGVTTIEGVQYLNNLIGLELKDN-QITDLA-PLKNLTKITELELSGNPLKNVS-AIAGLQSIKTLD  113 (227)
T ss_dssp             HHHHHTCCEEECTTSCCCCCTTGGGCTTCCEEECCSS-CCCCCG-GGTTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEE
T ss_pred             HHHcCCcCEEECCCCCCCcchhHhcCCCCcEeecCCc-eeeccc-cccccccccccccccccccccc-cccccccccccc
Confidence            3456789999999999988754322     3999999 888876 3899999999999999999887 588999999999


Q ss_pred             ccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCc
Q 004021          566 LEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPK  645 (779)
Q Consensus       566 l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~  645 (779)
                      +++| ....++.  +.....+..+.+..+.+..                ...+..+++|+.|+++.+...          
T Consensus       114 l~~~-~~~~~~~--~~~~~~~~~l~~~~~~~~~----------------~~~~~~~~~L~~L~l~~n~~~----------  164 (227)
T d1h6ua2         114 LTST-QITDVTP--LAGLSNLQVLYLDLNQITN----------------ISPLAGLTNLQYLSIGNAQVS----------  164 (227)
T ss_dssp             CTTS-CCCCCGG--GTTCTTCCEEECCSSCCCC----------------CGGGGGCTTCCEEECCSSCCC----------
T ss_pred             cccc-cccccch--hccccchhhhhchhhhhch----------------hhhhccccccccccccccccc----------
Confidence            9999 4555655  7788999999998877653                223567788999998754332          


Q ss_pred             ccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEe
Q 004021          646 LDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIG  725 (779)
Q Consensus       646 L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~  725 (779)
                       ....++++++|+.|+|++|. +..++                 .+..+++|++|+|+++ +++.++. +..+++|+.|+
T Consensus       165 -~~~~l~~l~~L~~L~Ls~n~-l~~l~-----------------~l~~l~~L~~L~Ls~N-~lt~i~~-l~~l~~L~~L~  223 (227)
T d1h6ua2         165 -DLTPLANLSKLTTLKADDNK-ISDIS-----------------PLASLPNLIEVHLKNN-QISDVSP-LANTSNLFIVT  223 (227)
T ss_dssp             -CCGGGTTCTTCCEEECCSSC-CCCCG-----------------GGGGCTTCCEEECTTS-CCCBCGG-GTTCTTCCEEE
T ss_pred             -cchhhcccccceecccCCCc-cCCCh-----------------hhcCCCCCCEEECcCC-cCCCCcc-cccCCCCCEEE
Confidence             12346778999999999974 45442                 4568899999999996 6888864 66899999999


Q ss_pred             eeC
Q 004021          726 VYG  728 (779)
Q Consensus       726 l~~  728 (779)
                      +++
T Consensus       224 lsn  226 (227)
T d1h6ua2         224 LTN  226 (227)
T ss_dssp             EEE
T ss_pred             eeC
Confidence            975

>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=99.45  E-value=5.2e-13  Score=141.66  Aligned_cols=171  Identities=19%  Similarity=0.283  Sum_probs=98.9

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      +++++| .+..+++ +..+.+|++|++++|.++.+| .+..+++|+.|++++| .+..+++  ++.+++|++|+++++.+
T Consensus       202 l~l~~n-~i~~~~~-~~~~~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~l~~n-~l~~~~~--~~~~~~L~~L~l~~~~l  275 (384)
T d2omza2         202 LIATNN-QISDITP-LGILTNLDELSLNGNQLKDIG-TLASLTNLTDLDLANN-QISNLAP--LSGLTKLTELKLGANQI  275 (384)
T ss_dssp             EECCSS-CCCCCGG-GGGCTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSS-CCCCCGG--GTTCTTCSEEECCSSCC
T ss_pred             eeccCC-ccCCCCc-ccccCCCCEEECCCCCCCCcc-hhhcccccchhccccC-ccCCCCc--ccccccCCEeeccCccc
Confidence            344444 4444432 344556666666666665554 4556666666666666 4555554  55666666666666555


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccc---cccCCCCCcc--------cCcccccccCcceEEeccc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLA---VQKFFKYPKL--------DLTWLVFVQNLKELEIIVC  665 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~---~~~~~~L~~L--------~~~~l~~l~~L~~L~L~~~  665 (779)
                      ..++                .+..++.++.+.+..+....   +..+.+++.|        ..+.+..+++|+.|++++|
T Consensus       276 ~~~~----------------~~~~~~~l~~l~~~~n~l~~~~~~~~~~~l~~L~ls~n~l~~l~~l~~l~~L~~L~L~~n  339 (384)
T d2omza2         276 SNIS----------------PLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFANN  339 (384)
T ss_dssp             CCCG----------------GGTTCTTCSEEECCSSCCSCCGGGGGCTTCSEEECCSSCCSCCGGGGGCTTCCEEECCSS
T ss_pred             CCCC----------------ccccccccccccccccccccccccchhcccCeEECCCCCCCCCcccccCCCCCEEECCCC
Confidence            4321                12233333333333222211   1122222222        1234678899999999987


Q ss_pred             cccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeCC
Q 004021          666 TEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYGC  729 (779)
Q Consensus       666 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~c  729 (779)
                      . ++.+                 ..+..+++|++|+++++ .++.++. +..+++|+.|+|+++
T Consensus       340 ~-l~~l-----------------~~l~~l~~L~~L~l~~N-~l~~l~~-l~~l~~L~~L~L~~N  383 (384)
T d2omza2         340 K-VSDV-----------------SSLANLTNINWLSAGHN-QISDLTP-LANLTRITQLGLNDQ  383 (384)
T ss_dssp             C-CCCC-----------------GGGGGCTTCCEEECCSS-CCCBCGG-GTTCTTCSEEECCCE
T ss_pred             C-CCCC-----------------hhHcCCCCCCEEECCCC-cCCCChh-hccCCCCCEeeCCCC
Confidence            4 4443                 24677999999999984 6777764 678999999999874

>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=99.44  E-value=2.5e-13  Score=129.58  Aligned_cols=62  Identities=19%  Similarity=0.281  Sum_probs=36.8

Q ss_pred             hcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCC
Q 004021          532 ISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      +..+++|++|++++|.++.++. ++++++|++|++++| .+..+|.  ++++++|+.|++++|...
T Consensus        58 l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n-~~~~~~~--l~~l~~L~~L~l~~~~~~  119 (199)
T d2omxa2          58 VEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNN-QIADITP--LANLTNLTGLTLFNNQIT  119 (199)
T ss_dssp             GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCCGG--GTTCTTCSEEECCSSCCC
T ss_pred             cccCCCcCcCccccccccCccc-ccCCccccccccccc-ccccccc--cccccccccccccccccc
Confidence            4556666666666666666553 566666666666666 3455554  556666666666655443

>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=99.41  E-value=3.1e-13  Score=130.08  Aligned_cols=161  Identities=24%  Similarity=0.261  Sum_probs=128.1

Q ss_pred             ccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeecc
Q 004021          493 EWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLE  567 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~  567 (779)
                      .+..+++|.+.++.+..++....     .|+|++| .++.+| .+++|++|++|++++|.++.+| .+.++++|+.|+++
T Consensus        44 ~L~~L~~L~l~~~~i~~l~~l~~l~~L~~L~L~~n-~i~~l~-~~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~  120 (210)
T d1h6ta2          44 ELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGN-KLTDIK-PLANLKNLGWLFLDENKVKDLS-SLKDLKKLKSLSLE  120 (210)
T ss_dssp             HHHTCCEEECTTSCCCCCTTGGGCTTCCEEECCSS-CCCCCG-GGTTCTTCCEEECCSSCCCCGG-GGTTCTTCCEEECT
T ss_pred             HhcCccEEECcCCCCCCchhHhhCCCCCEEeCCCc-cccCcc-ccccCccccccccccccccccc-cccccccccccccc
Confidence            35678889999988877654322     3899999 898887 4789999999999999999998 58999999999999


Q ss_pred             CCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCccc
Q 004021          568 YTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLD  647 (779)
Q Consensus       568 ~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~  647 (779)
                      +| .+..++.  +..+++|+.+++.+|.+..                +..+..+++|+.++++.+...         .+ 
T Consensus       121 ~~-~~~~~~~--l~~l~~l~~l~~~~n~l~~----------------~~~~~~l~~L~~l~l~~n~l~---------~i-  171 (210)
T d1h6ta2         121 HN-GISDING--LVHLPQLESLYLGNNKITD----------------ITVLSRLTKLDTLSLEDNQIS---------DI-  171 (210)
T ss_dssp             TS-CCCCCGG--GGGCTTCCEEECCSSCCCC----------------CGGGGGCTTCSEEECCSSCCC---------CC-
T ss_pred             cc-ccccccc--ccccccccccccccccccc----------------ccccccccccccccccccccc---------cc-
Confidence            99 5677765  8899999999999987764                234567889999999855432         22 


Q ss_pred             CcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccC
Q 004021          648 LTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILY  704 (779)
Q Consensus       648 ~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~  704 (779)
                       +.+..+++|+.|+|++|. ++++                 ..+..+++|+.|+|++
T Consensus       172 -~~l~~l~~L~~L~Ls~N~-i~~l-----------------~~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         172 -VPLAGLTKLQNLYLSKNH-ISDL-----------------RALAGLKNLDVLELFS  209 (210)
T ss_dssp             -GGGTTCTTCCEEECCSSC-CCBC-----------------GGGTTCTTCSEEEEEE
T ss_pred             -ccccCCCCCCEEECCCCC-CCCC-----------------hhhcCCCCCCEEEccC
Confidence             346778999999999974 5554                 2467899999999875

>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=99.41  E-value=8.7e-13  Score=137.97  Aligned_cols=93  Identities=26%  Similarity=0.314  Sum_probs=48.5

Q ss_pred             CccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCC
Q 004021          496 GAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYL  572 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l  572 (779)
                      ++++|+++++.++.+|..++   .|+|++| .++++|..+   .+|+.|++++|+++.++.-   .+.|++|++++| .+
T Consensus        39 ~l~~LdLs~~~L~~lp~~~~~L~~L~Ls~N-~l~~lp~~~---~~L~~L~l~~n~l~~l~~l---p~~L~~L~L~~n-~l  110 (353)
T d1jl5a_          39 QAHELELNNLGLSSLPELPPHLESLVASCN-SLTELPELP---QSLKSLLVDNNNLKALSDL---PPLLEYLGVSNN-QL  110 (353)
T ss_dssp             TCSEEECTTSCCSCCCSCCTTCSEEECCSS-CCSSCCCCC---TTCCEEECCSSCCSCCCSC---CTTCCEEECCSS-CC
T ss_pred             CCCEEEeCCCCCCCCCCCCCCCCEEECCCC-CCcccccch---hhhhhhhhhhcccchhhhh---cccccccccccc-cc
Confidence            34555666555555554432   2566665 566665443   3455555555555544321   123556666655 45


Q ss_pred             CCCchhhhcCCccCcEeeeccccCCC
Q 004021          573 SIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       573 ~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ..+|.  ++.+++|++|++.++.+..
T Consensus       111 ~~lp~--~~~l~~L~~L~l~~~~~~~  134 (353)
T d1jl5a_         111 EKLPE--LQNSSFLKIIDVDNNSLKK  134 (353)
T ss_dssp             SSCCC--CTTCTTCCEEECCSSCCSC
T ss_pred             ccccc--hhhhccceeeccccccccc
Confidence            55554  4555666666665554443

>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=99.40  E-value=5.8e-13  Score=126.95  Aligned_cols=146  Identities=20%  Similarity=0.271  Sum_probs=112.0

Q ss_pred             cccCCccEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeec
Q 004021          492 KEWEGAKRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNL  566 (779)
Q Consensus       492 ~~~~~lr~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l  566 (779)
                      ..+.+++.|++.++.+.++.....     .|+|++| .++.++. ++++++|++|++++|.+..+|. +.++++|+.|++
T Consensus        37 ~~l~~l~~L~l~~~~i~~l~~l~~l~nL~~L~Ls~N-~l~~~~~-l~~l~~L~~L~l~~n~~~~~~~-l~~l~~L~~L~l  113 (199)
T d2omxa2          37 TDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNN-QLTDITP-LKNLTKLVDILMNNNQIADITP-LANLTNLTGLTL  113 (199)
T ss_dssp             HHHTTCCEEECTTSCCCCCTTGGGCTTCCEEECCSS-CCCCCGG-GTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             HHhcCCCEEECCCCCCCCccccccCCCcCcCccccc-cccCccc-ccCCcccccccccccccccccc-cccccccccccc
Confidence            346789999999998887654322     3999999 8988875 9999999999999999999884 899999999999


Q ss_pred             cCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcc
Q 004021          567 EYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKL  646 (779)
Q Consensus       567 ~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L  646 (779)
                      ++| ....++.  +..+++|+.|++++|.+..                +..+..+++|+.|++.+|.         ++.+
T Consensus       114 ~~~-~~~~~~~--~~~l~~L~~L~l~~n~l~~----------------~~~l~~~~~L~~L~l~~n~---------l~~l  165 (199)
T d2omxa2         114 FNN-QITDIDP--LKNLTNLNRLELSSNTISD----------------ISALSGLTSLQQLNFSSNQ---------VTDL  165 (199)
T ss_dssp             CSS-CCCCCGG--GTTCTTCSEEECCSSCCCC----------------CGGGTTCTTCSEEECCSSC---------CCCC
T ss_pred             ccc-ccccccc--cchhhhhHHhhhhhhhhcc----------------ccccccccccccccccccc---------ccCC
Confidence            998 4555654  7899999999999987653                2346677788888777443         2222


Q ss_pred             cCcccccccCcceEEecccccccee
Q 004021          647 DLTWLVFVQNLKELEIIVCTEMEEI  671 (779)
Q Consensus       647 ~~~~l~~l~~L~~L~L~~~~~~~~~  671 (779)
                        +.++++++|++|++++|+ +.++
T Consensus       166 --~~l~~l~~L~~L~ls~N~-i~~i  187 (199)
T d2omxa2         166 --KPLANLTTLERLDISSNK-VSDI  187 (199)
T ss_dssp             --GGGTTCTTCCEEECCSSC-CCCC
T ss_pred             --ccccCCCCCCEEECCCCC-CCCC
Confidence              335667777888887764 4443

>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=99.38  E-value=9.7e-13  Score=129.85  Aligned_cols=100  Identities=14%  Similarity=0.193  Sum_probs=73.4

Q ss_pred             cEEEcccccccccccCcc----cccccccccccccch-hhcccccCceeeecCCccccc-c-hhhccCccCcEeeccCCc
Q 004021          498 KRISLMANEIESLSEIPT----LLSLRRNDSLTELPS-RISSLVSLHHLDLSLTHIRGL-P-QELKALEKLRYLNLEYTH  570 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~----lL~L~~~~~l~~lp~-~i~~L~~L~~L~L~~~~i~~l-p-~~~~~L~~L~~L~l~~~~  570 (779)
                      +.+..++.+++.+|...+    -|+|++| .++.+|. .|.++++|++|++++|.+... | ..|.+++++++|.+..+.
T Consensus        11 ~~i~c~~~~l~~iP~~l~~~l~~L~Ls~n-~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n   89 (242)
T d1xwdc1          11 RVFLCQESKVTEIPSDLPRNAIELRFVLT-KLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKAN   89 (242)
T ss_dssp             SEEEEESCSCSSCCSCSCSCCSEEEEESC-CCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCT
T ss_pred             CEEEEeCCCCCCcCCCCCCCCCEEECcCC-cCCccChhHhhccchhhhhhhccccccceeeccccccccccccccccccc
Confidence            455566666666654322    3788888 7888865 578889999999998877653 3 347888888888887665


Q ss_pred             CCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          571 YLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       571 ~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      .+..++.+.+.++++|++|++.+|.+..
T Consensus        90 ~l~~~~~~~~~~l~~L~~l~l~~~~l~~  117 (242)
T d1xwdc1          90 NLLYINPEAFQNLPNLQYLLISNTGIKH  117 (242)
T ss_dssp             TCCEECTTSEECCTTCCEEEEESCCCCS
T ss_pred             cccccccccccccccccccccchhhhcc
Confidence            6777776667888999999998887654

>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=99.36  E-value=5.1e-13  Score=116.07  Aligned_cols=100  Identities=28%  Similarity=0.342  Sum_probs=79.1

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .++.+| .++++.+|++|++++|.|+.+|+.++.+++|++|++++| .++.+|.  ++++++|++|++++|.+
T Consensus         3 L~Ls~n-~l~~l~-~l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N-~i~~l~~--~~~l~~L~~L~l~~N~i   77 (124)
T d1dcea3           3 LHLAHK-DLTVLC-HLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDN-ALENVDG--VANLPRLQELLLCNNRL   77 (124)
T ss_dssp             EECTTS-CCSSCC-CGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSS-CCCCCGG--GTTCSSCCEEECCSSCC
T ss_pred             EEcCCC-CCCCCc-ccccCCCCCEEECCCCccCcchhhhhhhhcccccccccc-cccccCc--cccccccCeEECCCCcc
Confidence            678888 888887 488899999999999999999988999999999999998 6788875  88999999999999887


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      ..             ...+..+..+++|+.|++++|..
T Consensus        78 ~~-------------~~~~~~l~~~~~L~~L~l~~N~i  102 (124)
T d1dcea3          78 QQ-------------SAAIQPLVSCPRLVLLNLQGNSL  102 (124)
T ss_dssp             CS-------------SSTTGGGGGCTTCCEEECTTSGG
T ss_pred             CC-------------CCCchhhcCCCCCCEEECCCCcC
Confidence            74             12234455666666666665543

>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=99.32  E-value=6.5e-12  Score=123.75  Aligned_cols=188  Identities=16%  Similarity=0.138  Sum_probs=126.5

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      ++.++. .++.+|..+.  .++++|++++|.|+.+|. .|.++++|++|++++|.....+|.+.+.+++++++|.+..+.
T Consensus        13 i~c~~~-~l~~iP~~l~--~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n   89 (242)
T d1xwdc1          13 FLCQES-KVTEIPSDLP--RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKAN   89 (242)
T ss_dssp             EEEESC-SCSSCCSCSC--SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCT
T ss_pred             EEEeCC-CCCCcCCCCC--CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeeccccccccccccccccccc
Confidence            566777 7889997764  589999999999999987 489999999999999966666776668899999999987643


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeeccccccc---CCCCCcc-------------cCcccccc-cCcc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQK---FFKYPKL-------------DLTWLVFV-QNLK  658 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~---~~~L~~L-------------~~~~l~~l-~~L~  658 (779)
                      ...             ...+..+.++++|+.|.++.+.......   +.+++.+             ....+..+ ..++
T Consensus        90 ~l~-------------~~~~~~~~~l~~L~~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~~~~~~l~  156 (242)
T d1xwdc1          90 NLL-------------YINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESV  156 (242)
T ss_dssp             TCC-------------EECTTSEECCTTCCEEEEESCCCCSCCCCTTTCBSSCEEEEEESCTTCCEECTTSSTTSBSSCE
T ss_pred             ccc-------------ccccccccccccccccccchhhhcccccccccccccccccccccccccccccccccccccccce
Confidence            221             2344567889999999999876644322   2223322             12223333 3566


Q ss_pred             eEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCC-CCCCCCccEEeeeCCCCCCCCCC
Q 004021          659 ELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPN-PLHFPKLKKIGVYGCPKLKKLPI  737 (779)
Q Consensus       659 ~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~-~~~l~~L~~L~l~~c~~L~~lP~  737 (779)
                      .|+++++ .+..+..                .....++++.+....++.++.++.. +..+++|++|++++++ ++.+|.
T Consensus       157 ~L~l~~n-~l~~i~~----------------~~~~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~-l~~l~~  218 (242)
T d1xwdc1         157 ILWLNKN-GIQEIHN----------------CAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPS  218 (242)
T ss_dssp             EEECCSS-CCCEECT----------------TTTTTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSC-CCCCCS
T ss_pred             eeecccc-ccccccc----------------ccccchhhhccccccccccccccHHHhcCCCCCCEEECCCCc-CCccCH
Confidence            7777663 3444433                2223455555555455667777654 3567777777777753 777775


Q ss_pred             C
Q 004021          738 N  738 (779)
Q Consensus       738 ~  738 (779)
                      .
T Consensus       219 ~  219 (242)
T d1xwdc1         219 Y  219 (242)
T ss_dssp             S
T ss_pred             H
Confidence            4

>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=99.25  E-value=3.3e-12  Score=128.91  Aligned_cols=177  Identities=20%  Similarity=0.170  Sum_probs=97.0

Q ss_pred             ccccccccccc--cchhhcccccCceeeecCCcccc-cchhhccCccCcEeeccCCcCCCC--CchhhhcCCccCcEeee
Q 004021          517 LSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIRG-LPQELKALEKLRYLNLEYTHYLSI--IPHQLISGFLKLEVLRL  591 (779)
Q Consensus       517 L~L~~~~~l~~--lp~~i~~L~~L~~L~L~~~~i~~-lp~~~~~L~~L~~L~l~~~~~l~~--lp~~~i~~L~~L~~L~l  591 (779)
                      |||++| .+..  ++..+.++++|++|++++|.+.. .+..++++++|++|++++|..++.  +.. +...+++|++|++
T Consensus        51 LdLs~~-~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c~~itd~~l~~-l~~~~~~L~~L~l  128 (284)
T d2astb2          51 MDLSNS-VIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQT-LLSSCSRLDELNL  128 (284)
T ss_dssp             EECTTC-EECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHH-HHHHCTTCCEEEC
T ss_pred             EECCCC-ccCHHHHHHHHHhCCCcccccccccCCCcHHHHHHhcCCCCcCccccccccccccccch-hhHHHHhcccccc
Confidence            666666 4432  34445566666666666665543 344566666666666666644432  111 1345666666666


Q ss_pred             ccccCCCcccccCCccCCCchhhHHhhc-CCCCCCceeEEeecccccccCCCCCcccCc-ccccccCcceEEeccccccc
Q 004021          592 LECGSEGVTKEEGNVLCDDAEPLMRELL-GLKRLNVLSWSFRSSLAVQKFFKYPKLDLT-WLVFVQNLKELEIIVCTEME  669 (779)
Q Consensus       592 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~-~l~~l~~L~~L~L~~~~~~~  669 (779)
                      ++|....            .......+. ..++|+.|+++++.       .++..-.+. ...++|+|++|++++|..++
T Consensus       129 s~c~~~~------------~~~~~~~~~~~~~~L~~L~l~~~~-------~~i~~~~l~~l~~~~~~L~~L~L~~~~~it  189 (284)
T d2astb2         129 SWCFDFT------------EKHVQVAVAHVSETITQLNLSGYR-------KNLQKSDLSTLVRRCPNLVHLDLSDSVMLK  189 (284)
T ss_dssp             CCCTTCC------------HHHHHHHHHHSCTTCCEEECCSCG-------GGSCHHHHHHHHHHCTTCSEEECTTCTTCC
T ss_pred             ccccccc------------cccchhhhcccccccchhhhcccc-------cccccccccccccccccccccccccccCCC
Confidence            6653221            011111222 23456666654221       011110111 12457888888888877665


Q ss_pred             eecccccccCcccchhhccCCCCCCCCccEEEccCCCCCcccc-CCCCCCCCccEEeeeCC
Q 004021          670 EIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIY-PNPLHFPKLKKIGVYGC  729 (779)
Q Consensus       670 ~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~-~~~~~l~~L~~L~l~~c  729 (779)
                      +...               ..+..+++|++|++++|+.+..-. ..+..+|+|+.|++++|
T Consensus       190 d~~~---------------~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~  235 (284)
T d2astb2         190 NDCF---------------QEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  235 (284)
T ss_dssp             GGGG---------------GGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             chhh---------------hhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCC
Confidence            3211               245678888888888887765432 24557888888888887

>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=99.23  E-value=2e-12  Score=118.12  Aligned_cols=102  Identities=22%  Similarity=0.178  Sum_probs=64.4

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .|+.+|..+..+.+|++|+|++|.|+.++ .+..+++|++|++++| .+..+|++++..+++|++|++.+|.+
T Consensus        23 L~L~~n-~I~~i~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N-~i~~l~~~~~~~l~~L~~L~L~~N~i   99 (162)
T d1a9na_          23 LDLRGY-KIPVIENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNN-RICRIGEGLDQALPDLTELILTNNSL   99 (162)
T ss_dssp             EECTTS-CCCSCCCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSS-CCCEECSCHHHHCTTCCEEECCSCCC
T ss_pred             EECCCC-CCCccCccccccccCCEEECCCCCCCccC-CcccCcchhhhhcccc-cccCCCccccccccccccceeccccc
Confidence            344444 55555555566777777777777777774 4677777777777777 56666665455677777777777766


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      ..             ...+..+..+++|+.|++++|..
T Consensus       100 ~~-------------~~~l~~l~~l~~L~~L~l~~N~i  124 (162)
T d1a9na_         100 VE-------------LGDLDPLASLKSLTYLCILRNPV  124 (162)
T ss_dssp             CC-------------GGGGGGGGGCTTCCEEECCSSGG
T ss_pred             cc-------------cccccccccccccchhhcCCCcc
Confidence            53             22234455666666666665543

>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=99.21  E-value=1.5e-11  Score=106.55  Aligned_cols=98  Identities=21%  Similarity=0.248  Sum_probs=85.0

Q ss_pred             cEEEcccccccccccCcc-----cccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCC
Q 004021          498 KRISLMANEIESLSEIPT-----LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYL  572 (779)
Q Consensus       498 r~l~l~~~~~~~l~~~~~-----lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l  572 (779)
                      |.|++++|+++.++....     .|++++| .++.+|+.++.+++|++|++++|.|+.+| .++++++|++|++++| .+
T Consensus         1 R~L~Ls~n~l~~l~~l~~l~~L~~L~ls~N-~l~~lp~~~~~l~~L~~L~l~~N~i~~l~-~~~~l~~L~~L~l~~N-~i   77 (124)
T d1dcea3           1 RVLHLAHKDLTVLCHLEQLLLVTHLDLSHN-RLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCNN-RL   77 (124)
T ss_dssp             SEEECTTSCCSSCCCGGGGTTCCEEECCSS-CCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCSS-CC
T ss_pred             CEEEcCCCCCCCCcccccCCCCCEEECCCC-ccCcchhhhhhhhcccccccccccccccC-ccccccccCeEECCCC-cc
Confidence            678899998887775433     3899999 99999999999999999999999999997 5999999999999999 67


Q ss_pred             CCCch-hhhcCCccCcEeeeccccCCC
Q 004021          573 SIIPH-QLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       573 ~~lp~-~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ..+|. ..++.+++|++|++.+|.+..
T Consensus        78 ~~~~~~~~l~~~~~L~~L~l~~N~i~~  104 (124)
T d1dcea3          78 QQSAAIQPLVSCPRLVLLNLQGNSLCQ  104 (124)
T ss_dssp             CSSSTTGGGGGCTTCCEEECTTSGGGG
T ss_pred             CCCCCchhhcCCCCCCEEECCCCcCCc
Confidence            77764 237899999999999998764

>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=99.13  E-value=3.8e-11  Score=113.37  Aligned_cols=122  Identities=19%  Similarity=0.157  Sum_probs=64.7

Q ss_pred             cccccccccccchhhcccccCceeeecCCcccc-c-chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          518 SLRRNDSLTELPSRISSLVSLHHLDLSLTHIRG-L-PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       518 ~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~-l-p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      +.+++ .++.+|..+.  .++++|+|++|.|+. + +..|.++++|++|++++| .+..++.+.+..+++|++|++++|.
T Consensus        14 ~Cs~~-~L~~iP~~lp--~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N-~i~~~~~~~~~~~~~L~~L~Ls~N~   89 (192)
T d1w8aa_          14 DCTGR-GLKEIPRDIP--LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRN-QLTGIEPNAFEGASHIQELQLGENK   89 (192)
T ss_dssp             ECTTS-CCSSCCSCCC--TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSS-CCCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             EEeCC-CcCccCCCCC--CCCCEEEeCCCCCcccccccccCCCceEeeeecccc-ccccccccccccccccceeeecccc
Confidence            33444 4555554442  456666666666643 2 233556666666666665 3444444445566666666666665


Q ss_pred             CCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          596 SEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       596 ~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                      +..              ..+..|.++++|+.|+++.         .+|+.+.+.++..+++|++|+|++|+
T Consensus        90 l~~--------------l~~~~F~~l~~L~~L~L~~---------N~l~~i~~~~f~~l~~L~~l~L~~N~  137 (192)
T d1w8aa_          90 IKE--------------ISNKMFLGLHQLKTLNLYD---------NQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCE--------------ECSSSSTTCTTCCEEECCS---------SCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             ccc--------------cCHHHHhCCCcccccccCC---------ccccccCHHHhcCCcccccccccccc
Confidence            553              1222345556666666652         23334444455566666666666654

>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=99.12  E-value=3.6e-11  Score=109.62  Aligned_cols=128  Identities=15%  Similarity=0.172  Sum_probs=100.0

Q ss_pred             ccccccCCccEEEcccccccccccCcc------cccccccccccccchhhcccccCceeeecCCcccccchh-hccCccC
Q 004021          489 PKVKEWEGAKRISLMANEIESLSEIPT------LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQE-LKALEKL  561 (779)
Q Consensus       489 ~~~~~~~~lr~l~l~~~~~~~l~~~~~------lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~-~~~L~~L  561 (779)
                      +......++|.|++++|.|..++....      .|+|++| .+..++ .+..+++|++|++++|.++.+|.. +..+++|
T Consensus        12 ~~~~n~~~lr~L~L~~n~I~~i~~~~~~l~~L~~L~Ls~N-~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L   89 (162)
T d1a9na_          12 AQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDN-EIRKLD-GFPLLRRLKTLLVNNNRICRIGEGLDQALPDL   89 (162)
T ss_dssp             CEEECTTSCEEEECTTSCCCSCCCGGGGTTCCSEEECCSS-CCCEEC-CCCCCSSCCEEECCSSCCCEECSCHHHHCTTC
T ss_pred             HhccCcCcCcEEECCCCCCCccCccccccccCCEEECCCC-CCCccC-CcccCcchhhhhcccccccCCCcccccccccc
Confidence            344455689999999999998865422      4999999 999995 589999999999999999999876 4679999


Q ss_pred             cEeeccCCcCCCCCch-hhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEE
Q 004021          562 RYLNLEYTHYLSIIPH-QLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       562 ~~L~l~~~~~l~~lp~-~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                      ++|++++| .+..++. ..+..+++|++|++.+|.+...+           ......+..+++|+.|+-.
T Consensus        90 ~~L~L~~N-~i~~~~~l~~l~~l~~L~~L~l~~N~i~~~~-----------~~r~~~i~~lp~L~~LD~~  147 (162)
T d1a9na_          90 TELILTNN-SLVELGDLDPLASLKSLTYLCILRNPVTNKK-----------HYRLYVIYKVPQVRVLDFQ  147 (162)
T ss_dssp             CEEECCSC-CCCCGGGGGGGGGCTTCCEEECCSSGGGGST-----------THHHHHHHHCTTCSEETTE
T ss_pred             ccceeccc-cccccccccccccccccchhhcCCCcccccc-----------chHHHHHHHCCCcCeeCCC
Confidence            99999999 6777775 23788999999999999876411           1122345566777776643

>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=99.10  E-value=2.7e-11  Score=122.05  Aligned_cols=202  Identities=17%  Similarity=0.134  Sum_probs=135.3

Q ss_pred             cCCccEEEcccccccc--c----ccCcc--cccccccccccc-cchhhcccccCceeeecCC-cccc--cchhhccCccC
Q 004021          494 WEGAKRISLMANEIES--L----SEIPT--LLSLRRNDSLTE-LPSRISSLVSLHHLDLSLT-HIRG--LPQELKALEKL  561 (779)
Q Consensus       494 ~~~lr~l~l~~~~~~~--l----~~~~~--lL~L~~~~~l~~-lp~~i~~L~~L~~L~L~~~-~i~~--lp~~~~~L~~L  561 (779)
                      ..++++|+++++.+..  +    ...+.  -|+|++| .+.. .+..++++++|++|++++| .++.  +..-..++++|
T Consensus        45 ~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~-~l~~~~~~~l~~~~~L~~L~Ls~c~~itd~~l~~l~~~~~~L  123 (284)
T d2astb2          45 PFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGL-RLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRL  123 (284)
T ss_dssp             CBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTC-BCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTTC
T ss_pred             CCCCCEEECCCCccCHHHHHHHHHhCCCccccccccc-CCCcHHHHHHhcCCCCcCccccccccccccccchhhHHHHhc
Confidence            3578999999877643  2    11222  3899999 6663 5778899999999999996 6653  44445789999


Q ss_pred             cEeeccCCcCCCC--Cchhhhc-CCccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccc
Q 004021          562 RYLNLEYTHYLSI--IPHQLIS-GFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQ  638 (779)
Q Consensus       562 ~~L~l~~~~~l~~--lp~~~i~-~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~  638 (779)
                      ++|++++|..+..  ++.. +. ..++|+.|++.++...-          . ......-..++++|++|+++.       
T Consensus       124 ~~L~ls~c~~~~~~~~~~~-~~~~~~~L~~L~l~~~~~~i----------~-~~~l~~l~~~~~~L~~L~L~~-------  184 (284)
T d2astb2         124 DELNLSWCFDFTEKHVQVA-VAHVSETITQLNLSGYRKNL----------Q-KSDLSTLVRRCPNLVHLDLSD-------  184 (284)
T ss_dssp             CEEECCCCTTCCHHHHHHH-HHHSCTTCCEEECCSCGGGS----------C-HHHHHHHHHHCTTCSEEECTT-------
T ss_pred             cccccccccccccccchhh-hcccccccchhhhccccccc----------c-ccccccccccccccccccccc-------
Confidence            9999999865542  2222 33 34789999999864211          0 122333345689999999873       


Q ss_pred             cCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCC
Q 004021          639 KFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHF  718 (779)
Q Consensus       639 ~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l  718 (779)
                       +.+++.-.+..+..+++|++|+|++|+.+.+...               ..++.+|+|+.|++.+|-.-..+......+
T Consensus       185 -~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l---------------~~L~~~~~L~~L~l~~~~~d~~l~~l~~~l  248 (284)
T d2astb2         185 -SVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETL---------------LELGEIPTLKTLQVFGIVPDGTLQLLKEAL  248 (284)
T ss_dssp             -CTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGG---------------GGGGGCTTCCEEECTTSSCTTCHHHHHHHS
T ss_pred             -ccCCCchhhhhhcccCcCCEEECCCCCCCChHHH---------------HHHhcCCCCCEEeeeCCCCHHHHHHHHHhC
Confidence             2334433455677899999999999987653211               245678999999999873222232222357


Q ss_pred             CCccEEeeeCCCCCCCC
Q 004021          719 PKLKKIGVYGCPKLKKL  735 (779)
Q Consensus       719 ~~L~~L~l~~c~~L~~l  735 (779)
                      |+|+   + +|+++..+
T Consensus       249 p~L~---i-~~~~ls~~  261 (284)
T d2astb2         249 PHLQ---I-NCSHFTTI  261 (284)
T ss_dssp             TTSE---E-SCCCSCCT
T ss_pred             cccc---c-cCccCCCC
Confidence            7776   3 67777765

>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=99.07  E-value=1.3e-09  Score=113.24  Aligned_cols=234  Identities=18%  Similarity=0.198  Sum_probs=143.6

Q ss_pred             cCcccccCccccccCCccEEEcccccccccccCcc---cccccccccccccchhhcccccCceeeecCCcccccchhhcc
Q 004021          481 AGVKLTEAPKVKEWEGAKRISLMANEIESLSEIPT---LLSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKA  557 (779)
Q Consensus       481 ~~~~~~~~~~~~~~~~lr~l~l~~~~~~~l~~~~~---lL~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~  557 (779)
                      .+.+++.+|..  ..++++|++++|.++.+|..+.   -|++++| .++.++.-   ...|++|++++|.+..+|. +++
T Consensus        46 s~~~L~~lp~~--~~~L~~L~Ls~N~l~~lp~~~~~L~~L~l~~n-~l~~l~~l---p~~L~~L~L~~n~l~~lp~-~~~  118 (353)
T d1jl5a_          46 NNLGLSSLPEL--PPHLESLVASCNSLTELPELPQSLKSLLVDNN-NLKALSDL---PPLLEYLGVSNNQLEKLPE-LQN  118 (353)
T ss_dssp             TTSCCSCCCSC--CTTCSEEECCSSCCSSCCCCCTTCCEEECCSS-CCSCCCSC---CTTCCEEECCSSCCSSCCC-CTT
T ss_pred             CCCCCCCCCCC--CCCCCEEECCCCCCcccccchhhhhhhhhhhc-ccchhhhh---ccccccccccccccccccc-hhh
Confidence            34445556643  4688999999999998887654   3888888 77776632   1468999999999988885 688


Q ss_pred             CccCcEeeccCCcCCCCCchh------------------hhcCCccCcEeeeccccCCCcccccCC----ccCCCchhhH
Q 004021          558 LEKLRYLNLEYTHYLSIIPHQ------------------LISGFLKLEVLRLLECGSEGVTKEEGN----VLCDDAEPLM  615 (779)
Q Consensus       558 L~~L~~L~l~~~~~l~~lp~~------------------~i~~L~~L~~L~l~~~~~~~~~~~~~~----~~~~~~~~~~  615 (779)
                      +++|++|++++| .+...|..                  .++.++.++.|.+..|....++.....    ..........
T Consensus       119 l~~L~~L~l~~~-~~~~~~~~~~~l~~l~~~~~~~~~~~~l~~l~~l~~L~l~~n~~~~~~~~~~~~~~l~~~~~~~~~~  197 (353)
T d1jl5a_         119 SSFLKIIDVDNN-SLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEEL  197 (353)
T ss_dssp             CTTCCEEECCSS-CCSCCCCCCTTCCEEECCSSCCSSCCCCTTCTTCCEEECCSSCCSSCCCCCTTCCEEECCSSCCSSC
T ss_pred             hccceeeccccc-cccccccccccccchhhccccccccccccccccceeccccccccccccccccccccccccccccccc
Confidence            899999999887 34433321                  134455666666666554443211111    0011111122


Q ss_pred             HhhcCCCCCCceeEEeecccccc----------------------------------cCCCCCcc------------cC-
Q 004021          616 RELLGLKRLNVLSWSFRSSLAVQ----------------------------------KFFKYPKL------------DL-  648 (779)
Q Consensus       616 ~~l~~L~~L~~L~l~~~~~~~~~----------------------------------~~~~L~~L------------~~-  648 (779)
                      ..+..++.|+.++++.+....+.                                  .+..+..+            .. 
T Consensus       198 ~~~~~l~~L~~l~l~~n~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~  277 (353)
T d1jl5a_         198 PELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIR  277 (353)
T ss_dssp             CCCTTCTTCCEEECCSSCCSSCCSCCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSEESCCCTTCCEEECCSSCCS
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhcccccccCccc
Confidence            33455667777776654332210                                  00111111            00 


Q ss_pred             cccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCCccEEEccCCCCCccccCCCCCCCCccEEeeeC
Q 004021          649 TWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQLESLGILYGPDLKSIYPNPLHFPKLKKIGVYG  728 (779)
Q Consensus       649 ~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~l~~l~~~~~~l~~L~~L~l~~  728 (779)
                      .....+++|++|+|++|. +..++.                   .+++|+.|+++++ .++++|.   .+++|++|++++
T Consensus       278 ~~~~~~~~L~~L~Ls~N~-l~~lp~-------------------~~~~L~~L~L~~N-~L~~l~~---~~~~L~~L~L~~  333 (353)
T d1jl5a_         278 SLCDLPPSLEELNVSNNK-LIELPA-------------------LPPRLERLIASFN-HLAEVPE---LPQNLKQLHVEY  333 (353)
T ss_dssp             EECCCCTTCCEEECCSSC-CSCCCC-------------------CCTTCCEEECCSS-CCSCCCC---CCTTCCEEECCS
T ss_pred             cccccCCCCCEEECCCCc-cCcccc-------------------ccCCCCEEECCCC-cCCcccc---ccCCCCEEECcC
Confidence            011235789999999874 344432                   4789999999974 6888875   357899999999


Q ss_pred             CCCCCCCCCCCCCcccccEEE
Q 004021          729 CPKLKKLPINSSSAKERRVVI  749 (779)
Q Consensus       729 c~~L~~lP~~~~~~~~~~l~i  749 (779)
                      |+ |+++|....  +++.+.|
T Consensus       334 N~-L~~lp~~~~--~L~~L~~  351 (353)
T d1jl5a_         334 NP-LREFPDIPE--SVEDLRM  351 (353)
T ss_dssp             SC-CSSCCCCCT--TCCEEEC
T ss_pred             Cc-CCCCCcccc--ccCeeEC
Confidence            97 999997543  3455544

>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=99.05  E-value=3.6e-12  Score=120.80  Aligned_cols=118  Identities=21%  Similarity=0.208  Sum_probs=91.6

Q ss_pred             cccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCccccc
Q 004021          524 SLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEE  603 (779)
Q Consensus       524 ~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~  603 (779)
                      .+..+|.+++.|++|++|+|++|.|+.++ .+.+|++|++|++++| .++.+|.. ...+.+|++|++.+|.+..     
T Consensus        36 ~i~~l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N-~i~~i~~~-~~~~~~L~~L~l~~N~i~~-----  107 (198)
T d1m9la_          36 PIEKMDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRN-LIKKIENL-DAVADTLEELWISYNQIAS-----  107 (198)
T ss_dssp             TCCCCHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEE-EECSCSSH-HHHHHHCCEEECSEEECCC-----
T ss_pred             chhhhhhHHhcccccceeECcccCCCCcc-cccCCccccChhhccc-cccccccc-ccccccccccccccccccc-----
Confidence            56778889999999999999999999886 5889999999999999 67888863 5566789999999987764     


Q ss_pred             CCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccccc
Q 004021          604 GNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEM  668 (779)
Q Consensus       604 ~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~  668 (779)
                                 +..+..+++|+.|+++.|....+..        +.++..+++|+.|+|++|+..
T Consensus       108 -----------l~~~~~l~~L~~L~L~~N~i~~~~~--------~~~l~~l~~L~~L~L~~N~l~  153 (198)
T d1m9la_         108 -----------LSGIEKLVNLRVLYMSNNKITNWGE--------IDKLAALDKLEDLLLAGNPLY  153 (198)
T ss_dssp             -----------HHHHHHHHHSSEEEESEEECCCHHH--------HHHHTTTTTCSEEEECSSHHH
T ss_pred             -----------cccccccccccccccccchhccccc--------cccccCCCccceeecCCCccc
Confidence                       2346667888889888776433211        235667888999999887543

>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=99.01  E-value=4.4e-10  Score=105.86  Aligned_cols=127  Identities=17%  Similarity=0.180  Sum_probs=100.7

Q ss_pred             CceeeecCCcccccchhhccCccCcEeeccCCcCCC-CCchhhhcCCccCcEeeeccccCCCcccccCCccCCCchhhHH
Q 004021          538 LHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLS-IIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMR  616 (779)
Q Consensus       538 L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~-~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~  616 (779)
                      .+.++.++++++.+|..+.  +++++|+|++| .+. .++...+.++++|++|++++|.+..              ....
T Consensus        10 ~~~v~Cs~~~L~~iP~~lp--~~l~~L~Ls~N-~i~~~~~~~~f~~l~~L~~L~L~~N~i~~--------------~~~~   72 (192)
T d1w8aa_          10 GTTVDCTGRGLKEIPRDIP--LHTTELLLNDN-ELGRISSDGLFGRLPHLVKLELKRNQLTG--------------IEPN   72 (192)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSC-CCCSBCCSCSGGGCTTCCEEECCSSCCCC--------------BCTT
T ss_pred             CCEEEEeCCCcCccCCCCC--CCCCEEEeCCC-CCcccccccccCCCceEeeeecccccccc--------------cccc
Confidence            4578999999999998774  68999999999 564 4666668899999999999998875              3455


Q ss_pred             hhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccccceecccccccCcccchhhccCCCCCCCC
Q 004021          617 ELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTEMEEIICVDKLRDVSDISEIIGSEHNFFTQ  696 (779)
Q Consensus       617 ~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  696 (779)
                      .+..+++|+.|+++.         .+++.+.+..|.++++|++|+|++| .+..++.               ..+..+++
T Consensus        73 ~~~~~~~L~~L~Ls~---------N~l~~l~~~~F~~l~~L~~L~L~~N-~l~~i~~---------------~~f~~l~~  127 (192)
T d1w8aa_          73 AFEGASHIQELQLGE---------NKIKEISNKMFLGLHQLKTLNLYDN-QISCVMP---------------GSFEHLNS  127 (192)
T ss_dssp             TTTTCTTCCEEECCS---------CCCCEECSSSSTTCTTCCEEECCSS-CCCEECT---------------TSSTTCTT
T ss_pred             ccccccccceeeecc---------ccccccCHHHHhCCCcccccccCCc-cccccCH---------------HHhcCCcc
Confidence            677888999999884         4556666667888899999999985 4566655               46778899


Q ss_pred             ccEEEccCCC
Q 004021          697 LESLGILYGP  706 (779)
Q Consensus       697 L~~L~l~~~~  706 (779)
                      |++|+|++.+
T Consensus       128 L~~l~L~~N~  137 (192)
T d1w8aa_         128 LTSLNLASNP  137 (192)
T ss_dssp             CCEEECTTCC
T ss_pred             cccccccccc
Confidence            9999998743

>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=98.93  E-value=2.6e-11  Score=114.75  Aligned_cols=127  Identities=19%  Similarity=0.213  Sum_probs=94.6

Q ss_pred             ccccccccccccchhhcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccC
Q 004021          517 LSLRRNDSLTELPSRISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGS  596 (779)
Q Consensus       517 L~L~~~~~l~~lp~~i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~  596 (779)
                      |+|++| .|+.++ .+.+|++|++|+|++|.|+.+|..+..+++|++|++++| .++.++.  +..+++|++|++++|.+
T Consensus        53 L~Ls~n-~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N-~i~~l~~--~~~l~~L~~L~L~~N~i  127 (198)
T d1m9la_          53 LALSTN-NIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYN-QIASLSG--IEKLVNLRVLYMSNNKI  127 (198)
T ss_dssp             EECSEE-EESCCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEE-ECCCHHH--HHHHHHSSEEEESEEEC
T ss_pred             eECccc-CCCCcc-cccCCccccChhhcccccccccccccccccccccccccc-ccccccc--ccccccccccccccchh
Confidence            666777 777776 588999999999999999999877777789999999999 6788765  88999999999999988


Q ss_pred             CCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCC-CcccCcccccccCcceEE
Q 004021          597 EGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKY-PKLDLTWLVFVQNLKELE  661 (779)
Q Consensus       597 ~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L-~~L~~~~l~~l~~L~~L~  661 (779)
                      ..             ...+..+..+++|+.|++++|.........+. .......+..+|+|+.|+
T Consensus       128 ~~-------------~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~~~~r~~vi~~lp~L~~LD  180 (198)
T d1m9la_         128 TN-------------WGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLD  180 (198)
T ss_dssp             CC-------------HHHHHHHTTTTTCSEEEECSSHHHHHHCTTTTHHHHHHHHHHHCSSCCEES
T ss_pred             cc-------------ccccccccCCCccceeecCCCccccCcccccchhhHHHHHHHHCCCcCEeC
Confidence            75             33456788999999999998765332111100 000011245678888775

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.88  E-value=1.3e-08  Score=101.66  Aligned_cols=182  Identities=16%  Similarity=0.180  Sum_probs=104.4

Q ss_pred             cccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----------chHHH
Q 004021          154 EQTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----------QTFQD  222 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----------~~i~~  222 (779)
                      ...|+||+++++++.+.      ..++|.|+|.+|+|||+|++++.++.   ...   ..|+.+           ..+..
T Consensus        11 ~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~~~---~~~---~~~i~~~~~~~~~~~~~~~~~~   78 (283)
T d2fnaa2          11 RKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGINEL---NLP---YIYLDLRKFEERNYISYKDFLL   78 (283)
T ss_dssp             GGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHHHH---TCC---EEEEEGGGGTTCSCCCHHHHHH
T ss_pred             hhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHHHC---CCC---eEEEEeccccccccccHHHHHH
Confidence            47899999999998753      34789999999999999999998876   222   344544           11222


Q ss_pred             HHHHHhC--------------CCc---------chh---hhhcchhhHHHHHHHhhCCCcceeehhhccccc--------
Q 004021          223 DIGKRIG--------------FSE---------DKK---WKEKSLQDKAVDISSILSPKKFRIDLTELGVPL--------  268 (779)
Q Consensus       223 ~i~~~l~--------------~~~---------~~~---~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~--------  268 (779)
                      .+.....              ...         ...   ....+..+....+. ...+++..+..|++....        
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~i~id~~~~~~~~~~~~~~  157 (283)
T d2fnaa2          79 ELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFE-QASKDNVIIVLDEAQELVKLRGVNLL  157 (283)
T ss_dssp             HHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHH-HTCSSCEEEEEETGGGGGGCTTCCCH
T ss_pred             HHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHH-hhcccccccccchhhhhcccchHHHH
Confidence            2221110              000         000   00111222222222 233555544444431110        


Q ss_pred             ------cccCCCcEEEEEeCchhhhhhc-----------C--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHH
Q 004021          269 ------QMLNAGFKIVLKTRSAGVCDQM-----------D--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAE  329 (779)
Q Consensus       269 ------~~~~~gs~IivTTR~~~va~~~-----------~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~  329 (779)
                            .........+++++........           +  ...+.|.+++.+++.+++.+.+.......+ +    ..
T Consensus       158 ~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~-~----~~  232 (283)
T d2fnaa2         158 PALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK-D----YE  232 (283)
T ss_dssp             HHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC-C----HH
T ss_pred             HHHHHHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHH-H----HH
Confidence                  0123445556665554332211           1  245789999999999999887655442221 1    46


Q ss_pred             HHHHHhCCChhHHHHHHHHhcCCC
Q 004021          330 TLARECGRLPLALKTVGRAMKSQK  353 (779)
Q Consensus       330 ~I~~~c~glPLai~~~g~~l~~~~  353 (779)
                      +|++.++|.|..+..+|..+....
T Consensus       233 ~i~~~~~G~P~~L~~~~~~~~~~~  256 (283)
T d2fnaa2         233 VVYEKIGGIPGWLTYFGFIYLDNK  256 (283)
T ss_dssp             HHHHHHCSCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcc
Confidence            999999999999999887665433

>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=98.59  E-value=2.9e-08  Score=89.25  Aligned_cols=79  Identities=19%  Similarity=0.201  Sum_probs=50.3

Q ss_pred             cccccccccccchhhcccccCceeeecCC-cccccch-hhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeecccc
Q 004021          518 SLRRNDSLTELPSRISSLVSLHHLDLSLT-HIRGLPQ-ELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECG  595 (779)
Q Consensus       518 ~L~~~~~l~~lp~~i~~L~~L~~L~L~~~-~i~~lp~-~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~  595 (779)
                      +.+++ .+...|..+..+++|+.|++.++ .++.++. .|.++++|+.|++++| .++.++++.|..+++|++|++++|.
T Consensus        14 ~c~~~-~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N-~l~~i~~~~f~~l~~L~~L~Ls~N~   91 (156)
T d2ifga3          14 RCTRD-GALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKS-GLRFVAPDAFHFTPRLSRLNLSFNA   91 (156)
T ss_dssp             ECCSS-CCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSS-CCCEECTTGGGSCSCCCEEECCSSC
T ss_pred             EecCC-CCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeecc-ccCCcccccccccccccceeccCCC
Confidence            34444 55556666666677777777554 4666654 3666777777777776 5666665556677777777777766


Q ss_pred             CCC
Q 004021          596 SEG  598 (779)
Q Consensus       596 ~~~  598 (779)
                      +..
T Consensus        92 l~~   94 (156)
T d2ifga3          92 LES   94 (156)
T ss_dssp             CSC
T ss_pred             Ccc
Confidence            654

>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=98.58  E-value=4.7e-08  Score=87.78  Aligned_cols=111  Identities=18%  Similarity=0.092  Sum_probs=88.2

Q ss_pred             cccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCCcccccCCccCCCch
Q 004021          533 SSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAE  612 (779)
Q Consensus       533 ~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~  612 (779)
                      +.......++.+++.+...|..+..+++|+.|++.++..++.++.+.|.++++|+.|++++|.+..              
T Consensus         5 C~c~~~~~l~c~~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~--------------   70 (156)
T d2ifga3           5 CCPHGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRF--------------   70 (156)
T ss_dssp             SCCSSSSCEECCSSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCE--------------
T ss_pred             CCcCCCCeEEecCCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccccCC--------------
Confidence            444556678889999999999999999999999988867999998779999999999999998875              


Q ss_pred             hhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccccc
Q 004021          613 PLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCTE  667 (779)
Q Consensus       613 ~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~~  667 (779)
                      ..+..+..+++|+.|+++.|.         |+.+....+.. .+|+.|+|++|+.
T Consensus        71 i~~~~f~~l~~L~~L~Ls~N~---------l~~l~~~~~~~-~~l~~L~L~~Np~  115 (156)
T d2ifga3          71 VAPDAFHFTPRLSRLNLSFNA---------LESLSWKTVQG-LSLQELVLSGNPL  115 (156)
T ss_dssp             ECTTGGGSCSCCCEEECCSSC---------CSCCCSTTTCS-CCCCEEECCSSCC
T ss_pred             cccccccccccccceeccCCC---------CcccChhhhcc-ccccccccCCCcc
Confidence            334568889999999998554         44443344433 3689999988654

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.45  E-value=7.7e-06  Score=80.55  Aligned_cols=157  Identities=11%  Similarity=0.140  Sum_probs=91.2

Q ss_pred             ccccchhhhHHHHHHHHhc----cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe------chHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITD----QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV------QTFQDDI  224 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v------~~i~~~i  224 (779)
                      ..++||+.++++|.++|..    .....+.+.|+|++|+||||+|+.+++.. .....+ ..+|+..      ......+
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l-~~~~~~-~~~~~~~~~~~~~~~~~~~~   93 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY-KDKTTA-RFVYINGFIYRNFTAIIGEI   93 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH-TTSCCC-EEEEEETTTCCSHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHH-hcccCC-cEEEecchhhhhhhhhhhhh
Confidence            4589999999999999864    23456789999999999999999999987 222223 2344443      4455556


Q ss_pred             HHHhCCCcchhhhhcchhhHHHHHHHhhCCC--cc---eeehhhccc-----------ccc-ccCCCcEEEEEeCchhhh
Q 004021          225 GKRIGFSEDKKWKEKSLQDKAVDISSILSPK--KF---RIDLTELGV-----------PLQ-MLNAGFKIVLKTRSAGVC  287 (779)
Q Consensus       225 ~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~---~~~ld~l~~-----------~~~-~~~~gs~IivTTR~~~va  287 (779)
                      ....+....  ............+.+.+...  ..   ....|++..           ... .......+|.+|......
T Consensus        94 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  171 (276)
T d1fnna2          94 ARSLNIPFP--RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVL  171 (276)
T ss_dssp             HHHTTCCCC--SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHH
T ss_pred             HHhhhhhhh--hhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhhh
Confidence            655544311  12223333444444433322  11   222232211           111 112333455555553332


Q ss_pred             h--------hcCCceeEccCCChHHHHHHHHHHhhc
Q 004021          288 D--------QMDSKNLEVYSLAHDEAWKLFQEMIER  315 (779)
Q Consensus       288 ~--------~~~~~~~~l~~L~~~~a~~Lf~~~a~~  315 (779)
                      .        .+....+.+.+.+.++.++++.+++..
T Consensus       172 ~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~  207 (276)
T d1fnna2         172 NNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKA  207 (276)
T ss_dssp             HTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             hhcchhhhhhhcchhccccchhHHHHHHHHHHHHHH
Confidence            2        122356889999999999999887653

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.17  E-value=3.4e-06  Score=80.54  Aligned_cols=163  Identities=15%  Similarity=0.195  Sum_probs=95.7

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .+++|.++.+++|.+++.++  ..+-+-++|++|+||||+|+.+++........++ +.-+..             .   
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~--~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~-~~~~n~-------------~---   75 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDG--NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADG-VLELNA-------------S---   75 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHH-EEEECT-------------T---
T ss_pred             HHhcCCHHHHHHHHHHHHcC--CCCeEEEECCCCCCchhhHHHHHHHHhccccccc-cccccc-------------c---
Confidence            56899999999999999877  4555779999999999999999887611000111 111111             0   


Q ss_pred             hhhhcchhhHHHHHHHhh------CCCcc-eeehhhcccc-----------ccccCCCcEEEEEeCc-hhhhhhc-C-Cc
Q 004021          235 KWKEKSLQDKAVDISSIL------SPKKF-RIDLTELGVP-----------LQMLNAGFKIVLKTRS-AGVCDQM-D-SK  293 (779)
Q Consensus       235 ~~~~~~~~~~~~~l~~~L------~~kr~-~~~ld~l~~~-----------~~~~~~gs~IivTTR~-~~va~~~-~-~~  293 (779)
                        ...........+....      ...++ .+..|++...           +......+++++||.+ ..+.... . ..
T Consensus        76 --~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~  153 (224)
T d1sxjb2          76 --DDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCA  153 (224)
T ss_dssp             --SCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             --ccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHH
Confidence              0000111111111111      11111 2333332111           1222445666666665 3443332 2 57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA  341 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa  341 (779)
                      .+++++++.++-...+.+.+.......+   .+....|++.|+|-+--
T Consensus       154 ~i~~~~~~~~~i~~~l~~i~~~e~~~i~---~~~l~~I~~~s~Gd~R~  198 (224)
T d1sxjb2         154 ILRYSKLSDEDVLKRLLQIIKLEDVKYT---NDGLEAIIFTAEGDMRQ  198 (224)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHHTTCHHH
T ss_pred             HhhhcccchhhhHHHHHHHHHhcccCCC---HHHHHHHHHHcCCcHHH
Confidence            8899999999999999988876553332   46678999999997653

>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=98.14  E-value=2.4e-07  Score=99.23  Aligned_cols=100  Identities=17%  Similarity=0.234  Sum_probs=73.1

Q ss_pred             CccEEEccccccccc------ccCcc--ccccccccccc-----ccchhhcccccCceeeecCCcccc-----cchhhc-
Q 004021          496 GAKRISLMANEIESL------SEIPT--LLSLRRNDSLT-----ELPSRISSLVSLHHLDLSLTHIRG-----LPQELK-  556 (779)
Q Consensus       496 ~lr~l~l~~~~~~~l------~~~~~--lL~L~~~~~l~-----~lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~-  556 (779)
                      +++.|+++++++.+.      |....  .|+|++| .++     .++..+..+++|++|+|++|.|+.     +...+. 
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~-~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~   81 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDC-GLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQT   81 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESS-CCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCS
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCC-CCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhc
Confidence            578899999888652      22222  4999999 776     346667889999999999998853     333333 


Q ss_pred             cCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeeeccccCCC
Q 004021          557 ALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       557 ~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ...+|++|++++| .++.     ++.. +..+++|++|++++|.+..
T Consensus        82 ~~~~L~~L~L~~n-~it~~~~~~l~~~-l~~~~~L~~L~L~~N~i~~  126 (460)
T d1z7xw1          82 PSCKIQKLSLQNC-CLTGAGCGVLSST-LRTLPTLQELHLSDNLLGD  126 (460)
T ss_dssp             TTCCCCEEECTTS-CCBGGGHHHHHHH-TTSCTTCCEEECCSSBCHH
T ss_pred             CCCCCCEEECCCC-Cccccccccccch-hhccccccccccccccchh
Confidence            2357999999999 4554     3444 7789999999999998653

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.12  E-value=7.8e-06  Score=78.11  Aligned_cols=164  Identities=13%  Similarity=0.186  Sum_probs=94.4

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .++||.++.++.|.+++..+  ..+.+-++|++|+||||+|+.+++.. ........+.-+....             ..
T Consensus        14 ~divg~~~~~~~L~~~i~~~--~~~~lLl~Gp~G~GKttl~~~la~~l-~~~~~~~~~~e~~~~~-------------~~   77 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEG--KLPHLLFYGPPGTGKTSTIVALAREI-YGKNYSNMVLELNASD-------------DR   77 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT--CCCCEEEECSSSSSHHHHHHHHHHHH-HTTSHHHHEEEECTTS-------------CC
T ss_pred             HHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCChhHHHHHHHHHh-hcCCCcceeEEecccc-------------cC
Confidence            56899999999999999876  44446799999999999999999876 2111111111111100             00


Q ss_pred             hhhhcchhhHHHHHHH--hh-CCCcceeehhhcccc-----------ccccCCCcEEEEEeCc-hhhhhhc-C-CceeEc
Q 004021          235 KWKEKSLQDKAVDISS--IL-SPKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRS-AGVCDQM-D-SKNLEV  297 (779)
Q Consensus       235 ~~~~~~~~~~~~~l~~--~L-~~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~-~~va~~~-~-~~~~~l  297 (779)
                        ..............  .+ .+++-.+.+|++...           +......++++++|.. ..+.... . ...+.+
T Consensus        78 --~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~~i~~  155 (227)
T d1sxjc2          78 --GIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCTRFRF  155 (227)
T ss_dssp             --SHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             --CeeeeecchhhccccccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHhhhcc
Confidence              00000000000000  01 111113333443211           2223456777777775 3333322 2 578899


Q ss_pred             cCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh
Q 004021          298 YSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP  339 (779)
Q Consensus       298 ~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP  339 (779)
                      .+++.++-.+.+.+.+.......+   .+....|++.++|-.
T Consensus       156 ~~~~~~~i~~~l~~I~~~e~i~i~---~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         156 QPLPQEAIERRIANVLVHEKLKLS---PNAEKALIELSNGDM  194 (227)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCCBC---HHHHHHHHHHHTTCH
T ss_pred             ccccccccccccccccccccccCC---HHHHHHHHHHcCCcH
Confidence            999999999999888766543322   466788999999854

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.11  E-value=7.5e-06  Score=78.79  Aligned_cols=172  Identities=10%  Similarity=0.123  Sum_probs=97.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe---c--h----HHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV---Q--T----FQDDIG  225 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v---~--~----i~~~i~  225 (779)
                      .+++|.++.++.+..++...  ..+.+.++|++|+||||+|+.+++..............+..   .  .    ......
T Consensus        12 ~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSA--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFA   89 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCT--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHh
Confidence            55899999999999999876  45557899999999999999998874111111111122222   0  0    111111


Q ss_pred             HHhCCCcchhhhhcchhhHHHHHHHhhCCCcc-eeehhhcccc-----------ccccCCCcEEEEEeCc-hhhhhhcC-
Q 004021          226 KRIGFSEDKKWKEKSLQDKAVDISSILSPKKF-RIDLTELGVP-----------LQMLNAGFKIVLKTRS-AGVCDQMD-  291 (779)
Q Consensus       226 ~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-~~~ld~l~~~-----------~~~~~~gs~IivTTR~-~~va~~~~-  291 (779)
                      ......       .    ....+... ...++ .+.+|++...           .......+++++||.. ..+..... 
T Consensus        90 ~~~~~~-------~----~~~~~~~~-~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~s  157 (237)
T d1sxjd2          90 RLTVSK-------P----SKHDLENY-PCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLAS  157 (237)
T ss_dssp             HSCCCC-------C----CTTHHHHS-CCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHH
T ss_pred             hhhhhh-------h----hHHHHhhc-cccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccc
Confidence            100000       0    00011111 22222 3444443221           1122345566666654 33333332 


Q ss_pred             -CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHHH
Q 004021          292 -SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LALK  343 (779)
Q Consensus       292 -~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai~  343 (779)
                       ...+.+++++.++....+.+.+.......+   .+..+.|++.++|-+ -|+.
T Consensus       158 r~~~i~f~~~~~~~~~~~L~~i~~~e~i~i~---~~~l~~ia~~s~gd~R~ai~  208 (237)
T d1sxjd2         158 QCSKFRFKALDASNAIDRLRFISEQENVKCD---DGVLERILDISAGDLRRGIT  208 (237)
T ss_dssp             HSEEEECCCCCHHHHHHHHHHHHHTTTCCCC---HHHHHHHHHHTSSCHHHHHH
T ss_pred             hhhhhccccccccccchhhhhhhhhhcCcCC---HHHHHHHHHHcCCCHHHHHH
Confidence             578899999999999999988766543322   567889999998754 4443

>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=98.06  E-value=5.4e-07  Score=92.66  Aligned_cols=78  Identities=24%  Similarity=0.194  Sum_probs=50.3

Q ss_pred             ccccccccccc-----cchhhcccccCceeeecCCcccc-----------cchhhccCccCcEeeccCCcCCCC-----C
Q 004021          517 LSLRRNDSLTE-----LPSRISSLVSLHHLDLSLTHIRG-----------LPQELKALEKLRYLNLEYTHYLSI-----I  575 (779)
Q Consensus       517 L~L~~~~~l~~-----lp~~i~~L~~L~~L~L~~~~i~~-----------lp~~~~~L~~L~~L~l~~~~~l~~-----l  575 (779)
                      |+|++| .+..     +-..+...++|+.|+++++....           +...+..+++|+.|++++| .+..     +
T Consensus        36 L~Ls~n-~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n-~i~~~~~~~l  113 (344)
T d2ca6a1          36 IVLSGN-TIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDN-AFGPTAQEPL  113 (344)
T ss_dssp             EECTTS-EECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSC-CCCTTTHHHH
T ss_pred             EECcCC-cCCHHHHHHHHHHHHhCCCCCEEECCCCcccccccccchHHHHHHHHHhhCCCccccccccc-ccccccccch
Confidence            778877 5542     34456677888888887764332           2233556778888888888 3333     3


Q ss_pred             chhhhcCCccCcEeeeccccCC
Q 004021          576 PHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       576 p~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      ... +...++|++|++++|.+.
T Consensus       114 ~~~-l~~~~~L~~L~l~~n~l~  134 (344)
T d2ca6a1         114 IDF-LSKHTPLEHLYLHNNGLG  134 (344)
T ss_dssp             HHH-HHHCTTCCEEECCSSCCH
T ss_pred             hhh-hcccccchheeccccccc
Confidence            332 556778888888877654

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.01  E-value=0.00011  Score=70.28  Aligned_cols=181  Identities=16%  Similarity=0.097  Sum_probs=94.6

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~  226 (779)
                      .++||.++.+++|..++...   ....+-+-++|++|+||||+|+.+++..   ...|   +.++.     ..-...++.
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~---~~~~---~~~~~~~~~~~~~~~~~~~   82 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL---QTNI---HVTSGPVLVKQGDMAAILT   82 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH---TCCE---EEEETTTCCSHHHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc---CCCc---ccccCcccccHHHHHHHHH
Confidence            56899999999999888532   2344567799999999999999999877   2222   22333     112222333


Q ss_pred             HhCCCcchhhhh-cch-hhHHHHHHHhhCCCcc--eeehhhccccccccCCCcEEEEEeCch-hhhhh--cC-CceeEcc
Q 004021          227 RIGFSEDKKWKE-KSL-QDKAVDISSILSPKKF--RIDLTELGVPLQMLNAGFKIVLKTRSA-GVCDQ--MD-SKNLEVY  298 (779)
Q Consensus       227 ~l~~~~~~~~~~-~~~-~~~~~~l~~~L~~kr~--~~~ld~l~~~~~~~~~gs~IivTTR~~-~va~~--~~-~~~~~l~  298 (779)
                      ..........+. ... ....+.+.........  ....+..........+...+|.+|... .+...  .. ...+.++
T Consensus        83 ~~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~~~~r~~~~~~~~  162 (238)
T d1in4a2          83 SLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELD  162 (238)
T ss_dssp             HCCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCHHHHTTCSEEEECC
T ss_pred             hhccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccccccceeeeeEEEEec
Confidence            222110000000 000 1111222222222111  000000000011112344555555543 33221  12 4567899


Q ss_pred             CCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          299 SLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       299 ~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      ..+.++...++...+.......   .++....|++.++|-+-.+..
T Consensus       163 ~~~~~~~~~~l~~~~~~~~~~~---~~~~l~~i~~~s~gd~R~ai~  205 (238)
T d1in4a2         163 FYTVKELKEIIKRAASLMDVEI---EDAAAEMIAKRSRGTPRIAIR  205 (238)
T ss_dssp             CCCHHHHHHHHHHHHHHTTCCB---CHHHHHHHHHTSTTCHHHHHH
T ss_pred             CCCHHHHHHHHHHhhhhccchh---hHHHHHHHHHhCCCCHHHHHH
Confidence            9999999999988876654222   256788999999998765543

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.01  E-value=3.5e-05  Score=74.73  Aligned_cols=174  Identities=13%  Similarity=0.091  Sum_probs=95.0

Q ss_pred             ccccchhhhHHHHHHHHhc---------------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe--
Q 004021          155 QTIVGQEKLLPRVWRCITD---------------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV--  217 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~---------------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v--  217 (779)
                      .+++|.++.+++|.+++..               +....+.+.++|++|+||||+|+++++..   .  ++ ..++..  
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~---~--~~-~~~~~~~~   87 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL---G--YD-ILEQNASD   87 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT---T--CE-EEEECTTS
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH---H--hh-hhcccccc
Confidence            5689999999999999853               12345689999999999999999999876   1  22 334444  


Q ss_pred             ---chHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhccccccc------------cCCCcEEEEEeC
Q 004021          218 ---QTFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQM------------LNAGFKIVLKTR  282 (779)
Q Consensus       218 ---~~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~~------------~~~gs~IivTTR  282 (779)
                         ...+....+..... ........  .  ........++...+..|++......            ......|++|+.
T Consensus        88 ~~~~~~~~~~~~~~~~~-~~~~~~~~--~--~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~i~~  162 (253)
T d1sxja2          88 VRSKTLLNAGVKNALDN-MSVVGYFK--H--NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICN  162 (253)
T ss_dssp             CCCHHHHHHTGGGGTTB-CCSTTTTT--C------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEEEES
T ss_pred             chhhHHHHHHHHHHhhc-chhhhhhh--h--hhhcccccccceEEEeeeccccccchhhhhHHHhhhhcccccccccccc
Confidence               12222222221111 00000000  0  0001112223333334433111100            012334555543


Q ss_pred             c--hhhhhhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh-hHH
Q 004021          283 S--AGVCDQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP-LAL  342 (779)
Q Consensus       283 ~--~~va~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP-Lai  342 (779)
                      .  ........  ...+++.+.+.++-...+...+.......++   +...+|++.++|-. -||
T Consensus       163 ~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~---~~l~~i~~~s~GDiR~ai  224 (253)
T d1sxja2         163 ERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDP---NVIDRLIQTTRGDIRQVI  224 (253)
T ss_dssp             CTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCT---THHHHHHHHTTTCHHHHH
T ss_pred             cccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCCH---HHHHHHHHhCCCcHHHHH
Confidence            3  22222233  5788999999999999888877554433332   45688999999965 444

>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=97.97  E-value=0.00015  Score=69.33  Aligned_cols=180  Identities=13%  Similarity=0.081  Sum_probs=94.2

Q ss_pred             ccccchhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-----chHHHHHHH
Q 004021          155 QTIVGQEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-----QTFQDDIGK  226 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-----~~i~~~i~~  226 (779)
                      .++||-++.++++..++...   +..++-+-++|++|+||||+|+.+++..   ...|   .+++.     .......+.
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~---~~~~---~~~~~~~~~~~~~~~~~~~   82 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL---GVNL---RVTSGPAIEKPGDLAAILA   82 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH---TCCE---EEEETTTCCSHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh---CCCe---EeccCCccccchhhHHHHH
Confidence            46899999999988887642   2345667799999999999999999877   2222   33333     111222222


Q ss_pred             H-hCCCcc---hhhhhcchhhHHHHHHHhhCCCcceeehhh--ccccccccCCCcEEEEEeCc-hhh-hhhc-C-CceeE
Q 004021          227 R-IGFSED---KKWKEKSLQDKAVDISSILSPKKFRIDLTE--LGVPLQMLNAGFKIVLKTRS-AGV-CDQM-D-SKNLE  296 (779)
Q Consensus       227 ~-l~~~~~---~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~--l~~~~~~~~~gs~IivTTR~-~~v-a~~~-~-~~~~~  296 (779)
                      . +....-   ....... ......+...+.+.......+.  .........+...++.+|-+ ... .... . ...+.
T Consensus        83 ~~~~~~~i~~iDe~~~~~-~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~  161 (239)
T d1ixsb2          83 NSLEEGDILFIDEIHRLS-RQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEH  161 (239)
T ss_dssp             TTCCTTCEEEEETGGGCC-HHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSCGGGGGCSEEEE
T ss_pred             hhccCCCeeeeecccccc-hhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCcccccchhhcccceeeE
Confidence            2 111100   0000000 1111222222211110000000  00000011233445544433 222 1222 2 56778


Q ss_pred             ccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHHHH
Q 004021          297 VYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLALKT  344 (779)
Q Consensus       297 l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai~~  344 (779)
                      +...+.++......+.+.......   ..+....|++.++|-+-.+..
T Consensus       162 ~~~~~~~~~~~i~~~~~~~~~i~~---~~~~l~~ia~~s~gd~R~a~~  206 (239)
T d1ixsb2         162 LEYYTPEELAQGVMRDARLLGVRI---TEEAALEIGRRSRGTMRVAKR  206 (239)
T ss_dssp             CCCCCHHHHHHHHHHHHGGGCCCB---CHHHHHHHHHHTTSSHHHHHH
T ss_pred             eeccChhhhhHHHHHHHHHhCCcc---chHHHHHHHHHcCCCHHHHHH
Confidence            999999999998888776554322   257889999999998765543

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=97.96  E-value=5.5e-05  Score=74.60  Aligned_cols=178  Identities=13%  Similarity=0.068  Sum_probs=91.6

Q ss_pred             ccccchhhhHHHHHHHHhc----cC---CCceEEEEEcCCCCcHHHHHHHHHhhhccc---cCCCCEEEEEEe------c
Q 004021          155 QTIVGQEKLLPRVWRCITD----QQ---KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQ---QHNFDVVIWAAV------Q  218 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~----~~---~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~---~~~F~~~~wv~v------~  218 (779)
                      +.++||+.++++|.+.+..    +.   ....++.|+|++|+|||++|+++++.....   ........++..      .
T Consensus        16 ~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   95 (287)
T d1w5sa2          16 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY   95 (287)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchh
Confidence            6789999999999987742    21   112356678999999999999999875211   111233445554      3


Q ss_pred             hHHHHHHHHhCCCcchhhhhcchhhHHHHHHHhhCCC--cceee---hhhccc--------------------cccccCC
Q 004021          219 TFQDDIGKRIGFSEDKKWKEKSLQDKAVDISSILSPK--KFRID---LTELGV--------------------PLQMLNA  273 (779)
Q Consensus       219 ~i~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~~~~---ld~l~~--------------------~~~~~~~  273 (779)
                      .....+...++....  ............+....+..  .....   .|.+..                    .......
T Consensus        96 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~  173 (287)
T d1w5sa2          96 TILSLIVRQTGYPIQ--VRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNR  173 (287)
T ss_dssp             HHHHHHHHHHTCCCC--CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCB
T ss_pred             hHHHHHhhhcccccc--cccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccc
Confidence            344445555443211  12223333344444433221  11111   111110                    0011112


Q ss_pred             CcEEEEEeCchhhh-------hhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHh
Q 004021          274 GFKIVLKTRSAGVC-------DQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLAREC  335 (779)
Q Consensus       274 gs~IivTTR~~~va-------~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c  335 (779)
                      -..|++++......       ....  ...+.+++.+.++..+++..++....... .--++..+.|+++.
T Consensus       174 ~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~-~~~~~al~~ia~~~  243 (287)
T d1w5sa2         174 IGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDT-VWEPRHLELISDVY  243 (287)
T ss_dssp             EEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTT-SCCHHHHHHHHHHH
T ss_pred             eeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccC-CCCHHHHHHHHHHH
Confidence            22334444332211       1111  45788999999999999998874322111 11145566666655

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.95  E-value=1.5e-05  Score=76.21  Aligned_cols=165  Identities=15%  Similarity=0.175  Sum_probs=91.9

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .+++|.++.++++..++..+  ..+-+-++|++|+||||+|+.+++........++.. -++.....             
T Consensus        24 ~diig~~~~~~~l~~~i~~~--~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~-e~n~s~~~-------------   87 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFL-ELNASDER-------------   87 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEE-EEETTCHH-------------
T ss_pred             HHccCcHHHHHHHHHHHHcC--CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCee-EEecCccc-------------
Confidence            56899999999999999877  566688999999999999999988651101111221 11110000             


Q ss_pred             hhhhcchhhHHHHHHHh--hCC-Ccceeehhhccc-----------cccccCCCcEEEEEeCc-hhhhhhcC--CceeEc
Q 004021          235 KWKEKSLQDKAVDISSI--LSP-KKFRIDLTELGV-----------PLQMLNAGFKIVLKTRS-AGVCDQMD--SKNLEV  297 (779)
Q Consensus       235 ~~~~~~~~~~~~~l~~~--L~~-kr~~~~ld~l~~-----------~~~~~~~gs~IivTTR~-~~va~~~~--~~~~~l  297 (779)
                        ...............  ..+ +...+..|++..           .+........+|.||.. ..+.....  ...+.+
T Consensus        88 --~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~i~~  165 (231)
T d1iqpa2          88 --GINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRF  165 (231)
T ss_dssp             --HHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEEEEC
T ss_pred             --chhHHHHHHHHHHhhhhccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCccccccc
Confidence              000000000000000  011 111222222211           11122234455555544 33433332  467899


Q ss_pred             cCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh
Q 004021          298 YSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL  340 (779)
Q Consensus       298 ~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL  340 (779)
                      .+.+.++....+.+.+......-+   .+....|++.|+|-.-
T Consensus       166 ~~~~~~~~~~~l~~~~~~e~i~i~---~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         166 RPLRDEDIAKRLRYIAENEGLELT---EEGLQAILYIAEGDMR  205 (231)
T ss_dssp             CCCCHHHHHHHHHHHHHTTTCEEC---HHHHHHHHHHHTTCHH
T ss_pred             cccchhhHHHHHHHHHHHhCCCCC---HHHHHHHHHHcCCCHH
Confidence            999999999999888765442221   4667889999988643

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.95  E-value=0.00012  Score=70.04  Aligned_cols=183  Identities=15%  Similarity=0.145  Sum_probs=99.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCcch
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSEDK  234 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~~~  234 (779)
                      .+++|.++.++.+..++..+. -...+-|+|.+|+||||+|+.+++.. ......+... ..+......+...-.....+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~l-~~~~~~~~~~-~~~~~~~~~i~~~~~~~~~~   88 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGL-NCETGITATP-CGVCDNCREIEQGRFVDLIE   88 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHHH-HCTTCSCSSC-CSCSHHHHHHHHTCCTTEEE
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHh-cCccccccCc-cccchHHHHHHcCCCCeEEE
Confidence            568999999999999998762 23567899999999999999988765 2111111000 00011122222211000000


Q ss_pred             --hhhhcchhhHHHHHHHhhC-----CCcceeehhhcccc-----------ccccCCCcEEEEEeCch-hhhhhcC--Cc
Q 004021          235 --KWKEKSLQDKAVDISSILS-----PKKFRIDLTELGVP-----------LQMLNAGFKIVLKTRSA-GVCDQMD--SK  293 (779)
Q Consensus       235 --~~~~~~~~~~~~~l~~~L~-----~kr~~~~ld~l~~~-----------~~~~~~gs~IivTTR~~-~va~~~~--~~  293 (779)
                        .......++ ...+.+...     +++..+++|++...           +.....++++|+||.+. .+.....  ..
T Consensus        89 ~~~~~~~~i~~-ir~~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~~i~~~i~SRc~  167 (239)
T d1njfa_          89 IDAASRTKVED-TRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCL  167 (239)
T ss_dssp             EETTCSSSHHH-HHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             ecchhcCCHHH-HHHHHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCccccChhHhhhhc
Confidence              000011111 112222221     11113344443211           11223566777777653 3322222  57


Q ss_pred             eeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChh-HHHH
Q 004021          294 NLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPL-ALKT  344 (779)
Q Consensus       294 ~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPL-ai~~  344 (779)
                      .+.+.+++.++-.+.+.+.+.......+   ++....|++.++|.+- |+..
T Consensus       168 ~i~~~~~~~~~i~~~l~~i~~~e~~~~~---~~~l~~i~~~s~Gd~R~ain~  216 (239)
T d1njfa_         168 QFHLKALDVEQIRHQLEHILNEEHIAHE---PRALQLLARAAEGSLRDALSL  216 (239)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCCBC---HHHHHHHHHHTTTCHHHHHHH
T ss_pred             ccccccCcHHHhhhHHHHHHhhhccCCC---HHHHHHHHHHcCCCHHHHHHH
Confidence            8899999999999988888765543222   4677889999999875 4443

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.94  E-value=6.2e-06  Score=80.26  Aligned_cols=183  Identities=8%  Similarity=0.119  Sum_probs=89.6

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc---ccCCCCEEEEEEechHHHHHHHHhCCC
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH---QQHNFDVVIWAAVQTFQDDIGKRIGFS  231 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~---~~~~F~~~~wv~v~~i~~~i~~~l~~~  231 (779)
                      .+++|.++..+.|..++.... ..+-+.|+|++|+||||+|+++++....   ....++...+.........+ ......
T Consensus        11 ~diig~~~~~~~L~~~~~~~~-~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~   88 (252)
T d1sxje2          11 NALSHNEELTNFLKSLSDQPR-DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLEL-NVVSSP   88 (252)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT-CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-------------------CCEECS
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhh-hhccCC
Confidence            468999988888888776543 3344669999999999999999987411   11122222222220000000 000000


Q ss_pred             c-----chhhhhcchhhHHHHHHHhhCC-------------Ccc-eeehhhccc-----------cccccCCCcEEEEEe
Q 004021          232 E-----DKKWKEKSLQDKAVDISSILSP-------------KKF-RIDLTELGV-----------PLQMLNAGFKIVLKT  281 (779)
Q Consensus       232 ~-----~~~~~~~~~~~~~~~l~~~L~~-------------kr~-~~~ld~l~~-----------~~~~~~~gs~IivTT  281 (779)
                      .     .......+.......+......             .++ .+.+|++..           .+......+++|+||
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~~~~~~~Il~t  168 (252)
T d1sxje2          89 YHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVC  168 (252)
T ss_dssp             SEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCHHHHHHHHHHHHHSTTTEEEEEEE
T ss_pred             ccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccccccchhhhcccccccccccceeee
Confidence            0     0000000000111111111111             111 223333211           122234567777777


Q ss_pred             Cchh-hhhhc-C-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhH
Q 004021          282 RSAG-VCDQM-D-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLA  341 (779)
Q Consensus       282 R~~~-va~~~-~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLa  341 (779)
                      .+.+ +.... . ...+++.+++.++..+.+...+........  .+++...|++.+.|-+-.
T Consensus       169 n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~--~~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         169 DSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLE--TKDILKRIAQASNGNLRV  229 (252)
T ss_dssp             SCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEEC--CSHHHHHHHHHHTTCHHH
T ss_pred             ccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCC--cHHHHHHHHHHcCCcHHH
Confidence            6532 22211 1 357899999999999999877654432222  246678899999887643

>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=97.93  E-value=2.7e-06  Score=87.24  Aligned_cols=158  Identities=19%  Similarity=0.108  Sum_probs=94.1

Q ss_pred             ccCCccEEEcccccccc-----c----ccCcc--cccccccccccc-----------cchhhcccccCceeeecCCcccc
Q 004021          493 EWEGAKRISLMANEIES-----L----SEIPT--LLSLRRNDSLTE-----------LPSRISSLVSLHHLDLSLTHIRG  550 (779)
Q Consensus       493 ~~~~lr~l~l~~~~~~~-----l----~~~~~--lL~L~~~~~l~~-----------lp~~i~~L~~L~~L~L~~~~i~~  550 (779)
                      ....++.|++++|.+..     +    .....  .|+++++ ....           +...+...++|+.|+|++|.+..
T Consensus        29 ~~~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~-~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~  107 (344)
T d2ca6a1          29 EDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDI-FTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGP  107 (344)
T ss_dssp             HCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSC-CTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCT
T ss_pred             hCCCCCEEECcCCcCCHHHHHHHHHHHHhCCCCCEEECCCC-cccccccccchHHHHHHHHHhhCCCccccccccccccc
Confidence            34678899999887633     1    11112  3677665 3322           22345667899999999997755


Q ss_pred             -----cchhhccCccCcEeeccCCcCCCC-----Cchh--------hhcCCccCcEeeeccccCCCcccccCCccCCCch
Q 004021          551 -----LPQELKALEKLRYLNLEYTHYLSI-----IPHQ--------LISGFLKLEVLRLLECGSEGVTKEEGNVLCDDAE  612 (779)
Q Consensus       551 -----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~--------~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~~~~  612 (779)
                           +...+...++|++|++++|. +..     +...        .......|+.|.+.+|.+..          ....
T Consensus       108 ~~~~~l~~~l~~~~~L~~L~l~~n~-l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~l~~n~i~~----------~~~~  176 (344)
T d2ca6a1         108 TAQEPLIDFLSKHTPLEHLYLHNNG-LGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLEN----------GSMK  176 (344)
T ss_dssp             TTHHHHHHHHHHCTTCCEEECCSSC-CHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTG----------GGHH
T ss_pred             ccccchhhhhcccccchheeccccc-ccccccccccccccccccccccccCcccceeecccccccc----------cccc
Confidence                 55567788999999999983 321     1010        01356789999998887653          1112


Q ss_pred             hhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEecccc
Q 004021          613 PLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVCT  666 (779)
Q Consensus       613 ~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~~  666 (779)
                      .....+...++|+.|+++.+....-+.    ..+....+...++|+.|+|++|.
T Consensus       177 ~l~~~l~~~~~L~~L~L~~n~i~~~g~----~~~l~~~l~~~~~L~~L~Ls~N~  226 (344)
T d2ca6a1         177 EWAKTFQSHRLLHTVKMVQNGIRPEGI----EHLLLEGLAYCQELKVLDLQDNT  226 (344)
T ss_dssp             HHHHHHHHCTTCCEEECCSSCCCHHHH----HHHHHTTGGGCTTCCEEECCSSC
T ss_pred             cccchhhhhhhhccccccccccccccc----ccchhhhhcchhhhccccccccc
Confidence            334456677889999988665421000    00001123445666666666643

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.89  E-value=0.00012  Score=68.35  Aligned_cols=161  Identities=17%  Similarity=0.241  Sum_probs=88.4

Q ss_pred             ccccchhhh--HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHHhCCCc
Q 004021          155 QTIVGQEKL--LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       155 ~~~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~l~~~~  232 (779)
                      ..++|....  ...+.++..........+-|+|..|+|||.|++++++..   ......+++++..++...+...+... 
T Consensus        11 nF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~-   86 (213)
T d1l8qa2          11 NFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEA---KKRGYRVIYSSADDFAQAMVEHLKKG-   86 (213)
T ss_dssp             SCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHH---HHTTCCEEEEEHHHHHHHHHHHHHHT-
T ss_pred             hccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHh---ccCccceEEechHHHHHHHHHHHHcc-
Confidence            445675332  233334443333334457899999999999999999988   33445677888766666665544321 


Q ss_pred             chhhhhcchhhHHHHHHHhhCCCcceeehhhccccc--------------cccCCCcEEEEEeCchh---------hhhh
Q 004021          233 DKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPL--------------QMLNAGFKIVLKTRSAG---------VCDQ  289 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~--------------~~~~~gs~IivTTR~~~---------va~~  289 (779)
                             .    ...+.+.+++-. .+.+|++....              .....|.+||+||+..-         +...
T Consensus        87 -------~----~~~~~~~~~~~d-ll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SR  154 (213)
T d1l8qa2          87 -------T----INEFRNMYKSVD-LLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSR  154 (213)
T ss_dssp             -------C----HHHHHHHHHTCS-EEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHH
T ss_pred             -------c----hhhHHHHHhhcc-chhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHH
Confidence                   1    111222232222 23333331110              01246889999998632         2233


Q ss_pred             cC-CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHh
Q 004021          290 MD-SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLAREC  335 (779)
Q Consensus       290 ~~-~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c  335 (779)
                      +. ...+.++ +++++-.+++++++.......+   +++..-|++++
T Consensus       155 L~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~---~~v~~yl~~~~  197 (213)
T d1l8qa2         155 FEGGILVEIE-LDNKTRFKIIKEKLKEFNLELR---KEVIDYLLENT  197 (213)
T ss_dssp             HHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCC---HHHHHHHHHHC
T ss_pred             hhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCC---HHHHHHHHHhc
Confidence            33 4567775 4777777777777755443322   34444444444

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.88  E-value=5.2e-05  Score=72.99  Aligned_cols=145  Identities=13%  Similarity=0.235  Sum_probs=84.7

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcccc--C-CCCEEEEE-EechHHHHHHHHhCCC
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQ--H-NFDVVIWA-AVQTFQDDIGKRIGFS  231 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~--~-~F~~~~wv-~v~~i~~~i~~~l~~~  231 (779)
                      .++||++++++++..|...  ...-+.++|.+|+|||+++..++++.....  . ..+..+|. ++..+..      +..
T Consensus        19 ~~igRd~Ei~~l~~iL~r~--~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~lia------g~~   90 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRR--RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLA------GTK   90 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---C------CCC
T ss_pred             cccChHHHHHHHHHHHhcC--ccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhc------cCc
Confidence            3699999999999999766  334556999999999999999988762211  1 12333443 3222110      000


Q ss_pred             cchhhhhcchhhHHHHHHHhhCC-Ccceeehhhcccccc-----------------c-cCCCcEEEEEeCchhhhhhcC-
Q 004021          232 EDKKWKEKSLQDKAVDISSILSP-KKFRIDLTELGVPLQ-----------------M-LNAGFKIVLKTRSAGVCDQMD-  291 (779)
Q Consensus       232 ~~~~~~~~~~~~~~~~l~~~L~~-kr~~~~ld~l~~~~~-----------------~-~~~gs~IivTTR~~~va~~~~-  291 (779)
                           .....++....+.+.+.. ....+..|++-..+.                 . ....-++|.||..++...... 
T Consensus        91 -----~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~  165 (268)
T d1r6bx2          91 -----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEK  165 (268)
T ss_dssp             -----CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCC
T ss_pred             -----cchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHHHHhh
Confidence                 122334444444444433 233343444322111                 0 123457888887766543322 


Q ss_pred             -------CceeEccCCChHHHHHHHHHHh
Q 004021          292 -------SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       292 -------~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                             ...+.+++.+.+++..++...+
T Consensus       166 d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         166 DRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             TTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             cHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence                   3577999999999999997654

>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=97.79  E-value=2.8e-06  Score=76.46  Aligned_cols=74  Identities=23%  Similarity=0.088  Sum_probs=56.6

Q ss_pred             cccccchhhcccccCceeeecCCccccc---chhhccCccCcEeeccCCcCCCCCchhhhcCCccCcEeeeccccCCC
Q 004021          524 SLTELPSRISSLVSLHHLDLSLTHIRGL---PQELKALEKLRYLNLEYTHYLSIIPHQLISGFLKLEVLRLLECGSEG  598 (779)
Q Consensus       524 ~l~~lp~~i~~L~~L~~L~L~~~~i~~l---p~~~~~L~~L~~L~l~~~~~l~~lp~~~i~~L~~L~~L~l~~~~~~~  598 (779)
                      ....++..+.++++|++|+|++|+|+.+   +..+.++++|+.|++++| .++.++.-...+..+|+.|++.+|.+..
T Consensus        53 ~~~~l~~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N-~i~~l~~l~~l~~~~L~~L~L~~Npl~~  129 (162)
T d1koha1          53 MAATLRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGN-ELKSERELDKIKGLKLEELWLDGNSLSD  129 (162)
T ss_dssp             HHHHHHHHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTS-CCCCGGGHHHHTTCCCSSCCCTTSTTSS
T ss_pred             HhhhhHHHHHhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccC-ccccchhhhhhhccccceeecCCCCcCc
Confidence            3333454556789999999999988876   455788999999999999 6788877323455679999999988764

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.63  E-value=0.00038  Score=67.19  Aligned_cols=163  Identities=16%  Similarity=0.116  Sum_probs=90.2

Q ss_pred             ccccchhhhHHHHHHHHh----c-------cCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHH
Q 004021          155 QTIVGQEKLLPRVWRCIT----D-------QQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDD  223 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~----~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~  223 (779)
                      .+++|.++.+++|.+.+.    .       +-...+-|-++|++|+|||++|+++++..   ..+|   +.++...+.  
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~---~~~~---~~i~~~~l~--   75 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET---GAFF---FLINGPEIM--   75 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT---TCEE---EEECHHHHT--
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh---CCeE---EEEEchhhc--
Confidence            457999999988888643    1       12235668899999999999999999876   2222   122211110  


Q ss_pred             HHHHhCCCcchhhhhcchhhHHHHHHHhhCCCcceeehhhcccccc------------------------ccCCCcEEEE
Q 004021          224 IGKRIGFSEDKKWKEKSLQDKAVDISSILSPKKFRIDLTELGVPLQ------------------------MLNAGFKIVL  279 (779)
Q Consensus       224 i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~kr~~~~ld~l~~~~~------------------------~~~~gs~Iiv  279 (779)
                            ..    +...........+...-+.++..+.+|++...+.                        ....+.-||.
T Consensus        76 ------~~----~~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~  145 (258)
T d1e32a2          76 ------SK----LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMA  145 (258)
T ss_dssp             ------TS----CTTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEE
T ss_pred             ------cc----ccccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEE
Confidence                  00    0000111111111111223344333333322110                        1223445566


Q ss_pred             EeCchhhh----hhcC--CceeEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCCh
Q 004021          280 KTRSAGVC----DQMD--SKNLEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLP  339 (779)
Q Consensus       280 TTR~~~va----~~~~--~~~~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glP  339 (779)
                      ||....-.    ...+  .+.+.++..+.++-..+|...........+.+    ...|++.+.|.-
T Consensus       146 tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~----~~~la~~t~G~s  207 (258)
T d1e32a2         146 ATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVD----LEQVANETHGHV  207 (258)
T ss_dssp             EESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCC----HHHHHHHCTTCC
T ss_pred             eCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccc----hhhhhhcccCCC
Confidence            88875432    2222  57889999999999999988775443222222    367888988853

>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=97.46  E-value=0.00092  Score=63.67  Aligned_cols=48  Identities=23%  Similarity=0.287  Sum_probs=36.0

Q ss_pred             ccccchhhhHHHHHHHH---hc-------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCI---TD-------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L---~~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|-++.+++|.+.+   ..       +....+-|-++|++|+|||+||+++++..
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~   66 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA   66 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc
Confidence            46889988777765543   22       12234568999999999999999999876

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.43  E-value=0.00039  Score=70.72  Aligned_cols=144  Identities=11%  Similarity=0.129  Sum_probs=77.9

Q ss_pred             ccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc--c-cCCCCEEEE-EEechHHHHHHHHhCCCc
Q 004021          157 IVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH--Q-QHNFDVVIW-AAVQTFQDDIGKRIGFSE  232 (779)
Q Consensus       157 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~--~-~~~F~~~~w-v~v~~i~~~i~~~l~~~~  232 (779)
                      ++||+++++++++.|....  -.-+.++|.+|||||+++..++++...  + ..-.+.++| +++..++...-       
T Consensus        24 ~~gr~~ei~~~~~~L~r~~--k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~-------   94 (387)
T d1qvra2          24 VIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAK-------   94 (387)
T ss_dssp             CCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC---------------
T ss_pred             CcCcHHHHHHHHHHHhcCC--CCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccC-------
Confidence            6999999999999998652  223367899999999999877766521  1 112244444 43333322110       


Q ss_pred             chhhhhcchhhHHHHHHHhhCC--Ccceeehhhcccccccc-----------------CCCcEEEEEeCchhhhhh----
Q 004021          233 DKKWKEKSLQDKAVDISSILSP--KKFRIDLTELGVPLQML-----------------NAGFKIVLKTRSAGVCDQ----  289 (779)
Q Consensus       233 ~~~~~~~~~~~~~~~l~~~L~~--kr~~~~ld~l~~~~~~~-----------------~~gs~IivTTR~~~va~~----  289 (779)
                          .....++....+...+..  ....+.+|++-..+..+                 ...-++|-||-.......    
T Consensus        95 ----~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~~~e~d~  170 (387)
T d1qvra2          95 ----YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYREIEKDP  170 (387)
T ss_dssp             -------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTTCCCEEEEECHHHHHHHTTCT
T ss_pred             ----cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHHHhcccH
Confidence                112233333333333322  23444555543222111                 122466766655443221    


Q ss_pred             --cC-CceeEccCCChHHHHHHHHHHh
Q 004021          290 --MD-SKNLEVYSLAHDEAWKLFQEMI  313 (779)
Q Consensus       290 --~~-~~~~~l~~L~~~~a~~Lf~~~a  313 (779)
                        .. ...+.+++.+.+++..++....
T Consensus       171 al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         171 ALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             TTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             HHHHhcccccCCCCcHHHHHHHHHHHH
Confidence              11 4678999999999999998665

>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=97.43  E-value=0.0012  Score=63.27  Aligned_cols=48  Identities=21%  Similarity=0.229  Sum_probs=36.6

Q ss_pred             ccccchhhhHHHHHHHH---hcc-------CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCI---TDQ-------QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L---~~~-------~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.+++|.+.+   ...       ....+-+-++|++|+|||++|+++++..
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~   69 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA   69 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc
Confidence            56899998887776543   321       2235678899999999999999999876

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.39  E-value=7.5e-05  Score=67.65  Aligned_cols=45  Identities=20%  Similarity=0.427  Sum_probs=38.6

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++||++++++++..|...  ...-+.++|.+|+|||+++..++++.
T Consensus        23 ~~igRd~Ei~~l~~iL~r~--~k~n~lLvG~pGVGKTalv~~LA~ri   67 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRR--TKNNPVLIGEPGVGKTAIVEGLAQRI   67 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSS--SSCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhcc--CCCCeEEEecCCcccHHHHHHHHHHH
Confidence            3699999999999999876  33456799999999999999988876

>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=97.31  E-value=2.9e-05  Score=69.46  Aligned_cols=89  Identities=17%  Similarity=0.078  Sum_probs=62.8

Q ss_pred             hcccccCceeeecCCcccccchhhccCccCcEeeccCCcCCCCCch--hhhcCCccCcEeeeccccCCCcccccCCccCC
Q 004021          532 ISSLVSLHHLDLSLTHIRGLPQELKALEKLRYLNLEYTHYLSIIPH--QLISGFLKLEVLRLLECGSEGVTKEEGNVLCD  609 (779)
Q Consensus       532 i~~L~~L~~L~L~~~~i~~lp~~~~~L~~L~~L~l~~~~~l~~lp~--~~i~~L~~L~~L~l~~~~~~~~~~~~~~~~~~  609 (779)
                      +..+..+..|+...+.+..++....++++|++|+|++| .++.++.  ..+.++++|+.|++++|.+..           
T Consensus        38 l~~~~~~~~l~~~~~~~~~l~~~~~~~~~L~~L~Ls~N-~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~-----------  105 (162)
T d1koha1          38 LVAQNIDVVLNRRSSMAATLRIIEENIPELLSLNLSNN-RLYRLDDMSSIVQKAPNLKILNLSGNELKS-----------  105 (162)
T ss_dssp             TTTTTCCCCTTSHHHHHHHHHHHHHHCTTCCCCCCCSS-CCCCCSGGGTHHHHSTTCCCCCCTTSCCCC-----------
T ss_pred             hhhccchhhcchhhhHhhhhHHHHHhCCCCCEeeCCCc-cccCCchhHHHHhhCCcccccccccCcccc-----------
Confidence            44455555666655555556555678999999999999 6777653  236789999999999999885           


Q ss_pred             CchhhHHhhcCCCCCCceeEEeeccc
Q 004021          610 DAEPLMRELLGLKRLNVLSWSFRSSL  635 (779)
Q Consensus       610 ~~~~~~~~l~~L~~L~~L~l~~~~~~  635 (779)
                        ......++. .+|+.|++++|...
T Consensus       106 --l~~l~~l~~-~~L~~L~L~~Npl~  128 (162)
T d1koha1         106 --ERELDKIKG-LKLEELWLDGNSLS  128 (162)
T ss_dssp             --GGGHHHHTT-CCCSSCCCTTSTTS
T ss_pred             --chhhhhhhc-cccceeecCCCCcC
Confidence              223334444 46899998877643

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.28  E-value=0.00039  Score=64.61  Aligned_cols=170  Identities=11%  Similarity=0.032  Sum_probs=88.6

Q ss_pred             hhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccC-CCCEEEEEEechHHHHHHHHhCCCc-----c
Q 004021          160 QEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH-NFDVVIWAAVQTFQDDIGKRIGFSE-----D  233 (779)
Q Consensus       160 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~-~F~~~~wv~v~~i~~~i~~~l~~~~-----~  233 (779)
                      .+...+++.+.+..+. -...+-++|..|+||||+|+.+++..-.... .....   ....-...+........     .
T Consensus         7 ~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~~~   82 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSC---GHCRGCQLMQAGTHPDYYTLAPE   82 (207)
T ss_dssp             GHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCC---SCSHHHHHHHHTCCTTEEEECCC
T ss_pred             cHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccc---cccchhhhhhhccccccchhhhh
Confidence            4556777888777662 2456899999999999999998876410000 00000   00001111111110000     0


Q ss_pred             hhhhhcchhhHHHHHHHhhCCC-----cceeehhhccc-----------cccccCCCcEEEEEeCch-hhhhhcC--Cce
Q 004021          234 KKWKEKSLQDKAVDISSILSPK-----KFRIDLTELGV-----------PLQMLNAGFKIVLKTRSA-GVCDQMD--SKN  294 (779)
Q Consensus       234 ~~~~~~~~~~~~~~l~~~L~~k-----r~~~~ld~l~~-----------~~~~~~~gs~IivTTR~~-~va~~~~--~~~  294 (779)
                      ........ +.+..+.+.+...     +-...+|++..           .+.....++.+|.||++. .+.....  ...
T Consensus        83 ~~~~~i~~-~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~tI~SRc~~  161 (207)
T d1a5ta2          83 KGKNTLGV-DAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRL  161 (207)
T ss_dssp             TTCSSBCH-HHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGGGSCHHHHTTSEE
T ss_pred             hccccccc-chhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChhhhhhhhcceeEE
Confidence            00000111 1122333333221     11333333311           112224567777777764 4544432  578


Q ss_pred             eEccCCChHHHHHHHHHHhhccCCCCCCChHHHHHHHHHHhCCChhHH
Q 004021          295 LEVYSLAHDEAWKLFQEMIERSTLDSHTSIPELAETLARECGRLPLAL  342 (779)
Q Consensus       295 ~~l~~L~~~~a~~Lf~~~a~~~~~~~~~~l~~~~~~I~~~c~glPLai  342 (779)
                      +.+.+++.++....+.+....        -++....|++.++|.|-.+
T Consensus       162 i~~~~~~~~~~~~~L~~~~~~--------~~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         162 HYLAPPPEQYAVTWLSREVTM--------SQDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             EECCCCCHHHHHHHHHHHCCC--------CHHHHHHHHHHTTTCHHHH
T ss_pred             EecCCCCHHHHHHHHHHcCCC--------CHHHHHHHHHHcCCCHHHH
Confidence            899999999998888654311        1466888999999988544

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.09  E-value=0.0012  Score=63.77  Aligned_cols=48  Identities=25%  Similarity=0.289  Sum_probs=36.4

Q ss_pred             ccccchhhhHHHHHHHHhc-----------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-----------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++.+++|.+.+..           +-...+-|-++|.+|.|||+||+++++..
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~   65 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC   65 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh
Confidence            4578888877777766531           12234568899999999999999999987

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.52  E-value=0.00058  Score=62.08  Aligned_cols=25  Identities=20%  Similarity=0.404  Sum_probs=23.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|+|.|++|+||||||+.+++..
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999998876

>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=96.51  E-value=0.0009  Score=60.31  Aligned_cols=39  Identities=18%  Similarity=0.072  Sum_probs=29.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ...+|.|+|++|+||||+|++++... . ..+++...++..
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L-~-~~~~~~~~~~~~   43 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTL-N-QQGGRSVSLLLG   43 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH-H-HHCSSCEEEEEH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH-h-hcCCCchhhhhh
Confidence            44789999999999999999999887 2 234555545443

>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=96.46  E-value=0.00041  Score=73.04  Aligned_cols=105  Identities=20%  Similarity=0.199  Sum_probs=76.0

Q ss_pred             ccccccccccc--cchhhcccccCceeeecCCccc-----ccchhhccCccCcEeeccCCcCCCC-----Cchhhhc-CC
Q 004021          517 LSLRRNDSLTE--LPSRISSLVSLHHLDLSLTHIR-----GLPQELKALEKLRYLNLEYTHYLSI-----IPHQLIS-GF  583 (779)
Q Consensus       517 L~L~~~~~l~~--lp~~i~~L~~L~~L~L~~~~i~-----~lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~-~L  583 (779)
                      ||++++ .++.  +..-+..+++|++|+|++|+++     .++..+..+++|++|+|++| .++.     +... +. ..
T Consensus         7 ld~~~~-~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N-~i~~~~~~~l~~~-l~~~~   83 (460)
T d1z7xw1           7 LDIQCE-ELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSN-ELGDVGVHCVLQG-LQTPS   83 (460)
T ss_dssp             EEEESC-CCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTC-CCHHHHHHHHHHT-TCSTT
T ss_pred             EEeeCC-cCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCC-cCChHHHHHHHHH-HhcCC
Confidence            788888 7765  2455677899999999999876     35667889999999999998 4432     2222 21 23


Q ss_pred             ccCcEeeeccccCCCcccccCCccCCCchhhHHhhcCCCCCCceeEEeecc
Q 004021          584 LKLEVLRLLECGSEGVTKEEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSS  634 (779)
Q Consensus       584 ~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~  634 (779)
                      .+|++|++++|.+..          .........+..+++|++|+++.|..
T Consensus        84 ~~L~~L~L~~n~it~----------~~~~~l~~~l~~~~~L~~L~L~~N~i  124 (460)
T d1z7xw1          84 CKIQKLSLQNCCLTG----------AGCGVLSSTLRTLPTLQELHLSDNLL  124 (460)
T ss_dssp             CCCCEEECTTSCCBG----------GGHHHHHHHTTSCTTCCEEECCSSBC
T ss_pred             CCCCEEECCCCCccc----------cccccccchhhccccccccccccccc
Confidence            579999999998764          10123455678899999999986653

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=96.43  E-value=0.00062  Score=60.40  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.+.|++|+||||+|+.++...
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            468888999999999999999876

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.38  E-value=0.00087  Score=58.57  Aligned_cols=24  Identities=29%  Similarity=0.293  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.|.|++|+||||+|+++....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            578899999999999999886644

>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=96.37  E-value=0.00087  Score=59.76  Aligned_cols=25  Identities=32%  Similarity=0.466  Sum_probs=23.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+||+|+|..|+|||||+.++.+..
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l   26 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPAL   26 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            5799999999999999999999876

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.32  E-value=0.0022  Score=58.63  Aligned_cols=39  Identities=26%  Similarity=0.428  Sum_probs=28.7

Q ss_pred             HHHHHHHHhcc-CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.|.+.+..- ....-+|+|.|.+|+||||||+.+....
T Consensus         7 ~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~~l   46 (198)
T d1rz3a_           7 IDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTL   46 (198)
T ss_dssp             HHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34444444332 3355689999999999999999998877

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.31  E-value=0.00097  Score=59.65  Aligned_cols=24  Identities=29%  Similarity=0.439  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.|.|++|+||||+|+++....
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            689999999999999999998765

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.20  E-value=0.001  Score=59.51  Aligned_cols=24  Identities=46%  Similarity=0.437  Sum_probs=21.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..|.|.|++|+||||+|+.++.+.
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            457799999999999999998876

>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=96.09  E-value=0.0017  Score=59.43  Aligned_cols=27  Identities=22%  Similarity=0.348  Sum_probs=24.3

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+.+|.|+|++|+||||+|+.++...
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            356899999999999999999998876

>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=96.04  E-value=0.0027  Score=61.48  Aligned_cols=43  Identities=21%  Similarity=0.135  Sum_probs=31.3

Q ss_pred             hhhhHHHHHHHHhcc---CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          160 QEKLLPRVWRCITDQ---QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       160 r~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -++.+.+.++.+..+   ...++.|.++|++|+||||||+.++...
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~~~   56 (273)
T d1gvnb_          11 FENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEET   56 (273)
T ss_dssp             HHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            344445555555433   3356778999999999999999999876

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.98  E-value=0.0017  Score=57.65  Aligned_cols=22  Identities=27%  Similarity=0.495  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.++||+|+||||+|+.++...
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            4456999999999999999887

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=95.93  E-value=0.0018  Score=57.25  Aligned_cols=22  Identities=32%  Similarity=0.566  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.||+|+||||+|+.++.+.
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            6788999999999999999987

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.92  E-value=0.0016  Score=58.90  Aligned_cols=24  Identities=38%  Similarity=0.481  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|.|+|.+|+|||||+++++...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            568999999999999999999887

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.91  E-value=0.0014  Score=59.81  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+|.++|++|+||||+|+.++...
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l   43 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYL   43 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4688899999999999999998877

>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=95.87  E-value=0.0025  Score=56.66  Aligned_cols=26  Identities=27%  Similarity=0.542  Sum_probs=23.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+++.|.|++|+||||+|+.+....
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            56899999999999999999998876

>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=95.86  E-value=0.0029  Score=62.46  Aligned_cols=48  Identities=25%  Similarity=0.305  Sum_probs=37.2

Q ss_pred             ccccchhhhHHHHHHHHhc------------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD------------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~------------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+...+..            .....+-+.++|++|+|||.||+++++..
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            4579999999888776621            01134667799999999999999999876

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=95.85  E-value=0.0025  Score=56.93  Aligned_cols=26  Identities=23%  Similarity=0.322  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ....|.|.|++|+||||+|+.++...
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            44578999999999999999998876

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.84  E-value=0.0025  Score=58.37  Aligned_cols=27  Identities=22%  Similarity=0.359  Sum_probs=24.5

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..++|.|.|++|+||||+|+.++..+
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            367899999999999999999998876

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.82  E-value=0.0022  Score=57.98  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=22.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|++|+||||+++.+....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l   25 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNL   25 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            689999999999999999999877

>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=95.82  E-value=0.0023  Score=59.34  Aligned_cols=25  Identities=24%  Similarity=0.381  Sum_probs=22.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+|.++|.+|+||||+|+++++..
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l   26 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYL   26 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3589999999999999999999876

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=95.75  E-value=0.0026  Score=56.88  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=23.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|.|.|.+|+||||+|+.+++..
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4799999999999999999998876

>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=95.70  E-value=0.0054  Score=58.12  Aligned_cols=48  Identities=19%  Similarity=0.113  Sum_probs=35.5

Q ss_pred             ccccchhhhHHHHHHHHh-------cc-CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCIT-------DQ-QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~-------~~-~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|..+.++.+++-..       .. ....+-|-++|++|+|||++|+++++..
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~   64 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES   64 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcc
Confidence            447887777766665443       22 2245568899999999999999999876

>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=95.70  E-value=0.0066  Score=55.48  Aligned_cols=52  Identities=21%  Similarity=0.342  Sum_probs=36.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      +.+||.++|+.|+||||.+..++... . +.. ..+..++.       .+-++...+.++.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~-~-~~g-~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYY-K-GKG-RRPLLVAADTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHH-H-HTT-CCEEEEECCSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH-H-HCC-CcEEEEecccccchHHHHHHHHHHhcCCc
Confidence            45899999999999999988887776 3 223 34666776       34455556666654

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=95.68  E-value=0.0029  Score=56.46  Aligned_cols=26  Identities=31%  Similarity=0.355  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|.|++|+||||+|+.+....
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~l   28 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLP   28 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35799999999999999999997654

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.67  E-value=0.003  Score=55.97  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=22.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++++|+|..|+|||||+.++....
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L   25 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAA   25 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHH
Confidence            689999999999999999998876

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.65  E-value=0.0078  Score=54.92  Aligned_cols=52  Identities=25%  Similarity=0.457  Sum_probs=38.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      ..++|.++|+.|+||||.+..++... .. .. ..+..|+.       .+-++..++.++.+
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~-~~-~g-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYY-QN-LG-KKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH-HT-TT-CCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH-HH-CC-CcEEEEEeccccccchhhHhhcccccCce
Confidence            56899999999999999988888776 32 22 35777777       34455666666654

>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=95.62  E-value=0.0025  Score=56.82  Aligned_cols=23  Identities=26%  Similarity=0.361  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.++|++|+||||+|+.++...
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            46688999999999999999887

>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=95.60  E-value=0.0033  Score=56.08  Aligned_cols=26  Identities=23%  Similarity=0.368  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|.++|++|+||||+|+......
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~~~   38 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLVSA   38 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            56899999999999999999886543

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.58  E-value=0.011  Score=53.81  Aligned_cols=52  Identities=29%  Similarity=0.369  Sum_probs=36.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      .+.||.++|+.|+||||.+..++... . +.. ..+..++.       .+-++..++.++.+
T Consensus         8 ~p~vi~lvGptGvGKTTTiAKLA~~~-~-~~g-~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   66 (211)
T d2qy9a2           8 APFVILMVGVNGVGKTTTIGKLARQF-E-QQG-KSVMLAAGDTFRAAAVEQLQVWGQRNNIP   66 (211)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHHH-H-TTT-CCEEEECCCTTCHHHHHHHHHHHHHTTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH-H-HCC-CcEEEEecccccccchhhhhhhhhhcCCc
Confidence            57899999999999999988888776 3 222 34555655       33455566666655

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=95.46  E-value=0.011  Score=54.21  Aligned_cols=53  Identities=26%  Similarity=0.337  Sum_probs=37.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      ..+.||.++|+.|+||||.+..++... ..++  ..+..++.       .+-++..++.++.+
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~-~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   68 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMF-VDEG--KSVVLAAADTFRAAAIEQLKIWGERVGAT   68 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHH-HHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH-HHCC--CceEEEeecccccchhHHHHHHhhhcCcc
Confidence            366899999999999999888887776 3222  45777777       33455556666554

>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=95.43  E-value=0.0037  Score=55.50  Aligned_cols=68  Identities=16%  Similarity=0.144  Sum_probs=38.2

Q ss_pred             cchhhcccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeeeccccCC
Q 004021          528 LPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRLLECGSE  597 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l~~~~~~  597 (779)
                      +-..+...++|++|+|++|.+..     +...+...+.|++|++++| .++.     +-.. +..-++|++|++.+|...
T Consensus        36 l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n-~i~~~g~~~l~~a-L~~n~sL~~L~l~~n~~~  113 (167)
T d1pgva_          36 LIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESN-FLTPELLARLLRS-TLVTQSIVEFKADNQRQS  113 (167)
T ss_dssp             HHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSS-BCCHHHHHHHHHH-TTTTCCCSEEECCCCSSC
T ss_pred             HHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehh-hcchHHHHHHHHH-HHhCCcCCEEECCCCcCC
Confidence            33345555667777777775542     3344555666777777777 3332     1222 445566777777665433

>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=95.39  E-value=0.0039  Score=58.20  Aligned_cols=41  Identities=20%  Similarity=0.256  Sum_probs=32.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHH
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGK  226 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~  226 (779)
                      .+||+|.|++|+||||+|+.+.+++     .|   .+++..+++++++.
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~-----gl---~~iStGdLlR~~a~   43 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEAL-----QW---HLLDSGAIYRVLAL   43 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH-----TC---EEEEHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh-----CC---cEECHHHHHHHHHH
Confidence            4699999999999999999999987     22   23555777777654

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.36  E-value=0.016  Score=55.07  Aligned_cols=90  Identities=16%  Similarity=0.215  Sum_probs=58.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcchhhHHHHHHHhh
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSLQDKAVDISSIL  252 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~~~~~~~l~~~L  252 (779)
                      ..-+++-|+|.+|+||||+|..++...   +..=..++|+.. ..+-.+.+++++.+.+.-  ....+.++..+.+....
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~---q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~  134 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANA---QAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLI  134 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHH---HHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHH---hcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHH
Confidence            356799999999999999998887665   233346899999 334455677777763321  12344556555555555


Q ss_pred             CCCcc-eeehhhccccc
Q 004021          253 SPKKF-RIDLTELGVPL  268 (779)
Q Consensus       253 ~~kr~-~~~ld~l~~~~  268 (779)
                      +.+++ +++||.+...+
T Consensus       135 ~~~~~~liIiDSi~al~  151 (269)
T d1mo6a1         135 RSGALDIVVIDSVAALV  151 (269)
T ss_dssp             HTTCEEEEEEECSTTCC
T ss_pred             hcCCCCEEEEecccccc
Confidence            54444 66677765443

>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=95.27  E-value=0.0048  Score=56.19  Aligned_cols=25  Identities=20%  Similarity=0.290  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.+|.|.|++|+||||.|+.+++..
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3689999999999999999999876

>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=95.17  E-value=0.0074  Score=54.53  Aligned_cols=24  Identities=42%  Similarity=0.526  Sum_probs=22.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.|.|++|+||||+|+.+....
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L   25 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            688999999999999999999887

>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=95.05  E-value=0.0085  Score=57.74  Aligned_cols=36  Identities=19%  Similarity=0.455  Sum_probs=27.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +.|+|+|-||+||||+|..++....  +..+ .++-|..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA--~~G~-rVllID~   37 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLH--AMGK-TIMVVGC   37 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHH--TTTC-CEEEEEE
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHH--hCCC-cEEEEec
Confidence            6899999999999999999988873  2233 3555555

>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=95.02  E-value=0.0056  Score=54.74  Aligned_cols=22  Identities=45%  Similarity=0.638  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |+|+|.+|+|||||++.+....
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l   24 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhcC
Confidence            8999999999999999999876

>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=95.00  E-value=0.0067  Score=53.70  Aligned_cols=119  Identities=12%  Similarity=0.019  Sum_probs=73.0

Q ss_pred             cccccCceeeecCC-cccc-----cchhhccCccCcEeeccCCcCCC-----CCchhhhcCCccCcEeeeccccCCCccc
Q 004021          533 SSLVSLHHLDLSLT-HIRG-----LPQELKALEKLRYLNLEYTHYLS-----IIPHQLISGFLKLEVLRLLECGSEGVTK  601 (779)
Q Consensus       533 ~~L~~L~~L~L~~~-~i~~-----lp~~~~~L~~L~~L~l~~~~~l~-----~lp~~~i~~L~~L~~L~l~~~~~~~~~~  601 (779)
                      .+.++|+.|+|+++ .+..     +-..+...++|++|++++| .++     .+... +...++|++|++++|.+..   
T Consensus        12 ~n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n-~l~~~~~~~la~~-L~~n~~L~~L~L~~n~i~~---   86 (167)
T d1pgva_          12 EDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANT-AISDSEARGLIEL-IETSPSLRVLNVESNFLTP---   86 (167)
T ss_dssp             TTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTS-CCBHHHHTTHHHH-HHHCSSCCEEECCSSBCCH---
T ss_pred             hCCCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeecccc-ccchhHHHHHhhh-hhhcccccceeeehhhcch---
Confidence            34588999999875 4532     3445777889999999998 443     23332 5667889999999998763   


Q ss_pred             ccCCccCCCchhhHHhhcCCCCCCceeEEeecccccccCCCCCcccCcccccccCcceEEeccc
Q 004021          602 EEGNVLCDDAEPLMRELLGLKRLNVLSWSFRSSLAVQKFFKYPKLDLTWLVFVQNLKELEIIVC  665 (779)
Q Consensus       602 ~~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~~~~~L~~L~~~~l~~l~~L~~L~L~~~  665 (779)
                             .........+...+.|++|+++.+....++.- .... ....+..-++|+.|+++.+
T Consensus        87 -------~g~~~l~~aL~~n~sL~~L~l~~n~~~~~g~~-~~~~-l~~~L~~n~sL~~l~l~~~  141 (167)
T d1pgva_          87 -------ELLARLLRSTLVTQSIVEFKADNQRQSVLGNQ-VEMD-MMMAIEENESLLRVGISFA  141 (167)
T ss_dssp             -------HHHHHHHHHTTTTCCCSEEECCCCSSCCCCHH-HHHH-HHHHHHHCSSCCEEECCCC
T ss_pred             -------HHHHHHHHHHHhCCcCCEEECCCCcCCCccHH-HHHH-HHHHHHhCCCccEeeCcCC
Confidence                   11123455677778899998875542211000 0000 0112334567777777653

>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=94.98  E-value=0.012  Score=57.84  Aligned_cols=48  Identities=27%  Similarity=0.370  Sum_probs=39.0

Q ss_pred             ccccchhhhHHHHHHHHhc-------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+...+..       .+....++.++|+.|+|||.||+.++...
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            5579999999999887742       23345588899999999999999998876

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=94.95  E-value=0.02  Score=54.46  Aligned_cols=89  Identities=11%  Similarity=0.152  Sum_probs=60.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchh--hhhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKK--WKEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~--~~~~~~~~~~~~l~~~L~  253 (779)
                      ..+++-|+|.+|+||||+|..++... ...+  ..++|++. ..+-..+++.++.+.+.-  ....+.++..+.+....+
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~a-qk~g--~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~  132 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQA-QKAG--GTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  132 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH-HHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CceEEEEecCCccchHHHHHHHHHHH-HhCC--CEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHh
Confidence            45799999999999999999888766 2222  45889998 344456788888763321  133455666666666665


Q ss_pred             CCcc-eeehhhccccc
Q 004021          254 PKKF-RIDLTELGVPL  268 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~~  268 (779)
                      ..++ ++++|.+...+
T Consensus       133 ~~~~~liIiDSi~al~  148 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALT  148 (268)
T ss_dssp             TTCCSEEEEECTTTCC
T ss_pred             cCCCcEEEEecccccc
Confidence            5544 66777775554

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.91  E-value=0.0073  Score=55.89  Aligned_cols=25  Identities=20%  Similarity=0.301  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-+|+|.|..|+||||+|+.+....
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l   26 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLL   26 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999998876

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=94.91  E-value=0.016  Score=57.10  Aligned_cols=51  Identities=24%  Similarity=0.178  Sum_probs=36.4

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ..++++.+....++..+|+|.|.+|+|||||.-.+.... .  ..-..++-+.+
T Consensus        40 ~~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~-~--~~g~~vavlav   90 (327)
T d2p67a1          40 STQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLL-I--REGLKVAVIAV   90 (327)
T ss_dssp             HHHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHH-H--HTTCCEEEEEE
T ss_pred             HHHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHH-H--hcCCceeeecC
Confidence            455666666555678999999999999999999988766 2  22234444555

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.87  E-value=0.011  Score=57.17  Aligned_cols=37  Identities=35%  Similarity=0.537  Sum_probs=30.2

Q ss_pred             HHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          164 LPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       164 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+.+.+...  ..++|.+.|-||+||||+|..++...
T Consensus         8 ~~~~~~~~~~~--~~~iii~sGKGGVGKTT~a~nLA~~l   44 (279)
T d1ihua2           8 LSALVDDIARN--EHGLIMLMGKGGVGKTTMAAAIAVRL   44 (279)
T ss_dssp             HHHHHHHHHTT--SCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcC--CCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            45566666655  78999999999999999998887766

>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=94.86  E-value=0.008  Score=54.45  Aligned_cols=25  Identities=32%  Similarity=0.470  Sum_probs=21.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.++| |.|++|+||||+|+.++...
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHHHh
Confidence            45566 78999999999999998876

>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=94.84  E-value=0.018  Score=56.64  Aligned_cols=40  Identities=20%  Similarity=0.347  Sum_probs=32.3

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...++++.+....++..+|+|.|.+|+|||||.-++....
T Consensus        36 ~~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~   75 (323)
T d2qm8a1          36 AVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLL   75 (323)
T ss_dssp             HHHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHH
Confidence            4556666666655678999999999999999999988765

>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=94.74  E-value=0.0071  Score=54.77  Aligned_cols=25  Identities=16%  Similarity=0.199  Sum_probs=21.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..|.|.|++|+||||+|+.+++..
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457799999999999999998876

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.74  E-value=0.024  Score=51.70  Aligned_cols=53  Identities=25%  Similarity=0.359  Sum_probs=33.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-------chHHHHHHHHhCCC
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-------QTFQDDIGKRIGFS  231 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-------~~i~~~i~~~l~~~  231 (779)
                      ..+.||.++|+.|+||||.+..++... . +... .+..|+.       .+-++..++.++.+
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~-~-~~g~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFY-K-KKGF-KVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHH-H-HTTC-CEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHH-H-HCCC-ceEEEEeeccccchhHHHHHhccccCcc
Confidence            367899999999999999888877766 3 2233 4677777       33345555666654

>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=94.67  E-value=0.0081  Score=55.94  Aligned_cols=41  Identities=20%  Similarity=0.271  Sum_probs=31.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEechHHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAVQTFQDDIGKR  227 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v~~i~~~i~~~  227 (779)
                      -+|+|-|++|+||||+|+.++.++     .|   .+++..+++++++..
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~l-----g~---~~istGdl~R~~a~~   44 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKDF-----GF---TYLDTGAMYRAATYM   44 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHH-----CC---EEEEHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh-----CC---cEECHHHHHHHHHHH
Confidence            368999999999999999999987     12   245556777776643

>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=94.67  E-value=0.0078  Score=53.98  Aligned_cols=22  Identities=27%  Similarity=0.520  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|++|+||||+|+.++...
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            7799999999999999998876

>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=94.58  E-value=0.078  Score=49.02  Aligned_cols=26  Identities=31%  Similarity=0.404  Sum_probs=22.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||.+.+..-.
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            34689999999999999999997654

>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=94.58  E-value=0.011  Score=54.36  Aligned_cols=26  Identities=27%  Similarity=0.372  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...+|-+.|++|+||||+|+++....
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~~l   48 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEHQL   48 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            56799999999999999999998765

>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=94.57  E-value=0.01  Score=53.61  Aligned_cols=25  Identities=24%  Similarity=0.377  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.|.|.|++|+||||+|+.++.++
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHH
Confidence            3456688999999999999998876

>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=94.52  E-value=0.0097  Score=54.09  Aligned_cols=26  Identities=27%  Similarity=0.353  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.|.|++|+||||+|+.++...
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45899999999999999999998865

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=94.52  E-value=0.02  Score=54.38  Aligned_cols=88  Identities=15%  Similarity=0.162  Sum_probs=53.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe-chHHHHHHHHhCCCcchhh--hhcchhhHHHHHHHhhC
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV-QTFQDDIGKRIGFSEDKKW--KEKSLQDKAVDISSILS  253 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v-~~i~~~i~~~l~~~~~~~~--~~~~~~~~~~~l~~~L~  253 (779)
                      .-+++-|+|.+|+||||||.+++... .  ..=..++|++. ..+-...++.++.+.+.-.  ...+.++..+.+....+
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~-q--~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~  129 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAA-Q--REGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  129 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHH-H--HTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHH-H--cCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHh
Confidence            44799999999999999999988776 2  22245788888 3444456777776532211  22334444444444443


Q ss_pred             CCcc-eeehhhcccc
Q 004021          254 PKKF-RIDLTELGVP  267 (779)
Q Consensus       254 ~kr~-~~~ld~l~~~  267 (779)
                      ..+. ++++|.+...
T Consensus       130 ~~~~~liViDSi~al  144 (263)
T d1u94a1         130 SGAVDVIVVDSVAAL  144 (263)
T ss_dssp             HTCCSEEEEECGGGC
T ss_pred             cCCCCEEEEECcccc
Confidence            3332 5556665443

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=94.48  E-value=0.05  Score=52.67  Aligned_cols=78  Identities=17%  Similarity=0.095  Sum_probs=45.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC--CEEEEEEechHH--HHHHHHhCCC-cchhhhhcchhhHHHHHHH
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF--DVVIWAAVQTFQ--DDIGKRIGFS-EDKKWKEKSLQDKAVDISS  250 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F--~~~~wv~v~~i~--~~i~~~l~~~-~~~~~~~~~~~~~~~~l~~  250 (779)
                      ..+-+|+|.|..|+||||+|+.+....   ...+  ..+.-++.....  .+.+..-+.. .-..+..-+.+.+...+..
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL---~~~~~~~~v~~Is~D~F~~~~~~l~~~~~~~~~g~Pes~D~~~L~~~L~~  154 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALL---SRWPEHRRVELITTDGFLHPNQVLKERGLMKKKGFPESYDMHRLVKFVSD  154 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHH---TTSTTCCCEEEEEGGGGBCCHHHHHHHTCTTCTTSGGGBCHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHH---hhhcCCCceEEEeeeeeECCchHHHHhcCCccCCchHhhhHHHHHHHHHH
Confidence            456799999999999999999998876   2322  234444541110  1111111111 0111245667777777777


Q ss_pred             hhCCCc
Q 004021          251 ILSPKK  256 (779)
Q Consensus       251 ~L~~kr  256 (779)
                      ...++.
T Consensus       155 lk~g~~  160 (308)
T d1sq5a_         155 LKSGVP  160 (308)
T ss_dssp             HTTTCS
T ss_pred             HHcCCC
Confidence            666654

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=94.46  E-value=0.024  Score=53.28  Aligned_cols=48  Identities=25%  Similarity=0.133  Sum_probs=36.6

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      |-+.|..+=....++.|+|.+|+|||++|.+++...   ..+...++|++.
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~---~~~~~~~~~is~   62 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENA---CANKERAILFAY   62 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHH---HTTTCCEEEEES
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHH---HHhccccceeec
Confidence            334444332345799999999999999999999887   466777888888

>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=94.37  E-value=0.011  Score=53.06  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.++...
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            37799999999999999999877

>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=94.34  E-value=0.01  Score=53.17  Aligned_cols=23  Identities=26%  Similarity=0.332  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|.|++|+||||+|+.++...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36788999999999999999876

>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=93.94  E-value=0.015  Score=52.60  Aligned_cols=23  Identities=35%  Similarity=0.446  Sum_probs=20.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHH
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVN  199 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~  199 (779)
                      .+-+|||.|+.|+||||+|..+.
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45689999999999999998873

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.93  E-value=0.014  Score=52.23  Aligned_cols=22  Identities=32%  Similarity=0.468  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|.|++|+||||+|+.++...
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4477999999999999998876

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.87  E-value=0.013  Score=52.69  Aligned_cols=24  Identities=38%  Similarity=0.555  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-|.|+|+.|+|||||++.+..+.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            347899999999999999998876

>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=93.86  E-value=0.014  Score=52.86  Aligned_cols=23  Identities=39%  Similarity=0.538  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|+|+.|+|||||++.+....
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            36799999999999999998876

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=93.78  E-value=0.028  Score=56.18  Aligned_cols=45  Identities=16%  Similarity=0.132  Sum_probs=32.5

Q ss_pred             cchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          158 VGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       158 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|-+..+-+..+.+..+.+..+.+.++|++|+|||++|..+++..
T Consensus       134 ~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~  178 (362)
T d1svma_         134 PKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELC  178 (362)
T ss_dssp             TTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHHHc
Confidence            344444434444444454466799999999999999999999987

>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=93.78  E-value=0.017  Score=51.83  Aligned_cols=24  Identities=25%  Similarity=0.477  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|.|+|++|+|||||++.+..+.
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            688999999999999999998765

>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=93.75  E-value=0.099  Score=49.78  Aligned_cols=41  Identities=22%  Similarity=0.191  Sum_probs=28.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHHhhhccccCCC-CEEEEEEe
Q 004021          176 KNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNF-DVVIWAAV  217 (779)
Q Consensus       176 ~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F-~~~~wv~v  217 (779)
                      ..+-+|||.|..|+||||||..+.... ..+..+ ..++-++.
T Consensus        25 ~~P~iIGi~G~qGSGKSTl~~~l~~~L-~~~~~~~~~v~~iS~   66 (286)
T d1odfa_          25 KCPLFIFFSGPQGSGKSFTSIQIYNHL-MEKYGGEKSIGYASI   66 (286)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHH-HHHHGGGSCEEEEEG
T ss_pred             CCCEEEEeECCCCCCHHHHHHHHHHHH-HHHhCCCcceEeecc
Confidence            345699999999999999999887765 211112 34556666

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=93.75  E-value=0.015  Score=56.53  Aligned_cols=36  Identities=22%  Similarity=0.402  Sum_probs=26.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +.|+|.|-||+||||+|..++....  +... .++-|..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~LA--~~G~-rVLlID~   38 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAALA--EMGK-KVMIVGC   38 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHH--HTTC-CEEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHH--HCCC-CEEEEec
Confidence            6788999999999999998887763  2222 2555555

>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=93.74  E-value=0.0066  Score=53.66  Aligned_cols=63  Identities=19%  Similarity=0.212  Sum_probs=34.5

Q ss_pred             cchhhcccccCceeeecCCcccc-----cchhhccCccCcEeeccCCcCCC-----CCchhhhcCCccCcEeeec
Q 004021          528 LPSRISSLVSLHHLDLSLTHIRG-----LPQELKALEKLRYLNLEYTHYLS-----IIPHQLISGFLKLEVLRLL  592 (779)
Q Consensus       528 lp~~i~~L~~L~~L~L~~~~i~~-----lp~~~~~L~~L~~L~l~~~~~l~-----~lp~~~i~~L~~L~~L~l~  592 (779)
                      +-..+...++|+.|+|++|.+..     +-..+...++|+.|++++|. +.     .+... +...++|+.+++.
T Consensus        38 l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~-~~~~g~~~l~~~-l~~~~~L~~l~L~  110 (166)
T d1io0a_          38 CAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNF-ISGSGILALVEA-LQSNTSLIELRID  110 (166)
T ss_dssp             HHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSC-CCHHHHHHHHHG-GGGCSSCCEEECC
T ss_pred             HHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhcccc-ccchhHHHHHHH-HHhCccccEEeec
Confidence            34445566677777777776543     33345556667777776662 22     12222 4455666665554

>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=93.73  E-value=0.015  Score=51.84  Aligned_cols=23  Identities=26%  Similarity=0.250  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|.|.|++|+||||+|+.++.+.
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36789999999999999998876

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=93.69  E-value=0.11  Score=48.08  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=22.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||.+.+..-.
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHcCc
Confidence            4699999999999999999997643

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.60  E-value=0.019  Score=55.86  Aligned_cols=26  Identities=27%  Similarity=0.303  Sum_probs=23.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.+.|-||+||||+|..++...
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~l   32 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRL   32 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHH
Confidence            57899999999999999999988777

>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=93.54  E-value=0.18  Score=46.74  Aligned_cols=26  Identities=38%  Similarity=0.589  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|+.|.|||||.+.+..-.
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34799999999999999999987654

>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=93.39  E-value=0.019  Score=50.56  Aligned_cols=87  Identities=15%  Similarity=0.053  Sum_probs=58.9

Q ss_pred             hcccccCceeeecCC-cccc-----cchhhccCccCcEeeccCCcCCCC-----CchhhhcCCccCcEeeeccccCCCcc
Q 004021          532 ISSLVSLHHLDLSLT-HIRG-----LPQELKALEKLRYLNLEYTHYLSI-----IPHQLISGFLKLEVLRLLECGSEGVT  600 (779)
Q Consensus       532 i~~L~~L~~L~L~~~-~i~~-----lp~~~~~L~~L~~L~l~~~~~l~~-----lp~~~i~~L~~L~~L~l~~~~~~~~~  600 (779)
                      ..+.+.|++|+|+++ .++.     +-..+...++|++|++++| .++.     +-.. +...++|+.|++.+|.+..  
T Consensus        13 ~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n-~l~~~~~~~L~~~-l~~~~~l~~l~l~~~~~~~--   88 (166)
T d1io0a_          13 QNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGT-RSNDPVAFALAEM-LKVNNTLKSLNVESNFISG--   88 (166)
T ss_dssp             HTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTS-CCCHHHHHHHHHH-HHHCSSCCEEECCSSCCCH--
T ss_pred             HhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCC-cccHHHHHHHHHH-Hhhcccchhhhhccccccc--
Confidence            356789999999874 4532     4455778889999999999 4432     2222 5667889999998887653  


Q ss_pred             cccCCccCCCchhhHHhhcCCCCCCceeEE
Q 004021          601 KEEGNVLCDDAEPLMRELLGLKRLNVLSWS  630 (779)
Q Consensus       601 ~~~~~~~~~~~~~~~~~l~~L~~L~~L~l~  630 (779)
                              +........+...++|+.+++.
T Consensus        89 --------~g~~~l~~~l~~~~~L~~l~L~  110 (166)
T d1io0a_          89 --------SGILALVEALQSNTSLIELRID  110 (166)
T ss_dssp             --------HHHHHHHHGGGGCSSCCEEECC
T ss_pred             --------hhHHHHHHHHHhCccccEEeec
Confidence                    1012344566777788876665

>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=93.39  E-value=0.022  Score=50.78  Aligned_cols=25  Identities=24%  Similarity=0.420  Sum_probs=22.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|.|+|+.|+|||||++.+..+.
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            3679999999999999999988765

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=93.37  E-value=0.029  Score=52.90  Aligned_cols=47  Identities=15%  Similarity=0.140  Sum_probs=37.2

Q ss_pred             cccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          156 TIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       156 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|||....++++.+.+..-.....-|.|.|..|+|||++|+.+.+.-
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s   47 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLS   47 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc
Confidence            37899999999998887643233446899999999999999997654

>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=93.29  E-value=0.016  Score=57.72  Aligned_cols=44  Identities=27%  Similarity=0.408  Sum_probs=32.8

Q ss_pred             ccccchhhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHh
Q 004021          155 QTIVGQEKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      +.++|.+..+..+.-.....  ...-|-+.|.+|+||||||+.+..
T Consensus         7 ~~I~Gq~~~kral~laa~~~--~~h~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHhcc--CCCeEEEECCCCccHHHHHHHHHH
Confidence            56899998777665444322  123478999999999999999875

>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=93.19  E-value=0.019  Score=52.13  Aligned_cols=26  Identities=27%  Similarity=0.202  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+-+|+|-|.-|+||||+|+.+.+..
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999987655

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.95  E-value=0.033  Score=51.89  Aligned_cols=36  Identities=25%  Similarity=0.268  Sum_probs=27.7

Q ss_pred             eEEEEE-cCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLY-GIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~-G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++|+|+ |-||+||||+|..++....   ..-..++.|..
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la---~~g~~VlliD~   38 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALA---QLGHDVTIVDA   38 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHH---HTTCCEEEEEC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHH---hCCCCEEEEeC
Confidence            788888 7899999999999988773   22234667766

>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=92.95  E-value=0.035  Score=54.38  Aligned_cols=48  Identities=29%  Similarity=0.436  Sum_probs=37.7

Q ss_pred             ccccchhhhHHHHHHHHhc-------cCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD-------QQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..++|.++.++.+.+.+..       ++....++.++|+.|+|||.+|+.+++..
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            4579999999988887642       12234478899999999999999998765

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=92.50  E-value=0.045  Score=54.63  Aligned_cols=49  Identities=20%  Similarity=0.312  Sum_probs=36.8

Q ss_pred             cccccchhhhHHHHHHHHh----------------------------ccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          154 EQTIVGQEKLLPRVWRCIT----------------------------DQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       154 ~~~~vGr~~~~~~l~~~L~----------------------------~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+||.++.++.+..++.                            +.+....-+-.+|+.|+|||.||+.++...
T Consensus        16 ~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          16 DNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhc
Confidence            3568999999888776552                            112244568888999999999999998654

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=92.44  E-value=0.05  Score=50.94  Aligned_cols=23  Identities=35%  Similarity=0.527  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ||+|.|..|+|||||..++.+..
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            78999999999999999987655

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=92.41  E-value=0.037  Score=50.12  Aligned_cols=25  Identities=36%  Similarity=0.680  Sum_probs=22.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||.+.++.-.
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhccc
Confidence            4689999999999999999998765

>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=92.02  E-value=0.023  Score=54.32  Aligned_cols=26  Identities=27%  Similarity=0.491  Sum_probs=20.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+||+|.|..|+||||+|+.+.+..
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~   28 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIF   28 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHH
Confidence            45799999999999999999987766

>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=91.88  E-value=0.042  Score=47.48  Aligned_cols=22  Identities=32%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.|+|.+|+|||||...+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            6799999999999999987553

>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=91.85  E-value=0.067  Score=49.43  Aligned_cols=34  Identities=18%  Similarity=0.156  Sum_probs=26.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEE
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAA  216 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~  216 (779)
                      .+++|+|+.|.|||||.+.++.-.    ..-.+.+|+.
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~----~p~~G~I~~~   58 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV----KPDRGEVRLN   58 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS----CCSEEEEEET
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC----CCCceEEEEC
Confidence            478999999999999999998865    2335666653

>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=91.76  E-value=0.059  Score=49.63  Aligned_cols=35  Identities=17%  Similarity=0.300  Sum_probs=26.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEE
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWA  215 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv  215 (779)
                      .-.+++|+|..|+|||||.+.++.-.    ..-.+.+++
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl~----~p~sG~I~~   64 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCLD----KPTEGEVYI   64 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS----CCSEEEEEE
T ss_pred             CCCEEEEECCCCCCcchhhHhccCCC----CCCcceeEE
Confidence            34699999999999999999887654    223455555

>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=91.73  E-value=0.045  Score=50.81  Aligned_cols=25  Identities=32%  Similarity=0.371  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||++.++.-.
T Consensus        29 Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          29 GEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCC
Confidence            4699999999999999999998755

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=91.73  E-value=0.049  Score=49.10  Aligned_cols=25  Identities=28%  Similarity=0.405  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .++.|+|+|.+|+|||||...+.+.
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcCC
Confidence            5678999999999999999999864

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=91.72  E-value=0.055  Score=47.97  Aligned_cols=34  Identities=26%  Similarity=0.417  Sum_probs=23.7

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      +.+.+.-.+... -|.++|.+|+|||||..++...
T Consensus         3 ~~~~~~~~~k~~-kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_           3 VLQFLGLYKKTG-KLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             HHHHHTCTTCCE-EEEEEEETTSSHHHHHHHHSCC
T ss_pred             hHHhccccCCCC-EEEEECCCCCCHHHHHHHHhCC
Confidence            344444444344 4779999999999999887543

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.70  E-value=0.047  Score=51.18  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=23.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++.|+|=|+-|+||||+++.+.+..
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            5799999999999999999998876

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.65  E-value=0.13  Score=47.81  Aligned_cols=48  Identities=13%  Similarity=0.137  Sum_probs=32.0

Q ss_pred             HHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccC----CCCEEEEEEe
Q 004021          169 RCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQH----NFDVVIWAAV  217 (779)
Q Consensus       169 ~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~----~F~~~~wv~v  217 (779)
                      +.|..+=..-+++-|.|.+|+||||||.++.... ....    .-...+|++.
T Consensus        25 ~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~-~~~~~~~~~~~~~~~i~~   76 (251)
T d1szpa2          25 TLLGGGVETGSITELFGEFRTGKSQLCHTLAVTC-QIPLDIGGGEGKCLYIDT   76 (251)
T ss_dssp             HHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTT-TSCTTTTCCSCEEEEEES
T ss_pred             hhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHh-hhhhhhccCCceEEEEee
Confidence            3343332345799999999999999999887654 1111    1246777776

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.63  E-value=0.067  Score=50.17  Aligned_cols=26  Identities=27%  Similarity=0.437  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.+..-.
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhccc
Confidence            34799999999999999999997755

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.61  E-value=0.069  Score=48.59  Aligned_cols=23  Identities=35%  Similarity=0.787  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .|+|-|+-|+||||+++.+.+..
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l   24 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAF   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            58999999999999999998876

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=91.60  E-value=0.049  Score=49.57  Aligned_cols=24  Identities=17%  Similarity=0.277  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+|.|+|+.|+|||||.+.+..+.
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            688999999999999999998765

>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=91.53  E-value=0.047  Score=47.59  Aligned_cols=23  Identities=35%  Similarity=0.494  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|+|+|.+|+|||||...+.++.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37899999999999999987654

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.44  E-value=0.073  Score=50.01  Aligned_cols=25  Identities=24%  Similarity=0.452  Sum_probs=22.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||++.+..-.
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhccc
Confidence            4689999999999999999997654

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.41  E-value=0.065  Score=49.87  Aligned_cols=36  Identities=28%  Similarity=0.360  Sum_probs=26.9

Q ss_pred             eEEEEE-cCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLY-GIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~-G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++|+|+ +-||+||||+|..++....  +... .++-+..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la--~~g~-~VlliD~   39 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALG--DRGR-KVLAVDG   39 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHH--HTTC-CEEEEEC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHH--hCCC-CEEEEeC
Confidence            789999 5699999999999988773  2222 4556654

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.39  E-value=0.071  Score=48.64  Aligned_cols=25  Identities=24%  Similarity=0.397  Sum_probs=22.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ...|+|-|+-|+||||+|+.+.+..
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L   27 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEAL   27 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHH
Confidence            3689999999999999999999887

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=91.30  E-value=0.049  Score=49.75  Aligned_cols=20  Identities=35%  Similarity=0.401  Sum_probs=18.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQV  198 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v  198 (779)
                      -+|+|+|+.|+||||.|+.+
T Consensus         4 ~iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           4 YIVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEEECCTTSCHHHHHHHH
T ss_pred             EEEEEECCCcCCHHHHHHHH
Confidence            38999999999999999865

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=91.28  E-value=0.05  Score=50.70  Aligned_cols=25  Identities=36%  Similarity=0.640  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -..|+|+|..|.|||||++.+..-.
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcC
Confidence            4689999999999999999997755

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.26  E-value=0.06  Score=49.61  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=22.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.++.-.
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34699999999999999999997754

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=91.19  E-value=0.069  Score=47.07  Aligned_cols=23  Identities=48%  Similarity=0.572  Sum_probs=19.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      ---|.|+|.+|+|||||...+..
T Consensus        16 ~~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          16 EVRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEEECCCCCCHHHHHHHHhc
Confidence            34578999999999999988754

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=91.18  E-value=0.045  Score=50.82  Aligned_cols=25  Identities=40%  Similarity=0.535  Sum_probs=22.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|+|||||++.++.-.
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCc
Confidence            4699999999999999999997654

>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=91.04  E-value=0.048  Score=51.42  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=22.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||++.+..-.
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            34699999999999999999997644

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.92  E-value=0.058  Score=47.01  Aligned_cols=22  Identities=32%  Similarity=0.271  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988764

>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=90.92  E-value=0.065  Score=49.99  Aligned_cols=26  Identities=27%  Similarity=0.487  Sum_probs=22.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|.|||||++.+..-.
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34799999999999999999987654

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.79  E-value=0.065  Score=51.22  Aligned_cols=26  Identities=27%  Similarity=0.478  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||++.+..-.
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            34789999999999999999998755

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.71  E-value=0.062  Score=47.30  Aligned_cols=22  Identities=36%  Similarity=0.448  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3679999999999999987654

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=90.67  E-value=0.18  Score=43.05  Aligned_cols=26  Identities=31%  Similarity=0.321  Sum_probs=23.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..-+|.+.|-=|+||||+++.+++..
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhc
Confidence            44689999999999999999999876

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.66  E-value=0.078  Score=48.58  Aligned_cols=26  Identities=19%  Similarity=0.275  Sum_probs=22.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.++.|.|.+|+|||+||.+++.+.
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            44799999999999999999987665

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.63  E-value=0.04  Score=51.54  Aligned_cols=25  Identities=20%  Similarity=0.199  Sum_probs=22.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+.|+|-|+-|+||||+|+.+.+..
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~l   26 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQLC   26 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGGC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4789999999999999999987765

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.59  E-value=0.065  Score=46.77  Aligned_cols=22  Identities=36%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999888754

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.53  E-value=1.4  Score=39.17  Aligned_cols=38  Identities=13%  Similarity=-0.030  Sum_probs=30.1

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++-+.+++..+  ....+.++|.+|+||||+|..+.+..
T Consensus         2 ~~~~l~~~i~~~--~~~~~l~~G~~g~gk~~~a~~l~~~i   39 (198)
T d2gnoa2           2 QLETLKRIIEKS--EGISILINGEDLSYPREVSLELPEYV   39 (198)
T ss_dssp             HHHHHHHHHHTC--SSEEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CCceEEEECCCCCCHHHHHHHHHHHH
Confidence            345555566555  67899999999999999999988765

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.52  E-value=0.085  Score=49.56  Aligned_cols=41  Identities=24%  Similarity=0.308  Sum_probs=29.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhcc---ccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCH---QQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~---~~~~F~~~~wv~v  217 (779)
                      .-+++.|.|.+|+||||+|.+++.....   ........+|+..
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~   78 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   78 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEec
Confidence            4579999999999999999998766511   0112345666666

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.46  E-value=0.068  Score=46.54  Aligned_cols=21  Identities=24%  Similarity=0.539  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999887653

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=90.46  E-value=0.066  Score=48.70  Aligned_cols=20  Identities=45%  Similarity=0.512  Sum_probs=18.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHH
Q 004021          179 GIIGLYGIGGVGKTTLLKQV  198 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v  198 (779)
                      -+|||.|..|+||||+|+.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            48999999999999999876

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=90.39  E-value=0.12  Score=45.41  Aligned_cols=33  Identities=36%  Similarity=0.650  Sum_probs=24.0

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ++..++...  .. -|.|+|.+|+|||||..++...
T Consensus         6 ~~~~~~~~k--~~-kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           6 RIWRLFNHQ--EH-KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHTTS--CE-EEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHhCCC--eE-EEEEECCCCCCHHHHHHHHhcC
Confidence            455455443  44 4679999999999999887654

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=90.24  E-value=0.057  Score=49.61  Aligned_cols=26  Identities=23%  Similarity=0.323  Sum_probs=22.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-.+++|+|..|+|||||.+.+..-.
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            34699999999999999999998754

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.05  E-value=0.074  Score=46.62  Aligned_cols=21  Identities=33%  Similarity=0.793  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |.|+|.+|+|||||...+.+.
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999887764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.02  E-value=0.075  Score=46.22  Aligned_cols=21  Identities=29%  Similarity=0.463  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |.|+|.+|+|||+|+..+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988754

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=89.99  E-value=0.064  Score=46.70  Aligned_cols=22  Identities=36%  Similarity=0.611  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3679999999999999987553

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=89.98  E-value=0.099  Score=50.67  Aligned_cols=24  Identities=29%  Similarity=0.577  Sum_probs=21.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++-++|.+|+|||.||++++...
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~  147 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEAL  147 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHHHh
Confidence            456678999999999999999986

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.96  E-value=0.079  Score=46.37  Aligned_cols=22  Identities=32%  Similarity=0.434  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||...+.+.
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987654

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.89  E-value=0.077  Score=46.54  Aligned_cols=22  Identities=41%  Similarity=0.602  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.87  E-value=0.079  Score=46.35  Aligned_cols=23  Identities=30%  Similarity=0.365  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|+|.+|+|||+|+..+.+..
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~~   25 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGVE   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC-
T ss_pred             EEEEECCCCcCHHHHHHHHhCCc
Confidence            37899999999999999876543

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=89.75  E-value=0.085  Score=46.24  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .|+|+|.+|+|||||..++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999998754

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.73  E-value=0.14  Score=48.08  Aligned_cols=49  Identities=14%  Similarity=0.066  Sum_probs=33.5

Q ss_pred             HHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhcc---ccCCCCEEEEEEe
Q 004021          169 RCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCH---QQHNFDVVIWAAV  217 (779)
Q Consensus       169 ~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~---~~~~F~~~~wv~v  217 (779)
                      +.|..+=..-+++.|.|.+|+|||++|.+++.....   ....+..+.|+..
T Consensus        28 ~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~   79 (258)
T d1v5wa_          28 KLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDT   79 (258)
T ss_dssp             HHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEES
T ss_pred             HhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEech
Confidence            344443335579999999999999999998865411   1234556777776

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.68  E-value=0.085  Score=46.02  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.|+|-+|+|||||...+.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36799999999999999987643

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.61  E-value=0.087  Score=45.97  Aligned_cols=22  Identities=41%  Similarity=0.522  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|-+|+|||+|+..+.+.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987653

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.61  E-value=0.1  Score=47.71  Aligned_cols=26  Identities=23%  Similarity=0.307  Sum_probs=23.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ..+.|+|-|+-|+||||+++.+.+..
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHH
Confidence            45789999999999999999999877

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.55  E-value=0.089  Score=46.06  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988754

>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=89.46  E-value=0.079  Score=49.29  Aligned_cols=25  Identities=36%  Similarity=0.506  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|+.|.|||||.+.+..-.
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            4699999999999999999997755

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.41  E-value=0.088  Score=45.85  Aligned_cols=22  Identities=41%  Similarity=0.510  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.34  E-value=0.093  Score=46.12  Aligned_cols=22  Identities=36%  Similarity=0.575  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            4789999999999999987654

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.29  E-value=0.095  Score=45.68  Aligned_cols=22  Identities=36%  Similarity=0.536  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|-+|+|||+|...+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=89.29  E-value=0.1  Score=45.98  Aligned_cols=24  Identities=33%  Similarity=0.552  Sum_probs=21.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ...|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999865

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.28  E-value=0.091  Score=46.17  Aligned_cols=22  Identities=32%  Similarity=0.419  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||+..+...
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987643

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.24  E-value=0.097  Score=45.74  Aligned_cols=22  Identities=27%  Similarity=0.585  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |.++|.+|+|||+|...+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5799999999999999987653

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=89.23  E-value=0.12  Score=48.34  Aligned_cols=36  Identities=19%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             HHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          167 VWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       167 l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |-+.|..+=..-.++.|.|.+|+|||++|..++...
T Consensus        23 LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          23 LDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             HHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             HHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            334443322244799999999999999999998765

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.22  E-value=0.092  Score=46.14  Aligned_cols=23  Identities=35%  Similarity=0.429  Sum_probs=19.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      --|.|+|.+|+|||+|+..+.+.
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            35779999999999999887754

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=89.09  E-value=0.086  Score=49.55  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=22.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -.+++|+|..|.|||||++.++.-.
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCCC
Confidence            3689999999999999999998765

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.06  E-value=0.11  Score=47.19  Aligned_cols=23  Identities=30%  Similarity=0.355  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      +.|+|+|.+|+|||||..++.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999988765

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.05  E-value=0.11  Score=45.79  Aligned_cols=24  Identities=38%  Similarity=0.584  Sum_probs=21.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ...|+|+|.+|+|||||..++.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999999864

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.05  E-value=0.093  Score=46.73  Aligned_cols=22  Identities=41%  Similarity=0.514  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            4779999999999999888754

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.00  E-value=0.098  Score=45.82  Aligned_cols=22  Identities=36%  Similarity=0.465  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999987654

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=88.94  E-value=0.11  Score=47.42  Aligned_cols=24  Identities=21%  Similarity=0.032  Sum_probs=21.4

Q ss_pred             eEEEEEcCC-CCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIG-GVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~g-GvGKTtLA~~v~~~~  202 (779)
                      +.+-|.|.| ||||||++..++...
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aL   26 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAA   26 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHH
Confidence            567899998 999999999998877

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.89  E-value=0.11  Score=45.38  Aligned_cols=22  Identities=36%  Similarity=0.534  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3789999999999999987654

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.88  E-value=0.11  Score=45.17  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=19.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .-|.|+|.+|+|||||...+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            46889999999999999987654

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.83  E-value=0.11  Score=45.77  Aligned_cols=22  Identities=41%  Similarity=0.611  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|..|+|||||+..+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987654

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.82  E-value=0.095  Score=48.24  Aligned_cols=26  Identities=38%  Similarity=0.465  Sum_probs=22.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++|..|.|.-|+|||||.+.+.+..
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhcC
Confidence            57899999999999999999987653

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=88.71  E-value=0.21  Score=46.96  Aligned_cols=42  Identities=21%  Similarity=0.306  Sum_probs=31.7

Q ss_pred             hhhHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          161 EKLLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       161 ~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +..+.++...+.+.....--|.++|..|+|||||...+..+.
T Consensus        15 ~~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~~   56 (257)
T d1h65a_          15 QTKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   56 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCCC
Confidence            355566667676654445568899999999999999998653

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=88.64  E-value=0.11  Score=46.11  Aligned_cols=22  Identities=36%  Similarity=0.493  Sum_probs=18.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      --|.++|.+|+|||||...+.+
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3466999999999999988744

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=88.63  E-value=0.15  Score=52.05  Aligned_cols=48  Identities=25%  Similarity=0.308  Sum_probs=36.6

Q ss_pred             ccccchhhhHHHHHHHHhc--------c----CCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          155 QTIVGQEKLLPRVWRCITD--------Q----QKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       155 ~~~vGr~~~~~~l~~~L~~--------~----~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++||.++.++.+--.+.+        +    +-..+=|-++|+.|+|||.||+.++...
T Consensus        14 ~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l   73 (443)
T d1g41a_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA   73 (443)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999988887776632        1    1113358899999999999999999865

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.46  E-value=0.11  Score=45.13  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|-+|+|||||...+.+.
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999988764

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=88.42  E-value=0.13  Score=48.04  Aligned_cols=24  Identities=29%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      ++|+|.|..|+||||+|+.+....
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999987654

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.41  E-value=0.12  Score=44.46  Aligned_cols=22  Identities=36%  Similarity=0.596  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|+++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999887664

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=88.40  E-value=0.13  Score=46.72  Aligned_cols=24  Identities=33%  Similarity=0.412  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +.|+|-|+.|+||||+++.+.+..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            578999999999999999998876

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=88.33  E-value=0.25  Score=46.91  Aligned_cols=24  Identities=29%  Similarity=0.404  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .++.|+|.+|+||||||.+++...
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHH
Confidence            578899999999999998887665

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.31  E-value=0.12  Score=45.09  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|..|+|||+|...+.+.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999987654

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.23  E-value=0.084  Score=46.73  Aligned_cols=21  Identities=33%  Similarity=0.631  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999998653

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.19  E-value=0.12  Score=45.72  Aligned_cols=22  Identities=41%  Similarity=0.442  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5889999999999999887654

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.16  E-value=0.12  Score=45.50  Aligned_cols=22  Identities=32%  Similarity=0.409  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999887654

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.99  E-value=0.12  Score=46.29  Aligned_cols=22  Identities=36%  Similarity=0.567  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            4789999999999999988754

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=87.82  E-value=0.099  Score=48.36  Aligned_cols=24  Identities=38%  Similarity=0.556  Sum_probs=21.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~Gl   48 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAGM   48 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            469999999999999999998763

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=87.77  E-value=0.12  Score=45.74  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|+|+|.+|+|||||..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998864

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.77  E-value=0.15  Score=46.26  Aligned_cols=24  Identities=21%  Similarity=0.254  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-|+|+|.+|+|||||..++....
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999998887643

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.73  E-value=0.14  Score=44.70  Aligned_cols=22  Identities=41%  Similarity=0.557  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999987654

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=87.71  E-value=0.092  Score=49.24  Aligned_cols=26  Identities=23%  Similarity=0.514  Sum_probs=22.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-..++|+|..|+|||||++.+..-.
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            34689999999999999998876644

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.71  E-value=0.13  Score=45.67  Aligned_cols=22  Identities=41%  Similarity=0.466  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4789999999999999887654

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=87.70  E-value=0.14  Score=45.60  Aligned_cols=23  Identities=35%  Similarity=0.463  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|-+|+|||+|...+....
T Consensus         4 KivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            36799999999999998876543

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=87.58  E-value=0.15  Score=44.27  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||...+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3668999999999999887654

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=87.33  E-value=0.15  Score=45.17  Aligned_cols=22  Identities=41%  Similarity=0.575  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988753

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.31  E-value=0.14  Score=44.79  Aligned_cols=22  Identities=36%  Similarity=0.412  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|.+|+|||+|+..+...
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988653

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.24  E-value=0.15  Score=44.78  Aligned_cols=21  Identities=38%  Similarity=0.654  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~  201 (779)
                      |.++|.+|+|||||...+.+.
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987654

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=87.12  E-value=0.16  Score=44.25  Aligned_cols=23  Identities=35%  Similarity=0.466  Sum_probs=19.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      --|.|+|-+|+|||||+..+.+.
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45789999999999999987653

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.05  E-value=0.14  Score=45.85  Aligned_cols=19  Identities=53%  Similarity=0.691  Sum_probs=17.3

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 004021          180 IIGLYGIGGVGKTTLLKQV  198 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v  198 (779)
                      -|.|+|.+|+|||||...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4679999999999999987

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=86.93  E-value=0.12  Score=45.88  Aligned_cols=22  Identities=45%  Similarity=0.665  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|+|+|.+|+|||||..++.+.
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEEE
T ss_pred             eEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999887543

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.73  E-value=0.17  Score=44.31  Aligned_cols=22  Identities=41%  Similarity=0.649  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|-+|+|||||+..+.+.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999877653

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.61  E-value=0.17  Score=44.67  Aligned_cols=23  Identities=30%  Similarity=0.342  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|..|+|||+|+..+.+..
T Consensus         4 KivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36799999999999999887643

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=86.59  E-value=0.17  Score=43.59  Aligned_cols=22  Identities=23%  Similarity=0.380  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|+|+|.+|+|||||..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999998754

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.54  E-value=0.18  Score=43.97  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|-.|+|||||...+.++.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36788999999999999987643

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.30  E-value=0.19  Score=44.17  Aligned_cols=23  Identities=22%  Similarity=0.393  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|.+|+|||||...+.+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            57899999999999999876643

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=86.27  E-value=0.61  Score=45.95  Aligned_cols=39  Identities=23%  Similarity=0.170  Sum_probs=25.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++..|.|.+|.||||++..+.....+....-...+.++.
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~A  202 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAA  202 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEB
T ss_pred             CeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEec
Confidence            689999999999999987655433111222234566666

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=86.20  E-value=0.18  Score=44.58  Aligned_cols=23  Identities=30%  Similarity=0.447  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|+|+|..|+|||||..++.+..
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~~   32 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNKE   32 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTST
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
Confidence            47999999999999999887643

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.11  E-value=0.18  Score=45.03  Aligned_cols=23  Identities=35%  Similarity=0.462  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      -|.++|.+|+|||+|...+....
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            36799999999999999885543

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.04  E-value=0.31  Score=44.24  Aligned_cols=35  Identities=26%  Similarity=0.464  Sum_probs=26.7

Q ss_pred             hHHHHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          163 LLPRVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       163 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .+++|.++|. +    +...++|..|+|||||..++..+.
T Consensus        85 g~~~L~~~l~-~----kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          85 GIEELKEYLK-G----KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             THHHHHHHHS-S----SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             hHhhHHHHhc-C----CeEEEECCCCCCHHHHHHhhcchh
Confidence            3566666663 2    577899999999999999886543

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.02  E-value=0.1  Score=45.73  Aligned_cols=22  Identities=41%  Similarity=0.539  Sum_probs=17.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.|+|.+|+|||+|...+.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4788999999999999776543

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.82  E-value=0.19  Score=44.77  Aligned_cols=22  Identities=41%  Similarity=0.442  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHhh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      -|.++|-+|+|||+|+..+.+.
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999887654

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=85.55  E-value=0.22  Score=45.86  Aligned_cols=39  Identities=18%  Similarity=0.020  Sum_probs=27.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      .-.++.|.|.+|+|||+||.+++....  ...-..++|++.
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~--~~~~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGI--IEFDEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH--HHHCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH--HhcCCCcccccc
Confidence            457999999999999999987654321  122224667776

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=85.33  E-value=0.23  Score=43.36  Aligned_cols=24  Identities=29%  Similarity=0.441  Sum_probs=19.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      ..+ |.++|.+|+|||||...+.+.
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            455 669999999999999987654

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=85.08  E-value=0.16  Score=44.88  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=20.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHHh
Q 004021          177 NRGIIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       177 ~~~vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      ....|+|+|.+++|||||..++..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            457799999999999999987744

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=84.95  E-value=0.25  Score=42.99  Aligned_cols=23  Identities=22%  Similarity=0.187  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      +-|.|.|.+|+||||+|.++..+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            56889999999999999887654

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.75  E-value=0.15  Score=44.76  Aligned_cols=21  Identities=38%  Similarity=0.485  Sum_probs=8.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHh
Q 004021          180 IIGLYGIGGVGKTTLLKQVNN  200 (779)
Q Consensus       180 vi~I~G~gGvGKTtLA~~v~~  200 (779)
                      -|.|+|-+|+|||||...+.+
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999987654

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=84.54  E-value=0.56  Score=44.37  Aligned_cols=38  Identities=21%  Similarity=0.203  Sum_probs=27.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      -.++.|.|.+|+||||+|.+++.+. .....+ .+++++.
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~-a~~~g~-~v~~~s~   72 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQW-GTAMGK-KVGLAML   72 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHH-HHTSCC-CEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhh-hhhccc-ceeEeee
Confidence            3688999999999999999988664 222233 4666676

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=84.05  E-value=0.26  Score=45.10  Aligned_cols=23  Identities=35%  Similarity=0.430  Sum_probs=19.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .-|.++|.+|+|||||...+...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999887543

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=83.59  E-value=0.29  Score=42.61  Aligned_cols=23  Identities=26%  Similarity=0.265  Sum_probs=19.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .-|.|.|.+|+||||+|..+..+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45789999999999999887654

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=82.94  E-value=0.33  Score=41.93  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          179 GIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       179 ~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      .-|.|.|.+|+||||+|.++..+-
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~g   39 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKRG   39 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHcC
Confidence            568899999999999998876653

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=82.53  E-value=0.58  Score=45.39  Aligned_cols=25  Identities=28%  Similarity=0.234  Sum_probs=22.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      +-.|.|=|.-|+||||+++.+.+..
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHh
Confidence            4567888999999999999999887

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.24  E-value=0.11  Score=44.75  Aligned_cols=22  Identities=36%  Similarity=0.466  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHhhh
Q 004021          181 IGLYGIGGVGKTTLLKQVNNNF  202 (779)
Q Consensus       181 i~I~G~gGvGKTtLA~~v~~~~  202 (779)
                      |+++|.+|+|||||..++....
T Consensus         3 I~liG~~n~GKSSLin~l~g~~   24 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNED   24 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999987653

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=81.29  E-value=1.3  Score=41.36  Aligned_cols=49  Identities=33%  Similarity=0.491  Sum_probs=33.9

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      +.++.+..=. .-+.++|.|..|+|||+|+..+.+.. . +.+=+.++++-+
T Consensus        57 raID~l~pig-kGQr~~If~~~g~GKt~l~~~i~~~~-~-~~~~~v~V~~~i  105 (276)
T d2jdid3          57 KVVDLLAPYA-KGGKIGLFGGAGVGKTVLIMELINNV-A-KAHGGYSVFAGV  105 (276)
T ss_dssp             HHHHHHSCEE-TTCEEEEEECTTSSHHHHHHHHHHHH-T-TTCSSEEEEEEE
T ss_pred             eeeeeecccc-CCCEEEeeCCCCCCHHHHHHHHHHHH-H-hhCCCeEEEEEe
Confidence            4555554311 23569999999999999999998774 1 344566777766

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=80.53  E-value=0.79  Score=43.16  Aligned_cols=49  Identities=18%  Similarity=0.143  Sum_probs=33.5

Q ss_pred             HHHHHHhccCCCceEEEEEcCCCCcHHHHHHHHHhhhccccCCCCEEEEEEe
Q 004021          166 RVWRCITDQQKNRGIIGLYGIGGVGKTTLLKQVNNNFCHQQHNFDVVIWAAV  217 (779)
Q Consensus       166 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLA~~v~~~~~~~~~~F~~~~wv~v  217 (779)
                      ++++.+..=. .-+.++|.|..|+|||+|+..+.+.. . ..+-++++.+.+
T Consensus        32 r~ID~l~Pig-rGQr~~I~g~~g~GKT~l~~~i~~~~-~-~~~~~~v~~~~~   80 (289)
T d1xpua3          32 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQSI-A-YNHPDCVLMVLL   80 (289)
T ss_dssp             HHHHHHSCCB-TTCEEEEEECSSSSHHHHHHHHHHHH-H-HHCTTSEEEEEE
T ss_pred             eeeeeccccc-CCCeeeEeCCCCCCHHHHHHHHHHHH-h-hcCCCeEEEEEe
Confidence            5677665421 34688999999999999999998866 2 234444444433

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=80.09  E-value=0.5  Score=43.24  Aligned_cols=24  Identities=33%  Similarity=0.499  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHHhh
Q 004021          178 RGIIGLYGIGGVGKTTLLKQVNNN  201 (779)
Q Consensus       178 ~~vi~I~G~gGvGKTtLA~~v~~~  201 (779)
                      .++|+|+|-.++|||||+.++...
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhh
Confidence            367999999999999999888654