Citrus Sinensis ID: 004895

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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----
Protein Sequence
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLGNR
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHccccHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccEEEEEccccccHHHHHHHHHHcccccccccEEEEEEEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHcccEEEEEEEccccccccccccccccccccccccccccccEEEEEEccccHHccccccccEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccccccccHHHHcccccccHHHHHHHHHHHcccccccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccEEEcHHHHHHHHHHHHHccEEEcccccccHHHHHHccccccEEEEcccccccccccccccccEEEEEEEccccccccccHHHHcccccEEEEEccccccccccccccccccccccccccccccccccccccccccEEcccccccccccHHHcccccccEEcccccccccccccccccccccccEEEccccccccccccccccccHHHHcccccccEEEEEEccccccHHHHccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcccccEEccccccccccccccccccccccccccHHHHHHHHHHHcccccEEEEEEccccccHHHHHHHHHccHHHHccccEEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccEEEEEEEccccHccHHHcccccccHccccccccccccEEEEEEccHHHHHHHcccccccEcccccHHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHHHccccHccccccccccHHHHccHHHccHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEHHHHHHHHHHHHHccccEEEEEccccccccccccccccEEEEEEcccccccccccccccccEEEEEcccccccccccHHHHHHcccEEEEEccccccccccccccccHcccEEEccccccccccccccccccEEEEEcccccHHccHHHHccccccEEEcccccccccccccHccccHHccEEEEEccccccccccccccccHHHHHccHHHcccccccccHHHHHHccccccc
Coil and Loop (DISEMBL)
MAEVCLAIFSSIVSegtktlsepiiGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIindedevrkpcfkglspnlmsRYKLSKRAVEDAKYAEHLLATGSLLIvsnvshppppkmrefgdmkdynifnSRKKIFQDVIEALKDdklniigvcgmggvgkTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAsdlgmnfdsndLIYHRAKQLCQRLKKEKRVLIILDNIWtkleldkigipygdvdekdknddprrctIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVgestkasdfrplAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNlreihgmdadvyspiklsyDFLDDEAKSLFLLCglhregrpiHVHYLLRYVMGLrydkglglfrNVYTLEAARNRVDALIDNLKASCLLldgdaedeaklHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIqkgpiaislpyrdiqelperlecpqlKLFLLFAKYDSTLQISDHFFegteelkvldftgirfsplpsslgrLINLQTLcldgwrleDIAIVGQLKKLEILSLRGaeikqlplqigqltrlqlldlsncsslvviapnVISKLSRLeelymgdsfsqwdkveggsnaslaelkglsklttleiDVRDAEMLRRIWSLGNR
Flexible Loop (DISEMBL)
MAEVCLAIFSSIvsegtktlsepiigRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHiindedevrkPCFKglspnlmsRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILdniwtkleldkigipygdvdekdknddprrctiiltsrsrdllcIDMNSQKMFWIDALSEEEALQLFEKIVgestkasdfrPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAAsiaeeklmfSIPNVVDFEREMEETiqkgpiaislPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASlaelkglsklttleidvrdaEMLRRIWSLGNR
Low Complexity Region (SEG)
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLGNR
Disordered region (IsUnstruct)
***VCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNV***********GDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN****KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVD********RRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS****
Disordered Region (DISOPRED)
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLAT*******************************RKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM****************QRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSS******GMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVV*FEREM*ETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLG**
Disordered Region (DISEMBL)
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLGNR
Disordered Region (DISPRO)
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVS********************IFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYxxxxxxxxxxxxxxxxxxxxxxxxxxxxGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLGNR
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	724	2.2.26 [Sep-21-2011]
Q9T048	985	Disease resistance protei	yes	no	0.725	0.532	0.316	1e-60
O81825	919	Probable disease resistan	no	no	0.696	0.548	0.310	6e-56
Q42484	909	Disease resistance protei	no	no	0.703	0.559	0.303	2e-53
O82484	892	Putative disease resistan	no	no	0.806	0.654	0.287	7e-45
P60838	894	Probable disease resistan	no	no	0.821	0.665	0.291	2e-44
O64789	925	Probable disease resistan	no	no	0.812	0.635	0.279	8e-44
Q940K0	889	Probable disease resistan	no	no	0.810	0.660	0.286	4e-41
Q8RXS5	888	Probable disease resistan	no	no	0.790	0.644	0.285	1e-40
Q9LVT4	843	Probable disease resistan	no	no	0.682	0.586	0.282	3e-40
Q9LMP6	851	Probable disease resistan	no	no	0.631	0.537	0.287	5e-40

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

 Score =  235 bits (599), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 179/566 (31%), Positives = 293/566 (51%), Gaps = 41/566 (7%)

Query: 174 EALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV---FDKVVMAEITKNPDAQKIQG 230
           + L  +K   IGV GMGGVGKTTLV+ +  ++ E+     F  V+   ++K  D +++Q 
Sbjct: 157 DGLTSEKAQKIGVWGMGGVGKTTLVRTLNNKLREEGATQPFGLVIFVIVSKEFDPREVQK 216

Query: 231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKD 290
           ++A  L ++    +     A+++   L KE++ L+ILD++W  ++LD +GIP  + ++  
Sbjct: 217 QIAERLDIDTQMEESEEKLARRIYVGLMKERKFLLILDDVWKPIDLDLLGIPRTEENKGS 276

Query: 291 KNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPL 350
           K        +ILTSR  ++ C  M +     +D L EE+A +LF K  G+  ++   R +
Sbjct: 277 K--------VILTSRFLEV-CRSMKTDLDVRVDCLLEEDAWELFCKNAGDVVRSDHVRKI 327

Query: 351 AEEIVGKCGGLPVALSTVANALKNKSPA-IWKDALNKLTSSNLREIHGMDADVYSPIKLS 409
           A+ +  +CGGLP+A+ TV  A++ K    +W   L+KL+ S +  I  ++  ++ P+KLS
Sbjct: 328 AKAVSQECGGLPLAIITVGTAMRGKKNVKLWNHVLSKLSKS-VPWIKSIEEKIFQPLKLS 386

Query: 410 YDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDA 469
           YDFL+D+AK  FLLC L  E   I V  ++RY M   + + LG      + E + N    
Sbjct: 387 YDFLEDKAKFCFLLCALFPEDYSIEVTEVVRYWMAEGFMEELG------SQEDSMNEGIT 440

Query: 470 LIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIA------EEKLMFSIPNVVDFEREMEE 523
            +++LK  CLL DGD  D  K+HDV+   A  I          L+ S   + D     ++
Sbjct: 441 TVESLKDYCLLEDGDRRDTVKMHDVVRDFAIWIMSSSQDDSHSLVMSGTGLQDIR---QD 497

Query: 524 TIQKGPIAISLPYRDIQELPERLE--CPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLD 581
            +      +SL    ++ LP+ +E  C +  + LL   +    ++   F +    L++L+
Sbjct: 498 KLAPSLRRVSLMNNKLESLPDLVEEFCVKTSVLLLQGNF-LLKEVPIGFLQAFPTLRILN 556

Query: 582 FTGIRFSPLPS-SLGRLINLQTLCL-DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQI 639
            +G R    PS SL RL +L +L L D ++L  +  +  L KLE+L L G  I + P  +
Sbjct: 557 LSGTRIKSFPSCSLLRLFSLHSLFLRDCFKLVKLPSLETLAKLELLDLCGTHILEFPRGL 616

Query: 640 GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGS---NASLAEL 696
            +L R + LDLS    L  I   V+S+LS LE L M  S  +W  V+G +    A++ E+
Sbjct: 617 EELKRFRHLDLSRTLHLESIPARVVSRLSSLETLDMTSSHYRWS-VQGETQKGQATVEEI 675

Query: 697 KGLSKLTTLEIDVRDAEML---RRIW 719
             L +L  L I +  +  L   R  W
Sbjct: 676 GCLQRLQVLSIRLHSSPFLLNKRNTW 701

Disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  219 bits (558), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 170/547 (31%), Positives = 276/547 (50%), Gaps = 43/547 (7%)

Query: 184 IGVCGMGGVGKTTLVKQIAKQVME---DNVFDKVVMAEITKNPDAQKIQGELASDLGMNF 240
           IGV GMGGVGKTTLV+ +   +++      F  V+   ++K+ D +++Q ++A  LG  F
Sbjct: 137 IGVWGMGGVGKTTLVRTLNNDLLKYAATQQFALVIWVTVSKDFDLKRVQMDIAKRLGKRF 196

Query: 241 DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTI 300
            + + +      +C+RL   K  L+ILD++W  ++LD++GIP      KD         +
Sbjct: 197 -TREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQLGIPLALERSKDSK-------V 248

Query: 301 ILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG 360
           +LTSR R  +C  M + +   +  L E+EA +LF   VGE   + + +P+A+++  +C G
Sbjct: 249 VLTSR-RLEVCQQMMTNENIKVACLQEKEAWELFCHNVGEVANSDNVKPIAKDVSHECCG 307

Query: 361 LPVALSTVANALKNKSPA-IWKDALNKLTSSNLREIHGMDAD--VYSPIKLSYDFLDDEA 417
           LP+A+ T+   L+ K    +WK  LN L     R    +D +  ++  +KLSYDFL D  
Sbjct: 308 LPLAIITIGRTLRGKPQVEVWKHTLNLLK----RSAPSIDTEEKIFGTLKLSYDFLQDNM 363

Query: 418 KSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKAS 477
           KS FL C L  E   I V  L+ Y +        GL    +  E   N    L++ LK S
Sbjct: 364 KSCFLFCALFPEDYSIKVSELIMYWV------AEGLLDGQHHYEDMMNEGVTLVERLKDS 417

Query: 478 CLLLDGDAEDEAKLHDVIHVVA----ASIAE--EKLMFSIPNVVDFERE-MEETIQKGPI 530
           CLL DGD+ D  K+HDV+   A    +S  E    L+ +   +++F ++    ++Q+   
Sbjct: 418 CLLEDGDSCDTVKMHDVVRDFAIWFMSSQGEGFHSLVMAGRGLIEFPQDKFVSSVQR--- 474

Query: 531 AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL 590
            +SL    ++ LP  +      L LL        ++ + F +    L++LD +G+R   L
Sbjct: 475 -VSLMANKLERLPNNVIEGVETLVLLLQGNSHVKEVPNGFLQAFPNLRILDLSGVRIRTL 533

Query: 591 PSSLGRLINLQTLCL-DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD 649
           P S   L +L++L L +  +L ++  +  L KL+ L L  + I++LP  +  L+ L+ + 
Sbjct: 534 PDSFSNLHSLRSLVLRNCKKLRNLPSLESLVKLQFLDLHESAIRELPRGLEALSSLRYIC 593

Query: 650 LSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW----DKVEGGSNASLAELKGLSKLTTL 705
           +SN   L  I    I +LS LE L M  S   W    ++ EG   A+L E+  L  L  L
Sbjct: 594 VSNTYQLQSIPAGTILQLSSLEVLDMAGSAYSWGIKGEEREG--QATLDEVTCLPHLQFL 651

Query: 706 EIDVRDA 712
            I + D 
Sbjct: 652 AIKLLDV 658

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  210 bits (535), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 174/573 (30%), Positives = 291/573 (50%), Gaps = 64/573 (11%)

Query: 168 IFQDVIEAL-KDDKLNIIGVCGMGGVGKTTLVKQIAKQ-VMEDNVFDKVVMAEITKNPDA 225
           + + V+E L ++++  IIGV G GGVGKTTL++ I  + + + + +D ++  ++++    
Sbjct: 161 MMEQVLEFLSEEEERGIIGVYGPGGVGKTTLMQSINNELITKGHQYDVLIWVQMSREFGE 220

Query: 226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGD 285
             IQ  + + LG+++D  +   +RA ++ + L+ +KR L++LD++W +++L+K G+P  D
Sbjct: 221 CTIQQAVGARLGLSWDEKETGENRALKIYRALR-QKRFLLLLDDVWEEIDLEKTGVPRPD 279

Query: 286 VDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGES--TK 343
            + K        C ++ T+RS  L C +M ++    ++ L ++ A +LF   V      +
Sbjct: 280 RENK--------CKVMFTTRSIAL-CNNMGAEYKLRVEFLEKKHAWELFCSKVWRKDLLE 330

Query: 344 ASDFRPLAEEIVGKCGGLPVALSTVANALKNK-SPAIWKDALNKLTSSNLREIHGMDADV 402
           +S  R LAE IV KCGGLP+AL T+  A+ ++ +   W  A   LT     E+ GM+  V
Sbjct: 331 SSSIRRLAEIIVSKCGGLPLALITLGGAMAHRETEEEWIHASEVLTRFP-AEMKGMNY-V 388

Query: 403 YSPIKLSYDFLD-DEAKSLFLLCGLHREGRPIHVHYLLRYVMG---LRYDKGLGLFRNVY 458
           ++ +K SYD L+ D  +S FL C L  E   I +  L+ Y +G   L    G+      Y
Sbjct: 389 FALLKFSYDNLESDLLRSCFLYCALFPEEHSIEIEQLVEYWVGEGFLTSSHGVNTIYKGY 448

Query: 459 TLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEK-----LMFSIPN 513
                      LI +LKA+CLL  GD + + K+H+V+   A  +A E+     L+   P+
Sbjct: 449 ----------FLIGDLKAACLLETGDEKTQVKMHNVVRSFALWMASEQGTYKELILVEPS 498

Query: 514 VVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEG 573
           +   E    E  ++  + ISL    IQ LPE+L CP+L   +L  +  S  +I   FF  
Sbjct: 499 MGHTEAPKAENWRQA-LVISLLDNRIQTLPEKLICPKLTTLML-QQNSSLKKIPTGFFMH 556

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIK 633
              L+VLD +    + +P S+  L+ L  L                      S+ G +I 
Sbjct: 557 MPVLRVLDLSFTSITEIPLSIKYLVELYHL----------------------SMSGTKIS 594

Query: 634 QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNAS- 692
            LP ++G L +L+ LDL     L  I  + I  LS+LE L +  S++ W+    G + + 
Sbjct: 595 VLPQELGNLRKLKHLDLQRTQFLQTIPRDAICWLSKLEVLNLYYSYAGWELQSFGEDEAE 654

Query: 693 ---LAELKGLSKLTTLEIDVRDAEMLRRIWSLG 722
               A+L+ L  LTTL I V   E L+ ++  G
Sbjct: 655 ELGFADLEYLENLTTLGITVLSLETLKTLFEFG 687

Disease resistance (R) protein that specifically recognizes the AvrRpt2 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is degraded by AvrRpt2.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  182 bits (463), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 188/654 (28%), Positives = 295/654 (45%), Gaps = 70/654 (10%)

Query: 29  SYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYA 88
           +Y+ K +  I  L++ +E+L   R  V   V     +G E    V  WL +VE     + 
Sbjct: 27  NYIHKLKDNIVALEKAIEDLTATRDDVLRRVQMEEGKGLERLQQVQVWLKRVEIIRNQFY 86

Query: 89  KHIINDEDEVRKPCF-KGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPP 147
             +     E+++ CF    S NL S Y   +R     K  E+L + G   IV+     P 
Sbjct: 87  DLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRVFLMIKEVENLNSNGFFEIVA----APA 142

Query: 148 PKMREFGDMKDYN-IFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM 206
           PK+    +M+        R+ IFQ     L DD +  +G+ GMGGVGKTTL+ QI   + 
Sbjct: 143 PKL----EMRPIQPTIMGRETIFQRAWNRLMDDGVGTMGLYGMGGVGKTTLLTQIHNTLH 198

Query: 207 ED-NVFDKVVMAEITKNPDAQKIQGELASDLGM-----NFDSNDLIYHRAKQLCQRLKKE 260
           +  N  D V+   ++ +    KIQ ++   LG      N         +A  +   L K 
Sbjct: 199 DTKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFIGKEWNKKQES---QKAVDILNCLSK- 254

Query: 261 KRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMF 320
           KR +++LD+IW K++L KIGIP    + K        C ++ T+RS D +C  M      
Sbjct: 255 KRFVLLLDDIWKKVDLTKIGIPSQTRENK--------CKVVFTTRSLD-VCARMGVHDPM 305

Query: 321 WIDALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANALKNKSPA 378
            +  LS  +A +LF++ VG+ +  S  D   LA+++ GKC GLP+AL+ +   +  K   
Sbjct: 306 EVQCLSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLALNVIGETMAGKRAV 365

Query: 379 I-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIHVH 436
             W  A++ LTS    E  GMD  +   +K SYD L+D+  +S F  C L+ E   I  +
Sbjct: 366 QEWHHAVDVLTSYA-AEFSGMDDHILLILKYSYDNLNDKHVRSCFQYCALYPEDYSIKKY 424

Query: 437 YLLRYVMGLRY-DKGLGLFRNVYTLEAARNRVDALIDNLKASCLLL-DGDAEDEAKLHDV 494
            L+ Y +   + D  +G        E A N+   ++  L  +CLL  +G  + E K+HDV
Sbjct: 425 RLIDYWICEGFIDGNIG-------KERAVNQGYEILGTLVRACLLSEEGKNKLEVKMHDV 477

Query: 495 IHVVA-------------ASIAEEKLMFSIPNVVDFEREMEETIQKGPI-AISLPYRDIQ 540
           +  +A               +     +  +P V D+          G +  +SL    I+
Sbjct: 478 VREMALWTLSDLGKNKERCIVQAGSGLRKVPKVEDW----------GAVRRLSLMNNGIE 527

Query: 541 ELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLIN 599
           E+    ECP+L   L   +  S + IS  FF    +L VLD +   +   LP  +  L+ 
Sbjct: 528 EISGSPECPELTT-LFLQENKSLVHISGEFFRHMRKLVVLDLSENHQLDGLPEQISELVA 586

Query: 600 LQTLCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN 652
           L+ L L    +E + A +  LK L  L+L           I +L+ L+ L L N
Sbjct: 587 LRYLDLSHTNIEGLPACLQDLKTLIHLNLECMRRLGSIAGISKLSSLRTLGLRN 640

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 =  181 bits (459), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 187/642 (29%), Positives = 303/642 (47%), Gaps = 47/642 (7%)

Query: 5   CLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVD-QAT 63
           CL +  S   E    +S+ +   + Y+ +    +  +K+ +E L ++R  VK  VD +  
Sbjct: 4   CLTLSFS-CDEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEF 62

Query: 64  EQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVE 122
            +  E  + V  WL  V      + + +  ++ E+++ C  G  S N+   Y   KR V 
Sbjct: 63  TRRRERLSQVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVL 122

Query: 123 DAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLN 182
             K  E L + G    V+  +  P  ++ E   M        ++ + + V   L +D   
Sbjct: 123 MLKEIESLSSQGDFDTVTLAT--PIARIEE---MPIQPTIVGQETMLERVWTRLTEDGDE 177

Query: 183 IIGVCGMGGVGKTTLVKQIAKQVMED-NVFDKVVMAEITKNPDAQKIQGELASDLGMNFD 241
           I+G+ GMGGVGKTTL+ +I  +  E  + F  V+   ++K+PD  +IQG++   L +  +
Sbjct: 178 IVGLYGMGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGE 237

Query: 242 SNDLI--YHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRR-- 297
             D +    RA  +   L K+K VL +LD+IW K+ L+ +G+PY           P R  
Sbjct: 238 EWDNVNENQRALDIYNVLGKQKFVL-LLDDIWEKVNLEVLGVPY-----------PSRQN 285

Query: 298 -CTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGEST--KASDFRPLAEEI 354
            C ++ T+RSRD +C  M       +  L   EA +LF+  VGE+T     D   LA ++
Sbjct: 286 GCKVVFTTRSRD-VCGRMRVDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKV 344

Query: 355 VGKCGGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFL 413
            GKC GLP+AL+ +   +  K     W++A++ L SS   E  GM+  +   +K SYD L
Sbjct: 345 AGKCCGLPLALNVIGETMACKRMVQEWRNAIDVL-SSYAAEFPGME-QILPILKYSYDNL 402

Query: 414 DDE-AKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALID 472
           + E  K  FL C L  E   +    L+ Y +        G      + E A ++   +I 
Sbjct: 403 NKEQVKPCFLYCSLFPEDYRMEKERLIDYWI------CEGFIDENESRERALSQGYEIIG 456

Query: 473 NLKASCLLL-DGDAEDEAKLHDVIHVVAASIAE---EKLMFSIPNVVDFEREMEETIQKG 528
            L  +CLLL +   +++ K+HDV+  +A  IA    E     I  V    RE+ +     
Sbjct: 457 ILVRACLLLEEAINKEQVKMHDVVREMALWIASDLGEHKERCIVQVGVGLREVPKVKNWS 516

Query: 529 PI-AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTG-IR 586
            +  +SL   +I+ L    EC +L   L   K DS L ISD FF     L VLD +G   
Sbjct: 517 SVRRMSLMENEIEILSGSPECLELTT-LFLQKNDSLLHISDEFFRCIPMLVVLDLSGNSS 575

Query: 587 FSPLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSL 627
              LP+ + +L++L+ L L    ++ + + + +LKKL  L L
Sbjct: 576 LRKLPNQISKLVSLRYLDLSWTYIKRLPVGLQELKKLRYLRL 617

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 =  179 bits (454), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 183/655 (27%), Positives = 312/655 (47%), Gaps = 67/655 (10%)

Query: 7   AIFSSIVSEGTKTLS---EPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQAT 63
           + FS  ++ G +T++   + +IG+ SY+   +  +  L+  +E+L   +  V+  V +  
Sbjct: 3   SCFSFQIAVGDQTMNRIFDCLIGK-SYIRTLEKNLRALQREMEDLRATQHEVQNKVAREE 61

Query: 64  EQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVE 122
            +  +    V  WL +V          +     E++K C  GL +  + S YK  K+   
Sbjct: 62  SRHQQRLEAVQVWLDRVNSIDIECKDLLSVSPVELQKLCLCGLCTKYVCSSYKYGKKVFL 121

Query: 123 DAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLN 182
             +  + L + G+      VS PPP   R   + +       ++++ +     L +D + 
Sbjct: 122 LLEEVKILKSEGNF---DEVSQPPP---RSEVEERPTQPTIGQEEMLEKAWNRLMEDGVG 175

Query: 183 IIGVCGMGGVGKTTLVKQIAKQVME-DNVFDKVVMAEITKNPDAQKIQGELAS------D 235
           I+G+ GMGGVGKTTL K+I  +  E    FD V+   +++     K+Q ++A       D
Sbjct: 176 IMGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDD 235

Query: 236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDP 295
           L  N + +D    +A  +  R+ K KR +++LD+IW K++L+ IGIPY          + 
Sbjct: 236 LWKNKNESD----KATDI-HRVLKGKRFVLMLDDIWEKVDLEAIGIPYP--------SEV 282

Query: 296 RRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASD--FRPLAEE 353
            +C +  T+RSR+ +C +M   K   ++ L  E+A +LF+  VG++T +SD     LA E
Sbjct: 283 NKCKVAFTTRSRE-VCGEMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVGLARE 341

Query: 354 IVGKCGGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDF 412
           +  KC GLP+AL+ +   + +K+    W+ A++ LT S   E  GM+  +   +K SYD 
Sbjct: 342 VAQKCRGLPLALNVIGETMASKTMVQEWEYAIDVLTRSA-AEFSGMENKILPILKYSYDS 400

Query: 413 LDDEA-KSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGL--GLFRNVYTLEAARNRVDA 469
           L DE  KS FL C L  E   I+   L+        DK +  G       ++ ARN+  A
Sbjct: 401 LGDEHIKSCFLYCALFPEDGQIYTETLI--------DKLICEGFIGEDQVIKRARNKGYA 452

Query: 470 LIDNLKASCLLLDGDAE----------DEAKLHDVIHVVAASIA----EEKLMFSIPNVV 515
           ++  L  + LL     E              +HDV+  +A  IA    ++K  F +    
Sbjct: 453 MLGTLTRANLLTKVGTELANLLTKVSIYHCVMHDVVREMALWIASDFGKQKENFVVQASA 512

Query: 516 DFEREMEETIQKGPI-AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGT 574
               E+ E    G +  +SL   +I+E+    +C +L    LF + +    +S  F    
Sbjct: 513 GL-HEIPEVKDWGAVRRMSLMRNEIEEITCESKCSELT--TLFLQSNQLKNLSGEFIRYM 569

Query: 575 EELKVLDFTGIR-FSPLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSL 627
           ++L VLD +  R F+ LP  +  L++LQ L L   R+E + + + +LKKL  L L
Sbjct: 570 QKLVVLDLSDNRDFNELPEQISGLVSLQYLDLSFTRIEQLPVGLKELKKLTFLDL 624

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 =  170 bits (430), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 184/643 (28%), Positives = 303/643 (47%), Gaps = 56/643 (8%)

Query: 7   AIFSSIVSEGT-KTLSEPIIGRMSYVLKCQSYIDGLKERVEELG--QRRKRVKILVDQAT 63
           + FS  VS+ T   +   +IG+ SY+   +  +  L+  +E+L   Q   + K+  D+A 
Sbjct: 3   SCFSLQVSDQTLNRIFNCLIGK-SYIRTLEKNLRALQREMEDLRAIQHEVQNKVARDEAR 61

Query: 64  EQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVE 122
            Q       V  WL +V          +     E++K C  GL S  + S YK  K+   
Sbjct: 62  HQ--RRLEAVQVWLDRVNSVDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFL 119

Query: 123 DAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLN 182
             +  + L + G+      VS PPP   R   + +       ++ + +     L +D + 
Sbjct: 120 LLEEVKKLNSEGNF---DEVSQPPP---RSEVEERPTQPTIGQEDMLEKAWNRLMEDGVG 173

Query: 183 IIGVCGMGGVGKTTLVKQIAKQVME-DNVFDKVVMAEITKNPDAQKIQGELAS------D 235
           I+G+ GMGGVGKTTL K+I  +  E    FD V+   ++K     K+Q ++A       D
Sbjct: 174 IMGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDD 233

Query: 236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDP 295
           L  N + +D    +A  +  R+ K KR +++LD+IW K++L+ IGIPY          + 
Sbjct: 234 LWKNKNESD----KATDI-HRVLKGKRFVLMLDDIWEKVDLEAIGIPYP--------SEV 280

Query: 296 RRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASD--FRPLAEE 353
            +C +  T+RSR+ +C +M   K   ++ L  E+A +LF+  VG++T +SD     LA E
Sbjct: 281 NKCKVAFTTRSRE-VCGEMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELARE 339

Query: 354 IVGKCGGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDF 412
           +  KC GLP+AL+ +   + +K+    W+ A++   +S   E   M   +   +K SYD 
Sbjct: 340 VAQKCRGLPLALNVIGETMSSKTMVQEWEHAIHVFNTS-AAEFSDMQNKILPILKYSYDS 398

Query: 413 LDDEA-KSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALI 471
           L DE  KS FL C L  E   I+   L+ Y +        G       ++ ARN+  A++
Sbjct: 399 LGDEHIKSCFLYCALFPEDGEIYNEKLIDYWI------CEGFIGEDQVIKRARNKGYAML 452

Query: 472 DNLKASCLLLDGDAEDEAKLHDVIHVVAASIA----EEKLMFSIPNVVDFEREMEETIQK 527
             L  + LL          +HDV+  +A  IA    ++K  F +   V    E+ +    
Sbjct: 453 GTLTRANLLTKVGTY-YCVMHDVVREMALWIASDFGKQKENFVVQAGVGL-HEIPKVKDW 510

Query: 528 GPI-AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR 586
           G +  +SL   DI+E+    +C +L    LF + +    +   F    ++L VLD +  R
Sbjct: 511 GAVRKMSLMDNDIEEITCESKCSELT--TLFLQSNKLKNLPGAFIRYMQKLVVLDLSYNR 568

Query: 587 -FSPLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSL 627
            F+ LP  +  L++LQ L L    +E + I + +LKKL  L L
Sbjct: 569 DFNKLPEQISGLVSLQFLDLSNTSIEHMPIGLKELKKLTFLDL 611

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  168 bits (426), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 185/649 (28%), Positives = 305/649 (46%), Gaps = 77/649 (11%)

Query: 37  YIDGLKERV-------EELGQRRKRV--KILVDQATEQGYEIFADVTEWLGKVEQFTQGY 87
           YI GL+E +       E++ QRR+ +  KIL ++   +G +  + V  W+ KVE      
Sbjct: 28  YIHGLEENLTALQRALEQIEQRREDLLRKILSEE--RRGLQRLSVVQGWVSKVEAIVPRV 85

Query: 88  AKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPP 146
            + +     +V++ C  G  S NL+S Y+  KR ++  +  E L   G   +V+      
Sbjct: 86  NELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVMKMIEEVEVLRYQGDFAVVAERVDAA 145

Query: 147 PPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM 206
             + R    M   +       + +     L +D++ I+G+ GMGGVGKTTL+  I  +  
Sbjct: 146 RVEERPTRPMVAMD------PMLESAWNRLMEDEIGILGLHGMGGVGKTTLLSHINNRFS 199

Query: 207 E-DNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK------- 258
                FD V+   ++K    Q+IQ E+   L  + +       + KQ  + +K       
Sbjct: 200 RVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDNE-------KWKQKTEDIKASNIYNV 252

Query: 259 -KEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRR---CTIILTSRSRDLLCIDM 314
            K KR +++LD+IW+K++L ++G+P+           P R   C I+ T+R ++ +C  M
Sbjct: 253 LKHKRFVLLLDDIWSKVDLTEVGVPF-----------PSRENGCKIVFTTRLKE-ICGRM 300

Query: 315 NSQKMFWIDALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANAL 372
                  +  L+ ++A  LF K VGE T  S  +   +A  +  KC GLP+AL+ +   +
Sbjct: 301 GVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVARTVAKKCRGLPLALNVIGETM 360

Query: 373 KNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEA-KSLFLLCGLHREG 430
             K     W+ A++ LTSS   E  GM+ ++   +K SYD L  E  K  F  C L  E 
Sbjct: 361 AYKRTVQEWRSAIDVLTSSAA-EFSGMEDEILPILKYSYDNLKSEQLKLCFQYCALFPED 419

Query: 431 RPIHVHYLLRYVMGLRY-DKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEA 489
             I  + L+ Y +G  + D+  G          A N+   +I  L  SCLL++ + E   
Sbjct: 420 HNIEKNDLVDYWIGEGFIDRNKG---------KAENQGYEIIGILVRSCLLMEENQET-V 469

Query: 490 KLHDVIHVVAASIA----EEKLMFSIPNVVDFEREMEETIQKGPIA--ISLPYRDIQELP 543
           K+HDV+  +A  IA    ++K  F +   +   R + E I+K  +A  +SL + +I+ + 
Sbjct: 470 KMHDVVREMALWIASDFGKQKENFIVQAGLQ-SRNIPE-IEKWKVARRVSLMFNNIESIR 527

Query: 544 ERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-FSPLPSSLGRLINLQT 602
           +  E PQL   LL   +     IS  FF     L VLD +  R    LP+ +   ++LQ 
Sbjct: 528 DAPESPQLITLLLRKNFLG--HISSSFFRLMPMLVVLDLSMNRDLRHLPNEISECVSLQY 585

Query: 603 LCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDL 650
           L L   R+    A + +L+KL  L+L    + +    I  LT L++L L
Sbjct: 586 LSLSRTRIRIWPAGLVELRKLLYLNLEYTRMVESICGISGLTSLKVLRL 634

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVT4|DRL37_ARATH Probable disease resistance protein At5g47250 OS=Arabidopsis thaliana GN=At5g47250 PE=2 SV=1

 Score =  167 bits (423), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 165/584 (28%), Positives = 277/584 (47%), Gaps = 90/584 (15%)

Query: 144 HPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAK 203
            PPPP +      +   +  + +K +    E+L+ D+  ++G+ GMGGVGKTTL+  I  
Sbjct: 143 QPPPPVVEVRLCQQTVGLDTTLEKTW----ESLRKDENRMLGIFGMGGVGKTTLLTLINN 198

Query: 204 QVME-DNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAK---QLCQRLKK 259
           + +E  + +D V+  E +K+ D  KIQ  +   L +  D+N   Y R K   ++ + L+ 
Sbjct: 199 KFVEVSDDYDVVIWVESSKDADVGKIQDAIGERLHI-CDNNWSTYSRGKKASEISRVLRD 257

Query: 260 EK-RVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQK 318
            K R +++LD++W  + L  IGIP             ++  ++ T+RS+D +C  M + +
Sbjct: 258 MKPRFVLLLDDLWEDVSLTAIGIPVLG----------KKYKVVFTTRSKD-VCSVMRANE 306

Query: 319 MFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPA 378
              +  LSE +A  LF+  V      ++   +A++IV KC GLP+AL  +   + +KS  
Sbjct: 307 DIEVQCLSENDAWDLFDMKV-HCDGLNEISDIAKKIVAKCCGLPLALEVIRKTMASKSTV 365

Query: 379 I-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHY 437
           I W+ AL+ L S    E+ G +  ++  +KLSYD+L  +    FL C L  +   I    
Sbjct: 366 IQWRRALDTLESYR-SEMKGTEKGIFQVLKLSYDYLKTKNAKCFLYCALFPKAYYIKQDE 424

Query: 438 LLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHV 497
           L+ Y +      G G        E A++R   +IDNL  + LLL+ +   +  +HD+I  
Sbjct: 425 LVEYWI------GEGFIDEKDGRERAKDRGYEIIDNLVGAGLLLESNK--KVYMHDMIRD 476

Query: 498 VAASIAEE------------KLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPER 545
           +A  I  E              +  +P+V D+      T+ K    +SL   +I+ +P+ 
Sbjct: 477 MALWIVSEFRDGERYVVKTDAGLSQLPDVTDW-----TTVTK----MSLFNNEIKNIPDD 527

Query: 546 LECP-QLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLINLQTL 603
            E P Q  L  LF + +  + I   FF     L VLD +   + + LP  +  L++L+  
Sbjct: 528 PEFPDQTNLVTLFLQNNRLVDIVGKFFLVMSTLVVLDLSWNFQITELPKGISALVSLR-- 585

Query: 604 CLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNV 663
                               +L+L G  IK LP  +G L++L  L+L + S+L  +   +
Sbjct: 586 --------------------LLNLSGTSIKHLPEGLGVLSKLIHLNLESTSNLRSVG--L 623

Query: 664 ISKLSRLEELYMGDSFSQWD----KVEGGSNASLAELKGLSKLT 703
           IS+L +L+ L    S +  D    K+       L +LKGL  LT
Sbjct: 624 ISELQKLQVLRFYGSAAALDCCLLKI-------LEQLKGLQLLT 660

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (420), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 140/487 (28%), Positives = 233/487 (47%), Gaps = 30/487 (6%)

Query: 24  IIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQF 83
           + G  +Y+LK ++ ++ L+  ++EL +RR  +   V    ++G +  A V  WL +V+  
Sbjct: 22  LFGDRNYILKMEANLEALQNTMQELEERRDDLLRRVVIEEDKGLQRLAQVQGWLSRVKDV 81

Query: 84  TQGYAKHIINDEDEVRKPCFKG-LSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNV 142
                  +     +  + C  G  S N +S        ++  K+ E LLA G   +V+  
Sbjct: 82  CSQVNDLLKAKSIQTERLCLCGYCSKNFISGRNYGINVLKKLKHVEGLLAKGVFEVVA-- 139

Query: 143 SHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIA 202
              P PK+ +    K          +      +L  D+   +G+ GMGGVGKTTL+  I 
Sbjct: 140 EKIPAPKVEK----KHIQTTVGLDAMVGRAWNSLMKDERRTLGLYGMGGVGKTTLLASIN 195

Query: 203 KQVMED-NVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLI-YHRAKQLCQRLKKE 260
            + +E  N FD V+   ++K+   + IQ ++   LG++     +    +A  +C  L  +
Sbjct: 196 NKFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGLHRGWKQVTEKEKASYICNILNVK 255

Query: 261 KRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMF 320
           K VL+ LD++W++++L+KIG+P    +   K        I+ T+RS+D+ C DM      
Sbjct: 256 KFVLL-LDDLWSEVDLEKIGVPPLTRENGSK--------IVFTTRSKDV-CRDMEVDGEM 305

Query: 321 WIDALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANALKNKSPA 378
            +D L  +EA +LF+K VG     S  D   LA ++  KC GLP+ALS +  A+ ++   
Sbjct: 306 KVDCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPLALSVIGKAMASRETV 365

Query: 379 I-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIHVH 436
             W+  ++ L SS+  E   M+  +   +K SYD L DE  K  FL C L  E   +   
Sbjct: 366 QEWQHVIHVLNSSS-HEFPSMEEKILPVLKFSYDDLKDEKVKLCFLYCSLFPEDYEVRKE 424

Query: 437 YLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIH 496
            L+ Y M        G        + A N+   +I +L  + LL+DG+   + K+HDVI 
Sbjct: 425 ELIEYWM------CEGFIDGNEDEDGANNKGHDIIGSLVRAHLLMDGELTTKVKMHDVIR 478

Query: 497 VVAASIA 503
            +A  IA
Sbjct: 479 EMALWIA 485

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	724
359488027	1520	PREDICTED: disease resistance protein At	0.943	0.449	0.450	1e-150
224111296	1315	cc-nbs-lrr resistance protein [Populus t	0.935	0.514	0.446	1e-144
147865073	1694	hypothetical protein VITISV_021876 [Viti	0.940	0.402	0.426	1e-144
359488103	1530	PREDICTED: disease resistance protein At	0.950	0.449	0.421	1e-143
359488095	1347	PREDICTED: probable disease resistance p	0.946	0.508	0.422	1e-142
147777048	1460	hypothetical protein VITISV_009359 [Viti	0.946	0.469	0.424	1e-141
359488288	1340	PREDICTED: LOW QUALITY PROTEIN: probable	0.928	0.501	0.431	1e-141
255563252	1603	Disease resistance protein RPS5, putativ	0.926	0.418	0.449	1e-138
359488101	1677	PREDICTED: disease resistance protein At	0.943	0.407	0.428	1e-137
359488108	1436	PREDICTED: disease resistance protein At	0.944	0.476	0.423	1e-137

>gi|359488027|ref|XP_002269288.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  540 bits (1390), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 321/712 (45%), Positives = 451/712 (63%), Gaps = 29/712 (4%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  +I ++  + L  PI     Y+   +S ID L+++VE+LG  R R++  VD+A   G 
Sbjct: 4   IVVTIAAKVAEYLVAPIGRSFGYLFNYRSNIDDLRQQVEKLGDARARLERSVDEAIRNGD 63

Query: 68  EIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYA 127
           EI ADV +WL +V  F +  A      E +  + CF G  PNL S+Y+LS+ A + A+  
Sbjct: 64  EIEADVDKWLLRVSGFMEE-AGIFFEVEKKANQSCFNGSCPNLKSQYQLSREAKKRARVV 122

Query: 128 EHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVC 187
             +   G       VS+  P         K +    SR     +++EAL+D  +NIIGV 
Sbjct: 123 AEIQGDGKF---ERVSYRAPLPGIGSAPFKGHEALESRMTTLDEIMEALRDAHVNIIGVW 179

Query: 188 GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY 247
           GM GVGKTTL+KQ+AKQ  E+ +FDKVVMA I+  P+ +KIQGELA  LG+ F+    + 
Sbjct: 180 GMAGVGKTTLMKQVAKQAEEEKLFDKVVMAYISSTPELKKIQGELADMLGLKFEEESEM- 238

Query: 248 HRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR 307
            RA +LC+RLKK K++LIILD+IWT+L+L+K+GIP+GD        D + C ++LTSR++
Sbjct: 239 GRAARLCERLKKVKKILIILDDIWTELDLEKVGIPFGD--------DHKGCKMVLTSRNK 290

Query: 308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST 367
            +L  +M +QK F ++ L EEEAL LF+K+ G+S +  D + +A ++  +C GLP+A+ T
Sbjct: 291 HILSNEMGTQKDFPVEHLQEEEALILFKKMAGDSIEEPDLQSIAIDVAKECAGLPIAIVT 350

Query: 368 VANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKSLFLLCGL 426
           VA ALKNK  +IW+DAL +L  S    I GMDA VYS ++LSY  L+ DE KSLFLLCGL
Sbjct: 351 VAKALKNKGLSIWEDALRQLKRSIPTNIKGMDAMVYSTLELSYKHLEGDEVKSLFLLCGL 410

Query: 427 HREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAE 486
                 I++  LL+Y MGLR      LF+   TLE A+NR+D L+D+LKAS LLLD    
Sbjct: 411 M--SNKIYIDDLLKYGMGLR------LFQGTNTLEEAKNRIDTLVDSLKASKLLLDTGHN 462

Query: 487 DEAKLHDVIHVVAASIAEE-KLMFSI--PNVVDFEREMEETIQKGPIAISLPYRDIQELP 543
              ++HDV+  VA +I  +   +FS+    +V++ + M+E   +    +SL Y DI ELP
Sbjct: 463 SFVRMHDVVRDVAIAIVSKVHRVFSLREDELVEWPK-MDEL--QTCTKMSLAYNDICELP 519

Query: 544 ERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL 603
             L CP+L+LFL +   D  L+I + FFE  ++LKVLD + + F+ LPSSL  L NL+TL
Sbjct: 520 IELVCPELELFLFYHTIDYHLKIPETFFEEMKKLKVLDLSNMHFTSLPSSLRCLTNLRTL 579

Query: 604 CLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNV 663
            L+  +L DI+I+ +LKKLE  S  G+ I++LP +I QLT L+L DL +CS L  I PNV
Sbjct: 580 SLNWCKLGDISIIVELKKLEFFSFMGSNIEKLPREIAQLTHLRLFDLRDCSKLREIPPNV 639

Query: 664 ISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEML 715
           IS LS+LE L M +SF+ W+ VEG SNAS+AE K L  LTTL+I + DAE+L
Sbjct: 640 ISSLSKLENLCMENSFTLWE-VEGKSNASIAEFKYLPYLTTLDIQIPDAELL 690

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 319/714 (44%), Positives = 432/714 (60%), Gaps = 37/714 (5%)

Query: 6   LAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQ 65
           + I  SIV++  + L  PI  ++ YVL C + I  LK  VE+L   R RV   +++A   
Sbjct: 1   MEIVISIVAKVAELLVVPIKRQIGYVLNCNTNIQNLKNEVEKLTDARTRVNHSIEEARRN 60

Query: 66  GYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAK 125
           G EI  +V  WLG V+    G    +    DE  K CF GL P+L  RY+L K A ++  
Sbjct: 61  GEEIEVEVFNWLGSVDGVIDGGGGGV---ADESSKKCFMGLCPDLKIRYRLGKAAKKELT 117

Query: 126 YAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIG 185
               L   G    VS  + P        G +KDY  F SR  +   +++ALKD  +N++G
Sbjct: 118 VVVDLQEKGRFDRVSYRAAPSG-----IGPVKDYEAFESRDSVLNAIVDALKDGGVNMVG 172

Query: 186 VCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDL 245
           V GM GVGKTTLVK++A+QV E  +FDK V+A ++  PD ++IQGE+A  LG+  D+ + 
Sbjct: 173 VYGMPGVGKTTLVKKVAEQVKEGRLFDKEVLAVVSHTPDIRRIQGEIADGLGLKLDA-ET 231

Query: 246 IYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSR 305
              RA QL +RLKK  RVL+ILD+IW +L+L+ +GIP G         D   C I+++SR
Sbjct: 232 DKGRASQLYERLKKVTRVLVILDDIWKELKLEDVGIPSGS--------DHEGCKILMSSR 283

Query: 306 SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL 365
           +  +L  +M S + F I  L   EA  LFEK+VG + K    R +A E+  +C GLP+ L
Sbjct: 284 NEYVLSREMGSNRNFPIQVLPASEAWNLFEKMVGVAVKKHSVRLVAAEVARRCAGLPILL 343

Query: 366 STVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFL-DDEAKSLFLLC 424
           +TVA ALKNK    WK AL +LT  +  +I   D  VY  ++LSY  L  DE KSLFLLC
Sbjct: 344 ATVARALKNKDLYAWKKALKQLTRFDKDDI---DDQVYLGLELSYKSLRGDEIKSLFLLC 400

Query: 425 GLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGD 484
           G  R    I +  LLRY +GL       LF+   TLE  RN +  L+D LKASCLLL+GD
Sbjct: 401 GQLRSNN-ILISDLLRYGIGL------DLFKGCSTLEETRNSLLTLVDELKASCLLLEGD 453

Query: 485 AEDEAKLHDVIHVVAASIA-EEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELP 543
            +   K+HDV+H  A S+A  +  + ++ +  +F+      + +   AISLP+R I +LP
Sbjct: 454 KDGSVKMHDVVHSFAISVALRDHHVLTVAD--EFKEWPANDVLQQYTAISLPFRKIPDLP 511

Query: 544 ERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL 603
             LECP L  FLL  K D +LQI D FF   +ELK+LD T +  SPLPSSL  L NLQTL
Sbjct: 512 AILECPNLNSFLLLNK-DPSLQIPDSFFREMKELKILDLTEVNLSPLPSSLQFLENLQTL 570

Query: 604 CLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNV 663
           CLD   LEDI+I+G+L KL++LSL  + I +LP +IG++TRLQLLDLSNC  L VI+PN 
Sbjct: 571 CLDHCVLEDISIIGELNKLKVLSLMSSNIVRLPREIGKVTRLQLLDLSNCERLEVISPNA 630

Query: 664 ISKLSRLEELYMGDSFSQWDKVEGGS----NASLAELKGLSKLTTLEIDVRDAE 713
           +S L+RLE+LYMG+SF +W+  EG S    NA L+ELK LS L+TL + + DA+
Sbjct: 631 LSSLTRLEDLYMGNSFVKWE-TEGSSSQRNNACLSELKHLSNLSTLHMQITDAD 683

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 310/727 (42%), Positives = 453/727 (62%), Gaps = 46/727 (6%)

Query: 1   MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVD 60
           M E+ L++ + +    ++ L +P I ++ Y+   ++ I+ L ++VE+L   R R++  VD
Sbjct: 1   MVEIVLSVAAKV----SEYLVDPAIRQLGYLFNYRANIEDLSQQVEKLRDARARLQHSVD 56

Query: 61  QATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRA 120
           +A   G+ I  DV +W+ + + F Q   K  + DE E RK CF GL PNL SRY+LS+ A
Sbjct: 57  EAIGNGHIIEDDVRKWMKRADGFIQNACK-FLEDEKEARKSCFNGLCPNLKSRYQLSREA 115

Query: 121 VEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDK 180
            + A  A  +   G       VS+  P  ++E           SR     +V+EAL+D  
Sbjct: 116 RKKAGVAVEIHGAGQF---ERVSYRAP--LQEIRTAPS-EALESRMLTLNEVMEALRDAN 169

Query: 181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF 240
           +N IGV GMGGVGK+TLVKQ+A+Q  ++ +F KVVM  + + PD + IQ ++A  LGM F
Sbjct: 170 INRIGVWGMGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVIQTPDFKGIQQQIADKLGMKF 229

Query: 241 DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTI 300
           +       RA +L QR+K+E  +LIILD++W +LEL+K+GIP          DD + C +
Sbjct: 230 EEVSE-QGRADRLHQRIKQENTILIILDDLWAELELEKVGIP--------SPDDHKGCKL 280

Query: 301 ILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG 360
           +LTSR++ +L  +M++QK F +  L E+E   LF+   G+S +  + +P+A ++  +C G
Sbjct: 281 VLTSRNKQVLSNEMSTQKDFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAG 340

Query: 361 LPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKS 419
           LP+A+ TVA ALKNK+ +IWKDAL +L S     I GM+  VYS +KLSY+ L+ DE KS
Sbjct: 341 LPIAIVTVAKALKNKNVSIWKDALQQLNSQTSTNITGMETKVYSSLKLSYEHLEGDEVKS 400

Query: 420 LFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCL 479
           LFLLCGL      I++  LL+Y MGLR      LF+   TLE A+NR+D L+DNLK+S L
Sbjct: 401 LFLLCGLF--SNYIYIRDLLKYGMGLR------LFQGTNTLEEAKNRIDTLVDNLKSSNL 452

Query: 480 LLDGDAEDEAKLHDVIHVVAASIA-EEKLMFSIPNVVDFEREMEETIQKGP--------I 530
           LL+       ++HDV+  VA  I+ ++  +F++       ++    ++K P        I
Sbjct: 453 LLETGHNAVVRMHDVVRSVALDISSKDHHVFTL-------QQTTGRVEKWPRIDELQKVI 505

Query: 531 AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL 590
            ++    DI ELPE L CP+LKLF+   K +S ++I + FFEG ++L+VLDFT +    L
Sbjct: 506 WVNQDECDIHELPEGLVCPKLKLFICCLKTNSAVKIPNTFFEGMKQLQVLDFTQMHLPSL 565

Query: 591 PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDL 650
           PSSL  L NLQTL L G +L DI I+ +LKKLEILSL  ++I+QLP +I QLT L+LLDL
Sbjct: 566 PSSLQCLANLQTLLLYGCKLGDIGIITELKKLEILSLIDSDIEQLPREIAQLTHLRLLDL 625

Query: 651 SNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVR 710
           S+ S++ VI   VIS LS+LE+L M +SF+QW+  EG SNA LAELK LS LT+L+I + 
Sbjct: 626 SDSSTIKVIPSGVISSLSQLEDLCMENSFTQWEG-EGKSNACLAELKHLSHLTSLDIQIP 684

Query: 711 DAEMLRR 717
           DA++L +
Sbjct: 685 DAKLLPK 691

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  514 bits (1325), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 303/719 (42%), Positives = 440/719 (61%), Gaps = 31/719 (4%)

Query: 1   MAEVCLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVD 60
           M E+ L++ + +    ++ L +P + ++ Y+   ++ I+ L ++V++L   R R++  VD
Sbjct: 1   MVEIVLSVAAKV----SEYLVDPAVRQLGYLFNYRANIEELSQQVQKLRDARARLQHSVD 56

Query: 61  QATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRA 120
           +A   G  I  DV +W+ + + F Q   K  + DE E RK CF GL PNL SRY+LS+ A
Sbjct: 57  EAIGNGLIIEDDVCKWMKRADGFIQNACK-FLEDEKEARKSCFNGLCPNLKSRYQLSREA 115

Query: 121 VEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDK 180
            + A  +  +L  G    V+     P   +R     +      SR     +V+EAL+D  
Sbjct: 116 SKKAGVSVQILGDGQFEKVA--YRAPLQGIR----CRPSEALESRMLTLNEVMEALRDAN 169

Query: 181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF 240
           +N IGV GMGGVGK+TLVKQ+A+Q  ++ +F+KVV   + + PD ++IQ ELA  LGM F
Sbjct: 170 INRIGVWGMGGVGKSTLVKQVAEQANQEKLFEKVVNVSVLQTPDLERIQRELADWLGMKF 229

Query: 241 DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTI 300
           +       RA +L QR+K EK +LIILD++W +LEL+K+GIP          DD + C +
Sbjct: 230 EEESE-QGRAARLHQRMKAEKTILIILDDLWAELELEKVGIP--------SPDDHKGCKL 280

Query: 301 ILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG 360
           +LTSR++ +L  +M++QK F +  L E+E   LF+   G+S +  + +P+A ++  +C G
Sbjct: 281 VLTSRNKQVLSNEMSTQKDFRVRHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAG 340

Query: 361 LPVALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKS 419
           LP+A+ TVA ALKNK+ +IWKDAL +L S     I GM+  VYS +KLSY+ L+ DE KS
Sbjct: 341 LPIAIVTVAKALKNKNVSIWKDALQQLKSQTSTNITGMETKVYSSLKLSYEHLEGDEVKS 400

Query: 420 LFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCL 479
           L LLCGL    R IH+  LL+Y +GLR      LF+   TLE  +NR+D L+DNLK+S  
Sbjct: 401 LCLLCGLF--SRYIHIRDLLKYGVGLR------LFQGTNTLEEVKNRIDTLVDNLKSSNF 452

Query: 480 LLDGDAEDEAKLHDVIHVVAASIA-EEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRD 538
           LL+       ++HD++   A  IA E+  +F+         E     +     + L + D
Sbjct: 453 LLETGRNAVVRMHDLVRSTARKIASEQHHVFTHQKTTVRVEEWSRIDELQVTWVKLHHCD 512

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLI 598
           I ELPE L CP+L+ F  F K +  ++I + FFEG ++LKVLD TG++   LP SL  L 
Sbjct: 513 IHELPEGLVCPKLEFFECFLKTNLAVKIPNTFFEGMKQLKVLDLTGMQLPSLPLSLQSLA 572

Query: 599 NLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV 658
           NL+TLCLDG +L DI I+ +LKKLEILSL  ++I+QLP +I QLT L+L DL +   L V
Sbjct: 573 NLRTLCLDGCKLGDIVIIAELKKLEILSLMDSDIEQLPREIAQLTHLRLFDLKSSFKLKV 632

Query: 659 IAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
           I  +VIS L RLE+L M +SF+QW+  EG SNA LAELK LS LT L+I + DA++L +
Sbjct: 633 IPSDVISSLFRLEDLCMENSFTQWEG-EGKSNACLAELKHLSHLTALDIQIPDAKLLPK 690

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  513 bits (1322), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 301/712 (42%), Positives = 440/712 (61%), Gaps = 27/712 (3%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  S+ ++ ++ L +P + ++ Y+   ++ I+ L  +VE+L   R R++  VD+A   G+
Sbjct: 4   IVVSVAAKVSEYLVDPAVRQLGYLFNYRANIEHLSLQVEKLRDARARLQHSVDEAIGNGH 63

Query: 68  EIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYA 127
            I  D  +W+ + ++F Q   K  + DE E RK CF GL PNL SRY+LS+ A + A  +
Sbjct: 64  IIEDDACKWMKRADEFIQNACK-FLEDEKEARKSCFNGLCPNLKSRYQLSREARKKAGVS 122

Query: 128 EHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVC 187
             +L          VS+  P  ++E           SR     +V+EAL+D  +N IGV 
Sbjct: 123 VQILGDRQF---EKVSYRAP--LQEIRSAPS-EALQSRMLTLNEVMEALRDANINRIGVW 176

Query: 188 GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY 247
           G+GGVGK+TLVKQ+A+Q  ++ +F KVVM  + + PD + IQ ++A  LGM F+      
Sbjct: 177 GLGGVGKSTLVKQVAEQAEQEKLFRKVVMVPVFQTPDFKGIQQQIADKLGMKFEEVSE-Q 235

Query: 248 HRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR 307
            RA +L QR+K+E  +LIILD++W +LEL+K+GIP          DD + C ++LTSR++
Sbjct: 236 GRADRLHQRIKQENTILIILDDLWAELELEKVGIP--------SPDDHKGCKLVLTSRNK 287

Query: 308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST 367
            +L  +M++QK F +  L E+E   LF+   G+S K  + +P+A ++  +C GLP+A+ T
Sbjct: 288 QVLSNEMSTQKDFRVQHLQEDETWILFKNTAGDSIKNPELQPIAVDVAKECAGLPIAIVT 347

Query: 368 VANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKSLFLLCGL 426
           VA ALKNK+ +IWKDAL +L S     I GM+  VYS +KLSY+ L+ DE KSL LLCGL
Sbjct: 348 VAKALKNKNVSIWKDALQQLKSQTSTNITGMETKVYSSLKLSYEHLEGDEVKSLCLLCGL 407

Query: 427 HREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAE 486
                 IH+  LL+Y +GLR      LF+   TLE A+NR+D L+DNLK+S  LL+ D  
Sbjct: 408 FSSD--IHIGDLLKYGVGLR------LFQGTNTLEEAKNRIDTLVDNLKSSNFLLETDHN 459

Query: 487 DEAKLHDVIHVVAASIA-EEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPER 545
              ++HD++   A  IA E++ +F+         E     +     + L   DI ELPE 
Sbjct: 460 AYVRMHDLVRSTARKIASEQRHVFTHQKTTVRVEEWSRIDELQVTWVKLHDCDIHELPEG 519

Query: 546 LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL 605
           L CP+L+ F  F K  S ++I + FFEG ++LKVLDF+ ++   LP S+  L NL+TLCL
Sbjct: 520 LVCPKLEFFECFLKTHSAVKIPNTFFEGMKQLKVLDFSRMQLPSLPLSIQCLANLRTLCL 579

Query: 606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVIS 665
           DG +L DI I+ +LKKLEILSL  ++++QLP +I QLT L+LLDLS+ S++ VI   VIS
Sbjct: 580 DGCKLGDIVIIAELKKLEILSLMSSDMEQLPREIAQLTHLRLLDLSDSSTIKVIPSGVIS 639

Query: 666 KLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
            L RLE+L M +SF+QW+  EG SNA LAELK LS LT L+I + DA++L +
Sbjct: 640 SLFRLEDLCMENSFTQWEG-EGKSNACLAELKHLSHLTFLDIQIPDAKLLPK 690

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147777048|emb|CAN65562.1| hypothetical protein VITISV_009359 [Vitis vinifera]

 Score =  510 bits (1313), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 303/713 (42%), Positives = 444/713 (62%), Gaps = 28/713 (3%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  S+ ++ ++ L +P + ++ ++   ++ I+ L  +VE+L   R R++  VD+A   G+
Sbjct: 4   IVVSVAAKVSEYLVDPAVRQLGHLFNYRANIEHLSLQVEKLRDARARLQHSVDEAIGNGH 63

Query: 68  EIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYA 127
            I  DV +W+ + ++FTQ   K  + DE E RK CF GL PNL SRY+LS+ A + A  A
Sbjct: 64  IIEDDVCKWMKRADEFTQNACK-FLEDEKEARKSCFNGLCPNLKSRYQLSREARKKAGVA 122

Query: 128 EHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVC 187
             +L          VS+  P  ++E           SR     +V+EAL+D  +N IGV 
Sbjct: 123 VQILGDRQF---EKVSYRAP--LQEIRSAPS-EALQSRMLTLNEVMEALRDADINRIGVW 176

Query: 188 GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY 247
           G+GGVGK+TLVK++A+Q  ++ +F KVV A + + PD ++IQ ++A  LGM F+      
Sbjct: 177 GLGGVGKSTLVKRVAEQAEQEELFHKVVTASVFQTPDYKEIQQQIAEKLGMKFEEVSE-Q 235

Query: 248 HRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR 307
            RA +L QR+K+E  +LIILD++W +LEL+K+GIP          DD + C ++LTSR++
Sbjct: 236 GRAGRLHQRIKQENTILIILDDLWAELELEKVGIP--------SPDDHKGCKLVLTSRNK 287

Query: 308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST 367
            +L  +M++QK F +  L E+E   LF+   G+S +  + +P+A ++  +C GLP+A+ T
Sbjct: 288 QVLSNEMSTQKDFRVQHLQEDETWILFKNTAGDSIENPELQPIAVDVAKECAGLPIAIVT 347

Query: 368 VANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKSLFLLCGL 426
           VA ALKNK+ AIWKDAL +L S     I GM+  VYS +KLSY+ L+ DE KSL LLCGL
Sbjct: 348 VAKALKNKNVAIWKDALQQLESQTSTNITGMETKVYSSLKLSYEHLEGDEMKSLCLLCGL 407

Query: 427 HREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAE 486
                 I++  LL+Y +GLR      LF+   TLE A+NR+D L+D LK+S  LL+    
Sbjct: 408 CYSQ--IYISDLLKYGVGLR------LFQGTNTLEEAKNRIDTLVDKLKSSNFLLETGHN 459

Query: 487 DEAKLHDVIHVVAASIAEEKL-MFSIPNVVDFEREMEETIQKGPIA-ISLPYRDIQELPE 544
              ++HD++   A  IA E+L +F+         E   T +   +  +SL   DI ELPE
Sbjct: 460 AVVRMHDLVRSTARKIASEQLHVFTHQKTTVRVEEWPRTDELQKVTWVSLGDCDIHELPE 519

Query: 545 RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC 604
            L CP+L+LF  + K  S ++I   FFEG ++L+VLDF+ ++   LP SL  L NL+TLC
Sbjct: 520 GLLCPELELFQCYQKTSSAVKIPHTFFEGMKQLEVLDFSNMQLPSLPLSLQCLANLRTLC 579

Query: 605 LDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVI 664
           LDG +L DI I+ +LKKLEILSL  ++I+QLP +I QLT L+L DL + S L VI P+VI
Sbjct: 580 LDGCKLGDIVIIAKLKKLEILSLIDSDIEQLPREIAQLTHLRLFDLKDSSKLKVIPPDVI 639

Query: 665 SKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
           S L RLE+L M +SF+QW+  EG SNA LAELK LS LT+L+I + DA++L +
Sbjct: 640 SSLFRLEDLCMENSFTQWEG-EGKSNACLAELKHLSHLTSLDIQIPDAKLLPK 691

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488288|ref|XP_003633735.1| PREDICTED: LOW QUALITY PROTEIN: probable disease resistance protein At1g61310-like [Vitis vinifera]

 Score =  508 bits (1307), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 309/716 (43%), Positives = 446/716 (62%), Gaps = 44/716 (6%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  S+ ++ ++ L  P+  ++ ++   ++ ++ L ++V +L   R R +  VD+A  +G+
Sbjct: 4   IVVSVAAKVSEYLVAPVGRQLGHLFNYRTNVEDLSQQVAKLRDARARQQHSVDEAIRKGH 63

Query: 68  EIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYA 127
           +I  DV +W  + + F Q   K  + +E E +K CF GL PNL SRY+LSK A + A  A
Sbjct: 64  KIEDDVCKWFTRADGFIQVACK-FLEEEKEAQKTCFNGLCPNLKSRYQLSKEARKKAGVA 122

Query: 128 EHLLATGSLLIVSNVSHPPPPKMREFGDM--KDYNIFNSRKKIFQDVIEALKDDKLNIIG 185
             +   G       VS+ PP  + E G    K   +  SR     +V++AL+D  +N IG
Sbjct: 123 VEIHGDGQF---ERVSYRPP--LLEIGSAPPKASKVLESRMLTLNEVMKALRDADINTIG 177

Query: 186 VCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDL 245
           + GMGGVGK TLVKQ+A+Q  ++ +FDKVVM  + + PD ++IQGE+A  LGM F+    
Sbjct: 178 IWGMGGVGKNTLVKQVAEQAAQEKLFDKVVMTSVFQTPDFRRIQGEIADMLGMKFEEESE 237

Query: 246 IYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSR 305
              RA +L +++ +EK +LIILD+IW +LEL+KIGIP          D+ + C ++LTSR
Sbjct: 238 -QGRAARLHRKINEEKTILIILDDIWAELELEKIGIP--------SPDNHKGCKLVLTSR 288

Query: 306 SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL 365
           ++ +L  +M++QK F ++ L  +EA  LF+ +VG+S +  D   +A ++  +C GLP+A+
Sbjct: 289 NKHVLSNEMSTQKDFGVEHLQGDEAWILFKNMVGDSIENPDLLLIATDVAKECTGLPIAI 348

Query: 366 STVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLD-DEAKSLFLLC 424
            TVA ALKNK+ +IWKDAL +L +     I GM   VYS +KLSY  L+ DE KSLFLLC
Sbjct: 349 VTVAKALKNKNVSIWKDALKQLKTQTSTNITGMGTKVYSTLKLSYKHLEGDEVKSLFLLC 408

Query: 425 GLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGD 484
           GL      I +  LL+Y MGLR      LF+   TLE A+NR++ L+DNLKAS LLL+  
Sbjct: 409 GLF--SNYIDIRDLLKYGMGLR------LFQGTNTLEEAKNRIETLVDNLKASNLLLETR 460

Query: 485 AEDEAKLHDVIHVVAASIA-EEKLMFSIPNVVDFER--EMEETIQKGPIAISLPYRDIQE 541
                ++HDV+  VA  IA +E  +F+    V  E    M+E +QK  + I L   DI+E
Sbjct: 461 YNAVFRMHDVVQNVAIEIASKEHHVFTFQTGVRMEEWPNMDE-LQKFTM-IYLDCCDIRE 518

Query: 542 LPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQ 601
           LPE L             ++S+L+I + FFEG ++LKVLDFT +    LPSSL  L NL+
Sbjct: 519 LPEGL------------NHNSSLKIPNTFFEGMKQLKVLDFTNMHLPSLPSSLHCLANLR 566

Query: 602 TLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAP 661
           TLCLD  +L DI I+ +LKKLEILSL  ++I+QLP ++ QLT L+LLDL   S L VI P
Sbjct: 567 TLCLDACKLGDITIIAELKKLEILSLMDSDIEQLPRELSQLTHLRLLDLKGSSKLKVIPP 626

Query: 662 NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
           +VIS LS+LE+L M +S++QW+ VEG SNA LAELK LS LTTL+I + DA++  +
Sbjct: 627 DVISSLSQLEDLCMENSYTQWE-VEGKSNAYLAELKHLSYLTTLDIQIPDAKLFPK 681

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563252|ref|XP_002522629.1| Disease resistance protein RPS5, putative [Ricinus communis] gi|223538105|gb|EEF39716.1| Disease resistance protein RPS5, putative [Ricinus communis]

 Score =  497 bits (1280), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 314/699 (44%), Positives = 435/699 (62%), Gaps = 28/699 (4%)

Query: 23  PIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQ 82
           PI   + Y    +S ++  K   E+L   R+R++  VD A   G EI  DV  W+  V++
Sbjct: 20  PIKRHLGYAFNYKSQVENFKNWTEKLVSARERLQHSVDYAVRGGEEIENDVKRWIIGVDK 79

Query: 83  FTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNV 142
             +   K I +D++E  K CF GL PN+ +RY L K+  + +K    L   G       V
Sbjct: 80  AIEEADKLIKDDQEEATKRCFIGLCPNVKARYNLCKKMEKYSKVIAELQNKGRF---DPV 136

Query: 143 SHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIA 202
           S+    +      +K+    +SR  + ++V++AL D  + ++GVCGMGGVGKTTL K++ 
Sbjct: 137 SYRVQLQQIVTSSVKNRGALHSRMSVLKEVMDALADPNVLMVGVCGMGGVGKTTLAKEVH 196

Query: 203 KQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKR 262
           +QV+E+ +FD VVMA +++ PD +KIQG +A  LG+ FD  +    RA +L QRL  EK+
Sbjct: 197 QQVIEEKLFDIVVMATVSEKPDIRKIQGNIADVLGLKFDE-ETETGRAYRLRQRLMTEKK 255

Query: 263 VLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWI 322
           +L+ILDNIW +LEL+++GIP G VD K        C I+LTSRSRDLL  DM  QK+F +
Sbjct: 256 ILVILDNIWAQLELEEVGIPCG-VDHKG-------CKILLTSRSRDLLSCDMGVQKVFRL 307

Query: 323 DALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKD 382
           + L EEEAL LFE +VG+  K  +F+  A E+  KC GLPV + T+A ALKNK   +WKD
Sbjct: 308 EVLQEEEALSLFEMMVGD-VKGGEFQSAASEVTKKCAGLPVLIVTIARALKNKDLYVWKD 366

Query: 383 ALNKLTSSNLREIHGMDADVYSPIKLSYDFL-DDEAKSLFLLCGLHREGRPIHVHYLLRY 441
           A+ +L+  +  EI      VYS ++LSY+ L   E KSLFLLCGL  +     +  L+  
Sbjct: 367 AVKQLSRCDNEEIQ---EKVYSALELSYNHLIGAEVKSLFLLCGLLGKSDIAILDLLM-- 421

Query: 442 VMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAAS 501
                Y  GLGLF+ + TL  ARNRV  LI +LKA+CLLLD D +   K+HDV+  VA S
Sbjct: 422 -----YSTGLGLFKGIDTLGDARNRVHKLISDLKAACLLLDSDIKGRVKIHDVVRDVAIS 476

Query: 502 IAEE-KLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKY 560
           IA   + +F++ N    +    + + K    ISLPY DI  LPE LECP+L+LFLLF + 
Sbjct: 477 IASRMQHLFTVRNGALLKEWPNKDVCKSCTRISLPYNDIHGLPEVLECPELELFLLFTQ- 535

Query: 561 DSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLK 620
           D +L++ D  FE T+ L+VL+FTG+ FS LP SLG L NL TLCLD   L D+AI+G+L 
Sbjct: 536 DISLKVPDLCFELTKNLRVLNFTGMHFSSLPPSLGFLKNLFTLCLDWCALRDVAIIGELT 595

Query: 621 KLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
            L ILS + ++I +LP +I QLT+L+ LDLS+C  L VI   +IS+L++LEELYM +SF 
Sbjct: 596 GLTILSFKHSDIVELPREIRQLTKLKFLDLSHCLKLKVIPAKIISELTQLEELYMNNSFD 655

Query: 681 QWD--KVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
            WD   +    NASLAEL+ L  LTTLEI V DA++L +
Sbjct: 656 LWDVQGINNQRNASLAELECLPYLTTLEICVLDAKILPK 694

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488101|ref|XP_002263761.2| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  496 bits (1278), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 307/717 (42%), Positives = 446/717 (62%), Gaps = 34/717 (4%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  S+ ++ ++ L + ++ ++ Y+   ++ I+ L ++VE+L   R R +  VD+A   G+
Sbjct: 4   IVVSVAAKVSEYLVDSVVRQLGYLSNYRTNIEDLSQKVEKLRDARARQQHSVDEAIRNGH 63

Query: 68  EIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYA 127
           +I  DV  W+ + + F Q   K  + DE E RK CFKGL PNL SRY+LS+ A + A  A
Sbjct: 64  KIEDDVCNWMTRADGFIQNVCK-FLEDEKEARKSCFKGLCPNLKSRYQLSREARKKAGVA 122

Query: 128 EHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVC 187
             +   G    VS     P  ++R            SR     +V+EAL+D K+N IGV 
Sbjct: 123 VQIHGDGQFERVS--YRAPQQEIRS----APSEALRSRVLTLDEVMEALRDAKINKIGVW 176

Query: 188 GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY 247
           G+GGVGKTTLVKQ+A+Q  ++ +FDKVV A + + PD +KIQGELA  LGM F+      
Sbjct: 177 GLGGVGKTTLVKQVAEQAAQEKLFDKVVKAAVLQTPDLKKIQGELADLLGMKFEEESE-Q 235

Query: 248 HRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR 307
            RA +L QR+ +EK +LIILD+IW KL+L+KIGIP          D  + C ++LTSR+ 
Sbjct: 236 GRAARLYQRMNEEKTILIILDDIWAKLDLEKIGIP--------SPDHHKGCKLVLTSRNE 287

Query: 308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST 367
            +L  +M++QK F +  L E+E   LF+   G S +  + +P+A ++  +C GLP+A+ T
Sbjct: 288 HILSSEMDTQKDFRVQPLQEDETWILFKNTAG-SIENPELQPIAVDVAKECAGLPLAIVT 346

Query: 368 VANALKNK-SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDD-EAKSLFLLCG 425
           VA ALK K S +IW+DA  +L S     I G+ A+VYS +KLSY+ L   E KS FLLCG
Sbjct: 347 VATALKGKKSVSIWEDARLQLKSQTSTNITGLTANVYSSLKLSYEHLKGVEVKSFFLLCG 406

Query: 426 LHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDA 485
           L  +   IH+  LL+Y +GLR      LF+   TLE A+NR+D L++ LK+S LLL+   
Sbjct: 407 LISQND-IHIWDLLKYGVGLR------LFQGTNTLEEAKNRIDTLVETLKSSNLLLETGH 459

Query: 486 EDEAKLHDVIHVVAASIA-EEKLMFSIPNV---VDFEREMEETIQKGPIAISLPYRDIQE 541
               ++HD++   A  IA ++  +F++ N    V+    ++E +QK   ++SL   DI+E
Sbjct: 460 NAVVRMHDLVRSTARKIASDQHHVFTLQNTTVRVEGWPRIDE-LQKV-TSVSLHDCDIRE 517

Query: 542 LPERLECPQLKLFLLF-AKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINL 600
           LPE L CP+L+LF  +    +  +QI + FFE  ++LKVLD + ++   LP SL  L NL
Sbjct: 518 LPEGLVCPKLELFGCYDVNTNLAVQIPNKFFEEMKQLKVLDLSRMQLPSLPLSLHCLTNL 577

Query: 601 QTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIA 660
           +TLCL+G ++ DI I+ +LKKLEILSL  ++++QLP +I QLT L+LLDLS  S L VI 
Sbjct: 578 RTLCLNGCKVGDIVIIAKLKKLEILSLIDSDMEQLPREIAQLTHLRLLDLSGSSKLKVIP 637

Query: 661 PNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
             VIS LS+LE L M +SF+QW+  EG SNA LAELK LS LT+L+I +RDA++L +
Sbjct: 638 SGVISSLSQLENLCMANSFTQWEG-EGKSNACLAELKHLSHLTSLDIQIRDAKLLPK 693

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488108|ref|XP_003633701.1| PREDICTED: disease resistance protein At4g27190-like [Vitis vinifera]

 Score =  495 bits (1275), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 305/720 (42%), Positives = 447/720 (62%), Gaps = 36/720 (5%)

Query: 8   IFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGY 67
           I  S+V++ ++ L  P++ ++ Y+   ++ I+ L ++V+ L   R R +  VD+A   G+
Sbjct: 4   IIGSVVAKVSEYLVGPVVRQLDYLFNYRTNIEDLSQKVDNLRDARARQQHSVDEAIGNGH 63

Query: 68  EIFADVTEWLGKVEQFTQ-GYAKH---IINDEDEVRKPCFKGLSPNLMSRYKLSKRAVED 123
            I  DV +W+ + + F Q G+ ++    + DE E RK CF  L PNL SRY+LS+ A + 
Sbjct: 64  IIEDDVCKWMKRADGFIQNGFIQNACKFLEDEKEARKSCFNRLCPNLKSRYQLSREARKR 123

Query: 124 AKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNI 183
           A  A  +L  G       VS+  P  ++E           SR     +V+ AL+D K+N 
Sbjct: 124 AGVAVEILGAGQF---ERVSYRAP--LQEIRSAPS-EALESRMLTLNEVMVALRDAKINK 177

Query: 184 IGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSN 243
           IGV G+GGVGKTTLVKQ+A+Q  ++ +FDKVV A + + PD +KIQGELA  LGM F+  
Sbjct: 178 IGVWGLGGVGKTTLVKQVAEQAAQEKLFDKVVTAAVLETPDLKKIQGELADLLGMKFEEE 237

Query: 244 DLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILT 303
                RA +L QR+ +EK +LIILD+IW KL+L+KIGIP          D  + C ++LT
Sbjct: 238 SE-QGRAARLYQRMNEEKTILIILDDIWAKLDLEKIGIP--------SPDHHKGCKLVLT 288

Query: 304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV 363
           SR+  +L  +M++QK F +  L E+E   LF+   G S +  + +P+A ++  +C GLP+
Sbjct: 289 SRNEHILSNEMDTQKDFRVQPLQEDETWILFKNTAG-SIENPELQPIAVDVAKECAGLPL 347

Query: 364 ALSTVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDD-EAKSLFL 422
           A+ TVA ALKNK+ +IWKDAL +L S  L  + G+  +VYS +KLSY+ L   E KS FL
Sbjct: 348 AIVTVAKALKNKNVSIWKDALQQLKSQTLTNVTGLTTNVYSSLKLSYEHLKGVEVKSFFL 407

Query: 423 LCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD 482
           LCGL  +   I +  LL+Y +GLR      LF+   TLE A+NR+DAL+DNLK+S  LL+
Sbjct: 408 LCGLISQND-ISIRDLLKYGVGLR------LFQGTNTLEEAKNRIDALVDNLKSSNFLLE 460

Query: 483 GDAEDEAKLHDVIHVVAASIA-EEKLMFSIPNV---VDFEREMEETIQKGPIAISLPYRD 538
                  ++HD++   A  IA ++  +F++ N    V+    ++E +QK    +SL   D
Sbjct: 461 TGHNAFVRMHDLVRSTARKIASDQHHVFTLQNTTVRVEGWPRIDE-LQK-VTWVSLHDCD 518

Query: 539 IQELPERLECPQLKLFLLF-AKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRL 597
           I+ELPE L CP+L+LF  +    +S +QI ++FFE  ++LKVLD + ++   LP S    
Sbjct: 519 IRELPEGLACPKLELFGCYDVNTNSAVQIPNNFFEEMKQLKVLDLSRMQLPSLPLSCHCR 578

Query: 598 INLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV 657
            NL+TLCLDG  L +I I+ +LKKLEILSL  ++I++LP +I QLT L+L DL     L 
Sbjct: 579 TNLRTLCLDGCNLGEIVIIAELKKLEILSLTYSDIEKLPREIAQLTHLRLFDLKGSYKLK 638

Query: 658 VIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR 717
           VI P+VIS LS+LE+L M +SF+QW+  EG SNA LAELK LS LT+L+I + DA++L +
Sbjct: 639 VIPPDVISSLSQLEDLCMENSFTQWEG-EGKSNACLAELKHLSHLTSLDIQIPDAKLLPK 697

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	724
TAIR|locus:2136447	985	AT4G27190 [Arabidopsis thalian	0.820	0.603	0.301	5.1e-62
TAIR|locus:2131689	919	AT4G27220 [Arabidopsis thalian	0.720	0.568	0.306	4.7e-57
TAIR|locus:2132741	892	AT4G10780 [Arabidopsis thalian	0.853	0.692	0.295	1.3e-49
TAIR|locus:2034770	894	SUMM2 "AT1G12280" [Arabidopsis	0.881	0.713	0.284	3.5e-49
TAIR|locus:2008440	899	AT1G61180 [Arabidopsis thalian	0.872	0.703	0.288	3.3e-47
TAIR|locus:2036214	851	AT1G15890 [Arabidopsis thalian	0.857	0.729	0.276	8.4e-47
TAIR|locus:2005517	909	RPS2 "RESISTANT TO P. SYRINGAE	0.636	0.507	0.311	1.1e-46
TAIR|locus:2008510	967	AT1G61190 "AT1G61190" [Arabido	0.848	0.634	0.279	2.1e-44
TAIR|locus:2166320	888	AT5G63020 [Arabidopsis thalian	0.868	0.708	0.277	3.5e-44
TAIR|locus:2201986	885	RFL1 "AT1G12210" [Arabidopsis	0.853	0.698	0.271	3.9e-43

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

 Score = 639 (230.0 bits), Expect = 5.1e-62, P = 5.1e-62
 Identities = 194/644 (30%), Positives = 327/644 (50%)

Query:    97 EVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDM 156
             E R  C   L P  MSR KL K  +++ K    +L    +  V  +S    P+  E    
Sbjct:    87 EERVSCGMSLRPR-MSR-KLVK-ILDEVK----MLEKDGIEFVDMLSVESTPERVEHVPG 139

Query:   157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV---FDK 213
                        +   + + L  +K   IGV GMGGVGKTTLV+ +  ++ E+     F  
Sbjct:   140 VSVVHQTMASNMLAKIRDGLTSEKAQKIGVWGMGGVGKTTLVRTLNNKLREEGATQPFGL 199

Query:   214 VVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK 273
             V+   ++K  D +++Q ++A  L ++    +     A+++   L KE++ L+ILD++W  
Sbjct:   200 VIFVIVSKEFDPREVQKQIAERLDIDTQMEESEEKLARRIYVGLMKERKFLLILDDVWKP 259

Query:   274 LELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQL 333
             ++LD +GIP        + ++ +   +ILTSR  ++ C  M +     +D L EE+A +L
Sbjct:   260 IDLDLLGIP--------RTEENKGSKVILTSRFLEV-CRSMKTDLDVRVDCLLEEDAWEL 310

Query:   334 FEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPA-IWKDALNKLTSSNL 392
             F K  G+  ++   R +A+ +  +CGGLP+A+ TV  A++ K    +W   L+KL+ S +
Sbjct:   311 FCKNAGDVVRSDHVRKIAKAVSQECGGLPLAIITVGTAMRGKKNVKLWNHVLSKLSKS-V 369

Query:   393 REIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLG 452
               I  ++  ++ P+KLSYDFL+D+AK  FLLC L  E   I V  ++RY M   + + LG
Sbjct:   370 PWIKSIEEKIFQPLKLSYDFLEDKAKFCFLLCALFPEDYSIEVTEVVRYWMAEGFMEELG 429

Query:   453 LFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIH-----VVAASIAEE-K 506
                   + E + N     +++LK  CLL DGD  D  K+HDV+      ++++S  +   
Sbjct:   430 ------SQEDSMNEGITTVESLKDYCLLEDGDRRDTVKMHDVVRDFAIWIMSSSQDDSHS 483

Query:   507 LMFSIPNVVDFERE-MEETIQKGPIAISLPYRDIQELPERLE--CPQLKLFLLFAKYDST 563
             L+ S   + D  ++ +  ++++    +SL    ++ LP+ +E  C +  + LL   +   
Sbjct:   484 LVMSGTGLQDIRQDKLAPSLRR----VSLMNNKLESLPDLVEEFCVKTSVLLLQGNF-LL 538

Query:   564 LQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCL-DGWRLEDIAIVGQLKK 621
              ++   F +    L++L+ +G R    PS SL RL +L +L L D ++L  +  +  L K
Sbjct:   539 KEVPIGFLQAFPTLRILNLSGTRIKSFPSCSLLRLFSLHSLFLRDCFKLVKLPSLETLAK 598

Query:   622 LEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ 681
             LE+L L G  I + P  + +L R + LDLS    L  I   V+S+LS LE L M  S  +
Sbjct:   599 LELLDLCGTHILEFPRGLEELKRFRHLDLSRTLHLESIPARVVSRLSSLETLDMTSSHYR 658

Query:   682 WDKVEGGSN---ASLAELKGLSKLTTLEIDVRDAEML---RRIW 719
             W  V+G +    A++ E+  L +L  L I +  +  L   R  W
Sbjct:   659 WS-VQGETQKGQATVEEIGCLQRLQVLSIRLHSSPFLLNKRNTW 701

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 592 (213.5 bits), Expect = 4.7e-57, P = 4.7e-57
 Identities = 174/567 (30%), Positives = 286/567 (50%)

Query:   166 KKIFQDVIEALKD--DKLNI--IGVCGMGGVGKTTLVKQIAKQVME---DNVFDKVVMAE 218
             +K   ++++ LKD   K N+  IGV GMGGVGKTTLV+ +   +++      F  V+   
Sbjct:   115 QKTALEMLDKLKDCLKKKNVQKIGVWGMGGVGKTTLVRTLNNDLLKYAATQQFALVIWVT 174

Query:   219 ITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDK 278
             ++K+ D +++Q ++A  LG  F + + +      +C+RL   K  L+ILD++W  ++LD+
Sbjct:   175 VSKDFDLKRVQMDIAKRLGKRF-TREQMNQLGLTICERLIDLKNFLLILDDVWHPIDLDQ 233

Query:   279 IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIV 338
             +GIP      KD         ++LTSR  ++ C  M + +   +  L E+EA +LF   V
Sbjct:   234 LGIPLALERSKDSK-------VVLTSRRLEV-CQQMMTNENIKVACLQEKEAWELFCHNV 285

Query:   339 GESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPA-IWKDALNKLTSSNLREIHG 397
             GE   + + +P+A+++  +C GLP+A+ T+   L+ K    +WK  LN L     R    
Sbjct:   286 GEVANSDNVKPIAKDVSHECCGLPLAIITIGRTLRGKPQVEVWKHTLNLLK----RSAPS 341

Query:   398 MDAD--VYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFR 455
             +D +  ++  +KLSYDFL D  KS FL C L  E   I V  L+ Y +        GL  
Sbjct:   342 IDTEEKIFGTLKLSYDFLQDNMKSCFLFCALFPEDYSIKVSELIMYWVAE------GLLD 395

Query:   456 NVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVA----ASIAE--EKLMF 509
               +  E   N    L++ LK SCLL DGD+ D  K+HDV+   A    +S  E    L+ 
Sbjct:   396 GQHHYEDMMNEGVTLVERLKDSCLLEDGDSCDTVKMHDVVRDFAIWFMSSQGEGFHSLVM 455

Query:   510 SIPNVVDFERE-MEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD 568
             +   +++F ++    ++Q+    +SL    ++ LP  +      L LL        ++ +
Sbjct:   456 AGRGLIEFPQDKFVSSVQR----VSLMANKLERLPNNVIEGVETLVLLLQGNSHVKEVPN 511

Query:   569 HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWR-LEDIAIVGQLKKLEILSL 627
              F +    L++LD +G+R   LP S   L +L++L L   + L ++  +  L KL+ L L
Sbjct:   512 GFLQAFPNLRILDLSGVRIRTLPDSFSNLHSLRSLVLRNCKKLRNLPSLESLVKLQFLDL 571

Query:   628 RGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEG 687
               + I++LP  +  L+ L+ + +SN   L  I    I +LS LE L M  S   W  ++G
Sbjct:   572 HESAIRELPRGLEALSSLRYICVSNTYQLQSIPAGTILQLSSLEVLDMAGSAYSWG-IKG 630

Query:   688 GSN---ASLAELKGLSKLTTLEIDVRD 711
                   A+L E+  L  L  L I + D
Sbjct:   631 EEREGQATLDEVTCLPHLQFLAIKLLD 657

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 = 530 (191.6 bits), Expect = 1.3e-49, P = 1.3e-49
 Identities = 196/663 (29%), Positives = 314/663 (47%)

Query:    29 SYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYA 88
             +Y+ K +  I  L++ +E+L   R  V   V     +G E    V  WL +VE     + 
Sbjct:    27 NYIHKLKDNIVALEKAIEDLTATRDDVLRRVQMEEGKGLERLQQVQVWLKRVEIIRNQFY 86

Query:    89 KHIINDEDEVRKPCF-KGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPP 147
               +     E+++ CF    S NL S Y   +R     K  E+L + G   IV+     P 
Sbjct:    87 DLLSARNIEIQRLCFYSNCSTNLSSSYTYGQRVFLMIKEVENLNSNGFFEIVA----APA 142

Query:   148 PKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME 207
             PK+ E   ++       R+ IFQ     L DD +  +G+ GMGGVGKTTL+ QI   + +
Sbjct:   143 PKL-EMRPIQP--TIMGRETIFQRAWNRLMDDGVGTMGLYGMGGVGKTTLLTQIHNTLHD 199

Query:   208 D-NVFDKVVMAEITKNPDAQKIQGELASDLG-MNFDSNDLIY-HRAKQLCQRLKKEKRVL 264
               N  D V+   ++ +    KIQ ++   LG +  + N      +A  +   L K KR +
Sbjct:   200 TKNGVDIVIWVVVSSDLQIHKIQEDIGEKLGFIGKEWNKKQESQKAVDILNCLSK-KRFV 258

Query:   265 IILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDA 324
             ++LD+IW K++L KIGIP     +  +N    +C ++ T+RS D+ C  M       +  
Sbjct:   259 LLLDDIWKKVDLTKIGIP----SQTREN----KCKVVFTTRSLDV-CARMGVHDPMEVQC 309

Query:   325 LSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANALKNKSPAI-WK 381
             LS  +A +LF++ VG+ +  S  D   LA+++ GKC GLP+AL+ +   +  K     W 
Sbjct:   310 LSTNDAWELFQEKVGQISLGSHPDILELAKKVAGKCRGLPLALNVIGETMAGKRAVQEWH 369

Query:   382 DALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIHVHYLLR 440
              A++ LTS    E  GMD  +   +K SYD L+D+  +S F  C L+ E   I  + L+ 
Sbjct:   370 HAVDVLTSY-AAEFSGMDDHILLILKYSYDNLNDKHVRSCFQYCALYPEDYSIKKYRLID 428

Query:   441 YVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD-GDAEDEAKLHDVIHVVA 499
             Y +   +  G     N+   E A N+   ++  L  +CLL + G  + E K+HDV+  +A
Sbjct:   429 YWICEGFIDG-----NIGK-ERAVNQGYEILGTLVRACLLSEEGKNKLEVKMHDVVREMA 482

Query:   500 ----ASIAEEKLMFSIPNVVDFEREMEETIQKGPIA-ISLPYRDIQELPERLECPQLK-L 553
                 + + + K    I       R++ +    G +  +SL    I+E+    ECP+L  L
Sbjct:   483 LWTLSDLGKNKER-CIVQAGSGLRKVPKVEDWGAVRRLSLMNNGIEEISGSPECPELTTL 541

Query:   554 FLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLINLQTLCLDGWRLED 612
             FL   K  S + IS  FF    +L VLD +   +   LP  +  L+ L+ L L    +E 
Sbjct:   542 FLQENK--SLVHISGEFFRHMRKLVVLDLSENHQLDGLPEQISELVALRYLDLSHTNIEG 599

Query:   613 I-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV-VIAPNVISKLSRL 670
             + A +  LK L  L+L           I +L+ L+ L L N + ++ V++   +  L  L
Sbjct:   600 LPACLQDLKTLIHLNLECMRRLGSIAGISKLSSLRTLGLRNSNIMLDVMSVKELHLLEHL 659

Query:   671 EEL 673
             E L
Sbjct:   660 EIL 662

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

 Score = 528 (190.9 bits), Expect = 3.5e-49, P = 3.5e-49
 Identities = 196/689 (28%), Positives = 326/689 (47%)

Query:     5 CLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVD-QAT 63
             CL +  S   E    +S+ +   + Y+ +    +  +K+ +E L ++R  VK  VD +  
Sbjct:     4 CLTLSFSC-DEVVNQISQGLCINVGYICELSKNVVAMKKDMEVLKKKRDDVKRRVDIEEF 62

Query:    64 EQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVE 122
              +  E  + V  WL  V      + + +  ++ E+++ C  G  S N+   Y   KR V 
Sbjct:    63 TRRRERLSQVQGWLTNVSTVENKFNELLTTNDAELQRLCLFGFCSKNVKMSYLYGKRVVL 122

Query:   123 DAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLN 182
               K  E L + G    V+  +  P  ++ E   M        ++ + + V   L +D   
Sbjct:   123 MLKEIESLSSQGDFDTVTLAT--PIARIEE---MPIQPTIVGQETMLERVWTRLTEDGDE 177

Query:   183 IIGVCGMGGVGKTTLVKQIAKQVMED-NVFDKVVMAEITKNPDAQKIQGELASDLGMNFD 241
             I+G+ GMGGVGKTTL+ +I  +  E  + F  V+   ++K+PD  +IQG++   L +  +
Sbjct:   178 IVGLYGMGGVGKTTLLTRINNKFSEKCSGFGVVIWVVVSKSPDIHRIQGDIGKRLDLGGE 237

Query:   242 SNDLIYH--RAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCT 299
               D +    RA  +   L K+K VL+ LD+IW K+ L+ +G+PY       +N     C 
Sbjct:   238 EWDNVNENQRALDIYNVLGKQKFVLL-LDDIWEKVNLEVLGVPY----PSRQNG----CK 288

Query:   300 IILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGK 357
             ++ T+RSRD+ C  M       +  L   EA +LF+  VGE+T     D   LA ++ GK
Sbjct:   289 VVFTTRSRDV-CGRMRVDDPMEVSCLEPNEAWELFQMKVGENTLKGHPDIPELARKVAGK 347

Query:   358 CGGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE 416
             C GLP+AL+ +   +  K     W++A++ L SS   E  GM+  +   +K SYD L+ E
Sbjct:   348 CCGLPLALNVIGETMACKRMVQEWRNAIDVL-SSYAAEFPGME-QILPILKYSYDNLNKE 405

Query:   417 -AKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLK 475
               K  FL C L  E   +    L+ Y +        G      + E A ++   +I  L 
Sbjct:   406 QVKPCFLYCSLFPEDYRMEKERLIDYWICE------GFIDENESRERALSQGYEIIGILV 459

Query:   476 ASCLLLDGDA-EDEAKLHDVIHV----VAASIAEEKLMFSIPNVVDFEREMEETIQKGPI 530
              +CLLL+    +++ K+HDV+      +A+ + E K    +   V   RE+ +      +
Sbjct:   460 RACLLLEEAINKEQVKMHDVVREMALWIASDLGEHKERCIVQVGVGL-REVPKVKNWSSV 518

Query:   531 A-ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTG-IRFS 588
               +SL   +I+ L    EC +L    L  K DS L ISD FF     L VLD +G     
Sbjct:   519 RRMSLMENEIEILSGSPECLELTTLFL-QKNDSLLHISDEFFRCIPMLVVLDLSGNSSLR 577

Query:   589 PLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSLRGAE-IKQLP--LQIGQLTR 644
              LP+ + +L++L+ L L    ++ + + + +LKKL  L L   + +K +     I  L +
Sbjct:   578 KLPNQISKLVSLRYLDLSWTYIKRLPVGLQELKKLRYLRLDYMKRLKSISGISNISSLRK 637

Query:   645 LQLLDLSNCSSLVVIAPNVISKLSRLEEL 673
             LQLL      S + +  +++ +L  LE L
Sbjct:   638 LQLLQ-----SKMSLDMSLVEELQLLEHL 661

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 511 (184.9 bits), Expect = 3.3e-47, Sum P(2) = 3.3e-47
 Identities = 197/684 (28%), Positives = 325/684 (47%)

Query:     9 FSSIVSEGT-KTLSEPIIGRMSYVLKCQSYIDGLKERVEELG--QRRKRVKILVDQATEQ 65
             FS  VS+ T   +   +IG+ SY+   +  +  L+  +E+L   Q   + K+  D+A  Q
Sbjct:     5 FSLQVSDQTLNRIFNCLIGK-SYIRTLEKNLRALQREMEDLRAIQHEVQNKVARDEARHQ 63

Query:    66 GYEIFADVTEWLGKVEQFTQGYAKHIINDED-EVRKPCFKGL-SPNLMSRYKLSKRAVED 123
                + A V  WL +V        K +++    E++K C  GL S  + S YK  K+    
Sbjct:    64 R-RLEA-VQVWLDRVNS-VDIECKDLLSVTPVELQKLCLCGLCSKYVCSSYKYGKKVFLL 120

Query:   124 AKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNI 183
              +  + L + G+      VS PPP   R   + +       ++ + +     L +D + I
Sbjct:   121 LEEVKKLNSEGNF---DEVSQPPP---RSEVEERPTQPTIGQEDMLEKAWNRLMEDGVGI 174

Query:   184 IGVCGMGGVGKTTLVKQIAKQVME-DNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD- 241
             +G+ GMGGVGKTTL K+I  +  E    FD V+   ++K     K+Q ++A  L +  D 
Sbjct:   175 MGLHGMGGVGKTTLFKKIHNKFAEIGGTFDIVIWIVVSKGVMISKLQEDIAEKLHLCDDL 234

Query:   242 -SNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTI 300
               N     +A  +  R+ K KR +++LD+IW K++L+ IGIPY          +  +C +
Sbjct:   235 WKNKNESDKATDI-HRVLKGKRFVLMLDDIWEKVDLEAIGIPYPS--------EVNKCKV 285

Query:   301 ILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASD--FRPLAEEIVGKC 358
               T+RSR++ C +M   K   ++ L  E+A +LF+  VG++T +SD     LA E+  KC
Sbjct:   286 AFTTRSREV-CGEMGDHKPMQVNCLEPEDAWELFKNKVGDNTLSSDPVIVELAREVAQKC 344

Query:   359 GGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE- 416
              GLP+AL+ +   + +K+    W+ A++   +S   E   M   +   +K SYD L DE 
Sbjct:   345 RGLPLALNVIGETMSSKTMVQEWEHAIHVFNTS-AAEFSDMQNKILPILKYSYDSLGDEH 403

Query:   417 AKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKA 476
              KS FL C L  E   I+   L+ Y +        G       ++ ARN+  A++  L  
Sbjct:   404 IKSCFLYCALFPEDGEIYNEKLIDYWICE------GFIGEDQVIKRARNKGYAMLGTLTR 457

Query:   477 SCLLLDGDAEDEAKLHDVIHVVAASIA----EEKLMFSIPNVVDFEREMEETIQKGPIA- 531
             + LL          +HDV+  +A  IA    ++K  F +   V    E+ +    G +  
Sbjct:   458 ANLLTKVGTY-YCVMHDVVREMALWIASDFGKQKENFVVQAGVGLH-EIPKVKDWGAVRK 515

Query:   532 ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-FSPL 590
             +SL   DI+E+    +C +L    LF + +    +   F    ++L VLD +  R F+ L
Sbjct:   516 MSLMDNDIEEITCESKCSELTT--LFLQSNKLKNLPGAFIRYMQKLVVLDLSYNRDFNKL 573

Query:   591 PSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD 649
             P  +  L++LQ L L    +E + I + +LKKL  L L   +       I +L  L+LL 
Sbjct:   574 PEQISGLVSLQFLDLSNTSIEHMPIGLKELKKLTFLDLTYTDRLCSISGISRLLSLRLLR 633

Query:   650 LSNCSSLVVIAPNVISKLSRLEEL 673
             L    S V    +V+ +L +L+ L
Sbjct:   634 L--LGSKVHGDASVLKELQQLQNL 655

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

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2036214 AT1G15890 [Arabidopsis thaliana (taxid:3702)]

 Score = 511 (184.9 bits), Expect = 8.4e-47, Sum P(2) = 8.4e-47
 Identities = 184/666 (27%), Positives = 315/666 (47%)

Query:    24 IIGRMSYVLKCQSYIDGLKERVEELGQRRKRV--KILVDQATEQGYEIFADVTEWLGKVE 81
             + G  +Y+LK ++ ++ L+  ++EL +RR  +  ++++++  ++G +  A V  WL +V+
Sbjct:    22 LFGDRNYILKMEANLEALQNTMQELEERRDDLLRRVVIEE--DKGLQRLAQVQGWLSRVK 79

Query:    82 QFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVS 140
                      +     +  + C  G  S N +S        ++  K+ E LLA G   +V+
Sbjct:    80 DVCSQVNDLLKAKSIQTERLCLCGYCSKNFISGRNYGINVLKKLKHVEGLLAKGVFEVVA 139

Query:   141 NVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQ 200
                  P PK+ +    K          +      +L  D+   +G+ GMGGVGKTTL+  
Sbjct:   140 EKI--PAPKVEK----KHIQTTVGLDAMVGRAWNSLMKDERRTLGLYGMGGVGKTTLLAS 193

Query:   201 IAKQVMED-NVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY-HRAKQLCQRLK 258
             I  + +E  N FD V+   ++K+   + IQ ++   LG++     +    +A  +C  L 
Sbjct:   194 INNKFLEGMNGFDLVIWVVVSKDLQNEGIQEQILGRLGLHRGWKQVTEKEKASYICNILN 253

Query:   259 KEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQK 318
              +K VL+ LD++W++++L+KIG+P    +   K        I+ T+RS+D+ C DM    
Sbjct:   254 VKKFVLL-LDDLWSEVDLEKIGVPPLTRENGSK--------IVFTTRSKDV-CRDMEVDG 303

Query:   319 MFWIDALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANALKNKS 376
                +D L  +EA +LF+K VG     S  D   LA ++  KC GLP+ALS +  A+ ++ 
Sbjct:   304 EMKVDCLPPDEAWELFQKKVGPIPLQSHEDIPTLARKVAEKCCGLPLALSVIGKAMASRE 363

Query:   377 PAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIH 434
                 W+  ++ L SS+  E   M+  +   +K SYD L DE  K  FL C L  E   + 
Sbjct:   364 TVQEWQHVIHVLNSSS-HEFPSMEEKILPVLKFSYDDLKDEKVKLCFLYCSLFPEDYEVR 422

Query:   435 VHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDV 494
                L+ Y M   +  G     N    + A N+   +I +L  + LL+DG+   + K+HDV
Sbjct:   423 KEELIEYWMCEGFIDG-----NEDE-DGANNKGHDIIGSLVRAHLLMDGELTTKVKMHDV 476

Query:   495 IHVVAASIA----EEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQ 550
             I  +A  IA    ++K    +   V      ++   +    +SL    I  +      P 
Sbjct:   477 IREMALWIASNFGKQKETLCVKPGVQLCHIPKDINWESLRRMSLMCNQIANISSSSNSPN 536

Query:   551 LKLFLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLINLQTLCLDGWR 609
             L   LL  + +  + IS  FF     L VLD +     S LP ++ +L +LQ + L    
Sbjct:   537 LSTLLL--QNNKLVHISCDFFRFMPALVVLDLSRNSSLSSLPEAISKLGSLQYINLSTTG 594

Query:   610 LEDIAI-VGQLKKLEILSLRGA-EIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKL 667
             ++ + +   +LKKL  L+L    E++ +      L  LQ+L L   SS V I  +++ +L
Sbjct:   595 IKWLPVSFKELKKLIHLNLEFTDELESIVGIATSLPNLQVLKLF--SSRVCIDGSLMEEL 652

Query:   668 SRLEEL 673
               LE L
Sbjct:   653 LLLEHL 658

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2005517 RPS2 "RESISTANT TO P. SYRINGAE 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 506 (183.2 bits), Expect = 1.1e-46, Sum P(3) = 1.1e-46
 Identities = 155/498 (31%), Positives = 274/498 (55%)

Query:   168 IFQDVIEAL-KDDKLNIIGVCGMGGVGKTTLVKQIAKQVM-EDNVFDKVVMAEITKNPDA 225
             + + V+E L ++++  IIGV G GGVGKTTL++ I  +++ + + +D ++  ++++    
Sbjct:   161 MMEQVLEFLSEEEERGIIGVYGPGGVGKTTLMQSINNELITKGHQYDVLIWVQMSREFGE 220

Query:   226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGD 285
               IQ  + + LG+++D  +   +RA ++ + L+ +KR L++LD++W +++L+K G+P  D
Sbjct:   221 CTIQQAVGARLGLSWDEKETGENRALKIYRALR-QKRFLLLLDDVWEEIDLEKTGVPRPD 279

Query:   286 VDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLF-EKIVGEST-K 343
              + K        C ++ T+RS   LC +M ++    ++ L ++ A +LF  K+  +   +
Sbjct:   280 RENK--------CKVMFTTRSI-ALCNNMGAEYKLRVEFLEKKHAWELFCSKVWRKDLLE 330

Query:   344 ASDFRPLAEEIVGKCGGLPVALSTVANALKNK-SPAIWKDALNKLTSSNLREIHGMDADV 402
             +S  R LAE IV KCGGLP+AL T+  A+ ++ +   W  A   LT     E+ GM+  V
Sbjct:   331 SSSIRRLAEIIVSKCGGLPLALITLGGAMAHRETEEEWIHASEVLTRFPA-EMKGMNY-V 388

Query:   403 YSPIKLSYDFLD-DEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLE 461
             ++ +K SYD L+ D  +S FL C L  E   I +  L+ Y +G  +   L     V T+ 
Sbjct:   389 FALLKFSYDNLESDLLRSCFLYCALFPEEHSIEIEQLVEYWVGEGF---LTSSHGVNTIY 445

Query:   462 AARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEK-----LMFSIPNVVD 516
                     LI +LKA+CLL  GD + + K+H+V+   A  +A E+     L+   P++  
Sbjct:   446 KGY----FLIGDLKAACLLETGDEKTQVKMHNVVRSFALWMASEQGTYKELILVEPSMGH 501

Query:   517 FEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQ-ISDHFFEGTE 575
              E    E  ++  + ISL    IQ LPE+L CP+L   +L  + +S+L+ I   FF    
Sbjct:   502 TEAPKAENWRQA-LVISLLDNRIQTLPEKLICPKLTTLML--QQNSSLKKIPTGFFMHMP 558

Query:   576 ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSLRGAEIKQ 634
              L+VLD +    + +P S+  L+ L  L + G ++  +   +G L+KL+ L L+  +  Q
Sbjct:   559 VLRVLDLSFTSITEIPLSIKYLVELYHLSMSGTKISVLPQELGNLRKLKHLDLQRTQFLQ 618

Query:   635 -LPLQ-IGQLTRLQLLDL 650
              +P   I  L++L++L+L
Sbjct:   619 TIPRDAICWLSKLEVLNL 636

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0043531 "ADP binding" evidence=IEA

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

GO:0016045 "detection of bacterium" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0042742 "defense response to bacterium" evidence=RCA;IMP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009595 "detection of biotic stimulus" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

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

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

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

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031347 "regulation of defense response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0043069 "negative regulation of programmed cell death" evidence=RCA

GO:0043900 "regulation of multi-organism process" evidence=RCA

GO:0045087 "innate immune response" evidence=RCA

GO:0050776 "regulation of immune response" evidence=RCA

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

GO:0051707 "response to other organism" evidence=RCA

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

 Score = 493 (178.6 bits), Expect = 2.1e-44, P = 2.1e-44
 Identities = 185/663 (27%), Positives = 311/663 (46%)

Query:    30 YVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAK 89
             Y+   +  +  L+  +E+L   +  V+  V +   +  +    V  WL +V        K
Sbjct:    27 YIRNLEKNLRALQREMEDLRATQHEVQNKVAREESRHQQRLEAVQVWLDRVNSIDIE-CK 85

Query:    90 HIINDED-EVRKPCFKGL-SPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPP 147
              +++    E++K C  GL S  + S YK  KR     +    L + G+      VS PPP
Sbjct:    86 DLLSVSPVELQKLCLCGLCSKYVCSSYKYGKRVFLLLEEVTKLKSEGNF---DEVSQPPP 142

Query:   148 PKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME 207
                R   + +       ++++ +     L +D + I+G+ GMGGVGKTTL K+I  +  E
Sbjct:   143 ---RSEVEERPTQPTIGQEEMLKKAWNRLMEDGVGIMGLHGMGGVGKTTLFKKIHNKFAE 199

Query:   208 DN-VFDKVVMAEITKNPDAQKIQGELASDLGMNFD--SNDLIYHRAKQLCQRLKKEKRVL 264
                 FD V+   +++     K+Q ++A  L +  D   N     +A  +  R+ K KR +
Sbjct:   200 TGGTFDIVIWIVVSQGAKLSKLQEDIAEKLHLCDDLWKNKNESDKATDI-HRVLKGKRFV 258

Query:   265 IILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDA 324
             ++LD+IW K++L+ IGIPY          +  +C +  T+R + + C  M   K   +  
Sbjct:   259 LMLDDIWEKVDLEAIGIPYPS--------EVNKCKVAFTTRDQKV-CGQMGDHKPMQVKC 309

Query:   325 LSEEEALQLFEKIVGESTKASD--FRPLAEEIVGKCGGLPVALSTVANALKNKSPAI-WK 381
             L  E+A +LF+  VG++T  SD     LA E+  KC GLP+ALS +   + +K+    W+
Sbjct:   310 LEPEDAWELFKNKVGDNTLRSDPVIVGLAREVAQKCRGLPLALSCIGETMASKTMVQEWE 369

Query:   382 DALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIHVHYLL- 439
              A++ LT S   E   M   +   +K SYD L+DE  KS FL C L  E   I    L+ 
Sbjct:   370 HAIDVLTRS-AAEFSDMQNKILPILKYSYDSLEDEHIKSCFLYCALFPEDDKIDTKTLIN 428

Query:   440 RYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNL-KASCLLLD-GDAEDEAKLHDVIHV 497
             +++         G       ++ ARN+   ++  L +A+ L  D G  +    +HDV+  
Sbjct:   429 KWICE-------GFIGEDQVIKRARNKGYEMLGTLIRANLLTNDRGFVKWHVVMHDVVRE 481

Query:   498 VAASIA----EEKLMFSIPNVVDFEREMEETIQKGPIA-ISLPYRDIQELPERLECPQLK 552
             +A  IA    ++K  + +   V    E+ +    G +  +SL   +I+E+    +C +L 
Sbjct:   482 MALWIASDFGKQKENYVVRARVGLH-EIPKVKDWGAVRRMSLMMNEIEEITCESKCSELT 540

Query:   553 LFLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLINLQTLCLDGWRLE 611
                LF + +    +S  F    ++L VLD +    F+ LP  +  L++LQ L L   R+E
Sbjct:   541 T--LFLQSNQLKNLSGEFIRYMQKLVVLDLSHNPDFNELPEQISGLVSLQYLDLSWTRIE 598

Query:   612 DIAI-VGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL 670
              + + + +LKKL  L+L   E       I +L  L+ L L    S V    +V+ +L +L
Sbjct:   599 QLPVGLKELKKLIFLNLCFTERLCSISGISRLLSLRWLSLRE--SNVHGDASVLKELQQL 656

Query:   671 EEL 673
             E L
Sbjct:   657 ENL 659

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 490 (177.5 bits), Expect = 3.5e-44, P = 3.5e-44
 Identities = 192/692 (27%), Positives = 327/692 (47%)

Query:     5 CLAIFSSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRV--KILVDQA 62
             C+++  S   + TK +   +     Y+   +  +  L+  +E++ QRR+ +  KIL ++ 
Sbjct:     4 CVSVSISC-DQLTKNVCSCLNRNGDYIHGLEENLTALQRALEQIEQRREDLLRKILSEE- 61

Query:    63 TEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAV 121
               +G +  + V  W+ KVE       + +     +V++ C  G  S NL+S Y+  KR +
Sbjct:    62 -RRGLQRLSVVQGWVSKVEAIVPRVNELVRMRSVQVQRLCLCGFCSKNLVSSYRYGKRVM 120

Query:   122 EDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKL 181
             +  +  E L   G   +V+        + R    M       +   + +     L +D++
Sbjct:   121 KMIEEVEVLRYQGDFAVVAERVDAARVEERPTRPMV------AMDPMLESAWNRLMEDEI 174

Query:   182 NIIGVCGMGGVGKTTLVKQIAKQVME-DNVFDKVVMAEITKNPDAQKIQGELASDLGMNF 240
              I+G+ GMGGVGKTTL+  I  +       FD V+   ++K    Q+IQ E+   L  + 
Sbjct:   175 GILGLHGMGGVGKTTLLSHINNRFSRVGGEFDIVIWIVVSKELQIQRIQDEIWEKLRSDN 234

Query:   241 D-----SNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDP 295
             +     + D+   +A  +   LK  KR +++LD+IW+K++L ++G+P+       +N   
Sbjct:   235 EKWKQKTEDI---KASNIYNVLK-HKRFVLLLDDIWSKVDLTEVGVPF----PSRENG-- 284

Query:   296 RRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKAS--DFRPLAEE 353
               C I+ T+R +++ C  M       +  L+ ++A  LF K VGE T  S  +   +A  
Sbjct:   285 --CKIVFTTRLKEI-CGRMGVDSDMEVRCLAPDDAWDLFTKKVGEITLGSHPEIPTVART 341

Query:   354 IVGKCGGLPVALSTVANALKNKSPAI-WKDALNKLTSSNLREIHGMDADVYSPIKLSYDF 412
             +  KC GLP+AL+ +   +  K     W+ A++ LTSS   E  GM+ ++   +K SYD 
Sbjct:   342 VAKKCRGLPLALNVIGETMAYKRTVQEWRSAIDVLTSS-AAEFSGMEDEILPILKYSYDN 400

Query:   413 LDDEAKSL-FLLCGLHREGRPIHVHYLLRYVMGLRY-DKGLGLFRNVYTLEAARNRVDAL 470
             L  E   L F  C L  E   I  + L+ Y +G  + D+  G          A N+   +
Sbjct:   401 LKSEQLKLCFQYCALFPEDHNIEKNDLVDYWIGEGFIDRNKG---------KAENQGYEI 451

Query:   471 IDNLKASCLLLDGDAEDEAKLHDVIHVVAASIA----EEKLMFSIPNVVDFEREMEETIQ 526
             I  L  SCLL++ + ++  K+HDV+  +A  IA    ++K  F +   +   R + E I+
Sbjct:   452 IGILVRSCLLME-ENQETVKMHDVVREMALWIASDFGKQKENFIVQAGLQ-SRNIPE-IE 508

Query:   527 KGPIA--ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTG 584
             K  +A  +SL + +I+ + +  E PQL   LL   +     IS  FF     L VLD + 
Sbjct:   509 KWKVARRVSLMFNNIESIRDAPESPQLITLLLRKNFLG--HISSSFFRLMPMLVVLDLSM 566

Query:   585 IR-FSPLPSSLGRLINLQTLCLDGWRLEDIAIVG--QLKKLEILSLRGAEIKQLPLQIGQ 641
              R    LP+ +   ++LQ L L   R+  I   G  +L+KL  L+L    + +    I  
Sbjct:   567 NRDLRHLPNEISECVSLQYLSLSRTRIR-IWPAGLVELRKLLYLNLEYTRMVESICGISG 625

Query:   642 LTRLQLLDLSNCSSLVVIAPNVISKLSRLEEL 673
             LT L++L L    S     P V+++L  LE L
Sbjct:   626 LTSLKVLRLF--VSGFPEDPCVLNELQLLENL 655

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 481 (174.4 bits), Expect = 3.9e-43, P = 3.9e-43
 Identities = 180/662 (27%), Positives = 298/662 (45%)

Query:    29 SYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEI-FADVTEWLGKVEQFTQGY 87
             SY+      +  L++ +  L  +R  V+  +++    G+    A V  WL +++     +
Sbjct:    27 SYIQNLSENLASLQKAMGVLNAKRDDVQGRINREEFTGHRRRLAQVQVWLTRIQTIENQF 86

Query:    88 AKHIINDEDEVRKPCFKGL-SPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPP 146
                +     E+++ C  G  S N+   Y   KR +   +  E L + G   IV+  +  P
Sbjct:    87 NDLLSTCNAEIQRLCLCGFCSKNVKMSYLYGKRVIVLLREVEGLSSQGVFDIVTEAA--P 144

Query:   147 PPKMREFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM 206
                + E  ++   +    +  +   V   L +DK+ I+G+ GMGGVGKTTL+ QI  +  
Sbjct:   145 ---IAEVEELPIQSTIVGQDSMLDKVWNCLMEDKVWIVGLYGMGGVGKTTLLTQINNKFS 201

Query:   207 E-DNVFDKVVMAEITKNPDAQKIQGELASDLGM---NFDSNDLIYHRAKQLCQRLKKEKR 262
             +    FD V+   ++KN    KIQ  +   LG+   N+D  +    RA  +   L+++K 
Sbjct:   202 KLGGGFDVVIWVVVSKNATVHKIQKSIGEKLGLVGKNWDEKNK-NQRALDIHNVLRRKKF 260

Query:   263 VLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWI 322
             VL+ LD+IW K+EL  IG+PY       +N     C +  T+ S+++ C  M       I
Sbjct:   261 VLL-LDDIWEKVELKVIGVPY----PSGENG----CKVAFTTHSKEV-CGRMGVDNPMEI 310

Query:   323 DALSEEEALQLFEKIVGESTKAS--DFRPLAEEIVGKCGGLPVALSTVANALKNKSPAI- 379
               L    A  L +K VGE+T  S  D   LA ++  KC GLP+AL+ +   +  K     
Sbjct:   311 SCLDTGNAWDLLKKKVGENTLGSHPDIPQLARKVSEKCCGLPLALNVIGETMSFKRTIQE 370

Query:   380 WKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE-AKSLFLLCGLHREGRPIHVHYL 438
             W+ A   LTS+   +  GM+ ++   +K SYD L+ E AKS FL C L  E   I    L
Sbjct:   371 WRHATEVLTSAT--DFSGMEDEILPILKYSYDSLNGEDAKSCFLYCSLFPEDFEIRKEML 428

Query:   439 LRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAE-DEAKLHDVIHV 497
             + Y +        G  +     E A N+   ++  L  S LLL+G  + D   +HD++  
Sbjct:   429 IEYWICE------GFIKEKQGREKAFNQGYDILGTLVRSSLLLEGAKDKDVVSMHDMVRE 482

Query:   498 VA----ASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKL 553
             +A    + + + K    +   +  +   E    +    +SL   + +++    EC +L  
Sbjct:   483 MALWIFSDLGKHKERCIVQAGIGLDELPEVENWRAVKRMSLMNNNFEKILGSPECVELIT 542

Query:   554 FLLFAKYDSTLQISDHFFEGTEELKVLDFT-GIRFSPLPSSLGRLINLQTLCLDGWRLED 612
               L   Y   + IS  FF     L VLD +     S LP  +  L++LQ L L G  +E 
Sbjct:   543 LFLQNNY-KLVDISMEFFRCMPSLAVLDLSENHSLSELPEEISELVSLQYLDLSGTYIER 601

Query:   613 IAI-VGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE 671
             +   + +L+KL  L L      +    I  L+ L+ L L +  S   +   ++ +L  LE
Sbjct:   602 LPHGLHELRKLVHLKLERTRRLESISGISYLSSLRTLRLRD--SKTTLDTGLMKELQLLE 659

Query:   672 EL 673
              L
Sbjct:   660 HL 661

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	724
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	6e-48
PLN03210	1153	PLN03210, PLN03210, Resistant to P	1e-09
smart00382	148	smart00382, AAA, ATPases associated with a variety	8e-08
COG4886	394	COG4886, COG4886, Leucine-rich repeat (LRR) protei	3e-06
COG4886	394	COG4886, COG4886, Leucine-rich repeat (LRR) protei	2e-05
COG4886	394	COG4886, COG4886, Leucine-rich repeat (LRR) protei	3e-05
pfam13401	124	pfam13401, AAA_22, AAA domain	4e-05
cd01120	165	cd01120, RecA-like_NTPases, RecA-like NTPases	3e-04
pfam13855	60	pfam13855, LRR_8, Leucine rich repeat	4e-04
TIGR00064	272	TIGR00064, ftsY, signal recognition particle-docki	0.004

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

 Score =  170 bits (433), Expect = 6e-48
 Identities = 90/288 (31%), Positives = 141/288 (48%), Gaps = 24/288 (8%)

Query: 169 FQDVIEALKD------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN 222
            +D+IEAL +      D L ++G+ GMGGVGKTTL KQI         FD V    ++K 
Sbjct: 1   REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKT 60

Query: 223 PDAQKIQGELASDLGM-NFDSNDLIYH-RAKQLCQRLKKEKRVLIILDNIWTKLELDKIG 280
               ++Q ++  +LG+ + D  +      A ++ + L   KR L++LD++W K + DKIG
Sbjct: 61  YTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEAL-LRKRFLLVLDDVWEKNDWDKIG 119

Query: 281 IPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQ-KMFWIDALSEEEALQLFEKIVG 339
           +P+ D +            +I+T+RS   +   M    K   +++L  EE+ +LF   V 
Sbjct: 120 VPFPDGEN--------GSRVIVTTRSES-VAGRMGGTSKPHEVESLEPEESWELFSNKVF 170

Query: 340 EST--KASDFRPLAEEIVGKCGGLPVALSTVANALKNKS-PAIWKDALNKLTSSNLREIH 396
           E       +   +A+EIV KC GLP+AL  +   L  KS    W+  L +L +  L    
Sbjct: 171 EKELPPCPELEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNE-LAGRD 229

Query: 397 GMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMG 444
           G++ +V S + LSYD L    K  FL   L  E   I    L++  + 
Sbjct: 230 GLN-EVLSILSLSYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIA 276

Length = 285

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

 Score = 61.8 bits (150), Expect = 1e-09
 Identities = 136/542 (25%), Positives = 239/542 (44%), Gaps = 97/542 (17%)

Query: 176 LKDDKLNIIGVCGMGGVGKTTLVKQIAKQV---MEDNVF-DKVVMAEITK-----NPDAQ 226
           L+ +++ ++G+ G  G+GKTT+ + +  ++    + +VF D+  +++  +     NPD  
Sbjct: 202 LESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSMEIYSSANPDDY 261

Query: 227 KIQGELASD-LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGD 285
            ++  L    L    D  D+  +    + +RLK  K VLI +D                D
Sbjct: 262 NMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRK-VLIFID----------------D 304

Query: 286 VDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFW----IDAL------SEEEALQLF- 334
           +D++D  D     T    S SR    I +   K F     ID +      S E AL++F 
Sbjct: 305 LDDQDVLDALAGQTQWFGSGSR---IIVITKDKHFLRAHGIDHIYEVCLPSNELALEMFC 361

Query: 335 EKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSNLRE 394
                +++    F  LA E+  + G LP+ L+ + + L+ +    W D L +L +     
Sbjct: 362 RSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDMLPRLRN----- 416

Query: 395 IHGMDADVYSPIKLSYDFLD---DEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGL 451
             G+D  +   +++SYD L+   D+A    + C  + E   ++   LL     L  + GL
Sbjct: 417 --GLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGE--KVNDIKLLLANSDLDVNIGL 472

Query: 452 GLFRNVYTLEAARNRVD-ALI----DNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEK 506
                       +N VD +LI    D ++   LL +   E       ++   +    E +
Sbjct: 473 ------------KNLVDKSLIHVREDIVEMHSLLQEMGKE-------IVRAQSNEPGERE 513

Query: 507 LMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLK-----LFLLF--AK 559
            +    ++ D   +   T  K  + I+L   +I EL   +     K     LFL F   K
Sbjct: 514 FLVDAKDICDVLEDNTGT--KKVLGITLDIDEIDEL--HIHENAFKGMRNLLFLKFYTKK 569

Query: 560 YDSTLQISDHFFEGTE----ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-A 614
           +D   ++  H  EG +    +L++L +       +PS+  R  NL  L + G +LE +  
Sbjct: 570 WDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLRCMPSNF-RPENLVKLQMQGSKLEKLWD 628

Query: 615 IVGQLKKLEILSLRGAE-IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEEL 673
            V  L  L  + LRG++ +K++P  +   T L+ L LS+CSSLV + P+ I  L++LE+L
Sbjct: 629 GVHSLTGLRNIDLRGSKNLKEIP-DLSMATNLETLKLSDCSSLVEL-PSSIQYLNKLEDL 686

Query: 674 YM 675
            M
Sbjct: 687 DM 688

syringae 6; Provisional. Length = 1153

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 51.6 bits (123), Expect = 8e-08
 Identities = 23/133 (17%), Positives = 48/133 (36%), Gaps = 6/133 (4%)

Query: 180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMN 239
              +I + G  G GKTTL + +A+++         +  E        ++   +      +
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 240 FDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWT--KLELDKIGIPYGDVDEKDKNDDPRR 297
                    R +      +K K  ++ILD I +    E + + +   ++         + 
Sbjct: 61  GSG----ELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN 116

Query: 298 CTIILTSRSRDLL 310
            T+ILT+     L
Sbjct: 117 LTVILTTNDEKDL 129

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. Length = 148

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

 Score = 50.0 bits (119), Expect = 3e-06
 Identities = 37/116 (31%), Positives = 53/116 (45%), Gaps = 3/116 (2%)

Query: 560 YDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIVGQ 618
            ++   I          LK LD +  +   LPS L  L NL+ L L    L D+  ++  
Sbjct: 125 NNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSN 184

Query: 619 LKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
           L  L  L L G +I  LP +I  L+ L+ LDLSN S + +   + +S L  L  L 
Sbjct: 185 LSNLNNLDLSGNKISDLPPEIELLSALEELDLSNNSIIEL--LSSLSNLKNLSGLE 238

Length = 394

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

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 44/142 (30%), Positives = 65/142 (45%), Gaps = 14/142 (9%)

Query: 538 DIQELPERLE-CPQLK-LFLLFAKYDSTLQISDHFFEGTE--ELKVLDFTGIRFSPLPSS 593
            I+ LP  L   P LK L L      S   +SD     +    L  LD +G + S LP  
Sbjct: 151 KIESLPSPLRNLPNLKNLDL------SFNDLSDLPKLLSNLSNLNNLDLSGNKISDLPPE 204

Query: 594 LGRLINLQTLCLDGWR-LEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN 652
           +  L  L+ L L     +E ++ +  LK L  L L   +++ LP  IG L+ L+ LDLSN
Sbjct: 205 IELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNKLEDLPESIGNLSNLETLDLSN 264

Query: 653 CSSLVVIAPNVISKLSRLEELY 674
                + + + +  L+ L EL 
Sbjct: 265 N---QISSISSLGSLTNLRELD 283

Length = 394

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

 Score = 46.5 bits (110), Expect = 3e-05
 Identities = 32/101 (31%), Positives = 45/101 (44%), Gaps = 4/101 (3%)

Query: 580 LDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQL--KKLEILSLRGAEIKQLPL 637
           LD    R     S L  L NL +L LD   + DI  +  L    L+ L L   +I+ LP 
Sbjct: 98  LDLNLNRLRSNISELLELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPS 157

Query: 638 QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS 678
            +  L  L+ LDLS     +   P ++S LS L  L +  +
Sbjct: 158 PLRNLPNLKNLDLSFND--LSDLPKLLSNLSNLNNLDLSGN 196

Length = 394

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 43.4 bits (103), Expect = 4e-05
 Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 186 VCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDL 245
           + G  G GKTTL++++A+Q+        VV  E       + +  ++   LG+       
Sbjct: 9   LTGESGSGKTTLLRRLARQLPNRR----VVYVEAPSLGTPKDLLRKILRALGLPLSGGT- 63

Query: 246 IYHRAKQLCQRLKKEKRVLIILDNI 270
                + +   LK+  R L+I+D  
Sbjct: 64  TAELLEAILDALKRRGRPLLIIDEA 88

Length = 124

>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 16/99 (16%)

Query: 183 IIGVCGMGGVGKTTLVKQIAKQV--MEDNVFDKVVMAEITKNPDAQKIQGELASD----- 235
           +I V G  G GKTTL  Q+A  +      V    V  E       +++ GE         
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIATKGGKVV--YVDIEEEIEELTERLIGESLKGALDNL 58

Query: 236 ----LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNI 270
                  +  +   +  +A++L +R       LIILD +
Sbjct: 59  IIVFATADDPAAARLLSKAERLRER---GGDDLIILDEL 94

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. Length = 165

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

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 621 KLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
            L+ L L    +  +P      L  L++LDLS   +L  I+P   S L  L  L +
Sbjct: 1   NLKSLDLSNNRLTVIPDGAFKGLPNLKVLDLSGN-NLTSISPEAFSGLPSLRSLDL 55

Length = 60

>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 14/54 (25%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 165 RKKIFQDVIEAL-KDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA 217
           ++ + +  +E + +++K N+I   G+ GVGKTT + ++A ++ +      V++A
Sbjct: 55  KEILKETDLELIVEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGK--SVLLA 106

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 [Protein fate, Protein and peptide secretion and trafficking]. Length = 272

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	724
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
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.61
PRK04841	903	transcriptional regulator MalT; Provisional	99.54
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.52
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.46
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.41
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.38
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.37
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.33
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.32
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.31
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.29
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.29
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.28
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.22
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.2
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.19
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.17
PF05729	166	NACHT: NACHT domain	99.13
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.09
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.05
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.05
COG3899	849	Predicted ATPase [General function prediction only	99.05
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	99.05
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.0
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.99
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.94
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.88
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.87
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.85
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.85
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.84
PRK13342	413	recombination factor protein RarA; Reviewed	98.84
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.82
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.8
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.79
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.75
PRK06893	229	DNA replication initiation factor; Validated	98.73
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.71
PRK12402	337	replication factor C small subunit 2; Reviewed	98.7
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.7
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.7
PRK04195	482	replication factor C large subunit; Provisional	98.67
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.67
PLN03025	319	replication factor C subunit; Provisional	98.66
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.63
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.62
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.61
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.61
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.6
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.6
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.59
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.59
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.59
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.58
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.58
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.58
PF13173	128	AAA_14: AAA domain	98.57
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.57
PTZ00202	550	tuzin; Provisional	98.57
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.56
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.55
COG3903	414	Predicted ATPase [General function prediction only	98.54
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.52
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.51
KOG2028	554	consensus ATPase related to the helicase subunit o	98.5
cd01128	249	rho_factor Transcription termination factor rho is	98.49
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.49
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.48
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.47
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.45
PLN03150	623	hypothetical protein; Provisional	98.45
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.44
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.43
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.42
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.4
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.39
PRK09376	416	rho transcription termination factor Rho; Provisio	98.39
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.38
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.36
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.36
PRK13341	725	recombination factor protein RarA/unknown domain f	98.36
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.35
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.35
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.35
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.34
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.33
PRK08084	235	DNA replication initiation factor; Provisional	98.32
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.31
PRK08727	233	hypothetical protein; Validated	98.31
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.3
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.3
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.3
PRK09087	226	hypothetical protein; Validated	98.29
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.27
PLN03150	623	hypothetical protein; Provisional	98.27
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	98.27
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.26
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.26
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.26
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.25
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.24
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.24
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.24
PF14516	331	AAA_35: AAA-like domain	98.23
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.22
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.22
TIGR00767	415	rho transcription termination factor Rho. Members	98.2
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.19
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.18
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.18
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.17
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	98.13
PRK05642	234	DNA replication initiation factor; Validated	98.13
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.13
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.12
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.12
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.11
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.11
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.11
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.09
PHA02544	316	44 clamp loader, small subunit; Provisional	98.08
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.08
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.05
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.05
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	98.04
CHL00095	821	clpC Clp protease ATP binding subunit	98.04
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	98.03
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.02
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.01
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.97
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.96
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.95
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.95
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.94
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	97.94
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.93
CHL00181	287	cbbX CbbX; Provisional	97.92
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.89
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.87
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.87
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.87
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.85
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	97.84
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.81
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.81
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.8
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.8
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.79
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.77
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.76
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.75
PRK10865	857	protein disaggregation chaperone; Provisional	97.73
PRK06620	214	hypothetical protein; Validated	97.71
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.71
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.7
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.69
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.65
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.65
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.65
PF00004	132	AAA: ATPase family associated with various cellula	97.57
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.55
PRK15386	426	type III secretion protein GogB; Provisional	97.54
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.54
PRK12422	445	chromosomal replication initiation protein; Provis	97.53
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.53
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.52
PRK15386	426	type III secretion protein GogB; Provisional	97.47
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.47
CHL00176	638	ftsH cell division protein; Validated	97.47
PRK08118	167	topology modulation protein; Reviewed	97.47
smart00382	148	AAA ATPases associated with a variety of cellular	97.46
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.45
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	97.45
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.44
PRK08181	269	transposase; Validated	97.43
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.41
PRK08116	268	hypothetical protein; Validated	97.4
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.4
CHL00195	489	ycf46 Ycf46; Provisional	97.4
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.39
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	97.38
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.37
PRK12608	380	transcription termination factor Rho; Provisional	97.37
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.34
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	97.33
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.3
PRK10536	262	hypothetical protein; Provisional	97.27
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.26
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.26
PHA00729	226	NTP-binding motif containing protein	97.25
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.24
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	97.23
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.23
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	97.21
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.2
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	97.2
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.19
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.17
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.14
PRK07261	171	topology modulation protein; Provisional	97.13
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.11
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.09
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.06
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.01
PRK04132	846	replication factor C small subunit; Provisional	97.0
PRK12377	248	putative replication protein; Provisional	97.0
KOG2123	388	consensus Uncharacterized conserved protein [Funct	97.0
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.99
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	96.98
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.97
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.96
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.96
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.94
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.92
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.89
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.88
KOG2982	418	consensus Uncharacterized conserved protein [Funct	96.88
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.81
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.8
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.8
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.77
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.76
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.76
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.74
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.72
KOG0736	953	consensus Peroxisome assembly factor 2 containing	96.71
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	96.71
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	96.67
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.66
PRK06696	223	uridine kinase; Validated	96.65
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.64
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.64
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.63
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	96.63
PRK07952	244	DNA replication protein DnaC; Validated	96.62
PRK05541	176	adenylylsulfate kinase; Provisional	96.6
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.59
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.59
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.59
PRK10865	857	protein disaggregation chaperone; Provisional	96.57
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.57
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	96.57
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	96.56
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.54
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.5
CHL00095	821	clpC Clp protease ATP binding subunit	96.49
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.48
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.47
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.46
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.46
PRK08939	306	primosomal protein DnaI; Reviewed	96.46
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.45
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.44
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.43
PRK09354	349	recA recombinase A; Provisional	96.43
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	96.4
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	96.39
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.38
PRK06526	254	transposase; Provisional	96.37
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.36
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.35
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.33
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.31
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.3
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.3
PTZ00494	664	tuzin-like protein; Provisional	96.28
PRK04296	190	thymidine kinase; Provisional	96.26
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.25
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.22
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.21
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	96.19
PTZ00301	210	uridine kinase; Provisional	96.16
PRK06921	266	hypothetical protein; Provisional	96.15
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.15
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.15
PRK07132	299	DNA polymerase III subunit delta'; Validated	96.15
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.15
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.14
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.14
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.13
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.12
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.12
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.12
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.12
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.1
PRK09183	259	transposase/IS protein; Provisional	96.08
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.03
PRK15455	644	PrkA family serine protein kinase; Provisional	96.01
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.01
PRK06547	172	hypothetical protein; Provisional	96.0
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.98
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.92
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.89
PRK07667	193	uridine kinase; Provisional	95.88
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	95.88
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.88
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.88
PTZ00035	337	Rad51 protein; Provisional	95.88
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.88
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.83
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.83
PRK13531	498	regulatory ATPase RavA; Provisional	95.83
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.83
PRK14974	336	cell division protein FtsY; Provisional	95.76
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.76
PRK06835	329	DNA replication protein DnaC; Validated	95.75
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	95.74
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	95.73
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.72
TIGR00959	428	ffh signal recognition particle protein. This mode	95.72
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	95.7
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.69
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	95.69
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.68
PRK06067	234	flagellar accessory protein FlaH; Validated	95.65
PRK10867	433	signal recognition particle protein; Provisional	95.63
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.6
PRK08233	182	hypothetical protein; Provisional	95.6
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	95.59
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.59
) 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	95.59
PRK05480	209	uridine/cytidine kinase; Provisional	95.58
PRK04328	249	hypothetical protein; Provisional	95.58
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.57
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	95.56
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.55
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.55
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.55
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.53
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.53
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.49
CHL00206	2281	ycf2 Ycf2; Provisional	95.49
KOG2982	418	consensus Uncharacterized conserved protein [Funct	95.48
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.48
PRK06762	166	hypothetical protein; Provisional	95.45
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.45
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.44
PF00154	322	RecA: recA bacterial DNA recombination protein; In	95.44
PRK00889	175	adenylylsulfate kinase; Provisional	95.44
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.44
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.43
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.42
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.4
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.39
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.37
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.36
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.35
PRK13765	637	ATP-dependent protease Lon; Provisional	95.35
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.33
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.33
PRK05439	311	pantothenate kinase; Provisional	95.3
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	95.3
PRK03839	180	putative kinase; Provisional	95.29
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.28
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.21
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	95.2
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.2
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.19
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.19
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.17
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	95.15
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.15
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	95.14
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.13
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.12
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.12
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	95.09
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.08
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.07
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	95.05
PRK00625	173	shikimate kinase; Provisional	95.04
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.03
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	95.02
PRK09519	790	recA DNA recombination protein RecA; Reviewed	95.0
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.99
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	94.99
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.97
PRK04040	188	adenylate kinase; Provisional	94.93
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.92
PRK00131	175	aroK shikimate kinase; Reviewed	94.9
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	94.88
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.88
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.87
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.87
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	94.86
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	94.82
PRK05022	509	anaerobic nitric oxide reductase transcription reg	94.78
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	94.77
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.76
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.75
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	94.72
PF13245	76	AAA_19: Part of AAA domain	94.71
PRK11823	446	DNA repair protein RadA; Provisional	94.67
PRK06851	367	hypothetical protein; Provisional	94.67
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	94.64
PRK12678	672	transcription termination factor Rho; Provisional	94.64
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	94.62
COG4240	300	Predicted kinase [General function prediction only	94.62
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	94.62
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	94.61
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.6
COG0714	329	MoxR-like ATPases [General function prediction onl	94.59
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	94.58
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.58
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	94.57
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	94.57
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	94.56
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.54
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	94.53
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.51
PRK14529	223	adenylate kinase; Provisional	94.5
PRK06217	183	hypothetical protein; Validated	94.5
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	94.5
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.49
PTZ00088	229	adenylate kinase 1; Provisional	94.48
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	94.47
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	94.44
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	94.44
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.41
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	94.4
PRK14530	215	adenylate kinase; Provisional	94.39
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.38
PRK10416	318	signal recognition particle-docking protein FtsY;	94.37
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.37
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.34
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	94.29
PRK13947	171	shikimate kinase; Provisional	94.27
PRK13949	169	shikimate kinase; Provisional	94.26
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.24
PRK14527	191	adenylate kinase; Provisional	94.23
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	94.23
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	94.21
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	94.19
PRK00409	782	recombination and DNA strand exchange inhibitor pr	94.18
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	94.18
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	94.17
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	94.17
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	94.16
PRK13695	174	putative NTPase; Provisional	94.15
PF07726	131	AAA_3: ATPase family associated with various cellu	94.14
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	94.12
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	94.12
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	94.12
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.09
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	94.07
PRK03846	198	adenylylsulfate kinase; Provisional	94.06
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	94.06
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	94.05
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	94.04
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.01
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.98
PRK00300	205	gmk guanylate kinase; Provisional	93.97
PTZ00185	574	ATPase alpha subunit; Provisional	93.97
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	93.95
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	93.94
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	93.92
PRK13975	196	thymidylate kinase; Provisional	93.91
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	93.91
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.9
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	93.89
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	93.89
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	93.89
PRK12339	197	2-phosphoglycerate kinase; Provisional	93.88
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	93.87
PRK05057	172	aroK shikimate kinase I; Reviewed	93.86
PRK08149	428	ATP synthase SpaL; Validated	93.85
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	93.84
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	93.82
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	93.8
PRK09435	332	membrane ATPase/protein kinase; Provisional	93.79
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	93.79
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	93.77
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	93.73
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	93.72
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.72
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.72
PRK07276	290	DNA polymerase III subunit delta'; Validated	93.69
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	93.66
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	93.63
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	93.63
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	93.6
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	93.6
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	93.58
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	93.57
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	93.56
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	93.53
PRK14737	186	gmk guanylate kinase; Provisional	93.52
PLN02200	234	adenylate kinase family protein	93.45
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	93.43
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	93.42
PRK00698	205	tmk thymidylate kinase; Validated	93.41
PRK13948	182	shikimate kinase; Provisional	93.38
PRK15453	290	phosphoribulokinase; Provisional	93.38
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	93.37
PRK13946	184	shikimate kinase; Provisional	93.37
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.36
PRK05922	434	type III secretion system ATPase; Validated	93.29

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.5e-81  Score=711.50  Aligned_cols=654  Identities=29%  Similarity=0.404  Sum_probs=507.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHhhhhcc----c-------------cc
Q 004895           38 IDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDE----V-------------RK  100 (724)
Q Consensus        38 ~~~~~~~~~~L~~~l~~i~~~l~~a~~~~~~~~~~v~~Wl~~l~~~~~~~~ed~ld~~~~----~-------------~~  100 (724)
                      +.+.++.+..|+..|..++.+++|+++++.+ ...+..|...+++++|+ +++.++.+.-    .             +.
T Consensus        23 ~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~-~~~~~~~~e~~~~~~~~-~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~  100 (889)
T KOG4658|consen   23 LDGKDNYILELKENLKALQSALEDLDAKRDD-LERRVNWEEDVGDLVYL-AEDIIWLFLVEEIERKANDLLSTRSVERQR  100 (889)
T ss_pred             HhchHHHHHHHHHHHHHHHHHHHHHHhhcch-HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhHHhhhhHHHHHH
Confidence            5677889999999999999999999998764 78899999999999999 9998764210    0             00


Q ss_pred             cccCCCC-CchhHHHHHhHHHHHHHHHHHHHHhcCCCcccccccc-CCCCCCcccCCCcccccccchHHHHHHHHHHhcC
Q 004895          101 PCFKGLS-PNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSH-PPPPKMREFGDMKDYNIFNSRKKIFQDVIEALKD  178 (724)
Q Consensus       101 ~~~~~~~-~~~~~r~~~~~~i~~~~~~l~~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~gR~~~~~~l~~~L~~  178 (724)
                      -|+...+ .....-+.+++++.++.+.++.+...+.|..   ++. ..++..++..|...... +|.+..++++.+.|.+
T Consensus       101 ~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~---~~~~~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~  176 (889)
T KOG4658|consen  101 LCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEV---VGESLDPREKVETRPIQSESD-VGLETMLEKLWNRLME  176 (889)
T ss_pred             HhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceec---ccccccchhhcccCCCCcccc-ccHHHHHHHHHHHhcc
Confidence            1111111 1222333445555555555555544444443   222 12222223333333333 8999999999999997


Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh-hccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCch--hHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM-EDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDL--IYHRAKQLCQ  255 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~--~~~~~~~l~~  255 (724)
                      ++..+++|+||||+||||||++++|+.. ++.+||.++||+||+.++..+++.+|++.++........  ..+.+..+.+
T Consensus       177 d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~  256 (889)
T KOG4658|consen  177 DDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLN  256 (889)
T ss_pred             CCCCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHH
Confidence            7779999999999999999999999998 899999999999999999999999999998874433221  2456667777


Q ss_pred             HHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchhhhhcCCCceEecCCCCHHHHHHHHH
Q 004895          256 RLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFE  335 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~  335 (724)
                      .|. ++||||||||||+..+|+.++.|+|.        ..+||||++|||+..|+...|++...++++.|+++|||+||+
T Consensus       257 ~L~-~krfllvLDDIW~~~dw~~I~~~~p~--------~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~  327 (889)
T KOG4658|consen  257 LLE-GKRFLLVLDDIWEEVDWDKIGVPFPS--------RENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQ  327 (889)
T ss_pred             Hhc-cCceEEEEecccccccHHhcCCCCCC--------ccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHH
Confidence            776 69999999999999999999999998        788999999999999986668888999999999999999999


Q ss_pred             HHhCCC--CCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCC-CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhh
Q 004895          336 KIVGES--TKASDFRPLAEEIVGKCGGLPVALSTVANALKNK-SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDF  412 (724)
Q Consensus       336 ~~~~~~--~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~-~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~  412 (724)
                      +.++..  ...+.++++|++++++|+|+|||++++|+.|+.+ +.++|+++.+.+.+....+..+..+.++++|++||+.
T Consensus       328 ~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~  407 (889)
T KOG4658|consen  328 KKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILKLSYDN  407 (889)
T ss_pred             HhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhhccHhh
Confidence            999854  3445589999999999999999999999999977 8889999999988875566556688999999999999


Q ss_pred             cHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcccccccccccccccHHHHHHHHHHHHHHHHhhcccccCC---CCCcc
Q 004895          413 LDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGD---AEDEA  489 (724)
Q Consensus       413 L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~~~---~~~~~  489 (724)
                      ||+++|.||+|||+||+||.|+++.|+.+|+      ||||+++....+.+++.+++++.+|++++|++...   ...+|
T Consensus       408 L~~~lK~CFLycalFPED~~I~~e~Li~yWi------aEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~~~~~~~  481 (889)
T KOG4658|consen  408 LPEELKSCFLYCALFPEDYEIKKEKLIEYWI------AEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDEGRKETV  481 (889)
T ss_pred             hhHHHHHHHHhhccCCcccccchHHHHHHHH------hccCcCccccccchhcchHHHHHHHHHHHHHhhcccccceeEE
Confidence            9999999999999999999999999999999      99999886556668888889999999999998654   44789


Q ss_pred             hhhHHHHHHHHHHhh-----hcceeeccCcchhhhhHhhhhccCceEEeccCCCcccCCCcccCCCccEEEEeccccccc
Q 004895          490 KLHDVIHVVAASIAE-----EKLMFSIPNVVDFEREMEETIQKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTL  564 (724)
Q Consensus       490 ~mHdlv~d~a~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~  564 (724)
                      +|||+|||+|.++|+     +++++...+.. .........+..+|+++++++.+..++....+++|++|.+..+.....
T Consensus       482 kmHDvvRe~al~ias~~~~~~e~~iv~~~~~-~~~~~~~~~~~~~rr~s~~~~~~~~~~~~~~~~~L~tLll~~n~~~l~  560 (889)
T KOG4658|consen  482 KMHDVVREMALWIASDFGKQEENQIVSDGVG-LSEIPQVKSWNSVRRMSLMNNKIEHIAGSSENPKLRTLLLQRNSDWLL  560 (889)
T ss_pred             EeeHHHHHHHHHHhccccccccceEEECCcC-ccccccccchhheeEEEEeccchhhccCCCCCCccceEEEeecchhhh
Confidence            999999999999999     66633332211 000001112578999999999999999888999999999954433467


Q ss_pred             ccchhhhcCCCCceEEEcCCCc-CCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCc-Ccccchhhhc
Q 004895          565 QISDHFFEGTEELKVLDFTGIR-FSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAE-IKQLPLQIGQ  641 (724)
Q Consensus       565 ~~~~~~~~~l~~L~~L~l~~~~-~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~-i~~lp~~i~~  641 (724)
                      .++..+|..++.|+||||++|. +.++|.+|++|.|||||+|+++.++. |..+++|..|.+||+..+. +..+|..+..
T Consensus       561 ~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~  640 (889)
T KOG4658|consen  561 EISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLE  640 (889)
T ss_pred             hcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccchhhh
Confidence            7888899999999999999764 56999999999999999999999998 8899999999999999984 4455666667


Q ss_pred             CCCCCeEccCCCC-CCcccChHHhhCCCCCcEEEccCCCC----ccccc------------c-CCccchHHhhcCCCCCc
Q 004895          642 LTRLQLLDLSNCS-SLVVIAPNVISKLSRLEELYMGDSFS----QWDKV------------E-GGSNASLAELKGLSKLT  703 (724)
Q Consensus       642 l~~L~~L~l~~~~-~l~~~~~~~i~~l~~L~~L~l~~~~~----~~~~~------------~-~~~~~~l~~L~~L~~L~  703 (724)
                      |++||+|.+.... ......-..+.+|.+|+.|.......    .....            . ......+..+..+.+|+
T Consensus       641 L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s~~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~~~l~~L~  720 (889)
T KOG4658|consen  641 LQSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISSVLLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSLGSLGNLE  720 (889)
T ss_pred             cccccEEEeeccccccchhhHHhhhcccchhhheeecchhHhHhhhhhhHHHHHHhHhhhhcccccceeecccccccCcc
Confidence            9999999997632 11111122234555555554433211    00000            0 01122344566778888


Q ss_pred             EEEeeccccc
Q 004895          704 TLEIDVRDAE  713 (724)
Q Consensus       704 ~L~l~~n~~~  713 (724)
                      .|.|..+...
T Consensus       721 ~L~i~~~~~~  730 (889)
T KOG4658|consen  721 ELSILDCGIS  730 (889)
T ss_pred             eEEEEcCCCc
Confidence            8888877764

>PLN03210 Resistant to P

Probab=100.00  E-value=7.9e-51  Score=489.53  Aligned_cols=503  Identities=21%  Similarity=0.331  Sum_probs=358.0

Q ss_pred             cccccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE---ecC---------
Q 004895          157 KDYNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI---TKN---------  222 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~---------  222 (724)
                      .+...++||+..++++..+|.  .+++++|+|+||||+||||||+.+|+...  .+|++.+|+..   +..         
T Consensus       181 ~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~--~~F~g~vfv~~~~v~~~~~~~~~~~~  258 (1153)
T PLN03210        181 NDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLS--RQFQSSVFIDRAFISKSMEIYSSANP  258 (1153)
T ss_pred             cccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHh--hcCCeEEEeeccccccchhhcccccc
Confidence            345678999999999998875  56789999999999999999999999875  45888877642   111         


Q ss_pred             --CC-hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcE
Q 004895          223 --PD-AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCT  299 (724)
Q Consensus       223 --~~-~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~  299 (724)
                        ++ ...+++.++..+........   .....+.+.+. ++|+||||||||+..+|+.+......        .++||+
T Consensus       259 ~~~~~~~~l~~~~l~~il~~~~~~~---~~~~~~~~~L~-~krvLLVLDdv~~~~~l~~L~~~~~~--------~~~Gsr  326 (1153)
T PLN03210        259 DDYNMKLHLQRAFLSEILDKKDIKI---YHLGAMEERLK-HRKVLIFIDDLDDQDVLDALAGQTQW--------FGSGSR  326 (1153)
T ss_pred             cccchhHHHHHHHHHHHhCCCCccc---CCHHHHHHHHh-CCeEEEEEeCCCCHHHHHHHHhhCcc--------CCCCcE
Confidence              01 12344444444322211110   01234555565 68999999999999889888655444        578999


Q ss_pred             EEEEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHH
Q 004895          300 IILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPA  378 (724)
Q Consensus       300 ilvTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~  378 (724)
                      ||||||+..++.. .+....|+++.+++++||+||+++||... +++++.+++++|+++|+|+|||++++|+.|++++..
T Consensus       327 IIiTTrd~~vl~~-~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~  405 (1153)
T PLN03210        327 IIVITKDKHFLRA-HGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKE  405 (1153)
T ss_pred             EEEEeCcHHHHHh-cCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHH
Confidence            9999999998633 45567999999999999999999998544 334578899999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHH-HHHHHHHhhccCCCCCcccHHHHHHHHhhccccccccccccc
Q 004895          379 IWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDD-EAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNV  457 (724)
Q Consensus       379 ~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~-~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~  457 (724)
                      +|+.+++++...       .+..+..+|++||+.|++ ..|.||+++|.|+.+..++   .+..|+      +.+...  
T Consensus       406 ~W~~~l~~L~~~-------~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l------~~~~~~--  467 (1153)
T PLN03210        406 DWMDMLPRLRNG-------LDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLL------ANSDLD--  467 (1153)
T ss_pred             HHHHHHHHHHhC-------ccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHH------HhcCCC--
Confidence            999999998653       234689999999999986 5999999999999875443   356677      443321  


Q ss_pred             ccHHHHHHHHHHHHHHHHhhcccccCCCCCcchhhHHHHHHHHHHhhhcce------eeccCcchhhhhHhh-hhccCce
Q 004895          458 YTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAASIAEEKLM------FSIPNVVDFEREMEE-TIQKGPI  530 (724)
Q Consensus       458 ~~~~~~~~~~~~~~~~L~~~~ll~~~~~~~~~~mHdlv~d~a~~~~~~~~~------~~~~~~~~~~~~~~~-~~~~~~~  530 (724)
                               ....++.|+++||++..  ...+.|||++|++|+.+++++..      +.... .++...+.. .....++
T Consensus       468 ---------~~~~l~~L~~ksLi~~~--~~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~-~di~~vl~~~~g~~~v~  535 (1153)
T PLN03210        468 ---------VNIGLKNLVDKSLIHVR--EDIVEMHSLLQEMGKEIVRAQSNEPGEREFLVDA-KDICDVLEDNTGTKKVL  535 (1153)
T ss_pred             ---------chhChHHHHhcCCEEEc--CCeEEhhhHHHHHHHHHHHhhcCCCCcceeEeCH-HHHHHHHHhCcccceee
Confidence                     11237778889999754  35699999999999999987630      11110 011001111 0134556


Q ss_pred             EEeccCCCcccCCC----cccCCCccEEEEecc-----------------------------cccccccchhhhcCCCCc
Q 004895          531 AISLPYRDIQELPE----RLECPQLKLFLLFAK-----------------------------YDSTLQISDHFFEGTEEL  577 (724)
Q Consensus       531 ~l~l~~~~~~~~~~----~~~~~~Lr~L~l~~~-----------------------------~~~~~~~~~~~~~~l~~L  577 (724)
                      .+++..+.+.++.-    ..++++|+.|.+..+                             .+....+|..+  .+.+|
T Consensus       536 ~i~l~~~~~~~~~i~~~aF~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f--~~~~L  613 (1153)
T PLN03210        536 GITLDIDEIDELHIHENAFKGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLRCMPSNF--RPENL  613 (1153)
T ss_pred             EEEeccCccceeeecHHHHhcCccccEEEEecccccccccceeecCcchhhcCcccEEEEecCCCCCCCCCcC--CccCC
Confidence            66554444332211    124555555555311                             11222333322  34678


Q ss_pred             eEEEcCCCcCCCCCccccCCCCCcEEEcCCcc-cCCcccccCCCCCcEEEccCC-cCcccchhhhcCCCCCeEccCCCCC
Q 004895          578 KVLDFTGIRFSPLPSSLGRLINLQTLCLDGWR-LEDIAIVGQLKKLEILSLRGA-EIKQLPLQIGQLTRLQLLDLSNCSS  655 (724)
Q Consensus       578 ~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~-l~~~~~~~~l~~L~~L~l~~~-~i~~lp~~i~~l~~L~~L~l~~~~~  655 (724)
                      +.|+++++.+..+|..+..+.+|++|+|++|. +..++.++.+++|++|++++| .+..+|..+.++++|++|++++|+.
T Consensus       614 ~~L~L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~ip~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~  693 (1153)
T PLN03210        614 VKLQMQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCEN  693 (1153)
T ss_pred             cEEECcCccccccccccccCCCCCEEECCCCCCcCcCCccccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCC
Confidence            88888888888888888888999999998875 566677888999999999988 6778899999999999999999888


Q ss_pred             CcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          656 LVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       656 l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      +..+|.. + ++++|+.|++++|.....         +..  ...+|+.|+++.|.+..+|..+
T Consensus       694 L~~Lp~~-i-~l~sL~~L~Lsgc~~L~~---------~p~--~~~nL~~L~L~~n~i~~lP~~~  744 (1153)
T PLN03210        694 LEILPTG-I-NLKSLYRLNLSGCSRLKS---------FPD--ISTNISWLDLDETAIEEFPSNL  744 (1153)
T ss_pred             cCccCCc-C-CCCCCCEEeCCCCCCccc---------ccc--ccCCcCeeecCCCccccccccc
Confidence            8888764 2 788999999888742111         111  1357788888888887777654

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=1.7e-43  Score=366.11  Aligned_cols=276  Identities=34%  Similarity=0.571  Sum_probs=222.3

Q ss_pred             hHHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-
Q 004895          165 RKKIFQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-  241 (724)
Q Consensus       165 R~~~~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-  241 (724)
                      |+.++++|.+.|.+  ++.++|+|+||||+||||||+.++++...+.+|+.++|+++++..+..+++..|+++++.... 
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            78999999999986  789999999999999999999999997788899999999999999999999999999988743 


Q ss_pred             --CCchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchhhhhcCCCce
Q 004895          242 --SNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKM  319 (724)
Q Consensus       242 --~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~~~~~~  319 (724)
                        ...........+.+.+. ++++||||||||+...|+.+...++.        ...+++||||||+..++.........
T Consensus        81 ~~~~~~~~~~~~~l~~~L~-~~~~LlVlDdv~~~~~~~~l~~~~~~--------~~~~~kilvTTR~~~v~~~~~~~~~~  151 (287)
T PF00931_consen   81 ISDPKDIEELQDQLRELLK-DKRCLLVLDDVWDEEDLEELREPLPS--------FSSGSKILVTTRDRSVAGSLGGTDKV  151 (287)
T ss_dssp             SSCCSSHHHHHHHHHHHHC-CTSEEEEEEEE-SHHHH-------HC--------HHSS-EEEEEESCGGGGTTHHSCEEE
T ss_pred             cccccccccccccchhhhc-cccceeeeeeeccccccccccccccc--------cccccccccccccccccccccccccc
Confidence              22224556777887776 57999999999999999888777665        66799999999999886433333679


Q ss_pred             EecCCCCHHHHHHHHHHHhCCCC--CCCCchhHHHHHHHHhCCchhHHHHHHHHhcCC-CHHHHHHHHHHHhcCcccccc
Q 004895          320 FWIDALSEEEALQLFEKIVGEST--KASDFRPLAEEIVGKCGGLPVALSTVANALKNK-SPAIWKDALNKLTSSNLREIH  396 (724)
Q Consensus       320 ~~l~~L~~~e~~~Lf~~~~~~~~--~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~-~~~~w~~~~~~l~~~~~~~~~  396 (724)
                      +++++|+++|+++||.+.++...  ..+.+++.+++|+++|+|+||||+++|++|+.+ +..+|+.+++++...... ..
T Consensus       152 ~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~-~~  230 (287)
T PF00931_consen  152 IELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRE-SR  230 (287)
T ss_dssp             EECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTC-SS
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-cc
Confidence            99999999999999999998543  445668899999999999999999999999644 788999999887765432 22


Q ss_pred             CCCcccchhhHhhhhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcccccccccccc
Q 004895          397 GMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRN  456 (724)
Q Consensus       397 ~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~  456 (724)
                      +....+..++..||+.||+++|+||+|||+||+++.|+++.|+++|+      ++|+|..
T Consensus       231 ~~~~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~------~e~~i~~  284 (287)
T PF00931_consen  231 DYDRSVFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWV------AEGFISS  284 (287)
T ss_dssp             GSCHHHHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHT------T-HHTC-
T ss_pred             cccccccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHH------HCCCCcc
Confidence            24678999999999999999999999999999999999999999999      9999864

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.

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

Probab=99.61  E-value=1.9e-17  Score=145.80  Aligned_cols=166  Identities=23%  Similarity=0.326  Sum_probs=133.9

Q ss_pred             ccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccC
Q 004895          540 QELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQ  618 (724)
Q Consensus       540 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~  618 (724)
                      .+++....+++...|.+  +.+....+|+. +..+.+|.+|++.+|+++++|.+|+.++.|+.|+++.|.+.. |..|+.
T Consensus        24 ~~~~gLf~~s~ITrLtL--SHNKl~~vppn-ia~l~nlevln~~nnqie~lp~~issl~klr~lnvgmnrl~~lprgfgs  100 (264)
T KOG0617|consen   24 EELPGLFNMSNITRLTL--SHNKLTVVPPN-IAELKNLEVLNLSNNQIEELPTSISSLPKLRILNVGMNRLNILPRGFGS  100 (264)
T ss_pred             hhcccccchhhhhhhhc--ccCceeecCCc-HHHhhhhhhhhcccchhhhcChhhhhchhhhheecchhhhhcCccccCC
Confidence            34455555666666666  34444555554 567889999999999999999999999999999999999877 789999


Q ss_pred             CCCCcEEEccCCcCc--ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhh
Q 004895          619 LKKLEILSLRGAEIK--QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL  696 (724)
Q Consensus       619 l~~L~~L~l~~~~i~--~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L  696 (724)
                      ++-|+.||+.+|.++  .+|..+..++.|+.|+++. +.++-+|+. +++|++||.|.+..|...         ....++
T Consensus       101 ~p~levldltynnl~e~~lpgnff~m~tlralyl~d-ndfe~lp~d-vg~lt~lqil~lrdndll---------~lpkei  169 (264)
T KOG0617|consen  101 FPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLGD-NDFEILPPD-VGKLTNLQILSLRDNDLL---------SLPKEI  169 (264)
T ss_pred             CchhhhhhccccccccccCCcchhHHHHHHHHHhcC-CCcccCChh-hhhhcceeEEeeccCchh---------hCcHHH
Confidence            999999999999877  7899999999999999998 567777776 799999999998876321         233567


Q ss_pred             cCCCCCcEEEeeccccccccccc
Q 004895          697 KGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       697 ~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      ..|.+|+.|.|.+|+++.+|..+
T Consensus       170 g~lt~lrelhiqgnrl~vlppel  192 (264)
T KOG0617|consen  170 GDLTRLRELHIQGNRLTVLPPEL  192 (264)
T ss_pred             HHHHHHHHHhcccceeeecChhh
Confidence            77788999999999999988654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.54  E-value=5.4e-13  Score=160.72  Aligned_cols=296  Identities=16%  Similarity=0.230  Sum_probs=183.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~  234 (724)
                      |.....++-|...++.+-+   ....+++.|+|++|.||||++.++.+.      ++.++|+++... .+...+...++.
T Consensus        10 p~~~~~~~~R~rl~~~l~~---~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~   80 (903)
T PRK04841         10 PVRLHNTVVRERLLAKLSG---ANNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIA   80 (903)
T ss_pred             CCCccccCcchHHHHHHhc---ccCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHH
Confidence            3444566788866666543   246789999999999999999998853      225899999744 466667677777


Q ss_pred             hhCCCCCCC-------------chhHHHHHHHHHHHhc-CCcEEEEEcccccccc--cc-ccccccCCCCcCCCCCCCCC
Q 004895          235 DLGMNFDSN-------------DLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE--LD-KIGIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       235 ~l~~~~~~~-------------~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~--~~-~l~~~~~~~~~~~~~~~~~~  297 (724)
                      .++......             .........+...+.. +.+++|||||+...++  .. .+...+..        ...+
T Consensus        81 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~--------~~~~  152 (903)
T PRK04841         81 ALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRH--------QPEN  152 (903)
T ss_pred             HHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHh--------CCCC
Confidence            764211110             1112233444444443 6789999999965431  11 22111222        3456


Q ss_pred             cEEEEEecccchhhh-h-cCCCceEecC----CCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHH
Q 004895          298 CTIILTSRSRDLLCI-D-MNSQKMFWID----ALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANA  371 (724)
Q Consensus       298 s~ilvTtR~~~v~~~-~-~~~~~~~~l~----~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~  371 (724)
                      .++|||||...-... . ........+.    +|+.+|+.++|....+...    -.+...+|.+.|+|+|+++..++..
T Consensus       153 ~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~----~~~~~~~l~~~t~Gwp~~l~l~~~~  228 (903)
T PRK04841        153 LTLVVLSRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPI----EAAESSRLCDDVEGWATALQLIALS  228 (903)
T ss_pred             eEEEEEeCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCC----CHHHHHHHHHHhCChHHHHHHHHHH
Confidence            788899998532110 0 0112244555    9999999999988765432    1456789999999999999999887


Q ss_pred             hcCCCHHHHHHHHHHHhcCccccccCCCcccchhhHh-hhhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcccccc
Q 004895          372 LKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPIKL-SYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKG  450 (724)
Q Consensus       372 l~~~~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~-sy~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~  450 (724)
                      +...... .......+..       .....+...+.. .++.||++.+..+...|+++   .++.+.+ ..-.      +
T Consensus       229 ~~~~~~~-~~~~~~~~~~-------~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~---~~~~~l~-~~l~------~  290 (903)
T PRK04841        229 ARQNNSS-LHDSARRLAG-------INASHLSDYLVEEVLDNVDLETRHFLLRCSVLR---SMNDALI-VRVT------G  290 (903)
T ss_pred             HhhCCCc-hhhhhHhhcC-------CCchhHHHHHHHHHHhcCCHHHHHHHHHhcccc---cCCHHHH-HHHc------C
Confidence            7543210 0011111100       011234554444 48999999999999999997   3564433 2211      1


Q ss_pred             cccccccccHHHHHHHHHHHHHHHHhhccccc-C-CCCCcchhhHHHHHHHHHHh
Q 004895          451 LGLFRNVYTLEAARNRVDALIDNLKASCLLLD-G-DAEDEAKLHDVIHVVAASIA  503 (724)
Q Consensus       451 ~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~-~-~~~~~~~mHdlv~d~a~~~~  503 (724)
                               .+++    .+.+++|.+.+++.. . +....|+.|++++++++...
T Consensus       291 ---------~~~~----~~~L~~l~~~~l~~~~~~~~~~~yr~H~L~r~~l~~~l  332 (903)
T PRK04841        291 ---------EENG----QMRLEELERQGLFIQRMDDSGEWFRYHPLFASFLRHRC  332 (903)
T ss_pred             ---------CCcH----HHHHHHHHHCCCeeEeecCCCCEEehhHHHHHHHHHHH
Confidence                     0112    356777888888653 2 23457899999999998775

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

Probab=99.52  E-value=5.2e-16  Score=161.86  Aligned_cols=151  Identities=22%  Similarity=0.279  Sum_probs=127.4

Q ss_pred             ccCceEEeccCCCcccCCC-cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPE-RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~  604 (724)
                      ..++.||++..|++..+.. ..++|.||++.+-.++.....+|++.| .+.-|.+||||+|++.+.|..+.+-+++-.|+
T Consensus        54 lqkLEHLs~~HN~L~~vhGELs~Lp~LRsv~~R~N~LKnsGiP~diF-~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLN  132 (1255)
T KOG0444|consen   54 LQKLEHLSMAHNQLISVHGELSDLPRLRSVIVRDNNLKNSGIPTDIF-RLKDLTILDLSHNQLREVPTNLEYAKNSIVLN  132 (1255)
T ss_pred             HhhhhhhhhhhhhhHhhhhhhccchhhHHHhhhccccccCCCCchhc-ccccceeeecchhhhhhcchhhhhhcCcEEEE
Confidence            5688999999999877754 348999999999666667778998866 58999999999999999999999999999999


Q ss_pred             cCCcccCC-c-ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          605 LDGWRLED-I-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       605 L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      |++|.|.. | +-+-+|.-|-+||||+|++..+|+.+.+|..|++|.|++| .+...--..+..|++|++|.+++.
T Consensus       133 LS~N~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~Ls~N-PL~hfQLrQLPsmtsL~vLhms~T  207 (1255)
T KOG0444|consen  133 LSYNNIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIRRLSMLQTLKLSNN-PLNHFQLRQLPSMTSLSVLHMSNT  207 (1255)
T ss_pred             cccCccccCCchHHHhhHhHhhhccccchhhhcCHHHHHHhhhhhhhcCCC-hhhHHHHhcCccchhhhhhhcccc
Confidence            99999988 4 3466899999999999999999999999999999999994 444433333456777788887764

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

Probab=99.46  E-value=2.6e-13  Score=164.54  Aligned_cols=150  Identities=25%  Similarity=0.301  Sum_probs=87.6

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~~L~  604 (724)
                      ..++++|++++|++........+++|++|.+.  .+......+..+.++++|++|++++|.+. .+|..++++.+|++|+
T Consensus       117 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        117 SSSLRYLNLSNNNFTGSIPRGSIPNLETLDLS--NNMLSGEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLT  194 (968)
T ss_pred             CCCCCEEECcCCccccccCccccCCCCEEECc--CCcccccCChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeee
Confidence            34666666666665432222345666666662  22222222233566667777777766665 5566666677777777


Q ss_pred             cCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          605 LDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       605 L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      |++|.+..  |..++++++|++|++++|.+. .+|..++++++|++|++++|. +....|..++++++|++|++++|
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~~L~~L~L~~n  270 (968)
T PLN00113        195 LASNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGLTSLNHLDLVYNN-LTGPIPSSLGNLKNLQYLFLYQN  270 (968)
T ss_pred             ccCCCCcCcCChHHcCcCCccEEECcCCccCCcCChhHhcCCCCCEEECcCce-eccccChhHhCCCCCCEEECcCC
Confidence            76666554  456666666666666666655 556666666666666666643 33233334666666666666654

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

Probab=99.41  E-value=1.3e-12  Score=158.27  Aligned_cols=179  Identities=22%  Similarity=0.292  Sum_probs=128.9

Q ss_pred             ccCceEEeccCCCcc-cCCCcc--cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCc
Q 004895          526 QKGPIAISLPYRDIQ-ELPERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~-~~~~~~--~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~  601 (724)
                      ...++.|.+++|.+. .+|...  .+++|+.|++. ++.....+|.   ..+++|++|++++|.+. .+|..++++.+|+
T Consensus        92 l~~L~~L~Ls~n~~~~~ip~~~~~~l~~L~~L~Ls-~n~l~~~~p~---~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~  167 (968)
T PLN00113         92 LPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLS-NNNFTGSIPR---GSIPNLETLDLSNNMLSGEIPNDIGSFSSLK  167 (968)
T ss_pred             CCCCCEEECCCCccCCcCChHHhccCCCCCEEECc-CCccccccCc---cccCCCCEEECcCCcccccCChHHhcCCCCC
Confidence            457777888777764 455432  67788888873 2222223332   34677888888888887 6788888889999


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +|+|++|.+..  |..++++++|++|++++|.+. .+|..++++++|++|++++|. +....|..++++++|++|++++|
T Consensus       168 ~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~-l~~~~p~~l~~l~~L~~L~L~~n  246 (968)
T PLN00113        168 VLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNN-LSGEIPYEIGGLTSLNHLDLVYN  246 (968)
T ss_pred             EEECccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCc-cCCcCChhHhcCCCCCEEECcCc
Confidence            99998888764  577888889999999888776 678888889999999988854 44334455888999999998876


Q ss_pred             CCccccccCCccchHHhhcCCCCCcEEEeeccccc-cccc
Q 004895          679 FSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE-MLRR  717 (724)
Q Consensus       679 ~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~-~lp~  717 (724)
                      .     +.+..+   ..+.++++|+.|+++.|.+. .+|.
T Consensus       247 ~-----l~~~~p---~~l~~l~~L~~L~L~~n~l~~~~p~  278 (968)
T PLN00113        247 N-----LTGPIP---SSLGNLKNLQYLFLYQNKLSGPIPP  278 (968)
T ss_pred             e-----eccccC---hhHhCCCCCCEEECcCCeeeccCch
Confidence            3     222223   34667788999999998874 3443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.38  E-value=2.9e-11  Score=132.69  Aligned_cols=301  Identities=17%  Similarity=0.209  Sum_probs=194.6

Q ss_pred             cCCCcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHH
Q 004895          153 FGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGE  231 (724)
Q Consensus       153 ~~~~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~  231 (724)
                      ..+|..+...+-|...++.+..   ..+.+++.|..|+|.|||||+.++......   =..+.|.++.+. .++..+...
T Consensus        12 ~~~P~~~~~~v~R~rL~~~L~~---~~~~RL~li~APAGfGKttl~aq~~~~~~~---~~~v~Wlslde~dndp~rF~~y   85 (894)
T COG2909          12 LVRPVRPDNYVVRPRLLDRLRR---ANDYRLILISAPAGFGKTTLLAQWRELAAD---GAAVAWLSLDESDNDPARFLSY   85 (894)
T ss_pred             cCCCCCcccccccHHHHHHHhc---CCCceEEEEeCCCCCcHHHHHHHHHHhcCc---ccceeEeecCCccCCHHHHHHH
Confidence            3344445666778766655543   347899999999999999999999873332   245999999865 567888888


Q ss_pred             HHHhhCCCCCCCc-------------hhHHHHHHHHHHHhc-CCcEEEEEcccccccc--c-cccccccCCCCcCCCCCC
Q 004895          232 LASDLGMNFDSND-------------LIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE--L-DKIGIPYGDVDEKDKNDD  294 (724)
Q Consensus       232 i~~~l~~~~~~~~-------------~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~--~-~~l~~~~~~~~~~~~~~~  294 (724)
                      ++..++.-.+.-.             ........+...+.. .++..+||||..-..+  . ..+...+..        .
T Consensus        86 Li~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~--------~  157 (894)
T COG2909          86 LIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKH--------A  157 (894)
T ss_pred             HHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHh--------C
Confidence            8888763322211             012233444444432 5689999999865532  1 122222223        5


Q ss_pred             CCCcEEEEEecccchhhhh--cCCCceEecC----CCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          295 PRRCTIILTSRSRDLLCID--MNSQKMFWID----ALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~~~~--~~~~~~~~l~----~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ..+-..|+|||+..-....  .-....+++.    .|+.+|+.++|....+..-+    +...+.+.+..+|.+-|+..+
T Consensus       158 P~~l~lvv~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld----~~~~~~L~~~teGW~~al~L~  233 (894)
T COG2909         158 PENLTLVVTSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLD----AADLKALYDRTEGWAAALQLI  233 (894)
T ss_pred             CCCeEEEEEeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCC----hHHHHHHHhhcccHHHHHHHH
Confidence            5688899999998632110  0111233333    58999999999987543222    345789999999999999999


Q ss_pred             HHHhcCC-CHHHHHHHHHHHhcCccccccCCCcccch-hhHhhhhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcc
Q 004895          369 ANALKNK-SPAIWKDALNKLTSSNLREIHGMDADVYS-PIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLR  446 (724)
Q Consensus       369 ~~~l~~~-~~~~w~~~~~~l~~~~~~~~~~~~~~i~~-~l~~sy~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~  446 (724)
                      +=.+++. +.+.-...++-           ...-+.. ...--++.||++++..+.-||+++.    --+.|+..-.   
T Consensus       234 aLa~~~~~~~~q~~~~LsG-----------~~~~l~dYL~eeVld~Lp~~l~~FLl~~svl~~----f~~eL~~~Lt---  295 (894)
T COG2909         234 ALALRNNTSAEQSLRGLSG-----------AASHLSDYLVEEVLDRLPPELRDFLLQTSVLSR----FNDELCNALT---  295 (894)
T ss_pred             HHHccCCCcHHHHhhhccc-----------hHHHHHHHHHHHHHhcCCHHHHHHHHHHHhHHH----hhHHHHHHHh---
Confidence            9888833 33322221110           1111222 2345688999999999999999965    2344555443   


Q ss_pred             cccccccccccccHHHHHHHHHHHHHHHHhhccccc--CCCCCcchhhHHHHHHHHHHhhh
Q 004895          447 YDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD--GDAEDEAKLHDVIHVVAASIAEE  505 (724)
Q Consensus       447 ~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~--~~~~~~~~mHdlv~d~a~~~~~~  505 (724)
                         +             ++....++++|.+++++..  ++....|+.|.++.||-+..-..
T Consensus       296 ---g-------------~~ng~amLe~L~~~gLFl~~Ldd~~~WfryH~LFaeFL~~r~~~  340 (894)
T COG2909         296 ---G-------------EENGQAMLEELERRGLFLQRLDDEGQWFRYHHLFAEFLRQRLQR  340 (894)
T ss_pred             ---c-------------CCcHHHHHHHHHhCCCceeeecCCCceeehhHHHHHHHHhhhcc
Confidence               2             2233467888999998752  35677899999999999877654

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

Probab=99.37  E-value=1.6e-14  Score=127.46  Aligned_cols=147  Identities=23%  Similarity=0.374  Sum_probs=80.6

Q ss_pred             cCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          527 KGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      +.++++.++.|.+..+|..+ ++.+|+.|++  .++...++|.+ ++.++.|+.|+++.|++..+|..++.++-|..|+|
T Consensus        33 s~ITrLtLSHNKl~~vppnia~l~nlevln~--~nnqie~lp~~-issl~klr~lnvgmnrl~~lprgfgs~p~levldl  109 (264)
T KOG0617|consen   33 SNITRLTLSHNKLTVVPPNIAELKNLEVLNL--SNNQIEELPTS-ISSLPKLRILNVGMNRLNILPRGFGSFPALEVLDL  109 (264)
T ss_pred             hhhhhhhcccCceeecCCcHHHhhhhhhhhc--ccchhhhcChh-hhhchhhhheecchhhhhcCccccCCCchhhhhhc
Confidence            44555555555555554332 5555565555  23334444433 45555666666666665556666666666666666


Q ss_pred             CCcccCC---cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          606 DGWRLED---IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       606 ~~~~l~~---~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      ++|.+.+   |..|..+..|+-|.++.|.++-+|+.+++|++|+.|.+.. +.+-.+|.+ ++.|+.|++|++.+|
T Consensus       110 tynnl~e~~lpgnff~m~tlralyl~dndfe~lp~dvg~lt~lqil~lrd-ndll~lpke-ig~lt~lrelhiqgn  183 (264)
T KOG0617|consen  110 TYNNLNENSLPGNFFYMTTLRALYLGDNDFEILPPDVGKLTNLQILSLRD-NDLLSLPKE-IGDLTRLRELHIQGN  183 (264)
T ss_pred             cccccccccCCcchhHHHHHHHHHhcCCCcccCChhhhhhcceeEEeecc-CchhhCcHH-HHHHHHHHHHhcccc
Confidence            6665544   3445555555555566665555566666666666665555 334444443 556666666655554

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

Probab=99.33  E-value=8.7e-14  Score=138.67  Aligned_cols=180  Identities=22%  Similarity=0.320  Sum_probs=129.2

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      ..+..++++.|++..+|+..+|+.|..|.+  +.+....+|....+++.+|.+||+..|++++.|+.++.+.+|.+|+++
T Consensus       206 ~~L~~LyL~~Nki~~lPef~gcs~L~Elh~--g~N~i~~lpae~~~~L~~l~vLDLRdNklke~Pde~clLrsL~rLDlS  283 (565)
T KOG0472|consen  206 ESLELLYLRRNKIRFLPEFPGCSLLKELHV--GENQIEMLPAEHLKHLNSLLVLDLRDNKLKEVPDEICLLRSLERLDLS  283 (565)
T ss_pred             hhhHHHHhhhcccccCCCCCccHHHHHHHh--cccHHHhhHHHHhcccccceeeeccccccccCchHHHHhhhhhhhccc
Confidence            456667788888888888778888888877  556667777777788888888888888888888888888888888888


Q ss_pred             CcccCC-cccccCCCCCcEEEccCCcCcccchhh------------------------------------------hcCC
Q 004895          607 GWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQI------------------------------------------GQLT  643 (724)
Q Consensus       607 ~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i------------------------------------------~~l~  643 (724)
                      +|.++. |.++++| +|+.|-+-||.+.++-.+|                                          ..+.
T Consensus       284 NN~is~Lp~sLgnl-hL~~L~leGNPlrTiRr~ii~~gT~~vLKyLrs~~~~dglS~se~~~e~~~t~~~~~~~~~~~~i  362 (565)
T KOG0472|consen  284 NNDISSLPYSLGNL-HLKFLALEGNPLRTIRREIISKGTQEVLKYLRSKIKDDGLSQSEGGTETAMTLPSESFPDIYAII  362 (565)
T ss_pred             CCccccCCcccccc-eeeehhhcCCchHHHHHHHHcccHHHHHHHHHHhhccCCCCCCcccccccCCCCCCcccchhhhh
Confidence            888888 6788888 8888877666543321111                                          1122


Q ss_pred             CCCeEccC-------------------------------------------------CCCCCcccChHHhhCCCCCcEEE
Q 004895          644 RLQLLDLS-------------------------------------------------NCSSLVVIAPNVISKLSRLEELY  674 (724)
Q Consensus       644 ~L~~L~l~-------------------------------------------------~~~~l~~~~~~~i~~l~~L~~L~  674 (724)
                      +.+.|+++                                                 . ++..+.+|..++.+++|..|+
T Consensus       363 ~tkiL~~s~~qlt~VPdEVfea~~~~~Vt~VnfskNqL~elPk~L~~lkelvT~l~ls-nn~isfv~~~l~~l~kLt~L~  441 (565)
T KOG0472|consen  363 TTKILDVSDKQLTLVPDEVFEAAKSEIVTSVNFSKNQLCELPKRLVELKELVTDLVLS-NNKISFVPLELSQLQKLTFLD  441 (565)
T ss_pred             hhhhhcccccccccCCHHHHHHhhhcceEEEecccchHhhhhhhhHHHHHHHHHHHhh-cCccccchHHHHhhhcceeee
Confidence            23333222                                                 2 122334466688999999999


Q ss_pred             ccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      +++|+..      ..|   .++..+..|+.|+|+.|+|..+|+..
T Consensus       442 L~NN~Ln------~LP---~e~~~lv~Lq~LnlS~NrFr~lP~~~  477 (565)
T KOG0472|consen  442 LSNNLLN------DLP---EEMGSLVRLQTLNLSFNRFRMLPECL  477 (565)
T ss_pred             cccchhh------hcc---hhhhhhhhhheecccccccccchHHH
Confidence            9987532      223   45556677999999999999999754

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

Probab=99.32  E-value=1.5e-13  Score=143.75  Aligned_cols=150  Identities=24%  Similarity=0.406  Sum_probs=127.2

Q ss_pred             ccCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~  604 (724)
                      ...+..|+++.|.+.+.|..+ ..+++-.|++  +++.+..+|...|-++.-|-.||||+|++..+|+.+..|.+|++|.
T Consensus       102 l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNL--S~N~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~  179 (1255)
T KOG0444|consen  102 LKDLTILDLSHNQLREVPTNLEYAKNSIVLNL--SYNNIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIRRLSMLQTLK  179 (1255)
T ss_pred             cccceeeecchhhhhhcchhhhhhcCcEEEEc--ccCccccCCchHHHhhHhHhhhccccchhhhcCHHHHHHhhhhhhh
Confidence            567888999999999998765 4677888888  6777889999999999999999999999999999999999999999


Q ss_pred             cCCcccCC--cccccCCCCCcEEEccCCc--CcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          605 LDGWRLED--IAIVGQLKKLEILSLRGAE--IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       605 L~~~~l~~--~~~~~~l~~L~~L~l~~~~--i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |++|.+..  +..+..+++|++|.++++.  +..+|.++..|.+|+.++++. +++..+| ..+-++++|+.|++++|.
T Consensus       180 Ls~NPL~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~-N~Lp~vP-ecly~l~~LrrLNLS~N~  256 (1255)
T KOG0444|consen  180 LSNNPLNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSE-NNLPIVP-ECLYKLRNLRRLNLSGNK  256 (1255)
T ss_pred             cCCChhhHHHHhcCccchhhhhhhcccccchhhcCCCchhhhhhhhhccccc-cCCCcch-HHHhhhhhhheeccCcCc
Confidence            99998765  4667778888899998884  447888899999999999987 5676665 457888999999988864

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

Probab=99.31  E-value=2.5e-13  Score=141.39  Aligned_cols=150  Identities=23%  Similarity=0.290  Sum_probs=107.3

Q ss_pred             ccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hh
Q 004895          565 QISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IG  640 (724)
Q Consensus       565 ~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~  640 (724)
                      .+-+..|-++..+..|+|+.|++..+- .++..|..|+.|+|++|.|..  +.++...++|+.|+|++|.|+++|++ +.
T Consensus       259 kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~lfgLt~L~~L~lS~NaI~rih~d~WsftqkL~~LdLs~N~i~~l~~~sf~  338 (873)
T KOG4194|consen  259 KLDDGAFYGLEKMEHLNLETNRLQAVNEGWLFGLTSLEQLDLSYNAIQRIHIDSWSFTQKLKELDLSSNRITRLDEGSFR  338 (873)
T ss_pred             cccCcceeeecccceeecccchhhhhhcccccccchhhhhccchhhhheeecchhhhcccceeEeccccccccCChhHHH
Confidence            344555666677777777777776553 356777788888888887776  46777778888888888888887554 77


Q ss_pred             cCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          641 QLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       641 ~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      .|..|+.|+|++ +.+..+..+.+..+++|++|++..|...|. ++    ..-.....|+.|++|.+.+|.++.+|+.-|
T Consensus       339 ~L~~Le~LnLs~-Nsi~~l~e~af~~lssL~~LdLr~N~ls~~-IE----Daa~~f~gl~~LrkL~l~gNqlk~I~krAf  412 (873)
T KOG4194|consen  339 VLSQLEELNLSH-NSIDHLAEGAFVGLSSLHKLDLRSNELSWC-IE----DAAVAFNGLPSLRKLRLTGNQLKSIPKRAF  412 (873)
T ss_pred             HHHHhhhhcccc-cchHHHHhhHHHHhhhhhhhcCcCCeEEEE-Ee----cchhhhccchhhhheeecCceeeecchhhh
Confidence            778888888888 567777777778888888888888765554 22    233345567888888888888877776543

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

Probab=99.29  E-value=1e-12  Score=136.96  Aligned_cols=180  Identities=21%  Similarity=0.251  Sum_probs=101.3

Q ss_pred             CceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEE
Q 004895          528 GPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLC  604 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~  604 (724)
                      -+|.++++.|.+.+++..  ..-.+++.|++  ..+.+..+..+.|.++.+|-+|.|+.|+++.+|. .|.+|++|+.|+
T Consensus       150 alrslDLSrN~is~i~~~sfp~~~ni~~L~L--a~N~It~l~~~~F~~lnsL~tlkLsrNrittLp~r~Fk~L~~L~~Ld  227 (873)
T KOG4194|consen  150 ALRSLDLSRNLISEIPKPSFPAKVNIKKLNL--ASNRITTLETGHFDSLNSLLTLKLSRNRITTLPQRSFKRLPKLESLD  227 (873)
T ss_pred             hhhhhhhhhchhhcccCCCCCCCCCceEEee--ccccccccccccccccchheeeecccCcccccCHHHhhhcchhhhhh
Confidence            345555666666555432  23345666666  4444555555556666666666666666666654 344466666666


Q ss_pred             cCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          605 LDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       605 L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      |..|.|...  -.|..|.+|+.|.+..|.|..+-.+ +..|.++++|+|.. +.+..+-.+.+..|++|+.|+++.|.+.
T Consensus       228 LnrN~irive~ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~-N~l~~vn~g~lfgLt~L~~L~lS~NaI~  306 (873)
T KOG4194|consen  228 LNRNRIRIVEGLTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLET-NRLQAVNEGWLFGLTSLEQLDLSYNAIQ  306 (873)
T ss_pred             ccccceeeehhhhhcCchhhhhhhhhhcCcccccCcceeeecccceeeccc-chhhhhhcccccccchhhhhccchhhhh
Confidence            666665542  4556666666666666666666444 45566666666666 4455555555566666666666665321


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      ..     .   +......++|+.|+++.|.++.+++.
T Consensus       307 ri-----h---~d~WsftqkL~~LdLs~N~i~~l~~~  335 (873)
T KOG4194|consen  307 RI-----H---IDSWSFTQKLKELDLSSNRITRLDEG  335 (873)
T ss_pred             ee-----e---cchhhhcccceeEeccccccccCChh
Confidence            11     1   11222334555666666655555544

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

Probab=99.29  E-value=6e-10  Score=114.04  Aligned_cols=186  Identities=17%  Similarity=0.241  Sum_probs=117.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHH---
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLC---  254 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~---  254 (724)
                      ....+++.|+|++|+||||+++.+++..... .+ .+.|+ +....+..+++..|+..++.+..... .......+.   
T Consensus        40 ~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~-~~-~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~~~-~~~~~~~l~~~l  115 (269)
T TIGR03015        40 SQREGFILITGEVGAGKTTLIRNLLKRLDQE-RV-VAAKL-VNTRVDAEDLLRMVAADFGLETEGRD-KAALLRELEDFL  115 (269)
T ss_pred             hcCCCEEEEEcCCCCCHHHHHHHHHHhcCCC-Ce-EEeee-eCCCCCHHHHHHHHHHHcCCCCCCCC-HHHHHHHHHHHH
Confidence            3445689999999999999999999887532 11 12233 23345777899999999887654332 222223333   


Q ss_pred             -HHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecC
Q 004895          255 -QRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWID  323 (724)
Q Consensus       255 -~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~  323 (724)
                       .....+++.++|+||++...  .++.+......     .........|++|.......        .........+.++
T Consensus       116 ~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~-----~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~  190 (269)
T TIGR03015       116 IEQFAAGKRALLVVDEAQNLTPELLEELRMLSNF-----QTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLG  190 (269)
T ss_pred             HHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCc-----ccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCC
Confidence             33335788999999998753  33333211110     00022233456665433110        1111224468899


Q ss_pred             CCCHHHHHHHHHHHhCCCC---CCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          324 ALSEEEALQLFEKIVGEST---KASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       324 ~L~~~e~~~Lf~~~~~~~~---~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      +++.+|..+++...+....   ...-.++..+.|++.|+|.|..|+.++..+
T Consensus       191 ~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       191 PLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            9999999999998774221   122235789999999999999999988877

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.28  E-value=8.5e-10  Score=119.54  Aligned_cols=296  Identities=16%  Similarity=0.110  Sum_probs=172.2

Q ss_pred             ccccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          158 DYNIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      .+..++||++++++|...+.    ......+.|+|++|+|||++++.++++.......-.++++++....+...++..|+
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~  107 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIA  107 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHH
Confidence            34568899999999988874    33456788999999999999999999886543223466777777778888999999


Q ss_pred             HhhCC-CCCCC-chhHHHHHHHHHHHhc-CCcEEEEEccccccc---cccccccccCCCCcCCCCCCCC--CcEEEEEec
Q 004895          234 SDLGM-NFDSN-DLIYHRAKQLCQRLKK-EKRVLIILDNIWTKL---ELDKIGIPYGDVDEKDKNDDPR--RCTIILTSR  305 (724)
Q Consensus       234 ~~l~~-~~~~~-~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~~~~~~~~~--~s~ilvTtR  305 (724)
                      +++.. ..+.. ....+....+.+.+.. +++.+||||+++...   ..+.+...+....      ...  ...+|.++.
T Consensus       108 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~------~~~~~~v~vI~i~~  181 (394)
T PRK00411        108 RQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHE------EYPGARIGVIGISS  181 (394)
T ss_pred             HHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhh------ccCCCeEEEEEEEC
Confidence            99865 22211 1133445556666643 456899999998753   1111111110000      112  233566665


Q ss_pred             ccchhhh------hcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHh----CCchhHHHHHHHHhc-
Q 004895          306 SRDLLCI------DMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKC----GGLPVALSTVANALK-  373 (724)
Q Consensus       306 ~~~v~~~------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c----~GlPLai~~~~~~l~-  373 (724)
                      ...+...      ..-....+.+++++.++..+++..++.... ...--++..+.|++.+    |..+.|+.++-.... 
T Consensus       182 ~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~  261 (394)
T PRK00411        182 DLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLI  261 (394)
T ss_pred             CcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            5433210      011235789999999999999998874211 1111133445555555    557777776644321 


Q ss_pred             ----CC---CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhccCCC--CCcccHHHHHHHHhh
Q 004895          374 ----NK---SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHRE--GRPIHVHYLLRYVMG  444 (724)
Q Consensus       374 ----~~---~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp~--~~~i~~~~Li~~W~~  444 (724)
                          +.   +.+.+..+.+...              .......+..||.+.|..+..++-.-+  ...+....+..... 
T Consensus       262 a~~~~~~~I~~~~v~~a~~~~~--------------~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~-  326 (394)
T PRK00411        262 AEREGSRKVTEEDVRKAYEKSE--------------IVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYK-  326 (394)
T ss_pred             HHHcCCCCcCHHHHHHHHHHHH--------------HHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH-
Confidence                11   5556665555431              123455788999988887776553321  12455555543211 


Q ss_pred             cccccccccccccccHHHHHHHHHHHHHHHHhhcccc
Q 004895          445 LRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLL  481 (724)
Q Consensus       445 ~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~  481 (724)
                       ...+..|..    +  -....+.++++.|...+++.
T Consensus       327 -~l~~~~~~~----~--~~~~~~~~~l~~L~~~glI~  356 (394)
T PRK00411        327 -ELCEELGYE----P--RTHTRFYEYINKLDMLGIIN  356 (394)
T ss_pred             -HHHHHcCCC----c--CcHHHHHHHHHHHHhcCCeE
Confidence             000011110    0  02344566778888888875

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.22  E-value=5.8e-09  Score=111.80  Aligned_cols=299  Identities=15%  Similarity=0.154  Sum_probs=169.6

Q ss_pred             ccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc-CC---CeEEEEEEecCCChHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN-VF---DKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F---~~~~wv~vs~~~~~~~l~~~  231 (724)
                      ..++||++++++|...+.    ....+.+.|+|++|+|||++++.+++...... ..   -.++|+++....+...++..
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            468899999999999886    24456889999999999999999999865321 11   13677888777778889999


Q ss_pred             HHHhh---CCCCCCCc-hhHHHHHHHHHHHh-cCCcEEEEEccccccc-cccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          232 LASDL---GMNFDSND-LIYHRAKQLCQRLK-KEKRVLIILDNIWTKL-ELDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       232 i~~~l---~~~~~~~~-~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~-~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      |++++   +...+... ...+....+.+.+. .+++++||||+++... ..+.+...+........ .......+|.++.
T Consensus        95 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~-~~~~~v~lI~i~n  173 (365)
T TIGR02928        95 LANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGD-LDNAKVGVIGISN  173 (365)
T ss_pred             HHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccC-CCCCeEEEEEEEC
Confidence            99988   43322211 12334455555554 3567899999998762 11111111100000000 0112334555554


Q ss_pred             ccchh----hhh--cCCCceEecCCCCHHHHHHHHHHHhCCC----CCCCCchhHHHHHHHHhCCchhHH-HHHHHHhc-
Q 004895          306 SRDLL----CID--MNSQKMFWIDALSEEEALQLFEKIVGES----TKASDFRPLAEEIVGKCGGLPVAL-STVANALK-  373 (724)
Q Consensus       306 ~~~v~----~~~--~~~~~~~~l~~L~~~e~~~Lf~~~~~~~----~~~~~l~~~~~~I~~~c~GlPLai-~~~~~~l~-  373 (724)
                      .....    ...  .-....+.+++++.+|..+++..++...    .-.++..+.+.+++..+.|.|..+ .++-.... 
T Consensus       174 ~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~  253 (365)
T TIGR02928       174 DLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEI  253 (365)
T ss_pred             CcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            43321    000  1112468899999999999999887411    111222234455666777888544 33222111 


Q ss_pred             ----CC---CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhccC--CCCCcccHHHHHHHHhh
Q 004895          374 ----NK---SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLH--REGRPIHVHYLLRYVMG  444 (724)
Q Consensus       374 ----~~---~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~f--p~~~~i~~~~Li~~W~~  444 (724)
                          +.   +.+..+.+.+.+.              .....-++..||.+.+..+..++..  ..+..+....+...+- 
T Consensus       254 a~~~~~~~it~~~v~~a~~~~~--------------~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~-  318 (365)
T TIGR02928       254 AEREGAERVTEDHVEKAQEKIE--------------KDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYK-  318 (365)
T ss_pred             HHHcCCCCCCHHHHHHHHHHHH--------------HHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHH-
Confidence                11   4455555544431              1234557788998888776665421  1333566666665332 


Q ss_pred             cccccccccccccccHHHHHHHHHHHHHHHHhhcccc
Q 004895          445 LRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLL  481 (724)
Q Consensus       445 ~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~  481 (724)
                       ...+..|. .+     -....+.++++.|...|++.
T Consensus       319 -~~~~~~~~-~~-----~~~~~~~~~l~~l~~~gli~  348 (365)
T TIGR02928       319 -EVCEDIGV-DP-----LTQRRISDLLNELDMLGLVE  348 (365)
T ss_pred             -HHHHhcCC-CC-----CcHHHHHHHHHHHHhcCCeE
Confidence             00001121 11     13355667888888899886

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.

>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=99.20  E-value=8.6e-11  Score=117.50  Aligned_cols=197  Identities=23%  Similarity=0.288  Sum_probs=104.6

Q ss_pred             ccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH---------
Q 004895          162 FNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL---------  232 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i---------  232 (724)
                      |+||++++++|.+++..+..+.+.|+|+.|+|||+|++.+.+..... .+ .++|+...+...... ...+         
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~-~~-~~~y~~~~~~~~~~~-~~~~~~~~~~~~~   77 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEK-GY-KVVYIDFLEESNESS-LRSFIEETSLADE   77 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT---EE-CCCHHCCTTBSHHHH-HHHHHHHHHHHCH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhc-CC-cEEEEecccchhhhH-HHHHHHHHHHHHH
Confidence            78999999999998887777899999999999999999999987432 11 344444433332221 1222         


Q ss_pred             -HHhh----CCC-C-----CCCchhHHHHHHHHHHHhc-CCcEEEEEccccccc-ccc---c----cccccCCCCcCCCC
Q 004895          233 -ASDL----GMN-F-----DSNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKL-ELD---K----IGIPYGDVDEKDKN  292 (724)
Q Consensus       233 -~~~l----~~~-~-----~~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~-~~~---~----l~~~~~~~~~~~~~  292 (724)
                       .+.+    ... .     ............+.+.+.+ +++++||+||+.... ...   .    +...+..      .
T Consensus        78 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~------~  151 (234)
T PF01637_consen   78 LSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDS------L  151 (234)
T ss_dssp             CHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH-------
T ss_pred             HHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhh------c
Confidence             1112    110 0     0111123344555555543 345999999997665 111   1    1111100      0


Q ss_pred             CCCCCcEEEEEecccchhhh-------hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          293 DDPRRCTIILTSRSRDLLCI-------DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      .......++++..+......       ..+....+.+++|+.+++++++...+.....-+.-++..++|+..+||+|..|
T Consensus       152 ~~~~~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P~~l  231 (234)
T PF01637_consen  152 LSQQNVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNPRYL  231 (234)
T ss_dssp             ---TTEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-HHHH
T ss_pred             cccCCceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCHHHH
Confidence            02233344455444332211       12334469999999999999999976433111122566799999999999987


Q ss_pred             HH
Q 004895          366 ST  367 (724)
Q Consensus       366 ~~  367 (724)
                      ..
T Consensus       232 ~~  233 (234)
T PF01637_consen  232 QE  233 (234)
T ss_dssp             HH
T ss_pred             hc
Confidence            64

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

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.19  E-value=1.4e-09  Score=113.40  Aligned_cols=274  Identities=15%  Similarity=0.127  Sum_probs=148.7

Q ss_pred             cccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ...|+|+++.++.|..++.     ......+.++|++|+|||+||+.+++.....  +   ..+..+......++ ...+
T Consensus         3 ~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~--~---~~~~~~~~~~~~~l-~~~l   76 (305)
T TIGR00635         3 LAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN--L---KITSGPALEKPGDL-AAIL   76 (305)
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC--E---EEeccchhcCchhH-HHHH
Confidence            4578999999999988875     2345678899999999999999999877532  1   22222211122222 2222


Q ss_pred             HhhCCCC----CC-CchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccc
Q 004895          234 SDLGMNF----DS-NDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD  308 (724)
Q Consensus       234 ~~l~~~~----~~-~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~  308 (724)
                      ..++...    ++ ..........+...+. +.+..+|+|+..+...+...              ..+.+-|..||+...
T Consensus        77 ~~~~~~~vl~iDEi~~l~~~~~e~l~~~~~-~~~~~~v~~~~~~~~~~~~~--------------~~~~~li~~t~~~~~  141 (305)
T TIGR00635        77 TNLEEGDVLFIDEIHRLSPAVEELLYPAME-DFRLDIVIGKGPSARSVRLD--------------LPPFTLVGATTRAGM  141 (305)
T ss_pred             HhcccCCEEEEehHhhhCHHHHHHhhHHHh-hhheeeeeccCccccceeec--------------CCCeEEEEecCCccc
Confidence            3332110    00 0000111222333332 34455566655444333211              123455667777654


Q ss_pred             hhhhh-cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHHHH
Q 004895          309 LLCID-MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKL  387 (724)
Q Consensus       309 v~~~~-~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~~l  387 (724)
                      +.... ......+.+++++.++..+++.+.+..... .--++....|++.|+|.|-.+..++..+       |..... .
T Consensus       142 l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~-~~~~~al~~ia~~~~G~pR~~~~ll~~~-------~~~a~~-~  212 (305)
T TIGR00635       142 LTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNV-EIEPEAALEIARRSRGTPRIANRLLRRV-------RDFAQV-R  212 (305)
T ss_pred             cCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHHhCCCcchHHHHHHHH-------HHHHHH-c
Confidence            43211 112346899999999999999998863222 1225678899999999997765554432       111000 0


Q ss_pred             hcCccccccCCCcccchhhHhhhhhcHHHHHHHHH-hhccCCCCCcccHHHHHHHHhhcccccccccccccccHHHHHHH
Q 004895          388 TSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFL-LCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNR  466 (724)
Q Consensus       388 ~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~-~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~  466 (724)
                      .......  ..-......+...|..|+++.+..+. .++.++.+ ++..+.+....         |     .+...+   
T Consensus       213 ~~~~it~--~~v~~~l~~l~~~~~~l~~~~~~~L~al~~~~~~~-~~~~~~ia~~l---------g-----~~~~~~---  272 (305)
T TIGR00635       213 GQKIINR--DIALKALEMLMIDELGLDEIDRKLLSVLIEQFQGG-PVGLKTLAAAL---------G-----EDADTI---  272 (305)
T ss_pred             CCCCcCH--HHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCC-cccHHHHHHHh---------C-----CCcchH---
Confidence            0000000  00011222255667888888887776 55777654 66666664433         1     111222   


Q ss_pred             HHHHHH-HHHhhcccccC
Q 004895          467 VDALID-NLKASCLLLDG  483 (724)
Q Consensus       467 ~~~~~~-~L~~~~ll~~~  483 (724)
                       ...++ .|++.+|+...
T Consensus       273 -~~~~e~~Li~~~li~~~  289 (305)
T TIGR00635       273 -EDVYEPYLLQIGFLQRT  289 (305)
T ss_pred             -HHhhhHHHHHcCCcccC
Confidence             23455 47788998643

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=99.17  E-value=7.9e-10  Score=116.00  Aligned_cols=277  Identities=14%  Similarity=0.108  Sum_probs=149.3

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      |.....|+|+++.++.+...+.     ......+.|+|++|+||||||+.+++.....     ..++..+.. .....+.
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l~~~-----~~~~~~~~~-~~~~~l~   94 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEMGVN-----IRITSGPAL-EKPGDLA   94 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHhCCC-----eEEEecccc-cChHHHH
Confidence            4456789999999998877664     2345678899999999999999999987532     122222211 1111222


Q ss_pred             HHHHhhCCCC----CC-CchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          231 ELASDLGMNF----DS-NDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       231 ~i~~~l~~~~----~~-~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      .++..++...    ++ ........+.+...+. +.+..+++|+..+...+..   .           -.+.+-|..|++
T Consensus        95 ~~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e-~~~~~~~l~~~~~~~~~~~---~-----------l~~~~li~at~~  159 (328)
T PRK00080         95 AILTNLEEGDVLFIDEIHRLSPVVEEILYPAME-DFRLDIMIGKGPAARSIRL---D-----------LPPFTLIGATTR  159 (328)
T ss_pred             HHHHhcccCCEEEEecHhhcchHHHHHHHHHHH-hcceeeeeccCccccceee---c-----------CCCceEEeecCC
Confidence            3333332110    00 0000011111222222 2334445554333221110   0           122455667777


Q ss_pred             ccchhhh-hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHH
Q 004895          306 SRDLLCI-DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDAL  384 (724)
Q Consensus       306 ~~~v~~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~  384 (724)
                      ...+... .......++++++++++..+++.+.+...... --++.+..|++.|+|.|-.+..+...+.     .|....
T Consensus       160 ~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~-~~~~~~~~ia~~~~G~pR~a~~~l~~~~-----~~a~~~  233 (328)
T PRK00080        160 AGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVE-IDEEGALEIARRSRGTPRIANRLLRRVR-----DFAQVK  233 (328)
T ss_pred             cccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHcCCCchHHHHHHHHHH-----HHHHHc
Confidence            5544311 11123578999999999999999988643221 2256789999999999975555544321     111110


Q ss_pred             HHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHH-hhccCCCCCcccHHHHHHHHhhcccccccccccccccHHHH
Q 004895          385 NKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFL-LCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAA  463 (724)
Q Consensus       385 ~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~-~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~  463 (724)
                         .......  ..-......+...+..|++..+..+. ....|+.+ ++..+.+....       +.       +.+.+
T Consensus       234 ---~~~~I~~--~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~~~-~~~~~~~a~~l-------g~-------~~~~~  293 (328)
T PRK00080        234 ---GDGVITK--EIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGG-PVGLDTLAAAL-------GE-------ERDTI  293 (328)
T ss_pred             ---CCCCCCH--HHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcCCC-ceeHHHHHHHH-------CC-------CcchH
Confidence               0000000  00112234455667788888888876 77778766 67777775543       11       12223


Q ss_pred             HHHHHHHHH-HHHhhcccccC
Q 004895          464 RNRVDALID-NLKASCLLLDG  483 (724)
Q Consensus       464 ~~~~~~~~~-~L~~~~ll~~~  483 (724)
                      +    +.++ .|++.+|++..
T Consensus       294 ~----~~~e~~Li~~~li~~~  310 (328)
T PRK00080        294 E----DVYEPYLIQQGFIQRT  310 (328)
T ss_pred             H----HHhhHHHHHcCCcccC
Confidence            3    2344 57778998644

>PF05729 NACHT: NACHT domain

Probab=99.13  E-value=5.3e-10  Score=105.23  Aligned_cols=145  Identities=24%  Similarity=0.323  Sum_probs=92.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEEEEecCCChH---HHHHHHHHhhCCCCCCCchhHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEITKNPDAQ---KIQGELASDLGMNFDSNDLIYHRAKQLC  254 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~---~l~~~i~~~l~~~~~~~~~~~~~~~~l~  254 (724)
                      +++.|+|.+|+||||+++.++.+......    +..++|++.+......   .+...|..+........      ...+.
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~------~~~~~   74 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPI------EELLQ   74 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhh------HHHHH
Confidence            58899999999999999999999876543    3456777776544332   33333433333221111      11233


Q ss_pred             HHHhcCCcEEEEEccccccccc---------cccccccCCCCcCCCCCCCCCcEEEEEecccchh--hhhcCCCceEecC
Q 004895          255 QRLKKEKRVLIILDNIWTKLEL---------DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--CIDMNSQKMFWID  323 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~~~~~---------~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~  323 (724)
                      ..+...++++||+|++++...-         ..+...+-.      ....++++++||+|.....  .........+.+.
T Consensus        75 ~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~------~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~  148 (166)
T PF05729_consen   75 ELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLP------QALPPGVKLIITSRPRAFPDLRRRLKQAQILELE  148 (166)
T ss_pred             HHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhh------hccCCCCeEEEEEcCChHHHHHHhcCCCcEEEEC
Confidence            3344578999999999776331         111111111      0135689999999998762  2223444689999


Q ss_pred             CCCHHHHHHHHHHHh
Q 004895          324 ALSEEEALQLFEKIV  338 (724)
Q Consensus       324 ~L~~~e~~~Lf~~~~  338 (724)
                      +|++++..+++.+..
T Consensus       149 ~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen  149 PFSEEDIKQYLRKYF  163 (166)
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999999998875

>PLN03210 Resistant to P

Probab=99.09  E-value=6.6e-10  Score=135.42  Aligned_cols=43  Identities=33%  Similarity=0.592  Sum_probs=23.5

Q ss_pred             ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          634 QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       634 ~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      .+|..++++++|++|++++|+.+..+|.. + .+++|+.|++++|
T Consensus       793 ~lP~si~~L~~L~~L~Ls~C~~L~~LP~~-~-~L~sL~~L~Ls~c  835 (1153)
T PLN03210        793 ELPSSIQNLHKLEHLEIENCINLETLPTG-I-NLESLESLDLSGC  835 (1153)
T ss_pred             ccChhhhCCCCCCEEECCCCCCcCeeCCC-C-CccccCEEECCCC
Confidence            44555555555666666555555555443 1 4555555555554

syringae 6; Provisional

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.05  E-value=4.7e-10  Score=127.94  Aligned_cols=168  Identities=18%  Similarity=0.225  Sum_probs=85.8

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      ..++.|.+++|.+..+|... .++|++|.+.  .+....+|..+.   .+|+.|++++|.+..+|..+.  .+|++|+++
T Consensus       199 ~~L~~L~Ls~N~LtsLP~~l-~~nL~~L~Ls--~N~LtsLP~~l~---~~L~~L~Ls~N~L~~LP~~l~--s~L~~L~Ls  270 (754)
T PRK15370        199 EQITTLILDNNELKSLPENL-QGNIKTLYAN--SNQLTSIPATLP---DTIQEMELSINRITELPERLP--SALQSLDLF  270 (754)
T ss_pred             cCCcEEEecCCCCCcCChhh-ccCCCEEECC--CCccccCChhhh---ccccEEECcCCccCcCChhHh--CCCCEEECc
Confidence            45556666666665555432 2456666552  222333443221   245555555555555554443  245555555


Q ss_pred             CcccCC-cccccCCCCCcEEEccCCcCcccchhhh-------------------cCCCCCeEccCCCCCCcccChHHhhC
Q 004895          607 GWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIG-------------------QLTRLQLLDLSNCSSLVVIAPNVISK  666 (724)
Q Consensus       607 ~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~-------------------~l~~L~~L~l~~~~~l~~~~~~~i~~  666 (724)
                      +|.++. |..+.  .+|++|++++|.++.+|..+.                   -.++|+.|++++| .+..+|.. +  
T Consensus       271 ~N~L~~LP~~l~--~sL~~L~Ls~N~Lt~LP~~lp~sL~~L~Ls~N~Lt~LP~~l~~sL~~L~Ls~N-~Lt~LP~~-l--  344 (754)
T PRK15370        271 HNKISCLPENLP--EELRYLSVYDNSIRTLPAHLPSGITHLNVQSNSLTALPETLPPGLKTLEAGEN-ALTSLPAS-L--  344 (754)
T ss_pred             CCccCccccccC--CCCcEEECCCCccccCcccchhhHHHHHhcCCccccCCccccccceeccccCC-ccccCChh-h--
Confidence            555544 22221  245555555555544443221                   1245666666663 45555432 2  


Q ss_pred             CCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          667 LSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       667 l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      .++|+.|++++|.+.      ..+..   +  .++|+.|+|++|.++.+|..+
T Consensus       345 ~~sL~~L~Ls~N~L~------~LP~~---l--p~~L~~LdLs~N~Lt~LP~~l  386 (754)
T PRK15370        345 PPELQVLDVSKNQIT------VLPET---L--PPTITTLDVSRNALTNLPENL  386 (754)
T ss_pred             cCcccEEECCCCCCC------cCChh---h--cCCcCEEECCCCcCCCCCHhH
Confidence            257777777775321      11211   1  257888999999988888654

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

Probab=99.05  E-value=2.3e-11  Score=121.72  Aligned_cols=151  Identities=24%  Similarity=0.329  Sum_probs=116.1

Q ss_pred             ccCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~  604 (724)
                      ..-+..++++.|.+.++|+.+ .++.+.+..+ .+ +.....++.+++.++.|..|++++|-+..+|..++.+..||.|+
T Consensus       387 ~~~Vt~VnfskNqL~elPk~L~~lkelvT~l~-ls-nn~isfv~~~l~~l~kLt~L~L~NN~Ln~LP~e~~~lv~Lq~Ln  464 (565)
T KOG0472|consen  387 SEIVTSVNFSKNQLCELPKRLVELKELVTDLV-LS-NNKISFVPLELSQLQKLTFLDLSNNLLNDLPEEMGSLVRLQTLN  464 (565)
T ss_pred             hcceEEEecccchHhhhhhhhHHHHHHHHHHH-hh-cCccccchHHHHhhhcceeeecccchhhhcchhhhhhhhhheec
Confidence            456888999999999998754 3444455444 22 23344556678888889999999888888898888888899999


Q ss_pred             cCCcccCC-cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          605 LDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       605 L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      ++.|.+.. |..+..+.-|+++-.+.|.+..+|++ +.++.+|..|++.+ +.+..+||. +|+|++|++|.+++|.+
T Consensus       465 lS~NrFr~lP~~~y~lq~lEtllas~nqi~~vd~~~l~nm~nL~tLDL~n-Ndlq~IPp~-LgnmtnL~hLeL~gNpf  540 (565)
T KOG0472|consen  465 LSFNRFRMLPECLYELQTLETLLASNNQIGSVDPSGLKNMRNLTTLDLQN-NDLQQIPPI-LGNMTNLRHLELDGNPF  540 (565)
T ss_pred             ccccccccchHHHhhHHHHHHHHhccccccccChHHhhhhhhcceeccCC-CchhhCChh-hccccceeEEEecCCcc
Confidence            98888877 55666677788888888888888665 88888888888887 567778775 78888888888888653

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.05  E-value=5.4e-09  Score=121.63  Aligned_cols=268  Identities=15%  Similarity=0.221  Sum_probs=158.2

Q ss_pred             ccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE---EecCCC---hHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE---ITKNPD---AQKIQGEL  232 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~---vs~~~~---~~~l~~~i  232 (724)
                      ++||+.+++.|...+.   .+...++.+.|..|+|||+++++|......+  +...+-..   ...+..   ..+.++++
T Consensus         2 l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~--~~~~i~~~f~q~~~~ipl~~lvq~~r~l   79 (849)
T COG3899           2 LYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQ--RGYFIKGKFDQFERNIPLSPLVQAFRDL   79 (849)
T ss_pred             CCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhcc--ceeeeHhhcccccCCCchHHHHHHHHHH
Confidence            6799999999998886   4566799999999999999999999987643  11111111   112221   12222333


Q ss_pred             HHhh-------------------CCC------------------CCC----CchhHH-----HHHHHHHHHhcCCcEEEE
Q 004895          233 ASDL-------------------GMN------------------FDS----NDLIYH-----RAKQLCQRLKKEKRVLII  266 (724)
Q Consensus       233 ~~~l-------------------~~~------------------~~~----~~~~~~-----~~~~l~~~l~~~kr~LlV  266 (724)
                      ..++                   +..                  .+.    +.....     ....+.......++.++|
T Consensus        80 ~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~  159 (849)
T COG3899          80 MGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIV  159 (849)
T ss_pred             HHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEE
Confidence            3222                   111                  000    000001     112233333456799999


Q ss_pred             Eccc-ccccc-ccccccccCCCCcCCCCCCCCCcEEEEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCC
Q 004895          267 LDNI-WTKLE-LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTK  343 (724)
Q Consensus       267 lDdv-~~~~~-~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~  343 (724)
                      +||+ |-+.. ++-+........  ......+..-.+.|.+.. ............+.|.||+..+...+.....+....
T Consensus       160 leDlhWaD~~SL~lL~~lm~~~~--~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~  237 (849)
T COG3899         160 LEDLHWADSASLKLLQLLMDRIA--IGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTKL  237 (849)
T ss_pred             EecccccChhHHHHHHHHHHhcc--hhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCccc
Confidence            9999 43321 111111111000  000001111123333332 111223345578999999999999999999875332


Q ss_pred             CCCchhHHHHHHHHhCCchhHHHHHHHHhcCC-------CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHH
Q 004895          344 ASDFRPLAEEIVGKCGGLPVALSTVANALKNK-------SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDE  416 (724)
Q Consensus       344 ~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~-------~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~  416 (724)
                      .+  .+....|+++..|+|+.+..+-..+...       +...|..-..++...      +..+++...+..-.+.||..
T Consensus       238 ~~--~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~------~~~~~vv~~l~~rl~kL~~~  309 (849)
T COG3899         238 LP--APLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGIL------ATTDAVVEFLAARLQKLPGT  309 (849)
T ss_pred             cc--chHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCc------hhhHHHHHHHHHHHhcCCHH
Confidence            22  4678999999999999999999988742       334444332222211      11222555688899999999


Q ss_pred             HHHHHHhhccCCCCCcccHHHHHHHHh
Q 004895          417 AKSLFLLCGLHREGRPIHVHYLLRYVM  443 (724)
Q Consensus       417 ~k~cf~~~s~fp~~~~i~~~~Li~~W~  443 (724)
                      .++.+...|++..  .|+.+.|...|-
T Consensus       310 t~~Vl~~AA~iG~--~F~l~~La~l~~  334 (849)
T COG3899         310 TREVLKAAACIGN--RFDLDTLAALAE  334 (849)
T ss_pred             HHHHHHHHHHhCc--cCCHHHHHHHHh
Confidence            9999999999987  677888877664

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

Probab=99.05  E-value=2.5e-10  Score=106.09  Aligned_cols=128  Identities=24%  Similarity=0.289  Sum_probs=40.9

Q ss_pred             CCCCceEEEcCCCcCCCCCcccc-CCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhhh-cCCCCCeEcc
Q 004895          573 GTEELKVLDFTGIRFSPLPSSLG-RLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIG-QLTRLQLLDL  650 (724)
Q Consensus       573 ~l~~L~~L~l~~~~~~~lp~~i~-~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~-~l~~L~~L~l  650 (724)
                      +...++.|+|++|.|+.+. .++ .+.+|+.|+|++|.++.++.+..+++|++|++++|.|++++..+. .+++|++|++
T Consensus        17 n~~~~~~L~L~~n~I~~Ie-~L~~~l~~L~~L~Ls~N~I~~l~~l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~L~~L~L   95 (175)
T PF14580_consen   17 NPVKLRELNLRGNQISTIE-NLGATLDKLEVLDLSNNQITKLEGLPGLPRLKTLDLSNNRISSISEGLDKNLPNLQELYL   95 (175)
T ss_dssp             --------------------S--TT-TT--EEE-TTS--S--TT----TT--EEE--SS---S-CHHHHHH-TT--EEE-
T ss_pred             ccccccccccccccccccc-chhhhhcCCCEEECCCCCCccccCccChhhhhhcccCCCCCCccccchHHhCCcCCEEEC
Confidence            3445677777777776553 344 466777777777777776667777777777777777777755543 5677777777


Q ss_pred             CCCCCCcccC-hHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEe
Q 004895          651 SNCSSLVVIA-PNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEI  707 (724)
Q Consensus       651 ~~~~~l~~~~-~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l  707 (724)
                      ++| .+..+. -..+..+++|+.|++.+|+.     ......-.--+..+++|+.||-
T Consensus        96 ~~N-~I~~l~~l~~L~~l~~L~~L~L~~NPv-----~~~~~YR~~vi~~lP~Lk~LD~  147 (175)
T PF14580_consen   96 SNN-KISDLNELEPLSSLPKLRVLSLEGNPV-----CEKKNYRLFVIYKLPSLKVLDG  147 (175)
T ss_dssp             TTS----SCCCCGGGGG-TT--EEE-TT-GG-----GGSTTHHHHHHHH-TT-SEETT
T ss_pred             cCC-cCCChHHhHHHHcCCCcceeeccCCcc-----cchhhHHHHHHHHcChhheeCC
Confidence            763 333221 12356677777777777542     2111222333445666666664

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

Probab=99.00  E-value=8.2e-11  Score=129.49  Aligned_cols=171  Identities=21%  Similarity=0.299  Sum_probs=116.6

Q ss_pred             CceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhc-------------------------CCCCceEEE
Q 004895          528 GPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFE-------------------------GTEELKVLD  581 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~-------------------------~l~~L~~L~  581 (724)
                      .++.+++..|++..+|... +.+.|++|.+..  +....+|+.+|.                         .+..|+.|.
T Consensus       288 ~L~~l~~~~nel~yip~~le~~~sL~tLdL~~--N~L~~lp~~~l~v~~~~l~~ln~s~n~l~~lp~~~e~~~~~Lq~Ly  365 (1081)
T KOG0618|consen  288 SLVSLSAAYNELEYIPPFLEGLKSLRTLDLQS--NNLPSLPDNFLAVLNASLNTLNVSSNKLSTLPSYEENNHAALQELY  365 (1081)
T ss_pred             hHHHHHhhhhhhhhCCCcccccceeeeeeehh--ccccccchHHHhhhhHHHHHHhhhhccccccccccchhhHHHHHHH
Confidence            4555555566666655444 366666666622  222233333222                         234466667


Q ss_pred             cCCCcCC-CCCccccCCCCCcEEEcCCcccCC-c-ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcc
Q 004895          582 FTGIRFS-PLPSSLGRLINLQTLCLDGWRLED-I-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV  658 (724)
Q Consensus       582 l~~~~~~-~lp~~i~~l~~L~~L~L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~  658 (724)
                      +.+|.++ ..-+-+.++.||+.|+|++|.+.. | ..+.++..|+.|+||||+++.+|..+.++..|++|...+ |.+..
T Consensus       366 lanN~Ltd~c~p~l~~~~hLKVLhLsyNrL~~fpas~~~kle~LeeL~LSGNkL~~Lp~tva~~~~L~tL~ahs-N~l~~  444 (1081)
T KOG0618|consen  366 LANNHLTDSCFPVLVNFKHLKVLHLSYNRLNSFPASKLRKLEELEELNLSGNKLTTLPDTVANLGRLHTLRAHS-NQLLS  444 (1081)
T ss_pred             HhcCcccccchhhhccccceeeeeecccccccCCHHHHhchHHhHHHhcccchhhhhhHHHHhhhhhHHHhhcC-Cceee
Confidence            7777776 222346788899999999999887 4 567889999999999999999999999999999998887 56777


Q ss_pred             cChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          659 IAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       659 ~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                      +| + +..++.|+.+|++.|.....        .+.+.-.-++|+.||+++|.
T Consensus       445 fP-e-~~~l~qL~~lDlS~N~L~~~--------~l~~~~p~p~LkyLdlSGN~  487 (1081)
T KOG0618|consen  445 FP-E-LAQLPQLKVLDLSCNNLSEV--------TLPEALPSPNLKYLDLSGNT  487 (1081)
T ss_pred             ch-h-hhhcCcceEEecccchhhhh--------hhhhhCCCcccceeeccCCc
Confidence            76 3 78999999999988743222        11111112789999999986

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.99  E-value=1.1e-09  Score=124.83  Aligned_cols=164  Identities=21%  Similarity=0.283  Sum_probs=101.6

Q ss_pred             CceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCC
Q 004895          528 GPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDG  607 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~  607 (724)
                      .++.|.+++|.+..+|... .++|+.|.+.  .+....+|..+.   .+|+.|++++|.++.+|..+.  .+|++|++++
T Consensus       242 ~L~~L~Ls~N~L~~LP~~l-~s~L~~L~Ls--~N~L~~LP~~l~---~sL~~L~Ls~N~Lt~LP~~lp--~sL~~L~Ls~  313 (754)
T PRK15370        242 TIQEMELSINRITELPERL-PSALQSLDLF--HNKISCLPENLP---EELRYLSVYDNSIRTLPAHLP--SGITHLNVQS  313 (754)
T ss_pred             cccEEECcCCccCcCChhH-hCCCCEEECc--CCccCccccccC---CCCcEEECCCCccccCcccch--hhHHHHHhcC
Confidence            4555555555555444332 2345555552  222233333221   356666666666665554432  2456666666


Q ss_pred             cccCCc-ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcccccc
Q 004895          608 WRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVE  686 (724)
Q Consensus       608 ~~l~~~-~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~  686 (724)
                      |.++.+ ..+  .++|++|++++|.++.+|..+.  ++|+.|++++| .+..+|.. +  .++|+.|++++|.+.     
T Consensus       314 N~Lt~LP~~l--~~sL~~L~Ls~N~Lt~LP~~l~--~sL~~L~Ls~N-~L~~LP~~-l--p~~L~~LdLs~N~Lt-----  380 (754)
T PRK15370        314 NSLTALPETL--PPGLKTLEAGENALTSLPASLP--PELQVLDVSKN-QITVLPET-L--PPTITTLDVSRNALT-----  380 (754)
T ss_pred             CccccCCccc--cccceeccccCCccccCChhhc--CcccEEECCCC-CCCcCChh-h--cCCcCEEECCCCcCC-----
Confidence            665552 222  3689999999999999998764  79999999995 57777653 3  368999999997432     


Q ss_pred             CCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          687 GGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       687 ~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                       ..|..+.     ..|+.|++++|.+..+|..
T Consensus       381 -~LP~~l~-----~sL~~LdLs~N~L~~LP~s  406 (754)
T PRK15370        381 -NLPENLP-----AALQIMQASRNNLVRLPES  406 (754)
T ss_pred             -CCCHhHH-----HHHHHHhhccCCcccCchh
Confidence             1222222     2588999999999988864

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

Probab=98.94  E-value=9.1e-10  Score=102.39  Aligned_cols=124  Identities=28%  Similarity=0.397  Sum_probs=45.9

Q ss_pred             CCCcCCCCCccccCCCCCcEEEcCCcccCCccccc-CCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccCh
Q 004895          583 TGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG-QLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAP  661 (724)
Q Consensus       583 ~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~-~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~  661 (724)
                      ..+.|...|. +.+..+++.|+|++|.|+.+..++ .+.+|+.|++++|.|+.++ ++..+++|+.|++++ |.++.+.+
T Consensus         5 t~~~i~~~~~-~~n~~~~~~L~L~~n~I~~Ie~L~~~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~-N~I~~i~~   81 (175)
T PF14580_consen    5 TANMIEQIAQ-YNNPVKLRELNLRGNQISTIENLGATLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSN-NRISSISE   81 (175)
T ss_dssp             --------------------------------S--TT-TT--EEE-TTS--S--T-T----TT--EEE--S-S---S-CH
T ss_pred             cccccccccc-cccccccccccccccccccccchhhhhcCCCEEECCCCCCcccc-CccChhhhhhcccCC-CCCCcccc
Confidence            3444454543 455667899999999999988888 6899999999999999985 588999999999999 67787765


Q ss_pred             HHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccc
Q 004895          662 NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       662 ~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                      .....+++|++|++++|.+..       ...+..|..+++|+.|++.+|.+...+
T Consensus        82 ~l~~~lp~L~~L~L~~N~I~~-------l~~l~~L~~l~~L~~L~L~~NPv~~~~  129 (175)
T PF14580_consen   82 GLDKNLPNLQELYLSNNKISD-------LNELEPLSSLPKLRVLSLEGNPVCEKK  129 (175)
T ss_dssp             HHHHH-TT--EEE-TTS---S-------CCCCGGGGG-TT--EEE-TT-GGGGST
T ss_pred             chHHhCCcCCEEECcCCcCCC-------hHHhHHHHcCCCcceeeccCCcccchh
Confidence            433579999999999875311       124677888999999999999875443

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.88  E-value=9.4e-09  Score=116.75  Aligned_cols=134  Identities=20%  Similarity=0.205  Sum_probs=97.3

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      +.+++.|++.+|.+..+|.  ..++|++|.+.  .+....+|.    ..++|+.|++++|.+..+|..   ..+|+.|++
T Consensus       221 ~~~L~~L~L~~N~Lt~LP~--lp~~Lk~LdLs--~N~LtsLP~----lp~sL~~L~Ls~N~L~~Lp~l---p~~L~~L~L  289 (788)
T PRK15387        221 PAHITTLVIPDNNLTSLPA--LPPELRTLEVS--GNQLTSLPV----LPPGLLELSIFSNPLTHLPAL---PSGLCKLWI  289 (788)
T ss_pred             hcCCCEEEccCCcCCCCCC--CCCCCcEEEec--CCccCcccC----cccccceeeccCCchhhhhhc---hhhcCEEEC
Confidence            4578888888888888875  35788888883  334445553    246788888888888877763   356788899


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      ++|.++.++.  .+++|++|++++|.++.+|...   .+|+.|++++ +.+..+|.    -..+|+.|++++|.+
T Consensus       290 s~N~Lt~LP~--~p~~L~~LdLS~N~L~~Lp~lp---~~L~~L~Ls~-N~L~~LP~----lp~~Lq~LdLS~N~L  354 (788)
T PRK15387        290 FGNQLTSLPV--LPPGLQELSVSDNQLASLPALP---SELCKLWAYN-NQLTSLPT----LPSGLQELSVSDNQL  354 (788)
T ss_pred             cCCccccccc--cccccceeECCCCccccCCCCc---cccccccccc-Cccccccc----cccccceEecCCCcc
Confidence            9998887443  3568999999999998887633   4577888888 45666653    125799999998753

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

Probab=98.87  E-value=3.3e-10  Score=109.24  Aligned_cols=134  Identities=19%  Similarity=0.215  Sum_probs=107.6

Q ss_pred             CCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCC
Q 004895          574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNC  653 (724)
Q Consensus       574 l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~  653 (724)
                      .+.|..|||++|.|+.+-.+..-++.++.|++++|.+....++..|++|+.|||++|.++++-..=.+|-|.++|.|++ 
T Consensus       283 Wq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~v~nLa~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKtL~La~-  361 (490)
T KOG1259|consen  283 WQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRTVQNLAELPQLQLLDLSGNLLAECVGWHLKLGNIKTLKLAQ-  361 (490)
T ss_pred             HhhhhhccccccchhhhhhhhhhccceeEEeccccceeeehhhhhcccceEeecccchhHhhhhhHhhhcCEeeeehhh-
Confidence            4679999999999998888888889999999999999888889999999999999998887755556778889999998 


Q ss_pred             CCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          654 SSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       654 ~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      |.+..+  .++++|.+|..|++.+|.+..       -.....+.+|+-|.+|.+.+|.+..+|.
T Consensus       362 N~iE~L--SGL~KLYSLvnLDl~~N~Ie~-------ldeV~~IG~LPCLE~l~L~~NPl~~~vd  416 (490)
T KOG1259|consen  362 NKIETL--SGLRKLYSLVNLDLSSNQIEE-------LDEVNHIGNLPCLETLRLTGNPLAGSVD  416 (490)
T ss_pred             hhHhhh--hhhHhhhhheeccccccchhh-------HHHhcccccccHHHHHhhcCCCccccch
Confidence            566665  347899999999998864311       1234456778888888888998877664

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.85  E-value=8.9e-09  Score=119.48  Aligned_cols=163  Identities=24%  Similarity=0.345  Sum_probs=121.2

Q ss_pred             cccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCc--CCCCCc-cccCCCCCcEEEcCCcc-cCC-c
Q 004895          539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR--FSPLPS-SLGRLINLQTLCLDGWR-LED-I  613 (724)
Q Consensus       539 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~--~~~lp~-~i~~l~~L~~L~L~~~~-l~~-~  613 (724)
                      ....|+.......|...+.  ++....++..  ...+.|+.|-+.+|.  +..++. .|..+++|++|+|++|. +.. |
T Consensus       513 ~~~~~~~~~~~~~rr~s~~--~~~~~~~~~~--~~~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP  588 (889)
T KOG4658|consen  513 LSEIPQVKSWNSVRRMSLM--NNKIEHIAGS--SENPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLP  588 (889)
T ss_pred             ccccccccchhheeEEEEe--ccchhhccCC--CCCCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCCCccCcCC
Confidence            3345655566677777662  2222333332  233468899988886  555554 47789999999999985 566 7


Q ss_pred             ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchH
Q 004895          614 AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASL  693 (724)
Q Consensus       614 ~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l  693 (724)
                      .+|+.|.+|++|+++++.++.+|.++.+|++|.+|++..+..+... ++.+..|++|++|.+....      .......+
T Consensus       589 ~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~-~~i~~~L~~Lr~L~l~~s~------~~~~~~~l  661 (889)
T KOG4658|consen  589 SSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESI-PGILLELQSLRVLRLPRSA------LSNDKLLL  661 (889)
T ss_pred             hHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccc-cchhhhcccccEEEeeccc------cccchhhH
Confidence            8999999999999999999999999999999999999987666655 5667779999999987642      11234467


Q ss_pred             HhhcCCCCCcEEEeecccc
Q 004895          694 AELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       694 ~~L~~L~~L~~L~l~~n~~  712 (724)
                      .++.+|++|+.|.+.....
T Consensus       662 ~el~~Le~L~~ls~~~~s~  680 (889)
T KOG4658|consen  662 KELENLEHLENLSITISSV  680 (889)
T ss_pred             Hhhhcccchhhheeecchh
Confidence            7888888888887765543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.85  E-value=3e-07  Score=102.39  Aligned_cols=243  Identities=17%  Similarity=0.178  Sum_probs=134.3

Q ss_pred             ccccchHHHHHHHHHHhc----C-CCccEEEEEcCCCCcHHHHHHHHHHHHhhc---cCCC--eEEEEEEecCCChHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK----D-DKLNIIGVCGMGGVGKTTLVKQIAKQVMED---NVFD--KVVMAEITKNPDAQKIQ  229 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~----~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~F~--~~~wv~vs~~~~~~~l~  229 (724)
                      ..+.||++++++|...|.    . ....++.|+|++|+|||+.++.|.+.....   ....  .+++|++....+...++
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIY  834 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAY  834 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHH
Confidence            456799999999988875    2 233577899999999999999999876432   1222  25778877777888899


Q ss_pred             HHHHHhhCCCCCCCc-hhHHHHHHHHHHHhc--CCcEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEE--
Q 004895          230 GELASDLGMNFDSND-LIYHRAKQLCQRLKK--EKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIIL--  302 (724)
Q Consensus       230 ~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~~--~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilv--  302 (724)
                      ..|.+++....+... ........++..+..  +...+||||+++....  -+.+...+.+       ....+++|++  
T Consensus       835 qvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~-------~~~s~SKLiLIG  907 (1164)
T PTZ00112        835 QVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDW-------PTKINSKLVLIA  907 (1164)
T ss_pred             HHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHH-------hhccCCeEEEEE
Confidence            999998844333222 123344555555422  2346999999975431  0111111110       0122444433  


Q ss_pred             Eecccchh----hh--hcCCCceEecCCCCHHHHHHHHHHHhCCCC---CCCCchhHHHHHHHHhCCchhHHHHHHHHhc
Q 004895          303 TSRSRDLL----CI--DMNSQKMFWIDALSEEEALQLFEKIVGEST---KASDFRPLAEEIVGKCGGLPVALSTVANALK  373 (724)
Q Consensus       303 TtR~~~v~----~~--~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~---~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~  373 (724)
                      +|......    ..  .......+..+|++.++..+++..++....   .+..++-+|+.++...|-.-.||.++-.+..
T Consensus       908 ISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAgE  987 (1164)
T PTZ00112        908 ISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAFE  987 (1164)
T ss_pred             ecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHh
Confidence            33321111    00  011123467799999999999999986321   1111222333333333444455555544443


Q ss_pred             CC-----CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHh
Q 004895          374 NK-----SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLL  423 (724)
Q Consensus       374 ~~-----~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~  423 (724)
                      .+     ..+....+.+.+.              ...+.-....||.+.|-.+..
T Consensus       988 ikegskVT~eHVrkAleeiE--------------~srI~e~IktLPlHqKLVLlA 1028 (1164)
T PTZ00112        988 NKRGQKIVPRDITEATNQLF--------------DSPLTNAINYLPWPFKMFLTC 1028 (1164)
T ss_pred             hcCCCccCHHHHHHHHHHHH--------------hhhHHHHHHcCCHHHHHHHHH
Confidence            21     2223333332221              122344556788887766553

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.84  E-value=1.3e-08  Score=115.52  Aligned_cols=169  Identities=20%  Similarity=0.172  Sum_probs=108.5

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      +.+++.|.+++|.+..+|..  .++|+.|.++.  +....+|.    ....|+.|++++|+++.+|..   +++|++|+|
T Consensus       241 p~~Lk~LdLs~N~LtsLP~l--p~sL~~L~Ls~--N~L~~Lp~----lp~~L~~L~Ls~N~Lt~LP~~---p~~L~~LdL  309 (788)
T PRK15387        241 PPELRTLEVSGNQLTSLPVL--PPGLLELSIFS--NPLTHLPA----LPSGLCKLWIFGNQLTSLPVL---PPGLQELSV  309 (788)
T ss_pred             CCCCcEEEecCCccCcccCc--ccccceeeccC--Cchhhhhh----chhhcCEEECcCCcccccccc---ccccceeEC
Confidence            57899999999999988753  47899999843  33344443    235788999999999998863   468999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++.++.+  ..+|..|++++|.++.+|..   ..+|++|++++ +.+..+|+.    .++|+.|++++|.+..  +
T Consensus       310 S~N~L~~Lp~l--p~~L~~L~Ls~N~L~~LP~l---p~~Lq~LdLS~-N~Ls~LP~l----p~~L~~L~Ls~N~L~~--L  377 (788)
T PRK15387        310 SDNQLASLPAL--PSELCKLWAYNNQLTSLPTL---PSGLQELSVSD-NQLASLPTL----PSELYKLWAYNNRLTS--L  377 (788)
T ss_pred             CCCccccCCCC--cccccccccccCcccccccc---ccccceEecCC-CccCCCCCC----Ccccceehhhcccccc--C
Confidence            99998874332  24577788888888877742   24678888887 456666531    1334444444432211  0


Q ss_pred             cCC---------ccchHHhhc-CCCCCcEEEeeccccccccc
Q 004895          686 EGG---------SNASLAELK-GLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~---------~~~~l~~L~-~L~~L~~L~l~~n~~~~lp~  717 (724)
                      ...         ....+..+. ..++|+.|++++|.++.+|.
T Consensus       378 P~l~~~L~~LdLs~N~Lt~LP~l~s~L~~LdLS~N~LssIP~  419 (788)
T PRK15387        378 PALPSGLKELIVSGNRLTSLPVLPSELKELMVSGNRLTSLPM  419 (788)
T ss_pred             cccccccceEEecCCcccCCCCcccCCCEEEccCCcCCCCCc
Confidence            000         000011111 12467788888888877775

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.84  E-value=5e-08  Score=105.56  Aligned_cols=181  Identities=15%  Similarity=0.173  Sum_probs=109.3

Q ss_pred             CcccccccchHHHHHH---HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQD---VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~---l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      |.....++|++..+..   +..++.......+.++|++|+||||+|+.+++.....       |+.++....-.+-++.+
T Consensus         8 P~~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~-------~~~l~a~~~~~~~ir~i   80 (413)
T PRK13342          8 PKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP-------FEALSAVTSGVKDLREV   80 (413)
T ss_pred             CCCHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCC-------EEEEecccccHHHHHHH
Confidence            3445678898887665   7777777777788999999999999999999876421       33333221111111222


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE--Eecccc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL--TSRSRD  308 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv--TtR~~~  308 (724)
                      ++                 ........+++.+|++|+++...  ..+.+...+           ..+..+++  ||.+..
T Consensus        81 i~-----------------~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~l-----------e~~~iilI~att~n~~  132 (413)
T PRK13342         81 IE-----------------EARQRRSAGRRTILFIDEIHRFNKAQQDALLPHV-----------EDGTITLIGATTENPS  132 (413)
T ss_pred             HH-----------------HHHHhhhcCCceEEEEechhhhCHHHHHHHHHHh-----------hcCcEEEEEeCCCChh
Confidence            21                 11111223577999999998653  233332221           12344444  334332


Q ss_pred             h--hhhhcCCCceEecCCCCHHHHHHHHHHHhCCCC-CC-CCchhHHHHHHHHhCCchhHHHHHHHH
Q 004895          309 L--LCIDMNSQKMFWIDALSEEEALQLFEKIVGEST-KA-SDFRPLAEEIVGKCGGLPVALSTVANA  371 (724)
Q Consensus       309 v--~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~-~~l~~~~~~I~~~c~GlPLai~~~~~~  371 (724)
                      .  ..........+.+.+++.++.+.++.+.+.... .. .--++..+.|++.|+|.|..+..+...
T Consensus       133 ~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~  199 (413)
T PRK13342        133 FEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLEL  199 (413)
T ss_pred             hhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            1  111123346899999999999999998764211 11 223567788999999999776544433

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

Probab=98.82  E-value=8.4e-08  Score=97.42  Aligned_cols=175  Identities=16%  Similarity=0.227  Sum_probs=108.7

Q ss_pred             CcccccccchHHHHH---HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQ---DVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGE  231 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~---~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~  231 (724)
                      |.....++|.+..+.   -|..++..+.+.-..+||++|+||||||+.+.......       |..+|... +.+++ ++
T Consensus        20 P~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~~~~-------f~~~sAv~~gvkdl-r~   91 (436)
T COG2256          20 PKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAA-------FEALSAVTSGVKDL-RE   91 (436)
T ss_pred             CCCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhhCCc-------eEEeccccccHHHH-HH
Confidence            444566677665542   23445556788888999999999999999999866432       34444433 33333 23


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE--Eeccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL--TSRSR  307 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv--TtR~~  307 (724)
                      +++                 .-.+....+++.+|++|.|..-+  +-+.+ .|.          -..|.-|+|  ||-++
T Consensus        92 i~e-----------------~a~~~~~~gr~tiLflDEIHRfnK~QQD~l-Lp~----------vE~G~iilIGATTENP  143 (436)
T COG2256          92 IIE-----------------EARKNRLLGRRTILFLDEIHRFNKAQQDAL-LPH----------VENGTIILIGATTENP  143 (436)
T ss_pred             HHH-----------------HHHHHHhcCCceEEEEehhhhcChhhhhhh-hhh----------hcCCeEEEEeccCCCC
Confidence            322                 12222233789999999997653  22333 332          445666665  55555


Q ss_pred             chh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCC-----CCCCc-hhHHHHHHHHhCCchhHHH
Q 004895          308 DLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGEST-----KASDF-RPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       308 ~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-----~~~~l-~~~~~~I~~~c~GlPLai~  366 (724)
                      ...  ..-.+...++.+++|+.+|..+++.+.+....     ....+ ++...-|++.++|--.++-
T Consensus       144 sF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aL  210 (436)
T COG2256         144 SFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRAL  210 (436)
T ss_pred             CeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHH
Confidence            431  22245567999999999999999999543111     11112 3467788899988775543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.80  E-value=2.5e-07  Score=102.61  Aligned_cols=188  Identities=18%  Similarity=0.221  Sum_probs=116.3

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      +.....++|.+..++.|..++..+++ ..+.++|+.|+||||+|+.+.+.......                   |..++
T Consensus        12 PqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~Dvi   91 (830)
T PRK07003         12 PKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYV   91 (830)
T ss_pred             CCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEE
Confidence            44567889999999999999886664 45679999999999999999987643211                   11133


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      +++.+....++++ +++++..                 ...-..++.-++|||++....  .++.+...+..        
T Consensus        92 EIDAas~rgVDdI-ReLIe~a-----------------~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEE--------  145 (830)
T PRK07003         92 EMDAASNRGVDEM-AALLERA-----------------VYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEE--------  145 (830)
T ss_pred             EecccccccHHHH-HHHHHHH-----------------HhccccCCceEEEEeChhhCCHHHHHHHHHHHHh--------
Confidence            3333222222221 1121111                 101112455689999998764  35544333322        


Q ss_pred             CCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch-hHHHHHHH
Q 004895          294 DPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP-VALSTVAN  370 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~~~~  370 (724)
                      .....++|+||.+.. +...-.+....+++++++.++..+.+.+.+..+... --.+..+.|++.++|.. -|+.++-.
T Consensus       146 PP~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~-id~eAL~lIA~~A~GsmRdALsLLdQ  223 (830)
T PRK07003        146 PPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIA-FEPQALRLLARAAQGSMRDALSLTDQ  223 (830)
T ss_pred             cCCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            334677777777654 322223445789999999999999999887543221 12567788999999866 45555433

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

Probab=98.79  E-value=3.7e-10  Score=118.10  Aligned_cols=170  Identities=24%  Similarity=0.325  Sum_probs=99.8

Q ss_pred             EeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCccc
Q 004895          532 ISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRL  610 (724)
Q Consensus       532 l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l  610 (724)
                      ..++.|.+.++|... .+..|.++.+.  .+..-.+|.. ..++..|.+|||+.|++..+|..+|.|+ |+.|-+++|++
T Consensus        80 aDlsrNR~~elp~~~~~f~~Le~liLy--~n~~r~ip~~-i~~L~~lt~l~ls~NqlS~lp~~lC~lp-Lkvli~sNNkl  155 (722)
T KOG0532|consen   80 ADLSRNRFSELPEEACAFVSLESLILY--HNCIRTIPEA-ICNLEALTFLDLSSNQLSHLPDGLCDLP-LKVLIVSNNKL  155 (722)
T ss_pred             hhccccccccCchHHHHHHHHHHHHHH--hccceecchh-hhhhhHHHHhhhccchhhcCChhhhcCc-ceeEEEecCcc
Confidence            445555555555433 34445555552  2222233332 4566667777777777777776666654 66677777766


Q ss_pred             CC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCc
Q 004895          611 ED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGS  689 (724)
Q Consensus       611 ~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~  689 (724)
                      +. |..++.+..|..||.+.|.+.++|..++.|.+|+.|++.. +.+..+|++ +..| .|..||++.|.+     .   
T Consensus       156 ~~lp~~ig~~~tl~~ld~s~nei~slpsql~~l~slr~l~vrR-n~l~~lp~E-l~~L-pLi~lDfScNki-----s---  224 (722)
T KOG0532|consen  156 TSLPEEIGLLPTLAHLDVSKNEIQSLPSQLGYLTSLRDLNVRR-NHLEDLPEE-LCSL-PLIRLDFSCNKI-----S---  224 (722)
T ss_pred             ccCCcccccchhHHHhhhhhhhhhhchHHhhhHHHHHHHHHhh-hhhhhCCHH-HhCC-ceeeeecccCce-----e---
Confidence            66 5666666677777777777777777777777777777666 455666655 3433 466666666421     1   


Q ss_pred             cchHHhhcCCCCCcEEEeeccccccccc
Q 004895          690 NASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       690 ~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                       ....++.+|++|+.|-+.+|.+.+=|.
T Consensus       225 -~iPv~fr~m~~Lq~l~LenNPLqSPPA  251 (722)
T KOG0532|consen  225 -YLPVDFRKMRHLQVLQLENNPLQSPPA  251 (722)
T ss_pred             -ecchhhhhhhhheeeeeccCCCCCChH
Confidence             122345566666777777776655554

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

Probab=98.75  E-value=1.2e-08  Score=107.28  Aligned_cols=185  Identities=17%  Similarity=0.101  Sum_probs=121.6

Q ss_pred             ccCceEEeccCCCcccC-CCc-ccC---CCccEEEEeccccccc--ccchhhhcCC-CCceEEEcCCCcCC-----CCCc
Q 004895          526 QKGPIAISLPYRDIQEL-PER-LEC---PQLKLFLLFAKYDSTL--QISDHFFEGT-EELKVLDFTGIRFS-----PLPS  592 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~-~~~-~~~---~~Lr~L~l~~~~~~~~--~~~~~~~~~l-~~L~~L~l~~~~~~-----~lp~  592 (724)
                      ..+++++++++|.+... +.. ..+   ++|+.|.+..+.....  ......+..+ ++|+.|++++|.++     .++.
T Consensus        80 ~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~  159 (319)
T cd00116          80 GCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEALAK  159 (319)
T ss_pred             cCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHHHHH
Confidence            35888899988877531 111 122   4599999943321111  1112234566 88999999999887     3455


Q ss_pred             cccCCCCCcEEEcCCcccCC------cccccCCCCCcEEEccCCcCc-----ccchhhhcCCCCCeEccCCCCCCcccCh
Q 004895          593 SLGRLINLQTLCLDGWRLED------IAIVGQLKKLEILSLRGAEIK-----QLPLQIGQLTRLQLLDLSNCSSLVVIAP  661 (724)
Q Consensus       593 ~i~~l~~L~~L~L~~~~l~~------~~~~~~l~~L~~L~l~~~~i~-----~lp~~i~~l~~L~~L~l~~~~~l~~~~~  661 (724)
                      .+..+.+|++|++++|.++.      +..+..+++|++|++++|.++     .++..+.++++|++|++++|. +.....
T Consensus       160 ~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~-l~~~~~  238 (319)
T cd00116         160 ALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNN-LTDAGA  238 (319)
T ss_pred             HHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCc-CchHHH
Confidence            66778899999999998874      234566679999999999876     344567778899999999964 443211


Q ss_pred             HHh-hC----CCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccc
Q 004895          662 NVI-SK----LSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEML  715 (724)
Q Consensus       662 ~~i-~~----l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~l  715 (724)
                      ..+ ..    .+.|++|++++|.+...    ........+..+++|+.++++.|.++.-
T Consensus       239 ~~l~~~~~~~~~~L~~L~l~~n~i~~~----~~~~l~~~~~~~~~L~~l~l~~N~l~~~  293 (319)
T cd00116         239 AALASALLSPNISLLTLSLSCNDITDD----GAKDLAEVLAEKESLLELDLRGNKFGEE  293 (319)
T ss_pred             HHHHHHHhccCCCceEEEccCCCCCcH----HHHHHHHHHhcCCCccEEECCCCCCcHH
Confidence            112 22    47899999988743211    1122234566778999999999987643

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).

>PRK06893 DNA replication initiation factor; Validated

Probab=98.73  E-value=1.7e-07  Score=92.84  Aligned_cols=155  Identities=14%  Similarity=0.189  Sum_probs=94.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      ...+.+.|+|++|+|||+|++.+++....+  ...+.|+++....   ..                     ...+.+.+.
T Consensus        37 ~~~~~l~l~G~~G~GKThL~~ai~~~~~~~--~~~~~y~~~~~~~---~~---------------------~~~~~~~~~   90 (229)
T PRK06893         37 LQQPFFYIWGGKSSGKSHLLKAVSNHYLLN--QRTAIYIPLSKSQ---YF---------------------SPAVLENLE   90 (229)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEeeHHHhh---hh---------------------hHHHHhhcc
Confidence            344678999999999999999999987653  2346777764210   00                     011222222


Q ss_pred             cCCcEEEEEcccccc---ccccc-cccccCCCCcCCCCCCCCCcEEEEEeccc----------chhhhhcCCCceEecCC
Q 004895          259 KEKRVLIILDNIWTK---LELDK-IGIPYGDVDEKDKNDDPRRCTIILTSRSR----------DLLCIDMNSQKMFWIDA  324 (724)
Q Consensus       259 ~~kr~LlVlDdv~~~---~~~~~-l~~~~~~~~~~~~~~~~~~s~ilvTtR~~----------~v~~~~~~~~~~~~l~~  324 (724)
                        +.-+|+|||+|..   ..|+. +...+...       ...+..+|++|.+.          .+.. .+.....+++++
T Consensus        91 --~~dlLilDDi~~~~~~~~~~~~l~~l~n~~-------~~~~~~illits~~~p~~l~~~~~~L~s-Rl~~g~~~~l~~  160 (229)
T PRK06893         91 --QQDLVCLDDLQAVIGNEEWELAIFDLFNRI-------KEQGKTLLLISADCSPHALSIKLPDLAS-RLTWGEIYQLND  160 (229)
T ss_pred             --cCCEEEEeChhhhcCChHHHHHHHHHHHHH-------HHcCCcEEEEeCCCChHHccccchhHHH-HHhcCCeeeCCC
Confidence              3359999999874   33442 21111110       12345555544433          2222 233456889999


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHH
Q 004895          325 LSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVAN  370 (724)
Q Consensus       325 L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~  370 (724)
                      +++++.++++++.+....-. --+++..-|++.+.|..-.+..+-.
T Consensus       161 pd~e~~~~iL~~~a~~~~l~-l~~~v~~~L~~~~~~d~r~l~~~l~  205 (229)
T PRK06893        161 LTDEQKIIVLQRNAYQRGIE-LSDEVANFLLKRLDRDMHTLFDALD  205 (229)
T ss_pred             CCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhccCCHHHHHHHHH
Confidence            99999999999988633211 1256788899999887766554433

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

Probab=98.71  E-value=6e-10  Score=116.53  Aligned_cols=147  Identities=20%  Similarity=0.240  Sum_probs=121.1

Q ss_pred             ccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccch
Q 004895          559 KYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPL  637 (724)
Q Consensus       559 ~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~  637 (724)
                      +.++...+|.. ++.|..|..+.|..|.+..+|..++++..|.||+|+.|.++. |..+|.|+ |+.|-+++|+++.+|.
T Consensus        83 srNR~~elp~~-~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lp-Lkvli~sNNkl~~lp~  160 (722)
T KOG0532|consen   83 SRNRFSELPEE-ACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGLCDLP-LKVLIVSNNKLTSLPE  160 (722)
T ss_pred             cccccccCchH-HHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhhhcCc-ceeEEEecCccccCCc
Confidence            33445556654 566788999999999999999999999999999999999988 67788776 9999999999999999


Q ss_pred             hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          638 QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       638 ~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .|+.+..|.+|+.+.| .+..+|+. ++.+.+|+.|.+..|..         .....+|..| .|.+||+++|++..+|-
T Consensus       161 ~ig~~~tl~~ld~s~n-ei~slpsq-l~~l~slr~l~vrRn~l---------~~lp~El~~L-pLi~lDfScNkis~iPv  228 (722)
T KOG0532|consen  161 EIGLLPTLAHLDVSKN-EIQSLPSQ-LGYLTSLRDLNVRRNHL---------EDLPEELCSL-PLIRLDFSCNKISYLPV  228 (722)
T ss_pred             ccccchhHHHhhhhhh-hhhhchHH-hhhHHHHHHHHHhhhhh---------hhCCHHHhCC-ceeeeecccCceeecch
Confidence            9999999999999985 56778776 89999999998877532         1223455544 48899999999999986


Q ss_pred             cc
Q 004895          718 IW  719 (724)
Q Consensus       718 ~~  719 (724)
                      .+
T Consensus       229 ~f  230 (722)
T KOG0532|consen  229 DF  230 (722)
T ss_pred             hh
Confidence            65

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.70  E-value=3.2e-07  Score=97.20  Aligned_cols=202  Identities=17%  Similarity=0.148  Sum_probs=112.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-eEEEEEEecCCCh-HHHHH---
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-KVVMAEITKNPDA-QKIQG---  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~-~~l~~---  230 (724)
                      |.....++|++..++.+..++..+..+.+.++|+.|+||||+|+.+++..... .+. ..+.+++++..+. .....   
T Consensus        11 P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~   89 (337)
T PRK12402         11 PALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD-PWENNFTEFNVADFFDQGKKYLVEDP   89 (337)
T ss_pred             CCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCc-ccccceEEechhhhhhcchhhhhcCc
Confidence            34456788999999999998887776778999999999999999999887532 222 2445555432110 00000   


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHh-----cCCcEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLK-----KEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~-----~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      .....++...............+.+...     .+.+-+||+||+.....  ...+...+..        ....+++|+|
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~--------~~~~~~~Il~  161 (337)
T PRK12402         90 RFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQ--------YSRTCRFIIA  161 (337)
T ss_pred             chhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHh--------ccCCCeEEEE
Confidence            0000000000000001112222222211     13345899999965421  2222222211        2334667777


Q ss_pred             ecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          304 SRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       304 tR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      +.... +..........+.+.+++.++...++.+.+...... --.+..+.+++.++|.+-.+..
T Consensus       162 ~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        162 TRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVD-YDDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             eCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            75432 211112334578899999999999998876532221 1256788999999987765543

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

Probab=98.70  E-value=5.7e-09  Score=106.20  Aligned_cols=185  Identities=23%  Similarity=0.146  Sum_probs=106.2

Q ss_pred             ccCceEEeccCCCcccCCC---cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc--ccCCCCC
Q 004895          526 QKGPIAISLPYRDIQELPE---RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS--LGRLINL  600 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~---~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~--i~~l~~L  600 (724)
                      .++++.+++.++.+...+.   ...|++++.|++..+-.........+...+++|+.|+++.|.+...-++  -..+.+|
T Consensus       120 ~kkL~~IsLdn~~V~~~~~~~~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~Nrl~~~~~s~~~~~l~~l  199 (505)
T KOG3207|consen  120 LKKLREISLDNYRVEDAGIEEYSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSNRLSNFISSNTTLLLSHL  199 (505)
T ss_pred             HHhhhheeecCccccccchhhhhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccccccCCccccchhhhhhh
Confidence            4678888888887766552   3478899999884333333334445677888999999998887633221  2357788


Q ss_pred             cEEEcCCcccCC---cccccCCCCCcEEEccCCc-CcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEcc
Q 004895          601 QTLCLDGWRLED---IAIVGQLKKLEILSLRGAE-IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG  676 (724)
Q Consensus       601 ~~L~L~~~~l~~---~~~~~~l~~L~~L~l~~~~-i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~  676 (724)
                      +.|.|+.|.++.   ....-.+++|+.|++.+|. +..--.....+..|+.|+|++|+.+..-....++.++.|+.|.++
T Consensus       200 K~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li~~~~~~~~~~l~~L~~Lnls  279 (505)
T KOG3207|consen  200 KQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNNLIDFDQGYKVGTLPGLNQLNLS  279 (505)
T ss_pred             heEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCcccccccccccccccchhhhhcc
Confidence            888888888765   2344456666666666662 221111223345566666666443322211235666666666665


Q ss_pred             CCCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          677 DSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       677 ~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      .|....  +......+......+++|+.|++.-|.+
T Consensus       280 ~tgi~s--i~~~d~~s~~kt~~f~kL~~L~i~~N~I  313 (505)
T KOG3207|consen  280 STGIAS--IAEPDVESLDKTHTFPKLEYLNISENNI  313 (505)
T ss_pred             ccCcch--hcCCCccchhhhcccccceeeecccCcc
Confidence            543211  1112222333344555666666666554

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

Probab=98.70  E-value=2.2e-09  Score=118.49  Aligned_cols=181  Identities=19%  Similarity=0.203  Sum_probs=113.9

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      ..+++|....|.+..+....-..+|+++.+  +.+....+| ++...+.+|..++..+|.+..+|..+..+.+|++|.+.
T Consensus       219 ~~l~~L~a~~n~l~~~~~~p~p~nl~~~di--s~n~l~~lp-~wi~~~~nle~l~~n~N~l~~lp~ri~~~~~L~~l~~~  295 (1081)
T KOG0618|consen  219 PSLTALYADHNPLTTLDVHPVPLNLQYLDI--SHNNLSNLP-EWIGACANLEALNANHNRLVALPLRISRITSLVSLSAA  295 (1081)
T ss_pred             cchheeeeccCcceeeccccccccceeeec--chhhhhcch-HHHHhcccceEecccchhHHhhHHHHhhhhhHHHHHhh
Confidence            356666666666654433333456777777  444555566 67777888888888888888888888888888888888


Q ss_pred             CcccCC-cccccCCCCCcEEEccCCcCcccchhhhc-CC-CCCeEc------------------------cCCCCCCccc
Q 004895          607 GWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQ-LT-RLQLLD------------------------LSNCSSLVVI  659 (724)
Q Consensus       607 ~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~-l~-~L~~L~------------------------l~~~~~l~~~  659 (724)
                      +|.++. |+....+.+|++|+|..|.+..+|..+-. +. .|+.|+                        +.+ |.++.-
T Consensus       296 ~nel~yip~~le~~~sL~tLdL~~N~L~~lp~~~l~v~~~~l~~ln~s~n~l~~lp~~~e~~~~~Lq~Lylan-N~Ltd~  374 (1081)
T KOG0618|consen  296 YNELEYIPPFLEGLKSLRTLDLQSNNLPSLPDNFLAVLNASLNTLNVSSNKLSTLPSYEENNHAALQELYLAN-NHLTDS  374 (1081)
T ss_pred             hhhhhhCCCcccccceeeeeeehhccccccchHHHhhhhHHHHHHhhhhccccccccccchhhHHHHHHHHhc-Cccccc
Confidence            888777 56666688888888888888777764322 11 133333                        333 222221


Q ss_pred             ChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          660 APNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       660 ~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      --..+-+..+|++|++++|..+.-        .-..+.++..|+.|++|+|.++.+|..+
T Consensus       375 c~p~l~~~~hLKVLhLsyNrL~~f--------pas~~~kle~LeeL~LSGNkL~~Lp~tv  426 (1081)
T KOG0618|consen  375 CFPVLVNFKHLKVLHLSYNRLNSF--------PASKLRKLEELEELNLSGNKLTTLPDTV  426 (1081)
T ss_pred             chhhhccccceeeeeecccccccC--------CHHHHhchHHhHHHhcccchhhhhhHHH
Confidence            111256666777777776543211        1134556667777777777777777544

>PRK04195 replication factor C large subunit; Provisional

Probab=98.67  E-value=2e-06  Score=95.06  Aligned_cols=186  Identities=19%  Similarity=0.174  Sum_probs=113.6

Q ss_pred             CcccccccchHHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD----DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      |.....++|+++.++.+.+|+..    ...+.+.|+|++|+||||+|+.++++..    |+ ++-++.++..+... +..
T Consensus        10 P~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el~----~~-~ielnasd~r~~~~-i~~   83 (482)
T PRK04195         10 PKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDYG----WE-VIELNASDQRTADV-IER   83 (482)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHcC----CC-EEEEcccccccHHH-HHH
Confidence            45567789999999999988862    2267899999999999999999999763    22 34445554433322 222


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------ccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------LDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      ++......   .            .+...++.+||+|+++....      +..+...+          ...+..||+|+.
T Consensus        84 ~i~~~~~~---~------------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l----------~~~~~~iIli~n  138 (482)
T PRK04195         84 VAGEAATS---G------------SLFGARRKLILLDEVDGIHGNEDRGGARAILELI----------KKAKQPIILTAN  138 (482)
T ss_pred             HHHHhhcc---C------------cccCCCCeEEEEecCcccccccchhHHHHHHHHH----------HcCCCCEEEecc
Confidence            22221100   0            01112568999999976532      22222111          122344666664


Q ss_pred             ccc-hhh-hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhc
Q 004895          306 SRD-LLC-IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALK  373 (724)
Q Consensus       306 ~~~-v~~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~  373 (724)
                      ... ... ........+.+.+++.++....+.+.+......-+ .+....|++.++|..-.+......+.
T Consensus       139 ~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i~-~eaL~~Ia~~s~GDlR~ain~Lq~~a  207 (482)
T PRK04195        139 DPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECD-DEALKEIAERSGGDLRSAINDLQAIA  207 (482)
T ss_pred             CccccchhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            432 111 11233467899999999999999887753222211 56789999999998776654444443

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

Probab=98.67  E-value=1.5e-05  Score=83.94  Aligned_cols=201  Identities=19%  Similarity=0.219  Sum_probs=126.9

Q ss_pred             ccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhC
Q 004895          162 FNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLG  237 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~  237 (724)
                      +.+|+++++++...|.    .+...-+.|+|.+|+|||+.++.+.+.......=..+++|++-...+..+++..|+++++
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~   98 (366)
T COG1474          19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLG   98 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcC
Confidence            7799999999998775    344445999999999999999999999876422222899999999999999999999997


Q ss_pred             CCCCCCchhHHHHHHHHHHHhc-CCcEEEEEcccccccccc--ccccccCCCCcCCCCCCCCCcEEEEEecccch--h--
Q 004895          238 MNFDSNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLELD--KIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL--L--  310 (724)
Q Consensus       238 ~~~~~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~~~--~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v--~--  310 (724)
                      ..+.......+....+.+.+.. ++.+++|||++.....-.  -+...+..       .....++|++-.-....  .  
T Consensus        99 ~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~-------~~~~~~~v~vi~i~n~~~~~~~  171 (366)
T COG1474          99 KVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRA-------PGENKVKVSIIAVSNDDKFLDY  171 (366)
T ss_pred             CCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccchHHHHHHhh-------ccccceeEEEEEEeccHHHHHH
Confidence            4333333245556666666653 678999999997653321  11111111       01224444333332222  1  


Q ss_pred             -----hhhcCCCceEecCCCCHHHHHHHHHHHhCC----CCCCCCchhHHHHHHHHhCC-chhHHHHHHH
Q 004895          311 -----CIDMNSQKMFWIDALSEEEALQLFEKIVGE----STKASDFRPLAEEIVGKCGG-LPVALSTVAN  370 (724)
Q Consensus       311 -----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~----~~~~~~l~~~~~~I~~~c~G-lPLai~~~~~  370 (724)
                           ....+ ...+..+|-+.+|-.+++..++..    ....++.-+.+..++..-+| .-.||..+-.
T Consensus       172 ld~rv~s~l~-~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~  240 (366)
T COG1474         172 LDPRVKSSLG-PSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRR  240 (366)
T ss_pred             hhhhhhhccC-cceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHH
Confidence                 11122 234789999999999999998742    22223323334444444443 3445544433

>PLN03025 replication factor C subunit; Provisional

Probab=98.66  E-value=4.2e-07  Score=94.98  Aligned_cols=185  Identities=12%  Similarity=0.100  Sum_probs=110.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-eEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-KVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.++.+..|..++..+..+.+.++|++|+||||+|+.+++..... .|. .++-++.++..+... .+++++
T Consensus         9 P~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~-~~~~~~~eln~sd~~~~~~-vr~~i~   86 (319)
T PLN03025          9 PTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGP-NYKEAVLELNASDDRGIDV-VRNKIK   86 (319)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcc-cCccceeeecccccccHHH-HHHHHH
Confidence            44566788999988888888777777778899999999999999999987432 222 223333333333322 222222


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLC  311 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~  311 (724)
                      .+.....              .+..++.-++|||+++....  .+.+...+..        ....+++++++.... +..
T Consensus        87 ~~~~~~~--------------~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~--------~~~~t~~il~~n~~~~i~~  144 (319)
T PLN03025         87 MFAQKKV--------------TLPPGRHKIVILDEADSMTSGAQQALRRTMEI--------YSNTTRFALACNTSSKIIE  144 (319)
T ss_pred             HHHhccc--------------cCCCCCeEEEEEechhhcCHHHHHHHHHHHhc--------ccCCceEEEEeCCccccch
Confidence            1110000              00113567999999976532  2222222211        234566776664432 211


Q ss_pred             hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          312 IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       312 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      .-......++++++++++....+...+......- -++....|++.++|..-.+
T Consensus       145 ~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~i-~~~~l~~i~~~~~gDlR~a  197 (319)
T PLN03025        145 PIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPY-VPEGLEAIIFTADGDMRQA  197 (319)
T ss_pred             hHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            1122345789999999999999988875332211 1467888999999877444

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

Probab=98.63  E-value=4.7e-09  Score=101.39  Aligned_cols=129  Identities=22%  Similarity=0.302  Sum_probs=104.4

Q ss_pred             cCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          527 KGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      .-+..+++++|.++.+..+. -.|++|.|++  +.+....+.+  +..+.+|..|||++|.++++-.+=.+|-|.++|.|
T Consensus       284 q~LtelDLS~N~I~~iDESvKL~Pkir~L~l--S~N~i~~v~n--La~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKtL~L  359 (490)
T KOG1259|consen  284 QELTELDLSGNLITQIDESVKLAPKLRRLIL--SQNRIRTVQN--LAELPQLQLLDLSGNLLAECVGWHLKLGNIKTLKL  359 (490)
T ss_pred             hhhhhccccccchhhhhhhhhhccceeEEec--cccceeeehh--hhhcccceEeecccchhHhhhhhHhhhcCEeeeeh
Confidence            46677889999998887666 4689999999  4444444433  67789999999999998877666677889999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCccc--chhhhcCCCCCeEccCCCCCCcccC
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQL--PLQIGQLTRLQLLDLSNCSSLVVIA  660 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~l--p~~i~~l~~L~~L~l~~~~~l~~~~  660 (724)
                      +.|.++.++.+++|.+|.+||+++|+|..+  -.+|++|+.|.+|.|.+ |.+..++
T Consensus       360 a~N~iE~LSGL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~-NPl~~~v  415 (490)
T KOG1259|consen  360 AQNKIETLSGLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTG-NPLAGSV  415 (490)
T ss_pred             hhhhHhhhhhhHhhhhheeccccccchhhHHHhcccccccHHHHHhhcC-CCccccc
Confidence            999999999999999999999999999876  35699999999999988 4455544

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

Probab=98.62  E-value=7.4e-09  Score=103.94  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=18.5

Q ss_pred             HhhcCCCCCcEEEeecccccccccc
Q 004895          694 AELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       694 ~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      +.+.+|..|++|++..|.++.+-..
T Consensus       316 ~~f~~ls~L~tL~L~~N~it~~~~~  340 (498)
T KOG4237|consen  316 GMFQGLSGLKTLSLYDNQITTVAPG  340 (498)
T ss_pred             HhhhccccceeeeecCCeeEEEecc
Confidence            3456788899999999988765443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=1.4e-06  Score=92.49  Aligned_cols=195  Identities=15%  Similarity=0.181  Sum_probs=109.3

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+..++.+...+..++. ..+.++|+.|+||||+|+.+++..........       ..+..-....++..
T Consensus        12 P~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~-------~pc~~c~~c~~~~~   84 (363)
T PRK14961         12 PQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITS-------NPCRKCIICKEIEK   84 (363)
T ss_pred             CCchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCC-------CCCCCCHHHHHHhc
Confidence            34456788999999999988876654 45689999999999999999987642111100       00000000111111


Q ss_pred             hhCCCC---CC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNF---DS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~---~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      ......   +. .....+....+.+.+.    .+++-++|+|++....  .++.+...+..        ....+++|++|
T Consensus        85 ~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe--------~~~~~~fIl~t  156 (363)
T PRK14961         85 GLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEE--------PPQHIKFILAT  156 (363)
T ss_pred             CCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhc--------CCCCeEEEEEc
Confidence            100000   00 0001111222222221    2345699999997654  34444333322        33455666666


Q ss_pred             cccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          305 RSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       305 R~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      .+.. +...-.+....+++.+++.++..+.+.+.+...... --++.+..|++.++|.|..+.
T Consensus       157 ~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~-i~~~al~~ia~~s~G~~R~al  218 (363)
T PRK14961        157 TDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESID-TDEYALKLIAYHAHGSMRDAL  218 (363)
T ss_pred             CChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHH
Confidence            4432 322212334689999999999999988876432211 124567889999999886443

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

Probab=98.61  E-value=3.7e-08  Score=103.52  Aligned_cols=179  Identities=23%  Similarity=0.239  Sum_probs=116.8

Q ss_pred             cCceEEeccCCCcccCCC--------cccCCCccEEEEecccccccccchhhhcCC---CCceEEEcCCCcCCC-----C
Q 004895          527 KGPIAISLPYRDIQELPE--------RLECPQLKLFLLFAKYDSTLQISDHFFEGT---EELKVLDFTGIRFSP-----L  590 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~--------~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l---~~L~~L~l~~~~~~~-----l  590 (724)
                      ..++++.+..+.+...+.        ...+++|+.|.+..  +.........+..+   ++|+.|++++|.+..     +
T Consensus        51 ~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~--~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l  128 (319)
T cd00116          51 PSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSD--NALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLL  128 (319)
T ss_pred             CCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccC--CCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHH
Confidence            457888888776652111        12467899998832  22222222333333   449999999998872     3


Q ss_pred             CccccCC-CCCcEEEcCCcccCC------cccccCCCCCcEEEccCCcCc-----ccchhhhcCCCCCeEccCCCCCCcc
Q 004895          591 PSSLGRL-INLQTLCLDGWRLED------IAIVGQLKKLEILSLRGAEIK-----QLPLQIGQLTRLQLLDLSNCSSLVV  658 (724)
Q Consensus       591 p~~i~~l-~~L~~L~L~~~~l~~------~~~~~~l~~L~~L~l~~~~i~-----~lp~~i~~l~~L~~L~l~~~~~l~~  658 (724)
                      +..+..+ .+|+.|++++|.++.      +..+..+.+|++|++++|.++     .++..+..+++|++|++++|. +..
T Consensus       129 ~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~-i~~  207 (319)
T cd00116         129 AKGLKDLPPALEKLVLGRNRLEGASCEALAKALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNG-LTD  207 (319)
T ss_pred             HHHHHhCCCCceEEEcCCCcCCchHHHHHHHHHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCc-cCh
Confidence            3456667 889999999998873      245677788999999999877     345566677899999999864 332


Q ss_pred             cC----hHHhhCCCCCcEEEccCCCCccccccCCccchHH-hh-cCCCCCcEEEeeccccc
Q 004895          659 IA----PNVISKLSRLEELYMGDSFSQWDKVEGGSNASLA-EL-KGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       659 ~~----~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~-~L-~~L~~L~~L~l~~n~~~  713 (724)
                      ..    ...+..+++|++|++++|..     .+.....+. .+ ...++|+.|++++|.++
T Consensus       208 ~~~~~l~~~~~~~~~L~~L~ls~n~l-----~~~~~~~l~~~~~~~~~~L~~L~l~~n~i~  263 (319)
T cd00116         208 EGASALAETLASLKSLEVLNLGDNNL-----TDAGAAALASALLSPNISLLTLSLSCNDIT  263 (319)
T ss_pred             HHHHHHHHHhcccCCCCEEecCCCcC-----chHHHHHHHHHHhccCCCceEEEccCCCCC
Confidence            21    23356788899999988642     211111111 11 13478999999999874

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).

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.60  E-value=9.2e-07  Score=100.20  Aligned_cols=186  Identities=13%  Similarity=0.208  Sum_probs=112.6

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccE-EEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNI-IGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~v-i~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      |.....++|.+..+..|..++..+++.- +.++|+.|+||||+|+.+++.......                   |.-++
T Consensus        12 P~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~Dvi   91 (944)
T PRK14949         12 PATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLI   91 (944)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEE
Confidence            3446778899999999999888777655 479999999999999999988643211                   11112


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      +++.+....+.++ ++|.+.+                 ...-..+++-++|||++....  ..+.+...+-.        
T Consensus        92 EidAas~~kVDdI-ReLie~v-----------------~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEE--------  145 (944)
T PRK14949         92 EVDAASRTKVDDT-RELLDNV-----------------QYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEE--------  145 (944)
T ss_pred             EeccccccCHHHH-HHHHHHH-----------------HhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhc--------
Confidence            2222111112111 2222211                 111113567899999997652  34443322222        


Q ss_pred             CCCCcEEEEEecc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          294 DPRRCTIILTSRS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       294 ~~~~s~ilvTtR~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ....+++|++|.. ..+...-......|++.+++.++..+.+.+.+..... ..-.+....|++.++|.|.-+..+
T Consensus       146 PP~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI-~~edeAL~lIA~~S~Gd~R~ALnL  220 (944)
T PRK14949        146 PPEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL-PFEAEALTLLAKAANGSMRDALSL  220 (944)
T ss_pred             cCCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            2334555555444 4443222334578999999999999999987753221 122467889999999988644433

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.60  E-value=3e-06  Score=93.29  Aligned_cols=184  Identities=14%  Similarity=0.195  Sum_probs=111.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      |.....++|.+...+.|..++..++. ..+.++|+.|+||||+|+.+++..-....                   |--++
T Consensus        11 PktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDvi   90 (702)
T PRK14960         11 PRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLI   90 (702)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceE
Confidence            44567889999999999999886664 56789999999999999999987642111                   11122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+....++++ ++++...                 ...-..+++-++|+|++....  ..+.+...+..        
T Consensus        91 EIDAAs~~~VddI-Reli~~~-----------------~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEE--------  144 (702)
T PRK14960         91 EIDAASRTKVEDT-RELLDNV-----------------PYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEE--------  144 (702)
T ss_pred             EecccccCCHHHH-HHHHHHH-----------------hhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhc--------
Confidence            2222222122111 1111111                 101112466799999997653  33333222222        


Q ss_pred             CCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          294 DPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      ...+.++|++|.+.. +..........+++.+++.++..+.+.+.+......- -.+....|++.++|.+..+.
T Consensus       145 PP~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~i-d~eAL~~IA~~S~GdLRdAL  217 (702)
T PRK14960        145 PPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAA-DQDAIWQIAESAQGSLRDAL  217 (702)
T ss_pred             CCCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence            234556777665532 2212234457899999999999999988875332221 24567889999999885543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.59  E-value=7.1e-07  Score=88.65  Aligned_cols=171  Identities=12%  Similarity=0.139  Sum_probs=103.3

Q ss_pred             chHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCC
Q 004895          164 SRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSN  243 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~  243 (724)
                      +.+..++.+..++.......+.|+|++|+|||+||+.+++.....  ....++++++.-.+      ..           
T Consensus        21 ~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~--~~~~~~i~~~~~~~------~~-----------   81 (226)
T TIGR03420        21 GNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER--GKSAIYLPLAELAQ------AD-----------   81 (226)
T ss_pred             CcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc--CCcEEEEeHHHHHH------hH-----------
Confidence            345567777777655566789999999999999999999987532  33456666543211      00           


Q ss_pred             chhHHHHHHHHHHHhcCCcEEEEEccccccc---ccc-ccccccCCCCcCCCCCCCCCcEEEEEecccchh--------h
Q 004895          244 DLIYHRAKQLCQRLKKEKRVLIILDNIWTKL---ELD-KIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------C  311 (724)
Q Consensus       244 ~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~---~~~-~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~  311 (724)
                             ..+...+.  +.-+||+||++...   .|. .+...+...       ...+..+|+||+.....        .
T Consensus        82 -------~~~~~~~~--~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~-------~~~~~~iIits~~~~~~~~~~~~~L~  145 (226)
T TIGR03420        82 -------PEVLEGLE--QADLVCLDDVEAIAGQPEWQEALFHLYNRV-------REAGGRLLIAGRAAPAQLPLRLPDLR  145 (226)
T ss_pred             -------HHHHhhcc--cCCEEEEeChhhhcCChHHHHHHHHHHHHH-------HHcCCeEEEECCCChHHCCcccHHHH
Confidence                   01112222  23489999997653   222 222111100       12234788888854311        1


Q ss_pred             hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHH
Q 004895          312 IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVAN  370 (724)
Q Consensus       312 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~  370 (724)
                      ........++++++++++...+++..+..... +--++..+.|++.+.|.|..+.-+..
T Consensus       146 ~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~-~~~~~~l~~L~~~~~gn~r~L~~~l~  203 (226)
T TIGR03420       146 TRLAWGLVFQLPPLSDEEKIAALQSRAARRGL-QLPDEVADYLLRHGSRDMGSLMALLD  203 (226)
T ss_pred             HHHhcCeeEecCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhccCCHHHHHHHHH
Confidence            11122357999999999999999876532111 11245678888889998877765543

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.

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

Probab=98.59  E-value=4.3e-09  Score=105.56  Aligned_cols=89  Identities=21%  Similarity=0.211  Sum_probs=69.6

Q ss_pred             cccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchH
Q 004895          615 IVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASL  693 (724)
Q Consensus       615 ~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l  693 (724)
                      .|+.|++|+.|+|++|.|+.+ +..+..+..++.|.|.. +.+..+....+..+..|++|++.+|.+...        ..
T Consensus       269 cf~~L~~L~~lnlsnN~i~~i~~~aFe~~a~l~eL~L~~-N~l~~v~~~~f~~ls~L~tL~L~~N~it~~--------~~  339 (498)
T KOG4237|consen  269 CFKKLPNLRKLNLSNNKITRIEDGAFEGAAELQELYLTR-NKLEFVSSGMFQGLSGLKTLSLYDNQITTV--------AP  339 (498)
T ss_pred             HHhhcccceEeccCCCccchhhhhhhcchhhhhhhhcCc-chHHHHHHHhhhccccceeeeecCCeeEEE--------ec
Confidence            367899999999999999977 55688899999999988 677888778888999999999998753221        23


Q ss_pred             HhhcCCCCCcEEEeecccc
Q 004895          694 AELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       694 ~~L~~L~~L~~L~l~~n~~  712 (724)
                      +.+..+..|.+|.+-.|.+
T Consensus       340 ~aF~~~~~l~~l~l~~Np~  358 (498)
T KOG4237|consen  340 GAFQTLFSLSTLNLLSNPF  358 (498)
T ss_pred             ccccccceeeeeehccCcc
Confidence            4556677788888877754

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.59  E-value=1.6e-06  Score=91.07  Aligned_cols=184  Identities=12%  Similarity=0.113  Sum_probs=109.0

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE--ecCCChHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI--TKNPDAQKIQGELA  233 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~l~~~i~  233 (724)
                      |.....++|+++.++.+..++..+..+.+.|+|+.|+||||+|+.+++...... +.. .++.+  +...... ...+.+
T Consensus        13 P~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~-~~~-~~i~~~~~~~~~~~-~~~~~i   89 (319)
T PRK00440         13 PRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGED-WRE-NFLELNASDERGID-VIRNKI   89 (319)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCc-ccc-ceEEeccccccchH-HHHHHH
Confidence            344566889999999999998877777789999999999999999999874322 211 22222  2222221 111111


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hh
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LL  310 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~  310 (724)
                      ..+....+               .....+-++++|++....  ....+...+..        ....+.+|+++.... +.
T Consensus        90 ~~~~~~~~---------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~--------~~~~~~lIl~~~~~~~l~  146 (319)
T PRK00440         90 KEFARTAP---------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEM--------YSQNTRFILSCNYSSKII  146 (319)
T ss_pred             HHHHhcCC---------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhc--------CCCCCeEEEEeCCccccc
Confidence            11110000               001235689999986542  22223222222        233456776664332 21


Q ss_pred             hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          311 CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       311 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      .........+++.++++++....+.+.+...... --++....+++.++|.+.-+.
T Consensus       147 ~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~-i~~~al~~l~~~~~gd~r~~~  201 (319)
T PRK00440        147 DPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIE-ITDDALEAIYYVSEGDMRKAI  201 (319)
T ss_pred             hhHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHH
Confidence            1112234578999999999999998887533221 125678899999999886643

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.58  E-value=1.6e-06  Score=95.19  Aligned_cols=197  Identities=15%  Similarity=0.157  Sum_probs=111.3

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+.....|..++..++.. .+.++|++|+||||+|+.+++.....+.+....|.|.+... +......-+.
T Consensus        10 P~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~-i~~~~h~dv~   88 (504)
T PRK14963         10 PITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLA-VRRGAHPDVL   88 (504)
T ss_pred             CCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHH-HhcCCCCceE
Confidence            344567889999998898888766654 55899999999999999999987532222222232221100 0000000000


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEec-cc
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSR-SR  307 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR-~~  307 (724)
                      .++..  ... ..+....+.+.+.    .+++-++|+|+++...  .++.+...+..        ....+.+|++|. ..
T Consensus        89 el~~~--~~~-~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEe--------p~~~t~~Il~t~~~~  157 (504)
T PRK14963         89 EIDAA--SNN-SVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEE--------PPEHVIFILATTEPE  157 (504)
T ss_pred             Eeccc--ccC-CHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHh--------CCCCEEEEEEcCChh
Confidence            00000  000 1111222222221    2456799999997552  34444333322        223445555443 33


Q ss_pred             chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       308 ~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      .+..........+++.++++++..+.+.+.+....... -++....|++.++|.+--+
T Consensus       158 kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i-~~~Al~~ia~~s~GdlR~a  214 (504)
T PRK14963        158 KMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREA-EPEALQLVARLADGAMRDA  214 (504)
T ss_pred             hCChHHhcceEEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            33222234456899999999999999998875332221 2467889999999988644

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.58  E-value=1.6e-06  Score=90.43  Aligned_cols=176  Identities=15%  Similarity=0.228  Sum_probs=114.1

Q ss_pred             ccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHh----hccCCCeEEEEEE-ecCCChHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVM----EDNVFDKVVMAEI-TKNPDAQKIQGELA  233 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~----~~~~F~~~~wv~v-s~~~~~~~l~~~i~  233 (724)
                      ..++|.+..++.+..++..++. ....++|+.|+||||+|+.+++..-    ...|+|...|... +.....+++ +++.
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~i-r~~~   82 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDI-RNII   82 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHH-HHHH
Confidence            4567989999999999876654 4668999999999999999998752    2356676666542 233344442 3333


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccc--cccccccccccCCCCcCCCCCCCCCcEEEEEecccchh-
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWT--KLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-  310 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~--~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-  310 (724)
                      +.+....                 ..+++-++|+|+++.  ...++.+...+..        ...++.+|++|.+.+.. 
T Consensus        83 ~~~~~~p-----------------~~~~~kv~iI~~ad~m~~~a~naLLK~LEe--------pp~~t~~il~~~~~~~ll  137 (313)
T PRK05564         83 EEVNKKP-----------------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEE--------PPKGVFIILLCENLEQIL  137 (313)
T ss_pred             HHHhcCc-----------------ccCCceEEEEechhhcCHHHHHHHHHHhcC--------CCCCeEEEEEeCChHhCc
Confidence            3332111                 013456777777644  3456666545544        55678888888665432 


Q ss_pred             hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          311 CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       311 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      ..-.+....+++.++++++....+.+.....     -.+.++.++..++|.|.-+.
T Consensus       138 ~TI~SRc~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~~l~~~~~g~~~~a~  188 (313)
T PRK05564        138 DTIKSRCQIYKLNRLSKEEIEKFISYKYNDI-----KEEEKKSAIAFSDGIPGKVE  188 (313)
T ss_pred             HHHHhhceeeeCCCcCHHHHHHHHHHHhcCC-----CHHHHHHHHHHcCCCHHHHH
Confidence            2113345789999999999988887664311     13457789999999986554

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.58  E-value=8.5e-07  Score=97.25  Aligned_cols=182  Identities=15%  Similarity=0.230  Sum_probs=111.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhcc------------------------C
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDN------------------------V  210 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~------------------------~  210 (724)
                      +.....++|.+..++.|..++..++.. .+.++|+.|+||||+|+.+.+......                        .
T Consensus        12 PqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~   91 (700)
T PRK12323         12 PRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGR   91 (700)
T ss_pred             CCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCC
Confidence            444677889999999999999876654 568899999999999999998764310                        0


Q ss_pred             CCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccC
Q 004895          211 FDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYG  284 (724)
Q Consensus       211 F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~  284 (724)
                      |..+++++.+...++++                      +..+.+.+    ..++.-++|+|+++...  .++.+...+.
T Consensus        92 hpDviEIdAas~~gVDd----------------------IReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLE  149 (700)
T PRK12323         92 FVDYIEMDAASNRGVDE----------------------MAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLE  149 (700)
T ss_pred             CCcceEecccccCCHHH----------------------HHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhc
Confidence            11122222222222221                      22222222    13566799999997653  3444333222


Q ss_pred             CCCcCCCCCCCCCcEEE-EEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          285 DVDEKDKNDDPRRCTII-LTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       285 ~~~~~~~~~~~~~s~il-vTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      .        ....+++| +||....+...-.+....+.+..++.++..+.+.+.+....... -.+..+.|++.++|.|.
T Consensus       150 E--------PP~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~-d~eAL~~IA~~A~Gs~R  220 (700)
T PRK12323        150 E--------PPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAH-EVNALRLLAQAAQGSMR  220 (700)
T ss_pred             c--------CCCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHH
Confidence            2        23345544 45544444322233456899999999999999988775332221 14556889999999996


Q ss_pred             HHHHH
Q 004895          364 ALSTV  368 (724)
Q Consensus       364 ai~~~  368 (724)
                      -...+
T Consensus       221 dALsL  225 (700)
T PRK12323        221 DALSL  225 (700)
T ss_pred             HHHHH
Confidence            54433

>PF13173 AAA_14: AAA domain

Probab=98.57  E-value=1.4e-07  Score=84.35  Aligned_cols=121  Identities=25%  Similarity=0.220  Sum_probs=79.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      .+++.|.|+.|+||||++++++++..   ....++|++..+........                 .+....+.+... +
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~-----------------~~~~~~~~~~~~-~   60 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLAD-----------------PDLLEYFLELIK-P   60 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhh-----------------hhhHHHHHHhhc-c
Confidence            36899999999999999999998875   23457788766432211000                 001122222222 3


Q ss_pred             CcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchhh-----hhcCCCceEecCCCCHHHH
Q 004895          261 KRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLC-----IDMNSQKMFWIDALSEEEA  330 (724)
Q Consensus       261 kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~-----~~~~~~~~~~l~~L~~~e~  330 (724)
                      ++.+++||++....+|......+.+        ..+..+|++|+.+.....     ...+....+++.||+..|.
T Consensus        61 ~~~~i~iDEiq~~~~~~~~lk~l~d--------~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPDWEDALKFLVD--------NGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             CCcEEEEehhhhhccHHHHHHHHHH--------hccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            6789999999988888776555544        445688999999876541     1223345789999998773

>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=98.57  E-value=4.2e-06  Score=79.71  Aligned_cols=187  Identities=18%  Similarity=0.187  Sum_probs=94.8

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      |.....|+|.++.+..+.-.+.     .+...-+.+||++|+||||||..+++.....  |   .+++.+.-....++ .
T Consensus        20 P~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~--~---~~~sg~~i~k~~dl-~   93 (233)
T PF05496_consen   20 PKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVN--F---KITSGPAIEKAGDL-A   93 (233)
T ss_dssp             -SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT----E---EEEECCC--SCHHH-H
T ss_pred             CCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCC--e---EeccchhhhhHHHH-H
Confidence            5567889999998887654433     3456788999999999999999999988653  2   22322111111222 1


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------cccccc--ccCCCCc-C-CCCCCCCC
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDKIGI--PYGDVDE-K-DKNDDPRR  297 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~l~~--~~~~~~~-~-~~~~~~~~  297 (724)
                      .                     +...+  +++-+|++|++.....         .++...  ..+.-.. . ....-.+=
T Consensus        94 ~---------------------il~~l--~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~F  150 (233)
T PF05496_consen   94 A---------------------ILTNL--KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPF  150 (233)
T ss_dssp             H---------------------HHHT----TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----
T ss_pred             H---------------------HHHhc--CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCc
Confidence            1                     12222  2345777788754311         111110  1110000 0 00000111


Q ss_pred             cEEEEEecccchhhhhc-CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          298 CTIILTSRSRDLLCIDM-NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       298 s~ilvTtR~~~v~~~~~-~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      +-|=.|||...+..... ...-..+++..+.+|-.++..+.+..-... --++.+.+|++.|.|-|--+.-+-...
T Consensus       151 TligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~-i~~~~~~~Ia~rsrGtPRiAnrll~rv  225 (233)
T PF05496_consen  151 TLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIE-IDEDAAEEIARRSRGTPRIANRLLRRV  225 (233)
T ss_dssp             EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-E-E-HHHHHHHHHCTTTSHHHHHHHHHHH
T ss_pred             eEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCC-cCHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            23667888766532212 222355899999999999998876422111 115789999999999997665544433

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.

>PTZ00202 tuzin; Provisional

Probab=98.57  E-value=5.4e-06  Score=86.05  Aligned_cols=167  Identities=13%  Similarity=0.176  Sum_probs=106.5

Q ss_pred             cCCCcccccccchHHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHH
Q 004895          153 FGDMKDYNIFNSRKKIFQDVIEALKD---DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQ  229 (724)
Q Consensus       153 ~~~~~~~~~~~gR~~~~~~l~~~L~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~  229 (724)
                      .+.|.+...|+||+.++.+|...|.+   ...+++.|+|++|+|||||++.+.....     ...++++..   +..+++
T Consensus       255 ~~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~-----~~qL~vNpr---g~eElL  326 (550)
T PTZ00202        255 QSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEG-----MPAVFVDVR---GTEDTL  326 (550)
T ss_pred             cCCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCC-----ceEEEECCC---CHHHHH
Confidence            34477788999999999999998853   2345899999999999999999996553     113333333   679999


Q ss_pred             HHHHHhhCCCCCCCchhHHHHHHHHHHHh----c-CCcEEEEEccccccc---cccccccccCCCCcCCCCCCCCCcEEE
Q 004895          230 GELASDLGMNFDSNDLIYHRAKQLCQRLK----K-EKRVLIILDNIWTKL---ELDKIGIPYGDVDEKDKNDDPRRCTII  301 (724)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~-~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~~~~~~~~~~s~il  301 (724)
                      +.|+.+||.+....  ..+....+.+.+.    . +++.+||+-==+..+   .+++. ..+..        ...-|.|+
T Consensus       327 r~LL~ALGV~p~~~--k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~-v~la~--------drr~ch~v  395 (550)
T PTZ00202        327 RSVVKALGVPNVEA--CGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEV-VALAC--------DRRLCHVV  395 (550)
T ss_pred             HHHHHHcCCCCccc--HHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHH-HHHHc--------cchhheee
Confidence            99999999743322  2334444444442    2 566677764321111   11111 12222        44557777


Q ss_pred             EEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      +---.+..-  ......-.-|-+++++.++|.++.++..
T Consensus       396 ~evpleslt~~~~~lprldf~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        396 IEVPLESLTIANTLLPRLDFYLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             eeehHhhcchhcccCccceeEecCCCCHHHHHHHHhhcc
Confidence            655444321  1122334578899999999999887764

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

Probab=98.56  E-value=6.7e-08  Score=104.80  Aligned_cols=176  Identities=27%  Similarity=0.341  Sum_probs=134.5

Q ss_pred             cCceEEeccCCCcccCCCcccCC--CccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEE
Q 004895          527 KGPIAISLPYRDIQELPERLECP--QLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC  604 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~--~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~  604 (724)
                      ..+..+.+.++.+..++......  +|+.|.+  ..+....++ .....++.|+.|++++|.+..+|...+.+.+|+.|+
T Consensus       116 ~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l--~~N~i~~l~-~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~L~  192 (394)
T COG4886         116 TNLTSLDLDNNNITDIPPLIGLLKSNLKELDL--SDNKIESLP-SPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNNLD  192 (394)
T ss_pred             cceeEEecCCcccccCccccccchhhcccccc--cccchhhhh-hhhhccccccccccCCchhhhhhhhhhhhhhhhhee
Confidence            46788889889998888766554  8999988  334444443 236788999999999999999988877899999999


Q ss_pred             cCCcccCCc-ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccc
Q 004895          605 LDGWRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD  683 (724)
Q Consensus       605 L~~~~l~~~-~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~  683 (724)
                      +++|.+..+ ..+..+.+|++|.+++|.+...|..+.++.++..|.+.+ +.+... +..++.+++|+.|++++|..   
T Consensus       193 ls~N~i~~l~~~~~~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~-n~~~~~-~~~~~~l~~l~~L~~s~n~i---  267 (394)
T COG4886         193 LSGNKISDLPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSN-NKLEDL-PESIGNLSNLETLDLSNNQI---  267 (394)
T ss_pred             ccCCccccCchhhhhhhhhhhhhhcCCcceecchhhhhcccccccccCC-ceeeec-cchhccccccceeccccccc---
Confidence            999998884 444677779999999997777788889999999998776 444443 34578899999999988642   


Q ss_pred             cccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          684 KVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       684 ~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                        .     .+..+..+.+|+.|++++|.+...+.
T Consensus       268 --~-----~i~~~~~~~~l~~L~~s~n~~~~~~~  294 (394)
T COG4886         268 --S-----SISSLGSLTNLRELDLSGNSLSNALP  294 (394)
T ss_pred             --c-----ccccccccCccCEEeccCccccccch
Confidence              1     12237778899999999987765543

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

Probab=98.55  E-value=2.7e-07  Score=82.92  Aligned_cols=117  Identities=20%  Similarity=0.298  Sum_probs=80.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc---CCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN---VFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQR  256 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~  256 (724)
                      +.+++.|+|++|+|||++++.+.+......   .-..++|++++...+...+...|+++++...............+.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~   82 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDA   82 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHH
Confidence            346889999999999999999999875310   12347799999888999999999999998776633355566777778


Q ss_pred             HhcCCcEEEEEcccccc-c--cccccccccCCCCcCCCCCCCCCcEEEEEecc
Q 004895          257 LKKEKRVLIILDNIWTK-L--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS  306 (724)
Q Consensus       257 l~~~kr~LlVlDdv~~~-~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~  306 (724)
                      +.+.+..+||+||+... .  .++.+....          +..+.++|+..+.
T Consensus        83 l~~~~~~~lviDe~~~l~~~~~l~~l~~l~----------~~~~~~vvl~G~~  125 (131)
T PF13401_consen   83 LDRRRVVLLVIDEADHLFSDEFLEFLRSLL----------NESNIKVVLVGTP  125 (131)
T ss_dssp             HHHCTEEEEEEETTHHHHTHHHHHHHHHHT----------CSCBEEEEEEESS
T ss_pred             HHhcCCeEEEEeChHhcCCHHHHHHHHHHH----------hCCCCeEEEEECh
Confidence            77666679999999765 2  122221111          3556677777665

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.54  E-value=4e-07  Score=93.25  Aligned_cols=291  Identities=23%  Similarity=0.263  Sum_probs=181.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..+.+.++|.|||||||++-.+.. ... .+-+.+.++.+....+...+.-.+...++....+..   .....+..... 
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~-~~~-~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~g~---~~~~~~~~~~~-   86 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH-AAS-EYADGVAFVDLAPITDPALVFPTLAGALGLHVQPGD---SAVDTLVRRIG-   86 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh-Hhh-hcccceeeeeccccCchhHhHHHHHhhcccccccch---HHHHHHHHHHh-
Confidence            356899999999999999999998 433 233567778887777777777777777877654422   12334444444 


Q ss_pred             CCcEEEEEcccccccc-ccccccccCCCCcCCCCCCCCCcEEEEEecccchhhhhcCCCceEecCCCCHH-HHHHHHHHH
Q 004895          260 EKRVLIILDNIWTKLE-LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEE-EALQLFEKI  337 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~-~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~~~~~~~~l~~L~~~-e~~~Lf~~~  337 (724)
                      ++|.++|+||.....+ -..+...+..        +...-.|+.|+|....    ......+.+++|+.. ++.++|...
T Consensus        87 ~rr~llvldncehl~~~~a~~i~all~--------~~~~~~~~atsre~~l----~~ge~~~~~~~L~~~d~a~~lf~~r  154 (414)
T COG3903          87 DRRALLVLDNCEHLLDACAALIVALLG--------ACPRLAILATSREAIL----VAGEVHRRVPSLSLFDEAIELFVCR  154 (414)
T ss_pred             hhhHHHHhcCcHHHHHHHHHHHHHHHc--------cchhhhhHHHhHhhhc----ccccccccCCccccCCchhHHHHHH
Confidence            5889999999876532 1111111211        4455678899998754    344567778888755 788998887


Q ss_pred             hCCCCC----CCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHHH----HhcCccccccCCCcccchhhHhh
Q 004895          338 VGESTK----ASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNK----LTSSNLREIHGMDADVYSPIKLS  409 (724)
Q Consensus       338 ~~~~~~----~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~~----l~~~~~~~~~~~~~~i~~~l~~s  409 (724)
                      +.....    ...-.....+|.++..|.|++|...++..+.....+...-++.    +... ..............+.+|
T Consensus       155 a~~~~~~f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~-~r~a~~~~qtl~asl~ws  233 (414)
T COG3903         155 AVLVALSFWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGG-ARLAVLRQQTLRASLDWS  233 (414)
T ss_pred             HHHhccceeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcc-cccchhHHHhccchhhhh
Confidence            642111    1222567889999999999999999999987766555444432    1111 111111234568899999


Q ss_pred             hhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcccccccccccccccHHHHHHHHHHHHHHHHhhcccccC--CCCC
Q 004895          410 YDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDG--DAED  487 (724)
Q Consensus       410 y~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~~--~~~~  487 (724)
                      |.-|..-.+-.|.-++.|...+.  .+  ...|.      +-|-.     .+...-.....+..+++.++..-.  ....
T Consensus       234 ~~lLtgwe~~~~~rLa~~~g~f~--~~--l~~~~------a~g~~-----~~~~~y~~~~a~~ll~~kslv~a~~~~~~a  298 (414)
T COG3903         234 YALLTGWERALFGRLAVFVGGFD--LG--LALAV------AAGAD-----VDVPRYLVLLALTLLVDKSLVVALDLLGRA  298 (414)
T ss_pred             hHhhhhHHHHHhcchhhhhhhhc--cc--HHHHH------hcCCc-----cccchHHHHHHHHHHhhccchhhhhhhhHH
Confidence            99999999999999999987533  33  23444      33211     101111122334446666665322  1223


Q ss_pred             cchhhHHHHHHHHHHhh
Q 004895          488 EAKLHDVIHVVAASIAE  504 (724)
Q Consensus       488 ~~~mHdlv~d~a~~~~~  504 (724)
                      .|+.-+-+|.|+..+-.
T Consensus       299 ~~Rl~eT~r~YalaeL~  315 (414)
T COG3903         299 RYRLLETGRRYALAELH  315 (414)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            46666666666665543

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.52  E-value=3.1e-06  Score=93.02  Aligned_cols=188  Identities=14%  Similarity=0.191  Sum_probs=111.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhcc-------------------CCCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDN-------------------VFDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~~  215 (724)
                      |.....++|.+..+..|...+..++. ..+.++|+.|+||||+|+.+++......                   .|..++
T Consensus        12 P~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dli   91 (546)
T PRK14957         12 PQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLI   91 (546)
T ss_pred             cCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceE
Confidence            34456788999999999988876555 4578999999999999999998664211                   122233


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      ++.......++++ +++++                 .+...-..+++-++|+|++....  ..+.+...+..        
T Consensus        92 eidaas~~gvd~i-r~ii~-----------------~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEe--------  145 (546)
T PRK14957         92 EIDAASRTGVEET-KEILD-----------------NIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEE--------  145 (546)
T ss_pred             EeecccccCHHHH-HHHHH-----------------HHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhc--------
Confidence            3333222222221 12221                 11111112566799999997543  33444333322        


Q ss_pred             CCCCcEEE-EEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHHHH
Q 004895          294 DPRRCTII-LTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTVAN  370 (724)
Q Consensus       294 ~~~~s~il-vTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~~~  370 (724)
                      ....+.+| +||....+...-......+++.+++.++....+.+.+..... ..-++....|++.++|.+- |+..+-.
T Consensus       146 pp~~v~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi-~~e~~Al~~Ia~~s~GdlR~alnlLek  223 (546)
T PRK14957        146 PPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENI-NSDEQSLEYIAYHAKGSLRDALSLLDQ  223 (546)
T ss_pred             CCCCceEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            23345455 555443333222344578999999999998888886643221 1124567889999999764 5444433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.51  E-value=2.9e-06  Score=92.70  Aligned_cols=179  Identities=16%  Similarity=0.221  Sum_probs=110.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCC----------------------
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD----------------------  212 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~----------------------  212 (724)
                      |.....++|.+..+..|...+..++. ..+.++|+.|+||||+|+.+++..-......                      
T Consensus        17 P~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h   96 (507)
T PRK06645         17 PSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNH   96 (507)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCC
Confidence            44466788999999988887766554 5788999999999999999999764321110                      


Q ss_pred             -eEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCC
Q 004895          213 -KVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGD  285 (724)
Q Consensus       213 -~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~  285 (724)
                       .++.++.+....+.+                      ...+.+...    .+++-++|+|+++...  .++.+...+..
T Consensus        97 ~Dv~eidaas~~~vd~----------------------Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEe  154 (507)
T PRK06645         97 PDIIEIDAASKTSVDD----------------------IRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEE  154 (507)
T ss_pred             CcEEEeeccCCCCHHH----------------------HHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhh
Confidence             011122211112211                      122222211    2466799999998753  35554333332


Q ss_pred             CCcCCCCCCCCCcEEE-EEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          286 VDEKDKNDDPRRCTII-LTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       286 ~~~~~~~~~~~~s~il-vTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                              ....+.+| +||+...+...-......+++.+++.++....+.+.+......- -.+....|++.++|.+.-
T Consensus       155 --------pp~~~vfI~aTte~~kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~i-e~eAL~~Ia~~s~GslR~  225 (507)
T PRK06645        155 --------PPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKT-DIEALRIIAYKSEGSARD  225 (507)
T ss_pred             --------cCCCEEEEEEeCChHHhhHHHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHH
Confidence                    33445555 45444444322233456899999999999999998886433221 145678899999998754


Q ss_pred             H
Q 004895          365 L  365 (724)
Q Consensus       365 i  365 (724)
                      +
T Consensus       226 a  226 (507)
T PRK06645        226 A  226 (507)
T ss_pred             H
Confidence            4

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

Probab=98.50  E-value=8.7e-07  Score=88.29  Aligned_cols=177  Identities=12%  Similarity=0.223  Sum_probs=108.1

Q ss_pred             cccccccchHHHHHH---HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          157 KDYNIFNSRKKIFQD---VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~---l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      .....++|.++.+.+   |.+.+.++.++-+.+||++|+||||||+.+....+...    ..||..|....-..-.+.|.
T Consensus       135 ktL~dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~if  210 (554)
T KOG2028|consen  135 KTLDDYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIF  210 (554)
T ss_pred             chHHHhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHH
Confidence            334455565544332   33444578889999999999999999999998776432    56888876654444445554


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE--Eecccch
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL--TSRSRDL  309 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv--TtR~~~v  309 (724)
                      ++-              .. ...+ .++|.+|++|.|..-.  +-+.+   +|.        -.+|.-++|  ||-++..
T Consensus       211 e~a--------------q~-~~~l-~krkTilFiDEiHRFNksQQD~f---LP~--------VE~G~I~lIGATTENPSF  263 (554)
T KOG2028|consen  211 EQA--------------QN-EKSL-TKRKTILFIDEIHRFNKSQQDTF---LPH--------VENGDITLIGATTENPSF  263 (554)
T ss_pred             HHH--------------HH-HHhh-hcceeEEEeHHhhhhhhhhhhcc---cce--------eccCceEEEecccCCCcc
Confidence            432              11 1122 3588999999997553  22222   333        445665554  6666543


Q ss_pred             h--hhhcCCCceEecCCCCHHHHHHHHHHHhC---CC------CCCCC--c-hhHHHHHHHHhCCchhH
Q 004895          310 L--CIDMNSQKMFWIDALSEEEALQLFEKIVG---ES------TKASD--F-RPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       310 ~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~---~~------~~~~~--l-~~~~~~I~~~c~GlPLa  364 (724)
                      -  ........++.|++|+.++...++.+...   +.      .+++.  + ..+.+-++..|.|-..+
T Consensus       264 qln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~  332 (554)
T KOG2028|consen  264 QLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARA  332 (554)
T ss_pred             chhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHH
Confidence            1  12244557899999999999999988542   11      11111  1 23556667777776643

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

Probab=98.49  E-value=3.2e-07  Score=91.00  Aligned_cols=94  Identities=17%  Similarity=0.152  Sum_probs=64.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC--CChHHHHHHHH-----HhhCCCCCCCch-hHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN--PDAQKIQGELA-----SDLGMNFDSNDL-IYHRA  250 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~l~~~i~-----~~l~~~~~~~~~-~~~~~  250 (724)
                      ..-..++|+|++|+|||||++.+++..... +|+.+.|+.+.++  .++.++++.+.     ..++.+...... .....
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~   92 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVL   92 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHH
Confidence            345689999999999999999999998764 8999999998877  78899999883     333321100000 00111


Q ss_pred             HHHHHHHhcCCcEEEEEcccccc
Q 004895          251 KQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       251 ~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .........+++.++++|++...
T Consensus        93 ~~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          93 EKAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHHCCCCEEEEEECHHHh
Confidence            22222223478999999999654

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=98.49  E-value=2.2e-06  Score=91.66  Aligned_cols=194  Identities=15%  Similarity=0.120  Sum_probs=112.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+..+..|..++..++.. .+.++|+.|+||||+|+.+++..........   ..+.....    ...+..
T Consensus        14 P~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~---~pCg~C~s----C~~i~~   86 (484)
T PRK14956         14 PQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN---EPCNECTS----CLEITK   86 (484)
T ss_pred             CCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc---cccCCCcH----HHHHHc
Confidence            445677889999999999888877754 5789999999999999999987643211100   00111101    112222


Q ss_pred             hhCCCC---CC-CchhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEE-EE
Q 004895          235 DLGMNF---DS-NDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTII-LT  303 (724)
Q Consensus       235 ~l~~~~---~~-~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~il-vT  303 (724)
                      ......   +. .....+.+..+.+.+    ..++.-++|+|++....  .++.+...+..        ......+| .|
T Consensus        87 g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEE--------Pp~~viFILaT  158 (484)
T PRK14956         87 GISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEE--------PPAHIVFILAT  158 (484)
T ss_pred             cCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhc--------CCCceEEEeec
Confidence            111110   00 000111222222222    23566799999997653  34544333322        22344444 45


Q ss_pred             ecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      |....+...-......|.+.+++.++..+.+.+.+...... --++....|++.++|.+.-+
T Consensus       159 te~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~-~e~eAL~~Ia~~S~Gd~RdA  219 (484)
T PRK14956        159 TEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQ-YDQEGLFWIAKKGDGSVRDM  219 (484)
T ss_pred             CChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCChHHHH
Confidence            54444432223445689999999999999998887533221 12567889999999998543

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.48  E-value=3.5e-06  Score=91.67  Aligned_cols=190  Identities=17%  Similarity=0.233  Sum_probs=110.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      |.....++|.+.....|...+..++. +.+.++|++|+||||+|+.+++.......                   +..++
T Consensus        10 P~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~   89 (472)
T PRK14962         10 PKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVI   89 (472)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccE
Confidence            44567789999888888888776666 45789999999999999999987643111                   00122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+...+..++ +.|.+...                 ..-..+++-++|+|++....  ..+.+...+..        
T Consensus        90 el~aa~~~gid~i-R~i~~~~~-----------------~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~--------  143 (472)
T PRK14962         90 ELDAASNRGIDEI-RKIRDAVG-----------------YRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEE--------  143 (472)
T ss_pred             EEeCcccCCHHHH-HHHHHHHh-----------------hChhcCCeEEEEEEChHHhHHHHHHHHHHHHHh--------
Confidence            2332222222222 12222111                 00012456799999996542  23333222221        


Q ss_pred             CCCCcEEEEEecc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHHHHHH
Q 004895          294 DPRRCTIILTSRS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALSTVANA  371 (724)
Q Consensus       294 ~~~~s~ilvTtR~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~~~~~  371 (724)
                      ....+.+|++|.+ ..+...-......+++.+++.++....+.+.+..... .--++....|++.++|. +.++..+-.+
T Consensus       144 p~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi-~i~~eal~~Ia~~s~GdlR~aln~Le~l  222 (472)
T PRK14962        144 PPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGI-EIDREALSFIAKRASGGLRDALTMLEQV  222 (472)
T ss_pred             CCCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            2223444444433 3332222344568999999999999999887743221 11246778899888654 6666666554


Q ss_pred             h
Q 004895          372 L  372 (724)
Q Consensus       372 l  372 (724)
                      .
T Consensus       223 ~  223 (472)
T PRK14962        223 W  223 (472)
T ss_pred             H
Confidence            3

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.47  E-value=1e-05  Score=84.77  Aligned_cols=199  Identities=14%  Similarity=0.174  Sum_probs=115.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccC--CCeEEEEEEecCCChHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV--FDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      |.....++|.++....+...+..++. ..+.|+|+.|+||||+|..+++..-....  +...   .....+..-...+.|
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~---~~~~~~~~c~~c~~i   95 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE---TLADPDPASPVWRQI   95 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc---ccCCCCCCCHHHHHH
Confidence            55567788999999999999886664 45889999999999999999998743110  1111   001111111233333


Q ss_pred             HHh-------hCCCCCC------CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          233 ASD-------LGMNFDS------NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       233 ~~~-------l~~~~~~------~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      ...       +..+.+.      .....+.+..+.+.+.    .+++-++|+|++....  ..+.+...+..        
T Consensus        96 ~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEE--------  167 (351)
T PRK09112         96 AQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEE--------  167 (351)
T ss_pred             HcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhc--------
Confidence            222       1111000      0111233344554443    3567799999997653  22333222221        


Q ss_pred             CCCCcE-EEEEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          294 DPRRCT-IILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       294 ~~~~s~-ilvTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ....+. |++|++...+...-.+....+++.+++.++..+++.+......   --++....|++.++|.|.....+
T Consensus       168 pp~~~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~~~---~~~~~~~~i~~~s~G~pr~Al~l  240 (351)
T PRK09112        168 PPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSSQG---SDGEITEALLQRSKGSVRKALLL  240 (351)
T ss_pred             CCCCceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcccC---CCHHHHHHHHHHcCCCHHHHHHH
Confidence            222334 4555444433322233456999999999999999988432211   11456788999999999866543

>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=98.45  E-value=1.6e-06  Score=79.44  Aligned_cols=60  Identities=20%  Similarity=0.229  Sum_probs=46.7

Q ss_pred             cchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          163 NSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .|++..+..+...+.....+.+.|+|++|+|||++++.+++.....  -..++++..++...
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~--~~~v~~~~~~~~~~   60 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP--GAPFLYLNASDLLE   60 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcC--CCCeEEEehhhhhh
Confidence            3788889999888876667789999999999999999999987522  23466777655433

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.

>PLN03150 hypothetical protein; Provisional

Probab=98.45  E-value=4.5e-07  Score=103.20  Aligned_cols=102  Identities=23%  Similarity=0.369  Sum_probs=78.1

Q ss_pred             CceEEEcCCCcCC-CCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccC
Q 004895          576 ELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLS  651 (724)
Q Consensus       576 ~L~~L~l~~~~~~-~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~  651 (724)
                      .+..|+|++|.+. .+|..++++.+|++|+|++|.+..  |..++.+++|++|+|++|.++ .+|..+++|++|++|+|+
T Consensus       419 ~v~~L~L~~n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~Ls  498 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNLN  498 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEECc
Confidence            3777888888887 678888888888888888888875  567888888888888888887 678888888888888888


Q ss_pred             CCCCCcccChHHhhC-CCCCcEEEccCC
Q 004895          652 NCSSLVVIAPNVISK-LSRLEELYMGDS  678 (724)
Q Consensus       652 ~~~~l~~~~~~~i~~-l~~L~~L~l~~~  678 (724)
                      +|.....+|. .++. +.++..+++.+|
T Consensus       499 ~N~l~g~iP~-~l~~~~~~~~~l~~~~N  525 (623)
T PLN03150        499 GNSLSGRVPA-ALGGRLLHRASFNFTDN  525 (623)
T ss_pred             CCcccccCCh-HHhhccccCceEEecCC
Confidence            8543334443 3554 346677777765

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.44  E-value=5.1e-06  Score=93.88  Aligned_cols=205  Identities=14%  Similarity=0.106  Sum_probs=113.8

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC---eEEEEEEecC---CChHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD---KVVMAEITKN---PDAQKIQG  230 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~---~~~wv~vs~~---~~~~~l~~  230 (724)
                      .....++|++..+..+.+.+.......+.|+|++|+||||+|+.+++.......+.   ..-|+.+...   .+...+..
T Consensus       151 ~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~  230 (615)
T TIGR02903       151 RAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTN  230 (615)
T ss_pred             CcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhH
Confidence            34456789999888888877666667899999999999999999988775433331   2345544321   12222211


Q ss_pred             HH---------------HHhhCCCC----------------C-CCchhHHHHHHHHHHHhcCCcEEEEEcccccc--ccc
Q 004895          231 EL---------------ASDLGMNF----------------D-SNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK--LEL  276 (724)
Q Consensus       231 ~i---------------~~~l~~~~----------------~-~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~--~~~  276 (724)
                      .+               +...+...                + ...........+...+. ++++.++-|+.|..  ..|
T Consensus       231 ~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le-~~~v~~~~~~~~~~~~~~~  309 (615)
T TIGR02903       231 PLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLE-DKRVEFSSSYYDPDDPNVP  309 (615)
T ss_pred             HhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHh-hCeEEeecceeccCCcccc
Confidence            11               11111100                0 01112233455555655 46677776666544  235


Q ss_pred             cccccccCCCCcCCCCCCCCCcEEEE--Eecccchh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHH
Q 004895          277 DKIGIPYGDVDEKDKNDDPRRCTIIL--TSRSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEE  353 (724)
Q Consensus       277 ~~l~~~~~~~~~~~~~~~~~~s~ilv--TtR~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~  353 (724)
                      +.+...+..        ..+...|++  ||++.... .........+.+.+++.+|.+.++.+.+...... --+++.+.
T Consensus       310 ~~ik~~~~~--------~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v~-ls~eal~~  380 (615)
T TIGR02903       310 KYIKKLFEE--------GAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVH-LAAGVEEL  380 (615)
T ss_pred             hhhhhhccc--------CccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHH
Confidence            555444332        333334444  56644321 1112233577899999999999999987532111 11345555


Q ss_pred             HHHHhCCchhHHHHHHHH
Q 004895          354 IVGKCGGLPVALSTVANA  371 (724)
Q Consensus       354 I~~~c~GlPLai~~~~~~  371 (724)
                      |.+.+..-+-|+..++..
T Consensus       381 L~~ys~~gRraln~L~~~  398 (615)
T TIGR02903       381 IARYTIEGRKAVNILADV  398 (615)
T ss_pred             HHHCCCcHHHHHHHHHHH
Confidence            555555445666555444

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.43  E-value=4.9e-06  Score=92.94  Aligned_cols=197  Identities=14%  Similarity=0.172  Sum_probs=110.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+..+..|...+..++.. .+.++|+.|+||||+|+.+++..-....+..       ..+..-...+.|..
T Consensus        12 P~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~-------~pCg~C~~C~~i~~   84 (647)
T PRK07994         12 PQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITA-------TPCGECDNCREIEQ   84 (647)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCC-------CCCCCCHHHHHHHc
Confidence            445677889999999999888876654 4579999999999999999987643211100       00111111111111


Q ss_pred             hhCCC---CCCC-chhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE-E
Q 004895          235 DLGMN---FDSN-DLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL-T  303 (724)
Q Consensus       235 ~l~~~---~~~~-~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv-T  303 (724)
                      .-..+   .+.. ....+....+.+.+    ..+++-++|+|++....  ..+.+...+..        ....+++|+ |
T Consensus        85 g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEE--------Pp~~v~FIL~T  156 (647)
T PRK07994         85 GRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE--------PPEHVKFLLAT  156 (647)
T ss_pred             CCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHc--------CCCCeEEEEec
Confidence            00000   0000 00111122222222    23567799999997653  33333222222        223444444 4


Q ss_pred             ecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      |....+...-.+....+++.+++.++....+.+.+...... .-.+....|++.++|.+.-+..+
T Consensus       157 t~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~-~e~~aL~~Ia~~s~Gs~R~Al~l  220 (647)
T PRK07994        157 TDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQIP-FEPRALQLLARAADGSMRDALSL  220 (647)
T ss_pred             CCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            44444432223345789999999999999998876422211 12456778999999988644433

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.42  E-value=4.9e-06  Score=92.51  Aligned_cols=185  Identities=14%  Similarity=0.211  Sum_probs=109.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      |.....++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+++.......                   |-.++
T Consensus        12 P~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~Dvl   91 (709)
T PRK08691         12 PKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLL   91 (709)
T ss_pred             CCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceE
Confidence            44567889999999999999886665 46789999999999999999887532211                   11112


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+....+++ ++++++..                 ...-..+++-++|+|++.....  .+.+...+..        
T Consensus        92 EidaAs~~gVd~-IRelle~a-----------------~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEE--------  145 (709)
T PRK08691         92 EIDAASNTGIDN-IREVLENA-----------------QYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEE--------  145 (709)
T ss_pred             EEeccccCCHHH-HHHHHHHH-----------------HhhhhhCCcEEEEEECccccCHHHHHHHHHHHHh--------
Confidence            222222222211 11111111                 0000124567999999975432  2222222221        


Q ss_pred             CCCCcEEEEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          294 DPRRCTIILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       294 ~~~~s~ilvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      ....+++|++|.+. .+.....+....+.+.+++.++....+.+.+......- -.+....|++.++|.+.-+..
T Consensus       146 Pp~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~i-d~eAL~~Ia~~A~GslRdAln  219 (709)
T PRK08691        146 PPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAY-EPPALQLLGRAAAGSMRDALS  219 (709)
T ss_pred             CCCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCc-CHHHHHHHHHHhCCCHHHHHH
Confidence            22345666666443 33211123345788999999999999998875332221 245778999999999854433

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

Probab=98.40  E-value=1.2e-06  Score=84.07  Aligned_cols=74  Identities=18%  Similarity=0.292  Sum_probs=43.5

Q ss_pred             cccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-----ChHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-----DAQKIQGEL  232 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~l~~~i  232 (724)
                      .|+||+++++++...+.   ....+.+.|+|++|+|||+|++.++........+  ++.+.+....     ....+++++
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l   78 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGY--VISINCDDSERNPYSPFRSALRQL   78 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT----EEEEEEETTTS-HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCE--EEEEEEeccccchhhHHHHHHHHH
Confidence            37899999999999983   4567899999999999999999999998775222  3444444331     124455555


Q ss_pred             HHhh
Q 004895          233 ASDL  236 (724)
Q Consensus       233 ~~~l  236 (724)
                      +.++
T Consensus        79 ~~~~   82 (185)
T PF13191_consen   79 IDQL   82 (185)
T ss_dssp             S---
T ss_pred             HHHh
Confidence            5443

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.39  E-value=7.7e-06  Score=86.89  Aligned_cols=172  Identities=11%  Similarity=0.106  Sum_probs=103.7

Q ss_pred             cccccchHHHHHHHHHHhcCCC----------ccEEEEEcCCCCcHHHHHHHHHHHHhhcc-------------------
Q 004895          159 YNIFNSRKKIFQDVIEALKDDK----------LNIIGVCGMGGVGKTTLVKQIAKQVMEDN-------------------  209 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~----------~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------  209 (724)
                      ...++|.+..++.|..++..+.          ...+.++|+.|+|||++|+.+++..-...                   
T Consensus         4 f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~   83 (394)
T PRK07940          4 WDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGT   83 (394)
T ss_pred             hhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCC
Confidence            3567899999999988887543          45688999999999999999988653211                   


Q ss_pred             CCCeEEEEEEe-cCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccc
Q 004895          210 VFDKVVMAEIT-KNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIP  282 (724)
Q Consensus       210 ~F~~~~wv~vs-~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~  282 (724)
                      |.| +.++... ....++                      .+..+.+...    .+++-++|+|+++...  ..+.+...
T Consensus        84 hpD-~~~i~~~~~~i~i~----------------------~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~  140 (394)
T PRK07940         84 HPD-VRVVAPEGLSIGVD----------------------EVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKA  140 (394)
T ss_pred             CCC-EEEeccccccCCHH----------------------HHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHH
Confidence            112 1122111 111111                      1222322221    2455688999997653  22333222


Q ss_pred             cCCCCcCCCCCCCCCcEEEEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc
Q 004895          283 YGDVDEKDKNDDPRRCTIILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL  361 (724)
Q Consensus       283 ~~~~~~~~~~~~~~~s~ilvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl  361 (724)
                      +..        ...++.+|++|.+. .+...-.+....+.+.+++.++..+.+.+..+.   +   .+.+..++..++|.
T Consensus       141 LEe--------p~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~---~---~~~a~~la~~s~G~  206 (394)
T PRK07940        141 VEE--------PPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV---D---PETARRAARASQGH  206 (394)
T ss_pred             hhc--------CCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC---C---HHHHHHHHHHcCCC
Confidence            222        23445555555554 333222344578999999999999888754321   1   35678899999999


Q ss_pred             hhHHHH
Q 004895          362 PVALST  367 (724)
Q Consensus       362 PLai~~  367 (724)
                      |.....
T Consensus       207 ~~~A~~  212 (394)
T PRK07940        207 IGRARR  212 (394)
T ss_pred             HHHHHH
Confidence            975543

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.39  E-value=1.3e-06  Score=90.17  Aligned_cols=101  Identities=19%  Similarity=0.228  Sum_probs=67.2

Q ss_pred             HHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC--ChHHHHHHHHHhhCC-CCCCCchhH
Q 004895          172 VIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP--DAQKIQGELASDLGM-NFDSNDLIY  247 (724)
Q Consensus       172 l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~l~~-~~~~~~~~~  247 (724)
                      +++.+. -+.-+...|+|++|+||||||+.+|+....+ +|+.++||.+.+..  .+.++++.|...+-. ..+.+....
T Consensus       159 vID~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~  237 (416)
T PRK09376        159 IIDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERH  237 (416)
T ss_pred             eeeeecccccCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHH
Confidence            444443 2345678999999999999999999998875 89999999999987  677777777632211 122222111


Q ss_pred             ----HHHHHHHHHH-hcCCcEEEEEcccccc
Q 004895          248 ----HRAKQLCQRL-KKEKRVLIILDNIWTK  273 (724)
Q Consensus       248 ----~~~~~l~~~l-~~~kr~LlVlDdv~~~  273 (724)
                          ..+....+.+ ..+++++|++|++...
T Consensus       238 ~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR~  268 (416)
T PRK09376        238 VQVAEMVIEKAKRLVEHGKDVVILLDSITRL  268 (416)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEEEChHHH
Confidence                1111122222 3578999999999654

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.38  E-value=9.7e-06  Score=87.89  Aligned_cols=183  Identities=13%  Similarity=0.132  Sum_probs=113.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhc-------------------cCCCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMED-------------------NVFDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~F~~~~  215 (724)
                      |.....++|.+...+.|...+..++.. .+.++|+.|+||||+|+.+++..-..                   ..+.-++
T Consensus         9 P~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~   88 (491)
T PRK14964          9 PSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVI   88 (491)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEE
Confidence            344677889999999888888766665 78899999999999999998754211                   1112234


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+...+++++ +++++.....                 -..+++-++|+|++....  ..+.+...+..        
T Consensus        89 eidaas~~~vddI-R~Iie~~~~~-----------------P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEe--------  142 (491)
T PRK14964         89 EIDAASNTSVDDI-KVILENSCYL-----------------PISSKFKVYIIDEVHMLSNSAFNALLKTLEE--------  142 (491)
T ss_pred             EEecccCCCHHHH-HHHHHHHHhc-----------------cccCCceEEEEeChHhCCHHHHHHHHHHHhC--------
Confidence            4554444444432 2333222100                 011456789999996543  23333222322        


Q ss_pred             CCCCcEEEEEec-ccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          294 DPRRCTIILTSR-SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       294 ~~~~s~ilvTtR-~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ....+++|++|. ...+...-......+++.+++.++..+.+.+.+......- -++....|++.++|.+..+
T Consensus       143 Pp~~v~fIlatte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i-~~eAL~lIa~~s~GslR~a  214 (491)
T PRK14964        143 PAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEH-DEESLKLIAENSSGSMRNA  214 (491)
T ss_pred             CCCCeEEEEEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence            234555555553 3344322234457899999999999999998875432221 1456788999999988644

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.36  E-value=1.8e-05  Score=83.49  Aligned_cols=200  Identities=11%  Similarity=0.111  Sum_probs=113.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEE---EEEecCCChHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVM---AEITKNPDAQKIQGE  231 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w---v~vs~~~~~~~l~~~  231 (724)
                      |.....++|.++..+.|.+.+..++.+ .+.++|+.|+||+|+|..+++..-..........   ...-..+..-...+.
T Consensus        15 P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c~~   94 (365)
T PRK07471         15 PRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARR   94 (365)
T ss_pred             CCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHHHH
Confidence            445567889999999999998876654 5889999999999999999998743221110000   000000000011111


Q ss_pred             HHHhhCCC-------CCC------CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCC
Q 004895          232 LASDLGMN-------FDS------NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       232 i~~~l~~~-------~~~------~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~  292 (724)
                      |...-..+       .++      .....+.+..+.+.+.    .+.+.++|+||++..+  ..+.+...+..       
T Consensus        95 i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEe-------  167 (365)
T PRK07471         95 IAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEE-------  167 (365)
T ss_pred             HHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhc-------
Confidence            11110000       000      0011223444444442    2567899999997553  23333222222       


Q ss_pred             CCCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          293 DDPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                       ...++.+|++|.+.. +...-.+....+.+.+++.++..+++.+.....   +  .+....+++.++|.|+.+..+
T Consensus       168 -pp~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~---~--~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        168 -PPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDL---P--DDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             -CCCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccC---C--HHHHHHHHHHcCCCHHHHHHH
Confidence             234555666666553 333334456789999999999999998864221   1  122367899999999865443

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

Probab=98.36  E-value=3.6e-07  Score=99.12  Aligned_cols=157  Identities=29%  Similarity=0.367  Sum_probs=102.4

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCC-CceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc-ccccCCCCCcE
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTE-ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIVGQLKKLEI  624 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~-~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~-~~~~~l~~L~~  624 (724)
                      ..+++..|.+  ..+....+++. ...+. +|+.|++++|.+..+|..++.+++|+.|+++.|.+... ...+.+.+|+.
T Consensus       114 ~~~~l~~L~l--~~n~i~~i~~~-~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~  190 (394)
T COG4886         114 ELTNLTSLDL--DNNNITDIPPL-IGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNN  190 (394)
T ss_pred             cccceeEEec--CCcccccCccc-cccchhhcccccccccchhhhhhhhhccccccccccCCchhhhhhhhhhhhhhhhh
Confidence            3455666666  33334444432 22332 67777777777777777777777777777777777774 34447777777


Q ss_pred             EEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcE
Q 004895          625 LSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTT  704 (724)
Q Consensus       625 L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~  704 (724)
                      |++++|.+..+|..+..+..|..|.++++.. ...+. .+.+++++..|.+.+|..         ...+..+..+++|+.
T Consensus       191 L~ls~N~i~~l~~~~~~~~~L~~l~~~~N~~-~~~~~-~~~~~~~l~~l~l~~n~~---------~~~~~~~~~l~~l~~  259 (394)
T COG4886         191 LDLSGNKISDLPPEIELLSALEELDLSNNSI-IELLS-SLSNLKNLSGLELSNNKL---------EDLPESIGNLSNLET  259 (394)
T ss_pred             eeccCCccccCchhhhhhhhhhhhhhcCCcc-eecch-hhhhcccccccccCCcee---------eeccchhccccccce
Confidence            7777777777777766667777777777322 23322 356777777776555321         111345667788999


Q ss_pred             EEeeccccccccc
Q 004895          705 LEIDVRDAEMLRR  717 (724)
Q Consensus       705 L~l~~n~~~~lp~  717 (724)
                      |+++.|.++.++.
T Consensus       260 L~~s~n~i~~i~~  272 (394)
T COG4886         260 LDLSNNQISSISS  272 (394)
T ss_pred             ecccccccccccc
Confidence            9999999888875

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.36  E-value=4.9e-06  Score=94.89  Aligned_cols=175  Identities=18%  Similarity=0.252  Sum_probs=101.0

Q ss_pred             CcccccccchHHHHH---HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQ---DVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~---~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      |.....|+|++..+.   .+...+..+....+.++|++|+||||+|+.+++....  +|.   .++.+. ....++ ++ 
T Consensus        24 P~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~--~f~---~lna~~-~~i~di-r~-   95 (725)
T PRK13341         24 PRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRA--HFS---SLNAVL-AGVKDL-RA-   95 (725)
T ss_pred             CCcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcC--cce---eehhhh-hhhHHH-HH-
Confidence            445667889988774   4556666677778899999999999999999987642  231   111110 011111 11 


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHh-cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEE--eccc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLK-KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILT--SRSR  307 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvT--tR~~  307 (724)
                                      ........+. .+++.+|||||++...  .++.+...           ...+..++++  |.+.
T Consensus        96 ----------------~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~-----------lE~g~IiLI~aTTenp  148 (725)
T PRK13341         96 ----------------EVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPW-----------VENGTITLIGATTENP  148 (725)
T ss_pred             ----------------HHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHH-----------hcCceEEEEEecCCCh
Confidence                            1111111111 1456899999997543  33333221           2234555554  3332


Q ss_pred             c--hhhhhcCCCceEecCCCCHHHHHHHHHHHhCC------CCCCCCchhHHHHHHHHhCCchhHH
Q 004895          308 D--LLCIDMNSQKMFWIDALSEEEALQLFEKIVGE------STKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       308 ~--v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~------~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      .  +..........+.+++++.++...++.+.+..      .....--++....|++.+.|..-.+
T Consensus       149 ~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~l  214 (725)
T PRK13341        149 YFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSL  214 (725)
T ss_pred             HhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHH
Confidence            1  11111223457999999999999999987641      1111112456788888898875433

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.35  E-value=2.1e-05  Score=78.56  Aligned_cols=192  Identities=17%  Similarity=0.213  Sum_probs=119.9

Q ss_pred             HHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC----eEEEEEEecCCChHHHHHHHHHhhCCC
Q 004895          167 KIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD----KVVMAEITKNPDAQKIQGELASDLGMN  239 (724)
Q Consensus       167 ~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~----~~~wv~vs~~~~~~~l~~~i~~~l~~~  239 (724)
                      +.++.+.+.+.   ..+.+-+.|||.+|.|||++++++.........-+    .++.|.....++...+...|+.+++.+
T Consensus        44 ~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP  123 (302)
T PF05621_consen   44 EALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAP  123 (302)
T ss_pred             HHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcc
Confidence            34555555554   34567899999999999999999998764321111    377888888999999999999999998


Q ss_pred             CCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEEEEecccchh
Q 004895          240 FDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL  310 (724)
Q Consensus       240 ~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~  310 (724)
                      ............+....++.-+--+||+|++.+...         ++.++ .+..        .-.=+-|.+-|+...-+
T Consensus       124 ~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK-~L~N--------eL~ipiV~vGt~~A~~a  194 (302)
T PF05621_consen  124 YRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALK-FLGN--------ELQIPIVGVGTREAYRA  194 (302)
T ss_pred             cCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHH-HHhh--------ccCCCeEEeccHHHHHH
Confidence            766553444444445555544567999999976421         11111 1111        22234466777654432


Q ss_pred             h----hhcCCCceEecCCCCHH-HHHHHHHHHhC----CCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          311 C----IDMNSQKMFWIDALSEE-EALQLFEKIVG----ESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       311 ~----~~~~~~~~~~l~~L~~~-e~~~Lf~~~~~----~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      -    .-.+....+.++....+ |...|+.....    .....-...++++.|...++|+.--+..
T Consensus       195 l~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~~  260 (302)
T PF05621_consen  195 LRTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGELSR  260 (302)
T ss_pred             hccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHHHHH
Confidence            1    11123456777776544 44555544332    1222223467899999999998755443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=9.2e-06  Score=89.42  Aligned_cols=199  Identities=14%  Similarity=0.183  Sum_probs=108.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|++..++.+..++..++. +.+.++|+.|+||||+|+.+++......      |... ..++.-...+.+..
T Consensus        12 P~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~------~~~~-~~Cg~C~sCr~i~~   84 (605)
T PRK05896         12 PHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLN------PKDG-DCCNSCSVCESINT   84 (605)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCC------CCCC-CCCcccHHHHHHHc
Confidence            44566788999999999998876554 4688999999999999999998864321      1110 01111111111111


Q ss_pred             hhCCC---CCCC-chhHHHHHHHHHHHh----cCCcEEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMN---FDSN-DLIYHRAKQLCQRLK----KEKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~---~~~~-~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      .....   .+.. ....+....+.....    .+++-++|+|++...  ..++.+...+..        ....+.+|++|
T Consensus        85 ~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEE--------Pp~~tvfIL~T  156 (605)
T PRK05896         85 NQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEE--------PPKHVVFIFAT  156 (605)
T ss_pred             CCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHh--------CCCcEEEEEEC
Confidence            11000   0000 000111122222111    124457999999764  233443322222        22344454444


Q ss_pred             -cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHHHH
Q 004895          305 -RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTVAN  370 (724)
Q Consensus       305 -R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~~~  370 (724)
                       ....+...-......+++.++++++....+.+.+......- -.+.+..+++.++|.+. |+..+-.
T Consensus       157 t~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~I-s~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        157 TEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKI-EDNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             CChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHHHHH
Confidence             43333222233456899999999999999988764322111 14567889999999765 4444443

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.35  E-value=9e-06  Score=90.64  Aligned_cols=199  Identities=12%  Similarity=0.173  Sum_probs=110.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCC--CeEEEEEEecCCChHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVF--DKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      |.....++|.+..+..|..++..++. ..+.++|+.|+||||+|+.+++..-.....  .+...    ..++.-...+.|
T Consensus        12 P~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~----~pCg~C~~C~~i   87 (618)
T PRK14951         12 PRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITA----TPCGVCQACRDI   87 (618)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCC----CCCCccHHHHHH
Confidence            34467788999999999998887665 456899999999999999998776321100  00000    001111111111


Q ss_pred             HHhhCCC---CCC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE
Q 004895          233 ASDLGMN---FDS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL  302 (724)
Q Consensus       233 ~~~l~~~---~~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv  302 (724)
                      ...-..+   .+. .....+....+.+...    .++.-++|||+++...  ..+.+...+..        ....+++|+
T Consensus        88 ~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEE--------PP~~~~fIL  159 (618)
T PRK14951         88 DSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEE--------PPEYLKFVL  159 (618)
T ss_pred             HcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhccc--------CCCCeEEEE
Confidence            1100000   000 0001111222222221    2455699999998653  33333332322        233455555


Q ss_pred             Ee-cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          303 TS-RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       303 Tt-R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      +| ....+...-......+++++++.++..+.+.+.+......- -.+....|++.++|.+.-+..
T Consensus       160 ~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~i-e~~AL~~La~~s~GslR~al~  224 (618)
T PRK14951        160 ATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPA-EPQALRLLARAARGSMRDALS  224 (618)
T ss_pred             EECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHH
Confidence            54 43444322234457899999999999999988775332221 145678899999998755443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.34  E-value=1.3e-05  Score=85.49  Aligned_cols=186  Identities=16%  Similarity=0.210  Sum_probs=110.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhcc--------------------CCCeE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDN--------------------VFDKV  214 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~~~  214 (724)
                      |.....++|.++.++.+.+++..++. ..+.++|++|+||||+|+.+.+......                    +++ +
T Consensus        10 p~~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~-~   88 (355)
T TIGR02397        10 PQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLD-V   88 (355)
T ss_pred             CCcHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCC-E
Confidence            34456778999999999998876654 4678999999999999999998864211                    222 1


Q ss_pred             EEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc--ccccccccccCCCCcCCCC
Q 004895          215 VMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       215 ~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~  292 (724)
                      ++++.+......+ .+++.+.+....                 ..+++-++|+|++...  ...+.+...+..       
T Consensus        89 ~~~~~~~~~~~~~-~~~l~~~~~~~p-----------------~~~~~~vviidea~~l~~~~~~~Ll~~le~-------  143 (355)
T TIGR02397        89 IEIDAASNNGVDD-IREILDNVKYAP-----------------SSGKYKVYIIDEVHMLSKSAFNALLKTLEE-------  143 (355)
T ss_pred             EEeeccccCCHHH-HHHHHHHHhcCc-----------------ccCCceEEEEeChhhcCHHHHHHHHHHHhC-------
Confidence            2332221111111 122222221000                 0134568999998654  223333222222       


Q ss_pred             CCCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          293 DDPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                       ....+.+|++|.+.. +...-......+++.++++++..+.+...+......- -++.+..+++.++|.|..+....
T Consensus       144 -~~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i-~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       144 -PPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKI-EDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             -CccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCChHHHHHHH
Confidence             234566666665443 2211123346789999999999999988774322111 14678889999999987664443

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=98.33  E-value=8.4e-06  Score=87.71  Aligned_cols=202  Identities=16%  Similarity=0.185  Sum_probs=111.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE-EecCCChHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE-ITKNPDAQKIQGELA  233 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~l~~~i~  233 (724)
                      |.....++|.+..++.|..++..++++ .+.++|+.|+||||+|..+++............|.. ....++.=...+.+.
T Consensus        12 P~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~   91 (397)
T PRK14955         12 PKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFD   91 (397)
T ss_pred             CCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHh
Confidence            344567889999999999888876665 488999999999999999998874322111111110 001111111111111


Q ss_pred             HhhCCC---CCC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          234 SDLGMN---FDS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       234 ~~l~~~---~~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      ......   .+. .....+.+..+.+.+.    .+++-++|+|++....  .++.+...+..        ....+.+|++
T Consensus        92 ~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEe--------p~~~t~~Il~  163 (397)
T PRK14955         92 AGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEE--------PPPHAIFIFA  163 (397)
T ss_pred             cCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhc--------CCCCeEEEEE
Confidence            111000   000 0001122223333331    2456789999987653  34444333332        3345555555


Q ss_pred             e-cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          304 S-RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       304 t-R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      | +...+...-......+++.++++++..+.+...+..... .--++.+..|++.++|.+--+.
T Consensus       164 t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~-~i~~~al~~l~~~s~g~lr~a~  226 (397)
T PRK14955        164 TTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGI-SVDADALQLIGRKAQGSMRDAQ  226 (397)
T ss_pred             eCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHH
Confidence            4 433332111222357889999999999888887642211 1125678899999999875443

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.32  E-value=2.1e-05  Score=78.24  Aligned_cols=166  Identities=13%  Similarity=0.130  Sum_probs=98.6

Q ss_pred             HHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhH
Q 004895          168 IFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY  247 (724)
Q Consensus       168 ~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~  247 (724)
                      .+..+..+......+.+.|+|+.|+|||+|++.+++.....  -..+.|+++.....                       
T Consensus        32 a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~--~~~v~y~~~~~~~~-----------------------   86 (235)
T PRK08084         32 LLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR--GRAVGYVPLDKRAW-----------------------   86 (235)
T ss_pred             HHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEEHHHHhh-----------------------
Confidence            44444444444455689999999999999999999987643  23466776643100                       


Q ss_pred             HHHHHHHHHHhcCCcEEEEEcccccc---cccccc-ccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcC
Q 004895          248 HRAKQLCQRLKKEKRVLIILDNIWTK---LELDKI-GIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMN  315 (724)
Q Consensus       248 ~~~~~l~~~l~~~kr~LlVlDdv~~~---~~~~~l-~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~  315 (724)
                       ....+.+.+.  +--+|++||+...   ..|+.. ...+...      ......++|+||+.....        .....
T Consensus        87 -~~~~~~~~~~--~~dlliiDdi~~~~~~~~~~~~lf~l~n~~------~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~  157 (235)
T PRK08084         87 -FVPEVLEGME--QLSLVCIDNIECIAGDELWEMAIFDLYNRI------LESGRTRLLITGDRPPRQLNLGLPDLASRLD  157 (235)
T ss_pred             -hhHHHHHHhh--hCCEEEEeChhhhcCCHHHHHHHHHHHHHH------HHcCCCeEEEeCCCChHHcCcccHHHHHHHh
Confidence             0011222222  1248999999654   234321 1111100      012234699999865321        11234


Q ss_pred             CCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          316 SQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       316 ~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ...+++++++++++-.+++.+++.... -.--+++..-|++.+.|..-.+..+
T Consensus       158 ~g~~~~l~~~~~~~~~~~l~~~a~~~~-~~l~~~v~~~L~~~~~~d~r~l~~~  209 (235)
T PRK08084        158 WGQIYKLQPLSDEEKLQALQLRARLRG-FELPEDVGRFLLKRLDREMRTLFMT  209 (235)
T ss_pred             CCceeeecCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHhhcCCHHHHHHH
Confidence            446899999999999999988764321 1122577888888888776655443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.31  E-value=1.1e-05  Score=77.52  Aligned_cols=160  Identities=24%  Similarity=0.252  Sum_probs=92.9

Q ss_pred             HHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhc--------------------cCCCeEEEEEEe-cCCChHHH
Q 004895          171 DVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMED--------------------NVFDKVVMAEIT-KNPDAQKI  228 (724)
Q Consensus       171 ~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs-~~~~~~~l  228 (724)
                      .+.+.+..++. ..+.++|+.|+||||+|+.+.+.....                    .+.|. .++... .....++ 
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~-~~~~~~~~~~~~~~-   80 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDL-HRLEPEGQSIKVDQ-   80 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcE-EEeccccCcCCHHH-
Confidence            34455555555 578899999999999999999886432                    12222 222211 1112211 


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecc
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS  306 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~  306 (724)
                      .+++.+.+....                 ..+.+-++|+||+....  .++.+...+..        ....+.+|++|++
T Consensus        81 i~~i~~~~~~~~-----------------~~~~~kviiide~~~l~~~~~~~Ll~~le~--------~~~~~~~il~~~~  135 (188)
T TIGR00678        81 VRELVEFLSRTP-----------------QESGRRVVIIEDAERMNEAAANALLKTLEE--------PPPNTLFILITPS  135 (188)
T ss_pred             HHHHHHHHccCc-----------------ccCCeEEEEEechhhhCHHHHHHHHHHhcC--------CCCCeEEEEEECC
Confidence            112222221100                 12456789999986643  23444333322        3345566666654


Q ss_pred             cc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          307 RD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       307 ~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      .. +..........+++.+++.++..+.+.+. +   -.   ++.+..|++.++|.|..
T Consensus       136 ~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~-g---i~---~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       136 PEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ-G---IS---EEAAELLLALAGGSPGA  187 (188)
T ss_pred             hHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc-C---CC---HHHHHHHHHHcCCCccc
Confidence            42 22211234468999999999999988886 2   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.

>PRK08727 hypothetical protein; Validated

Probab=98.31  E-value=1.3e-05  Score=79.53  Aligned_cols=170  Identities=11%  Similarity=0.066  Sum_probs=99.2

Q ss_pred             ccccchH-HHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC
Q 004895          160 NIFNSRK-KIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM  238 (724)
Q Consensus       160 ~~~~gR~-~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~  238 (724)
                      +.|++.. ..+..+...........+.|+|+.|+|||+|++.+++.....  ...+.|+++.+      ....+      
T Consensus        19 ~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~--~~~~~y~~~~~------~~~~~------   84 (233)
T PRK08727         19 DSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQA--GRSSAYLPLQA------AAGRL------   84 (233)
T ss_pred             hhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEeHHH------hhhhH------
Confidence            3444333 333333333333344579999999999999999999987643  23566776432      11111      


Q ss_pred             CCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc---cccc-cccccCCCCcCCCCCCCCCcEEEEEecccchh----
Q 004895          239 NFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL---ELDK-IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL----  310 (724)
Q Consensus       239 ~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~---~~~~-l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~----  310 (724)
                                  ....+.+.  +.-+||+||+....   .|.. +...+..       ....+..||+|++...-.    
T Consensus        85 ------------~~~~~~l~--~~dlLiIDDi~~l~~~~~~~~~lf~l~n~-------~~~~~~~vI~ts~~~p~~l~~~  143 (233)
T PRK08727         85 ------------RDALEALE--GRSLVALDGLESIAGQREDEVALFDFHNR-------ARAAGITLLYTARQMPDGLALV  143 (233)
T ss_pred             ------------HHHHHHHh--cCCEEEEeCcccccCChHHHHHHHHHHHH-------HHHcCCeEEEECCCChhhhhhh
Confidence                        11222332  34599999996542   2221 1111110       012356699999864321    


Q ss_pred             ----hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          311 ----CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       311 ----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                          .........+++++++.++-.+++.+++....- .--++...-|++.++|..-.+
T Consensus       144 ~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l-~l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        144 LPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGL-ALDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             hHHHHHHHhcCceEEecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHH
Confidence                111233468899999999999999987753211 112567788888888766555

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.30  E-value=1e-05  Score=89.17  Aligned_cols=184  Identities=14%  Similarity=0.177  Sum_probs=111.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccC-------------------CCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNV-------------------FDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~-------------------F~~~~  215 (724)
                      |.....++|.+..++.|..++..++.+ .+.++|+.|+||||+|+.+++..-....                   |.-++
T Consensus        12 P~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~   91 (509)
T PRK14958         12 PRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLF   91 (509)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEE
Confidence            445677889999999999999876655 4689999999999999999987643211                   11133


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+....++++ +++++.+...                 -..++.-++|+|++....  ..+.+...+..        
T Consensus        92 eidaas~~~v~~i-R~l~~~~~~~-----------------p~~~~~kV~iIDE~~~ls~~a~naLLk~LEe--------  145 (509)
T PRK14958         92 EVDAASRTKVEDT-RELLDNIPYA-----------------PTKGRFKVYLIDEVHMLSGHSFNALLKTLEE--------  145 (509)
T ss_pred             EEcccccCCHHHH-HHHHHHHhhc-----------------cccCCcEEEEEEChHhcCHHHHHHHHHHHhc--------
Confidence            3333333333332 2233222110                 012466799999997652  33333222222        


Q ss_pred             CCCCcEEEEEec-ccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          294 DPRRCTIILTSR-SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       294 ~~~~s~ilvTtR-~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      ....+++|++|. ...+...-.+....+++++++.++....+.+.+......- -.+....|++.++|.+.-+.
T Consensus       146 pp~~~~fIlattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~-~~~al~~ia~~s~GslR~al  218 (509)
T PRK14958        146 PPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEF-ENAALDLLARAANGSVRDAL  218 (509)
T ss_pred             cCCCeEEEEEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHH
Confidence            233455555544 3333222233346788999999998888777764332221 14567789999999885443

>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=98.30  E-value=6.1e-07  Score=68.38  Aligned_cols=56  Identities=29%  Similarity=0.425  Sum_probs=26.9

Q ss_pred             CceEEEcCCCcCCCCCc-cccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCc
Q 004895          576 ELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAE  631 (724)
Q Consensus       576 ~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~  631 (724)
                      +|++|++++|++..+|. .+..+++|++|++++|.++.  +..+..+++|++|++++|.
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCc
Confidence            34555555555554442 34445555555555554444  1334445555555554443

...

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

Probab=98.30  E-value=1e-07  Score=97.18  Aligned_cols=79  Identities=23%  Similarity=0.265  Sum_probs=35.4

Q ss_pred             CCCceEEEcCCCcCC--CCCccccCCCCCcEEEcCCcc-cCC-cccccCCCCCcEEEccCCcCcccc--hhhhcCCCCCe
Q 004895          574 TEELKVLDFTGIRFS--PLPSSLGRLINLQTLCLDGWR-LED-IAIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQL  647 (724)
Q Consensus       574 l~~L~~L~l~~~~~~--~lp~~i~~l~~L~~L~L~~~~-l~~-~~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~  647 (724)
                      +++|+.|.+++|+++  .+-.....+++|..|.|.+|. +.. -.+..-++.|+.|||++|.+-.+|  ..++.|+.|..
T Consensus       196 l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li~~~~~~~~~~l~~L~~  275 (505)
T KOG3207|consen  196 LSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNNLIDFDQGYKVGTLPGLNQ  275 (505)
T ss_pred             hhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhcccccceecchhhhhhHHhhccccCCcccccccccccccccchhh
Confidence            445555555555554  122222334455555555552 111 122233444555555555444433  23455555555


Q ss_pred             EccCC
Q 004895          648 LDLSN  652 (724)
Q Consensus       648 L~l~~  652 (724)
                      |+++.
T Consensus       276 Lnls~  280 (505)
T KOG3207|consen  276 LNLSS  280 (505)
T ss_pred             hhccc
Confidence            55554

>PRK09087 hypothetical protein; Validated

Probab=98.29  E-value=1.6e-05  Score=78.31  Aligned_cols=146  Identities=12%  Similarity=0.051  Sum_probs=88.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..+.+.|+|+.|+|||+|++.+++....       .|++..      .+..++                     ...+..
T Consensus        43 ~~~~l~l~G~~GsGKThLl~~~~~~~~~-------~~i~~~------~~~~~~---------------------~~~~~~   88 (226)
T PRK09087         43 PSPVVVLAGPVGSGKTHLASIWREKSDA-------LLIHPN------EIGSDA---------------------ANAAAE   88 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHhcCC-------EEecHH------HcchHH---------------------HHhhhc
Confidence            4567999999999999999988876422       244332      111111                     111111


Q ss_pred             CCcEEEEEcccccccc-ccccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHHHH
Q 004895          260 EKRVLIILDNIWTKLE-LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEEEA  330 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~-~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~e~  330 (724)
                         -+|++||+..... -+.+...+..       ....|..+|+|++...-.        .........+++++++.++-
T Consensus        89 ---~~l~iDDi~~~~~~~~~lf~l~n~-------~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~  158 (226)
T PRK09087         89 ---GPVLIEDIDAGGFDETGLFHLINS-------VRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALL  158 (226)
T ss_pred             ---CeEEEECCCCCCCCHHHHHHHHHH-------HHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHH
Confidence               3788899964321 1111111110       023366799998853321        11234457899999999999


Q ss_pred             HHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHH
Q 004895          331 LQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVAN  370 (724)
Q Consensus       331 ~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~  370 (724)
                      .+++++++....- .--+++..-|++.+.|..-++..+-.
T Consensus       159 ~~iL~~~~~~~~~-~l~~ev~~~La~~~~r~~~~l~~~l~  197 (226)
T PRK09087        159 SQVIFKLFADRQL-YVDPHVVYYLVSRMERSLFAAQTIVD  197 (226)
T ss_pred             HHHHHHHHHHcCC-CCCHHHHHHHHHHhhhhHHHHHHHHH
Confidence            9999998854321 11257888899999888877664333

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.27  E-value=1.2e-05  Score=85.72  Aligned_cols=179  Identities=16%  Similarity=0.196  Sum_probs=102.4

Q ss_pred             ccccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+.|+++.+++|.+.+.    .         ...+-+.++|++|+|||++|+.+++....  .|     +.+..   
T Consensus       120 ~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~--~~-----~~v~~---  189 (364)
T TIGR01242       120 SYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNA--TF-----IRVVG---  189 (364)
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCC--CE-----Eecch---
Confidence            34567899999999887763    1         12456899999999999999999987643  22     22221   


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~  291 (724)
                       .++....   ++     .  .......+.+......+.+|+|||++....             ...+...+..   .+.
T Consensus       190 -~~l~~~~---~g-----~--~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~---ld~  255 (364)
T TIGR01242       190 -SELVRKY---IG-----E--GARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAE---LDG  255 (364)
T ss_pred             -HHHHHHh---hh-----H--HHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHH---hhC
Confidence             1121111   11     0  112233344433445678999999975410             0011001100   001


Q ss_pred             CCCCCCcEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          292 NDDPRRCTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .....+.+||.||.........    ......+.++..+.++..++|+.++......++.  ....+++.+.|..
T Consensus       256 ~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~--~~~~la~~t~g~s  328 (364)
T TIGR01242       256 FDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDV--DLEAIAKMTEGAS  328 (364)
T ss_pred             CCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccC--CHHHHHHHcCCCC
Confidence            1123467788888765422111    1224578899999999999999887543322221  2467888887764

Many proteins may score above the trusted cutoff because an internal

>PLN03150 hypothetical protein; Provisional

Probab=98.27  E-value=1.9e-06  Score=98.10  Aligned_cols=108  Identities=21%  Similarity=0.322  Sum_probs=86.3

Q ss_pred             ccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEc
Q 004895          551 LKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSL  627 (724)
Q Consensus       551 Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l  627 (724)
                      ++.|.+ .++.....+|. .+..+++|+.|+|++|.+. .+|..++.+.+|++|+|++|.++.  |..+++|++|++|+|
T Consensus       420 v~~L~L-~~n~L~g~ip~-~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~L  497 (623)
T PLN03150        420 IDGLGL-DNQGLRGFIPN-DISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNL  497 (623)
T ss_pred             EEEEEC-CCCCccccCCH-HHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEEC
Confidence            566666 22222234444 5788999999999999998 789999999999999999999986  678999999999999


Q ss_pred             cCCcCc-ccchhhhcC-CCCCeEccCCCCCCcccC
Q 004895          628 RGAEIK-QLPLQIGQL-TRLQLLDLSNCSSLVVIA  660 (724)
Q Consensus       628 ~~~~i~-~lp~~i~~l-~~L~~L~l~~~~~l~~~~  660 (724)
                      ++|.++ .+|..+..+ .++..+++.+|..+...|
T Consensus       498 s~N~l~g~iP~~l~~~~~~~~~l~~~~N~~lc~~p  532 (623)
T PLN03150        498 NGNSLSGRVPAALGGRLLHRASFNFTDNAGLCGIP  532 (623)
T ss_pred             cCCcccccCChHHhhccccCceEEecCCccccCCC
Confidence            999988 889988764 567788888765555443

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

Probab=98.27  E-value=8.8e-09  Score=110.66  Aligned_cols=176  Identities=22%  Similarity=0.213  Sum_probs=99.6

Q ss_pred             ccCceEEeccCCCcccCCCcccC-CCccEEEEecccccccccchh---hhc---CCCCceEEEcCCCcCCCCCccccCCC
Q 004895          526 QKGPIAISLPYRDIQELPERLEC-PQLKLFLLFAKYDSTLQISDH---FFE---GTEELKVLDFTGIRFSPLPSSLGRLI  598 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~-~~Lr~L~l~~~~~~~~~~~~~---~~~---~l~~L~~L~l~~~~~~~lp~~i~~l~  598 (724)
                      .+.+|+|-+..+++.......++ ..|+.|++..+-.....+...   .++   ....|.+.+++.|.+..+-.++.-++
T Consensus       108 F~sLr~LElrg~~L~~~~GL~~lr~qLe~LIC~~Sl~Al~~v~ascggd~~ns~~Wn~L~~a~fsyN~L~~mD~SLqll~  187 (1096)
T KOG1859|consen  108 FRSLRVLELRGCDLSTAKGLQELRHQLEKLICHNSLDALRHVFASCGGDISNSPVWNKLATASFSYNRLVLMDESLQLLP  187 (1096)
T ss_pred             ccceeeEEecCcchhhhhhhHHHHHhhhhhhhhccHHHHHHHHHHhccccccchhhhhHhhhhcchhhHHhHHHHHHHHH
Confidence            35788888888888665443332 346666653211111100000   000   11235566666666666666666677


Q ss_pred             CCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          599 NLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       599 ~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      +|+.|+|+.|++.+...+..|++|.+|||++|.++.+|.- +..++ |+.|.+++ |-++.+  .+|.+|.+|+.||++.
T Consensus       188 ale~LnLshNk~~~v~~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc~-L~~L~lrn-N~l~tL--~gie~LksL~~LDlsy  263 (1096)
T KOG1859|consen  188 ALESLNLSHNKFTKVDNLRRLPKLKHLDLSYNCLRHVPQLSMVGCK-LQLLNLRN-NALTTL--RGIENLKSLYGLDLSY  263 (1096)
T ss_pred             HhhhhccchhhhhhhHHHHhcccccccccccchhccccccchhhhh-heeeeecc-cHHHhh--hhHHhhhhhhccchhH
Confidence            7777777777776666667777777777777777666642 23333 77777766 445554  2366777777777766


Q ss_pred             CCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          678 SFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       678 ~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      |.+     .+  -..+..|..|..|+.|.+.+|.+
T Consensus       264 Nll-----~~--hseL~pLwsLs~L~~L~LeGNPl  291 (1096)
T KOG1859|consen  264 NLL-----SE--HSELEPLWSLSSLIVLWLEGNPL  291 (1096)
T ss_pred             hhh-----hc--chhhhHHHHHHHHHHHhhcCCcc
Confidence            531     10  11233444555666777777654

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.26  E-value=2.1e-05  Score=87.94  Aligned_cols=200  Identities=10%  Similarity=0.142  Sum_probs=112.6

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCC--eEEEEEEecCCChHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFD--KVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~l~~~i  232 (724)
                      |.....++|.+..++.|..++..++.. .+.++|+.|+||||+|+.+++.........  ...+-    .+..-.-.+.|
T Consensus        20 P~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~----~cg~c~~C~~i   95 (598)
T PRK09111         20 PQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTID----LCGVGEHCQAI   95 (598)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccc----cCcccHHHHHH
Confidence            455677899999999999998876654 688999999999999999998764321110  00000    00000111122


Q ss_pred             HHhhCCCC---C-CCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE
Q 004895          233 ASDLGMNF---D-SNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL  302 (724)
Q Consensus       233 ~~~l~~~~---~-~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv  302 (724)
                      ......+.   + ......+.+..+.+.+.    .+++-++|+|++....  ..+.+...+..        ....+.+|+
T Consensus        96 ~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEe--------Pp~~~~fIl  167 (598)
T PRK09111         96 MEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEE--------PPPHVKFIF  167 (598)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHh--------CCCCeEEEE
Confidence            21111000   0 00001112222322221    2455689999996653  23333222222        234555555


Q ss_pred             Ee-cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          303 TS-RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       303 Tt-R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +| ....+...-......+++.+++.++....+.+.+......- -.+....|++.++|.+.-+...
T Consensus       168 ~tte~~kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i-~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        168 ATTEIRKVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEV-EDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             EeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            44 43433322233456899999999999999988775332111 1467788999999998665443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.26  E-value=3.3e-05  Score=82.66  Aligned_cols=183  Identities=15%  Similarity=0.228  Sum_probs=105.6

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhc------cCCCe-EEEEEEecCCChHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMED------NVFDK-VVMAEITKNPDAQK  227 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~------~~F~~-~~wv~vs~~~~~~~  227 (724)
                      |.....++|.+...+.+...+..+.. +.+.++|+.|+||||+|+.+.+.....      ..|.. ++-+......+..+
T Consensus        13 P~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   92 (367)
T PRK14970         13 PQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD   92 (367)
T ss_pred             CCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH
Confidence            34456778999999999999876654 478899999999999999998876431      11211 11111111111112


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEe-
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTS-  304 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt-  304 (724)
                      + +++++.+...                .. .+++-++++|++....  .++.+...+..        ....+.+|++| 
T Consensus        93 i-~~l~~~~~~~----------------p~-~~~~kiviIDE~~~l~~~~~~~ll~~le~--------~~~~~~~Il~~~  146 (367)
T PRK14970         93 I-RNLIDQVRIP----------------PQ-TGKYKIYIIDEVHMLSSAAFNAFLKTLEE--------PPAHAIFILATT  146 (367)
T ss_pred             H-HHHHHHHhhc----------------cc-cCCcEEEEEeChhhcCHHHHHHHHHHHhC--------CCCceEEEEEeC
Confidence            1 2222221100                00 1345689999986542  23333222221        22344555554 


Q ss_pred             cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          305 RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       305 R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ....+..........+++.++++++....+.+.+...... --++.+..|++.++|.+-.+
T Consensus       147 ~~~kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~-i~~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        147 EKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIK-FEDDALHIIAQKADGALRDA  206 (367)
T ss_pred             CcccCCHHHHhcceeEecCCccHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhCCCCHHHH
Confidence            3333322223344589999999999999998877532211 11467888999999876533

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.26  E-value=2.1e-05  Score=90.99  Aligned_cols=183  Identities=11%  Similarity=0.122  Sum_probs=108.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCC---------------------e
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFD---------------------K  213 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~---------------------~  213 (724)
                      +.....++|.+..++.|..++..+++. .+.++|+.|+||||+|+.+++.........                     .
T Consensus        11 P~~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~d   90 (824)
T PRK07764         11 PATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLD   90 (824)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCc
Confidence            344567889999999999998876664 578999999999999999998874321110                     0


Q ss_pred             EEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCC
Q 004895          214 VVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDK  291 (724)
Q Consensus       214 ~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~  291 (724)
                      +++++......++++ +++.+                 .+...-..++.-++|||+++...  ..+.+...+..      
T Consensus        91 v~eidaas~~~Vd~i-R~l~~-----------------~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEE------  146 (824)
T PRK07764         91 VTEIDAASHGGVDDA-RELRE-----------------RAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEE------  146 (824)
T ss_pred             EEEecccccCCHHHH-HHHHH-----------------HHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhC------
Confidence            122222111122221 11111                 11111112456689999997653  33343333322      


Q ss_pred             CCCCCCcEEEEEec-ccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          292 NDDPRRCTIILTSR-SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       292 ~~~~~~s~ilvTtR-~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                        -...+.+|++|. ...+...-......|++..++.++..+++.+.+....... -.+....|++.++|.+..+
T Consensus       147 --pP~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~i-d~eal~lLa~~sgGdlR~A  218 (824)
T PRK07764        147 --PPEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPV-EPGVLPLVIRAGGGSVRDS  218 (824)
T ss_pred             --CCCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHH
Confidence              234555555553 3333322234457899999999999998888764322211 1456678999999988433

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.25  E-value=2.3e-05  Score=86.83  Aligned_cols=187  Identities=17%  Similarity=0.208  Sum_probs=112.0

Q ss_pred             CcccccccchHHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-------------------eEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-------------------KVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-------------------~~~  215 (724)
                      |.....++|.+..+..|...+..++ ...+.++|+.|+||||+|+.+++..-.....+                   -++
T Consensus        12 P~sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpDv~   91 (624)
T PRK14959         12 PQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVV   91 (624)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCceE
Confidence            3445677899988888888887655 46788899999999999999998764321110                   022


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCCcC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEK  289 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~  289 (724)
                      ++..+....+++                      +..+.+.+    ..+++-++|+|++....  ..+.+...+..    
T Consensus        92 eId~a~~~~Id~----------------------iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEE----  145 (624)
T PRK14959         92 EIDGASNRGIDD----------------------AKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEE----  145 (624)
T ss_pred             EEecccccCHHH----------------------HHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhc----
Confidence            222211111111                      11222221    12466799999997652  23334322221    


Q ss_pred             CCCCCCCCcEEEEEecc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch-hHHHH
Q 004895          290 DKNDDPRRCTIILTSRS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP-VALST  367 (724)
Q Consensus       290 ~~~~~~~~s~ilvTtR~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~  367 (724)
                          ......+|++|.. ..+...-......+++.+++.++....+.+.+...... --.+.++.|++.++|.+ .|+..
T Consensus       146 ----P~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~-id~eal~lIA~~s~GdlR~Al~l  220 (624)
T PRK14959        146 ----PPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVD-YDPAAVRLIARRAAGSVRDSMSL  220 (624)
T ss_pred             ----cCCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence                2234445555544 33322212334688999999999999998876532211 12467889999999965 67777


Q ss_pred             HHHHhc
Q 004895          368 VANALK  373 (724)
Q Consensus       368 ~~~~l~  373 (724)
                      +...+.
T Consensus       221 Leqll~  226 (624)
T PRK14959        221 LGQVLA  226 (624)
T ss_pred             HHHHHH
Confidence            765543

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

Probab=98.24  E-value=1.6e-05  Score=77.88  Aligned_cols=163  Identities=18%  Similarity=0.161  Sum_probs=96.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      ...+.|+|+.|+|||.|.+.+++.......=..++|++.      .++...+...+..         .....+.+.+.  
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~------~~f~~~~~~~~~~---------~~~~~~~~~~~--   96 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSA------EEFIREFADALRD---------GEIEEFKDRLR--   96 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEH------HHHHHHHHHHHHT---------TSHHHHHHHHC--
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecH------HHHHHHHHHHHHc---------ccchhhhhhhh--
Confidence            456899999999999999999999865322234667753      4555566555532         11234555554  


Q ss_pred             CcEEEEEcccccccc---ccc-cccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHH
Q 004895          261 KRVLIILDNIWTKLE---LDK-IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEE  328 (724)
Q Consensus       261 kr~LlVlDdv~~~~~---~~~-l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~  328 (724)
                      .-=+|++||++....   |+. +...+...       ...|.+||+|++.....        .......-.+++++.+.+
T Consensus        97 ~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~-------~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~  169 (219)
T PF00308_consen   97 SADLLIIDDIQFLAGKQRTQEELFHLFNRL-------IESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDE  169 (219)
T ss_dssp             TSSEEEEETGGGGTTHHHHHHHHHHHHHHH-------HHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HH
T ss_pred             cCCEEEEecchhhcCchHHHHHHHHHHHHH-------HhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHH
Confidence            345899999976532   222 11111100       23466899999765321        112344568999999999


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +-.+++.+.+....-. --+++++-|++.+.+..-.+..+
T Consensus       170 ~r~~il~~~a~~~~~~-l~~~v~~~l~~~~~~~~r~L~~~  208 (219)
T PF00308_consen  170 DRRRILQKKAKERGIE-LPEEVIEYLARRFRRDVRELEGA  208 (219)
T ss_dssp             HHHHHHHHHHHHTT---S-HHHHHHHHHHTTSSHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC-CcHHHHHHHHHhhcCCHHHHHHH
Confidence            9999999988632221 12567777777777666554433

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.24  E-value=1.5e-05  Score=88.33  Aligned_cols=186  Identities=16%  Similarity=0.238  Sum_probs=108.3

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhcc-------------------CCCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDN-------------------VFDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~~  215 (724)
                      |.....++|.+..++.|..++..++.. .+.++|+.|+||||+|+.+++......                   .|..++
T Consensus        12 P~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~   91 (527)
T PRK14969         12 PKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLI   91 (527)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCcee
Confidence            344567889999999999988876655 467999999999999999998763211                   111122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~  293 (724)
                      ++..+....++++ +++++.....                 -..+++-++|+|++.....  .+.+...+..        
T Consensus        92 ei~~~~~~~vd~i-r~l~~~~~~~-----------------p~~~~~kVvIIDEad~ls~~a~naLLK~LEe--------  145 (527)
T PRK14969         92 EVDAASNTQVDAM-RELLDNAQYA-----------------PTRGRFKVYIIDEVHMLSKSAFNAMLKTLEE--------  145 (527)
T ss_pred             EeeccccCCHHHH-HHHHHHHhhC-----------------cccCCceEEEEcCcccCCHHHHHHHHHHHhC--------
Confidence            3322222222211 2222211100                 0124667999999976532  3333222222        


Q ss_pred             CCCCcEEEEEecc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHH
Q 004895          294 DPRRCTIILTSRS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTV  368 (724)
Q Consensus       294 ~~~~s~ilvTtR~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~  368 (724)
                      ....+.+|++|.+ ..+...-......+++++++.++..+.+.+.+...... .-++....|++.++|.+- |+..+
T Consensus       146 pp~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~-~~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        146 PPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIP-FDATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             CCCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            2234555555533 33321112234688999999999998888876432221 124567889999999875 44443

>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=98.24  E-value=7.7e-07  Score=67.79  Aligned_cols=57  Identities=33%  Similarity=0.560  Sum_probs=30.2

Q ss_pred             CCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          621 KLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       621 ~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +|++|++++|.++.+|. .+..+++|++|++++ +.+..+++..+..+++|++|++++|
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~-N~l~~i~~~~f~~l~~L~~L~l~~N   59 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSN-NNLTSIPPDAFSNLPNLRYLDLSNN   59 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETS-SSESEEETTTTTTSTTESEEEETSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccC-CccCccCHHHHcCCCCCCEEeCcCC
Confidence            45555555555555543 244555555555554 3445555555555555555555543

...

>PF14516 AAA_35: AAA-like domain

Probab=98.23  E-value=0.00038  Score=72.94  Aligned_cols=211  Identities=15%  Similarity=0.160  Sum_probs=121.3

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-----CChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-----PDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~l~~~  231 (724)
                      .+...++.|...-+.+.+.+.+. -..+.|.|+-.+|||+|...+.+..... .+. ++++++...     .+.+..++.
T Consensus         8 ~~~~~Yi~R~~~e~~~~~~i~~~-G~~~~I~apRq~GKTSll~~l~~~l~~~-~~~-~v~id~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen    8 LDSPFYIERPPAEQECYQEIVQP-GSYIRIKAPRQMGKTSLLLRLLERLQQQ-GYR-CVYIDLQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             CCCCcccCchHHHHHHHHHHhcC-CCEEEEECcccCCHHHHHHHHHHHHHHC-CCE-EEEEEeecCCCcccCCHHHHHHH
Confidence            34455678886677777777653 3589999999999999999999988764 343 557877652     245555555


Q ss_pred             HHH----hhCCCCCCC-------chhHHHHHHHHHHHh--cCCcEEEEEcccccccccc----ccccccCCCCcCCCCCC
Q 004895          232 LAS----DLGMNFDSN-------DLIYHRAKQLCQRLK--KEKRVLIILDNIWTKLELD----KIGIPYGDVDEKDKNDD  294 (724)
Q Consensus       232 i~~----~l~~~~~~~-------~~~~~~~~~l~~~l~--~~kr~LlVlDdv~~~~~~~----~l~~~~~~~~~~~~~~~  294 (724)
                      ++.    +++....-.       .........+.+.+.  .+++.+|+||+++......    ++...+...-.......
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            544    444332100       001112222333332  2689999999997653211    11100000000000000


Q ss_pred             C-CCcE-EEEEecccchh----hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          295 P-RRCT-IILTSRSRDLL----CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       295 ~-~~s~-ilvTtR~~~v~----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      . ..-+ |++.+......    .........++|++|+.+|...|+.+.-..- .    ....++|...+||+|.-+..+
T Consensus       165 ~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~-~----~~~~~~l~~~tgGhP~Lv~~~  239 (331)
T PF14516_consen  165 IWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEF-S----QEQLEQLMDWTGGHPYLVQKA  239 (331)
T ss_pred             ccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccC-C----HHHHHHHHHHHCCCHHHHHHH
Confidence            0 1111 22222111111    1112344688999999999999988763221 1    234889999999999999999


Q ss_pred             HHHhcCC
Q 004895          369 ANALKNK  375 (724)
Q Consensus       369 ~~~l~~~  375 (724)
                      +..+...
T Consensus       240 ~~~l~~~  246 (331)
T PF14516_consen  240 CYLLVEE  246 (331)
T ss_pred             HHHHHHc
Confidence            9999753

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.22  E-value=1.3e-05  Score=85.81  Aligned_cols=178  Identities=17%  Similarity=0.223  Sum_probs=101.1

Q ss_pred             cccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|+++.++++.+.+.    .         ...+-|.++|++|+|||++|+.+++.....       |+.++.    
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~-------~i~v~~----  198 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNAT-------FIRVVG----  198 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCC-------EEEeeh----
Confidence            4567799999988887653    1         235678999999999999999999876421       333321    


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~  292 (724)
                      .++....   .+     .  .......+++......+.+|+|||++....             ...+...+..   .+..
T Consensus       199 ~~l~~~~---~g-----~--~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~---ld~~  265 (389)
T PRK03992        199 SELVQKF---IG-----E--GARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAE---MDGF  265 (389)
T ss_pred             HHHhHhh---cc-----c--hHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHh---cccc
Confidence            1121111   11     0  112233444444445678999999975310             0011111100   1111


Q ss_pred             CCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          293 DDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ....+..||.||......... .   .....+.+++.+.++-.++|+.++......++.  ....+++.+.|.-
T Consensus       266 ~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~--~~~~la~~t~g~s  337 (389)
T PRK03992        266 DPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDV--DLEELAELTEGAS  337 (389)
T ss_pred             CCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcC--CHHHHHHHcCCCC
Confidence            123456788777765432111 1   223578999999999999999887543222221  2456777776644

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.22  E-value=4e-05  Score=85.85  Aligned_cols=199  Identities=17%  Similarity=0.196  Sum_probs=108.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE-EecCCChHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE-ITKNPDAQKIQGELA  233 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~~~~~l~~~i~  233 (724)
                      |.....++|.+..+..|..++..+++. .+.++|+.|+||||+|+.+++..-.....+.-.|.. +...++.-...+.+.
T Consensus        12 P~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~   91 (620)
T PRK14954         12 PSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFD   91 (620)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHh
Confidence            344677889999999999888776664 488999999999999999998874322111001110 001111111111111


Q ss_pred             HhhCCC---CCC-CchhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEE-E
Q 004895          234 SDLGMN---FDS-NDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTII-L  302 (724)
Q Consensus       234 ~~l~~~---~~~-~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~il-v  302 (724)
                      ..-...   .+. .....+.+..+.+.+    ..+++-++|+|+++...  ..+.+...+..        ....+.+| +
T Consensus        92 ~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEe--------Pp~~tv~IL~  163 (620)
T PRK14954         92 AGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEE--------PPPHAIFIFA  163 (620)
T ss_pred             ccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhC--------CCCCeEEEEE
Confidence            111000   000 000112222233333    12456689999987653  23333322322        22344444 4


Q ss_pred             EecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          303 TSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       303 TtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      |++...+...-......+++.+++.++....+.+.+...... --.+.+..|++.++|..-
T Consensus       164 t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~-I~~eal~~La~~s~Gdlr  223 (620)
T PRK14954        164 TTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQ-IDADALQLIARKAQGSMR  223 (620)
T ss_pred             eCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCCCHH
Confidence            444333322223456789999999999988888766422211 114678899999999665

>TIGR00767 rho transcription termination factor Rho

Probab=98.20  E-value=5.1e-06  Score=86.37  Aligned_cols=94  Identities=17%  Similarity=0.210  Sum_probs=65.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC--CChHHHHHHHHHhhCCC-CCCCchh-HHH----H
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN--PDAQKIQGELASDLGMN-FDSNDLI-YHR----A  250 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~l~~~i~~~l~~~-~~~~~~~-~~~----~  250 (724)
                      +.-..++|+|++|+|||||++.+++....+ +|+..+|+.+.+.  .++.++++.+...+-.. .+.+... ...    .
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            445689999999999999999999998764 8999999999977  68888988885433211 1211111 111    1


Q ss_pred             HHHHHHHhcCCcEEEEEcccccc
Q 004895          251 KQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       251 ~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .........+++++|++|++...
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHH
Confidence            12222223589999999999654

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

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.19  E-value=5.1e-05  Score=84.40  Aligned_cols=186  Identities=15%  Similarity=0.188  Sum_probs=111.0

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccE-EEEEcCCCCcHHHHHHHHHHHHhhccCCC---------------------e
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNI-IGVCGMGGVGKTTLVKQIAKQVMEDNVFD---------------------K  213 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~v-i~I~G~gGiGKTtLa~~v~~~~~~~~~F~---------------------~  213 (724)
                      |.....++|.+..++.|..++..++..- +.++|+.|+||||+|+.+++........+                     -
T Consensus         9 P~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~d   88 (584)
T PRK14952          9 PATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSID   88 (584)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCce
Confidence            4456778899999999999988776654 68999999999999999998764221111                     0


Q ss_pred             EEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCC
Q 004895          214 VVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVD  287 (724)
Q Consensus       214 ~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~  287 (724)
                      ++.++.+...++++                      ...+.+..    ..+++-++|+|++....  ..+.+...+..  
T Consensus        89 vieidaas~~gvd~----------------------iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEE--  144 (584)
T PRK14952         89 VVELDAASHGGVDD----------------------TRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEE--  144 (584)
T ss_pred             EEEeccccccCHHH----------------------HHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhc--
Confidence            11222211111111                      12222221    12456699999986542  33333222222  


Q ss_pred             cCCCCCCCCCcEEE-EEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HH
Q 004895          288 EKDKNDDPRRCTII-LTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-AL  365 (724)
Q Consensus       288 ~~~~~~~~~~s~il-vTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai  365 (724)
                            ....+.+| +||....+...-.+....+++.+++.++..+.+.+.+......- -.+....|++.++|.+- ++
T Consensus       145 ------pp~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i-~~~al~~Ia~~s~GdlR~al  217 (584)
T PRK14952        145 ------PPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGVVV-DDAVYPLVIRAGGGSPRDTL  217 (584)
T ss_pred             ------CCCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence                  23345555 45444444322233457899999999999988888765332211 14567889999999874 44


Q ss_pred             HHHHHHh
Q 004895          366 STVANAL  372 (724)
Q Consensus       366 ~~~~~~l  372 (724)
                      ..+-.++
T Consensus       218 n~Ldql~  224 (584)
T PRK14952        218 SVLDQLL  224 (584)
T ss_pred             HHHHHHH
Confidence            4444433

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=98.18  E-value=2e-05  Score=77.54  Aligned_cols=190  Identities=16%  Similarity=0.134  Sum_probs=120.3

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeE-EEEEEecCCChHHHHHHH--
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKV-VMAEITKNPDAQKIQGEL--  232 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~-~wv~vs~~~~~~~l~~~i--  232 (724)
                      |...+.++|.+...+-|...+.....++...+||+|.|||+.|..++...-..+.|.+. .=.++|......-+-..+  
T Consensus        32 Pkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~  111 (346)
T KOG0989|consen   32 PKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKN  111 (346)
T ss_pred             CCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcC
Confidence            66677888999999999999887778899999999999999999999987665566553 445666554433111111  


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHH-hcCCc-EEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEE-EEeccc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRL-KKEKR-VLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTII-LTSRSR  307 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l-~~~kr-~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~il-vTtR~~  307 (724)
                      ..++......             .. ..-++ -.+|||+++..  +.|..+...+..        ....++.+ ||+--.
T Consensus       112 fakl~~~~~~-------------~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~--------~s~~trFiLIcnyls  170 (346)
T KOG0989|consen  112 FAKLTVLLKR-------------SDGYPCPPFKIIILDECDSMTSDAQAALRRTMED--------FSRTTRFILICNYLS  170 (346)
T ss_pred             HHHHhhcccc-------------ccCCCCCcceEEEEechhhhhHHHHHHHHHHHhc--------cccceEEEEEcCChh
Confidence            0001000000             00 00123 48899999765  567777555443        44555544 444333


Q ss_pred             chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          308 DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       308 ~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      .+...-.....-+..++|.+++...-++..+..+.-.-+ .+..+.|++.++|.-.-+.+
T Consensus       171 rii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d-~~al~~I~~~S~GdLR~Ait  229 (346)
T KOG0989|consen  171 RIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDID-DDALKLIAKISDGDLRRAIT  229 (346)
T ss_pred             hCChHHHhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHcCCcHHHHHH
Confidence            332222334467889999999999999988864333222 45678899999986543333

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.18  E-value=4.5e-05  Score=86.00  Aligned_cols=182  Identities=15%  Similarity=0.216  Sum_probs=110.7

Q ss_pred             cccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhh---------------------ccCCCeE
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVME---------------------DNVFDKV  214 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~---------------------~~~F~~~  214 (724)
                      .....++|.+...+.|..++..++.. .+.++|+.|+||||+|+.++.....                     ..+|+ +
T Consensus        14 ~~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n-~   92 (614)
T PRK14971         14 STFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYN-I   92 (614)
T ss_pred             CCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCc-e
Confidence            34567889999999999998876664 4789999999999999999887631                     12333 2


Q ss_pred             EEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCC
Q 004895          215 VMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       215 ~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~  292 (724)
                      ..++.++..+.+++ ++++.++....                 ..+++-++|+|++....  .++.+...+..       
T Consensus        93 ~~ld~~~~~~vd~I-r~li~~~~~~P-----------------~~~~~KVvIIdea~~Ls~~a~naLLK~LEe-------  147 (614)
T PRK14971         93 HELDAASNNSVDDI-RNLIEQVRIPP-----------------QIGKYKIYIIDEVHMLSQAAFNAFLKTLEE-------  147 (614)
T ss_pred             EEecccccCCHHHH-HHHHHHHhhCc-----------------ccCCcEEEEEECcccCCHHHHHHHHHHHhC-------
Confidence            23333322222222 22222221100                 11355689999987653  34444333322       


Q ss_pred             CCCCCcEEEE-EecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          293 DDPRRCTIIL-TSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       293 ~~~~~s~ilv-TtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                       ....+.+|+ |+....+...-......+++.++++++....+.+.+....-.. -.+.+..|++.++|..--+.
T Consensus       148 -pp~~tifIL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i-~~~al~~La~~s~gdlr~al  220 (614)
T PRK14971        148 -PPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITA-EPEALNVIAQKADGGMRDAL  220 (614)
T ss_pred             -CCCCeEEEEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHH
Confidence             233455554 5444444322234457899999999999999988765332211 14567899999999775443

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.17  E-value=2.3e-05  Score=91.74  Aligned_cols=184  Identities=14%  Similarity=0.152  Sum_probs=105.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEE-EEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVM-AEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~w-v~vs~~~~~~~l~~  230 (724)
                      +....+++||++++.++++.|......-+.++|++|+||||+|+.+++.......    .+..+| +.++.-.       
T Consensus       183 ~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~-------  255 (852)
T TIGR03345       183 EGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQ-------  255 (852)
T ss_pred             CCCCCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhh-------
Confidence            3445788999999999999988666667779999999999999999998753211    122332 3322100       


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHh-cCCcEEEEEcccccccc-------cc--ccccccCCCCcCCCCCCCCCcEE
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLK-KEKRVLIILDNIWTKLE-------LD--KIGIPYGDVDEKDKNDDPRRCTI  300 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~-------~~--~l~~~~~~~~~~~~~~~~~~s~i  300 (724)
                         .  +.... .. .......+...+. .+++.+|++|++.....       -+  .+..|.-         ....-++
T Consensus       256 ---a--g~~~~-ge-~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l---------~~G~l~~  319 (852)
T TIGR03345       256 ---A--GASVK-GE-FENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPAL---------ARGELRT  319 (852)
T ss_pred             ---c--ccccc-hH-HHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHh---------hCCCeEE
Confidence               0  00000 00 1223333444433 24689999999965421       11  1111211         2233556


Q ss_pred             EEEecccch------hhhhcCCCceEecCCCCHHHHHHHHHHHhCC---CCCCCCchhHHHHHHHHhCCch
Q 004895          301 ILTSRSRDL------LCIDMNSQKMFWIDALSEEEALQLFEKIVGE---STKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       301 lvTtR~~~v------~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~---~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      |-||.....      ..........+.+++++.+++.++++.....   ...-.-..+....+++.+.++.
T Consensus       320 IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       320 IAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             EEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence            666654321      0111234568999999999999997655421   1111112456677777776654

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.

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

Probab=98.13  E-value=1.6e-06  Score=98.35  Aligned_cols=135  Identities=22%  Similarity=0.284  Sum_probs=73.0

Q ss_pred             CCceEEEcCCCcCC--CCCcccc-CCCCCcEEEcCCcccCC--c-ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeE
Q 004895          575 EELKVLDFTGIRFS--PLPSSLG-RLINLQTLCLDGWRLED--I-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL  648 (724)
Q Consensus       575 ~~L~~L~l~~~~~~--~lp~~i~-~l~~L~~L~L~~~~l~~--~-~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L  648 (724)
                      .+|+.||++|....  .-|..++ .|++|+.|.+++-.+..  . .-..+++||..||+|+|.++.+ .++++|++|+.|
T Consensus       122 ~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~TnI~nl-~GIS~LknLq~L  200 (699)
T KOG3665|consen  122 QNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGTNISNL-SGISRLKNLQVL  200 (699)
T ss_pred             HhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCCCccCc-HHHhccccHHHH
Confidence            45666676664432  1233333 35667777776655433  1 3344667777777777777766 667777777777


Q ss_pred             ccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          649 DLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       649 ~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      .+.+-..-...--..+.+|++|+.||++.......  .......+..-..|++||.||.|++.+
T Consensus       201 ~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~--~~ii~qYlec~~~LpeLrfLDcSgTdi  262 (699)
T KOG3665|consen  201 SMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDD--TKIIEQYLECGMVLPELRFLDCSGTDI  262 (699)
T ss_pred             hccCCCCCchhhHHHHhcccCCCeeeccccccccc--hHHHHHHHHhcccCccccEEecCCcch
Confidence            66552211111112356777777777765321111  001111223334577777777777664

>PRK05642 DNA replication initiation factor; Validated

Probab=98.13  E-value=8.1e-05  Score=73.89  Aligned_cols=154  Identities=14%  Similarity=0.158  Sum_probs=92.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      ...+.|+|..|+|||.|++.+++....+  -..++|++..+      +...                  ...+.+.+.+ 
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~--~~~v~y~~~~~------~~~~------------------~~~~~~~~~~-   97 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQR--GEPAVYLPLAE------LLDR------------------GPELLDNLEQ-   97 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC--CCcEEEeeHHH------HHhh------------------hHHHHHhhhh-
Confidence            3578999999999999999999877543  23467776532      2111                  0123333332 


Q ss_pred             CcEEEEEcccccc---ccccc-cccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHH
Q 004895          261 KRVLIILDNIWTK---LELDK-IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEE  328 (724)
Q Consensus       261 kr~LlVlDdv~~~---~~~~~-l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~  328 (724)
                      - =+||+||+...   ..|+. +...+..       ....|..+|+|++...-.        .........+++++++.+
T Consensus        98 ~-d~LiiDDi~~~~~~~~~~~~Lf~l~n~-------~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e  169 (234)
T PRK05642         98 Y-ELVCLDDLDVIAGKADWEEALFHLFNR-------LRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDE  169 (234)
T ss_pred             C-CEEEEechhhhcCChHHHHHHHHHHHH-------HHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHH
Confidence            1 27889999643   23432 2221111       023456788888865421        111223467899999999


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHH
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVAN  370 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~  370 (724)
                      +-.++++.++.... -.--+++..-|++.+.|..-.+..+-.
T Consensus       170 ~~~~il~~ka~~~~-~~l~~ev~~~L~~~~~~d~r~l~~~l~  210 (234)
T PRK05642        170 DKLRALQLRASRRG-LHLTDEVGHFILTRGTRSMSALFDLLE  210 (234)
T ss_pred             HHHHHHHHHHHHcC-CCCCHHHHHHHHHhcCCCHHHHHHHHH
Confidence            99999996664321 111156778888888887665544433

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.13  E-value=9.2e-05  Score=80.63  Aligned_cols=185  Identities=15%  Similarity=0.193  Sum_probs=107.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhcc---------------------CCCe
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDN---------------------VFDK  213 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------------------~F~~  213 (724)
                      |.....++|.+..+..+..++..++. ..+.++|+.|+||||+|+.+++......                     +++ 
T Consensus        13 P~~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d-   91 (451)
T PRK06305         13 PQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLD-   91 (451)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCc-
Confidence            34456788999999999998876665 5678999999999999999998764311                     111 


Q ss_pred             EEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCC
Q 004895          214 VVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDK  291 (724)
Q Consensus       214 ~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~  291 (724)
                      ++++........+++ +++.+.+                 ...-..+++-++|+|++....  ..+.+...+..      
T Consensus        92 ~~~i~g~~~~gid~i-r~i~~~l-----------------~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEe------  147 (451)
T PRK06305         92 VLEIDGASHRGIEDI-RQINETV-----------------LFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEE------  147 (451)
T ss_pred             eEEeeccccCCHHHH-HHHHHHH-----------------HhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhc------
Confidence            111211111112111 1111111                 000012466789999986542  22333222222      


Q ss_pred             CCCCCCcEEEEEecc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHH
Q 004895          292 NDDPRRCTIILTSRS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTV  368 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~  368 (724)
                        ....+.+|++|.. ..+...-......+++.++++++....+.+.+...... --++.+..|++.++|.+- |+..+
T Consensus       148 --p~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~-i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        148 --PPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIE-TSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             --CCCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence              2235556655533 32222113345689999999999999888876432211 124678899999999764 44443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.12  E-value=7.6e-05  Score=81.81  Aligned_cols=186  Identities=13%  Similarity=0.203  Sum_probs=110.6

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccC------------------CC-eEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNV------------------FD-KVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~------------------F~-~~~  215 (724)
                      |.....++|.+...+.|...+..++.. +..++|+.|+||||+|+.+++..-....                  +. .++
T Consensus        10 P~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~   89 (535)
T PRK08451         10 PKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDII   89 (535)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEE
Confidence            344667889999999999888776665 5689999999999999999887632111                  11 122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .+..+....++++ ++++.....                 .-..+++-++|+|++....  ..+.+...+..        
T Consensus        90 eldaas~~gId~I-Relie~~~~-----------------~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEE--------  143 (535)
T PRK08451         90 EMDAASNRGIDDI-RELIEQTKY-----------------KPSMARFKIFIIDEVHMLTKEAFNALLKTLEE--------  143 (535)
T ss_pred             EeccccccCHHHH-HHHHHHHhh-----------------CcccCCeEEEEEECcccCCHHHHHHHHHHHhh--------
Confidence            2222221222222 111111100                 0001456699999996552  23333222222        


Q ss_pred             CCCCcEEEEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          294 DPRRCTIILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       294 ~~~~s~ilvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ....+++|++|.+. .+...-......+++.+++.++....+.+.+......- -++.++.|++.++|.+.-+...
T Consensus       144 pp~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i-~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        144 PPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSY-EPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             cCCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHH
Confidence            23456666666543 22211123456899999999999999988775332221 2567889999999998555444

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.12  E-value=2.4e-05  Score=79.29  Aligned_cols=155  Identities=18%  Similarity=0.245  Sum_probs=79.6

Q ss_pred             ccccchHHHHHHHHH---Hhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          160 NIFNSRKKIFQDVIE---ALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~---~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ..++|.+..++++.+   +..            .+...-+.++|++|+||||+|+.+++.......-....++.++.   
T Consensus         6 ~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~---   82 (261)
T TIGR02881         6 SRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVER---   82 (261)
T ss_pred             HHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecH---
Confidence            346677666655543   321            12345678999999999999999998764322111112333322   


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc----------cccccccccCCCCcCCCCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL----------ELDKIGIPYGDVDEKDKNDD  294 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~----------~~~~l~~~~~~~~~~~~~~~  294 (724)
                       .++....   .+     ..  .   ..+.+.+......+|++|++....          ..+.+...+..        .
T Consensus        83 -~~l~~~~---~g-----~~--~---~~~~~~~~~a~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~--------~  140 (261)
T TIGR02881        83 -ADLVGEY---IG-----HT--A---QKTREVIKKALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMED--------N  140 (261)
T ss_pred             -HHhhhhh---cc-----ch--H---HHHHHHHHhccCCEEEEechhhhccCCccchHHHHHHHHHHHHhc--------c
Confidence             1221110   11     10  1   112222222234589999997532          11222222211        2


Q ss_pred             CCCcEEEEEecccchh-------hhhcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          295 PRRCTIILTSRSRDLL-------CIDMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~-------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                      .....+++++......       .........+.+++++.+|-.+++.+.+.
T Consensus       141 ~~~~~vila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~  192 (261)
T TIGR02881       141 RNEFVLILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVK  192 (261)
T ss_pred             CCCEEEEecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHH
Confidence            2333455555443220       11111234688999999999999988775

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.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.11  E-value=6.7e-05  Score=84.52  Aligned_cols=182  Identities=18%  Similarity=0.232  Sum_probs=107.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCC-C---------------eEEEEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVF-D---------------KVVMAE  218 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~---------------~~~wv~  218 (724)
                      |.....++|.+..++.|..++..+++ ..+.++|+.|+||||+|+.+++..-..... .               .++++.
T Consensus        14 P~~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~Dvieid   93 (725)
T PRK07133         14 PKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMD   93 (725)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCcEEEEe
Confidence            44456788999999999999876654 456789999999999999998875321110 0               011111


Q ss_pred             EecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCC
Q 004895          219 ITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       219 vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~  292 (724)
                      .+....                      .+.+..+.+.+.    .+++-++|+|++....  .++.+...+..       
T Consensus        94 aasn~~----------------------vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEE-------  144 (725)
T PRK07133         94 AASNNG----------------------VDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEE-------  144 (725)
T ss_pred             ccccCC----------------------HHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhc-------
Confidence            111111                      112223333322    2466799999986542  34343222222       


Q ss_pred             CCCCCcE-EEEEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHH
Q 004895          293 DDPRRCT-IILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTV  368 (724)
Q Consensus       293 ~~~~~s~-ilvTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~  368 (724)
                       ....+. |++|++...+...-......+++.+++.++....+...+....... -.+.+..|++.++|.+. |+..+
T Consensus       145 -PP~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~i-d~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        145 -PPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISY-EKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             -CCCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence             222344 4455554444322234456899999999999999888664322111 14567889999999775 44433

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.11  E-value=0.00033  Score=73.02  Aligned_cols=199  Identities=16%  Similarity=0.156  Sum_probs=122.9

Q ss_pred             cccccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ..+....||+.+++.+.+++.    ....+-+-|.|.+|.|||.+...++.+......=-.++++++..-.....++..|
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHH
Confidence            345668899999999888875    3456789999999999999999999988653221245777777656777888888


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCC-cEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEK-RVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~k-r~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      ...+...........+....+.++..+.+ .+|+|+|..+....  -..+...|.+       ...+++++|+.--....
T Consensus       227 ~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFew-------p~lp~sr~iLiGiANsl  299 (529)
T KOG2227|consen  227 FSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEW-------PKLPNSRIILIGIANSL  299 (529)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhc-------ccCCcceeeeeeehhhh
Confidence            88773322222223344555666665444 79999999865321  1111111111       02344554433222111


Q ss_pred             ---------hhh-hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          310 ---------LCI-DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       310 ---------~~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                               ... ..-....+..+|.+.++..++|..+.......+.+....+-+++||.|.-
T Consensus       300 DlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~S  362 (529)
T KOG2227|consen  300 DLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPS  362 (529)
T ss_pred             hHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCc
Confidence                     111 12234578889999999999999988654444444444555555655443

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

Probab=98.11  E-value=4e-05  Score=89.14  Aligned_cols=160  Identities=18%  Similarity=0.220  Sum_probs=93.5

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----CeEEEEEEecCCChHHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ...++++||++++.++++.|......-+.++|++|+|||++|+.+++........    +..+|..     +...    +
T Consensus       179 ~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~-----~~~~----l  249 (731)
T TIGR02639       179 GKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSL-----DMGS----L  249 (731)
T ss_pred             CCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEe-----cHHH----H
Confidence            3456789999999999998876666667899999999999999999987442211    3333321     1111    1


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------ccccccccCCCCcCCCCCCCCCcEEEE
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------LDKIGIPYGDVDEKDKNDDPRRCTIIL  302 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------~~~l~~~~~~~~~~~~~~~~~~s~ilv  302 (724)
                      ....  .... . .+.....+.+.+...++.+|++|++.....          ...+..+.-         ....-++|-
T Consensus       250 ~a~~--~~~g-~-~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l---------~~g~i~~Ig  316 (731)
T TIGR02639       250 LAGT--KYRG-D-FEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPAL---------SSGKLRCIG  316 (731)
T ss_pred             hhhc--cccc-h-HHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHH---------hCCCeEEEE
Confidence            1100  0001 1 233445555555444679999999974421          111111111         112234444


Q ss_pred             Eecccch----h--hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          303 TSRSRDL----L--CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       303 TtR~~~v----~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      +|.....    .  .........+.+++++.++..++++...
T Consensus       317 aTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       317 STTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             ecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHH
Confidence            4443211    0  1112234689999999999999999765

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.09  E-value=3.4e-05  Score=78.08  Aligned_cols=170  Identities=16%  Similarity=0.163  Sum_probs=105.3

Q ss_pred             ccccchHHHHHHHHHHhcCCC---ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          160 NIFNSRKKIFQDVIEALKDDK---LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~---~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      ..|-+|+.++..+...+.+..   ++.|.|+|.+|.|||.+.+++.+....     ..+|+++-+.++...++..|+.+.
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~-----~~vw~n~~ecft~~~lle~IL~~~   80 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNL-----ENVWLNCVECFTYAILLEKILNKS   80 (438)
T ss_pred             cCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCC-----cceeeehHHhccHHHHHHHHHHHh
Confidence            345689999999998886433   345589999999999999999988732     268999999999999999999998


Q ss_pred             C-CCCCCCchhH--HHHHHHHHHHh-------cCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecc
Q 004895          237 G-MNFDSNDLIY--HRAKQLCQRLK-------KEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS  306 (724)
Q Consensus       237 ~-~~~~~~~~~~--~~~~~l~~~l~-------~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~  306 (724)
                      + .+.++.....  +........+.       .++.++||||+++...+.+....+  .+.........+. -+|+++-.
T Consensus        81 ~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~--~l~~L~el~~~~~-i~iils~~  157 (438)
T KOG2543|consen   81 QLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQ--CLFRLYELLNEPT-IVIILSAP  157 (438)
T ss_pred             ccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHH--HHHHHHHHhCCCc-eEEEEecc
Confidence            6 2222211111  12222222221       246799999999877655443111  0000000112233 34444443


Q ss_pred             cchh--hhhcCC--CceEecCCCCHHHHHHHHHHH
Q 004895          307 RDLL--CIDMNS--QKMFWIDALSEEEALQLFEKI  337 (724)
Q Consensus       307 ~~v~--~~~~~~--~~~~~l~~L~~~e~~~Lf~~~  337 (724)
                      ..-.  ...++.  ..++..+.-+.+|..+++.+.
T Consensus       158 ~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~  192 (438)
T KOG2543|consen  158 SCEKQYLINTGTLEIVVLHFPQYSVEETQVILSRD  192 (438)
T ss_pred             ccHHHhhcccCCCCceEEecCCCCHHHHHHHHhcC
Confidence            3221  111233  346677889999999988764

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.08  E-value=3.5e-05  Score=80.73  Aligned_cols=150  Identities=12%  Similarity=0.144  Sum_probs=87.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.++..+.+..++..+.. .++.++|++|+||||+|+.+++....     .+..++.+. .....+ +..+.
T Consensus        17 P~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~-----~~~~i~~~~-~~~~~i-~~~l~   89 (316)
T PHA02544         17 PSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGA-----EVLFVNGSD-CRIDFV-RNRLT   89 (316)
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCc-----cceEeccCc-ccHHHH-HHHHH
Confidence            45567788999999999998876654 56666999999999999999887531     134455444 222111 11111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHH-hcCCcEEEEEccccccc--c-ccccccccCCCCcCCCCCCCCCcEEEEEecccchh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRL-KKEKRVLIILDNIWTKL--E-LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL  310 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l-~~~kr~LlVlDdv~~~~--~-~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~  310 (724)
                      .                 ..... ..+.+-++|+||+....  . ...+...+..        ...++++|+||......
T Consensus        90 ~-----------------~~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~--------~~~~~~~Ilt~n~~~~l  144 (316)
T PHA02544         90 R-----------------FASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEA--------YSKNCSFIITANNKNGI  144 (316)
T ss_pred             H-----------------HHHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHh--------cCCCceEEEEcCChhhc
Confidence            1                 01111 01345689999996541  1 1122221222        34567888888654321


Q ss_pred             -hhhcCCCceEecCCCCHHHHHHHHHHH
Q 004895          311 -CIDMNSQKMFWIDALSEEEALQLFEKI  337 (724)
Q Consensus       311 -~~~~~~~~~~~l~~L~~~e~~~Lf~~~  337 (724)
                       ..-......+.++..+.++..+++...
T Consensus       145 ~~~l~sR~~~i~~~~p~~~~~~~il~~~  172 (316)
T PHA02544        145 IEPLRSRCRVIDFGVPTKEEQIEMMKQM  172 (316)
T ss_pred             hHHHHhhceEEEeCCCCHHHHHHHHHHH
Confidence             111223346777778888877766543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.08  E-value=0.00011  Score=80.53  Aligned_cols=183  Identities=16%  Similarity=0.177  Sum_probs=106.7

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhcc-------------------CCCeEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDN-------------------VFDKVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~~  215 (724)
                      |.....++|.+.....+..++..++.. .+.++|+.|+||||+|+.++.......                   .|..++
T Consensus        12 P~~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~   91 (486)
T PRK14953         12 PKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLI   91 (486)
T ss_pred             CCcHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEE
Confidence            344567789999999999998766554 567899999999999999988753110                   011122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEK  289 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~  289 (724)
                      ++..+......+                      ...+.....    .+++-++|+|++....  ..+.+...+..    
T Consensus        92 eidaas~~gvd~----------------------ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEe----  145 (486)
T PRK14953         92 EIDAASNRGIDD----------------------IRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEE----  145 (486)
T ss_pred             EEeCccCCCHHH----------------------HHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhc----
Confidence            222221111111                      122222221    2456799999986542  23333222222    


Q ss_pred             CCCCCCCCcEEEE-EecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          290 DKNDDPRRCTIIL-TSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       290 ~~~~~~~~s~ilv-TtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                          ......+|+ ||+...+...-......+.+.+++.++....+.+.+...... --.+.+..|++.++|.+..+...
T Consensus       146 ----pp~~~v~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~-id~~al~~La~~s~G~lr~al~~  220 (486)
T PRK14953        146 ----PPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIE-YEEKALDLLAQASEGGMRDAASL  220 (486)
T ss_pred             ----CCCCeEEEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence                222344444 444333322112334689999999999999888876432211 12456788999999977655444


Q ss_pred             H
Q 004895          369 A  369 (724)
Q Consensus       369 ~  369 (724)
                      .
T Consensus       221 L  221 (486)
T PRK14953        221 L  221 (486)
T ss_pred             H
Confidence            3

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.05  E-value=3.6e-05  Score=76.41  Aligned_cols=164  Identities=9%  Similarity=0.074  Sum_probs=93.9

Q ss_pred             HHHHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhH
Q 004895          169 FQDVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIY  247 (724)
Q Consensus       169 ~~~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~  247 (724)
                      +..+.++.. ......+.|+|+.|+|||+||+.+++..... . ..+.+++......      .    +           
T Consensus        29 ~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~-~-~~~~~i~~~~~~~------~----~-----------   85 (227)
T PRK08903         29 VARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG-G-RNARYLDAASPLL------A----F-----------   85 (227)
T ss_pred             HHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-C-CcEEEEehHHhHH------H----H-----------
Confidence            344444433 2345678899999999999999999986432 1 2345555433110      0    0           


Q ss_pred             HHHHHHHHHHhcCCcEEEEEcccccccccc--ccccccCCCCcCCCCCCCCCc-EEEEEecccchhh-------hhcCCC
Q 004895          248 HRAKQLCQRLKKEKRVLIILDNIWTKLELD--KIGIPYGDVDEKDKNDDPRRC-TIILTSRSRDLLC-------IDMNSQ  317 (724)
Q Consensus       248 ~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~--~l~~~~~~~~~~~~~~~~~~s-~ilvTtR~~~v~~-------~~~~~~  317 (724)
                             ...  ...-+||+||+.....+.  .+...+...       ...+. .+|+|++......       ......
T Consensus        86 -------~~~--~~~~~liiDdi~~l~~~~~~~L~~~~~~~-------~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~  149 (227)
T PRK08903         86 -------DFD--PEAELYAVDDVERLDDAQQIALFNLFNRV-------RAHGQGALLVAGPAAPLALPLREDLRTRLGWG  149 (227)
T ss_pred             -------hhc--ccCCEEEEeChhhcCchHHHHHHHHHHHH-------HHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcC
Confidence                   011  233579999996543221  121111110       12233 4666666533210       012223


Q ss_pred             ceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          318 KMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       318 ~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      ..++++++++++-..++.+.+.... ..--++..+.+++.+.|.+..+..+...+
T Consensus       150 ~~i~l~pl~~~~~~~~l~~~~~~~~-v~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        150 LVYELKPLSDADKIAALKAAAAERG-LQLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             eEEEecCCCHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            6889999999988888777543221 11125678889999999998877666554

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.05  E-value=0.0001  Score=83.25  Aligned_cols=198  Identities=14%  Similarity=0.164  Sum_probs=111.7

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      +.....++|.+..++.|..++..++. ..+.++|+.|+||||+|+.+++.........      -...++.-...+.|..
T Consensus        12 P~~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~------~~~~c~~c~~c~~i~~   85 (585)
T PRK14950         12 SQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP------KGRPCGTCEMCRAIAE   85 (585)
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC------CCCCCccCHHHHHHhc
Confidence            34456788999999999888876655 4568999999999999999998764211100      0011111222333332


Q ss_pred             hhCCCC---CC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNF---DS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~---~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      ......   +. .....+....+.+.+.    .+++-++|+|++....  ..+.+...+..        ....+.+|+++
T Consensus        86 ~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEe--------pp~~tv~Il~t  157 (585)
T PRK14950         86 GSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEE--------PPPHAIFILAT  157 (585)
T ss_pred             CCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhc--------CCCCeEEEEEe
Confidence            221110   00 0001112222222221    1456799999996542  23333222222        22345566555


Q ss_pred             cc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          305 RS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       305 R~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      .. ..+...-......+.+.+++.++....+.+.+......- -.+.+..|++.++|.+..+...
T Consensus       158 ~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i-~~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        158 TEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINL-EPGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             CChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            43 333221123346788999999999999888775332211 1467889999999988655443

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.04  E-value=0.0001  Score=74.17  Aligned_cols=205  Identities=17%  Similarity=0.204  Sum_probs=118.4

Q ss_pred             ccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+-|-++.+++|.+...             -...+-|.++|++|.|||-||++|+++....       |+.|...  
T Consensus       149 tY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~At-------FIrvvgS--  219 (406)
T COG1222         149 TYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDAT-------FIRVVGS--  219 (406)
T ss_pred             ChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCce-------EEEeccH--
Confidence            34456678888888877764             1346678899999999999999999987543       4544432  


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--c-------ccc-ccccCCCCcCCCCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--L-------DKI-GIPYGDVDEKDKNDD  294 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~-------~~l-~~~~~~~~~~~~~~~  294 (724)
                        ++.+..   +|.       .......+++.-+...++.|++|.++....  .       .++ +..+.-+.+.+.+..
T Consensus       220 --ElVqKY---iGE-------GaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~  287 (406)
T COG1222         220 --ELVQKY---IGE-------GARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP  287 (406)
T ss_pred             --HHHHHH---hcc-------chHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC
Confidence              222222   221       233556666666667899999999965411  0       000 011112233455556


Q ss_pred             CCCcEEEEEecccchhhh----hcCCCceEecCCCCHHHH-HHHHHHHhCCCCCCCCchhHHHHHHHHhCCch----hHH
Q 004895          295 PRRCTIILTSRSRDLLCI----DMNSQKMFWIDALSEEEA-LQLFEKIVGESTKASDFRPLAEEIVGKCGGLP----VAL  365 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~~~----~~~~~~~~~l~~L~~~e~-~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP----Lai  365 (724)
                      ....|||..|-..++...    ...-...++++ +...++ .++|+=++..-.-..+.  -.+.|++.|.|.-    -|+
T Consensus       288 ~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfp-lPd~~gR~~Il~IHtrkM~l~~dv--d~e~la~~~~g~sGAdlkai  364 (406)
T COG1222         288 RGNVKVIMATNRPDILDPALLRPGRFDRKIEFP-LPDEEGRAEILKIHTRKMNLADDV--DLELLARLTEGFSGADLKAI  364 (406)
T ss_pred             CCCeEEEEecCCccccChhhcCCCcccceeecC-CCCHHHHHHHHHHHhhhccCccCc--CHHHHHHhcCCCchHHHHHH
Confidence            677899999988776411    11223456666 555554 45666665432222211  1456777777654    344


Q ss_pred             HHHHHHhc---CC---CHHHHHHHHHH
Q 004895          366 STVANALK---NK---SPAIWKDALNK  386 (724)
Q Consensus       366 ~~~~~~l~---~~---~~~~w~~~~~~  386 (724)
                      .+=|++++   .+   +.+.+..+.++
T Consensus       365 ctEAGm~AiR~~R~~Vt~~DF~~Av~K  391 (406)
T COG1222         365 CTEAGMFAIRERRDEVTMEDFLKAVEK  391 (406)
T ss_pred             HHHHhHHHHHhccCeecHHHHHHHHHH
Confidence            55555554   11   45555555554

>CHL00095 clpC Clp protease ATP binding subunit

Probab=98.04  E-value=6.1e-05  Score=88.68  Aligned_cols=180  Identities=17%  Similarity=0.230  Sum_probs=102.5

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----CeEEEEEEecCCChHHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ..+++||+++++++++.|......-+.++|++|+|||++|+.++.........    +..+|. +    +...+    +.
T Consensus       178 ~~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l----~~~~l----~a  248 (821)
T CHL00095        178 LDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-L----DIGLL----LA  248 (821)
T ss_pred             CCCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-e----eHHHH----hc
Confidence            45688999999999999986555566799999999999999999987532111    234442 1    11111    11


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                        +.+... . .++....+.+.+...++.+|++|++.....         ...+..|.-         ....-++|.+|.
T Consensus       249 --g~~~~g-e-~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l---------~rg~l~~IgaTt  315 (821)
T CHL00095        249 --GTKYRG-E-FEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPAL---------ARGELQCIGATT  315 (821)
T ss_pred             --cCCCcc-H-HHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHH---------hCCCcEEEEeCC
Confidence              111111 1 233455555555555789999999964321         111111111         122344555555


Q ss_pred             ccchh------hhhcCCCceEecCCCCHHHHHHHHHHHhC---CCCCCCCchhHHHHHHHHhCC
Q 004895          306 SRDLL------CIDMNSQKMFWIDALSEEEALQLFEKIVG---ESTKASDFRPLAEEIVGKCGG  360 (724)
Q Consensus       306 ~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~---~~~~~~~l~~~~~~I~~~c~G  360 (724)
                      .....      .........+.++..+.++...+++....   ......--++....+++.++|
T Consensus       316 ~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~  379 (821)
T CHL00095        316 LDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQ  379 (821)
T ss_pred             HHHHHHHHhcCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhc
Confidence            43321      11123446788999999999888876432   111111124556666666654

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

Probab=98.03  E-value=2.7e-06  Score=96.62  Aligned_cols=147  Identities=20%  Similarity=0.269  Sum_probs=99.3

Q ss_pred             ccCceEEeccCCCc--ccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCc
Q 004895          526 QKGPIAISLPYRDI--QELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~--~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~  601 (724)
                      ..++++|.+++...  ...+..  .-+|.|++|.+.+..-...+ ....+.++++|+.||+|+++++.+ ..|++|++|+
T Consensus       121 r~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~d-F~~lc~sFpNL~sLDIS~TnI~nl-~GIS~LknLq  198 (699)
T KOG3665|consen  121 RQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDD-FSQLCASFPNLRSLDISGTNISNL-SGISRLKNLQ  198 (699)
T ss_pred             HHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchh-HHHHhhccCccceeecCCCCccCc-HHHhccccHH
Confidence            46788888876433  122222  25899999999432221222 234567899999999999999988 7899999999


Q ss_pred             EEEcCCcccCC---cccccCCCCCcEEEccCCcCcccchh-------hhcCCCCCeEccCCCCCCcccChHHhhCCCCCc
Q 004895          602 TLCLDGWRLED---IAIVGQLKKLEILSLRGAEIKQLPLQ-------IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE  671 (724)
Q Consensus       602 ~L~L~~~~l~~---~~~~~~l~~L~~L~l~~~~i~~lp~~-------i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~  671 (724)
                      .|.+++-.+..   +..+.+|++|++||+|......-|..       -..|++||.|+.+++..-..+....+..-++|+
T Consensus       199 ~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLDcSgTdi~~~~le~ll~sH~~L~  278 (699)
T KOG3665|consen  199 VLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLDCSGTDINEEILEELLNSHPNLQ  278 (699)
T ss_pred             HHhccCCCCCchhhHHHHhcccCCCeeeccccccccchHHHHHHHHhcccCccccEEecCCcchhHHHHHHHHHhCccHh
Confidence            99998887765   46788999999999999754433321       234889999998874322222223334444554


Q ss_pred             EEE
Q 004895          672 ELY  674 (724)
Q Consensus       672 ~L~  674 (724)
                      .+.
T Consensus       279 ~i~  281 (699)
T KOG3665|consen  279 QIA  281 (699)
T ss_pred             hhh
Confidence            443

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

Probab=98.02  E-value=2.6e-05  Score=82.64  Aligned_cols=108  Identities=18%  Similarity=0.189  Sum_probs=72.2

Q ss_pred             ccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH-hhCC
Q 004895          160 NIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS-DLGM  238 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~-~l~~  238 (724)
                      ...++.+..++.+...|...  +.+.++|++|+|||++|+.+++.......|+.+.||++++..+..+++..+.- ..+.
T Consensus       175 ~d~~i~e~~le~l~~~L~~~--~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy  252 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK--KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGF  252 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCe
Confidence            34567788889998888643  46778999999999999999998876667888999999998887766543211 1111


Q ss_pred             CCCCCchhHHHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          239 NFDSNDLIYHRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       239 ~~~~~~~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ......    ....+..... .+++++||+|++...
T Consensus       253 ~~~~G~----f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        253 RRKDGI----FYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             EecCch----HHHHHHHHHhcccCCcEEEEehhhcc
Confidence            111110    1111122211 146799999999654

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.01  E-value=7.1e-05  Score=81.47  Aligned_cols=168  Identities=13%  Similarity=0.086  Sum_probs=102.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      .-+.|+|..|+|||+|++.+++.......-..+++++.      .++...+...++...       .....+.+.+.  +
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~------~~f~~~~~~~l~~~~-------~~~~~~~~~~~--~  206 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSG------DEFARKAVDILQKTH-------KEIEQFKNEIC--Q  206 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH------HHHHHHHHHHHHHhh-------hHHHHHHHHhc--c
Confidence            45889999999999999999997654322233555543      456667666654210       12233444443  3


Q ss_pred             cEEEEEccccccc---cc-cccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHHH
Q 004895          262 RVLIILDNIWTKL---EL-DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEEE  329 (724)
Q Consensus       262 r~LlVlDdv~~~~---~~-~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~e  329 (724)
                      .-+||+||+....   .+ +.+...+...       ...+..||+|+......        .......-.+.+++++.++
T Consensus       207 ~dvLiIDDiq~l~~k~~~~e~lf~l~N~~-------~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~  279 (450)
T PRK14087        207 NDVLIIDDVQFLSYKEKTNEIFFTIFNNF-------IENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKT  279 (450)
T ss_pred             CCEEEEeccccccCCHHHHHHHHHHHHHH-------HHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHH
Confidence            4589999996542   11 2221111110       22344688887654311        1113334578899999999


Q ss_pred             HHHHHHHHhCCCCC-CCCchhHHHHHHHHhCCchhHHHHHHHH
Q 004895          330 ALQLFEKIVGESTK-ASDFRPLAEEIVGKCGGLPVALSTVANA  371 (724)
Q Consensus       330 ~~~Lf~~~~~~~~~-~~~l~~~~~~I~~~c~GlPLai~~~~~~  371 (724)
                      -.+++.+++..... ..--+++..-|++.++|.|-.+.-+...
T Consensus       280 r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~  322 (450)
T PRK14087        280 ATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSR  322 (450)
T ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHH
Confidence            99999998853221 1223678899999999999877655443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.97  E-value=0.00021  Score=79.92  Aligned_cols=195  Identities=16%  Similarity=0.168  Sum_probs=108.0

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+...+.|..++..++. ..+.++|+.|+||||+|+.+++..-.....+.       ..++.-...+.|..
T Consensus        12 P~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~-------~pC~~C~~C~~i~~   84 (559)
T PRK05563         12 PQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDG-------EPCNECEICKAITN   84 (559)
T ss_pred             CCcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC-------CCCCccHHHHHHhc
Confidence            44567789999999999999876554 45678999999999999999887542211000       01111111112211


Q ss_pred             hhCCCC---CC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEE-EE
Q 004895          235 DLGMNF---DS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTII-LT  303 (724)
Q Consensus       235 ~l~~~~---~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~il-vT  303 (724)
                      ....+.   +. .....+....+.....    .++.-++|+|++....  .++.+...+..        ....+.+| .|
T Consensus        85 g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEe--------pp~~~ifIlat  156 (559)
T PRK05563         85 GSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEE--------PPAHVIFILAT  156 (559)
T ss_pred             CCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcC--------CCCCeEEEEEe
Confidence            111000   00 0001112222332221    2456789999997542  33333222222        22334444 44


Q ss_pred             ecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      |....+...-......+++.+++.++....+...+......-+ .+.+..|++.++|.+.-+.
T Consensus       157 t~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i~-~~al~~ia~~s~G~~R~al  218 (559)
T PRK05563        157 TEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYE-DEALRLIARAAEGGMRDAL  218 (559)
T ss_pred             CChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHcCCCHHHHH
Confidence            4444333222334567889999999999999887753221111 4567889999999876443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=0.00024  Score=80.22  Aligned_cols=199  Identities=13%  Similarity=0.155  Sum_probs=110.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      +.....++|.+.....|..++..++. ..+.++|+.|+||||+|+.+++..-...... ..    ...++.-+..+.+..
T Consensus        12 P~~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~-~~----~~~Cg~C~~C~~i~~   86 (620)
T PRK14948         12 PQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDK-PT----PEPCGKCELCRAIAA   86 (620)
T ss_pred             CCcHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCC-CC----CCCCcccHHHHHHhc
Confidence            34456778999999999988876553 5778999999999999999999874321110 00    011111122222322


Q ss_pred             hhCCCC---CC-CchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNF---DS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~---~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      ....+.   .. .....+.+..+.+...    .+++-++|+|++....  .++.+...+..        ....+.+|++|
T Consensus        87 g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEe--------Pp~~tvfIL~t  158 (620)
T PRK14948         87 GNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEE--------PPPRVVFVLAT  158 (620)
T ss_pred             CCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhc--------CCcCeEEEEEe
Confidence            211110   00 0001112222222221    2456799999997652  34444322222        22344444444


Q ss_pred             cc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          305 RS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       305 R~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      .+ ..+...-......+++..++.++....+.+.+......- -.+.+..|++.++|.+..+...
T Consensus       159 ~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~i-s~~al~~La~~s~G~lr~A~~l  222 (620)
T PRK14948        159 TDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEI-EPEALTLVAQRSQGGLRDAESL  222 (620)
T ss_pred             CChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHcCCCHHHHHHH
Confidence            33 333222233456788999999998888887765322111 1356889999999988655433

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.95  E-value=0.00026  Score=78.93  Aligned_cols=196  Identities=15%  Similarity=0.165  Sum_probs=108.5

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+..+..|..++..++.. .+.++|+.|+||||+|+.+++..-.......   ..+....+    .+.|..
T Consensus        12 P~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~---~pC~~C~~----C~~i~~   84 (563)
T PRK06647         12 PRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP---MPCGECSS----CKSIDN   84 (563)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC---CCCccchH----HHHHHc
Confidence            444667889999999999998766554 5789999999999999999987643211100   00000000    011111


Q ss_pred             hhCCC---CCCC-chhHHHHHHHHHHH----hcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMN---FDSN-DLIYHRAKQLCQRL----KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~---~~~~-~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      .-...   .+.. ....+.+..+.+.+    ..+++-++|+|++....  .++.+...+..        ....+.+|++|
T Consensus        85 ~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEe--------pp~~~vfI~~t  156 (563)
T PRK06647         85 DNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEE--------PPPYIVFIFAT  156 (563)
T ss_pred             CCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhcc--------CCCCEEEEEec
Confidence            00000   0000 00111112222111    12456789999986553  34444333322        33455555555


Q ss_pred             cc-cchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          305 RS-RDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       305 R~-~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      .. ..+...-......+++.+++.++....+.+.+...... --++.+..|++.++|.+..+..
T Consensus       157 te~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~-id~eAl~lLa~~s~GdlR~als  219 (563)
T PRK06647        157 TEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIK-YEDEALKWIAYKSTGSVRDAYT  219 (563)
T ss_pred             CChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHH
Confidence            33 33322223345678999999999999888876432211 1256778899999998854433

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=97.95  E-value=0.0026  Score=62.33  Aligned_cols=179  Identities=16%  Similarity=0.130  Sum_probs=105.0

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      |.....|+|.++.++++.=.+.     +...--+.++|++|.||||||.-+++...++  +    -++......-.    
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn--~----k~tsGp~leK~----   91 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANELGVN--L----KITSGPALEKP----   91 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHhcCC--e----EecccccccCh----
Confidence            5567889999998888765554     4567789999999999999999999998764  1    11111110000    


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCC----
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRR----  297 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~----  297 (724)
                                      . ....+...|.  ..=++++|.+.....         .+++....       .-+.+++    
T Consensus        92 ----------------g-DlaaiLt~Le--~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI-------~IG~gp~Arsv  145 (332)
T COG2255          92 ----------------G-DLAAILTNLE--EGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDI-------IIGKGPAARSI  145 (332)
T ss_pred             ----------------h-hHHHHHhcCC--cCCeEEEehhhhcChhHHHHhhhhhhheeEEE-------EEccCCccceE
Confidence                            0 1112222222  234566676644310         11110000       0001222    


Q ss_pred             -------cEEEEEecccchh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          298 -------CTIILTSRSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       298 -------s~ilvTtR~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                             +-|=.|||.-.+. +......-+.+++..+.+|-.++..+.+..-.- .--++-+.+|+++..|-|.-..-+-
T Consensus       146 ~ldLppFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i-~i~~~~a~eIA~rSRGTPRIAnRLL  224 (332)
T COG2255         146 RLDLPPFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI-EIDEEAALEIARRSRGTPRIANRLL  224 (332)
T ss_pred             eccCCCeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC-CCChHHHHHHHHhccCCcHHHHHHH
Confidence                   2355788876543 222233457789999999999999988742111 1114678999999999997655443


Q ss_pred             HH
Q 004895          370 NA  371 (724)
Q Consensus       370 ~~  371 (724)
                      +.
T Consensus       225 rR  226 (332)
T COG2255         225 RR  226 (332)
T ss_pred             HH
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=97.94  E-value=9.9e-06  Score=56.54  Aligned_cols=37  Identities=35%  Similarity=0.522  Sum_probs=16.7

Q ss_pred             CceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC
Q 004895          576 ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED  612 (724)
Q Consensus       576 ~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~  612 (724)
                      +|++|++++|+|+.+|..+++|++|++|++++|.+++
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~   38 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISD   38 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSB
T ss_pred             cceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCC
Confidence            3444555555555444444444444444444444443

...

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

Probab=97.94  E-value=5.5e-07  Score=87.43  Aligned_cols=58  Identities=24%  Similarity=0.254  Sum_probs=26.5

Q ss_pred             CCCCCcEEEccCC-cCc-ccchhhhcCCCCCeEccCCCCCCcccChHH---hhCCCCCcEEEccCC
Q 004895          618 QLKKLEILSLRGA-EIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNV---ISKLSRLEELYMGDS  678 (724)
Q Consensus       618 ~l~~L~~L~l~~~-~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~---i~~l~~L~~L~l~~~  678 (724)
                      .+++|-+|||+.| .++ .+-..+.+++.|+||.++.|..   ++|+.   +...++|.+|++.+|
T Consensus       311 rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY~---i~p~~~~~l~s~psl~yLdv~g~  373 (419)
T KOG2120|consen  311 RCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCYD---IIPETLLELNSKPSLVYLDVFGC  373 (419)
T ss_pred             hCCceeeeccccccccCchHHHHHHhcchheeeehhhhcC---CChHHeeeeccCcceEEEEeccc
Confidence            4455555555554 333 3333445555555555555432   22221   234455555555443

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.93  E-value=0.00012  Score=78.19  Aligned_cols=179  Identities=15%  Similarity=0.209  Sum_probs=98.8

Q ss_pred             ccccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+.|-+..+++|.+.+.    .         ...+-+.++|++|+|||++|+.+++....  .|     +.+..   
T Consensus       143 ~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~--~f-----i~i~~---  212 (398)
T PTZ00454        143 TYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTA--TF-----IRVVG---  212 (398)
T ss_pred             CHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCC--CE-----EEEeh---
Confidence            34557788887777766543    1         23567889999999999999999987642  12     22221   


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------------ccc-cccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------------LDK-IGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------------~~~-l~~~~~~~~~~~~  291 (724)
                       .++....   ++     .  .......++.......+.+|++|+++....            ... +...+.   ..+.
T Consensus       213 -s~l~~k~---~g-----e--~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~---~ld~  278 (398)
T PTZ00454        213 -SEFVQKY---LG-----E--GPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLN---QMDG  278 (398)
T ss_pred             -HHHHHHh---cc-----h--hHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHH---Hhhc
Confidence             1111111   11     0  112334444444456789999999864310            000 000000   0111


Q ss_pred             CCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          292 NDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .....+..||+||......... .   .....+.++..+.++-.++|+.........++.  ...++++.+.|+-
T Consensus       279 ~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dv--d~~~la~~t~g~s  351 (398)
T PTZ00454        279 FDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEV--DLEDFVSRPEKIS  351 (398)
T ss_pred             cCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCccc--CHHHHHHHcCCCC
Confidence            1133466788888765532111 1   223568888888998888888776432222221  2456677776654

>CHL00181 cbbX CbbX; Provisional

Probab=97.92  E-value=0.00023  Score=72.76  Aligned_cols=133  Identities=14%  Similarity=0.216  Sum_probs=72.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      ..+.++|++|+||||+|+.+++.......-...-|+.++.    .++....   .+..      . .....+.+.   ..
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~----~~l~~~~---~g~~------~-~~~~~~l~~---a~  122 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTR----DDLVGQY---IGHT------A-PKTKEVLKK---AM  122 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecH----HHHHHHH---hccc------h-HHHHHHHHH---cc
Confidence            3578899999999999999998765322211122454442    2222221   1110      0 111222222   23


Q ss_pred             cEEEEEccccccc------cc-----cccccccCCCCcCCCCCCCCCcEEEEEecccchh-------hhhcCCCceEecC
Q 004895          262 RVLIILDNIWTKL------EL-----DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-------CIDMNSQKMFWID  323 (724)
Q Consensus       262 r~LlVlDdv~~~~------~~-----~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-------~~~~~~~~~~~l~  323 (724)
                      .-+|++|++....      ++     +.+...+..        .....+||+++......       .........++++
T Consensus       123 ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~--------~~~~~~vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~  194 (287)
T CHL00181        123 GGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMEN--------QRDDLVVIFAGYKDRMDKFYESNPGLSSRIANHVDFP  194 (287)
T ss_pred             CCEEEEEccchhccCCCccchHHHHHHHHHHHHhc--------CCCCEEEEEeCCcHHHHHHHhcCHHHHHhCCceEEcC
Confidence            3599999996421      11     112122222        33456677777543321       1111234578999


Q ss_pred             CCCHHHHHHHHHHHhC
Q 004895          324 ALSEEEALQLFEKIVG  339 (724)
Q Consensus       324 ~L~~~e~~~Lf~~~~~  339 (724)
                      +++.+|..+++...+.
T Consensus       195 ~~t~~el~~I~~~~l~  210 (287)
T CHL00181        195 DYTPEELLQIAKIMLE  210 (287)
T ss_pred             CcCHHHHHHHHHHHHH
Confidence            9999999999988874

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

Probab=97.89  E-value=2.6e-06  Score=92.72  Aligned_cols=104  Identities=31%  Similarity=0.415  Sum_probs=47.7

Q ss_pred             cCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccC
Q 004895          572 EGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLS  651 (724)
Q Consensus       572 ~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~  651 (724)
                      ..+++|..|++.+|.+..+...+..+.+|++|+|++|.|+.+..+..+..|+.|++++|.|+.++ ++..+++|+.++++
T Consensus        92 ~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N~I~~i~~l~~l~~L~~L~l~~N~i~~~~-~~~~l~~L~~l~l~  170 (414)
T KOG0531|consen   92 SKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFNKITKLEGLSTLTLLKELNLSGNLISDIS-GLESLKSLKLLDLS  170 (414)
T ss_pred             ccccceeeeeccccchhhcccchhhhhcchheeccccccccccchhhccchhhheeccCcchhcc-CCccchhhhcccCC
Confidence            33444555555555554443334445555555555555555444445555555555555444432 23334555555555


Q ss_pred             CCCCCcccCh-HHhhCCCCCcEEEccCC
Q 004895          652 NCSSLVVIAP-NVISKLSRLEELYMGDS  678 (724)
Q Consensus       652 ~~~~l~~~~~-~~i~~l~~L~~L~l~~~  678 (724)
                      +| .+..+.+ . +..+.+|+.+++.+|
T Consensus       171 ~n-~i~~ie~~~-~~~~~~l~~l~l~~n  196 (414)
T KOG0531|consen  171 YN-RIVDIENDE-LSELISLEELDLGGN  196 (414)
T ss_pred             cc-hhhhhhhhh-hhhccchHHHhccCC
Confidence            42 2222222 1 244444444444443

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=0.00022  Score=80.21  Aligned_cols=201  Identities=13%  Similarity=0.182  Sum_probs=109.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+.....|..++..++.. .+.++|+.|+||||+|+.+++..-.....+.       ..++.-.....|..
T Consensus        12 P~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~-------~~c~~c~~c~~i~~   84 (576)
T PRK14965         12 PQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA-------EPCNVCPPCVEITE   84 (576)
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC-------CCCCccHHHHHHhc
Confidence            444677889999999999988876654 5689999999999999999987642211100       00000011111111


Q ss_pred             hhCCC---CCCC-chhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEE-EE
Q 004895          235 DLGMN---FDSN-DLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTII-LT  303 (724)
Q Consensus       235 ~l~~~---~~~~-~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~il-vT  303 (724)
                      .-..+   .+.. ....+....+...+.    .+++-++|+|++....  ..+.+...+..        ....+.+| +|
T Consensus        85 g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEe--------pp~~~~fIl~t  156 (576)
T PRK14965         85 GRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEE--------PPPHVKFIFAT  156 (576)
T ss_pred             CCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHc--------CCCCeEEEEEe
Confidence            00000   0000 000111222222221    2455689999996543  23333222222        22344555 45


Q ss_pred             ecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch-hHHHHHHHHh
Q 004895          304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP-VALSTVANAL  372 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~~~~~l  372 (724)
                      |....+...-......+++.+++.++....+...+......- -.+....|++.++|.. .|+..+-..+
T Consensus       157 ~~~~kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i-~~~al~~la~~a~G~lr~al~~Ldqli  225 (576)
T PRK14965        157 TEPHKVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISI-SDAALALVARKGDGSMRDSLSTLDQVL  225 (576)
T ss_pred             CChhhhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            444444322233456888999999999888887664322111 1456788999999966 4555544433

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.87  E-value=9.9e-05  Score=75.47  Aligned_cols=132  Identities=15%  Similarity=0.223  Sum_probs=71.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCc
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKR  262 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr  262 (724)
                      -+.++|++|+||||+|+.+++..........--|+.++.    .++...+   .+.     . . .....+.+.   -..
T Consensus        60 ~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~----~~l~~~~---~g~-----~-~-~~~~~~~~~---a~~  122 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR----DDLVGQY---IGH-----T-A-PKTKEILKR---AMG  122 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH----HHHhHhh---ccc-----c-h-HHHHHHHHH---ccC
Confidence            578999999999999999988775432222112444442    1222111   111     1 1 112222222   234


Q ss_pred             EEEEEcccccc------cc-----ccccccccCCCCcCCCCCCCCCcEEEEEecccchhhh-------hcCCCceEecCC
Q 004895          263 VLIILDNIWTK------LE-----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCI-------DMNSQKMFWIDA  324 (724)
Q Consensus       263 ~LlVlDdv~~~------~~-----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~-------~~~~~~~~~l~~  324 (724)
                      -+|+||++...      ..     ++.+...+..        ...+.+||+++........       .......+++++
T Consensus       123 gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~--------~~~~~~vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~  194 (284)
T TIGR02880       123 GVLFIDEAYYLYRPDNERDYGQEAIEILLQVMEN--------QRDDLVVILAGYKDRMDSFFESNPGFSSRVAHHVDFPD  194 (284)
T ss_pred             cEEEEechhhhccCCCccchHHHHHHHHHHHHhc--------CCCCEEEEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCC
Confidence            68999999632      01     1222222222        3345667776654322100       011235789999


Q ss_pred             CCHHHHHHHHHHHhC
Q 004895          325 LSEEEALQLFEKIVG  339 (724)
Q Consensus       325 L~~~e~~~Lf~~~~~  339 (724)
                      ++.+|..+++.+.+.
T Consensus       195 l~~edl~~I~~~~l~  209 (284)
T TIGR02880       195 YSEAELLVIAGLMLK  209 (284)
T ss_pred             cCHHHHHHHHHHHHH
Confidence            999999999988764

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.87  E-value=0.00033  Score=76.44  Aligned_cols=164  Identities=15%  Similarity=0.213  Sum_probs=91.5

Q ss_pred             cccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC---CCeEEEEEEe
Q 004895          157 KDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV---FDKVVMAEIT  220 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---F~~~~wv~vs  220 (724)
                      .....+.|.+..++++.+.+.             -...+-+.++|++|+|||++|+.+++.......   .....|++++
T Consensus       179 v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl~v~  258 (512)
T TIGR03689       179 VTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFLNIK  258 (512)
T ss_pred             CCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEEecc
Confidence            334566788888888877653             123456889999999999999999998753211   1234455544


Q ss_pred             cCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH----hcCCcEEEEEcccccccc---------c-----cccccc
Q 004895          221 KNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL----KKEKRVLIILDNIWTKLE---------L-----DKIGIP  282 (724)
Q Consensus       221 ~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l----~~~kr~LlVlDdv~~~~~---------~-----~~l~~~  282 (724)
                      ..    +++..        ...+  .......+++..    ..+++++|+||+++....         .     ..+...
T Consensus       259 ~~----eLl~k--------yvGe--te~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~  324 (512)
T TIGR03689       259 GP----ELLNK--------YVGE--TERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSE  324 (512)
T ss_pred             ch----hhccc--------ccch--HHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHH
Confidence            32    11111        0000  111222222222    235789999999975311         0     111111


Q ss_pred             cCCCCcCCCCCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCC
Q 004895          283 YGDVDEKDKNDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGE  340 (724)
Q Consensus       283 ~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~  340 (724)
                      +      +......+..||.||......... .   .....++++..+.++..++|+++...
T Consensus       325 L------Dgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~  380 (512)
T TIGR03689       325 L------DGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTD  380 (512)
T ss_pred             h------cccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhc
Confidence            1      111122345566666554432111 1   22346899999999999999998743

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.

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=97.85  E-value=0.00032  Score=75.45  Aligned_cols=179  Identities=17%  Similarity=0.195  Sum_probs=98.8

Q ss_pred             ccccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+.|.+..+++|.+.+.    .         ....-+.++|++|+|||++|+.+++....  .|     +.+...  
T Consensus       181 ~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~--~f-----i~V~~s--  251 (438)
T PTZ00361        181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSA--TF-----LRVVGS--  251 (438)
T ss_pred             CHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCC--CE-----EEEecc--
Confidence            34556788888888877653    1         23456889999999999999999997643  22     222211  


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc-------------cccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL-------------DKIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~-------------~~l~~~~~~~~~~~~  291 (724)
                        ++....   ++     .  .......++.......+.+|+||+++....-             ..+...+.   ..+.
T Consensus       252 --eL~~k~---~G-----e--~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~---~Ldg  316 (438)
T PTZ00361        252 --ELIQKY---LG-----D--GPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLN---QLDG  316 (438)
T ss_pred             --hhhhhh---cc-----h--HHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHH---HHhh
Confidence              111110   11     0  1122334444444457899999998643110             00000000   0011


Q ss_pred             CCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          292 NDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .....+.+||+||......... .   .....++++..+.++-.++|..++......++.  ....++..+.|+-
T Consensus       317 ~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dv--dl~~la~~t~g~s  389 (438)
T PTZ00361        317 FDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDV--DLEEFIMAKDELS  389 (438)
T ss_pred             hcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCc--CHHHHHHhcCCCC
Confidence            1123456788888765543111 1   223578899999999999999876533222211  2345666665544

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

Probab=97.84  E-value=1.9e-05  Score=72.93  Aligned_cols=75  Identities=27%  Similarity=0.348  Sum_probs=34.1

Q ss_pred             ceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc-ccc-cCCCCCcEEEccCCcCcccc--hhhhcCCCCCeEccCC
Q 004895          577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIV-GQLKKLEILSLRGAEIKQLP--LQIGQLTRLQLLDLSN  652 (724)
Q Consensus       577 L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~-~~~-~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~L~l~~  652 (724)
                      ...+||++|.+-.++ .+..+..|.+|.|.+|.|+.+ +.+ ..+++|.+|.+.+|+|.++-  ..+..+++|++|.+-+
T Consensus        44 ~d~iDLtdNdl~~l~-~lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll~  122 (233)
T KOG1644|consen   44 FDAIDLTDNDLRKLD-NLPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLLG  122 (233)
T ss_pred             cceecccccchhhcc-cCCCccccceEEecCCcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceeeecC
Confidence            444555555544332 234455555555555555442 222 23344555555555444331  1234444555555444

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.81  E-value=0.00078  Score=69.68  Aligned_cols=195  Identities=15%  Similarity=0.184  Sum_probs=111.3

Q ss_pred             ccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhc--------------cCCCeEEEEEEecCCC
Q 004895          160 NIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMED--------------NVFDKVVMAEITKNPD  224 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------~~F~~~~wv~vs~~~~  224 (724)
                      ..++|.+..++.+...+..++. ....++|+.|+||+++|..+++..-..              .|.| ..|+.-....+
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPD-l~~i~p~~~~~   82 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPD-LLWVEPTYQHQ   82 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCC-EEEEecccccc
Confidence            4578999999999999887764 789999999999999999998876322              1222 23432110000


Q ss_pred             hHHHHHHHHHhhCCCCC-CCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCC
Q 004895          225 AQKIQGELASDLGMNFD-SNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~-~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~  297 (724)
                      -..+-...++..+.... ......+.+..+.+.+.    .+++-++|+|+++...  ..+.+...+..        .. .
T Consensus        83 g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEE--------Pp-~  153 (314)
T PRK07399         83 GKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEE--------PG-N  153 (314)
T ss_pred             ccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhC--------CC-C
Confidence            00000111112221000 00111223344544443    2567799999986653  23333222222        22 3


Q ss_pred             cEEEEEe-cccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          298 CTIILTS-RSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       298 s~ilvTt-R~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +.+|++| ....+...-.+....+.+.++++++..+.+.+......    .......++..++|.|..+...
T Consensus       154 ~~fILi~~~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~----~~~~~~~l~~~a~Gs~~~al~~  221 (314)
T PRK07399        154 GTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI----LNINFPELLALAQGSPGAAIAN  221 (314)
T ss_pred             CeEEEEECChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc----chhHHHHHHHHcCCCHHHHHHH
Confidence            3445444 44444333345567999999999999999998743211    1112468899999999766543

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.81  E-value=0.00028  Score=76.82  Aligned_cols=161  Identities=14%  Similarity=0.193  Sum_probs=95.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-eEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-KVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..-+.|+|++|+|||+|++.+++..... +++ .++|++.      .++..++...+...    .     ...+.+.+. 
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~-~~~~~v~yi~~------~~f~~~~~~~~~~~----~-----~~~f~~~~~-  192 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQN-EPDLRVMYITS------EKFLNDLVDSMKEG----K-----LNEFREKYR-  192 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHh-CCCCeEEEEEH------HHHHHHHHHHHhcc----c-----HHHHHHHHH-
Confidence            3458999999999999999999987643 233 4677764      34556666555321    1     122333333 


Q ss_pred             CCcEEEEEcccccccc---c-cccccccCCCCcCCCCCCCCCcEEEEEecccc-hh-------hhhcCCCceEecCCCCH
Q 004895          260 EKRVLIILDNIWTKLE---L-DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LL-------CIDMNSQKMFWIDALSE  327 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~---~-~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~-------~~~~~~~~~~~l~~L~~  327 (724)
                      .+.-+|++||+.....   + +.+...+..+       ...+..||+||.... -.       .........+++++.+.
T Consensus       193 ~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l-------~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~  265 (440)
T PRK14088        193 KKVDVLLIDDVQFLIGKTGVQTELFHTFNEL-------HDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDE  265 (440)
T ss_pred             hcCCEEEEechhhhcCcHHHHHHHHHHHHHH-------HHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCH
Confidence            2346899999974311   1 1121111100       123446888885332 11       01123345788999999


Q ss_pred             HHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          328 EEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       328 ~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      +.-.+++++.+...... --+++..-|++.+.|..-.+.
T Consensus       266 e~r~~IL~~~~~~~~~~-l~~ev~~~Ia~~~~~~~R~L~  303 (440)
T PRK14088        266 ETRKKIARKMLEIEHGE-LPEEVLNFVAENVDDNLRRLR  303 (440)
T ss_pred             HHHHHHHHHHHHhcCCC-CCHHHHHHHHhccccCHHHHH
Confidence            99999999887532111 125678888888887655443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.80  E-value=0.00039  Score=82.25  Aligned_cols=159  Identities=16%  Similarity=0.260  Sum_probs=92.1

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----CeEEE-EEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DKVVM-AEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~~~w-v~vs~~~~~~~l~~~  231 (724)
                      ....+++||++++.++++.|......-+.++|++|+|||++|+.+++.......+    +..+| +.++      .+   
T Consensus       170 ~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~------~l---  240 (852)
T TIGR03346       170 GKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMG------AL---  240 (852)
T ss_pred             CCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEEeeHH------HH---
Confidence            3456789999999999999876665667799999999999999999886432111    22233 2211      11   


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhc-CCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEE
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTII  301 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~il  301 (724)
                       +.  +..... . .......+...+.. +++.+|++|++.....         ...+..+..         ....-++|
T Consensus       241 -~a--~~~~~g-~-~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l---------~~g~i~~I  306 (852)
T TIGR03346       241 -IA--GAKYRG-E-FEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPAL---------ARGELHCI  306 (852)
T ss_pred             -hh--cchhhh-h-HHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhh---------hcCceEEE
Confidence             10  101111 1 22334444444432 4689999999975421         011111111         12223455


Q ss_pred             EEecccch------hhhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDL------LCIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v------~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      .+|.....      -.........+.++..+.++..++++...
T Consensus       307 gaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       307 GATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             EeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence            44443322      01112344678899999999999998764

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.80  E-value=0.00025  Score=76.91  Aligned_cols=160  Identities=19%  Similarity=0.195  Sum_probs=94.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      ...+.|+|+.|+|||+|++.+++.......=..++|++.      .++...+...+...    .     ...+.+.+.  
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~------~~~~~~~~~~~~~~----~-----~~~~~~~~~--  198 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS------EKFTNDFVNALRNN----K-----MEEFKEKYR--  198 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH------HHHHHHHHHHHHcC----C-----HHHHHHHHH--
Confidence            356889999999999999999998765321123666653      34444555544321    1     123334443  


Q ss_pred             CcEEEEEcccccccc---c-cccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHH
Q 004895          261 KRVLIILDNIWTKLE---L-DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEE  328 (724)
Q Consensus       261 kr~LlVlDdv~~~~~---~-~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~  328 (724)
                      +.-+|+|||+.....   + +.+...+...       ...+..+|+|+....-.        .........+.+++.+.+
T Consensus       199 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~-------~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~  271 (405)
T TIGR00362       199 SVDLLLIDDIQFLAGKERTQEEFFHTFNAL-------HENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLE  271 (405)
T ss_pred             hCCEEEEehhhhhcCCHHHHHHHHHHHHHH-------HHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHH
Confidence            234899999975421   1 1121111100       12345688887653211        111222347899999999


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      +-..++.+.+...... --+++...|++.+.|.+-.+
T Consensus       272 ~r~~il~~~~~~~~~~-l~~e~l~~ia~~~~~~~r~l  307 (405)
T TIGR00362       272 TRLAILQKKAEEEGLE-LPDEVLEFIAKNIRSNVREL  307 (405)
T ss_pred             HHHHHHHHHHHHcCCC-CCHHHHHHHHHhcCCCHHHH
Confidence            9999999988643211 12567788888888876544

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).

>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=97.79  E-value=3.4e-05  Score=53.86  Aligned_cols=32  Identities=41%  Similarity=0.633  Sum_probs=14.8

Q ss_pred             CCcEEEccCCcCcccchhhhcCCCCCeEccCC
Q 004895          621 KLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       621 ~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~  652 (724)
                      +|++|++++|.|+.+|+.+.+|++|+.|++++
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~   33 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELSNLPNLETLNLSN   33 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGTTCTTSSEEEETS
T ss_pred             cceEEEccCCCCcccCchHhCCCCCCEEEecC
Confidence            34444444444444444444555555555544

...

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.77  E-value=0.00024  Score=78.02  Aligned_cols=161  Identities=18%  Similarity=0.164  Sum_probs=95.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      ..-+.|+|+.|+|||+|++.+++.......-..++|++..      ++...+...+...         ....+.+.+.  
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~------~~~~~~~~~~~~~---------~~~~~~~~~~--  210 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSE------KFTNDFVNALRNN---------TMEEFKEKYR--  210 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHH------HHHHHHHHHHHcC---------cHHHHHHHHh--
Confidence            3568899999999999999999998653212235666543      3344444444211         1123344444  


Q ss_pred             CcEEEEEcccccccc---c-cccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHH
Q 004895          261 KRVLIILDNIWTKLE---L-DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEE  328 (724)
Q Consensus       261 kr~LlVlDdv~~~~~---~-~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~  328 (724)
                      +.-+|||||+.....   + +.+...+..+       ...+..||+||....-.        .........+++++.+.+
T Consensus       211 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l-------~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~  283 (450)
T PRK00149        211 SVDVLLIDDIQFLAGKERTQEEFFHTFNAL-------HEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLE  283 (450)
T ss_pred             cCCEEEEehhhhhcCCHHHHHHHHHHHHHH-------HHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHH
Confidence            345899999965321   1 1221111100       11244578887654211        111233457899999999


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                      +-..++++.+..... .--+++..-|++.++|..-.+.
T Consensus       284 ~r~~il~~~~~~~~~-~l~~e~l~~ia~~~~~~~R~l~  320 (450)
T PRK00149        284 TRIAILKKKAEEEGI-DLPDEVLEFIAKNITSNVRELE  320 (450)
T ss_pred             HHHHHHHHHHHHcCC-CCCHHHHHHHHcCcCCCHHHHH
Confidence            999999998853211 1125678889999888776543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.76  E-value=0.00081  Score=69.99  Aligned_cols=152  Identities=17%  Similarity=0.175  Sum_probs=89.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhcc--------------------CCCeEEEEEEe---cCCChHHHHHHHHHhhC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDN--------------------VFDKVVMAEIT---KNPDAQKIQGELASDLG  237 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~~~~wv~vs---~~~~~~~l~~~i~~~l~  237 (724)
                      ...+.++|+.|+||||+|+.+++..--..                    |.| ..|+.-.   +...+            
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~~~~~~~~i~i------------   88 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPD-NFVLEPEEADKTIKV------------   88 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccCCCCCCCH------------
Confidence            44678999999999999999998864321                    122 1222111   11111            


Q ss_pred             CCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hh
Q 004895          238 MNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LL  310 (724)
Q Consensus       238 ~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~  310 (724)
                                +.+..+.+.+.    .+++-++|+|+++...  ..+.+...+..        ...++.+|+||.+.. +.
T Consensus        89 ----------d~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEE--------Pp~~~~fiL~t~~~~~ll  150 (328)
T PRK05707         89 ----------DQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEE--------PSGDTVLLLISHQPSRLL  150 (328)
T ss_pred             ----------HHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhC--------CCCCeEEEEEECChhhCc
Confidence                      22223333321    2345566789997653  33333222322        334566777776654 33


Q ss_pred             hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          311 CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       311 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ..-.+....+.+.+++.+++.+.+.......     ..+.+..++..++|.|+.+..+
T Consensus       151 ~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~~-----~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        151 PTIKSRCQQQACPLPSNEESLQWLQQALPES-----DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             HHHHhhceeeeCCCcCHHHHHHHHHHhcccC-----ChHHHHHHHHHcCCCHHHHHHH
Confidence            3324445789999999999999888764211     1344667899999999765443

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

Probab=97.75  E-value=1.5e-06  Score=93.96  Aligned_cols=107  Identities=26%  Similarity=0.274  Sum_probs=63.6

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCC-CCCcEEEccCCcCcccchhhhcCCCCCeEc
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQL-KKLEILSLRGAEIKQLPLQIGQLTRLQLLD  649 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l-~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~  649 (724)
                      +.-++.|+.|+|++|++.+.- .+..|.+|++|+|++|.++..+.++.- .+|+.|++++|.++++ .+|.+|++|++|+
T Consensus       183 Lqll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc~L~~L~lrnN~l~tL-~gie~LksL~~LD  260 (1096)
T KOG1859|consen  183 LQLLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYNCLRHVPQLSMVGCKLQLLNLRNNALTTL-RGIENLKSLYGLD  260 (1096)
T ss_pred             HHHHHHhhhhccchhhhhhhH-HHHhcccccccccccchhccccccchhhhhheeeeecccHHHhh-hhHHhhhhhhccc
Confidence            444566667777777666553 566666777777777776664333321 1377777777776666 4566777777777


Q ss_pred             cCCCCCCcc-cChHHhhCCCCCcEEEccCCCC
Q 004895          650 LSNCSSLVV-IAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       650 l~~~~~l~~-~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      +++| .+.. ---..++.|..|..|++.+|..
T Consensus       261 lsyN-ll~~hseL~pLwsLs~L~~L~LeGNPl  291 (1096)
T KOG1859|consen  261 LSYN-LLSEHSELEPLWSLSSLIVLWLEGNPL  291 (1096)
T ss_pred             hhHh-hhhcchhhhHHHHHHHHHHHhhcCCcc
Confidence            7663 2221 1112256666677777766643

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.73  E-value=0.00033  Score=82.56  Aligned_cols=159  Identities=16%  Similarity=0.245  Sum_probs=91.2

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----Ce-EEEEEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DK-VVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~-~~wv~vs~~~~~~~l~~~  231 (724)
                      ....+++||++++.++++.|......-+.++|++|+|||++|+.++.........    +. +++++++.      +   
T Consensus       175 ~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~------l---  245 (857)
T PRK10865        175 GKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------L---  245 (857)
T ss_pred             CCCCcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhh------h---
Confidence            3456789999999999999876666677799999999999999999987432111    22 23333321      1   


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHh-cCCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEE
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLK-KEKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTII  301 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~il  301 (724)
                       ..  +......  .+.....+...+. .+++.+|++|++.....         ...+..|.-         ....-++|
T Consensus       246 -~a--g~~~~g~--~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l---------~~g~l~~I  311 (857)
T PRK10865        246 -VA--GAKYRGE--FEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL---------ARGELHCV  311 (857)
T ss_pred             -hh--ccchhhh--hHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchh---------hcCCCeEE
Confidence             10  0011111  1223344444432 24679999999975421         111111211         22234555


Q ss_pred             EEecccch------hhhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDL------LCIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v------~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      -+|.....      -.......+.+.+..-+.++...+++...
T Consensus       312 gaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        312 GATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             EcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHh
Confidence            55554432      01112233466777779999999887654

>PRK06620 hypothetical protein; Validated

Probab=97.71  E-value=0.00017  Score=70.32  Aligned_cols=136  Identities=15%  Similarity=0.039  Sum_probs=79.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      +.+.|+|++|+|||+|++.+++....       .++.  ..+.                   . .        +.+.  .
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~~-------~~~~--~~~~-------------------~-~--------~~~~--~   85 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSNA-------YIIK--DIFF-------------------N-E--------EILE--K   85 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccCC-------EEcc--hhhh-------------------c-h--------hHHh--c
Confidence            56899999999999999987665421       1221  0000                   0 0        0111  2


Q ss_pred             cEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchh------hhhcCCCceEecCCCCHHHHHHHHH
Q 004895          262 RVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL------CIDMNSQKMFWIDALSEEEALQLFE  335 (724)
Q Consensus       262 r~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf~  335 (724)
                      .-++++||+....+ ..+...+..       ....|..+|+|++.....      .......-.++++++++++-..++.
T Consensus        86 ~d~lliDdi~~~~~-~~lf~l~N~-------~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~~~~~l~  157 (214)
T PRK06620         86 YNAFIIEDIENWQE-PALLHIFNI-------INEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDELIKILIF  157 (214)
T ss_pred             CCEEEEeccccchH-HHHHHHHHH-------HHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHHHHHHHH
Confidence            35788999963321 011111100       023466899999865431      1122334589999999999888888


Q ss_pred             HHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          336 KIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       336 ~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      +.+....- .--+++..-|++.+.|.--.+
T Consensus       158 k~~~~~~l-~l~~ev~~~L~~~~~~d~r~l  186 (214)
T PRK06620        158 KHFSISSV-TISRQIIDFLLVNLPREYSKI  186 (214)
T ss_pred             HHHHHcCC-CCCHHHHHHHHHHccCCHHHH
Confidence            87653211 111567778888887765544

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.71  E-value=0.0013  Score=63.94  Aligned_cols=53  Identities=19%  Similarity=0.226  Sum_probs=41.7

Q ss_pred             CcccccccchHHHHHHHHHHh----cCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          156 MKDYNIFNSRKKIFQDVIEAL----KDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +.....++|-+..++.|++-.    ......-+.++|..|+|||++++.+.+....+
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~   79 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ   79 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc
Confidence            445667889888888877643    34455677889999999999999999988764

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

Probab=97.70  E-value=7.4e-06  Score=89.11  Aligned_cols=79  Identities=30%  Similarity=0.399  Sum_probs=37.0

Q ss_pred             CCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccC
Q 004895          573 GTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLS  651 (724)
Q Consensus       573 ~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~  651 (724)
                      .+.+|++|++++|.|..+. .+..+..|+.|++++|.++.+..+..+.+|+.+++++|.+..++.. +..+.+|+.+.+.
T Consensus       116 ~~~~L~~L~ls~N~I~~i~-~l~~l~~L~~L~l~~N~i~~~~~~~~l~~L~~l~l~~n~i~~ie~~~~~~~~~l~~l~l~  194 (414)
T KOG0531|consen  116 SLVNLQVLDLSFNKITKLE-GLSTLTLLKELNLSGNLISDISGLESLKSLKLLDLSYNRIVDIENDELSELISLEELDLG  194 (414)
T ss_pred             hhhcchheecccccccccc-chhhccchhhheeccCcchhccCCccchhhhcccCCcchhhhhhhhhhhhccchHHHhcc
Confidence            3444555555555544442 2344444555555555554444444455555555555544444332 3444444444444


Q ss_pred             C
Q 004895          652 N  652 (724)
Q Consensus       652 ~  652 (724)
                      +
T Consensus       195 ~  195 (414)
T KOG0531|consen  195 G  195 (414)
T ss_pred             C
Confidence            4

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.69  E-value=0.00081  Score=74.84  Aligned_cols=180  Identities=14%  Similarity=0.149  Sum_probs=95.5

Q ss_pred             cccccccchHHHHHHHHHHh---cC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEAL---KD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....+.|-++.++++.+.+   ..         ...+-+.++|++|+|||++|+.+++.....       ++.++.   
T Consensus        52 ~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~-------~~~i~~---  121 (495)
T TIGR01241        52 VTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP-------FFSISG---  121 (495)
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCC-------eeeccH---
Confidence            34456677776655554433   21         223458899999999999999999875321       233321   


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc------------ccc-ccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL------------DKI-GIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~------------~~l-~~~~~~~~~~~~  291 (724)
                       .++....   .+.       .......+++......+.+|+|||++....-            ... ...+..   .+.
T Consensus       122 -~~~~~~~---~g~-------~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~---~d~  187 (495)
T TIGR01241       122 -SDFVEMF---VGV-------GASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVE---MDG  187 (495)
T ss_pred             -HHHHHHH---hcc-------cHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhh---hcc
Confidence             1121111   010       1122334444444456799999999653110            000 000000   011


Q ss_pred             CCCCCCcEEEEEecccchhhh----hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          292 NDDPRRCTIILTSRSRDLLCI----DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~~----~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .....+..||.||........    ...-...+.++..+.++-.++|+..+......+  ......+++.+.|.-
T Consensus       188 ~~~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~--~~~l~~la~~t~G~s  260 (495)
T TIGR01241       188 FGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAP--DVDLKAVARRTPGFS  260 (495)
T ss_pred             ccCCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCc--chhHHHHHHhCCCCC
Confidence            113344556666755432111    112345788888898888899988775332222  123457888888743

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.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.65  E-value=7.3e-05  Score=85.91  Aligned_cols=158  Identities=19%  Similarity=0.273  Sum_probs=93.0

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc-C---CCeEEEEEEecCCChHHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN-V---FDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~---F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ..+++||++++.++++.|......-+.++|++|+|||++|+.+++...... .   .++.+|..     +...    ++.
T Consensus       185 ~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l-----~~~~----lla  255 (758)
T PRK11034        185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL-----DIGS----LLA  255 (758)
T ss_pred             CCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec-----cHHH----Hhc
Confidence            456889999999999988765455667899999999999999998754321 1   13444421     1111    111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc----------cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL----------ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~----------~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                        +......  .+.....+...+.+.++.+|++|++....          +...+..++.         ....-+||.+|
T Consensus       256 --G~~~~Ge--~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L---------~~g~i~vIgAT  322 (758)
T PRK11034        256 --GTKYRGD--FEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL---------SSGKIRVIGST  322 (758)
T ss_pred             --ccchhhh--HHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHH---------hCCCeEEEecC
Confidence              1111111  22334455555554567899999997531          1111112221         22234455555


Q ss_pred             cccchh------hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          305 RSRDLL------CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       305 R~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      ......      .........+.+++.+.++..++++...
T Consensus       323 t~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        323 TYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             ChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHH
Confidence            443320      1112334689999999999999998765

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.65  E-value=0.00052  Score=73.58  Aligned_cols=166  Identities=23%  Similarity=0.260  Sum_probs=96.5

Q ss_pred             chHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCC
Q 004895          164 SRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSN  243 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~  243 (724)
                      .|.+...++++.+..... ++.|.|+-++||||+++.+.......     .++++.-+......-+.+..          
T Consensus        21 ~~~~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~-----~iy~~~~d~~~~~~~l~d~~----------   84 (398)
T COG1373          21 ERRKLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLLEE-----IIYINFDDLRLDRIELLDLL----------   84 (398)
T ss_pred             hHHhhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCCcc-----eEEEEecchhcchhhHHHHH----------
Confidence            344556666666543333 99999999999999997766655432     55555433211111101111          


Q ss_pred             chhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchh-----hhhcCCCc
Q 004895          244 DLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-----CIDMNSQK  318 (724)
Q Consensus       244 ~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-----~~~~~~~~  318 (724)
                             ...... ...++..++||.|.....|......+.+        ..+. +|++|+-+....     ....+...
T Consensus        85 -------~~~~~~-~~~~~~yifLDEIq~v~~W~~~lk~l~d--------~~~~-~v~itgsss~ll~~~~~~~L~GR~~  147 (398)
T COG1373          85 -------RAYIEL-KEREKSYIFLDEIQNVPDWERALKYLYD--------RGNL-DVLITGSSSSLLSKEISESLAGRGK  147 (398)
T ss_pred             -------HHHHHh-hccCCceEEEecccCchhHHHHHHHHHc--------cccc-eEEEECCchhhhccchhhhcCCCce
Confidence                   111111 1125689999999999999877566555        3344 788888876643     22234467


Q ss_pred             eEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          319 MFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       319 ~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      .+++.|||..|...+-...+    ..... +..-+-.-.+||.|-++..
T Consensus       148 ~~~l~PlSF~Efl~~~~~~~----~~~~~-~~~f~~Yl~~GGfP~~v~~  191 (398)
T COG1373         148 DLELYPLSFREFLKLKGEEI----EPSKL-ELLFEKYLETGGFPESVKA  191 (398)
T ss_pred             eEEECCCCHHHHHhhccccc----chhHH-HHHHHHHHHhCCCcHHHhC
Confidence            89999999999766533000    00011 1122223357899987654

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.65  E-value=0.00088  Score=74.20  Aligned_cols=159  Identities=14%  Similarity=0.125  Sum_probs=93.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      ..+.|+|..|+|||.|++.+++.......--.++|++.      .++..++...+...         ....+.+.+.  +
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yita------eef~~el~~al~~~---------~~~~f~~~y~--~  377 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSS------EEFTNEFINSIRDG---------KGDSFRRRYR--E  377 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH------HHHHHHHHHHHHhc---------cHHHHHHHhh--c
Confidence            45899999999999999999998754211123566654      34444554443211         1222333443  2


Q ss_pred             cEEEEEccccccc---ccc-ccccccCCCCcCCCCCCCCCcEEEEEecccch--------hhhhcCCCceEecCCCCHHH
Q 004895          262 RVLIILDNIWTKL---ELD-KIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL--------LCIDMNSQKMFWIDALSEEE  329 (724)
Q Consensus       262 r~LlVlDdv~~~~---~~~-~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v--------~~~~~~~~~~~~l~~L~~~e  329 (724)
                      -=+|||||+....   .|+ .+...+..+       ...+..|||||+...-        ........-.+++.+.+.+.
T Consensus       378 ~DLLlIDDIq~l~gke~tqeeLF~l~N~l-------~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~Et  450 (617)
T PRK14086        378 MDILLVDDIQFLEDKESTQEEFFHTFNTL-------HNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELET  450 (617)
T ss_pred             CCEEEEehhccccCCHHHHHHHHHHHHHH-------HhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHH
Confidence            3589999996542   222 121111110       2234568888886421        01223445688999999999


Q ss_pred             HHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          330 ALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       330 ~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      -.+++++++....-. --++++.-|++.+.+..-.+
T Consensus       451 R~aIL~kka~~r~l~-l~~eVi~yLa~r~~rnvR~L  485 (617)
T PRK14086        451 RIAILRKKAVQEQLN-APPEVLEFIASRISRNIREL  485 (617)
T ss_pred             HHHHHHHHHHhcCCC-CCHHHHHHHHHhccCCHHHH
Confidence            999999987533211 11567777777776654433

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.57  E-value=0.00016  Score=64.73  Aligned_cols=69  Identities=20%  Similarity=0.256  Sum_probs=41.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC-c
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK-R  262 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k-r  262 (724)
                      |.|+|++|+||||+|+.+++.....     ++.++.+...+.               .... .......+.+...... +
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~-----~~~i~~~~~~~~---------------~~~~-~~~~i~~~~~~~~~~~~~   59 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFP-----FIEIDGSELISS---------------YAGD-SEQKIRDFFKKAKKSAKP   59 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSE-----EEEEETTHHHTS---------------STTH-HHHHHHHHHHHHHHTSTS
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccc-----cccccccccccc---------------cccc-cccccccccccccccccc
Confidence            5799999999999999999987421     344443321100               0011 2223334444443333 7


Q ss_pred             EEEEEcccccc
Q 004895          263 VLIILDNIWTK  273 (724)
Q Consensus       263 ~LlVlDdv~~~  273 (724)
                      .+|++||++..
T Consensus        60 ~vl~iDe~d~l   70 (132)
T PF00004_consen   60 CVLFIDEIDKL   70 (132)
T ss_dssp             EEEEEETGGGT
T ss_pred             eeeeeccchhc
Confidence            99999999654

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 ....

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.55  E-value=0.0051  Score=59.62  Aligned_cols=194  Identities=19%  Similarity=0.244  Sum_probs=109.9

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe-cCCChHHHHHHHHHhhCCCCCCC--ch
Q 004895          169 FQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT-KNPDAQKIQGELASDLGMNFDSN--DL  245 (724)
Q Consensus       169 ~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~l~~~i~~~l~~~~~~~--~~  245 (724)
                      +..+...+ ..+.+++.++|.-|.|||++.+........    +.++-+.+. ...+...+...|+..+..+....  ..
T Consensus        40 l~~l~~~i-~d~qg~~~vtGevGsGKTv~~Ral~~s~~~----d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~  114 (269)
T COG3267          40 LLMLHAAI-ADGQGILAVTGEVGSGKTVLRRALLASLNE----DQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAV  114 (269)
T ss_pred             HHHHHHHH-hcCCceEEEEecCCCchhHHHHHHHHhcCC----CceEEEEecCcchhHHHHHHHHHHHhccCccchhHHH
Confidence            33443333 445579999999999999999955443332    122223333 33566778888888887632211  11


Q ss_pred             hHHHHHHHHHHHhcCCc-EEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEEEecccc--------hhhhhc
Q 004895          246 IYHRAKQLCQRLKKEKR-VLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD--------LLCIDM  314 (724)
Q Consensus       246 ~~~~~~~l~~~l~~~kr-~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~--------v~~~~~  314 (724)
                      .......+.....+++| ..+++||....  +.++.++.....    .. ....--+|+..-..+-        ......
T Consensus       115 ~e~~~~~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl----~~-~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~  189 (269)
T COG3267         115 LEQIDRELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNL----EE-DSSKLLSIVLIGQPKLRPRLRLPVLRELEQ  189 (269)
T ss_pred             HHHHHHHHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhh----cc-cccCceeeeecCCcccchhhchHHHHhhhh
Confidence            22233444555556777 99999998654  222222111100    00 0111112332222111        101111


Q ss_pred             CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCc--hhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          315 NSQKMFWIDALSEEEALQLFEKIVGESTKASDF--RPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       315 ~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l--~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      ...-.|++.|++.++...+++.+......++++  .+....|.....|.|.+|..++...
T Consensus       190 R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~A  249 (269)
T COG3267         190 RIDIRIELPPLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLATLA  249 (269)
T ss_pred             eEEEEEecCCcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHHHH
Confidence            122238999999999999999988644333332  4567889999999999998876543

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.54  E-value=0.00019  Score=75.33  Aligned_cols=83  Identities=17%  Similarity=0.282  Sum_probs=52.0

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCC-cCCCCCccccCCCCCcEEEcCCc-ccCCcccccCCCCCcE
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGI-RFSPLPSSLGRLINLQTLCLDGW-RLEDIAIVGQLKKLEI  624 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~~~~lp~~i~~l~~L~~L~L~~~-~l~~~~~~~~l~~L~~  624 (724)
                      .+.+++.|.+.  .+....+|.  +  -.+|+.|.+++| .++.+|..+.  .+|++|.+++| .+..++     .+|++
T Consensus        50 ~~~~l~~L~Is--~c~L~sLP~--L--P~sLtsL~Lsnc~nLtsLP~~LP--~nLe~L~Ls~Cs~L~sLP-----~sLe~  116 (426)
T PRK15386         50 EARASGRLYIK--DCDIESLPV--L--PNELTEITIENCNNLTTLPGSIP--EGLEKLTVCHCPEISGLP-----ESVRS  116 (426)
T ss_pred             HhcCCCEEEeC--CCCCcccCC--C--CCCCcEEEccCCCCcccCCchhh--hhhhheEccCcccccccc-----cccce
Confidence            46788888883  224444441  1  246888898875 3456776553  57889999888 454421     34777


Q ss_pred             EEccCCc---CcccchhhhcC
Q 004895          625 LSLRGAE---IKQLPLQIGQL  642 (724)
Q Consensus       625 L~l~~~~---i~~lp~~i~~l  642 (724)
                      |+++++.   +..+|.++..|
T Consensus       117 L~L~~n~~~~L~~LPssLk~L  137 (426)
T PRK15386        117 LEIKGSATDSIKNVPNGLTSL  137 (426)
T ss_pred             EEeCCCCCcccccCcchHhhe
Confidence            7777654   45677765544

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.54  E-value=0.0024  Score=68.76  Aligned_cols=181  Identities=17%  Similarity=0.202  Sum_probs=100.1

Q ss_pred             cccccchHHHHHHHHHHhc---C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          159 YNIFNSRKKIFQDVIEALK---D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ...+-|-++.+.++.+.+.   .         ...+-|.++|++|+|||.||+.++.+..+-       ++.++..    
T Consensus       189 f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vP-------f~~isAp----  257 (802)
T KOG0733|consen  189 FSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVP-------FLSISAP----  257 (802)
T ss_pred             hhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCc-------eEeecch----
Confidence            4456688888888777653   1         235678899999999999999999988753       3444332    


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc---ccc-----c-c-ccccCCCCcCCCCC-CC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL---ELD-----K-I-GIPYGDVDEKDKND-DP  295 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~---~~~-----~-l-~~~~~~~~~~~~~~-~~  295 (724)
                          +|+....    .+  .++.+..++..-.+.-++++++|+++...   +|.     . + ...+..++...... .+
T Consensus       258 ----eivSGvS----GE--SEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g  327 (802)
T KOG0733|consen  258 ----EIVSGVS----GE--SEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKG  327 (802)
T ss_pred             ----hhhcccC----cc--cHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCC
Confidence                2232221    11  34556677777666789999999997542   110     0 0 01111111111111 12


Q ss_pred             CCcEEEEEecccchh----hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          296 RRCTIILTSRSRDLL----CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       296 ~~s~ilvTtR~~~v~----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .+.-||-+|-.++..    .........|.|.--++..-.++++..+.+-.-+..+.  .++|++.+-|+-
T Consensus       328 ~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d--~~qlA~lTPGfV  396 (802)
T KOG0733|consen  328 DPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFD--FKQLAKLTPGFV  396 (802)
T ss_pred             CCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcC--HHHHHhcCCCcc
Confidence            334444444444332    12223345666776666666667776664322222222  456777666653

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.53  E-value=0.0011  Score=71.96  Aligned_cols=153  Identities=12%  Similarity=0.104  Sum_probs=88.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      .-+.|+|+.|+|||+|++.+++.....  --.+++++.      .++...+...+...         ....+...+.  .
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~--~~~v~yi~~------~~f~~~~~~~l~~~---------~~~~f~~~~~--~  202 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRES--GGKILYVRS------ELFTEHLVSAIRSG---------EMQRFRQFYR--N  202 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHc--CCCEEEeeH------HHHHHHHHHHHhcc---------hHHHHHHHcc--c
Confidence            568899999999999999999987643  233566653      34444555554321         1122333332  3


Q ss_pred             cEEEEEccccccccc----cccccccCCCCcCCCCCCCCCcEEEEEecccch-----h---hhhcCCCceEecCCCCHHH
Q 004895          262 RVLIILDNIWTKLEL----DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL-----L---CIDMNSQKMFWIDALSEEE  329 (724)
Q Consensus       262 r~LlVlDdv~~~~~~----~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v-----~---~~~~~~~~~~~l~~L~~~e  329 (724)
                      .-+|++||+......    +.+...+..+       ...|..||+||.....     .   .........+++.+++.++
T Consensus       203 ~dvLiIDDiq~l~~k~~~qeelf~l~N~l-------~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~  275 (445)
T PRK12422        203 VDALFIEDIEVFSGKGATQEEFFHTFNSL-------HTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEG  275 (445)
T ss_pred             CCEEEEcchhhhcCChhhHHHHHHHHHHH-------HHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHH
Confidence            458899998654221    1221111110       1134568888865321     0   1112334688999999999


Q ss_pred             HHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc
Q 004895          330 ALQLFEKIVGESTKASDFRPLAEEIVGKCGGL  361 (724)
Q Consensus       330 ~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl  361 (724)
                      -..++.+++..... .--+++..-|++.+.|.
T Consensus       276 r~~iL~~k~~~~~~-~l~~evl~~la~~~~~d  306 (445)
T PRK12422        276 LRSFLERKAEALSI-RIEETALDFLIEALSSN  306 (445)
T ss_pred             HHHHHHHHHHHcCC-CCCHHHHHHHHHhcCCC
Confidence            99999988753221 11145566666666644

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.53  E-value=0.00047  Score=77.32  Aligned_cols=205  Identities=15%  Similarity=0.128  Sum_probs=105.6

Q ss_pred             CcccccccchHHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec---CCChHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD-----DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK---NPDAQK  227 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~---~~~~~~  227 (724)
                      |.....++|.++.+..+..++..     ...+++.|+|++|+||||+++.++.....    +..-|++-..   ..+...
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~----~~~Ew~npv~~~~~~~~~~  155 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGI----QVQEWSNPTLPDFQKNDHK  155 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhh----HHHHHhhhhhhcccccccc
Confidence            56677889999999999888863     23457999999999999999999987532    2233422110   000111


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHH------hcCCcEEEEEccccccc-----ccccccc-ccCCCCcCCCCCCC
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRL------KKEKRVLIILDNIWTKL-----ELDKIGI-PYGDVDEKDKNDDP  295 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l------~~~kr~LlVlDdv~~~~-----~~~~l~~-~~~~~~~~~~~~~~  295 (724)
                      +...+.+++.........-..........+      ..+++.+|+||++.+..     .+..+.. .+..        .+
T Consensus       156 ~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~~~lq~lLr~~~~e--------~~  227 (637)
T TIGR00602       156 VTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVS--------IG  227 (637)
T ss_pred             cchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhHHHHHHHHHHHhhc--------CC
Confidence            111222222211110000000011111100      12467899999995432     1222212 1111        22


Q ss_pred             CCcEEEEEecccc---------hh------hhhc--CCCceEecCCCCHHHHHHHHHHHhCCCCC---CC---CchhHHH
Q 004895          296 RRCTIILTSRSRD---------LL------CIDM--NSQKMFWIDALSEEEALQLFEKIVGESTK---AS---DFRPLAE  352 (724)
Q Consensus       296 ~~s~ilvTtR~~~---------v~------~~~~--~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~---~~---~l~~~~~  352 (724)
                      .-.-|++||-+..         ..      ....  .....+.+.+++..+..+.+.+.+.....   ..   .-.+...
T Consensus       228 ~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p~~~~l~  307 (637)
T TIGR00602       228 RCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVE  307 (637)
T ss_pred             CceEEEEecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccCCHHHHH
Confidence            2234555663211         00      0001  12346899999999988888777642211   11   0135677


Q ss_pred             HHHHHhCCchhHHHHHHHHh
Q 004895          353 EIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       353 ~I~~~c~GlPLai~~~~~~l  372 (724)
                      .|+..++|--..+...-..+
T Consensus       308 ~I~~~s~GDiRsAIn~LQf~  327 (637)
T TIGR00602       308 LLCQGCSGDIRSAINSLQFS  327 (637)
T ss_pred             HHHHhCCChHHHHHHHHHHH
Confidence            88888888765544444443

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.52  E-value=0.0019  Score=67.60  Aligned_cols=146  Identities=12%  Similarity=0.142  Sum_probs=85.5

Q ss_pred             ccc-hHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhcc--------------------CCCeEEEEEE
Q 004895          162 FNS-RKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDN--------------------VFDKVVMAEI  219 (724)
Q Consensus       162 ~~g-R~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~~~~wv~v  219 (724)
                      ++| .+...+.+...+..++. ....++|+.|+||||+|+.+.+..-...                    |.|..+...-
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~   86 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPD   86 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccc
Confidence            445 67777788887776655 4568999999999999999988764221                    2222111111


Q ss_pred             ecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          220 TKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       220 s~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      +....+                      +.+..+.+.+.    .+.+-++|+|++....  ..+.+...+..        
T Consensus        87 ~~~i~i----------------------d~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEE--------  136 (329)
T PRK08058         87 GQSIKK----------------------DQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEE--------  136 (329)
T ss_pred             cccCCH----------------------HHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcC--------
Confidence            111111                      12222333221    2455689999986553  22333223322        


Q ss_pred             CCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHH
Q 004895          294 DPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKI  337 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~  337 (724)
                      ...++.+|++|.+.. +...-.+....+++.++++++..+.+.+.
T Consensus       137 Pp~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        137 PSGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             CCCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            334566666666543 32322445678999999999998888653

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.47  E-value=0.00037  Score=73.16  Aligned_cols=130  Identities=18%  Similarity=0.294  Sum_probs=72.9

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCC-cCCCCCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGI-RFSPLPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~~~~lp~~i~~l~~L~~L~  604 (724)
                      ..+.++|++++|.+..+|.  -.++|++|.+. +......+|.. +  ..+|+.|++++| .+..+|.+      |++|.
T Consensus        51 ~~~l~~L~Is~c~L~sLP~--LP~sLtsL~Ls-nc~nLtsLP~~-L--P~nLe~L~Ls~Cs~L~sLP~s------Le~L~  118 (426)
T PRK15386         51 ARASGRLYIKDCDIESLPV--LPNELTEITIE-NCNNLTTLPGS-I--PEGLEKLTVCHCPEISGLPES------VRSLE  118 (426)
T ss_pred             hcCCCEEEeCCCCCcccCC--CCCCCcEEEcc-CCCCcccCCch-h--hhhhhheEccCcccccccccc------cceEE
Confidence            3678899999998888883  22469999993 33333444432 2  257999999998 66677764      56666


Q ss_pred             cCCcccCCcccccCC-CCCcEEEccCCc-Cc--ccchhhhcC-CCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          605 LDGWRLEDIAIVGQL-KKLEILSLRGAE-IK--QLPLQIGQL-TRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       605 L~~~~l~~~~~~~~l-~~L~~L~l~~~~-i~--~lp~~i~~l-~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      ++++....   +..| .+|+.|.+.++. ..  .+|.   .| .+|++|++++|..+ .+|+. +.  .+|+.|+++.
T Consensus       119 L~~n~~~~---L~~LPssLk~L~I~~~n~~~~~~lp~---~LPsSLk~L~Is~c~~i-~LP~~-LP--~SLk~L~ls~  186 (426)
T PRK15386        119 IKGSATDS---IKNVPNGLTSLSINSYNPENQARIDN---LISPSLKTLSLTGCSNI-ILPEK-LP--ESLQSITLHI  186 (426)
T ss_pred             eCCCCCcc---cccCcchHhheecccccccccccccc---ccCCcccEEEecCCCcc-cCccc-cc--ccCcEEEecc
Confidence            66554322   1222 235555554321 11  1111   12 45667776665533 22221 11  3566666654

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.0044  Score=63.97  Aligned_cols=173  Identities=16%  Similarity=0.224  Sum_probs=97.2

Q ss_pred             HHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhcc-----------------CCCeEEEEEEecCCChHHH
Q 004895          167 KIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDN-----------------VFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       167 ~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~-----------------~F~~~~wv~vs~~~~~~~l  228 (724)
                      ...+.+...+..++.+ .+.++|+.|+||+++|..+++..-...                 |.| ..|+......     
T Consensus        11 ~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD-~~~i~~~p~~-----   84 (319)
T PRK08769         11 RAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPD-LQLVSFIPNR-----   84 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCC-EEEEecCCCc-----
Confidence            3455666666666654 588999999999999999988764321                 111 1122100000     


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL  302 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv  302 (724)
                             -+.+. ......+.+..+.+.+.    .+++-++|+|+++...  .-+.+.-.+..        ...++.+|+
T Consensus        85 -------~~~k~-~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE--------Pp~~~~fiL  148 (319)
T PRK08769         85 -------TGDKL-RTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEE--------PSPGRYLWL  148 (319)
T ss_pred             -------ccccc-cccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhC--------CCCCCeEEE
Confidence                   00000 00011223333433332    2466799999997653  22222222222        334566666


Q ss_pred             Eeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          303 TSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       303 TtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +|.+. .+...-.+....+.+.+++.+++.+.+... +   .+   ...+..++..++|.|+.+..+
T Consensus       149 ~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~-~---~~---~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        149 ISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQ-G---VS---ERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             EECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHc-C---CC---hHHHHHHHHHcCCCHHHHHHH
Confidence            66654 333332444578899999999999888753 1   11   233668899999999866443

>CHL00176 ftsH cell division protein; Validated

Probab=97.47  E-value=0.002  Score=72.96  Aligned_cols=175  Identities=16%  Similarity=0.176  Sum_probs=94.0

Q ss_pred             ccccchHHHHHH---HHHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHH
Q 004895          160 NIFNSRKKIFQD---VIEALKDD---------KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       160 ~~~~gR~~~~~~---l~~~L~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  227 (724)
                      ..+.|.++..++   +++.+...         ..+-+.++|++|+|||+||+.++.....       -|+.++..    +
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~-------p~i~is~s----~  251 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEV-------PFFSISGS----E  251 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC-------CeeeccHH----H
Confidence            445566554444   44444321         2346889999999999999999887632       13333211    1


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------------ccc-cccccCCCCcCCCCCC
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------------LDK-IGIPYGDVDEKDKNDD  294 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------------~~~-l~~~~~~~~~~~~~~~  294 (724)
                      +....   .+.       .......+........+++|++||++....            .+. +...+..   .+....
T Consensus       252 f~~~~---~g~-------~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~---~dg~~~  318 (638)
T CHL00176        252 FVEMF---VGV-------GAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTE---MDGFKG  318 (638)
T ss_pred             HHHHh---hhh-------hHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhh---hccccC
Confidence            11100   010       111233444444456789999999964310            100 1011100   011113


Q ss_pred             CCCcEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC
Q 004895          295 PRRCTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG  360 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G  360 (724)
                      ..+..||.||.........    ......+.++..+.++-.++++.++......+  ......+++.+.|
T Consensus       319 ~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~--d~~l~~lA~~t~G  386 (638)
T CHL00176        319 NKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSP--DVSLELIARRTPG  386 (638)
T ss_pred             CCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccch--hHHHHHHHhcCCC
Confidence            3455677777664432111    12235788888899999999988875422222  2345678888887

>PRK08118 topology modulation protein; Reviewed

Probab=97.47  E-value=6.9e-05  Score=70.06  Aligned_cols=35  Identities=29%  Similarity=0.460  Sum_probs=29.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc-cCCCeEEE
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED-NVFDKVVM  216 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~w  216 (724)
                      +.|.|+|++|+||||||+.+++..... -+||..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            368999999999999999999987653 45677776

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.46  E-value=0.00044  Score=62.44  Aligned_cols=90  Identities=23%  Similarity=0.176  Sum_probs=51.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      ..+.|+|++|+||||+|+.++.......  ..+++++.+........... ............ .......+.......+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   78 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILEEVLDQLL-LIIVGGKKASGS-GELRLRLALALARKLK   78 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCC--CCEEEECCEEccccCHHHHH-hhhhhccCCCCC-HHHHHHHHHHHHHhcC
Confidence            5789999999999999999998875432  24666666554332222111 111111111111 2223334444444333


Q ss_pred             cEEEEEcccccccc
Q 004895          262 RVLIILDNIWTKLE  275 (724)
Q Consensus       262 r~LlVlDdv~~~~~  275 (724)
                      ..+|++|++.....
T Consensus        79 ~~viiiDei~~~~~   92 (148)
T smart00382       79 PDVLILDEITSLLD   92 (148)
T ss_pred             CCEEEEECCcccCC
Confidence            48999999987643

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.

>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=97.45  E-value=0.0086  Score=62.92  Aligned_cols=203  Identities=20%  Similarity=0.249  Sum_probs=125.6

Q ss_pred             hHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHH-HHHHHHHhhccCCCeEEEEEEecC---CChHHHHHHHHHhhCCC-
Q 004895          165 RKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLV-KQIAKQVMEDNVFDKVVMAEITKN---PDAQKIQGELASDLGMN-  239 (724)
Q Consensus       165 R~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~~wv~vs~~---~~~~~l~~~i~~~l~~~-  239 (724)
                      |.+.+++|..||.+..-..|.|.||-|+||+.|+ .++.++.+      .++.++|.+-   .+-..++..++.++|.- 
T Consensus         1 R~e~~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~d~~L~~r~------~vL~IDC~~i~~ar~D~~~I~~lA~qvGY~P   74 (431)
T PF10443_consen    1 RKEAIEQLKSWLNENPNTFIVVQGPRGSGKRELVMDHVLKDRK------NVLVIDCDQIVKARGDAAFIKNLASQVGYFP   74 (431)
T ss_pred             CchHHHHHHHHHhcCCCeEEEEECCCCCCccHHHHHHHHhCCC------CEEEEEChHhhhccChHHHHHHHHHhcCCCc
Confidence            5677899999999888889999999999999999 77766543      2777877643   34455666666665421 


Q ss_pred             -----------------------CCCCchhHHHHHHHHH----HHh-------------------------cCCcEEEEE
Q 004895          240 -----------------------FDSNDLIYHRAKQLCQ----RLK-------------------------KEKRVLIIL  267 (724)
Q Consensus       240 -----------------------~~~~~~~~~~~~~l~~----~l~-------------------------~~kr~LlVl  267 (724)
                                             ..-....+.....+.+    .|+                         ..++=+||+
T Consensus        75 vFsw~nSiss~IDLa~qGltGqKaGfSes~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PVVVI  154 (431)
T PF10443_consen   75 VFSWMNSISSFIDLAVQGLTGQKAGFSESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPVVVI  154 (431)
T ss_pred             chHHHHHHHHHHHHHHhhccccccCCCCChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCEEEE
Confidence                                   1111111222211111    111                         022568999


Q ss_pred             ccccccc-----------cccccccccCCCCcCCCCCCCCCcEEEEEecccchh-----hhhcCCCceEecCCCCHHHHH
Q 004895          268 DNIWTKL-----------ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-----CIDMNSQKMFWIDALSEEEAL  331 (724)
Q Consensus       268 Ddv~~~~-----------~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-----~~~~~~~~~~~l~~L~~~e~~  331 (724)
                      |+.-...           +|...   +.         ..+=.+||++|-+....     .........+.|...+++.|.
T Consensus       155 dnF~~k~~~~~~iy~~laeWAa~---Lv---------~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak  222 (431)
T PF10443_consen  155 DNFLHKAEENDFIYDKLAEWAAS---LV---------QNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAK  222 (431)
T ss_pred             cchhccCcccchHHHHHHHHHHH---HH---------hcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHH
Confidence            9984431           24332   11         33456788888776543     122345678899999999999


Q ss_pred             HHHHHHhCCCCCC-------------------CCchhHHHHHHHHhCCchhHHHHHHHHhcC-CCH-HHHHHHHH
Q 004895          332 QLFEKIVGESTKA-------------------SDFRPLAEEIVGKCGGLPVALSTVANALKN-KSP-AIWKDALN  385 (724)
Q Consensus       332 ~Lf~~~~~~~~~~-------------------~~l~~~~~~I~~~c~GlPLai~~~~~~l~~-~~~-~~w~~~~~  385 (724)
                      .+...+.......                   .....-....++.+||=-.-+..+++.++. .++ +..+.+.+
T Consensus       223 ~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p~~Av~~iI~  297 (431)
T PF10443_consen  223 QYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESPEEAVEEIIS  297 (431)
T ss_pred             HHHHHHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            9999988532110                   123344567788888888888888888873 333 33444443

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 [].

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

Probab=97.45  E-value=0.00023  Score=65.96  Aligned_cols=102  Identities=24%  Similarity=0.230  Sum_probs=75.2

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC--ccccCCCCCcEEE
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP--SSLGRLINLQTLC  604 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp--~~i~~l~~L~~L~  604 (724)
                      +....+++++|++..++....++.|.+|.+  +++++..+.+..-.-+++|..|.|.+|++..+-  .-+..++.|+||.
T Consensus        42 d~~d~iDLtdNdl~~l~~lp~l~rL~tLll--~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Lt  119 (233)
T KOG1644|consen   42 DQFDAIDLTDNDLRKLDNLPHLPRLHTLLL--NNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLT  119 (233)
T ss_pred             cccceecccccchhhcccCCCccccceEEe--cCCcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceee
Confidence            455567888888877777777888888888  566666666665566778888888888887542  3456677888888


Q ss_pred             cCCcccCCc-----ccccCCCCCcEEEccCC
Q 004895          605 LDGWRLEDI-----AIVGQLKKLEILSLRGA  630 (724)
Q Consensus       605 L~~~~l~~~-----~~~~~l~~L~~L~l~~~  630 (724)
                      +-+|.++.-     --++.+++|++||+++-
T Consensus       120 ll~Npv~~k~~YR~yvl~klp~l~~LDF~kV  150 (233)
T KOG1644|consen  120 LLGNPVEHKKNYRLYVLYKLPSLRTLDFQKV  150 (233)
T ss_pred             ecCCchhcccCceeEEEEecCcceEeehhhh
Confidence            888887662     34778888888888764

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.44  E-value=0.0035  Score=67.50  Aligned_cols=140  Identities=18%  Similarity=0.282  Sum_probs=85.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ...-|.++|++|+|||-||+.|+|.....       |++|.+.    +++....   |     +  .+..+..++++-+.
T Consensus       544 ~PsGvLL~GPPGCGKTLlAKAVANEag~N-------FisVKGP----ELlNkYV---G-----E--SErAVR~vFqRAR~  602 (802)
T KOG0733|consen  544 APSGVLLCGPPGCGKTLLAKAVANEAGAN-------FISVKGP----ELLNKYV---G-----E--SERAVRQVFQRARA  602 (802)
T ss_pred             CCCceEEeCCCCccHHHHHHHHhhhccCc-------eEeecCH----HHHHHHh---h-----h--HHHHHHHHHHHhhc
Confidence            35668899999999999999999988654       5666543    3332221   1     1  34456677777777


Q ss_pred             CCcEEEEEccccccc-------cccccccccCCCCcCCCCCCCCCcEEEEEecccchhhhhc----CCCceEecCCCCHH
Q 004895          260 EKRVLIILDNIWTKL-------ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEE  328 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~-------~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~  328 (724)
                      ..+|+|+||.++...       .|..-+..-.-+..++......|.-||-.|-.+++...++    .-...+-++.-+.+
T Consensus       603 saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~  682 (802)
T KOG0733|consen  603 SAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAE  682 (802)
T ss_pred             CCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCCCHH
Confidence            889999999996531       1110000000011222333556777888887776531111    12245556667788


Q ss_pred             HHHHHHHHHhCC
Q 004895          329 EALQLFEKIVGE  340 (724)
Q Consensus       329 e~~~Lf~~~~~~  340 (724)
                      |-.++++.....
T Consensus       683 eR~~ILK~~tkn  694 (802)
T KOG0733|consen  683 ERVAILKTITKN  694 (802)
T ss_pred             HHHHHHHHHhcc
Confidence            888888888763

>PRK08181 transposase; Validated

Probab=97.43  E-value=0.0036  Score=63.06  Aligned_cols=79  Identities=22%  Similarity=0.199  Sum_probs=48.9

Q ss_pred             HHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHH
Q 004895          174 EALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQL  253 (724)
Q Consensus       174 ~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l  253 (724)
                      +|+.  ...-+.++|++|+|||.||..+.+....+  ...++|+++      .+++..+.....    ..     .....
T Consensus       101 ~~~~--~~~nlll~Gp~GtGKTHLa~Aia~~a~~~--g~~v~f~~~------~~L~~~l~~a~~----~~-----~~~~~  161 (269)
T PRK08181        101 SWLA--KGANLLLFGPPGGGKSHLAAAIGLALIEN--GWRVLFTRT------TDLVQKLQVARR----EL-----QLESA  161 (269)
T ss_pred             HHHh--cCceEEEEecCCCcHHHHHHHHHHHHHHc--CCceeeeeH------HHHHHHHHHHHh----CC-----cHHHH
Confidence            4554  33468999999999999999999987543  234566653      455555543321    11     12233


Q ss_pred             HHHHhcCCcEEEEEcccccc
Q 004895          254 CQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       254 ~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .+.+.  +.=||||||+...
T Consensus       162 l~~l~--~~dLLIIDDlg~~  179 (269)
T PRK08181        162 IAKLD--KFDLLILDDLAYV  179 (269)
T ss_pred             HHHHh--cCCEEEEeccccc
Confidence            44443  3459999999543

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

Probab=97.41  E-value=3.9e-05  Score=76.69  Aligned_cols=136  Identities=17%  Similarity=0.164  Sum_probs=81.6

Q ss_pred             CCCCceEEEcCCCcCCCCC-----ccccCCCCCcEEEcCCcccCCc------ccccCCCCCcEEEccCCcCc-----ccc
Q 004895          573 GTEELKVLDFTGIRFSPLP-----SSLGRLINLQTLCLDGWRLEDI------AIVGQLKKLEILSLRGAEIK-----QLP  636 (724)
Q Consensus       573 ~l~~L~~L~l~~~~~~~lp-----~~i~~l~~L~~L~L~~~~l~~~------~~~~~l~~L~~L~l~~~~i~-----~lp  636 (724)
                      .-+.|||+..+.|++..-|     ..+...+.|..+.+..|.|...      ..+..+++|+.|||+.|-++     .+.
T Consensus       155 ~~~~Lrv~i~~rNrlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~La  234 (382)
T KOG1909|consen  155 SKPKLRVFICGRNRLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALA  234 (382)
T ss_pred             CCcceEEEEeeccccccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHH
Confidence            3466788887777776433     2345556777777777776541      45677788888888887655     234


Q ss_pred             hhhhcCCCCCeEccCCCCCCcc----cChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          637 LQIGQLTRLQLLDLSNCSSLVV----IAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       637 ~~i~~l~~L~~L~l~~~~~l~~----~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ..+..+++|+.|++++|..-..    +....-...++|+.|.+.+|.....    ........+...+.|..|++++|++
T Consensus       235 kaL~s~~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNeIt~d----a~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  235 KALSSWPHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNEITRD----AALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             HHhcccchheeecccccccccccHHHHHHHHhccCCCCceeccCcchhHHH----HHHHHHHHHhcchhhHHhcCCcccc
Confidence            4556677788888887742111    1111123467788888877643211    0011112334467888888888877

>PRK08116 hypothetical protein; Validated

Probab=97.40  E-value=0.00055  Score=69.29  Aligned_cols=74  Identities=22%  Similarity=0.266  Sum_probs=47.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      ..+.++|..|+|||.||..+++....+  -..++++++      .+++..+..........      ....+.+.+.+ -
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~--~~~v~~~~~------~~ll~~i~~~~~~~~~~------~~~~~~~~l~~-~  179 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK--GVPVIFVNF------PQLLNRIKSTYKSSGKE------DENEIIRSLVN-A  179 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEH------HHHHHHHHHHHhccccc------cHHHHHHHhcC-C
Confidence            458899999999999999999998653  234666653      34555555444321111      12234444442 2


Q ss_pred             cEEEEEcccc
Q 004895          262 RVLIILDNIW  271 (724)
Q Consensus       262 r~LlVlDdv~  271 (724)
                       =||||||+.
T Consensus       180 -dlLviDDlg  188 (268)
T PRK08116        180 -DLLILDDLG  188 (268)
T ss_pred             -CEEEEeccc
Confidence             389999994

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

Probab=97.40  E-value=0.0004  Score=65.57  Aligned_cols=103  Identities=16%  Similarity=0.174  Sum_probs=69.0

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      |.....+||-++.++.+.-.-.+++.+-+.|.||+|+||||-+..+++..-....=+.+.=.+.|+...++-+-..|-.-
T Consensus        23 P~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~F  102 (333)
T KOG0991|consen   23 PSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMF  102 (333)
T ss_pred             chHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHH
Confidence            45566788999888888777678899999999999999999999999887543333455556666655544332222111


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .               +-.-.+..++.-.+|||..++.
T Consensus       103 A---------------Q~kv~lp~grhKIiILDEADSM  125 (333)
T KOG0991|consen  103 A---------------QKKVTLPPGRHKIIILDEADSM  125 (333)
T ss_pred             H---------------HhhccCCCCceeEEEeeccchh
Confidence            0               0011112356678999999765

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.40  E-value=0.0026  Score=69.66  Aligned_cols=178  Identities=13%  Similarity=0.114  Sum_probs=92.3

Q ss_pred             cccccchHHHHHHHHHHhc----------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHH
Q 004895          159 YNIFNSRKKIFQDVIEALK----------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l  228 (724)
                      ...+.|.+..++.+.+...          -...+-|.++|++|+|||.+|+.+++.....     .+-++.+.      +
T Consensus       227 ~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~-----~~~l~~~~------l  295 (489)
T CHL00195        227 ISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLP-----LLRLDVGK------L  295 (489)
T ss_pred             HHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEEhHH------h
Confidence            3456677766665554211          1234578899999999999999999987532     12222221      1


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----ccc------c-ccccCCCCcCCCCCCCCC
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----LDK------I-GIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----~~~------l-~~~~~~~~~~~~~~~~~~  297 (724)
                      .    .    .....  .......+.+......+++|++|+++....    ...      + ...+..+.     ....+
T Consensus       296 ~----~----~~vGe--se~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~-----~~~~~  360 (489)
T CHL00195        296 F----G----GIVGE--SESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLS-----EKKSP  360 (489)
T ss_pred             c----c----cccCh--HHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHh-----cCCCc
Confidence            1    1    01111  122334444444445789999999975311    000      0 00000000     01233


Q ss_pred             cEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          298 CTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       298 s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .-||.||.........    ......+.++.-+.++-.++|+.+.........-......+++.+.|+-
T Consensus       361 V~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfS  429 (489)
T CHL00195        361 VFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFS  429 (489)
T ss_pred             eEEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCC
Confidence            4466677655422111    1233567788888899999998877532211100122456666666654

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.39  E-value=0.0073  Score=62.47  Aligned_cols=176  Identities=10%  Similarity=0.103  Sum_probs=95.4

Q ss_pred             HHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCC-----C-C
Q 004895          169 FQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMN-----F-D  241 (724)
Q Consensus       169 ~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~-----~-~  241 (724)
                      -+.+...+..++. ..+.+.|+.|+||+++|..+++..--......       ..++.=.-.+.+...-..+     . .
T Consensus        11 ~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~-------~~Cg~C~sC~~~~~g~HPD~~~i~p~~   83 (325)
T PRK06871         11 YQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGD-------QPCGQCHSCHLFQAGNHPDFHILEPID   83 (325)
T ss_pred             HHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCC-------CCCCCCHHHHHHhcCCCCCEEEEcccc
Confidence            4556666665554 56778999999999999999987643211100       0000000011111000000     0 0


Q ss_pred             CCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEeccc-chhhhhc
Q 004895          242 SNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR-DLLCIDM  314 (724)
Q Consensus       242 ~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~-~v~~~~~  314 (724)
                      ......+.+..+.+.+.    .+++-++|+|+++...  ..+.+.-.+..        ...++.+|++|.+. .+...-.
T Consensus        84 ~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEE--------Pp~~~~fiL~t~~~~~llpTI~  155 (325)
T PRK06871         84 NKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEE--------PRPNTYFLLQADLSAALLPTIY  155 (325)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcC--------CCCCeEEEEEECChHhCchHHH
Confidence            00111223333444332    2566788999997653  23333222222        33455666666654 3433323


Q ss_pred             CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          315 NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       315 ~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      +....+.+.++++++..+.+.......      ...+...+..++|.|+.+
T Consensus       156 SRC~~~~~~~~~~~~~~~~L~~~~~~~------~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        156 SRCQTWLIHPPEEQQALDWLQAQSSAE------ISEILTALRINYGRPLLA  200 (325)
T ss_pred             hhceEEeCCCCCHHHHHHHHHHHhccC------hHHHHHHHHHcCCCHHHH
Confidence            445789999999999999888764211      223567788999999643

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=97.38  E-value=0.0029  Score=71.11  Aligned_cols=181  Identities=15%  Similarity=0.114  Sum_probs=109.5

Q ss_pred             ccccchH---HHHHHHHHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHH
Q 004895          160 NIFNSRK---KIFQDVIEALKDD---------KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       160 ~~~~gR~---~~~~~l~~~L~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  227 (724)
                      .++.|-+   +|++++++.|.++         -++=+.++|++|+|||-||++++-...+-       |+++|..     
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVP-------F~svSGS-----  378 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVP-------FFSVSGS-----  378 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCc-------eeeechH-----
Confidence            3445544   4566666777632         24668899999999999999999877653       5666643     


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccccc--------------cccccCCCCcCCCCC
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDK--------------IGIPYGDVDEKDKND  293 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~--------------l~~~~~~~~~~~~~~  293 (724)
                         ++++.+...      ....+..++..-+...++.+.+|+++....-..              +...+   .+.+...
T Consensus       379 ---EFvE~~~g~------~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll---~emDgf~  446 (774)
T KOG0731|consen  379 ---EFVEMFVGV------GASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLL---VEMDGFE  446 (774)
T ss_pred             ---HHHHHhccc------chHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHH---HHhcCCc
Confidence               223322211      122455666666667889999999865421110              00011   1112333


Q ss_pred             CCCCcEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          294 DPRRCTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ...+.-++-+|...++.+.+    ..-...+.++.=+...-.++|.-++.......+..++.+ |+...-|.+=|.
T Consensus       447 ~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~-~a~~t~gf~gad  521 (774)
T KOG0731|consen  447 TSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSK-LASLTPGFSGAD  521 (774)
T ss_pred             CCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHH-HHhcCCCCcHHH
Confidence            34445566667766664221    122356777777788888899988865444344456666 999998888554

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.37  E-value=0.012  Score=60.71  Aligned_cols=164  Identities=13%  Similarity=0.181  Sum_probs=94.9

Q ss_pred             HHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhc-------------------cCCCeEEEEEEecCCChHH
Q 004895          168 IFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMED-------------------NVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       168 ~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~  227 (724)
                      ..+++...+..++. ..+.++|+.|+||+++|..+++..--.                   .|.|. .|+.-..      
T Consensus        11 ~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~-~~i~p~~------   83 (319)
T PRK06090         11 VWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDL-HVIKPEK------   83 (319)
T ss_pred             HHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCE-EEEecCc------
Confidence            34556666655554 578899999999999999998875321                   12221 1221100      


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEE
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTII  301 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~il  301 (724)
                                   .......+.+..+.+.+.    .+++-++|+|+++...  ..+.+.-.+..        ...++.+|
T Consensus        84 -------------~~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE--------Pp~~t~fi  142 (319)
T PRK06090         84 -------------EGKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEE--------PAPNCLFL  142 (319)
T ss_pred             -------------CCCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcC--------CCCCeEEE
Confidence                         000001122233333331    2456799999997653  33333222222        33455555


Q ss_pred             EEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          302 LTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       302 vTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ++|.+. .+...-.+....+.+.+++.+++.+.+... +.   .     .+..++..++|.|+.+..+
T Consensus       143 L~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~-~~---~-----~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        143 LVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQ-GI---T-----VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             EEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHc-CC---c-----hHHHHHHHcCCCHHHHHHH
Confidence            555544 444333455678999999999999988764 11   1     2457889999999876543

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.37  E-value=0.002  Score=66.96  Aligned_cols=104  Identities=17%  Similarity=0.160  Sum_probs=68.3

Q ss_pred             HHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe-EEEEEEecC-CChHHHHHHHHHhhCCCCCCCch
Q 004895          169 FQDVIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK-VVMAEITKN-PDAQKIQGELASDLGMNFDSNDL  245 (724)
Q Consensus       169 ~~~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~~~~  245 (724)
                      ..++++.+.. ++-..+.|+|.+|+|||||++.+++..... +-+. ++|+.+.+. ..+.++.+.+...+.....+...
T Consensus       120 ~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~~i~~~-~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~  198 (380)
T PRK12608        120 SMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAAAVAAN-HPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPP  198 (380)
T ss_pred             hHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCH
Confidence            3446776652 344577999999999999999999987643 4454 467777765 46788888888777654332221


Q ss_pred             hH-----HHHHHHHHHH-hcCCcEEEEEcccccc
Q 004895          246 IY-----HRAKQLCQRL-KKEKRVLIILDNIWTK  273 (724)
Q Consensus       246 ~~-----~~~~~l~~~l-~~~kr~LlVlDdv~~~  273 (724)
                      ..     .......+++ .++++++||+|++...
T Consensus       199 ~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr~  232 (380)
T PRK12608        199 DEHIRVAELVLERAKRLVEQGKDVVILLDSLTRL  232 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHHH
Confidence            11     1122233333 3589999999999543

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

Probab=97.34  E-value=0.0048  Score=72.01  Aligned_cols=102  Identities=17%  Similarity=0.254  Sum_probs=60.5

Q ss_pred             cccchHHHHHHHHHHhcC-------C--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD-------D--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.++.++.+...+..       +  ...++.++|+.|+|||+||+.+++...     ...+.++.++.....    .
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~-----~~~~~~d~se~~~~~----~  525 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG-----VHLERFDMSEYMEKH----T  525 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc-----CCeEEEeCchhhhcc----c
Confidence            356888888887777651       1  234688999999999999999998762     335666665432211    1


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +...++......  ..+....+.+.+......+++||+++..
T Consensus       526 ~~~lig~~~gyv--g~~~~~~l~~~~~~~p~~VvllDEieka  565 (731)
T TIGR02639       526 VSRLIGAPPGYV--GFEQGGLLTEAVRKHPHCVLLLDEIEKA  565 (731)
T ss_pred             HHHHhcCCCCCc--ccchhhHHHHHHHhCCCeEEEEechhhc
Confidence            122223221110  0111233444554445679999999765

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.33  E-value=0.003  Score=60.88  Aligned_cols=178  Identities=16%  Similarity=0.208  Sum_probs=101.4

Q ss_pred             cccccchHHHHHH---HHHHhcC------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHH
Q 004895          159 YNIFNSRKKIFQD---VIEALKD------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQ  229 (724)
Q Consensus       159 ~~~~~gR~~~~~~---l~~~L~~------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~  229 (724)
                      .+.++|.++.+.+   |++.|.+      -..+-|..+|++|.|||.+|+.+++..++-       ++.+.    ..+++
T Consensus       120 ~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp-------~l~vk----at~li  188 (368)
T COG1223         120 LDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVP-------LLLVK----ATELI  188 (368)
T ss_pred             HhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCc-------eEEec----hHHHH
Confidence            4567787766543   5566653      357889999999999999999999987653       22221    11221


Q ss_pred             HHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc---ccccc-------ccccCCCCcCCCCCCCCCcE
Q 004895          230 GELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL---ELDKI-------GIPYGDVDEKDKNDDPRRCT  299 (724)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~---~~~~l-------~~~~~~~~~~~~~~~~~~s~  299 (724)
                         -+..|    +   ....+.++++.-.+.-+|++++|.++...   .++.+       ..++  +..+++...+.|..
T Consensus       189 ---GehVG----d---gar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNAL--LTelDgi~eneGVv  256 (368)
T COG1223         189 ---GEHVG----D---GARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNAL--LTELDGIKENEGVV  256 (368)
T ss_pred             ---HHHhh----h---HHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHH--HHhccCcccCCceE
Confidence               12222    1   23355666666666789999999986541   11111       1111  11122223455666


Q ss_pred             EEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc
Q 004895          300 IILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL  361 (724)
Q Consensus       300 ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl  361 (724)
                      .|-.|.+....  .........++..--+++|-.+++...+..-.-+-  ..-.+.++++.+|.
T Consensus       257 tIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv--~~~~~~~~~~t~g~  318 (368)
T COG1223         257 TIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPV--DADLRYLAAKTKGM  318 (368)
T ss_pred             EEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCcc--ccCHHHHHHHhCCC
Confidence            66666655543  11122234566666778888888888774221111  12255677777664

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

Probab=97.30  E-value=0.0026  Score=70.05  Aligned_cols=161  Identities=22%  Similarity=0.264  Sum_probs=92.1

Q ss_pred             cchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          163 NSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .|-++.+++|++.|.      .-+-+++.+|||+|+|||+|++.+++-...+     .+-+++++-.|..++-..=-..+
T Consensus       326 YGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al~Rk-----fvR~sLGGvrDEAEIRGHRRTYI  400 (782)
T COG0466         326 YGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKALGRK-----FVRISLGGVRDEAEIRGHRRTYI  400 (782)
T ss_pred             cCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHhCCC-----EEEEecCccccHHHhcccccccc
Confidence            388899999999885      2345799999999999999999999987543     34556667667665522111111


Q ss_pred             CCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc-cc-----cc---cccc-----cCC-CCcCCCCCCCCCcEEE
Q 004895          237 GMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL-EL-----DK---IGIP-----YGD-VDEKDKNDDPRRCTII  301 (724)
Q Consensus       237 ~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~-~~-----~~---l~~~-----~~~-~~~~~~~~~~~~s~il  301 (724)
                      |.      ......+.+.+.  +.++=|++||.++... ++     ..   +..|     |.+ +...  .-.-.....|
T Consensus       401 Ga------mPGrIiQ~mkka--~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev--~yDLS~VmFi  470 (782)
T COG0466         401 GA------MPGKIIQGMKKA--GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEV--PYDLSKVMFI  470 (782)
T ss_pred             cc------CChHHHHHHHHh--CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccC--ccchhheEEE
Confidence            11      011122222222  2466799999986541 10     00   0000     000 0000  0011122233


Q ss_pred             EEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      .|.-+-+ +..........+++.+.+++|-.++-+++.
T Consensus       471 aTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         471 ATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             eecCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence            4444333 333335666899999999999988887765

>PRK10536 hypothetical protein; Provisional

Probab=97.27  E-value=0.0011  Score=65.29  Aligned_cols=56  Identities=18%  Similarity=0.289  Sum_probs=41.8

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEE
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVM  216 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w  216 (724)
                      ...+.+|......++.++.+.  .++.+.|++|+|||+||..++.+.-..+.|+.++-
T Consensus        54 ~~~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         54 TSPILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             CccccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            345667888888888888653  49999999999999999999986432344554443

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.26  E-value=0.0071  Score=70.80  Aligned_cols=178  Identities=17%  Similarity=0.203  Sum_probs=96.6

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|.+..++.|.+.+.             -...+-+.++|++|+|||++|+.+++....  .     ++.++..   
T Consensus       452 ~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~--~-----fi~v~~~---  521 (733)
T TIGR01243       452 WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGA--N-----FIAVRGP---  521 (733)
T ss_pred             hhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCC--C-----EEEEehH---
Confidence            3456677777666665542             123456889999999999999999997642  1     2333221   


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc----------ccccc-ccCCCCcCCCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL----------DKIGI-PYGDVDEKDKNDD  294 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~----------~~l~~-~~~~~~~~~~~~~  294 (724)
                       ++    +..    ...+  .+.....++.......+.+|++|+++....-          +.+.. .+..   .+....
T Consensus       522 -~l----~~~----~vGe--se~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~---ldg~~~  587 (733)
T TIGR01243       522 -EI----LSK----WVGE--SEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTE---MDGIQE  587 (733)
T ss_pred             -HH----hhc----ccCc--HHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHH---hhcccC
Confidence             11    111    1111  2234455555555567899999999643110          00000 0000   001112


Q ss_pred             CCCcEEEEEecccchhh-hhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          295 PRRCTIILTSRSRDLLC-IDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~~-~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ..+.-||.||....... ...   .....+.++..+.++-.++|+.........++  .....+++.|.|+-
T Consensus       588 ~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~--~~l~~la~~t~g~s  657 (733)
T TIGR01243       588 LSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAED--VDLEELAEMTEGYT  657 (733)
T ss_pred             CCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCcc--CCHHHHHHHcCCCC
Confidence            33455666776554321 111   23457888888888888898876543222221  12456777787754

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.26  E-value=0.0062  Score=61.62  Aligned_cols=58  Identities=22%  Similarity=0.332  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          166 KKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       166 ~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      .+.++++..++..+  .-+.+.|++|+|||++|+.+++...     ...+.++++...+..+++.
T Consensus         8 ~~l~~~~l~~l~~g--~~vLL~G~~GtGKT~lA~~la~~lg-----~~~~~i~~~~~~~~~dllg   65 (262)
T TIGR02640         8 KRVTSRALRYLKSG--YPVHLRGPAGTGKTTLAMHVARKRD-----RPVMLINGDAELTTSDLVG   65 (262)
T ss_pred             HHHHHHHHHHHhcC--CeEEEEcCCCCCHHHHHHHHHHHhC-----CCEEEEeCCccCCHHHHhh
Confidence            34455566655443  2456899999999999999987442     1245666666666555543

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).

>PHA00729 NTP-binding motif containing protein

Probab=97.25  E-value=0.0017  Score=62.81  Aligned_cols=36  Identities=25%  Similarity=0.444  Sum_probs=28.7

Q ss_pred             HHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          171 DVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       171 ~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+++.+...+...|.|+|.+|+||||||..+.+...
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            345555555666889999999999999999999753

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.24  E-value=0.0041  Score=65.59  Aligned_cols=135  Identities=16%  Similarity=0.198  Sum_probs=83.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ....+.|+|..|.|||.|++.+.+.......=..+++++.      ++...+++..+..         .......+.. +
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~s------e~f~~~~v~a~~~---------~~~~~Fk~~y-~  175 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTS------EDFTNDFVKALRD---------NEMEKFKEKY-S  175 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccH------HHHHHHHHHHHHh---------hhHHHHHHhh-c
Confidence            4778999999999999999999999875322123555532      3444444444321         2234444444 2


Q ss_pred             CCcEEEEEcccccccc---cc-ccccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCH
Q 004895          260 EKRVLIILDNIWTKLE---LD-KIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSE  327 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~---~~-~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~  327 (724)
                        -=++++||++-...   |+ .+...+..+       ...|-.||+|++...-.        .......-.+++.+.+.
T Consensus       176 --~dlllIDDiq~l~gk~~~qeefFh~FN~l-------~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~  246 (408)
T COG0593         176 --LDLLLIDDIQFLAGKERTQEEFFHTFNAL-------LENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDD  246 (408)
T ss_pred             --cCeeeechHhHhcCChhHHHHHHHHHHHH-------HhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCH
Confidence              23899999976432   22 121111110       22344799999765421        11234456899999999


Q ss_pred             HHHHHHHHHHhC
Q 004895          328 EEALQLFEKIVG  339 (724)
Q Consensus       328 ~e~~~Lf~~~~~  339 (724)
                      +.-..++.+++.
T Consensus       247 e~r~aiL~kka~  258 (408)
T COG0593         247 ETRLAILRKKAE  258 (408)
T ss_pred             HHHHHHHHHHHH
Confidence            999999999775

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.23  E-value=0.0038  Score=61.28  Aligned_cols=178  Identities=17%  Similarity=0.190  Sum_probs=95.8

Q ss_pred             cccchHHHHHHHHHHhc----------C--CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHH
Q 004895          161 IFNSRKKIFQDVIEALK----------D--DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~----------~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l  228 (724)
                      .+.|-+..++.|.+...          .  ...+-|.++|++|.||+.||+.|+.....       -|++||..    ++
T Consensus       134 DVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnS-------TFFSvSSS----DL  202 (439)
T KOG0739|consen  134 DVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANS-------TFFSVSSS----DL  202 (439)
T ss_pred             hhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhcCC-------ceEEeehH----HH
Confidence            34455555555555532          1  23578899999999999999999987653       24555543    23


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc---------cccccccccCCCCcCCCCCCCCCcE
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL---------ELDKIGIPYGDVDEKDKNDDPRRCT  299 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~---------~~~~l~~~~~~~~~~~~~~~~~~s~  299 (724)
                      ....   +|     +  .+.++..|++.-+..++.+|++|.++...         .-..+..-+. ++.+..-.+..|.-
T Consensus       203 vSKW---mG-----E--SEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKTEfL-VQMqGVG~d~~gvL  271 (439)
T KOG0739|consen  203 VSKW---MG-----E--SEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFL-VQMQGVGNDNDGVL  271 (439)
T ss_pred             HHHH---hc-----c--HHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHH-HhhhccccCCCceE
Confidence            2222   11     1  34566777777777899999999996431         1111110000 00000001345556


Q ss_pred             EEEEecccchhhhhc--CCCceEecCCCCHHHHHH-HHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          300 IILTSRSRDLLCIDM--NSQKMFWIDALSEEEALQ-LFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       300 ilvTtR~~~v~~~~~--~~~~~~~l~~L~~~e~~~-Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      |+-.|..+-+.....  .....|- =||.+..|+. +|+-+.|... ..-.++..+++.++..|+-
T Consensus       272 VLgATNiPw~LDsAIRRRFekRIY-IPLPe~~AR~~MF~lhlG~tp-~~LT~~d~~eL~~kTeGyS  335 (439)
T KOG0739|consen  272 VLGATNIPWVLDSAIRRRFEKRIY-IPLPEAHARARMFKLHLGDTP-HVLTEQDFKELARKTEGYS  335 (439)
T ss_pred             EEecCCCchhHHHHHHHHhhccee-ccCCcHHHhhhhheeccCCCc-cccchhhHHHHHhhcCCCC
Confidence            666666654431111  1111222 2566666665 5655555332 2222455677888887754

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.23  E-value=0.0023  Score=59.43  Aligned_cols=137  Identities=18%  Similarity=0.224  Sum_probs=73.9

Q ss_pred             chHHHHHHHHHHhcCCCcc-EEEEEcCCCCcHHHHHHHHHHHHhhccCC------------------CeEEEEEEecC--
Q 004895          164 SRKKIFQDVIEALKDDKLN-IIGVCGMGGVGKTTLVKQIAKQVMEDNVF------------------DKVVMAEITKN--  222 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~-vi~I~G~gGiGKTtLa~~v~~~~~~~~~F------------------~~~~wv~vs~~--  222 (724)
                      |.++..+.|.+.+..++.+ .+.++|+.|+||+++|..+++..-.....                  .-+.|+.-.+.  
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~   80 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKK   80 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSS
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccc
Confidence            5567777787777766654 67999999999999999999876432211                  11333322221  


Q ss_pred             -CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcE
Q 004895          223 -PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCT  299 (724)
Q Consensus       223 -~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~  299 (724)
                       ...+++ +++.+.+.....                 .+++-++|+||++...  ..+.+.-.+..        ....+.
T Consensus        81 ~i~i~~i-r~i~~~~~~~~~-----------------~~~~KviiI~~ad~l~~~a~NaLLK~LEe--------pp~~~~  134 (162)
T PF13177_consen   81 SIKIDQI-REIIEFLSLSPS-----------------EGKYKVIIIDEADKLTEEAQNALLKTLEE--------PPENTY  134 (162)
T ss_dssp             SBSHHHH-HHHHHHCTSS-T-----------------TSSSEEEEEETGGGS-HHHHHHHHHHHHS--------TTTTEE
T ss_pred             hhhHHHH-HHHHHHHHHHHh-----------------cCCceEEEeehHhhhhHHHHHHHHHHhcC--------CCCCEE
Confidence             222222 233333322111                 1356799999998752  34444333333        445788


Q ss_pred             EEEEecccc-hhhhhcCCCceEecCCCC
Q 004895          300 IILTSRSRD-LLCIDMNSQKMFWIDALS  326 (724)
Q Consensus       300 ilvTtR~~~-v~~~~~~~~~~~~l~~L~  326 (724)
                      +|++|.+.. +...-.+....+.+.++|
T Consensus       135 fiL~t~~~~~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  135 FILITNNPSKILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             EEEEES-GGGS-HHHHTTSEEEEE----
T ss_pred             EEEEECChHHChHHHHhhceEEecCCCC
Confidence            888888765 333334445677776664

...

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

Probab=97.21  E-value=3.2e-05  Score=75.49  Aligned_cols=175  Identities=21%  Similarity=0.138  Sum_probs=117.1

Q ss_pred             cCceEEeccCCCccc--CCCc-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCc-CCC--CCccccCCCCC
Q 004895          527 KGPIAISLPYRDIQE--LPER-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-FSP--LPSSLGRLINL  600 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~--~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~-~~~--lp~~i~~l~~L  600 (724)
                      .+++|++++...++.  +... ..|.+|+.|.+.  +.....-.-..+..-.+|+.|++++|. +++  +---+.++..|
T Consensus       185 sRlq~lDLS~s~it~stl~~iLs~C~kLk~lSlE--g~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~ll~~scs~L  262 (419)
T KOG2120|consen  185 SRLQHLDLSNSVITVSTLHGILSQCSKLKNLSLE--GLRLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQLLLSSCSRL  262 (419)
T ss_pred             hhhHHhhcchhheeHHHHHHHHHHHHhhhhcccc--ccccCcHHHHHHhccccceeeccccccccchhHHHHHHHhhhhH
Confidence            357777777666632  2221 267777777772  222111111224455789999999875 342  22345788899


Q ss_pred             cEEEcCCcccCCc---ccccCC-CCCcEEEccCCc----CcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcE
Q 004895          601 QTLCLDGWRLEDI---AIVGQL-KKLEILSLRGAE----IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEE  672 (724)
Q Consensus       601 ~~L~L~~~~l~~~---~~~~~l-~~L~~L~l~~~~----i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~  672 (724)
                      ..|+|++|.+..+   -.+... ++|.-|+++|+.    .+.+..-..++++|.+|+|+.|..++.--...+.+++-|++
T Consensus       263 ~~LNlsWc~l~~~~Vtv~V~hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~  342 (419)
T KOG2120|consen  263 DELNLSWCFLFTEKVTVAVAHISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQH  342 (419)
T ss_pred             hhcCchHhhccchhhhHHHhhhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchhee
Confidence            9999999986652   112222 478889999973    22333345689999999999988776644456789999999


Q ss_pred             EEccCCCCccccccCCccchHHhhcCCCCCcEEEeecc
Q 004895          673 LYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVR  710 (724)
Q Consensus       673 L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n  710 (724)
                      |.++.|+.       ..|..+-++...+.|..|++.+.
T Consensus       343 lSlsRCY~-------i~p~~~~~l~s~psl~yLdv~g~  373 (419)
T KOG2120|consen  343 LSLSRCYD-------IIPETLLELNSKPSLVYLDVFGC  373 (419)
T ss_pred             eehhhhcC-------CChHHeeeeccCcceEEEEeccc
Confidence            99999863       33556678888899999998765

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.20  E-value=0.01  Score=61.93  Aligned_cols=164  Identities=13%  Similarity=0.170  Sum_probs=95.5

Q ss_pred             HHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhc--------------------cCCCeEEEEEEecCCChH
Q 004895          168 IFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMED--------------------NVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       168 ~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~  226 (724)
                      .-+++...+..++ ...+.+.|+.|+||+++|..++...--.                    .|.|. .++.-...    
T Consensus        10 ~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~-~~i~p~~~----   84 (334)
T PRK07993         10 DYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDY-YTLTPEKG----   84 (334)
T ss_pred             HHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCE-EEEecccc----
Confidence            3456667666555 4567799999999999999998876321                    12221 11110000    


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEE
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTI  300 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~i  300 (724)
                                     ......+.+..+.+.+.    .+++-++|+|+++...  .-+.+.-.+..        ...++.+
T Consensus        85 ---------------~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE--------Pp~~t~f  141 (334)
T PRK07993         85 ---------------KSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEE--------PPENTWF  141 (334)
T ss_pred             ---------------cccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcC--------CCCCeEE
Confidence                           00011223333444332    2567799999997653  23333222222        3345566


Q ss_pred             EEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          301 ILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       301 lvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      |++|.+. .+...-.+..+.+.+.+++.+++.+.+....+   .+   .+.+..++..++|.|..+
T Consensus       142 iL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~---~~---~~~a~~~~~la~G~~~~A  201 (334)
T PRK07993        142 FLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVT---MS---QDALLAALRLSAGAPGAA  201 (334)
T ss_pred             EEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccC---CC---HHHHHHHHHHcCCCHHHH
Confidence            6666554 34333244456889999999999988865422   11   334678899999999644

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.0057  Score=66.81  Aligned_cols=180  Identities=12%  Similarity=0.177  Sum_probs=91.8

Q ss_pred             cccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      .....+-|-++.+.+|-+...             -...+-|..+|++|+|||++|+.+++.....       |+.++.. 
T Consensus       431 v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n-------Flsvkgp-  502 (693)
T KOG0730|consen  431 VSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMN-------FLSVKGP-  502 (693)
T ss_pred             CChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCC-------eeeccCH-
Confidence            334455566665555554432             1456788999999999999999999987643       3444332 


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccccc---------ccc-cccCCCCcCCCCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELD---------KIG-IPYGDVDEKDKND  293 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~---------~l~-~~~~~~~~~~~~~  293 (724)
                         +++...        -.+  .+..+..++..-++--+++|+||.++....-.         .+. ..+.   ..+...
T Consensus       503 ---EL~sk~--------vGe--SEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLt---EmDG~e  566 (693)
T KOG0730|consen  503 ---ELFSKY--------VGE--SERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLT---EMDGLE  566 (693)
T ss_pred             ---HHHHHh--------cCc--hHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHH---Hccccc
Confidence               221111        111  23344555555555567999999986542111         000 0000   011111


Q ss_pred             CCCCcEEEEEecccchh-hhhcC---CCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          294 DPRRCTIILTSRSRDLL-CIDMN---SQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~v~-~~~~~---~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ...+.-||-.|-.++.. ...+.   ....+.++.=+.+.-.++|+.++....-.++  -...+|++++.|.-
T Consensus       567 ~~k~V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~--vdl~~La~~T~g~S  637 (693)
T KOG0730|consen  567 ALKNVLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSED--VDLEELAQATEGYS  637 (693)
T ss_pred             ccCcEEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCcc--ccHHHHHHHhccCC
Confidence            22333344444444322 11122   2345555555555666788888754332222  12345566555543

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.19  E-value=0.0053  Score=68.58  Aligned_cols=49  Identities=18%  Similarity=0.272  Sum_probs=39.8

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .....++|.+..++.+...+......-+.|+|++|+|||++|+.+++..
T Consensus        62 ~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~  110 (531)
T TIGR02902        62 KSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEA  110 (531)
T ss_pred             CCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHh
Confidence            3455688999999988877765555667899999999999999998764

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.

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

Probab=97.17  E-value=0.0004  Score=69.66  Aligned_cols=162  Identities=20%  Similarity=0.266  Sum_probs=110.2

Q ss_pred             cCCCccEEEEecccccccc--cchhhhcCCCCceEEEcCCCcCCCC--------------CccccCCCCCcEEEcCCccc
Q 004895          547 ECPQLKLFLLFAKYDSTLQ--ISDHFFEGTEELKVLDFTGIRFSPL--------------PSSLGRLINLQTLCLDGWRL  610 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~--~~~~~~~~l~~L~~L~l~~~~~~~l--------------p~~i~~l~~L~~L~L~~~~l  610 (724)
                      .+|+|++|+++.+......  .....++++..|+.|.|.+|.+...              ...+++-..||++...+|.+
T Consensus        90 ~~~~L~~ldLSDNA~G~~g~~~l~~ll~s~~~L~eL~L~N~Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~rNrl  169 (382)
T KOG1909|consen   90 GCPKLQKLDLSDNAFGPKGIRGLEELLSSCTDLEELYLNNCGLGPEAGGRLGRALFELAVNKKAASKPKLRVFICGRNRL  169 (382)
T ss_pred             cCCceeEeeccccccCccchHHHHHHHHhccCHHHHhhhcCCCChhHHHHHHHHHHHHHHHhccCCCcceEEEEeecccc
Confidence            6778888888543332222  2234567788899999999987621              12345567899999999998


Q ss_pred             CC-c-----ccccCCCCCcEEEccCCcCc-----ccchhhhcCCCCCeEccCCCCCCccc----ChHHhhCCCCCcEEEc
Q 004895          611 ED-I-----AIVGQLKKLEILSLRGAEIK-----QLPLQIGQLTRLQLLDLSNCSSLVVI----APNVISKLSRLEELYM  675 (724)
Q Consensus       611 ~~-~-----~~~~~l~~L~~L~l~~~~i~-----~lp~~i~~l~~L~~L~l~~~~~l~~~----~~~~i~~l~~L~~L~l  675 (724)
                      .+ +     ..+...+.|+.+.++.|.|.     -+-..+.++++|+.|+|..|. ++.-    ....+..+++|+.|++
T Consensus       170 en~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNt-ft~egs~~LakaL~s~~~L~El~l  248 (382)
T KOG1909|consen  170 ENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNT-FTLEGSVALAKALSSWPHLRELNL  248 (382)
T ss_pred             ccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccch-hhhHHHHHHHHHhcccchheeecc
Confidence            76 2     45677789999999999765     224567899999999999853 3321    1234678889999999


Q ss_pred             cCCCCccccccCCccchHHhhc-CCCCCcEEEeeccccc
Q 004895          676 GDSFSQWDKVEGGSNASLAELK-GLSKLTTLEIDVRDAE  713 (724)
Q Consensus       676 ~~~~~~~~~~~~~~~~~l~~L~-~L~~L~~L~l~~n~~~  713 (724)
                      ++|.....    ........+. ..+.|+.|.+.+|.++
T Consensus       249 ~dcll~~~----Ga~a~~~al~~~~p~L~vl~l~gNeIt  283 (382)
T KOG1909|consen  249 GDCLLENE----GAIAFVDALKESAPSLEVLELAGNEIT  283 (382)
T ss_pred             cccccccc----cHHHHHHHHhccCCCCceeccCcchhH
Confidence            99853222    1112223332 3579999999999753

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

Probab=97.14  E-value=3.9e-05  Score=66.32  Aligned_cols=75  Identities=17%  Similarity=0.230  Sum_probs=37.5

Q ss_pred             cccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchh
Q 004895          564 LQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQ  638 (724)
Q Consensus       564 ~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~  638 (724)
                      ...|..+-..++.+..|++++|.+..+|..+..++.||.|+++.|.+.. |.-+..|.+|-+|+..+|.+..+|-.
T Consensus        66 k~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~~L~~l~~Lds~~na~~eid~d  141 (177)
T KOG4579|consen   66 KKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFNPLNAEPRVIAPLIKLDMLDSPENARAEIDVD  141 (177)
T ss_pred             hhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccCccccchHHHHHHHhHHHhcCCCCccccCcHH
Confidence            3344444444445555555555555555555555555555555555443 33444455555555555544444443

>PRK07261 topology modulation protein; Provisional

Probab=97.13  E-value=0.0016  Score=61.26  Aligned_cols=34  Identities=24%  Similarity=0.410  Sum_probs=25.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhc-cCCCeEEE
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMED-NVFDKVVM  216 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~w  216 (724)
                      .|.|+|++|+||||||+.+....... -+.|...|
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~   36 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHF   36 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEe
Confidence            58899999999999999998775431 23455555

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.11  E-value=0.019  Score=59.96  Aligned_cols=103  Identities=17%  Similarity=0.214  Sum_probs=61.1

Q ss_pred             HHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecc-cchhhhhcCCCceEe
Q 004895          249 RAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS-RDLLCIDMNSQKMFW  321 (724)
Q Consensus       249 ~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~-~~v~~~~~~~~~~~~  321 (724)
                      .+..+.+.+.    .+++-++|+|+++...  ..+.+...+..        ...++.+|++|.+ ..+...-.+....+.
T Consensus       116 qiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE--------Pp~~t~fiL~t~~~~~LLpTI~SRcq~i~  187 (342)
T PRK06964        116 QVRALLDFCGVGTHRGGARVVVLYPAEALNVAAANALLKTLEE--------PPPGTVFLLVSARIDRLLPTILSRCRQFP  187 (342)
T ss_pred             HHHHHHHHhccCCccCCceEEEEechhhcCHHHHHHHHHHhcC--------CCcCcEEEEEECChhhCcHHHHhcCEEEE
Confidence            3444444442    2456689999997653  33443333322        3445555555554 444333234457899


Q ss_pred             cCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          322 IDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       322 l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +.+++.++..+.+... +.    +.    ...++..++|.|+.+..+
T Consensus       188 ~~~~~~~~~~~~L~~~-~~----~~----~~~~l~~~~Gsp~~Al~~  225 (342)
T PRK06964        188 MTVPAPEAAAAWLAAQ-GV----AD----ADALLAEAGGAPLAALAL  225 (342)
T ss_pred             ecCCCHHHHHHHHHHc-CC----Ch----HHHHHHHcCCCHHHHHHH
Confidence            9999999999988775 21    11    234678899999755433

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=97.09  E-value=0.0043  Score=67.47  Aligned_cols=192  Identities=15%  Similarity=0.198  Sum_probs=110.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+.....|...+..++. .--...|+-|+||||+|+.++.-.--..      | .....++.=...++|..
T Consensus        12 P~~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~------~-~~~ePC~~C~~Ck~I~~   84 (515)
T COG2812          12 PKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCEN------G-PTAEPCGKCISCKEINE   84 (515)
T ss_pred             cccHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCC------C-CCCCcchhhhhhHhhhc
Confidence            34456678999999999998876553 4556789999999999999988763221      1 11111221122223322


Q ss_pred             hhCCC---CCC-CchhHHHHHHHHHHHh----cCCcEEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEE-E
Q 004895          235 DLGMN---FDS-NDLIYHRAKQLCQRLK----KEKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIIL-T  303 (724)
Q Consensus       235 ~l~~~---~~~-~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilv-T  303 (724)
                      .-..+   .+. .....+....+.+...    .++.-+.|+|+|.-.  ..|+.+.--+..        .....+.|+ |
T Consensus        85 g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEE--------PP~hV~FIlAT  156 (515)
T COG2812          85 GSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEE--------PPSHVKFILAT  156 (515)
T ss_pred             CCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhccccc--------CccCeEEEEec
Confidence            21000   000 0001222334444332    345569999999654  345554333322        233445444 4


Q ss_pred             ecccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          304 SRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      |-...+...-.+..+.|.++.++.++....+...+..+.-..+ ++....|++..+|...
T Consensus       157 Te~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~e-~~aL~~ia~~a~Gs~R  215 (515)
T COG2812         157 TEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIE-EDALSLIARAAEGSLR  215 (515)
T ss_pred             CCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHcCCChh
Confidence            4445554444566789999999999999999988864433322 4556667777777544

>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=97.06  E-value=0.0031  Score=61.75  Aligned_cols=37  Identities=27%  Similarity=0.400  Sum_probs=29.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      -.++|+|..|+|||||+..+.....  +.|+.+++++-.
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~--~~f~~I~l~t~~   50 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLR--HKFDHIFLITPE   50 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhc--ccCCEEEEEecC
Confidence            3678999999999999999998765  458777777543

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.01  E-value=0.012  Score=69.06  Aligned_cols=176  Identities=14%  Similarity=0.145  Sum_probs=94.5

Q ss_pred             cccccchHHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALKD-------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|.++.++++.+.+.-             ...+-+.++|++|+|||+||+.+++.....     .+.++.+     
T Consensus       177 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~-----~i~i~~~-----  246 (733)
T TIGR01243       177 YEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY-----FISINGP-----  246 (733)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCe-----EEEEecH-----
Confidence            44577999988888776531             234578899999999999999999876421     2223221     


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~  292 (724)
                       ++.    ..    ....  .......+++......+.+|+||++.....             ...+...+..      .
T Consensus       247 -~i~----~~----~~g~--~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~------l  309 (733)
T TIGR01243       247 -EIM----SK----YYGE--SEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDG------L  309 (733)
T ss_pred             -HHh----cc----cccH--HHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhc------c
Confidence             111    10    0001  122334444444445678999999864311             0111111110      0


Q ss_pred             CCCCCcEEEE-Eecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          293 DDPRRCTIIL-TSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       293 ~~~~~s~ilv-TtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                       ...+..++| ||....-.....    .....+.+...+.++-.++++.........+  ......+++.+.|.--+
T Consensus       310 -~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~--d~~l~~la~~t~G~~ga  383 (733)
T TIGR01243       310 -KGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAE--DVDLDKLAEVTHGFVGA  383 (733)
T ss_pred             -ccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCcc--ccCHHHHHHhCCCCCHH
Confidence             122333444 444332111101    1234677888888888888886553222111  12356788888887543

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.

>PRK04132 replication factor C small subunit; Provisional

Probab=97.00  E-value=0.011  Score=68.48  Aligned_cols=157  Identities=11%  Similarity=0.052  Sum_probs=95.2

Q ss_pred             Ec--CCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEE
Q 004895          187 CG--MGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVL  264 (724)
Q Consensus       187 ~G--~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~L  264 (724)
                      .|  |.++||||+|..++++.-....-..++-++.|+..+...+ ++++..+....+               +...+.-+
T Consensus       570 ~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~I-R~iIk~~a~~~~---------------~~~~~~KV  633 (846)
T PRK04132        570 GGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVI-REKVKEFARTKP---------------IGGASFKI  633 (846)
T ss_pred             cCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHH-HHHHHHHHhcCC---------------cCCCCCEE
Confidence            36  8899999999999998743211123677888876666544 333332211000               00124579


Q ss_pred             EEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCC
Q 004895          265 IILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGES  341 (724)
Q Consensus       265 lVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~  341 (724)
                      +|+|+++...  ..+.+...+..        ....+++|++|.+.. +...-.+....+.+.+++.++....+...+...
T Consensus       634 vIIDEaD~Lt~~AQnALLk~lEe--------p~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~E  705 (846)
T PRK04132        634 IFLDEADALTQDAQQALRRTMEM--------FSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENE  705 (846)
T ss_pred             EEEECcccCCHHHHHHHHHHhhC--------CCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhc
Confidence            9999998763  33333322221        234556666655543 322223446789999999999998888776432


Q ss_pred             CCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          342 TKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       342 ~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      .-. --++....|++.|+|.+..+..+
T Consensus       706 gi~-i~~e~L~~Ia~~s~GDlR~AIn~  731 (846)
T PRK04132        706 GLE-LTEEGLQAILYIAEGDMRRAINI  731 (846)
T ss_pred             CCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            211 11567889999999988554433

>PRK12377 putative replication protein; Provisional

Probab=97.00  E-value=0.0035  Score=62.27  Aligned_cols=75  Identities=20%  Similarity=0.295  Sum_probs=48.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ....+.++|++|+|||+||..+++....+  ...++++++.      +++..+-.....    ..    ....+.+.+. 
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~~l~~~--g~~v~~i~~~------~l~~~l~~~~~~----~~----~~~~~l~~l~-  162 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGNRLLAK--GRSVIVVTVP------DVMSRLHESYDN----GQ----SGEKFLQELC-  162 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCCeEEEEHH------HHHHHHHHHHhc----cc----hHHHHHHHhc-
Confidence            34678999999999999999999998753  2336677654      455554443321    10    1123444443 


Q ss_pred             CCcEEEEEccccc
Q 004895          260 EKRVLIILDNIWT  272 (724)
Q Consensus       260 ~kr~LlVlDdv~~  272 (724)
                       +--||||||+..
T Consensus       163 -~~dLLiIDDlg~  174 (248)
T PRK12377        163 -KVDLLVLDEIGI  174 (248)
T ss_pred             -CCCEEEEcCCCC
Confidence             457999999943

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.00  E-value=7.1e-05  Score=72.44  Aligned_cols=100  Identities=22%  Similarity=0.236  Sum_probs=51.4

Q ss_pred             CCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccc--hhhhcCCCCCeEccC
Q 004895          574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQLLDLS  651 (724)
Q Consensus       574 l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~L~l~  651 (724)
                      +.+.+.|++-||.+..+. -+.+|+.|..|.|+-|.|+.+..+..+++|+.|+|+.|.|..+-  ..+.+|++|+.|.|.
T Consensus        18 l~~vkKLNcwg~~L~DIs-ic~kMp~lEVLsLSvNkIssL~pl~rCtrLkElYLRkN~I~sldEL~YLknlpsLr~LWL~   96 (388)
T KOG2123|consen   18 LENVKKLNCWGCGLDDIS-ICEKMPLLEVLSLSVNKISSLAPLQRCTRLKELYLRKNCIESLDELEYLKNLPSLRTLWLD   96 (388)
T ss_pred             HHHhhhhcccCCCccHHH-HHHhcccceeEEeeccccccchhHHHHHHHHHHHHHhcccccHHHHHHHhcCchhhhHhhc
Confidence            344455555555555331 12345556666666666666555666666666666666555442  234555566666555


Q ss_pred             CCCCCcccCh----HHhhCCCCCcEEE
Q 004895          652 NCSSLVVIAP----NVISKLSRLEELY  674 (724)
Q Consensus       652 ~~~~l~~~~~----~~i~~l~~L~~L~  674 (724)
                      .|.....-++    ..+.-|++|+.||
T Consensus        97 ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   97 ENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             cCCcccccchhHHHHHHHHcccchhcc
Confidence            5433333221    1244555555554

>TIGR00763 lon ATP-dependent protease La

Probab=96.99  E-value=0.0069  Score=71.13  Aligned_cols=46  Identities=37%  Similarity=0.385  Sum_probs=36.8

Q ss_pred             cccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|.++.++.+.+++.      ..+.+++.++|++|+|||++|+.+++...
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l~  372 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALN  372 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHhc
Confidence            35688888888887653      22345899999999999999999999874

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.

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

Probab=96.98  E-value=0.00016  Score=62.67  Aligned_cols=90  Identities=21%  Similarity=0.255  Sum_probs=69.4

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCC-CCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeE
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRL-INLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL  648 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l-~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L  648 (724)
                      +.....|...+|++|.+.++|+.+... +-+..|+|++|.+++ |..+..++.|+.|+++.|.+...|.-|..|.+|-.|
T Consensus        49 l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~~L~~l~~L  128 (177)
T KOG4579|consen   49 LSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFNPLNAEPRVIAPLIKLDML  128 (177)
T ss_pred             HhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccCccccchHHHHHHHhHHHh
Confidence            345567788888999888888876544 478888888888888 667888888888888888888888888888888888


Q ss_pred             ccCCCCCCcccCh
Q 004895          649 DLSNCSSLVVIAP  661 (724)
Q Consensus       649 ~l~~~~~l~~~~~  661 (724)
                      +..+ +....++-
T Consensus       129 ds~~-na~~eid~  140 (177)
T KOG4579|consen  129 DSPE-NARAEIDV  140 (177)
T ss_pred             cCCC-CccccCcH
Confidence            8777 34444543

>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=96.97  E-value=0.0047  Score=59.27  Aligned_cols=88  Identities=23%  Similarity=0.287  Sum_probs=53.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCC---CCchhHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFD---SNDLIYHRAKQLCQR  256 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~---~~~~~~~~~~~l~~~  256 (724)
                      ++|+.++|+.|+||||.+.+++.....+  -..+..++.... ....+-++..++.++.+..   ......+...+..+.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~--~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~   78 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK--GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEK   78 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT--T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc--cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHH
Confidence            3689999999999999999999888754  344677775422 2445566778888886532   111122233333333


Q ss_pred             HhcCCcEEEEEccc
Q 004895          257 LKKEKRVLIILDNI  270 (724)
Q Consensus       257 l~~~kr~LlVlDdv  270 (724)
                      ...++.=++++|=.
T Consensus        79 ~~~~~~D~vlIDT~   92 (196)
T PF00448_consen   79 FRKKGYDLVLIDTA   92 (196)
T ss_dssp             HHHTTSSEEEEEE-
T ss_pred             HhhcCCCEEEEecC
Confidence            33223347777765

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 ....

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.96  E-value=0.01  Score=69.17  Aligned_cols=165  Identities=19%  Similarity=0.223  Sum_probs=88.8

Q ss_pred             cccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ..+|.++.++.|+++|.      .....++.++|++|+||||+|+.++......  |   +-++.+...+..++...-..
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~--~---~~i~~~~~~d~~~i~g~~~~  397 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRK--Y---VRMALGGVRDEAEIRGHRRT  397 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHhCCC--E---EEEEcCCCCCHHHhccchhc
Confidence            35699999999988875      1345689999999999999999999866421  2   22444444444333221111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-c-----cccccccCCCCc---C----CCCCCCCCcEEE
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-L-----DKIGIPYGDVDE---K----DKNDDPRRCTII  301 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-~-----~~l~~~~~~~~~---~----~~~~~~~~s~il  301 (724)
                      ..+..      .......+...  ...+-+++||+++.... .     ..+...+..-..   .    ...-.-....+|
T Consensus       398 ~~g~~------~G~~~~~l~~~--~~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i  469 (784)
T PRK10787        398 YIGSM------PGKLIQKMAKV--GVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFV  469 (784)
T ss_pred             cCCCC------CcHHHHHHHhc--CCCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEE
Confidence            11110      11112222211  11334789999965421 0     111100000000   0    000012344566


Q ss_pred             EEecccchhhhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      .|+.+..+..........+.+.+++++|-.++.+++.
T Consensus       470 ~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        470 ATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             EcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            6665554433334445688999999999998887765

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.96  E-value=0.0046  Score=60.40  Aligned_cols=89  Identities=18%  Similarity=0.215  Sum_probs=54.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh-C---CC-----CCCCchhHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL-G---MN-----FDSNDLIYHRA  250 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l-~---~~-----~~~~~~~~~~~  250 (724)
                      .-+++.|+|++|+|||++|.+++......  -..++|++... ++...+.+ +++.. .   ..     ...........
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~--g~~v~yi~~e~-~~~~rl~~-~~~~~~~~~~~~i~~~~~~~~~~~~~~~   86 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ--GKKVVYIDTEG-LSPERFKQ-IAEDRPERALSNFIVFEVFDFDEQGVAI   86 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCC-CCHHHHHH-HHHhChHHHhcCEEEEECCCHHHHHHHH
Confidence            35799999999999999999998876532  45789999876 66555543 33321 0   00     00101011224


Q ss_pred             HHHHHHHhcCCcEEEEEccccc
Q 004895          251 KQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       251 ~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                      ..+...+...+.-+||+|.+..
T Consensus        87 ~~l~~~~~~~~~~lvVIDSis~  108 (209)
T TIGR02237        87 QKTSKFIDRDSASLVVVDSFTA  108 (209)
T ss_pred             HHHHHHHhhcCccEEEEeCcHH
Confidence            4444444444566899999843

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.94  E-value=0.012  Score=59.18  Aligned_cols=169  Identities=18%  Similarity=0.211  Sum_probs=96.4

Q ss_pred             ccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC-CeEEEEEEecCCCh-HHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF-DKVVMAEITKNPDA-QKIQGELA  233 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~-~~l~~~i~  233 (724)
                      ..++|-.++-..+-.++.    .++..-+.|+||.|.|||+|...+..+.+   .| ...+-|...+..-. .-.++.|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q---~~~E~~l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQ---ENGENFLLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHH---hcCCeEEEEEECccchhhHHHHHHHH
Confidence            345677777777766665    35556778999999999999999888832   23 23444555554332 22345555


Q ss_pred             HhhC----CCCCCCchhHHHHHHHHHHHhc-----CCcEEEEEcccccccc-------ccccccccCCCCcCCCCCCCCC
Q 004895          234 SDLG----MNFDSNDLIYHRAKQLCQRLKK-----EKRVLIILDNIWTKLE-------LDKIGIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       234 ~~l~----~~~~~~~~~~~~~~~l~~~l~~-----~kr~LlVlDdv~~~~~-------~~~l~~~~~~~~~~~~~~~~~~  297 (724)
                      +++.    ........-.+....+...|..     +-++.+|+|.++-...       ++-+...-..        ..+-
T Consensus       101 rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~--------r~Pi  172 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSA--------RAPI  172 (408)
T ss_pred             HHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhc--------CCCe
Confidence            5542    2211111123455666666653     2358888888754311       1111111111        4566


Q ss_pred             cEEEEEecccchh------hhhcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          298 CTIILTSRSRDLL------CIDMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       298 s~ilvTtR~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                      |-|.+|||-....      ........++-++.++-++...++++...
T Consensus       173 ciig~Ttrld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  173 CIIGVTTRLDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             EEEEeeccccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhc
Confidence            7788999975432      11123333555677788888888877653

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.92  E-value=0.0051  Score=61.30  Aligned_cols=92  Identities=22%  Similarity=0.251  Sum_probs=57.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEEEEecCCChHHHHHHHHHhhCCCCC------------CC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEITKNPDAQKIQGELASDLGMNFD------------SN  243 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~------------~~  243 (724)
                      .-.++.|+|++|+|||+||.+++........    -..++|++..+.++..++ .++++..+....            ..
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl-~~~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL-VQIAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH-HHHHHHhccChHhHhcCEEEEecCCH
Confidence            3469999999999999999999865332211    256899998887766554 344444332211            00


Q ss_pred             chhHHHHHHHHHHHhcC-CcEEEEEccccc
Q 004895          244 DLIYHRAKQLCQRLKKE-KRVLIILDNIWT  272 (724)
Q Consensus       244 ~~~~~~~~~l~~~l~~~-kr~LlVlDdv~~  272 (724)
                      .........+...+.+. +.-+||+|.+..
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcHH
Confidence            00122334444555545 778999999854

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 .

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

Probab=96.89  E-value=0.00043  Score=67.01  Aligned_cols=57  Identities=32%  Similarity=0.478  Sum_probs=26.4

Q ss_pred             CCCCCcEEEcCCcc--cCC--cccccCCCCCcEEEccCCcCc---ccchhhhcCCCCCeEccCCC
Q 004895          596 RLINLQTLCLDGWR--LED--IAIVGQLKKLEILSLRGAEIK---QLPLQIGQLTRLQLLDLSNC  653 (724)
Q Consensus       596 ~l~~L~~L~L~~~~--l~~--~~~~~~l~~L~~L~l~~~~i~---~lp~~i~~l~~L~~L~l~~~  653 (724)
                      .|++|++|.++.|.  +..  ....-.+++|++|++++|+++   ++++ +..+.+|..|++..|
T Consensus        63 ~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~p-l~~l~nL~~Ldl~n~  126 (260)
T KOG2739|consen   63 KLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRP-LKELENLKSLDLFNC  126 (260)
T ss_pred             CcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccch-hhhhcchhhhhcccC
Confidence            44555555555552  222  122233355555555555444   2221 344455555555554

>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=96.88  E-value=0.00093  Score=58.82  Aligned_cols=23  Identities=39%  Similarity=0.674  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ||.|+|++|+||||+|+.+.+..
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

...

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.88  E-value=0.00058  Score=66.94  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=18.1

Q ss_pred             cchHHhhcCCCCCcEEEeecccc
Q 004895          690 NASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       690 ~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ..++.+|.++++|+.|.++.+.+
T Consensus       239 wasvD~Ln~f~~l~dlRv~~~Pl  261 (418)
T KOG2982|consen  239 WASVDALNGFPQLVDLRVSENPL  261 (418)
T ss_pred             HHHHHHHcCCchhheeeccCCcc
Confidence            44678888889999888887764

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.81  E-value=0.002  Score=66.79  Aligned_cols=47  Identities=21%  Similarity=0.359  Sum_probs=40.7

Q ss_pred             cccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          161 IFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++|.++.++++++++.      ....+++.++|++|+||||||+.+++....
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~  104 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEE  104 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            57899999999999886      234578999999999999999999998864

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

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

Probab=96.80  E-value=0.0032  Score=71.27  Aligned_cols=161  Identities=20%  Similarity=0.291  Sum_probs=95.7

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC----eEEEEEEecCCChHHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD----KVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~----~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ...++++||++|+.++++.|....-.--.++|.+|+|||+++.-++.+.-...-..    ..++. +    ++    ..+
T Consensus       167 gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~s-L----D~----g~L  237 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYS-L----DL----GSL  237 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEE-e----cH----HHH
Confidence            34567889999999999999743323335789999999999999988875432211    11110 0    11    111


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--------ccccccccCCCCcCCCCCCCCC-cE-EEE
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--------LDKIGIPYGDVDEKDKNDDPRR-CT-IIL  302 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--------~~~l~~~~~~~~~~~~~~~~~~-s~-ilv  302 (724)
                      ..  |.+...+  -++....+.+.+.+.++..|++|.+.....        .+.-...-|.        -..| -+ |-.
T Consensus       238 vA--GakyRGe--FEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPa--------LARGeL~~IGA  305 (786)
T COG0542         238 VA--GAKYRGE--FEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPA--------LARGELRCIGA  305 (786)
T ss_pred             hc--cccccCc--HHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHH--------HhcCCeEEEEe
Confidence            11  2222222  355667777777766689999999976421        1111111111        1222 23 556


Q ss_pred             Eecccchh-----hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          303 TSRSRDLL-----CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       303 TtR~~~v~-----~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      ||-++.--     .......+.+.+..-+.+++..+++...
T Consensus       306 TT~~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk  346 (786)
T COG0542         306 TTLDEYRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGLK  346 (786)
T ss_pred             ccHHHHHHHhhhchHHHhcCceeeCCCCCHHHHHHHHHHHH
Confidence            66554320     1123456789999999999999988764

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=96.80  E-value=0.063  Score=56.39  Aligned_cols=43  Identities=28%  Similarity=0.499  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          166 KKIFQDVIEALKD---DKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       166 ~~~~~~l~~~L~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +...+.|.+.+.+   ....+|+|.|.=|+||||+.+.+.+.....
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            3445566666653   567899999999999999999999988764

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.77  E-value=0.0026  Score=70.00  Aligned_cols=75  Identities=25%  Similarity=0.366  Sum_probs=54.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      .-+++.++|++|+||||||+.++++..    | .++=|++|+..+...+-..|...+....-..              ..
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaG----Y-sVvEINASDeRt~~~v~~kI~~avq~~s~l~--------------ad  385 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAG----Y-SVVEINASDERTAPMVKEKIENAVQNHSVLD--------------AD  385 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcC----c-eEEEecccccccHHHHHHHHHHHHhhccccc--------------cC
Confidence            457999999999999999999998653    2 2677889988887777666655543221110              12


Q ss_pred             CCcEEEEEcccccc
Q 004895          260 EKRVLIILDNIWTK  273 (724)
Q Consensus       260 ~kr~LlVlDdv~~~  273 (724)
                      +++..||+|.++..
T Consensus       386 srP~CLViDEIDGa  399 (877)
T KOG1969|consen  386 SRPVCLVIDEIDGA  399 (877)
T ss_pred             CCcceEEEecccCC
Confidence            57888999998754

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.76  E-value=0.016  Score=60.84  Aligned_cols=140  Identities=16%  Similarity=0.137  Sum_probs=78.7

Q ss_pred             ccchHHHHHHHHHHhc-CCCccE-EEEEcCCCCcHHHHHHHHHHHHhhcc-------------------CCCeEEEEEEe
Q 004895          162 FNSRKKIFQDVIEALK-DDKLNI-IGVCGMGGVGKTTLVKQIAKQVMEDN-------------------VFDKVVMAEIT  220 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~-~~~~~v-i~I~G~gGiGKTtLa~~v~~~~~~~~-------------------~F~~~~wv~vs  220 (724)
                      ++|-+.....+..+.. .++.+- +.++|+.|+||||+|..+++......                   ....+..++.+
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s   82 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS   82 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEeccc
Confidence            3456666777777766 344444 99999999999999999999875322                   12334555555


Q ss_pred             cCCC---hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCCCC
Q 004895          221 KNPD---AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDP  295 (724)
Q Consensus       221 ~~~~---~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~  295 (724)
                      +...   ..+..+++.+.......                 .++.-++++|+++....  -+.+...+..        ..
T Consensus        83 ~~~~~~i~~~~vr~~~~~~~~~~~-----------------~~~~kviiidead~mt~~A~nallk~lEe--------p~  137 (325)
T COG0470          83 DLRKIDIIVEQVRELAEFLSESPL-----------------EGGYKVVIIDEADKLTEDAANALLKTLEE--------PP  137 (325)
T ss_pred             ccCCCcchHHHHHHHHHHhccCCC-----------------CCCceEEEeCcHHHHhHHHHHHHHHHhcc--------CC
Confidence            4444   23333333333322111                 24668999999976532  2222222222        34


Q ss_pred             CCcEEEEEecccc-hhhhhcCCCceEecCCCC
Q 004895          296 RRCTIILTSRSRD-LLCIDMNSQKMFWIDALS  326 (724)
Q Consensus       296 ~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~  326 (724)
                      ..+.+|++|.... +...-.+....+++.+.+
T Consensus       138 ~~~~~il~~n~~~~il~tI~SRc~~i~f~~~~  169 (325)
T COG0470         138 KNTRFILITNDPSKILPTIRSRCQRIRFKPPS  169 (325)
T ss_pred             CCeEEEEEcCChhhccchhhhcceeeecCCch
Confidence            5566777776433 322223344567776633

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.76  E-value=0.007  Score=60.64  Aligned_cols=81  Identities=23%  Similarity=0.345  Sum_probs=52.8

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHH
Q 004895          172 VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAK  251 (724)
Q Consensus       172 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~  251 (724)
                      +.+++.  +..-+.++|.+|+|||.||..+.++.. +..+ .+.++++      .+++.++......    ..    ...
T Consensus        98 ~~~~~~--~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~-sv~f~~~------~el~~~Lk~~~~~----~~----~~~  159 (254)
T COG1484          98 LVEFFE--RGENLVLLGPPGVGKTHLAIAIGNELL-KAGI-SVLFITA------PDLLSKLKAAFDE----GR----LEE  159 (254)
T ss_pred             HHHHhc--cCCcEEEECCCCCcHHHHHHHHHHHHH-HcCC-eEEEEEH------HHHHHHHHHHHhc----Cc----hHH
Confidence            334443  566789999999999999999999987 4333 3566654      3566666655442    11    223


Q ss_pred             HHHHHHhcCCcEEEEEccccc
Q 004895          252 QLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       252 ~l~~~l~~~kr~LlVlDdv~~  272 (724)
                      ++.+.+.  +-=||||||+-.
T Consensus       160 ~l~~~l~--~~dlLIiDDlG~  178 (254)
T COG1484         160 KLLRELK--KVDLLIIDDIGY  178 (254)
T ss_pred             HHHHHhh--cCCEEEEecccC
Confidence            3444343  345999999954

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.74  E-value=0.0032  Score=74.10  Aligned_cols=106  Identities=15%  Similarity=0.262  Sum_probs=61.0

Q ss_pred             ccccchHHHHHHHHHHhc-------C--CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK-------D--DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~-------~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      ..++|.+..++.+.+.+.       +  ....++.++|+.|+|||.+|+.++......  ....+-++++.....    .
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~--~~~~~~~dmse~~~~----~  639 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGG--EQNLITINMSEFQEA----H  639 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCC--CcceEEEeHHHhhhh----h
Confidence            346799988888888764       1  134578999999999999999998876421  222333343322111    1


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .+.+-+|.+..-..  ......+.+.+++....+|+||++...
T Consensus       640 ~~~~l~g~~~gyvg--~~~~g~L~~~v~~~p~svvllDEieka  680 (852)
T TIGR03345       640 TVSRLKGSPPGYVG--YGEGGVLTEAVRRKPYSVVLLDEVEKA  680 (852)
T ss_pred             hhccccCCCCCccc--ccccchHHHHHHhCCCcEEEEechhhc
Confidence            11122332221110  011123444555556789999999654

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.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.72  E-value=0.0026  Score=60.06  Aligned_cols=75  Identities=25%  Similarity=0.357  Sum_probs=45.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ...-+.++|+.|+|||.||..+.+....+ .+ .+.|+++      .+++..+-.    ......     ...+.+.+. 
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~~~~~-g~-~v~f~~~------~~L~~~l~~----~~~~~~-----~~~~~~~l~-  107 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANEAIRK-GY-SVLFITA------SDLLDELKQ----SRSDGS-----YEELLKRLK-  107 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHHHHHT-T---EEEEEH------HHHHHHHHC----CHCCTT-----HCHHHHHHH-
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHHhccC-Cc-ceeEeec------Cceeccccc----cccccc-----hhhhcCccc-
Confidence            34579999999999999999999987653 22 3667754      345555432    211111     123344554 


Q ss_pred             CCcEEEEEcccccc
Q 004895          260 EKRVLIILDNIWTK  273 (724)
Q Consensus       260 ~kr~LlVlDdv~~~  273 (724)
                       +-=||||||+...
T Consensus       108 -~~dlLilDDlG~~  120 (178)
T PF01695_consen  108 -RVDLLILDDLGYE  120 (178)
T ss_dssp             -TSSCEEEETCTSS
T ss_pred             -cccEeccccccee
Confidence             3458889999543

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.

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.71  E-value=0.0085  Score=66.44  Aligned_cols=95  Identities=15%  Similarity=0.273  Sum_probs=66.7

Q ss_pred             ccccccchHHHHHHHHHHhc---------CC---CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          158 DYNIFNSRKKIFQDVIEALK---------DD---KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~---------~~---~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...++-|-++.+..|.+.+.         ..   +.+-|.++|++|.|||-+|++|+.+..-       -|++|-+.   
T Consensus       670 ~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEcsL-------~FlSVKGP---  739 (953)
T KOG0736|consen  670 SWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATECSL-------NFLSVKGP---  739 (953)
T ss_pred             chhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhcee-------eEEeecCH---
Confidence            34556677888888887764         11   2457889999999999999999987754       35666543   


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                       +++.--   +|.       .++...+++++-+..++|+|++|.+++.
T Consensus       740 -ELLNMY---VGq-------SE~NVR~VFerAR~A~PCVIFFDELDSl  776 (953)
T KOG0736|consen  740 -ELLNMY---VGQ-------SEENVREVFERARSAAPCVIFFDELDSL  776 (953)
T ss_pred             -HHHHHH---hcc-------hHHHHHHHHHHhhccCCeEEEecccccc
Confidence             222211   111       3456777888878889999999999764

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.71  E-value=0.052  Score=53.19  Aligned_cols=207  Identities=12%  Similarity=0.151  Sum_probs=115.7

Q ss_pred             ccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc----cCCCeEEEEEEecC----------C--
Q 004895          160 NIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED----NVFDKVVMAEITKN----------P--  223 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~----------~--  223 (724)
                      ....++++....+......++.+-..++|+.|.||-|.+..+.++.-..    -.-+...|.+-|..          .  
T Consensus        13 ~~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHl   92 (351)
T KOG2035|consen   13 DELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHL   92 (351)
T ss_pred             hhcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceE
Confidence            3455677777777766556778899999999999999999988876421    11233445443332          1  


Q ss_pred             ---------ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcE-EEEEcccccc--ccccccccccCCCCcCCC
Q 004895          224 ---------DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRV-LIILDNIWTK--LELDKIGIPYGDVDEKDK  291 (724)
Q Consensus       224 ---------~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~-LlVlDdv~~~--~~~~~l~~~~~~~~~~~~  291 (724)
                               .-.-+.++|++......+-           -.  ...+.| ++|+-.+++.  +.-..++.-...      
T Consensus        93 EitPSDaG~~DRvViQellKevAQt~qi-----------e~--~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEk------  153 (351)
T KOG2035|consen   93 EITPSDAGNYDRVVIQELLKEVAQTQQI-----------ET--QGQRPFKVVVINEADELTRDAQHALRRTMEK------  153 (351)
T ss_pred             EeChhhcCcccHHHHHHHHHHHHhhcch-----------hh--ccccceEEEEEechHhhhHHHHHHHHHHHHH------
Confidence                     1122344444433221110           00  112344 5555555432  111111111111      


Q ss_pred             CCCCCCcEEEEEecccc--hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          292 NDDPRRCTIILTSRSRD--LLCIDMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~--v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                        -...+|+|+..-+-+  +.+. .+..-.++++..+++|....+++.+..+. .-|  .+++.+|+++++|.-.-.-.+
T Consensus       154 --Ys~~~RlIl~cns~SriIepI-rSRCl~iRvpaps~eeI~~vl~~v~~kE~l~lp--~~~l~rIa~kS~~nLRrAllm  228 (351)
T KOG2035|consen  154 --YSSNCRLILVCNSTSRIIEPI-RSRCLFIRVPAPSDEEITSVLSKVLKKEGLQLP--KELLKRIAEKSNRNLRRALLM  228 (351)
T ss_pred             --HhcCceEEEEecCcccchhHH-hhheeEEeCCCCCHHHHHHHHHHHHHHhcccCc--HHHHHHHHHHhcccHHHHHHH
Confidence              123566666544432  2121 22234678999999999999999885332 223  689999999999876444444


Q ss_pred             HHHhc--CC---------CHHHHHHHHHHHhcC
Q 004895          369 ANALK--NK---------SPAIWKDALNKLTSS  390 (724)
Q Consensus       369 ~~~l~--~~---------~~~~w~~~~~~l~~~  390 (724)
                      -...+  +.         ..-+|+-++.+....
T Consensus       229 lE~~~~~n~~~~a~~~~i~~~dWe~~i~e~a~~  261 (351)
T KOG2035|consen  229 LEAVRVNNEPFTANSQVIPKPDWEIYIQEIARV  261 (351)
T ss_pred             HHHHHhccccccccCCCCCCccHHHHHHHHHHH
Confidence            33333  11         456898888775543

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=96.67  E-value=0.02  Score=54.91  Aligned_cols=156  Identities=13%  Similarity=0.180  Sum_probs=86.7

Q ss_pred             ccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHH
Q 004895          162 FNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l  228 (724)
                      +-|-++.+++|.+.+.             -.+.+-+.++|++|.|||-||+.|+++.       .+.|+.||+.    ++
T Consensus       149 iGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht-------~c~firvsgs----el  217 (404)
T KOG0728|consen  149 IGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT-------DCTFIRVSGS----EL  217 (404)
T ss_pred             hccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc-------ceEEEEechH----HH
Confidence            3355666666555443             1346678899999999999999998754       3557777763    33


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc--cc-------c-ccccCCCCcCCCCCCCCCc
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL--DK-------I-GIPYGDVDEKDKNDDPRRC  298 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~--~~-------l-~~~~~~~~~~~~~~~~~~s  298 (724)
                      .+..+-.          .......++---+.--+..|+.|.+++...-  +.       + ...+..+.+++.+-..+.-
T Consensus       218 vqk~ige----------gsrmvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeatkni  287 (404)
T KOG0728|consen  218 VQKYIGE----------GSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEATKNI  287 (404)
T ss_pred             HHHHhhh----------hHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccccce
Confidence            3222110          1122333333333345788999988664210  00       0 0111112233344456777


Q ss_pred             EEEEEecccchhhh----hcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          299 TIILTSRSRDLLCI----DMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       299 ~ilvTtR~~~v~~~----~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      +||+.|..-++...    .......++.++-+++.-.++++-+.
T Consensus       288 kvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihs  331 (404)
T KOG0728|consen  288 KVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHS  331 (404)
T ss_pred             EEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhh
Confidence            88888877665411    11223466777777776666666543

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

Probab=96.66  E-value=0.0012  Score=64.01  Aligned_cols=83  Identities=22%  Similarity=0.318  Sum_probs=63.6

Q ss_pred             cCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCC--cCc-ccchhhhcCCCCCeEccCCCCC--CcccChHHhhCCCC
Q 004895          595 GRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGA--EIK-QLPLQIGQLTRLQLLDLSNCSS--LVVIAPNVISKLSR  669 (724)
Q Consensus       595 ~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~--~i~-~lp~~i~~l~~L~~L~l~~~~~--l~~~~~~~i~~l~~  669 (724)
                      -.+..|++|++.++.++....+-.|++|++|+++.|  ++. .++.-..++++|++|++++|..  +..+.|  +..+.+
T Consensus        40 d~~~~le~ls~~n~gltt~~~~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~p--l~~l~n  117 (260)
T KOG2739|consen   40 DEFVELELLSVINVGLTTLTNFPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRP--LKELEN  117 (260)
T ss_pred             ccccchhhhhhhccceeecccCCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccch--hhhhcc
Confidence            445667777788877777778888999999999999  555 6666667779999999999532  334444  578888


Q ss_pred             CcEEEccCCC
Q 004895          670 LEELYMGDSF  679 (724)
Q Consensus       670 L~~L~l~~~~  679 (724)
                      |..|++.+|.
T Consensus       118 L~~Ldl~n~~  127 (260)
T KOG2739|consen  118 LKSLDLFNCS  127 (260)
T ss_pred             hhhhhcccCC
Confidence            8899988874

>PRK06696 uridine kinase; Validated

Probab=96.65  E-value=0.0029  Score=62.39  Aligned_cols=44  Identities=23%  Similarity=0.427  Sum_probs=36.7

Q ss_pred             chHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          164 SRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       164 gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .|++.+++|.+.+.   .+...+|+|.|.+|+||||||+.+.+....
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~   48 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKK   48 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46777788887764   456789999999999999999999998754

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.64  E-value=0.005  Score=65.29  Aligned_cols=88  Identities=25%  Similarity=0.308  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHHhcCC--------C-ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          165 RKKIFQDVIEALKDD--------K-LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       165 R~~~~~~l~~~L~~~--------~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -+.|+++|++.|.++        + .+-|.++|++|.|||-||+.|+-...+-  |    |......|+      ++.-.
T Consensus       312 AK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP--F----F~~sGSEFd------Em~VG  379 (752)
T KOG0734|consen  312 AKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP--F----FYASGSEFD------EMFVG  379 (752)
T ss_pred             HHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC--e----Eeccccchh------hhhhc
Confidence            445788889998743        2 4578899999999999999999877653  1    222222333      22211


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .         ....+..|+..-+..-+|+|++|.++..
T Consensus       380 v---------GArRVRdLF~aAk~~APcIIFIDEiDav  408 (752)
T KOG0734|consen  380 V---------GARRVRDLFAAAKARAPCIIFIDEIDAV  408 (752)
T ss_pred             c---------cHHHHHHHHHHHHhcCCeEEEEechhhh
Confidence            1         1234556666666678999999999754

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.64  E-value=0.009  Score=61.73  Aligned_cols=91  Identities=21%  Similarity=0.231  Sum_probs=57.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc----cCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC---------Cchh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED----NVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS---------NDLI  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~---------~~~~  246 (724)
                      .-+++-|+|++|+|||+|+.+++-.....    ..=..++||+..+.++.+++. ++++.++...+.         ....
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~-~~a~~~g~d~~~~l~~i~~~~~~~~  173 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR-AIAERFGVDPDAVLDNILYARAYTS  173 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH-HHHHHcCCChHHhcCcEEEecCCCH
Confidence            34688999999999999999877543211    112368999999988888774 567777654221         0001


Q ss_pred             H---HHHHHHHHHHhcCCcEEEEEcccc
Q 004895          247 Y---HRAKQLCQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       247 ~---~~~~~l~~~l~~~kr~LlVlDdv~  271 (724)
                      +   +....+...+...+--|||+|.+-
T Consensus       174 e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       174 EHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence            1   122333334444455689999884

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.

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

Probab=96.63  E-value=0.025  Score=62.45  Aligned_cols=97  Identities=23%  Similarity=0.330  Sum_probs=63.9

Q ss_pred             ccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          162 FNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -+|.++.++.|++.+.      +.+-+++..+||+|+|||++|+.++.....+ +    +-++|++-.|..+|-..=-..
T Consensus       413 HYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRk-F----fRfSvGG~tDvAeIkGHRRTY  487 (906)
T KOG2004|consen  413 HYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRK-F----FRFSVGGMTDVAEIKGHRRTY  487 (906)
T ss_pred             ccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCc-e----EEEeccccccHHhhcccceee
Confidence            3488999999999875      3456799999999999999999999987532 2    356777777776652111111


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                      +|.          .-.++.+.|+  +..+=|+.||.|+..
T Consensus       488 VGA----------MPGkiIq~LK~v~t~NPliLiDEvDKl  517 (906)
T KOG2004|consen  488 VGA----------MPGKIIQCLKKVKTENPLILIDEVDKL  517 (906)
T ss_pred             ecc----------CChHHHHHHHhhCCCCceEEeehhhhh
Confidence            111          1123334443  234568999998653

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=96.63  E-value=0.015  Score=64.93  Aligned_cols=157  Identities=17%  Similarity=0.183  Sum_probs=84.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..+.+.++|++|.|||.||+.+++.....       ++.+...    +++...   +|     +  .+.....++..-.+
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~~~~~~-------fi~v~~~----~l~sk~---vG-----e--sek~ir~~F~~A~~  333 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVALESRSR-------FISVKGS----ELLSKW---VG-----E--SEKNIRELFEKARK  333 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHhhCCCe-------EEEeeCH----HHhccc---cc-----h--HHHHHHHHHHHHHc
Confidence            45689999999999999999999965432       2333221    111110   11     1  23344455555455


Q ss_pred             CCcEEEEEcccccccccccc----------ccccCCCCcCCCCCCCCCcEEEEEecccchhhhh----cCCCceEecCCC
Q 004895          260 EKRVLIILDNIWTKLELDKI----------GIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCID----MNSQKMFWIDAL  325 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~~~~l----------~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L  325 (724)
                      ..++.|++|+++....+..-          ...+..   .+......+..||-||-........    ..-...+.+++-
T Consensus       334 ~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~---~d~~e~~~~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~p  410 (494)
T COG0464         334 LAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTE---LDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLP  410 (494)
T ss_pred             CCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHH---hcCCCccCceEEEecCCCccccCHhhcccCccceEeecCCC
Confidence            68899999999765322211          000000   0111133344455555554432111    123457888888


Q ss_pred             CHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC
Q 004895          326 SEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG  360 (724)
Q Consensus       326 ~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G  360 (724)
                      +.++..+.|+.+.......-.-.-..+++++.+.|
T Consensus       411 d~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~  445 (494)
T COG0464         411 DLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEG  445 (494)
T ss_pred             CHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcC
Confidence            99999999999886332211112234455555554

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.62  E-value=0.015  Score=57.60  Aligned_cols=89  Identities=16%  Similarity=0.303  Sum_probs=52.8

Q ss_pred             HHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCch
Q 004895          168 IFQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDL  245 (724)
Q Consensus       168 ~~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~  245 (724)
                      .+..+.+...+  .....+.++|.+|+|||+||..+++.....+  ..++++++      .+++..+-.....  ...  
T Consensus        84 al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g--~~v~~it~------~~l~~~l~~~~~~--~~~--  151 (244)
T PRK07952         84 ALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRG--KSVLIITV------ADIMSAMKDTFSN--SET--  151 (244)
T ss_pred             HHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEEH------HHHHHHHHHHHhh--ccc--
Confidence            44444444432  2345788999999999999999999886532  34566643      4555554443321  111  


Q ss_pred             hHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          246 IYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       246 ~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                         ....+.+.+.  +.=+|||||+...
T Consensus       152 ---~~~~~l~~l~--~~dlLvIDDig~~  174 (244)
T PRK07952        152 ---SEEQLLNDLS--NVDLLVIDEIGVQ  174 (244)
T ss_pred             ---cHHHHHHHhc--cCCEEEEeCCCCC
Confidence               1123444454  3458899999543

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.60  E-value=0.0082  Score=56.82  Aligned_cols=36  Identities=25%  Similarity=0.442  Sum_probs=29.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      ...+|.++|+.|+||||+|+.+++....  .+..++++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~--~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKL--KYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHH--cCCcEEEE
Confidence            4569999999999999999999998864  24555555

>TIGR02012 tigrfam_recA protein RecA

Probab=96.59  E-value=0.01  Score=61.12  Aligned_cols=86  Identities=19%  Similarity=0.214  Sum_probs=55.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~  254 (724)
                      .-+++-|+|++|+||||||.+++......  -..++|++..+.++..     .+++++...+     .....++....+.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~--g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~  126 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAE  126 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            34699999999999999999988776532  3457899877665542     4555554311     1111233333333


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ..+..+..-++|+|-+-.
T Consensus       127 ~li~~~~~~lIVIDSv~a  144 (321)
T TIGR02012       127 TLVRSGAVDIIVVDSVAA  144 (321)
T ss_pred             HHhhccCCcEEEEcchhh
Confidence            334445677999999853

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.59  E-value=0.011  Score=62.04  Aligned_cols=88  Identities=17%  Similarity=0.169  Sum_probs=53.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..++.++|+.|+||||++.+++.....+.....+..++.... ....+-++...+.++.+........+. ......+. 
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l-~~~l~~l~-  214 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDL-QLALAELR-  214 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccH-HHHHHHhc-
Confidence            469999999999999999999988653322234666654322 234555666677777654322211122 22233333 


Q ss_pred             CCcEEEEEcccc
Q 004895          260 EKRVLIILDNIW  271 (724)
Q Consensus       260 ~kr~LlVlDdv~  271 (724)
                       +.-++++|..-
T Consensus       215 -~~DlVLIDTaG  225 (374)
T PRK14722        215 -NKHMVLIDTIG  225 (374)
T ss_pred             -CCCEEEEcCCC
Confidence             34567799884

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.59  E-value=0.0051  Score=71.02  Aligned_cols=102  Identities=18%  Similarity=0.265  Sum_probs=60.0

Q ss_pred             cccchHHHHHHHHHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.++.++.+.+.+..         .....+.++|++|+|||++|+.++.....     ..+.+++++.....    .
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~-----~~i~id~se~~~~~----~  529 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGI-----ELLRFDMSEYMERH----T  529 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhCC-----CcEEeechhhcccc----c
Confidence            367888888888877651         12457889999999999999999887731     23455555432211    1


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +.+-+|.+.....  ......+.+.+......+|+||+++..
T Consensus       530 ~~~LiG~~~gyvg--~~~~g~L~~~v~~~p~sVlllDEieka  569 (758)
T PRK11034        530 VSRLIGAPPGYVG--FDQGGLLTDAVIKHPHAVLLLDEIEKA  569 (758)
T ss_pred             HHHHcCCCCCccc--ccccchHHHHHHhCCCcEEEeccHhhh
Confidence            2222332211100  011122334444445679999999765

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.57  E-value=0.019  Score=67.88  Aligned_cols=105  Identities=18%  Similarity=0.276  Sum_probs=59.5

Q ss_pred             cccchHHHHHHHHHHhcC-------C--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD-------D--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.+..++.+...+..       +  ...++.++|+.|+|||++|+.+++.....  -...+.++++.... ..   .
T Consensus       569 ~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~--~~~~i~id~se~~~-~~---~  642 (857)
T PRK10865        569 RVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDS--DDAMVRIDMSEFME-KH---S  642 (857)
T ss_pred             eEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcC--CCcEEEEEhHHhhh-hh---h
Confidence            467888888888777641       1  12478899999999999999999866321  12345555543221 11   1


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +.+-+|.+.....  ......+.+.+.....-+|+|||+...
T Consensus       643 ~~~LiG~~pgy~g--~~~~g~l~~~v~~~p~~vLllDEieka  682 (857)
T PRK10865        643 VSRLVGAPPGYVG--YEEGGYLTEAVRRRPYSVILLDEVEKA  682 (857)
T ss_pred             HHHHhCCCCcccc--cchhHHHHHHHHhCCCCeEEEeehhhC
Confidence            1222332221111  011122334444334479999999754

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.57  E-value=0.012  Score=58.22  Aligned_cols=55  Identities=25%  Similarity=0.246  Sum_probs=38.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      .-.++.|+|++|+|||+||.+++.......    .=..++|++....++...+. .+.+.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~-~~~~~   76 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLV-QLAVR   76 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHH-HHHHH
Confidence            356999999999999999999987654221    01458899987777765543 34443

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.

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.57  E-value=0.019  Score=55.59  Aligned_cols=130  Identities=15%  Similarity=0.216  Sum_probs=73.2

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+-|=++.+++|.+...             -+..+-|.++|++|.|||-+|+.|+|+...       .|+.|-+.   
T Consensus       176 y~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtda-------cfirvigs---  245 (435)
T KOG0729|consen  176 YSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDA-------CFIRVIGS---  245 (435)
T ss_pred             cccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCc-------eEEeehhH---
Confidence            3445567777777766543             134567889999999999999999987643       23333211   


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--cc-------cc-ccccCCCCcCCCCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LD-------KI-GIPYGDVDEKDKNDDP  295 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~-------~l-~~~~~~~~~~~~~~~~  295 (724)
                       ++.+..   .|.       .......+++--+.+|-|+|++|.++....  ++       ++ ...+..+.+++.+...
T Consensus       246 -elvqky---vge-------garmvrelf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdpr  314 (435)
T KOG0729|consen  246 -ELVQKY---VGE-------GARMVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPR  314 (435)
T ss_pred             -HHHHHH---hhh-------hHHHHHHHHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCCC
Confidence             222211   110       223445556555667889999999854310  00       00 0011111222333344


Q ss_pred             CCcEEEEEecccch
Q 004895          296 RRCTIILTSRSRDL  309 (724)
Q Consensus       296 ~~s~ilvTtR~~~v  309 (724)
                      ..-+|++.|...+.
T Consensus       315 gnikvlmatnrpdt  328 (435)
T KOG0729|consen  315 GNIKVLMATNRPDT  328 (435)
T ss_pred             CCeEEEeecCCCCC
Confidence            56689988877654

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.56  E-value=0.35  Score=51.18  Aligned_cols=161  Identities=17%  Similarity=0.199  Sum_probs=84.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      +--.++||+|.|||++..++++...    ||. .=..++...+-.+ +                     .+|...  ...
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L~----ydI-ydLeLt~v~~n~d-L---------------------r~LL~~--t~~  286 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYLN----YDI-YDLELTEVKLDSD-L---------------------RHLLLA--TPN  286 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhcC----Cce-EEeeeccccCcHH-H---------------------HHHHHh--CCC
Confidence            3457899999999999999999774    432 2233332222111 2                     222221  135


Q ss_pred             cEEEEEccccccccccccc-------------ccc-CCCCcCCCCCCCC--CcEEEEEecccchh---hhh-cCCCceEe
Q 004895          262 RVLIILDNIWTKLELDKIG-------------IPY-GDVDEKDKNDDPR--RCTIILTSRSRDLL---CID-MNSQKMFW  321 (724)
Q Consensus       262 r~LlVlDdv~~~~~~~~l~-------------~~~-~~~~~~~~~~~~~--~s~ilvTtR~~~v~---~~~-~~~~~~~~  321 (724)
                      +-+||+.|++...+...-.             ..+ +-+.-.++.+.++  .--|+.||-..+-.   -.. ..-...+.
T Consensus       287 kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~  366 (457)
T KOG0743|consen  287 KSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIY  366 (457)
T ss_pred             CcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEE
Confidence            6788888886442211000             000 0111122333334  23466677665432   111 12234678


Q ss_pred             cCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH-HHhcCC
Q 004895          322 IDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA-NALKNK  375 (724)
Q Consensus       322 l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~-~~l~~~  375 (724)
                      +.--+.+....|+....+...++    .++.+|.+...|--+.=..++ .++.++
T Consensus       367 mgyCtf~~fK~La~nYL~~~~~h----~L~~eie~l~~~~~~tPA~V~e~lm~~~  417 (457)
T KOG0743|consen  367 MGYCTFEAFKTLASNYLGIEEDH----RLFDEIERLIEETEVTPAQVAEELMKNK  417 (457)
T ss_pred             cCCCCHHHHHHHHHHhcCCCCCc----chhHHHHHHhhcCccCHHHHHHHHhhcc
Confidence            89999999999999998754322    345566665555443333334 444554

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=96.54  E-value=0.096  Score=57.99  Aligned_cols=200  Identities=14%  Similarity=0.169  Sum_probs=114.0

Q ss_pred             cccchHHHHHHHHHHhc----C-CCccEEEEEcCCCCcHHHHHHHHHHHHhh---c---cCCCeEEEEEEecCCChHHHH
Q 004895          161 IFNSRKKIFQDVIEALK----D-DKLNIIGVCGMGGVGKTTLVKQIAKQVME---D---NVFDKVVMAEITKNPDAQKIQ  229 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~----~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~---~~F~~~~wv~vs~~~~~~~l~  229 (724)
                      .+-+|+.+..+|-..+.    + +..+.+-|.|.+|+|||..+..|.+....   +   ..|+ .+.|+.-.-....++.
T Consensus       397 sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveINgm~l~~~~~~Y  475 (767)
T KOG1514|consen  397 SLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEINGLRLASPREIY  475 (767)
T ss_pred             cccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEcceeecCHHHHH
Confidence            34579999888887765    3 34458999999999999999999997652   1   2232 2344444456788999


Q ss_pred             HHHHHhhCCCCCCCchhHHHHHHHHHHHh----cCCcEEEEEcccccccc-ccc-cccccCCCCcCCCCCCCCCcEEEEE
Q 004895          230 GELASDLGMNFDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKLE-LDK-IGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~~-~~~-l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      ..|..++........   .....+..+..    +.+.+++++|+++..-. -++ +...|.+       ...++||++|-
T Consensus       476 ~~I~~~lsg~~~~~~---~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdW-------pt~~~sKLvvi  545 (767)
T KOG1514|consen  476 EKIWEALSGERVTWD---AALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDW-------PTLKNSKLVVI  545 (767)
T ss_pred             HHHHHhcccCcccHH---HHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcC-------CcCCCCceEEE
Confidence            999999876544332   12233333332    34678999999854311 011 1111111       03456665554


Q ss_pred             ecccc--hh-h------hhcCCCceEecCCCCHHHHHHHHHHHhCCC--CCCCCchhHHHHHHHHhCCchhHHHHHHHH
Q 004895          304 SRSRD--LL-C------IDMNSQKMFWIDALSEEEALQLFEKIVGES--TKASDFRPLAEEIVGKCGGLPVALSTVANA  371 (724)
Q Consensus       304 tR~~~--v~-~------~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~--~~~~~l~~~~~~I~~~c~GlPLai~~~~~~  371 (724)
                      +=...  .. .      ...-+...+...|.+.++--++...+..+.  ..+...+-++++|+.-.|-.-.|+.+.-+.
T Consensus       546 ~IaNTmdlPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic~RA  624 (767)
T KOG1514|consen  546 AIANTMDLPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDICRRA  624 (767)
T ss_pred             EecccccCHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHHHHH
Confidence            43221  11 0      001223567788888888888777766432  112222334555555555555555444333

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.50  E-value=0.0091  Score=53.57  Aligned_cols=45  Identities=31%  Similarity=0.560  Sum_probs=36.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCC
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF  240 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~  240 (724)
                      +|.|.|++|+||||+|+.++++..-.       .+      +...++++|++..|.+.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~gl~-------~v------saG~iFR~~A~e~gmsl   46 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLGLK-------LV------SAGTIFREMARERGMSL   46 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHHhCCc-------ee------eccHHHHHHHHHcCCCH
Confidence            78999999999999999999987543       11      23478899999888763

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.49  E-value=0.01  Score=70.21  Aligned_cols=106  Identities=18%  Similarity=0.273  Sum_probs=61.1

Q ss_pred             ccccchHHHHHHHHHHhc-------CC--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK-------DD--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~-------~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      ..++|.++.+..+...+.       +.  ...++.++|+.|+|||+||+.+++.....  -...+-++.++..+...+  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~--~~~~~~~d~s~~~~~~~~--  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGS--EDAMIRLDMSEYMEKHTV--  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCC--ccceEEEEchhccccccH--
Confidence            456798988888887764       11  23467789999999999999999876321  123444555543222111  


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                        ...+|.+..-.  .......+.+.+......+++||+++..
T Consensus       585 --~~l~g~~~gyv--g~~~~~~l~~~~~~~p~~VvllDeieka  623 (821)
T CHL00095        585 --SKLIGSPPGYV--GYNEGGQLTEAVRKKPYTVVLFDEIEKA  623 (821)
T ss_pred             --HHhcCCCCccc--CcCccchHHHHHHhCCCeEEEECChhhC
Confidence              11223221100  0011223445555444579999999765

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.48  E-value=0.013  Score=60.27  Aligned_cols=86  Identities=22%  Similarity=0.224  Sum_probs=54.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~  254 (724)
                      .-+++-|+|++|+||||||.+++......  -..++|++..+.++..     .++.++.+.+     .....++....+.
T Consensus        54 ~G~iteI~Gp~GsGKTtLal~~~~~~~~~--g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~  126 (325)
T cd00983          54 KGRIIEIYGPESSGKTTLALHAIAEAQKL--GGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIAD  126 (325)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHH
Confidence            35688999999999999999988776532  3458899887766642     3455554311     1111233333333


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ..+..+..-++|+|-+-.
T Consensus       127 ~li~s~~~~lIVIDSvaa  144 (325)
T cd00983         127 SLVRSGAVDLIVVDSVAA  144 (325)
T ss_pred             HHHhccCCCEEEEcchHh
Confidence            333445667999999843

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.47  E-value=0.008  Score=71.32  Aligned_cols=105  Identities=19%  Similarity=0.315  Sum_probs=61.6

Q ss_pred             cccchHHHHHHHHHHhcC-------C--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD-------D--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~-------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.+..++.+...+..       +  ...++.++|+.|+|||++|+.+.......  -...+.++++.......    
T Consensus       566 ~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~--~~~~i~~d~s~~~~~~~----  639 (852)
T TIGR03346       566 RVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD--EDAMVRIDMSEYMEKHS----  639 (852)
T ss_pred             ccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC--CCcEEEEechhhcccch----
Confidence            467999888888887752       1  23578899999999999999999876432  22345555554322111    


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      ....+|.+.....  ......+...+......+|+||++...
T Consensus       640 ~~~l~g~~~g~~g--~~~~g~l~~~v~~~p~~vlllDeieka  679 (852)
T TIGR03346       640 VARLIGAPPGYVG--YEEGGQLTEAVRRKPYSVVLFDEVEKA  679 (852)
T ss_pred             HHHhcCCCCCccC--cccccHHHHHHHcCCCcEEEEeccccC
Confidence            1122232211100  011123444444444569999999765

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.46  E-value=0.015  Score=59.44  Aligned_cols=88  Identities=23%  Similarity=0.284  Sum_probs=49.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      ..+++.|+|++|+||||++..++.....+..-..+..++..... ...+-+....+.++.+........ ........+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~-~l~~~l~~~~  271 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPK-ELRKALDRLR  271 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHH-HHHHHHHHcc
Confidence            35699999999999999999999887643111245566543221 223334444555555443222122 2233333332


Q ss_pred             cCCcEEEEEccc
Q 004895          259 KEKRVLIILDNI  270 (724)
Q Consensus       259 ~~kr~LlVlDdv  270 (724)
                        ..=+|++|..
T Consensus       272 --~~d~vliDt~  281 (282)
T TIGR03499       272 --DKDLILIDTA  281 (282)
T ss_pred             --CCCEEEEeCC
Confidence              2347777753

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.46  E-value=0.02  Score=53.02  Aligned_cols=40  Identities=38%  Similarity=0.428  Sum_probs=30.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ++.|+|++|+||||++..+......  .-..++|++......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~--~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHh--cCCEEEEEECCcchH
Confidence            3689999999999999999988754  234577887765543

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.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.46  E-value=0.015  Score=59.95  Aligned_cols=91  Identities=20%  Similarity=0.310  Sum_probs=56.6

Q ss_pred             chHHHHHHHHHHhcC----CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCC
Q 004895          164 SRKKIFQDVIEALKD----DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMN  239 (724)
Q Consensus       164 gR~~~~~~l~~~L~~----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~  239 (724)
                      +|........+++.+    ....-+.|+|..|+|||.||..+++....+ .+ .+.+++++      +++.++....+. 
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~-g~-~v~~~~~~------~l~~~lk~~~~~-  205 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKK-GV-SSTLLHFP------EFIRELKNSISD-  205 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-CC-CEEEEEHH------HHHHHHHHHHhc-
Confidence            455555555555542    234678999999999999999999998743 33 35666653      455555554421 


Q ss_pred             CCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          240 FDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       240 ~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                         ..     .....+.+.  +-=||||||+...
T Consensus       206 ---~~-----~~~~l~~l~--~~dlLiIDDiG~e  229 (306)
T PRK08939        206 ---GS-----VKEKIDAVK--EAPVLMLDDIGAE  229 (306)
T ss_pred             ---Cc-----HHHHHHHhc--CCCEEEEecCCCc
Confidence               11     123333443  4569999999543

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.45  E-value=0.00027  Score=68.55  Aligned_cols=98  Identities=21%  Similarity=0.202  Sum_probs=70.8

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC---cccccCCCCCc
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED---IAIVGQLKKLE  623 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~---~~~~~~l~~L~  623 (724)
                      ++.+.+.|+++++.....    ++...|+.|.||.|+-|+|+.+- .+..+++|+.|.|+.|.|..   +..+.+|++|+
T Consensus        17 dl~~vkKLNcwg~~L~DI----sic~kMp~lEVLsLSvNkIssL~-pl~rCtrLkElYLRkN~I~sldEL~YLknlpsLr   91 (388)
T KOG2123|consen   17 DLENVKKLNCWGCGLDDI----SICEKMPLLEVLSLSVNKISSLA-PLQRCTRLKELYLRKNCIESLDELEYLKNLPSLR   91 (388)
T ss_pred             HHHHhhhhcccCCCccHH----HHHHhcccceeEEeeccccccch-hHHHHHHHHHHHHHhcccccHHHHHHHhcCchhh
Confidence            355677777754443222    24567899999999999998773 47788899999999998877   46788899999


Q ss_pred             EEEccCCcCc-ccc-----hhhhcCCCCCeEc
Q 004895          624 ILSLRGAEIK-QLP-----LQIGQLTRLQLLD  649 (724)
Q Consensus       624 ~L~l~~~~i~-~lp-----~~i~~l~~L~~L~  649 (724)
                      +|.|..|.-. +-+     .-+.-|++|+.|+
T Consensus        92 ~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   92 TLWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             hHhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            9999887322 222     2356688888886

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.44  E-value=0.015  Score=57.49  Aligned_cols=46  Identities=22%  Similarity=0.338  Sum_probs=35.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l  228 (724)
                      .-.++.|+|++|+|||++|.+++......  -..++|++.. .++...+
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~~~--~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAAKN--GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEECC-CCCHHHH
Confidence            35699999999999999999999877543  3568899887 5554443

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.43  E-value=0.022  Score=57.32  Aligned_cols=90  Identities=27%  Similarity=0.345  Sum_probs=56.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHhhCCCCC------------CCc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASDLGMNFD------------SND  244 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~------------~~~  244 (724)
                      -.+.=|+|++|+|||.|+.+++-......    .=..++|++-...++.+++. +|++..+....            ...
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~  116 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLE  116 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHH
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCHH
Confidence            45899999999999999998876543211    12359999999999887774 56766543210            000


Q ss_pred             hhHHHHHHHHHHHhcCCcEEEEEcccc
Q 004895          245 LIYHRAKQLCQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       245 ~~~~~~~~l~~~l~~~kr~LlVlDdv~  271 (724)
                      ........+...+.+.+--|||+|.+-
T Consensus       117 ~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  117 ELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHhhccccceEEEEecchH
Confidence            011223333344444566799999873

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 ....

>PRK09354 recA recombinase A; Provisional

Probab=96.43  E-value=0.015  Score=60.47  Aligned_cols=86  Identities=19%  Similarity=0.214  Sum_probs=56.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~  254 (724)
                      .-+++-|+|++|+||||||.+++......  -..++||+....++.     ..+++++.+.+     .....++....+.
T Consensus        59 ~G~IteI~G~~GsGKTtLal~~~~~~~~~--G~~~~yId~E~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~~  131 (349)
T PRK09354         59 RGRIVEIYGPESSGKTTLALHAIAEAQKA--GGTAAFIDAEHALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIAD  131 (349)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            35689999999999999999998776533  355889988877665     34555654321     1111333333333


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ..+..+..-+||+|-+-.
T Consensus       132 ~li~s~~~~lIVIDSvaa  149 (349)
T PRK09354        132 TLVRSGAVDLIVVDSVAA  149 (349)
T ss_pred             HHhhcCCCCEEEEeChhh
Confidence            444445677999999853

>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=96.40  E-value=0.043  Score=49.52  Aligned_cols=106  Identities=11%  Similarity=0.148  Sum_probs=68.7

Q ss_pred             HHHHHhhHhHhhHhhhhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHH
Q 004895           10 SSIVSEGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAK   89 (724)
Q Consensus        10 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~i~~~l~~a~~~~~~~~~~v~~Wl~~l~~~~~~~~e   89 (724)
                      +++++.+++.+...+......       ....+.-+++|...+..|...+++.+..+...+.+-+.-++++.+...+ ++
T Consensus         8 gaalG~~~~eLlk~v~~~~~k-------~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~-g~   79 (147)
T PF05659_consen    8 GAALGAVFGELLKAVIDASKK-------SLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEK-GK   79 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHH-HH
Confidence            344555555555554433332       2234556666777777777777777766555566667888899999999 99


Q ss_pred             HHhhhhccccccccCCCCCchhHHHHHhHHHHHHHHHHHHH
Q 004895           90 HIINDEDEVRKPCFKGLSPNLMSRYKLSKRAVEDAKYAEHL  130 (724)
Q Consensus        90 d~ld~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~l~~i  130 (724)
                      ++++.+...+       .+++...++.+++|+++.+.+...
T Consensus        80 ~LV~k~sk~~-------r~n~~kk~~y~~Ki~~le~~l~~f  113 (147)
T PF05659_consen   80 ELVEKCSKVR-------RWNLYKKPRYARKIEELEESLRRF  113 (147)
T ss_pred             HHHHHhcccc-------HHHHHhhHhHHHHHHHHHHHHHHH
Confidence            9988765433       234556667788888777766554

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 [].

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=96.39  E-value=0.014  Score=55.89  Aligned_cols=128  Identities=19%  Similarity=0.227  Sum_probs=70.8

Q ss_pred             cccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHH
Q 004895          161 IFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  227 (724)
                      .+-|-+-.++++.+...             -+..+-+.++|++|.|||.||+.|+++....       |+.|-+.    +
T Consensus       156 diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~-------firvvgs----e  224 (408)
T KOG0727|consen  156 DIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAA-------FIRVVGS----E  224 (408)
T ss_pred             ccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchh-------eeeeccH----H
Confidence            34455555555555432             2356778899999999999999999976532       3433321    2


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccc-------c-ccccCCCCcCCCCCCCCC
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDK-------I-GIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~-------l-~~~~~~~~~~~~~~~~~~  297 (724)
                      ..+   +.+|...       .....+++.-+.+.+-.|++|.++....  ++.       + ...+..+.+.+.+.....
T Consensus       225 fvq---kylgegp-------rmvrdvfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~n  294 (408)
T KOG0727|consen  225 FVQ---KYLGEGP-------RMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTN  294 (408)
T ss_pred             HHH---HHhccCc-------HHHHHHHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccc
Confidence            211   1233211       1233444444556788999999865411  000       0 011111223344456677


Q ss_pred             cEEEEEecccch
Q 004895          298 CTIILTSRSRDL  309 (724)
Q Consensus       298 s~ilvTtR~~~v  309 (724)
                      .|||+.|...+.
T Consensus       295 vkvimatnradt  306 (408)
T KOG0727|consen  295 VKVIMATNRADT  306 (408)
T ss_pred             eEEEEecCcccc
Confidence            888888876553

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.38  E-value=0.031  Score=56.00  Aligned_cols=93  Identities=19%  Similarity=0.300  Sum_probs=57.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCC--------CCCCCchhH---
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGM--------NFDSNDLIY---  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~--------~~~~~~~~~---  247 (724)
                      +-+.++|+|..|+|||||++.+++..+.+ +-+.++++-+.+.. ...++.+++...-..        ..++.....   
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~~i~~~-~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~  146 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELINNIAKA-HGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARV  146 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHHHHHhc-CCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHH
Confidence            44578999999999999999999988753 23456677776654 345555555443111        111211111   


Q ss_pred             -HHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          248 -HRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       248 -~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                       ..+-.+.+++.  +++++|+++||+-..
T Consensus       147 ~~~a~~~AEyfr~~~g~~Vl~~~Dsltr~  175 (274)
T cd01133         147 ALTGLTMAEYFRDEEGQDVLLFIDNIFRF  175 (274)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEEeChhHH
Confidence             11233445553  278999999998543

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.

>PRK06526 transposase; Provisional

Probab=96.37  E-value=0.0088  Score=59.88  Aligned_cols=74  Identities=20%  Similarity=0.214  Sum_probs=44.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      ..-+.|+|++|+|||+||..+.+..... .+ .+.|+      +..+++..+.....    ...     .......+.  
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~-g~-~v~f~------t~~~l~~~l~~~~~----~~~-----~~~~l~~l~--  158 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQA-GH-RVLFA------TAAQWVARLAAAHH----AGR-----LQAELVKLG--  158 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHC-CC-chhhh------hHHHHHHHHHHHHh----cCc-----HHHHHHHhc--
Confidence            4468999999999999999999887543 22 23443      33445555543211    111     111222332  


Q ss_pred             CcEEEEEcccccc
Q 004895          261 KRVLIILDNIWTK  273 (724)
Q Consensus       261 kr~LlVlDdv~~~  273 (724)
                      +.-+||+||+...
T Consensus       159 ~~dlLIIDD~g~~  171 (254)
T PRK06526        159 RYPLLIVDEVGYI  171 (254)
T ss_pred             cCCEEEEcccccC
Confidence            3469999999643

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.36  E-value=0.029  Score=61.81  Aligned_cols=160  Identities=18%  Similarity=0.127  Sum_probs=85.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC--ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP--DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      ..-|.|.|+.|+|||+||+.+++... +.+.-.+.+++++.-.  ..+.+++.+-.                 ...+.+.
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~-----------------vfse~~~  492 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNN-----------------VFSEALW  492 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHH-----------------HHHHHHh
Confidence            45788999999999999999999987 4444456677776432  23333322211                 1222233


Q ss_pred             cCCcEEEEEccccccc--------cccccc---c-ccCCCCcCCCCCCCCCcEEEEEecccchhh----hhcCCCceEec
Q 004895          259 KEKRVLIILDNIWTKL--------ELDKIG---I-PYGDVDEKDKNDDPRRCTIILTSRSRDLLC----IDMNSQKMFWI  322 (724)
Q Consensus       259 ~~kr~LlVlDdv~~~~--------~~~~l~---~-~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~----~~~~~~~~~~l  322 (724)
                       -.+-+|||||++...        +|....   . .+..+ ..++...++.-++|.|.....-..    ..........|
T Consensus       493 -~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqv-i~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L  570 (952)
T KOG0735|consen  493 -YAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQV-IKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIAL  570 (952)
T ss_pred             -hCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHH-HHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEec
Confidence             367899999995431        221100   0 00000 000000122224555555443211    11122346788


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc
Q 004895          323 DALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL  361 (724)
Q Consensus       323 ~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl  361 (724)
                      ..+...+-.++++.......... ......-+..+|+|+
T Consensus       571 ~ap~~~~R~~IL~~~~s~~~~~~-~~~dLd~ls~~TEGy  608 (952)
T KOG0735|consen  571 PAPAVTRRKEILTTIFSKNLSDI-TMDDLDFLSVKTEGY  608 (952)
T ss_pred             CCcchhHHHHHHHHHHHhhhhhh-hhHHHHHHHHhcCCc
Confidence            89998888888877654322111 123334488888875

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=96.35  E-value=0.015  Score=60.01  Aligned_cols=29  Identities=24%  Similarity=0.279  Sum_probs=25.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .....++|+|++|+|||.+|+.+++....
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~elg~  174 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKMGI  174 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHcCC
Confidence            34678999999999999999999998864

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.33  E-value=0.029  Score=58.39  Aligned_cols=59  Identities=25%  Similarity=0.286  Sum_probs=36.5

Q ss_pred             CcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          297 RCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       297 ~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      ++.+|++|.+.. +..........+.+.+++.+++.+.+.+. +.   ..  .  . ..+..++|.|+.
T Consensus       143 ~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~-~~---~~--~--~-~~l~~~~g~p~~  202 (325)
T PRK08699        143 QVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER-GV---AE--P--E-ERLAFHSGAPLF  202 (325)
T ss_pred             CCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc-CC---Cc--H--H-HHHHHhCCChhh
Confidence            455666666654 43333445578999999999998888654 11   11  1  1 123568898964

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.31  E-value=0.022  Score=59.39  Aligned_cols=91  Identities=21%  Similarity=0.198  Sum_probs=57.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh---ccC-CCeEEEEEEecCCChHHHHHHHHHhhCCCCCC---------Cchh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME---DNV-FDKVVMAEITKNPDAQKIQGELASDLGMNFDS---------NDLI  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~-F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~---------~~~~  246 (724)
                      .-+++-|+|++|+|||+|+.+++-....   ... -..++||+..+.|+.+++. ++++.++.+.+.         ....
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~-~ia~~~g~d~~~~l~~I~~~~~~~~  203 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIV-PIAERFGMDADAVLDNIIYARAYTY  203 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHH-HHHHHcCCChhhhcCeEEEecCCCH
Confidence            3468889999999999999998654321   111 2468999999999988874 466776654211         0001


Q ss_pred             HH---HHHHHHHHHhcCCcEEEEEcccc
Q 004895          247 YH---RAKQLCQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       247 ~~---~~~~l~~~l~~~kr~LlVlDdv~  271 (724)
                      ++   ....+...+...+--|||+|.+-
T Consensus       204 e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        204 EHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            11   22223233333455688999874

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.30  E-value=0.025  Score=59.12  Aligned_cols=58  Identities=26%  Similarity=0.328  Sum_probs=42.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEEEEecCCChHHHHHHHHHhhCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEITKNPDAQKIQGELASDLGM  238 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~l~~~i~~~l~~  238 (724)
                      ...++-|+|++|+|||+|+.+++........    =..++||+..+.++..++. ++++.++.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~-~~~~~~g~  162 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE-QMAEALGL  162 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH-HHHHHcCC
Confidence            3568899999999999999999876532111    1368999998888877764 45555553

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.30  E-value=0.016  Score=61.46  Aligned_cols=85  Identities=21%  Similarity=0.259  Sum_probs=46.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..++.++|++|+||||++..++........+ .+..++... .....+.++..++.++.+.....    ....+.+.+..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~-~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~~----~~~~l~~~l~~  297 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGK-SVSLYTTDNYRIAAIEQLKRYADTMGMPFYPVK----DIKKFKETLAR  297 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCC-eEEEecccchhhhHHHHHHHHHHhcCCCeeehH----HHHHHHHHHHh
Confidence            4689999999999999999999865332222 233333221 11223344455555555432211    12334444433


Q ss_pred             CCcEEEEEccc
Q 004895          260 EKRVLIILDNI  270 (724)
Q Consensus       260 ~kr~LlVlDdv  270 (724)
                      ...-++|+|-.
T Consensus       298 ~~~D~VLIDTa  308 (432)
T PRK12724        298 DGSELILIDTA  308 (432)
T ss_pred             CCCCEEEEeCC
Confidence            23346888843

>PTZ00494 tuzin-like protein; Provisional

Probab=96.28  E-value=0.14  Score=53.84  Aligned_cols=164  Identities=12%  Similarity=0.147  Sum_probs=100.0

Q ss_pred             CCcccccccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          155 DMKDYNIFNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       155 ~~~~~~~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .+.....++.|+.+-..+.+.|.   ...++++.+.|.-|.||++|.+........     ..++|++...   ++-++.
T Consensus       366 a~a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE~~-----paV~VDVRg~---EDtLrs  437 (664)
T PTZ00494        366 AAAAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVEGV-----ALVHVDVGGT---EDTLRS  437 (664)
T ss_pred             cccccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHcCC-----CeEEEEecCC---cchHHH
Confidence            35556678899988887777775   356889999999999999999999887654     2678888765   456788


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHH------hcCCcEEEEEcccccccc----ccccccccCCCCcCCCCCCCCCcEEE
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRL------KKEKRVLIILDNIWTKLE----LDKIGIPYGDVDEKDKNDDPRRCTII  301 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l------~~~kr~LlVlDdv~~~~~----~~~l~~~~~~~~~~~~~~~~~~s~il  301 (724)
                      +.+.++.+.-+.  -.+..+.+.+..      .+++.=+||+-== +-..    +++. ..+..        ...-|.|+
T Consensus       438 VVKALgV~nve~--CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLR-EGssL~RVYnE~-vaLac--------DrRlCHvv  505 (664)
T PTZ00494        438 VVRALGVSNVEV--CGDLLGFVEEAMRGATVKASDGVPFLVMRLR-EGSDLGRVYGEV-VSLVS--------DCQACHIV  505 (664)
T ss_pred             HHHHhCCCChhh--hccHHHHHHHHHHHHHHhcCCCCCEEEEEec-cCCcHHHHHHHH-HHHHc--------cchhheee
Confidence            999998764321  111222222211      1244445554321 1111    1111 11222        34556677


Q ss_pred             EEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      +---.+.+-  ......-.-|.+++|+.++|.++.++..
T Consensus       506 ~EVplESLT~~n~~LPRLDFy~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        506 LAVPMKALTPLNVSSRRLDFYCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             eechHhhhchhhccCccceeEecCCcCHHHHHHHHhccc
Confidence            654443321  1122334578899999999999888764

>PRK04296 thymidine kinase; Provisional

Probab=96.26  E-value=0.0071  Score=57.92  Aligned_cols=112  Identities=17%  Similarity=0.111  Sum_probs=61.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC--CchhHHHHHHHHHHHhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS--NDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~--~~~~~~~~~~l~~~l~~  259 (724)
                      .++.|+|+.|.||||+|..++.+....  -..++.+.  ..++.......+++.++.....  .....+....+.+  ..
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~--g~~v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~~--~~   76 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEER--GMKVLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIEE--EG   76 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHc--CCeEEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHHh--hC
Confidence            467899999999999999999987643  22334342  1112222233456666644322  1112222333333  23


Q ss_pred             CCcEEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          260 EKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       260 ~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      ++.-+||+|.+.-.  ++..++...+          ...|..|++|.+..+.
T Consensus        77 ~~~dvviIDEaq~l~~~~v~~l~~~l----------~~~g~~vi~tgl~~~~  118 (190)
T PRK04296         77 EKIDCVLIDEAQFLDKEQVVQLAEVL----------DDLGIPVICYGLDTDF  118 (190)
T ss_pred             CCCCEEEEEccccCCHHHHHHHHHHH----------HHcCCeEEEEecCccc
Confidence            34458999999432  1122221111          3457789999988653

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.25  E-value=0.056  Score=57.63  Aligned_cols=165  Identities=21%  Similarity=0.252  Sum_probs=87.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH--
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL--  257 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l--  257 (724)
                      ....+.+.|++|+|||+||..++..-    .|..+--++..+-....                   +......+.+..  
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~S----~FPFvKiiSpe~miG~s-------------------EsaKc~~i~k~F~D  593 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALSS----DFPFVKIISPEDMIGLS-------------------ESAKCAHIKKIFED  593 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhhc----CCCeEEEeChHHccCcc-------------------HHHHHHHHHHHHHH
Confidence            45567789999999999999998643    36544333221111111                   111222222222  


Q ss_pred             -hcCCcEEEEEccccccccccccccccCCCCc-----CCCCCCCCCcE--EEEEecccchhhhhcC----CCceEecCCC
Q 004895          258 -KKEKRVLIILDNIWTKLELDKIGIPYGDVDE-----KDKNDDPRRCT--IILTSRSRDLLCIDMN----SQKMFWIDAL  325 (724)
Q Consensus       258 -~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~-----~~~~~~~~~s~--ilvTtR~~~v~~~~~~----~~~~~~l~~L  325 (724)
                       .+..=-.||+||++...+|-.++.-+.....     ..+.....|-|  |+-||....+.. .|+    ....|.++.+
T Consensus       594 AYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~-~m~i~~~F~~~i~Vpnl  672 (744)
T KOG0741|consen  594 AYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQ-EMGILDCFSSTIHVPNL  672 (744)
T ss_pred             hhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHH-HcCHHHhhhheeecCcc
Confidence             1234579999999988888766543221100     01111233333  555666665542 122    2357889999


Q ss_pred             CH-HHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          326 SE-EEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       326 ~~-~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      +. ++..+.++..-  ...+.+.+.++.+...+|-  -..|+-+-.++
T Consensus       673 ~~~~~~~~vl~~~n--~fsd~~~~~~~~~~~~~~~--~vgIKklL~li  716 (744)
T KOG0741|consen  673 TTGEQLLEVLEELN--IFSDDEVRAIAEQLLSKKV--NVGIKKLLMLI  716 (744)
T ss_pred             CchHHHHHHHHHcc--CCCcchhHHHHHHHhcccc--chhHHHHHHHH
Confidence            87 77777776642  1122334556666666662  23344444433

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.22  E-value=0.036  Score=54.92  Aligned_cols=30  Identities=30%  Similarity=0.589  Sum_probs=26.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ++..+++|.|+.|+|||||++.+....+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~~l~~~   60 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEALLQQD   60 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            567799999999999999999999888653

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.21  E-value=0.042  Score=57.58  Aligned_cols=88  Identities=18%  Similarity=0.179  Sum_probs=47.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC--hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD--AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRL  257 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  257 (724)
                      +.++|+++|++|+||||++..++.....+ .+ .+..++.. .+.  ..+-++...+.++.+........... .....+
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~L~~~-Gk-kVglI~aD-t~RiaAvEQLk~yae~lgipv~v~~d~~~L~-~aL~~l  315 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQFHGK-KK-TVGFITTD-HSRIGTVQQLQDYVKTIGFEVIAVRDEAAMT-RALTYF  315 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHHHHHc-CC-cEEEEecC-CcchHHHHHHHHHhhhcCCcEEecCCHHHHH-HHHHHH
Confidence            45799999999999999999999877543 22 34455543 222  22233444455554432111122222 223333


Q ss_pred             hcC-CcEEEEEcccc
Q 004895          258 KKE-KRVLIILDNIW  271 (724)
Q Consensus       258 ~~~-kr~LlVlDdv~  271 (724)
                      ... +.=++++|-.-
T Consensus       316 k~~~~~DvVLIDTaG  330 (436)
T PRK11889        316 KEEARVDYILIDTAG  330 (436)
T ss_pred             HhccCCCEEEEeCcc
Confidence            321 22467777764

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=96.19  E-value=0.06  Score=61.77  Aligned_cols=153  Identities=18%  Similarity=0.150  Sum_probs=79.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      +-|.++|++|+|||++|+.++......  |   +.++.++      +.. +.  .+.       .......+........
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~~~~--f---~~is~~~------~~~-~~--~g~-------~~~~~~~~f~~a~~~~  244 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEAKVP--F---FTISGSD------FVE-MF--VGV-------GASRVRDMFEQAKKAA  244 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHcCCC--E---EEEehHH------hHH-hh--hcc-------cHHHHHHHHHHHHhcC
Confidence            348899999999999999998876432  2   2232221      111 10  010       1112233333334457


Q ss_pred             cEEEEEcccccccccc------------cc-ccccCCCCcCCCCCCCCCcEEEEEecccchhhhh----cCCCceEecCC
Q 004895          262 RVLIILDNIWTKLELD------------KI-GIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCID----MNSQKMFWIDA  324 (724)
Q Consensus       262 r~LlVlDdv~~~~~~~------------~l-~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~  324 (724)
                      +++|++|+++....-.            .. ...+.   ..+......+.-||.||.........    ......+.++.
T Consensus       245 P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~---~mdg~~~~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~  321 (644)
T PRK10733        245 PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLV---EMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGL  321 (644)
T ss_pred             CcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHH---hhhcccCCCCeeEEEecCChhhcCHHHhCCcccceEEEcCC
Confidence            8999999996541100            00 00000   01111133455566677765532111    12245777888


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC
Q 004895          325 LSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG  360 (724)
Q Consensus       325 L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G  360 (724)
                      -+.++-.+++..+.......++.  ....+++.+.|
T Consensus       322 Pd~~~R~~Il~~~~~~~~l~~~~--d~~~la~~t~G  355 (644)
T PRK10733        322 PDVRGREQILKVHMRRVPLAPDI--DAAIIARGTPG  355 (644)
T ss_pred             CCHHHHHHHHHHHhhcCCCCCcC--CHHHHHhhCCC
Confidence            88888888888876533222221  13356666666

>PTZ00301 uridine kinase; Provisional

Probab=96.16  E-value=0.015  Score=56.42  Aligned_cols=26  Identities=35%  Similarity=0.723  Sum_probs=23.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.+|+|.|.+|+||||||+.+.+...
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~~l~   28 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVSELM   28 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHHHHH
Confidence            56899999999999999999988764

>PRK06921 hypothetical protein; Provisional

Probab=96.15  E-value=0.028  Score=56.81  Aligned_cols=39  Identities=28%  Similarity=0.369  Sum_probs=30.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      ....+.++|..|+|||+||..+++....+.. ..++|++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g-~~v~y~~~  154 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKG-VPVLYFPF  154 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcC-ceEEEEEH
Confidence            4567899999999999999999998764312 34667764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.15  E-value=0.033  Score=58.01  Aligned_cols=58  Identities=26%  Similarity=0.312  Sum_probs=42.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHhhCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASDLGM  238 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~l~~  238 (724)
                      .-.++-|+|++|+|||+|+.+++.......    .=..++||+..+.++.+++. ++++.++.
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~gl  155 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARGL  155 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcCC
Confidence            356889999999999999999987753211    01368999998888877654 45555543

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.15  E-value=0.15  Score=56.43  Aligned_cols=154  Identities=18%  Similarity=0.222  Sum_probs=86.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      .-|.++|++|.|||.||.+++.....+       +|+|.+.    +++..   .+|.       .++....++++-+.-+
T Consensus       702 ~giLLyGppGcGKT~la~a~a~~~~~~-------fisvKGP----ElL~K---yIGa-------SEq~vR~lF~rA~~a~  760 (952)
T KOG0735|consen  702 TGILLYGPPGCGKTLLASAIASNSNLR-------FISVKGP----ELLSK---YIGA-------SEQNVRDLFERAQSAK  760 (952)
T ss_pred             cceEEECCCCCcHHHHHHHHHhhCCee-------EEEecCH----HHHHH---Hhcc-------cHHHHHHHHHHhhccC
Confidence            458899999999999999998766432       5676653    33222   2232       3455667777777789


Q ss_pred             cEEEEEcccccccc-------------ccccccccCCCCcCCCCCCCCCcEEEEEecccchh-hhhcCCC---ceEecCC
Q 004895          262 RVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-CIDMNSQ---KMFWIDA  324 (724)
Q Consensus       262 r~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-~~~~~~~---~~~~l~~  324 (724)
                      +|.|++|.+++...             .+.+...+      ++.-+-.|..|+..|...+.. +....+.   ..+.-+.
T Consensus       761 PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTel------DG~Egl~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~  834 (952)
T KOG0735|consen  761 PCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTEL------DGAEGLDGVYILAATSRPDLIDPALLRPGRLDKLVYCPL  834 (952)
T ss_pred             CeEEEeccccccCcccCCCCCCchHHHHHHHHHhh------ccccccceEEEEEecCCccccCHhhcCCCccceeeeCCC
Confidence            99999999976521             11111111      111134566666555544432 1111111   2223333


Q ss_pred             CCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          325 LSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       325 L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      -++.|-.++|+........+.  ....+.++.+.+|..-|
T Consensus       835 P~~~eRl~il~~ls~s~~~~~--~vdl~~~a~~T~g~tgA  872 (952)
T KOG0735|consen  835 PDEPERLEILQVLSNSLLKDT--DVDLECLAQKTDGFTGA  872 (952)
T ss_pred             CCcHHHHHHHHHHhhccCCcc--ccchHHHhhhcCCCchh
Confidence            456666777777654211111  12355677777776644

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=96.15  E-value=0.19  Score=51.55  Aligned_cols=166  Identities=10%  Similarity=0.087  Sum_probs=91.5

Q ss_pred             HHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHH--------hhccCCCeEEEEEE-ecCCChHHHHHHHHHhhCCC
Q 004895          170 QDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQV--------MEDNVFDKVVMAEI-TKNPDAQKIQGELASDLGMN  239 (724)
Q Consensus       170 ~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~--------~~~~~F~~~~wv~v-s~~~~~~~l~~~i~~~l~~~  239 (724)
                      +.+...+..++. .+..++|..|.||+++|..+.+..        ....|.+.+.++.. .+....+++. ++.+.+...
T Consensus         6 ~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~~   84 (299)
T PRK07132          6 KFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYFS   84 (299)
T ss_pred             HHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhccC
Confidence            344445544444 566799999999999999999886        22223333444432 1223333332 333333211


Q ss_pred             CCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecc-cchhhhhcCC
Q 004895          240 FDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS-RDLLCIDMNS  316 (724)
Q Consensus       240 ~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~-~~v~~~~~~~  316 (724)
                      .-                ..+.+-++|+|++....  ..+.+...+..        ....+.+|++|.+ ..+...-.+.
T Consensus        85 ~~----------------~~~~~KvvII~~~e~m~~~a~NaLLK~LEE--------Pp~~t~~il~~~~~~kll~TI~SR  140 (299)
T PRK07132         85 SF----------------VQSQKKILIIKNIEKTSNSLLNALLKTIEE--------PPKDTYFLLTTKNINKVLPTIVSR  140 (299)
T ss_pred             Cc----------------ccCCceEEEEecccccCHHHHHHHHHHhhC--------CCCCeEEEEEeCChHhChHHHHhC
Confidence            10                11466788999986543  23333223322        3345556655543 3333322455


Q ss_pred             CceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          317 QKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       317 ~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      ...+++.++++++..+.+... +   .+   ++.++.++...+|.--|+..
T Consensus       141 c~~~~f~~l~~~~l~~~l~~~-~---~~---~~~a~~~a~~~~~~~~a~~~  184 (299)
T PRK07132        141 CQVFNVKEPDQQKILAKLLSK-N---KE---KEYNWFYAYIFSNFEQAEKY  184 (299)
T ss_pred             eEEEECCCCCHHHHHHHHHHc-C---CC---hhHHHHHHHHcCCHHHHHHH
Confidence            678999999999998877664 1   11   24466677777763344444

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.15  E-value=0.046  Score=54.46  Aligned_cols=49  Identities=12%  Similarity=0.234  Sum_probs=35.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      .-+++.|.|++|+|||+||.++......+  -..++|++..+  +..++.+.+
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~--ge~~lyvs~ee--~~~~i~~~~   68 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGIYVALEE--HPVQVRRNM   68 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc--CCcEEEEEeeC--CHHHHHHHH
Confidence            45699999999999999999987664322  34588888765  444555543

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.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.14  E-value=0.024  Score=59.17  Aligned_cols=59  Identities=19%  Similarity=0.198  Sum_probs=43.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc---c-CCCeEEEEEEecCCChHHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED---N-VFDKVVMAEITKNPDAQKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~  239 (724)
                      ...++-|+|.+|+|||+|+..++-.....   . .-..++|++..+.++.+++ .+|++.++..
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl-~qia~~~~~~  184 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRL-IQIAERFGLN  184 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHH-HHHHHHcCCC
Confidence            35688899999999999999887543211   1 1136999999999988776 5667776644

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.14  E-value=0.01  Score=53.61  Aligned_cols=75  Identities=23%  Similarity=0.396  Sum_probs=45.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC-CCCCCchhHHHHHHHHHHHhcCCc
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM-NFDSNDLIYHRAKQLCQRLKKEKR  262 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~-~~~~~~~~~~~~~~l~~~l~~~kr  262 (724)
                      |.++|++|+|||+||+.+++....     ...-+.++...+..++....--.-+. ......        +.+.+  .+.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~~-----~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~--------l~~a~--~~~   66 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLGR-----PVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGP--------LVRAM--RKG   66 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHTC-----EEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-C--------CCTTH--HEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhc-----ceEEEEeccccccccceeeeeeccccccccccc--------ccccc--cce
Confidence            578999999999999999998832     24557788888877765433221000 000000        11111  157


Q ss_pred             EEEEEcccccc
Q 004895          263 VLIILDNIWTK  273 (724)
Q Consensus       263 ~LlVlDdv~~~  273 (724)
                      .++|||++...
T Consensus        67 ~il~lDEin~a   77 (139)
T PF07728_consen   67 GILVLDEINRA   77 (139)
T ss_dssp             EEEEESSCGG-
T ss_pred             eEEEECCcccC
Confidence            99999999743

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.13  E-value=0.042  Score=59.91  Aligned_cols=89  Identities=19%  Similarity=0.315  Sum_probs=49.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      ...+|+|+|++|+||||++..++.....+.....+..++.... ....+.+....+.++....... .........+.+.
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~-d~~~L~~aL~~l~  427 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEAD-SAESLLDLLERLR  427 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecC-cHHHHHHHHHHhc
Confidence            3579999999999999999999887654322334555554321 1222333334444444332221 1122233333333


Q ss_pred             cCCcEEEEEcccc
Q 004895          259 KEKRVLIILDNIW  271 (724)
Q Consensus       259 ~~kr~LlVlDdv~  271 (724)
                        +.-+||+|..-
T Consensus       428 --~~DLVLIDTaG  438 (559)
T PRK12727        428 --DYKLVLIDTAG  438 (559)
T ss_pred             --cCCEEEecCCC
Confidence              34588888874

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.12  E-value=0.037  Score=54.76  Aligned_cols=53  Identities=17%  Similarity=0.246  Sum_probs=35.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLG  237 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~  237 (724)
                      ...++.|.|++|+||||||.+++.....+.  ..++|++...  +..++.+.+ .+++
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g--~~~~yi~~e~--~~~~~~~~~-~~~g   75 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNG--YSVSYVSTQL--TTTEFIKQM-MSLG   75 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCC--CcEEEEeCCC--CHHHHHHHH-HHhC
Confidence            345999999999999999877766653222  3466776333  445666665 3344

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.12  E-value=0.0081  Score=53.87  Aligned_cols=30  Identities=43%  Similarity=0.571  Sum_probs=25.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD  212 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~  212 (724)
                      .-|.|.||+|+||||+++.+.+..+.+. |.
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g-~k   35 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKG-YK   35 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcC-ce
Confidence            4689999999999999999999988643 54

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.12  E-value=0.022  Score=52.68  Aligned_cols=35  Identities=26%  Similarity=0.321  Sum_probs=28.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      .-..+.|+|+.|.|||||.+.+|...+..   .+.+|+
T Consensus        27 ~Gef~fl~GpSGAGKSTllkLi~~~e~pt---~G~i~~   61 (223)
T COG2884          27 KGEFVFLTGPSGAGKSTLLKLIYGEERPT---RGKILV   61 (223)
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhhhcCC---CceEEE
Confidence            44588999999999999999999988653   345555

>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=96.12  E-value=0.028  Score=52.96  Aligned_cols=26  Identities=35%  Similarity=0.528  Sum_probs=23.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ++.++|++|+||||++..++......
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~   27 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            68899999999999999999887653

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.

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

Probab=96.10  E-value=0.015  Score=65.96  Aligned_cols=105  Identities=20%  Similarity=0.335  Sum_probs=64.6

Q ss_pred             ccccchHHHHHHHHHHhc---------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK---------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~---------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      ..++|.++.+..+.+.+.         +....+...+||.|||||-||+.++...-...  +..+-++.|+....    .
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e--~aliR~DMSEy~Ek----H  564 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDE--QALIRIDMSEYMEK----H  564 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCC--ccceeechHHHHHH----H
Confidence            346799999999888875         22456788899999999999999998773211  33455555543211    2


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcE-EEEEcccccc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRV-LIILDNIWTK  273 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~-LlVlDdv~~~  273 (724)
                      .+.+-+|.++.--.  .+....|-+..++ ++| +|+||+++..
T Consensus       565 sVSrLIGaPPGYVG--yeeGG~LTEaVRr-~PySViLlDEIEKA  605 (786)
T COG0542         565 SVSRLIGAPPGYVG--YEEGGQLTEAVRR-KPYSVILLDEIEKA  605 (786)
T ss_pred             HHHHHhCCCCCCce--eccccchhHhhhc-CCCeEEEechhhhc
Confidence            23333444432111  1112345555554 555 9999999765

>PRK09183 transposase/IS protein; Provisional

Probab=96.08  E-value=0.027  Score=56.74  Aligned_cols=27  Identities=30%  Similarity=0.365  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+.|+|++|+|||+||..+++....
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~  128 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVR  128 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            346789999999999999999887654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.03  E-value=0.038  Score=59.65  Aligned_cols=88  Identities=26%  Similarity=0.322  Sum_probs=51.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCCC---chhHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFDSN---DLIYHRAKQLCQ  255 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~~---~~~~~~~~~l~~  255 (724)
                      ...+|.++|++|+||||+|..++...... .+ .+..+++... +...+.++.+++.++.+....   ...........+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~-g~-kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~  171 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKK-GL-KVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLE  171 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHc-CC-eEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHH
Confidence            46799999999999999999999888753 22 3444544321 223445666777776543221   111222233333


Q ss_pred             HHhcCCcEEEEEcccc
Q 004895          256 RLKKEKRVLIILDNIW  271 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~  271 (724)
                      .+. +. -++|+|..-
T Consensus       172 ~~~-~~-DvVIIDTAG  185 (437)
T PRK00771        172 KFK-KA-DVIIVDTAG  185 (437)
T ss_pred             Hhh-cC-CEEEEECCC
Confidence            333 22 568888773

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.01  E-value=0.0098  Score=64.96  Aligned_cols=47  Identities=17%  Similarity=0.361  Sum_probs=41.1

Q ss_pred             cccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          161 IFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++|.++.+++|++.|.      +.+-+++.++||+|+||||||+.+++-...
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            46799999999999883      456689999999999999999999998754

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.01  E-value=0.029  Score=58.21  Aligned_cols=59  Identities=19%  Similarity=0.191  Sum_probs=41.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh---cc-CCCeEEEEEEecCCChHHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME---DN-VFDKVVMAEITKNPDAQKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~-~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~  239 (724)
                      ...++.|+|.+|+|||||+..++.....   .. .-..++|++..+.++..++ ..+++.++..
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~~  157 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGLN  157 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCCC
Confidence            3578999999999999999998764321   11 1135799998887777764 4556655543

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).

>PRK06547 hypothetical protein; Provisional

Probab=96.00  E-value=0.01  Score=55.63  Aligned_cols=35  Identities=26%  Similarity=0.300  Sum_probs=28.4

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          172 VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       172 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +...+......+|+|.|++|+||||+|+.+.+...
T Consensus         6 ~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~~~~   40 (172)
T PRK06547          6 IAARLCGGGMITVLIDGRSGSGKTTLAGALAARTG   40 (172)
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            33445567788999999999999999999998753

>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=95.98  E-value=0.0082  Score=54.72  Aligned_cols=36  Identities=28%  Similarity=0.466  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      ..||.|+|.+|+||||||+.+.+......  ..+.+++
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~g--~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFARG--IKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHTT--S-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHcC--CcEEEec
Confidence            35899999999999999999999997643  3355554

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 ....

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.92  E-value=0.016  Score=54.54  Aligned_cols=25  Identities=40%  Similarity=0.482  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .|.|.|++|+||||+|+.+.+....
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i   26 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGL   26 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4789999999999999999998654

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

Probab=95.89  E-value=0.0074  Score=58.12  Aligned_cols=25  Identities=48%  Similarity=0.768  Sum_probs=23.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ||+|.|++|+||||+|+.+......
T Consensus         1 IIgI~G~sgSGKTTla~~L~~~L~~   25 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQILNK   25 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCc
Confidence            7999999999999999999999875

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 ....

>PRK07667 uridine kinase; Provisional

Probab=95.88  E-value=0.013  Score=56.37  Aligned_cols=37  Identities=27%  Similarity=0.551  Sum_probs=28.8

Q ss_pred             HHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          171 DVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       171 ~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .|.+.+.  .+...+|+|.|.+|+||||+|+.+......
T Consensus         5 ~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~~l~~   43 (193)
T PRK07667          5 ELINIMKKHKENRFILGIDGLSRSGKTTFVANLKENMKQ   43 (193)
T ss_pred             HHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3444443  344579999999999999999999998764

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.88  E-value=0.18  Score=51.69  Aligned_cols=47  Identities=26%  Similarity=0.190  Sum_probs=33.7

Q ss_pred             cccchHHHHHHHHHHhc--------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          161 IFNSRKKIFQDVIEALK--------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~--------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+-|-+..++.+.+...              -..+.-|.++||+|.|||-||+.++.+...
T Consensus        93 DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga  153 (386)
T KOG0737|consen   93 DIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGA  153 (386)
T ss_pred             hccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCC
Confidence            34455666666555432              124567889999999999999999998754

>cd01394 radB RadB

Probab=95.88  E-value=0.038  Score=54.29  Aligned_cols=43  Identities=23%  Similarity=0.258  Sum_probs=32.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .-.++.|.|.+|+||||||.+++......  -..++|++....+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~~--g~~v~yi~~e~~~~   60 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQ--GKKVAYIDTEGLSS   60 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCCCCH
Confidence            35689999999999999999999876532  23577887655543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.88  E-value=0.0035  Score=36.35  Aligned_cols=21  Identities=29%  Similarity=0.586  Sum_probs=15.3

Q ss_pred             CCcEEEccCCcCcccchhhhc
Q 004895          621 KLEILSLRGAEIKQLPLQIGQ  641 (724)
Q Consensus       621 ~L~~L~l~~~~i~~lp~~i~~  641 (724)
                      +|++||+++|.++.+|+++++
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSN   21 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT
T ss_pred             CccEEECCCCcCEeCChhhcC
Confidence            467788888877777776654

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 ....

>PTZ00035 Rad51 protein; Provisional

Probab=95.88  E-value=0.053  Score=56.77  Aligned_cols=92  Identities=18%  Similarity=0.214  Sum_probs=55.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh---cc-CCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC---------Cchh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME---DN-VFDKVVMAEITKNPDAQKIQGELASDLGMNFDS---------NDLI  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~---~~-~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~---------~~~~  246 (724)
                      .-.++.|+|++|+|||||+..++-....   .. .-..++|++..+.++.+++ ..+++.++.....         ....
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g~~~~~~l~nI~~~~~~~~  195 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFGLDPEDVLDNIAYARAYNH  195 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhCCChHhHhhceEEEccCCH
Confidence            3568999999999999999988765431   00 1234779998887777764 4556665543210         0001


Q ss_pred             HHH---HHHHHHHHhcCCcEEEEEccccc
Q 004895          247 YHR---AKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       247 ~~~---~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                      ++.   ...+...+...+--|||+|-+..
T Consensus       196 e~~~~~l~~~~~~l~~~~~~lvVIDSita  224 (337)
T PTZ00035        196 EHQMQLLSQAAAKMAEERFALLIVDSATA  224 (337)
T ss_pred             HHHHHHHHHHHHHhhccCccEEEEECcHH
Confidence            112   22223333344556899998843

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.88  E-value=0.067  Score=56.83  Aligned_cols=89  Identities=18%  Similarity=0.199  Sum_probs=52.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc--CCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN--VFDKVVMAEITKN-PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQR  256 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~  256 (724)
                      ..++|.++|+.|+||||.+..++.......  .-..+..+++... ....+-++..++.++.+.............+ ..
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L-~~  251 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEI-TQ  251 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHH-HH
Confidence            457999999999999999999998765321  1223555555432 1223336666777776543322122222222 22


Q ss_pred             HhcCCcEEEEEcccc
Q 004895          257 LKKEKRVLIILDNIW  271 (724)
Q Consensus       257 l~~~kr~LlVlDdv~  271 (724)
                      +  .+.-++++|...
T Consensus       252 ~--~~~DlVLIDTaG  264 (388)
T PRK12723        252 S--KDFDLVLVDTIG  264 (388)
T ss_pred             h--CCCCEEEEcCCC
Confidence            2  244688889874

>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=95.83  E-value=0.0079  Score=53.35  Aligned_cols=22  Identities=45%  Similarity=0.897  Sum_probs=20.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|.|++|+||||+|+.+.+..
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            6899999999999999999885

...

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.83  E-value=0.051  Score=58.83  Aligned_cols=87  Identities=22%  Similarity=0.222  Sum_probs=48.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      .+++.++|++|+||||++..++........-..+..++..... ...+-+....+.++.+........+....+ ..+. 
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l-~~~~-  298 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKAL-EQLR-  298 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHH-HHhC-
Confidence            3599999999999999999998876511122346666653221 122334444555555432222122222222 2222 


Q ss_pred             CCcEEEEEccc
Q 004895          260 EKRVLIILDNI  270 (724)
Q Consensus       260 ~kr~LlVlDdv  270 (724)
                       ..=++|+|..
T Consensus       299 -~~DlVlIDt~  308 (424)
T PRK05703        299 -DCDVILIDTA  308 (424)
T ss_pred             -CCCEEEEeCC
Confidence             3468888876

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.83  E-value=0.014  Score=62.99  Aligned_cols=50  Identities=12%  Similarity=0.181  Sum_probs=39.7

Q ss_pred             ccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC
Q 004895          160 NIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF  211 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  211 (724)
                      ..++||++.++.+...+..+.  -|.|.|++|+|||++|+.+.........|
T Consensus        20 ~~i~gre~vI~lll~aalag~--hVLL~GpPGTGKT~LAraLa~~~~~~~~F   69 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQNARAF   69 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC--CEEEECCCChhHHHHHHHHHHHhcccCcc
Confidence            357799999999988876444  57899999999999999999876543334

>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=95.83  E-value=0.044  Score=53.76  Aligned_cols=41  Identities=22%  Similarity=0.217  Sum_probs=28.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      +|+|.|..|+||||||+.+.........=..+..++..+.+
T Consensus         1 IigI~G~sGSGKTTla~~L~~~l~~~~~~~~v~vi~~D~f~   41 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLSRWPDHPNVELITTDGFL   41 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHHHHhhcCCCCcEEEEecCccc
Confidence            58999999999999999999887531001224455554443

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK14974 cell division protein FtsY; Provisional

Probab=95.76  E-value=0.1  Score=54.43  Aligned_cols=57  Identities=32%  Similarity=0.370  Sum_probs=37.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC--hHHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD--AQKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~l~~~i~~~l~~~  239 (724)
                      +..+|.++|++|+||||++..++...... .+ .++.++. +.+.  ..+-++..++.++.+
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~~-g~-~V~li~~-Dt~R~~a~eqL~~~a~~lgv~  197 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKN-GF-SVVIAAG-DTFRAGAIEQLEEHAERLGVK  197 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc-CC-eEEEecC-CcCcHHHHHHHHHHHHHcCCc
Confidence            46799999999999999999999877643 33 2334432 2232  233455667777754

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.76  E-value=0.019  Score=55.41  Aligned_cols=108  Identities=12%  Similarity=0.178  Sum_probs=56.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC--hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD--AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      .+|.|+|+.|+||||++..+.......  ....+++ +.+...  ... ...+..+-....+.    ......+...+..
T Consensus         2 GlilI~GptGSGKTTll~~ll~~~~~~--~~~~i~t-~e~~~E~~~~~-~~~~i~q~~vg~~~----~~~~~~i~~aLr~   73 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINKN--KTHHILT-IEDPIEFVHES-KRSLINQREVGLDT----LSFENALKAALRQ   73 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhhhc--CCcEEEE-EcCCccccccC-ccceeeecccCCCc----cCHHHHHHHHhcC
Confidence            478999999999999999888776432  2333332 211110  000 00111111111111    1123345555554


Q ss_pred             CCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          260 EKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                       .+=.+++|++.+.+........           ...|..++.|+-..++
T Consensus        74 -~pd~ii~gEird~e~~~~~l~~-----------a~~G~~v~~t~Ha~~~  111 (198)
T cd01131          74 -DPDVILVGEMRDLETIRLALTA-----------AETGHLVMSTLHTNSA  111 (198)
T ss_pred             -CcCEEEEcCCCCHHHHHHHHHH-----------HHcCCEEEEEecCCcH
Confidence             4669999999766544332111           2235557777776654

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.75  E-value=0.046  Score=56.90  Aligned_cols=38  Identities=26%  Similarity=0.340  Sum_probs=30.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      ...+.++|+.|+|||+||..+++....++  ..++|+++.
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g--~~V~y~t~~  220 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRG--KSVIYRTAD  220 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCC--CeEEEEEHH
Confidence            36799999999999999999999886542  246777653

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.049  Score=56.61  Aligned_cols=86  Identities=28%  Similarity=0.363  Sum_probs=59.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSND-LIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~~  259 (724)
                      -++|.|-|-+|+|||||.-+++.+...+.   .++||+--+  +..++ +--++.|+...+.-. ..+...+.+...+.+
T Consensus        93 Gs~iLIgGdPGIGKSTLLLQva~~lA~~~---~vLYVsGEE--S~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~~  166 (456)
T COG1066          93 GSVILIGGDPGIGKSTLLLQVAARLAKRG---KVLYVSGEE--SLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELEQ  166 (456)
T ss_pred             ccEEEEccCCCCCHHHHHHHHHHHHHhcC---cEEEEeCCc--CHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHHh
Confidence            46899999999999999999999987653   677776544  33332 333556665432211 123345667777777


Q ss_pred             CCcEEEEEccccc
Q 004895          260 EKRVLIILDNIWT  272 (724)
Q Consensus       260 ~kr~LlVlDdv~~  272 (724)
                      .++-++|+|-+..
T Consensus       167 ~~p~lvVIDSIQT  179 (456)
T COG1066         167 EKPDLVVIDSIQT  179 (456)
T ss_pred             cCCCEEEEeccce
Confidence            7899999999854

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.73  E-value=0.034  Score=57.03  Aligned_cols=28  Identities=29%  Similarity=0.315  Sum_probs=24.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .-+-|..+|++|.|||-||+.|+.....
T Consensus       244 PWkgvLm~GPPGTGKTlLAKAvATEc~t  271 (491)
T KOG0738|consen  244 PWKGVLMVGPPGTGKTLLAKAVATECGT  271 (491)
T ss_pred             ccceeeeeCCCCCcHHHHHHHHHHhhcC
Confidence            3467889999999999999999998764

>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=95.72  E-value=0.0094  Score=46.39  Aligned_cols=23  Identities=43%  Similarity=0.746  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +|.|.|..|+||||+++.+.+..
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999886

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.

>TIGR00959 ffh signal recognition particle protein

Probab=95.72  E-value=0.072  Score=57.39  Aligned_cols=91  Identities=20%  Similarity=0.197  Sum_probs=49.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCC---CchhHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFDS---NDLIYHRAKQLCQ  255 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~l~~  255 (724)
                      ...++.++|++|+||||.|..++.....+..+ .++-|++... +...+-+....+..+.+.-.   ............+
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~-kV~lV~~D~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~~al~  176 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYYLKKKQGK-KVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIARRALE  176 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhCCC-eEEEEeccccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHHHHHH
Confidence            46799999999999999999999886432222 3444444321 12233344555665544211   1112233333333


Q ss_pred             HHhcCCcEEEEEcccc
Q 004895          256 RLKKEKRVLIILDNIW  271 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~  271 (724)
                      .......=++|+|-.-
T Consensus       177 ~~~~~~~DvVIIDTaG  192 (428)
T TIGR00959       177 YAKENGFDVVIVDTAG  192 (428)
T ss_pred             HHHhcCCCEEEEeCCC
Confidence            3332232377777764

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.

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.70  E-value=0.066  Score=59.29  Aligned_cols=179  Identities=17%  Similarity=0.161  Sum_probs=90.7

Q ss_pred             ccccchHHH---HHHHHHHhcCCC---------ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHH
Q 004895          160 NIFNSRKKI---FQDVIEALKDDK---------LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       160 ~~~~gR~~~---~~~l~~~L~~~~---------~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  227 (724)
                      ..+.|.++.   +.++++.|.++.         ++-+.++|++|.|||.||+.++-...+-       +.+.|... .. 
T Consensus       150 ~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VP-------Ff~iSGS~-FV-  220 (596)
T COG0465         150 ADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP-------FFSISGSD-FV-  220 (596)
T ss_pred             hhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCC-------ceeccchh-hh-
Confidence            344576654   455566666432         4568899999999999999999988763       22333221 00 


Q ss_pred             HHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccccc------------c-cccccCCCCcCCCCCC
Q 004895          228 IQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELD------------K-IGIPYGDVDEKDKNDD  294 (724)
Q Consensus       228 l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~------------~-l~~~~~~~~~~~~~~~  294 (724)
                         ++.-..         .......++..-++.-++.+++|.++....-.            + +...+   ...+.+..
T Consensus       221 ---emfVGv---------GAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlL---vEmDGF~~  285 (596)
T COG0465         221 ---EMFVGV---------GASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLL---VEMDGFGG  285 (596)
T ss_pred             ---hhhcCC---------CcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHH---hhhccCCC
Confidence               111111         11234445555444568999999986542111            1 11111   11223333


Q ss_pred             CCCcEEEEEecccchhh----hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          295 PRRCTIILTSRSRDLLC----IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~~----~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      +.|-.|+..|-..+|..    ........+.++.-+-..-.++++-++....-.+. .+ ...|++.+-|.-.|
T Consensus       286 ~~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~-Vd-l~~iAr~tpGfsGA  357 (596)
T COG0465         286 NEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAED-VD-LKKIARGTPGFSGA  357 (596)
T ss_pred             CCceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCc-CC-HHHHhhhCCCcccc
Confidence            44555555555555531    11122234444444445555566655543222222 12 23377777776543

>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=95.69  E-value=0.0099  Score=53.96  Aligned_cols=24  Identities=46%  Similarity=0.758  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +|.++|++|+||||+|+.+.....
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~   24 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG   24 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Confidence            688999999999999999986553

...

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=95.69  E-value=0.054  Score=49.54  Aligned_cols=25  Identities=24%  Similarity=0.662  Sum_probs=22.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|.|+|.+|+||||+|+.+......
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~l~~   25 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEKLFQ   25 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            5789999999999999999998753

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.68  E-value=0.07  Score=54.32  Aligned_cols=28  Identities=25%  Similarity=0.322  Sum_probs=23.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+|+|.|+.|+||||+|+.+..-..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~ll~   87 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQALLS   87 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567999999999999999998876654

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.65  E-value=0.079  Score=52.68  Aligned_cols=87  Identities=16%  Similarity=0.258  Sum_probs=53.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----------------
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----------------  242 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----------------  242 (724)
                      .-+++.|+|.+|+|||+||.++......+  =..++|++..+.  ..++.+.+ ++++....+                 
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~--g~~~~y~~~e~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~   98 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ--GKKVYVITTENT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGF   98 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC--CCEEEEEEcCCC--HHHHHHHH-HHCCCChhHHHhCCCceEEecccccc
Confidence            45799999999999999999997654322  245888888654  34555543 333322110                 


Q ss_pred             ---CchhHHHHHHHHHHHhcCCcEEEEEcccc
Q 004895          243 ---NDLIYHRAKQLCQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       243 ---~~~~~~~~~~l~~~l~~~kr~LlVlDdv~  271 (724)
                         ..........+.+.+...+.-++|+|.+-
T Consensus        99 ~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         99 EWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             ccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence               01113344555555544456689999985

>PRK10867 signal recognition particle protein; Provisional

Probab=95.63  E-value=0.062  Score=57.93  Aligned_cols=58  Identities=22%  Similarity=0.322  Sum_probs=35.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh--HHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA--QKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~l~~~i~~~l~~~  239 (724)
                      ...+|.++|++|+||||+|..++.....+.. ..++.|++. .+..  .+-++...+..+.+
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~~l~~~~G-~kV~lV~~D-~~R~aa~eQL~~~a~~~gv~  158 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAKYLKKKKK-KKVLLVAAD-VYRPAAIEQLKTLGEQIGVP  158 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHhcC-CcEEEEEcc-ccchHHHHHHHHHHhhcCCe
Confidence            4679999999999999999999887764311 224444443 2222  22334445555543

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.60  E-value=0.23  Score=57.91  Aligned_cols=61  Identities=13%  Similarity=0.187  Sum_probs=41.1

Q ss_pred             ccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          160 NIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      ..++|+...+..+.+.+.  .....-|.|+|..|+|||++|+.+++.....  -...+.+++..-
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~--~~~~v~i~c~~~  438 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRN--NRRMVKMNCAAM  438 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCC--CCCeEEEecccC
Confidence            357788877777765554  2333467899999999999999998765321  123555666543

>PRK08233 hypothetical protein; Provisional

Probab=95.60  E-value=0.0099  Score=56.52  Aligned_cols=26  Identities=31%  Similarity=0.555  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|+|.|++|+||||||+.++....
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999998764

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=95.59  E-value=0.77  Score=47.60  Aligned_cols=47  Identities=26%  Similarity=0.201  Sum_probs=33.6

Q ss_pred             eEecCCCCHHHHHHHHHHHhCCCCC--CCCchhHHHHHHHHhCCchhHH
Q 004895          319 MFWIDALSEEEALQLFEKIVGESTK--ASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       319 ~~~l~~L~~~e~~~Lf~~~~~~~~~--~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ++++++++.+|+..++.......-.  ...-+...+++.-..+|+|.-+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHh
Confidence            7899999999999999987742211  1233456667777779999643

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.59  E-value=0.053  Score=52.04  Aligned_cols=41  Identities=27%  Similarity=0.428  Sum_probs=29.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCC--------CeEEEEEEecC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVF--------DKVVMAEITKN  222 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--------~~~~wv~vs~~  222 (724)
                      .++.|+|++|+||||++..++........|        ..++|++....
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            488999999999999999999987643222        35788876654

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=95.59  E-value=0.16  Score=44.14  Aligned_cols=45  Identities=22%  Similarity=0.347  Sum_probs=32.4

Q ss_pred             ccchHHHHHHHHHHhc-------CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          162 FNSRKKIFQDVIEALK-------DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~-------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++|..-..+.+++.+.       ..+.-|++..|++|+|||.+++.+++..-
T Consensus        27 l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly   78 (127)
T PF06309_consen   27 LFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLY   78 (127)
T ss_pred             ccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHH
Confidence            4455544455554443       23556999999999999999999999843

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

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.58  E-value=0.012  Score=57.36  Aligned_cols=27  Identities=41%  Similarity=0.608  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+..+|+|+|++|+||||||+.++...
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            356799999999999999999999876

>PRK04328 hypothetical protein; Provisional

Probab=95.58  E-value=0.07  Score=53.52  Aligned_cols=41  Identities=17%  Similarity=0.227  Sum_probs=32.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      .-+++.|.|.+|+|||+||.++......+  -..++|++..+.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~--ge~~lyis~ee~   62 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM--GEPGVYVALEEH   62 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc--CCcEEEEEeeCC
Confidence            45689999999999999999987764322  345788887664

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.57  E-value=0.052  Score=57.54  Aligned_cols=87  Identities=25%  Similarity=0.317  Sum_probs=53.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSND-LIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~~  259 (724)
                      -.++.|.|.+|+|||||+.+++......  -..++|++..+  +..++ ..-++.++...+.-. ........+.+.+..
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~--g~~VlYvs~EE--s~~qi-~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~  156 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR--GGKVLYVSGEE--SPEQI-KLRADRLGISTENLYLLAETNLEDILASIEE  156 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc--CCeEEEEECCc--CHHHH-HHHHHHcCCCcccEEEEccCcHHHHHHHHHh
Confidence            4689999999999999999999877543  24577887643  33333 222445554322110 001123445555554


Q ss_pred             CCcEEEEEccccc
Q 004895          260 EKRVLIILDNIWT  272 (724)
Q Consensus       260 ~kr~LlVlDdv~~  272 (724)
                      .+.-++|+|.+..
T Consensus       157 ~~~~lVVIDSIq~  169 (372)
T cd01121         157 LKPDLVIIDSIQT  169 (372)
T ss_pred             cCCcEEEEcchHH
Confidence            5677899999843

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.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=95.56  E-value=0.025  Score=49.95  Aligned_cols=44  Identities=25%  Similarity=0.288  Sum_probs=31.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .+-|.|.|-+|+||||||.+++....       .-|+++|+-....++...
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~-------~~~i~isd~vkEn~l~~g   50 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTG-------LEYIEISDLVKENNLYEG   50 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhC-------CceEehhhHHhhhcchhc
Confidence            35688999999999999999996543       237888765444444333

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.55  E-value=1.2  Score=46.99  Aligned_cols=58  Identities=26%  Similarity=0.308  Sum_probs=39.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC--ChHHHHHHHHHhhCCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP--DAQKIQGELASDLGMNF  240 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~l~~~~  240 (724)
                      .+.||..+|.-|.||||.|-.+++.++.+ .+  ..-+...+.+  ..-+-++.+.++++.+.
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~~lkk~-~~--kvllVaaD~~RpAA~eQL~~La~q~~v~~  158 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAKYLKKK-GK--KVLLVAADTYRPAAIEQLKQLAEQVGVPF  158 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHHHHHHc-CC--ceEEEecccCChHHHHHHHHHHHHcCCce
Confidence            46799999999999999999999998762 22  2223233333  33445677777777653

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.55  E-value=0.13  Score=53.92  Aligned_cols=73  Identities=21%  Similarity=0.297  Sum_probs=42.5

Q ss_pred             HHHHHHHhcCC----CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCC
Q 004895          169 FQDVIEALKDD----KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFD  241 (724)
Q Consensus       169 ~~~l~~~L~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~  241 (724)
                      ...+..++.++    +.++|++||+.|+||||-....+..+.-...=..+..|+.... ....+-++..++-++.+..
T Consensus       187 l~~~~~~~~~~~~~~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~  264 (407)
T COG1419         187 LRKLLLSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLE  264 (407)
T ss_pred             HHHHHHhhccccccccCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceE
Confidence            33444444433    4789999999999996654444444431112244677766432 2344455666677776654

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.55  E-value=0.022  Score=53.86  Aligned_cols=47  Identities=26%  Similarity=0.304  Sum_probs=32.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ..+|+|-||-|+||||||+.++++....     +++-.+.+++=++....++
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~~~-----~~~E~vednp~L~~FY~d~   50 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLGFK-----VFYELVEDNPFLDLFYEDP   50 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHhCCc-----eeeecccCChHHHHHHHhH
Confidence            4689999999999999999999988643     3334444544344444443

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.53  E-value=0.016  Score=56.36  Aligned_cols=60  Identities=22%  Similarity=0.323  Sum_probs=38.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE---------ecCCChHHH--HHHHHHhhCCCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI---------TKNPDAQKI--QGELASDLGMNFD  241 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v---------s~~~~~~~l--~~~i~~~l~~~~~  241 (724)
                      +...|.++||+|+||||+.+.++.+...++...  .-|++         .-+.++.+.  .++..++.+..+.
T Consensus        18 ~p~~ilVvGMAGSGKTTF~QrL~~hl~~~~~pp--YviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LGPN   88 (366)
T KOG1532|consen   18 RPVIILVVGMAGSGKTTFMQRLNSHLHAKKTPP--YVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLGPN   88 (366)
T ss_pred             CCcEEEEEecCCCCchhHHHHHHHHHhhccCCC--eEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCCCC
Confidence            455788899999999999999999987653322  22232         223345443  3566666655443

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.53  E-value=0.035  Score=55.49  Aligned_cols=28  Identities=32%  Similarity=0.427  Sum_probs=25.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .++|.++||+|.|||+|++..++...++
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR  204 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIR  204 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheee
Confidence            4789999999999999999999998663

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.49  E-value=0.022  Score=56.65  Aligned_cols=63  Identities=22%  Similarity=0.422  Sum_probs=47.2

Q ss_pred             HHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          170 QDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       170 ~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      .+|+..+.  .++..+|+|.|.+|+|||||.-.+...+..+.+--.++=|+-|..++-..++.+=
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TGGsiLGDR  102 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGDR  102 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCCccccccH
Confidence            34554443  5677899999999999999999999999877665566777777777655555443

>CHL00206 ycf2 Ycf2; Provisional

Probab=95.49  E-value=0.12  Score=63.95  Aligned_cols=28  Identities=32%  Similarity=0.275  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+-|.++|++|+|||.||++++.+..+
T Consensus      1629 pPKGILLiGPPGTGKTlLAKALA~es~V 1656 (2281)
T CHL00206       1629 PSRGILVIGSIGTGRSYLVKYLATNSYV 1656 (2281)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHhcCC
Confidence            3567889999999999999999998754

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.48  E-value=0.0046  Score=60.82  Aligned_cols=86  Identities=22%  Similarity=0.186  Sum_probs=46.7

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccc-cCCCCCcEEEcCCcccCC---cccccCCCCC
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSL-GRLINLQTLCLDGWRLED---IAIVGQLKKL  622 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i-~~l~~L~~L~L~~~~l~~---~~~~~~l~~L  622 (724)
                      .+++++.|++.++......-....+.+++.|++|+++.|++.+.-.++ -.+.+|++|-|.++.+..   -..+..++.+
T Consensus        69 ~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~L~w~~~~s~l~~lP~v  148 (418)
T KOG2982|consen   69 SVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTGLSWTQSTSSLDDLPKV  148 (418)
T ss_pred             HhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCCCChhhhhhhhhcchhh
Confidence            455666666633222222222344566777777777777665321222 235567777776666554   2445566666


Q ss_pred             cEEEccCCcC
Q 004895          623 EILSLRGAEI  632 (724)
Q Consensus       623 ~~L~l~~~~i  632 (724)
                      +.|.++.|.+
T Consensus       149 telHmS~N~~  158 (418)
T KOG2982|consen  149 TELHMSDNSL  158 (418)
T ss_pred             hhhhhccchh
Confidence            6666666643

>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=95.48  E-value=0.021  Score=54.68  Aligned_cols=51  Identities=24%  Similarity=0.390  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          166 KKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       166 ~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      ..+-...++.|.  ...++.+.|++|.|||.||...+-+.-..+.|+.++++.
T Consensus         6 ~~~Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~R   56 (205)
T PF02562_consen    6 NEEQKFALDALL--NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITR   56 (205)
T ss_dssp             SHHHHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE
T ss_pred             CHHHHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            344445556555  456999999999999999999998776668899888774

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK06762 hypothetical protein; Provisional

Probab=95.45  E-value=0.014  Score=54.64  Aligned_cols=25  Identities=36%  Similarity=0.581  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|+|++|+||||+|+.+.+..
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3589999999999999999999876

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.45  E-value=0.091  Score=54.95  Aligned_cols=90  Identities=20%  Similarity=0.185  Sum_probs=53.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      +.+++.++|+.|+||||++..++.....+.  ..+.+++..... ...+-++..++.++.+........+. ......+.
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g--~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL-~~al~~l~  281 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQN--RTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAEL-EEAVQYMT  281 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHH-HHHHHHHH
Confidence            457999999999999999999998765432  346666664322 23445566677676553222212222 22233333


Q ss_pred             c-CCcEEEEEccccc
Q 004895          259 K-EKRVLIILDNIWT  272 (724)
Q Consensus       259 ~-~kr~LlVlDdv~~  272 (724)
                      . +..=++++|-.-.
T Consensus       282 ~~~~~D~VLIDTAGr  296 (407)
T PRK12726        282 YVNCVDHILIDTVGR  296 (407)
T ss_pred             hcCCCCEEEEECCCC
Confidence            1 2345778887743

>TIGR00235 udk uridine kinase

Probab=95.44  E-value=0.014  Score=56.92  Aligned_cols=28  Identities=43%  Similarity=0.536  Sum_probs=24.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+|+|+|++|+||||||+.++....
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~~l~   31 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYEQLG   31 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3457999999999999999999998764

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=95.44  E-value=0.069  Score=54.89  Aligned_cols=86  Identities=20%  Similarity=0.208  Sum_probs=51.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLCQ  255 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~~  255 (724)
                      -+++-|+|+.|+||||||..+.......  -..++||+....++.     ..++.+|.+.+.     +...++....+.+
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia~~q~~--g~~~a~ID~e~~ld~-----~~a~~lGvdl~rllv~~P~~~E~al~~~e~  125 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIAEAQKQ--GGICAFIDAEHALDP-----EYAESLGVDLDRLLVVQPDTGEQALWIAEQ  125 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--T-EEEEEESSS---H-----HHHHHTT--GGGEEEEE-SSHHHHHHHHHH
T ss_pred             CceEEEeCCCCCchhhhHHHHHHhhhcc--cceeEEecCcccchh-----hHHHhcCccccceEEecCCcHHHHHHHHHH
Confidence            4699999999999999999999876543  345899998776654     445666654321     1112223333333


Q ss_pred             HHhcCCcEEEEEcccccc
Q 004895          256 RLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~~~  273 (724)
                      .++.+.--++|+|-|-..
T Consensus       126 lirsg~~~lVVvDSv~al  143 (322)
T PF00154_consen  126 LIRSGAVDLVVVDSVAAL  143 (322)
T ss_dssp             HHHTTSESEEEEE-CTT-
T ss_pred             HhhcccccEEEEecCccc
Confidence            334455568999988543

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 ....

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.44  E-value=0.067  Score=50.47  Aligned_cols=28  Identities=29%  Similarity=0.507  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+|.|+|++|+||||+|+.++.....
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~   30 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLRE   30 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4568999999999999999999998864

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.44  E-value=0.014  Score=55.80  Aligned_cols=26  Identities=35%  Similarity=0.431  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++++|.|+|++|+||||+|+.+....
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.

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=95.43  E-value=0.026  Score=56.92  Aligned_cols=26  Identities=38%  Similarity=0.570  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +.|.|+|.+|+||||+|+.+......
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~~~~   27 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKYLEE   27 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHHHh
Confidence            47899999999999999999998775

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.42  E-value=0.1  Score=47.86  Aligned_cols=116  Identities=20%  Similarity=0.233  Sum_probs=61.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec---CCChHHHHHHHHHhh-----CCC--CCCCchhH----
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK---NPDAQKIQGELASDL-----GMN--FDSNDLIY----  247 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~---~~~~~~l~~~i~~~l-----~~~--~~~~~~~~----  247 (724)
                      ..|-|++..|.||||+|.-.+-+.... .+ .+.++-.-+   ..+....++.+ ..+     +..  ........    
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 GLIQVYTGNGKGKTTAALGLALRALGH-GY-RVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHC-CC-eEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            468888889999999999998877643 22 234433322   23333333333 111     111  11111111    


Q ss_pred             --HHHHHHHHHHhcCCcEEEEEcccccccc-----ccccccccCCCCcCCCCCCCCCcEEEEEecccc
Q 004895          248 --HRAKQLCQRLKKEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD  308 (724)
Q Consensus       248 --~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~  308 (724)
                        .......+.+..+.-=|+|||++-....     .+.+...+..        ...+.-||+|.|+..
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~--------rp~~~evIlTGr~~p  139 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKA--------KPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHc--------CCCCCEEEEECCCCC
Confidence              1122333344445556999999965422     2333233332        445678999999975

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.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.40  E-value=0.078  Score=53.05  Aligned_cols=94  Identities=20%  Similarity=0.185  Sum_probs=58.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh--ccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchh--
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME--DNVFDKVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLI--  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~--  246 (724)
                      +-+.++|.|-.|+|||+|+..+.++...  +..-+.++++-+.+.. ...++..++...=..+        .++....  
T Consensus        68 ~GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~  147 (276)
T cd01135          68 RGQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERI  147 (276)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHH
Confidence            4457899999999999999999887641  1224678888887764 4566666665432111        1111101  


Q ss_pred             --HHHHHHHHHHHhc--CCcEEEEEcccccc
Q 004895          247 --YHRAKQLCQRLKK--EKRVLIILDNIWTK  273 (724)
Q Consensus       247 --~~~~~~l~~~l~~--~kr~LlVlDdv~~~  273 (724)
                        ....-.+.++++.  ++++|+++||+-..
T Consensus       148 ~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         148 ITPRMALTTAEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHHHHHHHHHHhccCCeEEEEEcChhHH
Confidence              1112334555542  68999999999554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.39  E-value=0.089  Score=56.37  Aligned_cols=57  Identities=25%  Similarity=0.230  Sum_probs=36.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGM  238 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~  238 (724)
                      ...+|.++|+.|+||||+|..++...+.+ .+ .++.|+.... ....+-++...+..+.
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~-G~-kV~lV~~D~~R~aA~eQLk~~a~~~~v  156 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRK-GF-KPCLVCADTFRAGAFDQLKQNATKARI  156 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC-CC-CEEEEcCcccchhHHHHHHHHhhccCC
Confidence            46799999999999999999999877643 22 3455544221 1222333444555444

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.

>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=95.37  E-value=0.023  Score=55.75  Aligned_cols=62  Identities=18%  Similarity=0.323  Sum_probs=38.9

Q ss_pred             HHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHH
Q 004895          168 IFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQ  229 (724)
Q Consensus       168 ~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~  229 (724)
                      ....+++.+.  .++..+|+|.|++|+|||||...+...+..+.+=-.++=|+-|..++-..++
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tGGAlL   77 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTGGALL   77 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC---SS
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCCCccc
Confidence            3445555544  3567899999999999999999999998865443345556656666544443

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.36  E-value=0.12  Score=52.32  Aligned_cols=58  Identities=31%  Similarity=0.418  Sum_probs=37.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh--HHHHHHHHHhhCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA--QKIQGELASDLGMN  239 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~l~~~i~~~l~~~  239 (724)
                      .+.+++.++|++|+||||++..++...... . ..+.+++.. .+..  .+-+....+..+..
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~-g-~~V~li~~D-~~r~~a~~ql~~~~~~~~i~  129 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQ-G-KSVLLAAGD-TFRAAAIEQLEEWAKRLGVD  129 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc-C-CEEEEEeCC-CCCHHHHHHHHHHHHhCCeE
Confidence            346799999999999999999999877543 2 245566543 2322  23334455555543

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.35  E-value=0.037  Score=54.72  Aligned_cols=90  Identities=16%  Similarity=0.233  Sum_probs=52.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCC--------------CC---
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF--------------DS---  242 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~--------------~~---  242 (724)
                      .-+++.|.|++|+|||+|+.++......+. =..++|++..+.  ..++.+.+- .++.+.              ..   
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~-ge~vlyvs~ee~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF-GEKVLYVSFEEP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH-T--EEEEESSS---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc-CCcEEEEEecCC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEecccccc
Confidence            457999999999999999999876553320 134788887554  344444432 333210              00   


Q ss_pred             ---CchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          243 ---NDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       243 ---~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                         ..........+.+.+...+...+|+|.+...
T Consensus        94 ~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l  127 (226)
T PF06745_consen   94 GWSPNDLEELLSKIREAIEELKPDRVVIDSLSAL  127 (226)
T ss_dssp             T-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHH
T ss_pred             cccccCHHHHHHHHHHHHHhcCCCEEEEECHHHH
Confidence               1113344555555555445579999998544

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 ....

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=95.35  E-value=0.034  Score=62.91  Aligned_cols=79  Identities=13%  Similarity=0.171  Sum_probs=58.8

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .....++|+++.++.|...+...  +.+.++|++|+||||+|+.+.+.... .+++..+|..- ...+..++++.++.++
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~--~~~l~~G~~G~GKttla~~l~~~l~~-~~~~~~~~~~n-p~~~~~~~~~~v~~~~  103 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQR--RHVMMIGSPGTGKSMLAKAMAELLPK-EELQDILVYPN-PEDPNNPKIRTVPAGK  103 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhC--CeEEEECCCCCcHHHHHHHHHHHcCh-HhHHHheEeeC-CCcchHHHHHHHHHhc
Confidence            34566889998888887776554  36889999999999999999987643 34677788655 3346677788888776


Q ss_pred             CCC
Q 004895          237 GMN  239 (724)
Q Consensus       237 ~~~  239 (724)
                      |..
T Consensus       104 G~~  106 (637)
T PRK13765        104 GKQ  106 (637)
T ss_pred             CHH
Confidence            643

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.33  E-value=0.088  Score=53.12  Aligned_cols=40  Identities=20%  Similarity=0.377  Sum_probs=31.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      .-+++.|.|++|+|||+||.+++.....+  =..++|++...
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR--GNPVLFVTVES   74 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC--CCcEEEEEecC
Confidence            45689999999999999999987765432  23578888764

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.33  E-value=0.031  Score=50.39  Aligned_cols=39  Identities=21%  Similarity=0.404  Sum_probs=28.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      ++|.|+|+.|+|||||++.+.+....+ .+...+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~l~~~-g~~v~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINELKRR-GYRVAVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhHc-CCceEEEEEccC
Confidence            489999999999999999999998753 455555555544

>PRK05439 pantothenate kinase; Provisional

Probab=95.30  E-value=0.13  Score=52.74  Aligned_cols=45  Identities=22%  Similarity=0.181  Sum_probs=30.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      +..-+|+|.|.+|+||||+|+.+.........-..+.-++..+-.
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~~l~~~~~~~~v~vi~~DdFy  128 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQALLSRWPEHPKVELVTTDGFL  128 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHhhCCCCceEEEeccccc
Confidence            456799999999999999999998866432111234445554433

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=95.30  E-value=0.059  Score=49.97  Aligned_cols=25  Identities=40%  Similarity=0.502  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..++.|.||.|+|||||++.+..+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            3578899999999999999998876

>PRK03839 putative kinase; Provisional

Probab=95.29  E-value=0.016  Score=55.08  Aligned_cols=24  Identities=46%  Similarity=0.679  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|+|++|+||||+|+.+++...
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~   25 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLG   25 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            588999999999999999999874

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=95.28  E-value=0.014  Score=49.99  Aligned_cols=24  Identities=42%  Similarity=0.733  Sum_probs=21.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      |.|+|++|+|||+||+.++.+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~   24 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLK   24 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHH
Confidence            468999999999999999988754

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

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.21  E-value=0.099  Score=56.98  Aligned_cols=60  Identities=20%  Similarity=0.226  Sum_probs=38.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCCC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMNF  240 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~  240 (724)
                      ..|++++|+.|+||||++.+++.....+..-..+..++... .....+-++...+.++...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv  316 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPV  316 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCe
Confidence            36999999999999999999998775432222355555432 1223344455566666543

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=95.20  E-value=0.29  Score=47.45  Aligned_cols=48  Identities=25%  Similarity=0.285  Sum_probs=37.7

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+-|-++.++++++++.             -...+-+..+|++|.|||-+|+..+.+..
T Consensus       170 YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~  230 (424)
T KOG0652|consen  170 YSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTN  230 (424)
T ss_pred             ccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhcc
Confidence            4456688999999988864             12456788999999999999999887654

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.20  E-value=0.07  Score=50.88  Aligned_cols=44  Identities=16%  Similarity=0.176  Sum_probs=31.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      +.|.|++|+|||+||.++.......  =..++|++...  +..++.+.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~--g~~v~~~s~e~--~~~~~~~~   45 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLEE--SPEELIEN   45 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC--CCcEEEEECCC--CHHHHHHH
Confidence            6789999999999999998876432  13477887654  34444433

A related protein is found in archaea.

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=95.19  E-value=0.013  Score=59.33  Aligned_cols=88  Identities=15%  Similarity=0.298  Sum_probs=46.4

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh-hCCCCCCCchhHH
Q 004895          170 QDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD-LGMNFDSNDLIYH  248 (724)
Q Consensus       170 ~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~-l~~~~~~~~~~~~  248 (724)
                      ..+++.+...+. -+.++|+.|+|||++++...+...... | .+.-++.+...+...++ .+++. +.... ...    
T Consensus        23 ~~ll~~l~~~~~-pvLl~G~~GtGKT~li~~~l~~l~~~~-~-~~~~~~~s~~Tts~~~q-~~ie~~l~k~~-~~~----   93 (272)
T PF12775_consen   23 SYLLDLLLSNGR-PVLLVGPSGTGKTSLIQNFLSSLDSDK-Y-LVITINFSAQTTSNQLQ-KIIESKLEKRR-GRV----   93 (272)
T ss_dssp             HHHHHHHHHCTE-EEEEESSTTSSHHHHHHHHHHCSTTCC-E-EEEEEES-TTHHHHHHH-HCCCTTECECT-TEE----
T ss_pred             HHHHHHHHHcCC-cEEEECCCCCchhHHHHhhhccCCccc-c-ceeEeeccCCCCHHHHH-HHHhhcEEcCC-CCC----
Confidence            345555544444 457999999999999999886543321 1 13344555443333332 22221 11100 000    


Q ss_pred             HHHHHHHHHhcCCcEEEEEccccc
Q 004895          249 RAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       249 ~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                           . .-..+|+.++++||+.-
T Consensus        94 -----~-gP~~~k~lv~fiDDlN~  111 (272)
T PF12775_consen   94 -----Y-GPPGGKKLVLFIDDLNM  111 (272)
T ss_dssp             -----E-EEESSSEEEEEEETTT-
T ss_pred             -----C-CCCCCcEEEEEecccCC
Confidence                 0 00136889999999853

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.19  E-value=0.018  Score=55.10  Aligned_cols=28  Identities=43%  Similarity=0.659  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ++-+|+|.|.+|+||||+|+.++..+..
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~~~~~   34 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSEQLGV   34 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHhCc
Confidence            4579999999999999999999998864

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.17  E-value=0.14  Score=54.80  Aligned_cols=61  Identities=21%  Similarity=0.229  Sum_probs=37.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFD  241 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~  241 (724)
                      ..+++++|+.|+||||++..++.........+.+..++.... ....+-+..+.+.++.+..
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~  252 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVR  252 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHHHHHHHcCCcee
Confidence            469999999999999999998876533222334444443321 2233334555666665543

>TIGR01817 nifA Nif-specific regulatory protein

Probab=95.15  E-value=0.16  Score=57.32  Aligned_cols=63  Identities=13%  Similarity=0.120  Sum_probs=42.8

Q ss_pred             ccccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          158 DYNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      ....++|+...+.++.+.+.  .....-|.|+|..|+|||++|+.+.+.-...  -...+.++++.-
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~--~~pfv~i~c~~~  258 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRA--KRPFVKVNCAAL  258 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCCC--CCCeEEeecCCC
Confidence            34567898888888877664  2233356799999999999999998864321  122455555543

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.15  E-value=0.077  Score=51.52  Aligned_cols=97  Identities=28%  Similarity=0.360  Sum_probs=56.7

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCC-------C-CC
Q 004895          172 VIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGM-------N-FD  241 (724)
Q Consensus       172 l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~-------~-~~  241 (724)
                      .++.+.. .+-..++|.|.+|+|||+|+..+.+....    +.++++.+.+.. ...++.+++...-..       . .+
T Consensus         5 ~ID~l~Pig~Gqr~~I~g~~g~GKt~Ll~~i~~~~~~----d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~   80 (215)
T PF00006_consen    5 AIDLLFPIGRGQRIGIFGGAGVGKTVLLQEIANNQDA----DVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSD   80 (215)
T ss_dssp             HHHHHSCEETTSEEEEEESTTSSHHHHHHHHHHHCTT----TEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETT
T ss_pred             eeccccccccCCEEEEEcCcccccchhhHHHHhcccc----cceeeeeccccchhHHHHHHHHhhcccccccccccccch
Confidence            3444431 23357899999999999999999998743    445788887653 455555555432100       0 11


Q ss_pred             CCchhH----HHHHHHHHHHh-cCCcEEEEEccccc
Q 004895          242 SNDLIY----HRAKQLCQRLK-KEKRVLIILDNIWT  272 (724)
Q Consensus       242 ~~~~~~----~~~~~l~~~l~-~~kr~LlVlDdv~~  272 (724)
                      +.....    ...-.+.+++. +++++|+++||+-.
T Consensus        81 ~~~~~r~~~~~~a~t~AEyfrd~G~dVlli~Dsltr  116 (215)
T PF00006_consen   81 EPPAARYRAPYTALTIAEYFRDQGKDVLLIIDSLTR  116 (215)
T ss_dssp             S-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHH
T ss_pred             hhHHHHhhhhccchhhhHHHhhcCCceeehhhhhHH
Confidence            111011    01122233332 47999999999843

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=95.14  E-value=0.012  Score=57.47  Aligned_cols=24  Identities=29%  Similarity=0.403  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .+++.|+|+.|.|||||.+.+...
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~   52 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALI   52 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHH
Confidence            488999999999999999999854

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.13  E-value=0.058  Score=57.04  Aligned_cols=47  Identities=26%  Similarity=0.303  Sum_probs=36.0

Q ss_pred             cccchHHHHHHHHHHhcCC--------------CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          161 IFNSRKKIFQDVIEALKDD--------------KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~~--------------~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++|.++.++.+.-++...              ..+.|.++|++|+|||++|+.++.....
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~   73 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANA   73 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4678888777776554421              2367899999999999999999998754

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.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.12  E-value=0.044  Score=52.57  Aligned_cols=51  Identities=25%  Similarity=0.508  Sum_probs=36.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD  241 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~  241 (724)
                      .|+|+|-||+||||+|.........++.| .++-|+...++++       .++||...+
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~~~-~VLvVDaDpd~nL-------~~~LGve~~   52 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKGGY-NVLVVDADPDSNL-------PEALGVEEP   52 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHHHHhcCCc-eEEEEeCCCCCCh-------HHhcCCCCC
Confidence            68999999999999999977777665433 3555666665554       445666654

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.12  E-value=0.088  Score=49.14  Aligned_cols=80  Identities=16%  Similarity=0.193  Sum_probs=45.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC-Cc
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE-KR  262 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~-kr  262 (724)
                      +.|.|.+|+|||++|.++....     ...++|+.-.+.++. ++.+.|.+--........ ..+....+.+.+... +.
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~-----~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~-t~E~~~~l~~~l~~~~~~   74 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL-----GGPVTYIATAEAFDD-EMAERIARHRKRRPAHWR-TIETPRDLVSALKELDPG   74 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc-----CCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCce-EeecHHHHHHHHHhcCCC
Confidence            6789999999999999998652     235777776666654 344444332211111111 111223344444221 33


Q ss_pred             EEEEEccc
Q 004895          263 VLIILDNI  270 (724)
Q Consensus       263 ~LlVlDdv  270 (724)
                      -.+++|.+
T Consensus        75 ~~VLIDcl   82 (169)
T cd00544          75 DVVLIDCL   82 (169)
T ss_pred             CEEEEEcH
Confidence            47999997

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.09  E-value=0.16  Score=48.88  Aligned_cols=52  Identities=17%  Similarity=0.247  Sum_probs=38.9

Q ss_pred             cccccccchHHHHHHHHHHh----cCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          157 KDYNIFNSRKKIFQDVIEAL----KDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L----~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .+...++|-+...+.|++.-    ......-|.+||.-|+|||+|++.+.+....+
T Consensus        57 i~L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~  112 (287)
T COG2607          57 IDLADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE  112 (287)
T ss_pred             cCHHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc
Confidence            34456678777777666543    34445678899999999999999999998764

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.08  E-value=0.091  Score=58.27  Aligned_cols=87  Identities=17%  Similarity=0.273  Sum_probs=56.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC---------------CCc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD---------------SND  244 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~---------------~~~  244 (724)
                      .-+++.|.|++|+|||||+.+++.....+  =..++|++..+  +..++...+ +.++.+..               ...
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~f~~~~~~~--ge~~~y~s~eE--s~~~i~~~~-~~lg~~~~~~~~~g~l~~~~~~p~~~  336 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSKFLENACAN--KERAILFAYEE--SRAQLLRNA-YSWGIDFEEMEQQGLLKIICAYPESA  336 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC--CCeEEEEEeeC--CHHHHHHHH-HHcCCChHHHhhCCcEEEEEcccccC
Confidence            45799999999999999999999887543  23567776654  444555553 44543211               111


Q ss_pred             hhHHHHHHHHHHHhcCCcEEEEEcccc
Q 004895          245 LIYHRAKQLCQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       245 ~~~~~~~~l~~~l~~~kr~LlVlDdv~  271 (724)
                      ..++.+..+.+.+...+.-.+|+|.+.
T Consensus       337 ~~~~~~~~i~~~i~~~~~~~vvIDsi~  363 (484)
T TIGR02655       337 GLEDHLQIIKSEIADFKPARIAIDSLS  363 (484)
T ss_pred             ChHHHHHHHHHHHHHcCCCEEEEcCHH
Confidence            124456666666665566688888874

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.07  E-value=0.084  Score=52.14  Aligned_cols=90  Identities=18%  Similarity=0.161  Sum_probs=52.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-----CCChHHHHHHHHHhhCCCC------CCCchh-H
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-----NPDAQKIQGELASDLGMNF------DSNDLI-Y  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-----~~~~~~l~~~i~~~l~~~~------~~~~~~-~  247 (724)
                      +-.+++|||..|+||||+++.+..-....   .+.+++.-.+     .....+...++++.++...      +.+-.. .
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~L~~pt---~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQ  114 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILGLEEPT---SGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQ  114 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHcCcCCC---CceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchh
Confidence            45689999999999999999998876532   3344443221     1123344566677666432      111001 1


Q ss_pred             HHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          248 HRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       248 ~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .+.-.+.+.+. -++-++|.|..-+.
T Consensus       115 rQRi~IARALa-l~P~liV~DEpvSa  139 (268)
T COG4608         115 RQRIGIARALA-LNPKLIVADEPVSA  139 (268)
T ss_pred             hhhHHHHHHHh-hCCcEEEecCchhh
Confidence            11223344444 47889999997554

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

Probab=95.05  E-value=0.033  Score=54.31  Aligned_cols=20  Identities=15%  Similarity=0.099  Sum_probs=15.2

Q ss_pred             hhcCCCCCcEEEeecccccc
Q 004895          695 ELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       695 ~L~~L~~L~~L~l~~n~~~~  714 (724)
                      .+..+++|+.|||.-|-++.
T Consensus       209 gl~y~~~LevLDlqDNtft~  228 (388)
T COG5238         209 GLFYSHSLEVLDLQDNTFTL  228 (388)
T ss_pred             HHHHhCcceeeeccccchhh
Confidence            35567889999999887654

>PRK00625 shikimate kinase; Provisional

Probab=95.04  E-value=0.02  Score=53.70  Aligned_cols=24  Identities=42%  Similarity=0.584  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.++||+|+||||+++.+.+...
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~   25 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLS   25 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999988764

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.03  E-value=0.089  Score=56.61  Aligned_cols=93  Identities=18%  Similarity=0.324  Sum_probs=59.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchh----
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLI----  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~----  246 (724)
                      +-..++|.|.+|+|||+|+..+.+.... .+-+.++|+-+.+.. ...++..++...-..+        .+++...    
T Consensus       137 kGQr~~Ifg~~G~GKt~l~~~~~~~~~~-~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~  215 (449)
T TIGR03305       137 RGGKAGLFGGAGVGKTVLLTEMIHNMVG-QHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRV  215 (449)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHHh-cCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHH
Confidence            4457899999999999999999888653 234678888887654 3455555555431111        1111111    


Q ss_pred             HHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          247 YHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 ~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                      ...+-.+.++++  +++++|+++||+-..
T Consensus       216 ~~~a~tiAEyfrd~~G~~VLl~~DslTR~  244 (449)
T TIGR03305       216 GHTALTMAEYFRDDEKQDVLLLIDNIFRF  244 (449)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEecChHHH
Confidence            112334556665  379999999999543

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=95.02  E-value=0.31  Score=50.98  Aligned_cols=43  Identities=16%  Similarity=0.226  Sum_probs=29.4

Q ss_pred             cchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          163 NSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +|+...+.++.+.+.  .....-|.|+|..|+||+++|+.+.+.-
T Consensus         2 iG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s   46 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLS   46 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhc
Confidence            455555555555443  1223356899999999999999998754

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=95.00  E-value=0.1  Score=60.00  Aligned_cols=86  Identities=16%  Similarity=0.201  Sum_probs=56.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      .-+++-|+|++|+||||||.+++......  =..++|++..+.++.     ..++++|.+.+.     ....+.....+.
T Consensus        59 ~GsiteI~G~~GsGKTtLal~~~~~a~~~--G~~v~yId~E~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~  131 (790)
T PRK09519         59 RGRVIEIYGPESSGKTTVALHAVANAQAA--GGVAAFIDAEHALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (790)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEECCccchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHH
Confidence            35788999999999999998877654332  245899988777663     367777765321     111233333344


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ..+..++.-|||+|-+-.
T Consensus       132 ~lv~~~~~~LVVIDSI~a  149 (790)
T PRK09519        132 MLIRSGALDIVVIDSVAA  149 (790)
T ss_pred             HHhhcCCCeEEEEcchhh
Confidence            444455678999999853

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.99  E-value=0.16  Score=51.17  Aligned_cols=88  Identities=20%  Similarity=0.252  Sum_probs=55.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh-hCC---CCC-CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD-LGM---NFD-SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~-l~~---~~~-~~~~~~~~~~~l~  254 (724)
                      .-+++=|+|+.|+||||+|.+++-.....  -..++|++.-..++++.+ +.+... +..   ..+ ........+..+.
T Consensus        59 ~g~ItEiyG~~gsGKT~lal~~~~~aq~~--g~~a~fIDtE~~l~p~r~-~~l~~~~~d~l~v~~~~~~e~q~~i~~~~~  135 (279)
T COG0468          59 RGRITEIYGPESSGKTTLALQLVANAQKP--GGKAAFIDTEHALDPERA-KQLGVDLLDNLLVSQPDTGEQQLEIAEKLA  135 (279)
T ss_pred             cceEEEEecCCCcchhhHHHHHHHHhhcC--CCeEEEEeCCCCCCHHHH-HHHHHhhhcceeEecCCCHHHHHHHHHHHH
Confidence            45688999999999999999988776532  347899999998988765 444444 321   111 1111122222232


Q ss_pred             HHHhcCCcEEEEEcccc
Q 004895          255 QRLKKEKRVLIILDNIW  271 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~  271 (724)
                      ....+ +--|+|+|.+-
T Consensus       136 ~~~~~-~i~LvVVDSva  151 (279)
T COG0468         136 RSGAE-KIDLLVVDSVA  151 (279)
T ss_pred             HhccC-CCCEEEEecCc
Confidence            22221 35699999884

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=94.99  E-value=0.11  Score=51.12  Aligned_cols=127  Identities=20%  Similarity=0.237  Sum_probs=70.7

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+-|-+..+++|.+...             -...+-|.++|.+|.|||-||++|+|.....  |-.+           
T Consensus       184 y~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSAT--FlRv-----------  250 (440)
T KOG0726|consen  184 YADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSAT--FLRV-----------  250 (440)
T ss_pred             hcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchh--hhhh-----------
Confidence            3445577888888877654             1235567799999999999999999976542  3111           


Q ss_pred             HHHHHHHH-HhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--cc-------cc-ccccCCCCcCCCCCC
Q 004895          226 QKIQGELA-SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LD-------KI-GIPYGDVDEKDKNDD  294 (724)
Q Consensus       226 ~~l~~~i~-~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~-------~l-~~~~~~~~~~~~~~~  294 (724)
                        +-.+++ ..+|.       ......++++.-....+..+++|.++....  ++       ++ ...+..+++++.+..
T Consensus       251 --vGseLiQkylGd-------GpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFds  321 (440)
T KOG0726|consen  251 --VGSELIQKYLGD-------GPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDS  321 (440)
T ss_pred             --hhHHHHHHHhcc-------chHHHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccc
Confidence              111222 22321       122445555554445678888898854311  00       00 011111223334445


Q ss_pred             CCCcEEEEEeccc
Q 004895          295 PRRCTIILTSRSR  307 (724)
Q Consensus       295 ~~~s~ilvTtR~~  307 (724)
                      ....+||+.|..-
T Consensus       322 rgDvKvimATnri  334 (440)
T KOG0726|consen  322 RGDVKVIMATNRI  334 (440)
T ss_pred             cCCeEEEEecccc
Confidence            5567888777653

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.97  E-value=0.2  Score=57.54  Aligned_cols=60  Identities=20%  Similarity=0.230  Sum_probs=38.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNF  240 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~  240 (724)
                      ..|++++|+.|+||||++.+++...........+..++.... ....+-++...+.++.+.
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPV  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCc
Confidence            469999999999999999999987743222234555554321 123445566666666544

>PRK04040 adenylate kinase; Provisional

Probab=94.93  E-value=0.024  Score=54.06  Aligned_cols=25  Identities=32%  Similarity=0.600  Sum_probs=22.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|+|++|+||||+++.+.+...
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            5899999999999999999998874

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.92  E-value=0.019  Score=54.72  Aligned_cols=23  Identities=30%  Similarity=0.390  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ||.|+|++|+||||+|+.++...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHc
Confidence            57899999999999999998866

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.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=94.90  E-value=0.027  Score=53.09  Aligned_cols=26  Identities=31%  Similarity=0.351  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|+|++|+||||+|+.+++...
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999998874

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=94.88  E-value=0.16  Score=58.79  Aligned_cols=101  Identities=18%  Similarity=0.230  Sum_probs=64.3

Q ss_pred             ccchHHHHHHHHHHhcC------C--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALKD------D--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~~------~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ++|.++.+..|.+.+..      .  ....+.+.|+.|+|||-||+.++......  .+..+-++.|+.      .. +.
T Consensus       564 V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs--e~~~IriDmse~------~e-vs  634 (898)
T KOG1051|consen  564 VIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGS--EENFIRLDMSEF------QE-VS  634 (898)
T ss_pred             ccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCC--ccceEEechhhh------hh-hh
Confidence            55677777777776641      1  35577889999999999999999877432  344555555432      22 33


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +.++.+..--  ..+...++-+.+++....+|+||||+..
T Consensus       635 kligsp~gyv--G~e~gg~LteavrrrP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  635 KLIGSPPGYV--GKEEGGQLTEAVKRRPYSVVLFEEIEKA  672 (898)
T ss_pred             hccCCCcccc--cchhHHHHHHHHhcCCceEEEEechhhc
Confidence            3334332111  1234557777887666679999999765

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.88  E-value=0.096  Score=52.87  Aligned_cols=116  Identities=17%  Similarity=0.138  Sum_probs=62.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC-CC-------CCCchhHHH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM-NF-------DSNDLIYHR  249 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~-~~-------~~~~~~~~~  249 (724)
                      ..+..-++|+|+.|.|||||.+.+......   ..+.+++.-.+-... +-..++...... ..       +-.+ ....
T Consensus       108 ~~~~~~~~i~g~~g~GKttl~~~l~~~~~~---~~G~i~~~g~~v~~~-d~~~ei~~~~~~~~q~~~~~r~~v~~-~~~k  182 (270)
T TIGR02858       108 NNRVLNTLIISPPQCGKTTLLRDLARILST---GISQLGLRGKKVGIV-DERSEIAGCVNGVPQHDVGIRTDVLD-GCPK  182 (270)
T ss_pred             CCCeeEEEEEcCCCCCHHHHHHHHhCccCC---CCceEEECCEEeecc-hhHHHHHHHhcccccccccccccccc-cchH
Confidence            344568899999999999999999987653   233444421111111 111233322211 10       0000 0111


Q ss_pred             HHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          250 AKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       250 ~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      ...+...+..-.+-++++|.+-....+..+...+           ..|..||+||-...+
T Consensus       183 ~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~-----------~~G~~vI~ttH~~~~  231 (270)
T TIGR02858       183 AEGMMMLIRSMSPDVIVVDEIGREEDVEALLEAL-----------HAGVSIIATAHGRDV  231 (270)
T ss_pred             HHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHH-----------hCCCEEEEEechhHH
Confidence            2234444443467899999987655444442222           246779999987655

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.87  E-value=0.09  Score=56.92  Aligned_cols=94  Identities=19%  Similarity=0.304  Sum_probs=59.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchh---
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLI---  246 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~---  246 (724)
                      .+-..++|.|.+|+|||||+..+.+..... +-+.++++-+.+.. ...++..++...-..+        .+++...   
T Consensus       141 gkGQR~gIfa~~G~GKt~Ll~~~~~~~~~~-~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~  219 (461)
T PRK12597        141 AKGGKTGLFGGAGVGKTVLMMELIFNISKQ-HSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMR  219 (461)
T ss_pred             ccCCEEEeecCCCCChhHHHHHHHHHHHhh-CCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHH
Confidence            345689999999999999999999887643 56778888776553 3455555555432111        1221111   


Q ss_pred             -HHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          247 -YHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 -~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                       ...+-.+.++++  +++++|+++|++-..
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLl~~DslTR~  249 (461)
T PRK12597        220 VVLTGLTIAEYLRDEEKEDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEeccchHH
Confidence             112234455554  278999999999543

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.87  E-value=0.036  Score=57.84  Aligned_cols=50  Identities=18%  Similarity=0.313  Sum_probs=42.9

Q ss_pred             ccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          158 DYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +...++|.++.+..|+..+.++...-|.|.|..|+||||+|+.+++-...
T Consensus        15 pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~   64 (350)
T CHL00081         15 PFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPE   64 (350)
T ss_pred             CHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            45677899999999888888888888889999999999999999887643

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=94.86  E-value=0.046  Score=57.07  Aligned_cols=47  Identities=21%  Similarity=0.330  Sum_probs=39.8

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...++|.++.+..++-.+.++...-+.|.|..|+|||||++.+..-.
T Consensus         3 f~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            34678999999888777777777778899999999999999998765

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.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=94.82  E-value=0.066  Score=57.50  Aligned_cols=91  Identities=19%  Similarity=0.262  Sum_probs=49.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh-----CC--CCCCCchhH----H
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL-----GM--NFDSNDLIY----H  248 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l-----~~--~~~~~~~~~----~  248 (724)
                      .-..++|+|+.|+|||||++.+......   ...+++..--...++.++....+...     +.  +.+++....    .
T Consensus       164 ~Gqri~I~G~SGsGKTTLL~~Ia~l~~p---d~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~  240 (450)
T PRK06002        164 AGQRIGIFAGSGVGKSTLLAMLARADAF---DTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPL  240 (450)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCCC---CeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHH
Confidence            3458999999999999999988764432   22344443323344444444333322     11  111111111    1


Q ss_pred             HHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          249 RAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       249 ~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ..-.+.+++. +++++|+++||+-..
T Consensus       241 ~a~~iAEyfrd~G~~Vll~~DslTr~  266 (450)
T PRK06002        241 TATAIAEYFRDRGENVLLIVDSVTRF  266 (450)
T ss_pred             HHHHHHHHHHHcCCCEEEeccchHHH
Confidence            1222334442 478999999998543

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=94.78  E-value=0.56  Score=52.46  Aligned_cols=63  Identities=14%  Similarity=0.129  Sum_probs=43.5

Q ss_pred             cccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          159 YNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      ...++|+...+.++.+.+.  .....-|.|+|..|+|||++|+.+.+.....  -...+.|+++.-+
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~--~~p~v~v~c~~~~  250 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRA--DKPLVYLNCAALP  250 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcC--CCCeEEEEcccCC
Confidence            3457788888877777665  2334467799999999999999998865321  1235566666543

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=94.77  E-value=0.033  Score=51.82  Aligned_cols=28  Identities=25%  Similarity=0.526  Sum_probs=25.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+++|+|..|+|||||++.+......
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~~l~~   32 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIPALCA   32 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHHHHhh
Confidence            4569999999999999999999998865

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.76  E-value=0.021  Score=55.15  Aligned_cols=23  Identities=48%  Similarity=0.809  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +|+|.|+.|+||||||+.+....
T Consensus         1 iigi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            58999999999999999998876

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.

>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=94.75  E-value=0.01  Score=34.32  Aligned_cols=21  Identities=33%  Similarity=0.678  Sum_probs=13.7

Q ss_pred             CceEEEcCCCcCCCCCccccC
Q 004895          576 ELKVLDFTGIRFSPLPSSLGR  596 (724)
Q Consensus       576 ~L~~L~l~~~~~~~lp~~i~~  596 (724)
                      +|++||+++|.++.+|+++++
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~   21 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSN   21 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT
T ss_pred             CccEEECCCCcCEeCChhhcC
Confidence            366777777777766666544

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 ....

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=94.72  E-value=0.067  Score=50.64  Aligned_cols=27  Identities=26%  Similarity=0.429  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|.|||||++.+.-...
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            345899999999999999999987653

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PF13245 AAA_19: Part of AAA domain

Probab=94.71  E-value=0.077  Score=42.05  Aligned_cols=26  Identities=27%  Similarity=0.273  Sum_probs=18.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +.+++.|.|++|.|||+++.......
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l   34 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAEL   34 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            45678889999999995554444443

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.67  E-value=0.11  Score=56.71  Aligned_cols=87  Identities=26%  Similarity=0.332  Sum_probs=52.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSND-LIYHRAKQLCQRLKK  259 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~~  259 (724)
                      -.++.|.|.+|+|||||+.+++......  -..++|++..+.  ..++.. -++.++...+.-. ........+.+.+.+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~--g~~vlYvs~Ees--~~qi~~-ra~rlg~~~~~l~~~~e~~l~~i~~~i~~  154 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA--GGKVLYVSGEES--ASQIKL-RAERLGLPSDNLYLLAETNLEAILATIEE  154 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEcccc--HHHHHH-HHHHcCCChhcEEEeCCCCHHHHHHHHHh
Confidence            4589999999999999999999877532  235788876543  334322 2455554321100 000123344455544


Q ss_pred             CCcEEEEEccccc
Q 004895          260 EKRVLIILDNIWT  272 (724)
Q Consensus       260 ~kr~LlVlDdv~~  272 (724)
                      .+.-++|+|.+..
T Consensus       155 ~~~~lVVIDSIq~  167 (446)
T PRK11823        155 EKPDLVVIDSIQT  167 (446)
T ss_pred             hCCCEEEEechhh
Confidence            4667899999843

>PRK06851 hypothetical protein; Provisional

Probab=94.67  E-value=0.41  Score=50.33  Aligned_cols=44  Identities=32%  Similarity=0.262  Sum_probs=33.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      .+--+++.|.|++|+|||||++.++.....+ .++..++-|.+.+
T Consensus       211 ~~~~~~~~i~G~pG~GKstl~~~i~~~a~~~-G~~v~~~hC~~dP  254 (367)
T PRK06851        211 EGVKNRYFLKGRPGTGKSTMLKKIAKAAEER-GFDVEVYHCGFDP  254 (367)
T ss_pred             cccceEEEEeCCCCCcHHHHHHHHHHHHHhC-CCeEEEEeCCCCC
Confidence            3445789999999999999999999998754 4665555554443

>TIGR01069 mutS2 MutS2 family protein

Probab=94.64  E-value=0.056  Score=62.97  Aligned_cols=191  Identities=16%  Similarity=0.196  Sum_probs=89.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH-hhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCC----CCCchhHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV-MEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF----DSNDLIYHRAKQL  253 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~----~~~~~~~~~~~~l  253 (724)
                      .+.+++.|+|+.|.|||||.+.+.-.. .....    .+|.+.....+ ..+..+...++...    .... -......+
T Consensus       320 ~~~~~liItGpNg~GKSTlLK~i~~~~l~aq~G----~~Vpa~~~~~~-~~~d~i~~~i~~~~si~~~LSt-fS~~m~~~  393 (771)
T TIGR01069       320 FEKRVLAITGPNTGGKTVTLKTLGLLALMFQSG----IPIPANEHSEI-PYFEEIFADIGDEQSIEQNLST-FSGHMKNI  393 (771)
T ss_pred             CCceEEEEECCCCCCchHHHHHHHHHHHHHHhC----CCccCCccccc-cchhheeeecChHhHHhhhhhH-HHHHHHHH
Confidence            345799999999999999999998762 11111    12222111000 00111111111100    0000 01111222


Q ss_pred             HHHHhc-CCcEEEEEcccccccccc---cccc-ccCCCCcCCCCCCCCCcEEEEEecccchhhhhcCCCc--eEecCCCC
Q 004895          254 CQRLKK-EKRVLIILDNIWTKLELD---KIGI-PYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQK--MFWIDALS  326 (724)
Q Consensus       254 ~~~l~~-~kr~LlVlDdv~~~~~~~---~l~~-~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~~~~~--~~~l~~L~  326 (724)
                      ...+.. ..+-|+++|..-...+..   .+.. .+..+       ...|+.+|+||-...+.........  ...+. ++
T Consensus       394 ~~il~~~~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l-------~~~g~~viitTH~~eL~~~~~~~~~v~~~~~~-~d  465 (771)
T TIGR01069       394 SAILSKTTENSLVLFDELGAGTDPDEGSALAISILEYL-------LKQNAQVLITTHYKELKALMYNNEGVENASVL-FD  465 (771)
T ss_pred             HHHHHhcCCCcEEEecCCCCCCCHHHHHHHHHHHHHHH-------HhcCCEEEEECChHHHHHHhcCCCCeEEeEEE-Ec
Confidence            222221 467999999986543321   1110 11000       2357889999998776422111111  11111 11


Q ss_pred             HHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHHHHhc
Q 004895          327 EEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTS  389 (724)
Q Consensus       327 ~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~~l~~  389 (724)
                      . +... |..+.-...  +. ...|-+|++++ |+|-.+.--|..+.......++.+++.+..
T Consensus       466 ~-~~l~-p~Ykl~~G~--~g-~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~L~~  522 (771)
T TIGR01069       466 E-ETLS-PTYKLLKGI--PG-ESYAFEIAQRY-GIPHFIIEQAKTFYGEFKEEINVLIEKLSA  522 (771)
T ss_pred             C-CCCc-eEEEECCCC--CC-CcHHHHHHHHh-CcCHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            1 1000 000010011  11 34577888887 788888777777765555667777666544

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.

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.64  E-value=0.12  Score=56.62  Aligned_cols=90  Identities=21%  Similarity=0.241  Sum_probs=51.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEE-EEEEecCCChHHHHHHHHHhhC-----CCCCCCchh----HH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVV-MAEITKNPDAQKIQGELASDLG-----MNFDSNDLI----YH  248 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~-wv~vs~~~~~~~l~~~i~~~l~-----~~~~~~~~~----~~  248 (724)
                      +.-....|+|++|+|||||++.+++.... .+-++.+ .+-|.+.+...   .+|-+.+.     ...+.....    ..
T Consensus       414 GkGQR~LIvgpp~aGKTtLL~~IAn~i~~-n~~~~~~ivvLIgERpeEV---tdm~rsVkgeVVasT~D~p~~~~~~~a~  489 (672)
T PRK12678        414 GKGQRGLIVSPPKAGKTTILQNIANAITT-NNPECHLMVVLVDERPEEV---TDMQRSVKGEVIASTFDRPPSDHTTVAE  489 (672)
T ss_pred             ccCCEeEEeCCCCCCHHHHHHHHHHHHhh-cCCCeEEEEEEEeCchhhH---HHHHHhccceEEEECCCCCHHHHHHHHH
Confidence            34457899999999999999999987754 3445543 44455443221   22333331     112222211    11


Q ss_pred             HHHHHHHHH-hcCCcEEEEEccccc
Q 004895          249 RAKQLCQRL-KKEKRVLIILDNIWT  272 (724)
Q Consensus       249 ~~~~l~~~l-~~~kr~LlVlDdv~~  272 (724)
                      .+..+.+++ ..++.+||++|++-.
T Consensus       490 ~ai~~Ae~fre~G~dVlillDSlTR  514 (672)
T PRK12678        490 LAIERAKRLVELGKDVVVLLDSITR  514 (672)
T ss_pred             HHHHHHHHHHHcCCCEEEEEeCchH
Confidence            222333444 247899999999854

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=94.62  E-value=0.026  Score=53.55  Aligned_cols=23  Identities=39%  Similarity=0.712  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +|+|.|.+|+||||+|+.+....
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.

>COG4240 Predicted kinase [General function prediction only]

Probab=94.62  E-value=0.25  Score=47.04  Aligned_cols=83  Identities=13%  Similarity=0.119  Sum_probs=51.5

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC----CCCCCchhHHHHHHH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM----NFDSNDLIYHRAKQL  253 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~----~~~~~~~~~~~~~~l  253 (724)
                      .++.-+++|.|+-|+||||++..+++....+.. ..++..++.+-+-...-...++++...    .......+......+
T Consensus        47 ~grPli~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lSLDDlYlthadrl~La~q~npllq~RGlpGTHD~tlglnV  125 (300)
T COG4240          47 RGRPLIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLSLDDLYLTHADRLRLARQVNPLLQTRGLPGTHDPTLGLNV  125 (300)
T ss_pred             cCCceEEEeecCCCCchhhHHHHHHHHHHHhcc-cceEEeehhhhhcchHHHHHHHHhcCchhcccCCCCCCchHHHHHH
Confidence            356679999999999999999999999887643 356666665544333334455555321    111112234455556


Q ss_pred             HHHHhcCC
Q 004895          254 CQRLKKEK  261 (724)
Q Consensus       254 ~~~l~~~k  261 (724)
                      .+.+.+++
T Consensus       126 Lnai~~g~  133 (300)
T COG4240         126 LNAIARGG  133 (300)
T ss_pred             HHHHhcCC
Confidence            66665554

>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=94.62  E-value=0.027  Score=51.29  Aligned_cols=24  Identities=42%  Similarity=0.614  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +|.|+|+.|+||||+|+.+.....
T Consensus         1 ~I~i~G~~GsGKst~a~~la~~~~   24 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLG   24 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            589999999999999999998764

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=94.61  E-value=0.27  Score=53.12  Aligned_cols=94  Identities=19%  Similarity=0.333  Sum_probs=58.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchhH--
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLIY--  247 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~~--  247 (724)
                      .+-..++|.|..|+|||||+..+........ -+.++++-+.+.. .+.++..++...-..+        .+.+....  
T Consensus       142 gkGQR~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~  220 (463)
T PRK09280        142 AKGGKIGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLR  220 (463)
T ss_pred             ccCCEEEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            3456899999999999999999988775432 2457777776554 3455666665432111        11211111  


Q ss_pred             --HHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          248 --HRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       248 --~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                        ..+-.+.++++  +++++||++|++-..
T Consensus       221 a~~~a~tiAEyfrd~~G~~VLll~DslTR~  250 (463)
T PRK09280        221 VALTGLTMAEYFRDVEGQDVLLFIDNIFRF  250 (463)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecchHHH
Confidence              11233455552  479999999999543

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.60  E-value=0.075  Score=60.31  Aligned_cols=76  Identities=16%  Similarity=0.218  Sum_probs=51.8

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM  238 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~  238 (724)
                      ...++|+++.+..+...+....  -+.++|++|+||||+|+.+.+..... .|..++++.-+ ..+..++++.+..+++.
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~--~~ll~G~pG~GKT~la~~la~~l~~~-~~~~~~~~~n~-~~~~~~~~~~v~~~~g~   92 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR--NVLLIGEPGVGKSMLAKAMAELLPDE-ELEDILVYPNP-EDPNMPRIVEVPAGEGR   92 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC--CEEEECCCCCCHHHHHHHHHHHcCch-hheeEEEEeCC-CCCchHHHHHHHHhhch
Confidence            4567799988887777666543  55599999999999999999877543 33333333222 23455667777777764

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=94.59  E-value=0.077  Score=55.76  Aligned_cols=65  Identities=22%  Similarity=0.227  Sum_probs=48.3

Q ss_pred             ccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ++|+++.+..+...+..++  -+.+.|++|+|||+||+.++.....     ...+|.+.......++.....
T Consensus        26 ~~g~~~~~~~~l~a~~~~~--~vll~G~PG~gKT~la~~lA~~l~~-----~~~~i~~t~~l~p~d~~G~~~   90 (329)
T COG0714          26 VVGDEEVIELALLALLAGG--HVLLEGPPGVGKTLLARALARALGL-----PFVRIQCTPDLLPSDLLGTYA   90 (329)
T ss_pred             eeccHHHHHHHHHHHHcCC--CEEEECCCCccHHHHHHHHHHHhCC-----CeEEEecCCCCCHHHhcCchh
Confidence            6688887777766665433  4779999999999999999988752     256777777777777655443

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=94.58  E-value=0.067  Score=52.96  Aligned_cols=23  Identities=39%  Similarity=0.455  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +..|+|++|.||||++..+....
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHHh
Confidence            78899999999998888777776

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=94.58  E-value=0.031  Score=52.96  Aligned_cols=25  Identities=32%  Similarity=0.474  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++.|+|+.|+||||+++.+.....
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~~~   26 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARARLA   26 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4789999999999999999988754

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=94.57  E-value=0.054  Score=59.86  Aligned_cols=60  Identities=28%  Similarity=0.318  Sum_probs=43.2

Q ss_pred             CcccccccchHHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD-----DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      |.....++-..+-++++..||.+     ...+++.+.||+|+||||.++.+++...    |+.+=|.+-
T Consensus        15 P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~elg----~~v~Ew~np   79 (519)
T PF03215_consen   15 PKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKELG----FEVQEWINP   79 (519)
T ss_pred             CCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHhC----CeeEEecCC
Confidence            33344455556667777777762     3357999999999999999999998863    566667643

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=94.57  E-value=0.092  Score=49.03  Aligned_cols=27  Identities=22%  Similarity=0.297  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|.|||||++.+.....
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            445899999999999999999987653

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=94.56  E-value=0.072  Score=47.21  Aligned_cols=28  Identities=29%  Similarity=0.239  Sum_probs=24.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+|.+.|.-|+|||||++.+++....
T Consensus        21 ~~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        21 FGTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            3458999999999999999999998654

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.54  E-value=0.64  Score=47.17  Aligned_cols=38  Identities=16%  Similarity=0.308  Sum_probs=29.0

Q ss_pred             HHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          169 FQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       169 ~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -++|...+..+++ ....++|+.|+||+++|..++...-
T Consensus         6 ~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~ll   44 (290)
T PRK05917          6 WEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLIL   44 (290)
T ss_pred             HHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHh
Confidence            3456666665554 4667899999999999999988764

>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=94.53  E-value=0.031  Score=52.91  Aligned_cols=25  Identities=36%  Similarity=0.717  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|+|.|.+|+||||||+.+......
T Consensus         1 ii~i~G~sgsGKttla~~l~~~l~~   25 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRV   25 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            5899999999999999999988763

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.51  E-value=0.035  Score=52.44  Aligned_cols=25  Identities=20%  Similarity=0.379  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++|.+.|++|+||||+|+.+.....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~   27 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLA   27 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhC
Confidence            5899999999999999999987753

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK14529 adenylate kinase; Provisional

Probab=94.50  E-value=0.094  Score=51.21  Aligned_cols=85  Identities=16%  Similarity=0.080  Sum_probs=45.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCe--EEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcC
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK--VVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKE  260 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~  260 (724)
                      .|.|.|++|+||||+|+.++...... +.+.  .+.-.+..........++++.+-. -.+    .+-....+.+.+.+.
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~~~-~is~gdllr~~i~~~t~lg~~i~~~i~~G~-lvp----dei~~~lv~~~l~~~   75 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYDLA-HIESGAIFREHIGGGTELGKKAKEYIDRGD-LVP----DDITIPMILETLKQD   75 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCC-CcccchhhhhhccCCChHHHHHHHHHhccC-cch----HHHHHHHHHHHHhcc
Confidence            37889999999999999999887542 3321  111122222223333444443211 111    222334455555432


Q ss_pred             CcEEEEEcccccc
Q 004895          261 KRVLIILDNIWTK  273 (724)
Q Consensus       261 kr~LlVlDdv~~~  273 (724)
                      ...=+|||..-..
T Consensus        76 ~~~g~iLDGfPRt   88 (223)
T PRK14529         76 GKNGWLLDGFPRN   88 (223)
T ss_pred             CCCcEEEeCCCCC
Confidence            2445899998543

>PRK06217 hypothetical protein; Validated

Probab=94.50  E-value=0.029  Score=53.37  Aligned_cols=33  Identities=27%  Similarity=0.333  Sum_probs=25.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCC--CeEEE
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVF--DKVVM  216 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~w  216 (724)
                      .|.|.|.+|+||||+|+.+.+.... .+|  |..+|
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~-~~~~~D~~~~   37 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDI-PHLDTDDYFW   37 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCC-cEEEcCceee
Confidence            5899999999999999999988753 233  34555

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

Probab=94.50  E-value=0.1  Score=46.20  Aligned_cols=41  Identities=15%  Similarity=0.392  Sum_probs=15.4

Q ss_pred             ccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcC
Q 004895          565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLD  606 (724)
Q Consensus       565 ~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~  606 (724)
                      .+....|.+++.|+.+.+.++ +..++. .+..+.+|+++.+.
T Consensus        25 ~I~~~~F~~~~~l~~i~~~~~-~~~i~~~~F~~~~~l~~i~~~   66 (129)
T PF13306_consen   25 KIGENAFSNCTSLKSINFPNN-LTSIGDNAFSNCKSLESITFP   66 (129)
T ss_dssp             EE-TTTTTT-TT-SEEEESST-TSCE-TTTTTT-TT-EEEEET
T ss_pred             EeChhhccccccccccccccc-ccccceeeeeccccccccccc
Confidence            344444555555555555442 333322 23333344444443

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.49  E-value=0.028  Score=51.52  Aligned_cols=23  Identities=43%  Similarity=0.673  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++.|+|++|+||||+|+.+.+..
T Consensus         1 li~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhhc
Confidence            47899999999999999998764

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PTZ00088 adenylate kinase 1; Provisional

Probab=94.48  E-value=0.043  Score=54.00  Aligned_cols=24  Identities=33%  Similarity=0.432  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|+|++|+||||+|+.+++...
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g   31 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKEN   31 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999988764

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=94.47  E-value=0.054  Score=56.38  Aligned_cols=48  Identities=21%  Similarity=0.307  Sum_probs=38.4

Q ss_pred             ccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          158 DYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +...++|.++.+..+.-.+.+.+..-+.+.|.+|+||||+|+.+..-.
T Consensus         6 ~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407          6 PFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             CHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            456678999988887765544455568899999999999999998765

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=94.44  E-value=0.08  Score=54.60  Aligned_cols=49  Identities=27%  Similarity=0.359  Sum_probs=37.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .+++.+.|.||+||||+|...+-.....+  ..++-|+.....++.+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~~lA~~g--~kvLlvStDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAVKLAESG--KKVLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHHHHHHcC--CcEEEEEeCCCCchHhhhcc
Confidence            46899999999999999999877776543  45777777777676666544

>TIGR00416 sms DNA repair protein RadA

Probab=94.44  E-value=0.12  Score=56.47  Aligned_cols=88  Identities=27%  Similarity=0.323  Sum_probs=51.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSND-LIYHRAKQLCQRLK  258 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~  258 (724)
                      .-.++.|.|.+|+|||||+.+++.......  ..++|++..+  +..++.. -++.++...+.-. ........+...+.
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~g--~kvlYvs~EE--s~~qi~~-ra~rlg~~~~~l~~~~e~~~~~I~~~i~  167 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKNQ--MKVLYVSGEE--SLQQIKM-RAIRLGLPEPNLYVLSETNWEQICANIE  167 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhcC--CcEEEEECcC--CHHHHHH-HHHHcCCChHHeEEcCCCCHHHHHHHHH
Confidence            346899999999999999999988765432  3578887644  3333322 2334443211100 00112344455554


Q ss_pred             cCCcEEEEEccccc
Q 004895          259 KEKRVLIILDNIWT  272 (724)
Q Consensus       259 ~~kr~LlVlDdv~~  272 (724)
                      +.+.-++|+|.+..
T Consensus       168 ~~~~~~vVIDSIq~  181 (454)
T TIGR00416       168 EENPQACVIDSIQT  181 (454)
T ss_pred             hcCCcEEEEecchh
Confidence            44667899998843

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.41  E-value=0.063  Score=54.35  Aligned_cols=54  Identities=17%  Similarity=0.262  Sum_probs=41.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLG  237 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~  237 (724)
                      +.-+++.|+|.+|+|||+++.++.......  ...++||+..+.  ..++.+.+.+ ++
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~--ge~vlyvs~~e~--~~~l~~~~~~-~g   74 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE--GEPVLYVSTEES--PEELLENARS-FG   74 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc--CCcEEEEEecCC--HHHHHHHHHH-cC
Confidence            356799999999999999999999988654  677999998764  3344444333 44

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=94.40  E-value=0.043  Score=53.41  Aligned_cols=32  Identities=25%  Similarity=0.441  Sum_probs=27.6

Q ss_pred             HhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          175 ALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       175 ~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+.++++++|+++|+.|+|||||..++.+...
T Consensus        16 ~~~~~~~~~i~~~G~~gsGKTTli~~l~~~~~   47 (207)
T TIGR00073        16 RLDKHGLVVLNFMSSPGSGKTTLIEKLIDNLK   47 (207)
T ss_pred             HhhhcCcEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34467899999999999999999999998753

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK14530 adenylate kinase; Provisional

Probab=94.39  E-value=0.037  Score=54.24  Aligned_cols=25  Identities=28%  Similarity=0.291  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.|.|+|++|+||||+|+.++....
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~   28 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFG   28 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3689999999999999999988763

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.38  E-value=0.21  Score=49.84  Aligned_cols=24  Identities=25%  Similarity=0.469  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +..|+|++|+|||+||..++-...
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va   26 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMA   26 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHh
Confidence            567899999999999999987654

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.37  E-value=0.36  Score=50.15  Aligned_cols=29  Identities=38%  Similarity=0.520  Sum_probs=25.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +..+++++|++|+||||++..++......
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~l~~~  141 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHKYKAQ  141 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            46799999999999999999999988643

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.37  E-value=0.25  Score=45.84  Aligned_cols=120  Identities=16%  Similarity=0.122  Sum_probs=64.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeE--EEEEEecCCChHHHHHHHH---HhhCCC--CC--CCchhH----
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKV--VMAEITKNPDAQKIQGELA---SDLGMN--FD--SNDLIY----  247 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~--~wv~vs~~~~~~~l~~~i~---~~l~~~--~~--~~~~~~----  247 (724)
                      ...|-|++..|.||||.|.-.+-+.... .+...  -|+--.........+..+.   .+.+..  +.  +.....    
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~ra~~~-g~~v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~~~~   83 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMALRALGH-GKKVGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTAIAK   83 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHHHHHHC-CCeEEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHHHHH
Confidence            4578888899999999999998887653 23321  2333322234333443320   011111  11  111111    


Q ss_pred             HHHHHHHHHHhcCCcEEEEEcccccccc-----ccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          248 HRAKQLCQRLKKEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       248 ~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      .......+.+..+.-=|+|||.+-....     .+++...+..        ...+.-||+|-|+..-
T Consensus        84 ~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~--------rp~~~evVlTGR~~p~  142 (173)
T TIGR00708        84 AAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQE--------RPGHQHVIITGRGCPQ  142 (173)
T ss_pred             HHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHh--------CCCCCEEEEECCCCCH
Confidence            1223334444445556999999864432     2233333333        4556789999998753

Alternate name: corrinoid adenosyltransferase.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.34  E-value=0.11  Score=48.59  Aligned_cols=47  Identities=21%  Similarity=0.292  Sum_probs=30.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      ++.|.|.+|+||||+|..+......     .++++.-....+ .+..+.|...
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~-----~~~~iat~~~~~-~e~~~ri~~h   49 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGL-----QVLYIATAQPFD-DEMAARIAHH   49 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCC-----CcEeCcCCCCCh-HHHHHHHHHH
Confidence            6899999999999999999876421     234444433333 3444555443

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=94.29  E-value=0.07  Score=53.92  Aligned_cols=36  Identities=19%  Similarity=0.273  Sum_probs=29.8

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          172 VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       172 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+.+...+..++.|+|.+|+|||||+..+.+....
T Consensus        95 ~r~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~~l~~  130 (290)
T PRK10463         95 NRARFAARKQLVLNLVSSPGSGKTTLLTETLMRLKD  130 (290)
T ss_pred             HHHHHHhcCCeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            334444677899999999999999999999998754

>PRK13947 shikimate kinase; Provisional

Probab=94.27  E-value=0.038  Score=51.90  Aligned_cols=24  Identities=38%  Similarity=0.472  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -|.|+|++|+||||+|+.+++...
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg   26 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLS   26 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhC
Confidence            488999999999999999998874

>PRK13949 shikimate kinase; Provisional

Probab=94.26  E-value=0.037  Score=51.81  Aligned_cols=24  Identities=42%  Similarity=0.476  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -|.|+|+.|+||||+++.+++...
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~   26 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELG   26 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            588999999999999999998774

>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=94.24  E-value=0.082  Score=54.45  Aligned_cols=77  Identities=17%  Similarity=0.404  Sum_probs=55.0

Q ss_pred             ccccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE----ecCC---ChH
Q 004895          160 NIFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI----TKNP---DAQ  226 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v----s~~~---~~~  226 (724)
                      ..|.|-++.++++++.+.      +.+-+|+.++||.|.||||||..+.+-.+.   |  .+|.-.    .+.+   =+.
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~---y--~~Y~l~~~Pm~e~PL~L~P~  135 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKRGLEE---Y--PIYTLKGCPMHEEPLHLFPK  135 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHHHhhe---E--EEEEecCCccccChhhhCCH
Confidence            468899999999999886      456789999999999999999999988864   2  333321    1111   134


Q ss_pred             HHHHHHHHhhCCCCC
Q 004895          227 KIQGELASDLGMNFD  241 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~  241 (724)
                      ++-..+.+.++....
T Consensus       136 ~~r~~~~~~~~~~i~  150 (358)
T PF08298_consen  136 ELRREFEDELGIRIE  150 (358)
T ss_pred             hHHHHHHHHhCcccC
Confidence            555666666766443

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK14527 adenylate kinase; Provisional

Probab=94.23  E-value=0.048  Score=52.34  Aligned_cols=29  Identities=24%  Similarity=0.311  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ....+|.|+|++|+||||+|+.+++....
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La~~~~~   32 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLAQELGL   32 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            34578999999999999999999887743

>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=94.23  E-value=0.03  Score=30.04  Aligned_cols=16  Identities=31%  Similarity=0.586  Sum_probs=8.0

Q ss_pred             CCcEEEccCCcCcccc
Q 004895          621 KLEILSLRGAEIKQLP  636 (724)
Q Consensus       621 ~L~~L~l~~~~i~~lp  636 (724)
                      +|++|++++|.++++|
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            5666777777666665

...

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.21  E-value=0.046  Score=51.19  Aligned_cols=27  Identities=37%  Similarity=0.612  Sum_probs=24.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +.|.+.|.+|+||||+|+++++..+.+
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHHHHHh
Confidence            467889999999999999999988764

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=94.19  E-value=0.093  Score=48.05  Aligned_cols=32  Identities=25%  Similarity=0.496  Sum_probs=27.7

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          177 KDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       177 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ..++..+|.+.|.+|.||||+|..+++.....
T Consensus        19 ~~~~~~viW~TGLSGsGKSTiA~ale~~L~~~   50 (197)
T COG0529          19 KGQKGAVIWFTGLSGSGKSTIANALEEKLFAK   50 (197)
T ss_pred             hCCCCeEEEeecCCCCCHHHHHHHHHHHHHHc
Confidence            34566799999999999999999999998764

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=94.18  E-value=0.2  Score=58.59  Aligned_cols=193  Identities=17%  Similarity=0.208  Sum_probs=89.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC---CchhHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS---NDLIYHRAKQLCQ  255 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~l~~  255 (724)
                      ...+++.|+|+.+.||||+.+.+.-..--   .++-.+|++..... -.++..|...++....-   .+.-.....++..
T Consensus       325 ~~~~~~iITGpN~gGKTt~lktigl~~~m---aq~G~~vpa~~~~~-i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~  400 (782)
T PRK00409        325 FDKTVLVITGPNTGGKTVTLKTLGLAALM---AKSGLPIPANEPSE-IPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVR  400 (782)
T ss_pred             CCceEEEEECCCCCCcHHHHHHHHHHHHH---HHhCCCcccCCCcc-ccccceEEEecCCccchhhchhHHHHHHHHHHH
Confidence            34578899999999999999999754211   00111222221000 00111111111111000   0001111122222


Q ss_pred             HHhc-CCcEEEEEcccccccccc---ccccc-cCCCCcCCCCCCCCCcEEEEEecccchhhhhcCCCc--eEecCCCCHH
Q 004895          256 RLKK-EKRVLIILDNIWTKLELD---KIGIP-YGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQK--MFWIDALSEE  328 (724)
Q Consensus       256 ~l~~-~kr~LlVlDdv~~~~~~~---~l~~~-~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~~~~~--~~~l~~L~~~  328 (724)
                      .+.. ..+-|+++|......+..   .+... +..+       ...|+.+|+||....+.........  ...+. ++. 
T Consensus       401 Il~~~~~~sLvLlDE~~~GtDp~eg~ala~aile~l-------~~~~~~vIitTH~~el~~~~~~~~~v~~~~~~-~d~-  471 (782)
T PRK00409        401 ILEKADKNSLVLFDELGAGTDPDEGAALAISILEYL-------RKRGAKIIATTHYKELKALMYNREGVENASVE-FDE-  471 (782)
T ss_pred             HHHhCCcCcEEEecCCCCCCCHHHHHHHHHHHHHHH-------HHCCCEEEEECChHHHHHHHhcCCCeEEEEEE-Eec-
Confidence            2221 367899999986543321   11110 1000       2347889999998776432111111  11111 111 


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHHHHhc
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTS  389 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~~l~~  389 (724)
                      +......+...+.   + -...|-+|++++ |+|-.+.--|..+.......++.++..+..
T Consensus       472 ~~l~~~Ykl~~G~---~-g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~l~~  527 (782)
T PRK00409        472 ETLRPTYRLLIGI---P-GKSNAFEIAKRL-GLPENIIEEAKKLIGEDKEKLNELIASLEE  527 (782)
T ss_pred             CcCcEEEEEeeCC---C-CCcHHHHHHHHh-CcCHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            1100000000011   1 134577888887 788888777777766556677777766554

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=94.18  E-value=0.33  Score=52.18  Aligned_cols=91  Identities=20%  Similarity=0.258  Sum_probs=54.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC-hHHHHHHHHHhhCCC--------CCCCchh---
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD-AQKIQGELASDLGMN--------FDSNDLI---  246 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~l~~~i~~~l~~~--------~~~~~~~---  246 (724)
                      .+-..++|+|..|+|||||++.+++...    .+.++++-+.+... ..++..+.+..-+.+        .+++...   
T Consensus       156 ~~Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~  231 (442)
T PRK08927        156 CRGQRMGIFAGSGVGKSVLLSMLARNAD----ADVSVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQ  231 (442)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhccC----CCEEEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHH
Confidence            3456899999999999999999987653    24555666665543 334444444332211        1111111   


Q ss_pred             -HHHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          247 -YHRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 -~~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                       ...+-.+.+++. +++++|+++||+-..
T Consensus       232 a~~~a~tiAEyfrd~G~~Vll~~DslTr~  260 (442)
T PRK08927        232 AAYLTLAIAEYFRDQGKDVLCLMDSVTRF  260 (442)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCcHHH
Confidence             111223444442 478999999999543

>TIGR03263 guanyl_kin guanylate kinase

Probab=94.17  E-value=0.037  Score=52.52  Aligned_cols=24  Identities=42%  Similarity=0.613  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++|+|+|+.|+||||||+.+++..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            478999999999999999998854

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.

>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=94.17  E-value=0.074  Score=49.59  Aligned_cols=24  Identities=42%  Similarity=0.641  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      |.|.|.+|+|||||++.+++..+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l~~   25 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEELKK   25 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhhc
Confidence            689999999999999999998854

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=94.16  E-value=0.14  Score=52.70  Aligned_cols=63  Identities=21%  Similarity=0.255  Sum_probs=43.0

Q ss_pred             cccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      .|+=..+....++.++..+  +-|.|.|++|+||||+|+.++......     .+.|.++...+..++..
T Consensus        46 ~y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~~l~~~-----~~rV~~~~~l~~~DliG  108 (327)
T TIGR01650        46 AYLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAARLNWP-----CVRVNLDSHVSRIDLVG  108 (327)
T ss_pred             CccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHHHHCCC-----eEEEEecCCCChhhcCC
Confidence            3444444556676666533  368999999999999999999988532     34666666665555543

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.

>PRK13695 putative NTPase; Provisional

Probab=94.15  E-value=0.07  Score=50.28  Aligned_cols=34  Identities=41%  Similarity=0.487  Sum_probs=25.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      .++|+|.+|+|||||++.+++.... ..+....|+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~-~G~~~~g~~   35 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKE-EGYKVGGFY   35 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH-CCCeEEEEE
Confidence            4789999999999999999988764 234434344

>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=94.14  E-value=0.071  Score=46.49  Aligned_cols=24  Identities=42%  Similarity=0.551  Sum_probs=18.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      |.|+|.+|+||||+|+.++.....
T Consensus         2 vLleg~PG~GKT~la~~lA~~~~~   25 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALARSLGL   25 (131)
T ss_dssp             EEEES---HHHHHHHHHHHHHTT-
T ss_pred             EeeECCCccHHHHHHHHHHHHcCC
Confidence            679999999999999999988653

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.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=94.12  E-value=0.23  Score=53.44  Aligned_cols=94  Identities=19%  Similarity=0.320  Sum_probs=58.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchh---
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLI---  246 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~---  246 (724)
                      .+-..++|.|.+|+|||||+..+....... +-+.++++-+.+.. ...+++.++...-..+        .+++...   
T Consensus       141 g~GQr~~If~~~G~GKt~L~~~~~~~~~~~-~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~  219 (461)
T TIGR01039       141 AKGGKIGLFGGAGVGKTVLIQELINNIAKE-HGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMR  219 (461)
T ss_pred             ccCCEEEeecCCCCChHHHHHHHHHHHHhc-CCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            345688999999999999999998876542 23467777776653 3456666665432111        1121111   


Q ss_pred             -HHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          247 -YHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 -~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                       ...+-.+.++++  +++++||++||+-..
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLll~DslTR~  249 (461)
T TIGR01039       220 VALTGLTMAEYFRDEQGQDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCeeEEEecchhHH
Confidence             112234555664  368999999999553

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=94.12  E-value=0.18  Score=54.60  Aligned_cols=94  Identities=19%  Similarity=0.187  Sum_probs=57.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC--eEEEEEEecCC-ChHHHHHHHHHhhCCC--------CCCCchh--
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD--KVVMAEITKNP-DAQKIQGELASDLGMN--------FDSNDLI--  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~-~~~~l~~~i~~~l~~~--------~~~~~~~--  246 (724)
                      +-..++|.|..|+|||||+..+.+.....+.+.  .++++-+.+.. ...+++.++...=..+        .+++...  
T Consensus       140 ~GQR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~  219 (458)
T TIGR01041       140 RGQKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERI  219 (458)
T ss_pred             cCCEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHH
Confidence            445789999999999999999988765321121  45666666543 4555666655432111        1111111  


Q ss_pred             --HHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          247 --YHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 --~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                        ...+..+.++++  +++++||++||+-..
T Consensus       220 ~a~~~a~tiAEyfr~d~G~~VLli~DslTR~  250 (458)
T TIGR01041       220 VTPRMALTAAEYLAFEKDMHVLVILTDMTNY  250 (458)
T ss_pred             HHHHHHHHHHHHHHHccCCcEEEEEcChhHH
Confidence              112334566666  588999999999543

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=94.12  E-value=0.048  Score=50.14  Aligned_cols=33  Identities=21%  Similarity=0.440  Sum_probs=26.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEE
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVM  216 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~w  216 (724)
                      |++|+|+.|+|||||+..+....+.+ .+...+.
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~~l~~~-G~~V~vi   33 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVKALKAR-GYRVATI   33 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhc-CCeEEEE
Confidence            58899999999999999999988753 4444333

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.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.09  E-value=0.04  Score=50.29  Aligned_cols=20  Identities=45%  Similarity=0.745  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIA  202 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~  202 (724)
                      .|+|.|.+|+||||++..+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999987

>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=94.07  E-value=0.046  Score=50.26  Aligned_cols=23  Identities=43%  Similarity=0.528  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      |.|+|++|+||||+|+.+.....
T Consensus         2 i~l~G~~GsGKstla~~la~~l~   24 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhC
Confidence            67999999999999999988763

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=94.06  E-value=0.078  Score=51.18  Aligned_cols=30  Identities=23%  Similarity=0.405  Sum_probs=25.9

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+..+|.|+|++|+||||||+.+......
T Consensus        21 ~~~~~~i~i~G~~GsGKSTla~~l~~~l~~   50 (198)
T PRK03846         21 GHKGVVLWFTGLSGSGKSTVAGALEEALHE   50 (198)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            356679999999999999999999987753

>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=94.06  E-value=0.047  Score=47.59  Aligned_cols=23  Identities=39%  Similarity=0.618  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      |.|+|..|+|||||.+.+.....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS-
T ss_pred             EEEECcCCCCHHHHHHHHhcCCC
Confidence            78999999999999999987654

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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=94.05  E-value=0.066  Score=50.94  Aligned_cols=36  Identities=31%  Similarity=0.455  Sum_probs=27.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      .+++.|+|+.|+|||||++.+......  .|..+++.+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~--~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPD--KFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTT--TEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhccc--ccccceeec
Confidence            468999999999999999999997753  364444443

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 ....

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=94.04  E-value=0.2  Score=53.71  Aligned_cols=93  Identities=20%  Similarity=0.222  Sum_probs=58.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc--cCCC---------eEEEEEEecCCChHHHHHHHHHhhC-CC--------
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED--NVFD---------KVVMAEITKNPDAQKIQGELASDLG-MN--------  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~---------~~~wv~vs~~~~~~~l~~~i~~~l~-~~--------  239 (724)
                      +-+.++|.|-+|+|||||+..+.+.....  ...|         .++++-+.+.....+.+.+.+..-+ ..        
T Consensus       140 ~GQRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~at  219 (466)
T TIGR01040       140 RGQKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNL  219 (466)
T ss_pred             cCCeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEEC
Confidence            45678999999999999999998876410  0012         5677777777655555555555544 11        


Q ss_pred             CCCCchh----HHHHHHHHHHHh--cCCcEEEEEccccc
Q 004895          240 FDSNDLI----YHRAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       240 ~~~~~~~----~~~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                      .+++...    ...+-.+.+++.  +++++|+++||+-.
T Consensus       220 sd~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr  258 (466)
T TIGR01040       220 ANDPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMSS  258 (466)
T ss_pred             CCCCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHH
Confidence            1111111    111233556665  47999999999954

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.01  E-value=0.13  Score=54.58  Aligned_cols=46  Identities=26%  Similarity=0.283  Sum_probs=36.3

Q ss_pred             cccchHHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALKD--------------DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|.++.++.+..++..              .....|.++|++|+|||++|+.+.....
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~   75 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            467888888887766632              0136789999999999999999998864

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.98  E-value=0.42  Score=48.63  Aligned_cols=52  Identities=19%  Similarity=0.215  Sum_probs=37.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -.++.|.|++|+||||++.+++...... +=..++|++...  +..++...+...
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~-~g~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQ-HGVRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHh-cCceEEEEEccc--CHHHHHHHHHHH
Confidence            4588899999999999999998876432 123588888765  345566665544

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK00300 gmk guanylate kinase; Provisional

Probab=93.97  E-value=0.053  Score=52.69  Aligned_cols=26  Identities=35%  Similarity=0.483  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|+|+|+.|+||||||+.++...
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34689999999999999999999865

>PTZ00185 ATPase alpha subunit; Provisional

Probab=93.97  E-value=0.35  Score=52.46  Aligned_cols=95  Identities=13%  Similarity=0.095  Sum_probs=54.8

Q ss_pred             CCccEEEEEcCCCCcHHHHH-HHHHHHHhhc-----cCCCeEEEEEEecCCChHHHHHHHHHhhCC-C--------CCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLV-KQIAKQVMED-----NVFDKVVMAEITKNPDAQKIQGELASDLGM-N--------FDSN  243 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~-----~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~-~--------~~~~  243 (724)
                      .+-..++|.|..|+|||+|| ..+.+.....     +.-+.++++-+.+..+...-+.+.+++-+. .        .+++
T Consensus       187 GRGQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep  266 (574)
T PTZ00185        187 GRGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEP  266 (574)
T ss_pred             cCCCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCC
Confidence            34567899999999999997 6667765321     234567888888765433223444444331 1        1111


Q ss_pred             chhH----HHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          244 DLIY----HRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       244 ~~~~----~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ....    -..-.+.+++. +++.+|+|+||+-..
T Consensus       267 ~~~r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        267 AGLQYLAPYSGVTMGEYFMNRGRHCLCVYDDLSKQ  301 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEcCchHH
Confidence            1010    01222334442 478999999999553

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=93.95  E-value=0.058  Score=49.46  Aligned_cols=29  Identities=28%  Similarity=0.655  Sum_probs=26.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhcc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDN  209 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~  209 (724)
                      .+|++|+|+.|+|||||...+....+.++
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G   30 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARG   30 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHHHHHhCC
Confidence            46999999999999999999999998753

>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=93.94  E-value=0.049  Score=54.05  Aligned_cols=33  Identities=27%  Similarity=0.460  Sum_probs=23.3

Q ss_pred             EEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          186 VCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       186 I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      |+||+|+||||+++.+.+.....+  ..++-|+..
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~--~~~~~vNLD   33 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLESNG--RDVYIVNLD   33 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHTTT---S-EEEEE--
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcc--CCceEEEcc
Confidence            689999999999999999887542  335555554

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=93.92  E-value=0.042  Score=49.47  Aligned_cols=22  Identities=41%  Similarity=0.699  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |+|+|+.|+|||||++.+.+..
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~   23 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEF   23 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcC
Confidence            7899999999999999998765

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.

>PRK13975 thymidylate kinase; Provisional

Probab=93.91  E-value=0.052  Score=52.27  Aligned_cols=26  Identities=35%  Similarity=0.473  Sum_probs=23.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..|+|.|+.|+||||+|+.+++....
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~l~~   28 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEKLNA   28 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999998753

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=93.91  E-value=0.31  Score=52.20  Aligned_cols=90  Identities=19%  Similarity=0.334  Sum_probs=53.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC-hHHHHHHHHHhhCCC--------CCCCchhH---
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD-AQKIQGELASDLGMN--------FDSNDLIY---  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~l~~~i~~~l~~~--------~~~~~~~~---  247 (724)
                      .-..++|+|..|+|||||++.++....    .+.++.+-+.+... ..++..+++..-+..        .+++....   
T Consensus       161 ~GqrigI~G~sG~GKSTLL~~I~~~~~----~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a  236 (444)
T PRK08972        161 KGQRMGLFAGSGVGKSVLLGMMTRGTT----ADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKG  236 (444)
T ss_pred             CCCEEEEECCCCCChhHHHHHhccCCC----CCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHH
Confidence            456899999999999999999986432    35556666665543 344555554432211        11111111   


Q ss_pred             -HHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          248 -HRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       248 -~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                       ..+-.+.+++. +++++|+++||+-..
T Consensus       237 ~~~A~tiAEyfrd~G~~VLl~~DslTR~  264 (444)
T PRK08972        237 CETATTIAEYFRDQGLNVLLLMDSLTRY  264 (444)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEEcChHHH
Confidence             11222444442 478999999999543

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.90  E-value=0.041  Score=51.23  Aligned_cols=22  Identities=27%  Similarity=0.585  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|++|+||||+|+.+.+..
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4689999999999999998775

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.

>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=93.89  E-value=0.097  Score=54.06  Aligned_cols=45  Identities=22%  Similarity=0.379  Sum_probs=31.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l  228 (724)
                      +++.+.|-||+||||+|...+-....++  ..+.-++.....++.++
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G--~rtLlvS~Dpa~~L~d~   46 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRG--KRTLLVSTDPAHSLSDV   46 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTT--S-EEEEESSTTTHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCC--CCeeEeecCCCccHHHH
Confidence            6899999999999999999888876543  23555554444444333

...

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=93.89  E-value=0.18  Score=50.58  Aligned_cols=96  Identities=15%  Similarity=0.153  Sum_probs=53.8

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHHHHHhhccCCCeE-EEEEEecCC-ChHHHHHHHHHhhCC--------CCCCCchhH-
Q 004895          180 KLNIIGVCGMGGVGKTTLV-KQIAKQVMEDNVFDKV-VMAEITKNP-DAQKIQGELASDLGM--------NFDSNDLIY-  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~l~~~i~~~l~~--------~~~~~~~~~-  247 (724)
                      +-+.++|.|..|+|||+|| ..+.+..    .-+.+ +++-+.+.. ...++.+++...-..        ..++..... 
T Consensus        68 rGQr~~Ifg~~g~GKt~L~l~~i~~~~----~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  143 (274)
T cd01132          68 RGQRELIIGDRQTGKTAIAIDTIINQK----GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQY  143 (274)
T ss_pred             cCCEEEeeCCCCCCccHHHHHHHHHhc----CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHH
Confidence            4457899999999999996 5555543    23444 666666553 345555555543211        111111110 


Q ss_pred             ---HHHHHHHHHHh-cCCcEEEEEcccccc-cccccc
Q 004895          248 ---HRAKQLCQRLK-KEKRVLIILDNIWTK-LELDKI  279 (724)
Q Consensus       248 ---~~~~~l~~~l~-~~kr~LlVlDdv~~~-~~~~~l  279 (724)
                         ..+-.+.+++. +++++|+++||+-.. ..++++
T Consensus       144 ~a~~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEi  180 (274)
T cd01132         144 LAPYTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQM  180 (274)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHH
Confidence               01223334443 478999999999654 344444

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=93.89  E-value=0.56  Score=48.56  Aligned_cols=49  Identities=20%  Similarity=0.233  Sum_probs=36.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGEL  232 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i  232 (724)
                      +-..++|.|..|+|||+|++++.+...    -+.++++-+.+.. ...+++.++
T Consensus       156 kGqr~~I~G~~G~GKT~L~~~Iak~~~----~dvvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         156 KGGTAAIPGPFGCGKTVIQQSLSKYSN----SDIVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             CCCEEEEECCCCCChHHHHHHHHhCCC----CCEEEEEEeCCChHHHHHHHHHH
Confidence            445899999999999999999988542    3578888887654 345555554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=93.88  E-value=0.057  Score=51.81  Aligned_cols=25  Identities=36%  Similarity=0.464  Sum_probs=22.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|.|.+|+||||+|+.++...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4589999999999999999998875

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=93.87  E-value=0.25  Score=52.99  Aligned_cols=90  Identities=22%  Similarity=0.381  Sum_probs=50.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCC--------CCCCchhH---
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMN--------FDSNDLIY---  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~--------~~~~~~~~---  247 (724)
                      +-..++|+|..|+|||||++.+......    +....+.+.+ .....++..+.+..-+.+        .+++....   
T Consensus       139 ~Gq~i~I~G~sG~GKTtLl~~I~~~~~~----~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a  214 (418)
T TIGR03498       139 RGQRLGIFAGSGVGKSTLLSMLARNTDA----DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQA  214 (418)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCCCC----CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHH
Confidence            4468999999999999999988865432    2323333333 333444555444332211        11111111   


Q ss_pred             -HHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          248 -HRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       248 -~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                       ..+-.+.+++. +++++|+++||+-..
T Consensus       215 ~~~a~~iAEyfrd~G~~Vll~~DslTr~  242 (418)
T TIGR03498       215 AYTATAIAEYFRDQGKDVLLLMDSVTRF  242 (418)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchhHH
Confidence             11223444443 478999999998543

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=93.86  E-value=0.059  Score=50.63  Aligned_cols=26  Identities=35%  Similarity=0.400  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|+|+.|+||||+++.+.+...
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~   29 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcC
Confidence            34689999999999999999998753

>PRK08149 ATP synthase SpaL; Validated

Probab=93.85  E-value=0.3  Score=52.37  Aligned_cols=90  Identities=18%  Similarity=0.249  Sum_probs=53.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCC--------CCCCchh----
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMN--------FDSNDLI----  246 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~--------~~~~~~~----  246 (724)
                      +-..++|+|..|+|||||+..++....    .+.++...+... .+..++..+........        .+.+...    
T Consensus       150 ~Gq~i~I~G~sG~GKTTLl~~i~~~~~----~dv~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~a  225 (428)
T PRK08149        150 VGQRMGIFASAGCGKTSLMNMLIEHSE----ADVFVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCNA  225 (428)
T ss_pred             cCCEEEEECCCCCChhHHHHHHhcCCC----CCeEEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHhH
Confidence            456899999999999999999887442    244444445433 34556666665543211        1111101    


Q ss_pred             HHHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          247 YHRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 ~~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ...+..+.+++. +++++||++||+-..
T Consensus       226 ~~~a~tiAE~fr~~G~~Vll~~DslTr~  253 (428)
T PRK08149        226 ALVATTVAEYFRDQGKRVVLFIDSMTRY  253 (428)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEccchHHH
Confidence            112223344442 478999999999543

>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=93.84  E-value=0.27  Score=48.92  Aligned_cols=25  Identities=28%  Similarity=0.489  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|+|.|..|+||||+++.+.+....
T Consensus         1 IIgItG~SGSGKTTv~~~l~~~l~~   25 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAR   25 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHh
Confidence            5899999999999999999988764

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.82  E-value=0.05  Score=51.61  Aligned_cols=37  Identities=22%  Similarity=0.308  Sum_probs=28.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      .-.|++|+|+.|+|||||.+.+..-....   ++.+|+.-
T Consensus        27 ~Gevv~iiGpSGSGKSTlLRclN~LE~~~---~G~I~i~g   63 (240)
T COG1126          27 KGEVVVIIGPSGSGKSTLLRCLNGLEEPD---SGSITVDG   63 (240)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCcCCC---CceEEECC
Confidence            44699999999999999999986654432   45777753

>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=93.80  E-value=0.1  Score=49.72  Aligned_cols=45  Identities=16%  Similarity=0.194  Sum_probs=32.0

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...++|.+..+..+.-....  ..-+.++|++|+|||++|+.+..-.
T Consensus         2 f~dI~GQe~aKrAL~iAAaG--~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    2 FSDIVGQEEAKRALEIAAAG--GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             TCCSSSTHHHHHHHHHHHHC--C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             hhhhcCcHHHHHHHHHHHcC--CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            34677888777776655443  3478899999999999999997643

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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=93.79  E-value=0.16  Score=52.80  Aligned_cols=38  Identities=29%  Similarity=0.616  Sum_probs=29.9

Q ss_pred             HHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          171 DVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       171 ~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .+++.+.  .++..+|+|.|++|+|||||+..+.......
T Consensus        44 ~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~~l~~~   83 (332)
T PRK09435         44 ELLDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQ   83 (332)
T ss_pred             HHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            4444443  3567799999999999999999999888753

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=93.79  E-value=0.72  Score=49.28  Aligned_cols=79  Identities=19%  Similarity=0.257  Sum_probs=63.2

Q ss_pred             ccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-------ChHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-------DAQKIQGE  231 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~l~~~  231 (724)
                      -|||+.+++.|.+.|.   +++..+-.|.|.=|.|||.+++.+.+....+ .| .+..+.+|...       ....+.++
T Consensus        27 ~VGr~~e~~~l~~~l~~v~~G~s~~kfi~G~YGsGKTf~l~~i~~~A~~~-~f-vvs~v~ls~e~~lh~~~g~~~~~Yr~  104 (416)
T PF10923_consen   27 AVGREREIEALDRDLDRVADGGSSFKFIRGEYGSGKTFFLRLIRERALEK-GF-VVSEVDLSPERPLHGTGGQLEALYRE  104 (416)
T ss_pred             eechHHHHHHHHHHHHHHhCCCCeEEEEEeCCCCcHHHHHHHHHHHHHHc-CC-EEEEEecCCCcccccccccHHHHHHH
Confidence            4699999999988776   6777788999999999999999999988764 34 36677777642       45679999


Q ss_pred             HHHhhCCCCCC
Q 004895          232 LASDLGMNFDS  242 (724)
Q Consensus       232 i~~~l~~~~~~  242 (724)
                      |++.+..+..+
T Consensus       105 l~~nL~t~~~p  115 (416)
T PF10923_consen  105 LMRNLSTKTKP  115 (416)
T ss_pred             HHHhcCCCCCC
Confidence            99999876543

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=93.77  E-value=0.15  Score=54.22  Aligned_cols=41  Identities=32%  Similarity=0.476  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          167 KIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       167 ~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+.+++.+.......+.|.|+||+|||+|.+.+.+..+.
T Consensus         8 ~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen    8 RVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             HHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            34556666666566778999999999999999999998865

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=93.73  E-value=0.13  Score=52.38  Aligned_cols=53  Identities=25%  Similarity=0.280  Sum_probs=40.2

Q ss_pred             cccccchHHHHH---HHHHHhcCC--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCC
Q 004895          159 YNIFNSRKKIFQ---DVIEALKDD--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF  211 (724)
Q Consensus       159 ~~~~~gR~~~~~---~l~~~L~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  211 (724)
                      ..+++|..+..+   -+++++.++  .-+.|.|+|++|.|||+||-.+.+.....-+|
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF   95 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDVPF   95 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCc
Confidence            467888766544   345555544  34789999999999999999999999766555

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=93.72  E-value=0.34  Score=50.14  Aligned_cols=89  Identities=25%  Similarity=0.369  Sum_probs=51.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCC--------CCCCchhH---
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMN--------FDSNDLIY---  247 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~--------~~~~~~~~---  247 (724)
                      .-..++|+|..|+|||||++.+.....    .+.....-+.. ..+..++.......-+..        .+++....   
T Consensus        68 ~Gqri~I~G~sG~GKTtLl~~Ia~~~~----~~~~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~  143 (326)
T cd01136          68 KGQRLGIFAGSGVGKSTLLGMIARGTT----ADVNVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKA  143 (326)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCCCC----CCEEEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHH
Confidence            446889999999999999998887543    23334444443 334555555555432211        11211111   


Q ss_pred             -HHHHHHHHHHh-cCCcEEEEEccccc
Q 004895          248 -HRAKQLCQRLK-KEKRVLIILDNIWT  272 (724)
Q Consensus       248 -~~~~~l~~~l~-~~kr~LlVlDdv~~  272 (724)
                       ..+-.+.+++. +++++|+++||+-.
T Consensus       144 ~~~a~~~AEyfr~~g~~Vll~~Dsltr  170 (326)
T cd01136         144 AYTATAIAEYFRDQGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHHHcCCCeEEEeccchH
Confidence             11222333332 47899999999854

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.72  E-value=0.57  Score=46.73  Aligned_cols=51  Identities=16%  Similarity=0.263  Sum_probs=36.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      -.++.|.|.+|+|||+++.+++.+...... ..++|++...  +..++...++.
T Consensus        13 G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g-~~vly~s~E~--~~~~~~~r~~~   63 (242)
T cd00984          13 GDLIIIAARPSMGKTAFALNIAENIAKKQG-KPVLFFSLEM--SKEQLLQRLLA   63 (242)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhCC-CceEEEeCCC--CHHHHHHHHHH
Confidence            358999999999999999999887654312 3477777654  45566666543

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.72  E-value=0.052  Score=51.84  Aligned_cols=24  Identities=25%  Similarity=0.480  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++.|+|+.|+|||||++.++...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~   26 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQRE   26 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccC
Confidence            478999999999999999997654

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=93.69  E-value=2.4  Score=43.20  Aligned_cols=68  Identities=15%  Similarity=0.171  Sum_probs=39.4

Q ss_pred             CCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEeccc-chhhhhcCCCceEecCCCCHHHHHHHHHH
Q 004895          260 EKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR-DLLCIDMNSQKMFWIDALSEEEALQLFEK  336 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~-~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~  336 (724)
                      +++-++|+||++...  ..+.+.-.+..        ...++.+|++|.+. .+.+.-.+....+.+.+ +.++..+.+..
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEE--------Pp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~~  173 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEE--------PQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLEQ  173 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcC--------CCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHHH
Confidence            566799999997653  34444333322        33445566666554 44433344556788876 66766666653

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=93.66  E-value=0.27  Score=53.99  Aligned_cols=124  Identities=19%  Similarity=0.279  Sum_probs=64.7

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHH-HHHHHHHHHhhccCCCeEEEEEEecCCCh--HHHHHHHHHhhCCCCCCCc--
Q 004895          170 QDVIEALKDDKLNIIGVCGMGGVGKTT-LVKQIAKQVMEDNVFDKVVMAEITKNPDA--QKIQGELASDLGMNFDSND--  244 (724)
Q Consensus       170 ~~l~~~L~~~~~~vi~I~G~gGiGKTt-La~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~l~~~i~~~l~~~~~~~~--  244 (724)
                      ++|++.+.  ...||.|+|..|+|||| |++.+|.+--..   ++  -|-+.+...+  -.+.+.+.+.++.......  
T Consensus       362 ~~ll~~ir--~n~vvvivgETGSGKTTQl~QyL~edGY~~---~G--mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGY  434 (1042)
T KOG0924|consen  362 DQLLSVIR--ENQVVVIVGETGSGKTTQLAQYLYEDGYAD---NG--MIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGY  434 (1042)
T ss_pred             HHHHHHHh--hCcEEEEEecCCCCchhhhHHHHHhccccc---CC--eeeecCchHHHHHHHHHHHHHHhCCccccccce
Confidence            34444443  34599999999999976 666666654222   22  3444444433  3345566666643321100  


Q ss_pred             --------hhH------HHHHHHHHHHhc---CCcEEEEEccccccccccc-----cccccCCCCcCCCCCCCCCcEEEE
Q 004895          245 --------LIY------HRAKQLCQRLKK---EKRVLIILDNIWTKLELDK-----IGIPYGDVDEKDKNDDPRRCTIIL  302 (724)
Q Consensus       245 --------~~~------~~~~~l~~~l~~---~kr~LlVlDdv~~~~~~~~-----l~~~~~~~~~~~~~~~~~~s~ilv  302 (724)
                              ...      ....-|++.|..   .|--.||+|...+...--+     +...+.         ....-|+||
T Consensus       435 sIRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~la---------rRrdlKliV  505 (1042)
T KOG0924|consen  435 SIRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLA---------RRRDLKLIV  505 (1042)
T ss_pred             EEEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHH---------hhccceEEE
Confidence                    000      011223333321   3556899999976532111     111111         345678999


Q ss_pred             Eecccch
Q 004895          303 TSRSRDL  309 (724)
Q Consensus       303 TtR~~~v  309 (724)
                      ||-.-+.
T Consensus       506 tSATm~a  512 (1042)
T KOG0924|consen  506 TSATMDA  512 (1042)
T ss_pred             eeccccH
Confidence            9987653

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=93.63  E-value=0.33  Score=48.45  Aligned_cols=98  Identities=21%  Similarity=0.245  Sum_probs=55.2

Q ss_pred             ccchHHHHHHHHHHhc----C---CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC-CeE-EEEEEecCCChHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK----D---DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF-DKV-VMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~----~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~-~wv~vs~~~~~~~l~~~i  232 (724)
                      +.|..-..+.++..+.    +   .+.=|++.+|.+|+||...++.+++......-- +.+ .++..-.-+....+ .. 
T Consensus        84 lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~i-e~-  161 (344)
T KOG2170|consen   84 LFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKI-ED-  161 (344)
T ss_pred             hhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHH-HH-
Confidence            3454444455555443    2   345699999999999999999999987542110 111 11111111111111 00 


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                                  -..+...+++..+..-+|-|+|+|+++..
T Consensus       162 ------------Yk~eL~~~v~~~v~~C~rslFIFDE~DKm  190 (344)
T KOG2170|consen  162 ------------YKEELKNRVRGTVQACQRSLFIFDEVDKL  190 (344)
T ss_pred             ------------HHHHHHHHHHHHHHhcCCceEEechhhhc
Confidence                        02234455555555568899999999765

>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=93.63  E-value=0.11  Score=47.71  Aligned_cols=34  Identities=26%  Similarity=0.486  Sum_probs=27.1

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          169 FQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       169 ~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++.|.+.+.+   +++.++|..|+|||||+..+....
T Consensus        26 ~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   26 IEELKELLKG---KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             HHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             HHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhhc
Confidence            4566666643   689999999999999999887653

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.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=93.60  E-value=0.057  Score=52.20  Aligned_cols=27  Identities=30%  Similarity=0.494  Sum_probs=23.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|..|+|||||++.++--.+
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~Gl~~   58 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAGLEK   58 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhcccC
Confidence            445899999999999999999976554

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=93.60  E-value=0.073  Score=48.18  Aligned_cols=46  Identities=26%  Similarity=0.380  Sum_probs=32.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGM  238 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~  238 (724)
                      ..++.|+|.+|+||||+.+.+.... +..+           ..+..++.-+++...|.
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l-~~~~-----------ivNyG~~Mle~A~k~gl   49 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL-VKHK-----------IVNYGDLMLEIAKKKGL   49 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHHHH-hhce-----------eeeHhHHHHHHHHHhCC
Confidence            4789999999999999999888776 2111           11344666677666654

>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=93.58  E-value=0.063  Score=45.46  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=19.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIA  202 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~  202 (724)
                      -..++|+|+.|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4589999999999999999976

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

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=93.57  E-value=0.19  Score=48.32  Aligned_cols=26  Identities=35%  Similarity=0.468  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..|+|.|..|+||||+++.+.+....
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~l~~   29 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKLLQE   29 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            47999999999999999999998765

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.

>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=93.56  E-value=0.2  Score=48.23  Aligned_cols=25  Identities=36%  Similarity=0.586  Sum_probs=23.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|+|.|+.|+||||+++.+.+....
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~l~~   26 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEA   26 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999998864

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=93.53  E-value=0.2  Score=48.23  Aligned_cols=31  Identities=29%  Similarity=0.364  Sum_probs=26.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .++-++..|.|++|+||||+++.+.......
T Consensus        15 ~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~   45 (196)
T PF13604_consen   15 TSGDRVSVLQGPAGTGKTTLLKALAEALEAA   45 (196)
T ss_dssp             HCTCSEEEEEESTTSTHHHHHHHHHHHHHHT
T ss_pred             hcCCeEEEEEECCCCCHHHHHHHHHHHHHhC
Confidence            3455788999999999999999998887764

>PRK14737 gmk guanylate kinase; Provisional

Probab=93.52  E-value=0.065  Score=51.01  Aligned_cols=26  Identities=15%  Similarity=0.391  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +..+|.|+|++|+|||||++.+.+..
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcC
Confidence            45689999999999999999998754

>PLN02200 adenylate kinase family protein

Probab=93.45  E-value=0.074  Score=52.65  Aligned_cols=26  Identities=31%  Similarity=0.253  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|.|.|++|+||||+|+.+++..
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            34588999999999999999998765

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.43  E-value=1.8  Score=46.17  Aligned_cols=73  Identities=22%  Similarity=0.254  Sum_probs=44.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      .++-+.+.|++|.|||.|++.|+-+....       +.++|.            ..|..++.++.  +..+..++..-+.
T Consensus       185 p~rglLLfGPpgtGKtmL~~aiAsE~~at-------ff~iSa------------ssLtsK~~Ge~--eK~vralf~vAr~  243 (428)
T KOG0740|consen  185 PVRGLLLFGPPGTGKTMLAKAIATESGAT-------FFNISA------------SSLTSKYVGES--EKLVRALFKVARS  243 (428)
T ss_pred             ccchhheecCCCCchHHHHHHHHhhhcce-------EeeccH------------HHhhhhccChH--HHHHHHHHHHHHh
Confidence            45566799999999999999999887653       223321            11112222221  2233444444444


Q ss_pred             CCcEEEEEcccccc
Q 004895          260 EKRVLIILDNIWTK  273 (724)
Q Consensus       260 ~kr~LlVlDdv~~~  273 (724)
                      .++.++++|+++..
T Consensus       244 ~qPsvifidEidsl  257 (428)
T KOG0740|consen  244 LQPSVIFIDEIDSL  257 (428)
T ss_pred             cCCeEEEechhHHH
Confidence            67889999998643

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=93.42  E-value=0.72  Score=53.37  Aligned_cols=45  Identities=20%  Similarity=0.362  Sum_probs=32.8

Q ss_pred             ccccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..++|....+.++.+...   .... -|.|+|..|+||+++|+.+.+.-
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~-pvli~Ge~GtGK~~~A~~ih~~s  372 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSF-PVLLCGEEGVGKALLAQAIHNES  372 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCC-CEEEECCCCcCHHHHHHHHHHhC
Confidence            446677776666665544   3333 36799999999999999998754

>PRK00698 tmk thymidylate kinase; Validated

Probab=93.41  E-value=0.19  Score=48.67  Aligned_cols=26  Identities=23%  Similarity=0.464  Sum_probs=23.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+|+|.|+.|+||||+++.+.+....
T Consensus         4 ~~I~ieG~~gsGKsT~~~~L~~~l~~   29 (205)
T PRK00698          4 MFITIEGIDGAGKSTQIELLKELLEQ   29 (205)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            58999999999999999999998764

>PRK13948 shikimate kinase; Provisional

Probab=93.38  E-value=0.085  Score=49.88  Aligned_cols=28  Identities=18%  Similarity=0.455  Sum_probs=24.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+.|.++|+.|+||||+++.+.+...
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcC
Confidence            3557899999999999999999998764

>PRK15453 phosphoribulokinase; Provisional

Probab=93.38  E-value=0.09  Score=52.65  Aligned_cols=28  Identities=36%  Similarity=0.463  Sum_probs=24.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+..+|+|.|.+|+||||+|+.+.+.+.
T Consensus         3 ~k~piI~ItG~SGsGKTTva~~l~~if~   30 (290)
T PRK15453          3 AKHPIIAVTGSSGAGTTTVKRAFEKIFR   30 (290)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3567999999999999999999997664

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=93.37  E-value=0.085  Score=43.79  Aligned_cols=25  Identities=48%  Similarity=0.728  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ++.+.|.+|+||||++..++.....
T Consensus         1 ~~~~~g~~G~Gktt~~~~l~~~l~~   25 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALAK   25 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4788999999999999999999865

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK13946 shikimate kinase; Provisional

Probab=93.37  E-value=0.071  Score=50.79  Aligned_cols=26  Identities=23%  Similarity=0.397  Sum_probs=23.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+.|.++|+.|+||||+++.+.+...
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg   35 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLG   35 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999999874

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.36  E-value=0.38  Score=53.43  Aligned_cols=87  Identities=16%  Similarity=0.151  Sum_probs=52.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC------------------
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD------------------  241 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~------------------  241 (724)
                      .-+++.|.|++|+||||||.++...-..+ .=..++||+..+  +.+++.+.+ +.++....                  
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~-~ge~~lyvs~eE--~~~~l~~~~-~~~G~~~~~~~~~g~l~~~~~~~~~~   95 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH-FDEPGVFVTFEE--SPQDIIKNA-RSFGWDLQKLVDEGKLFILDASPDPE   95 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh-CCCCEEEEEEec--CHHHHHHHH-HHcCCCHHHHhhcCceEEEecCchhc
Confidence            45799999999999999999997653221 014588888864  334444332 33332110                  


Q ss_pred             -----CCchhHHHHHHHHHHHhcCCcEEEEEccc
Q 004895          242 -----SNDLIYHRAKQLCQRLKKEKRVLIILDNI  270 (724)
Q Consensus       242 -----~~~~~~~~~~~l~~~l~~~kr~LlVlDdv  270 (724)
                           ...........+...+..+++-.+|+|-+
T Consensus        96 ~~~~~~~~~l~~~l~~i~~~ls~g~~qRVvIDSl  129 (484)
T TIGR02655        96 GQDVVGGFDLSALIERINYAIRKYKAKRVSIDSV  129 (484)
T ss_pred             cccccccCCHHHHHHHHHHHHHHhCCcEEEEeeh
Confidence                 00112334556666666666778999954

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK05922 type III secretion system ATPase; Validated

Probab=93.29  E-value=0.42  Score=51.40  Aligned_cols=91  Identities=23%  Similarity=0.254  Sum_probs=50.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCC--------CCCCchh---
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMN--------FDSNDLI---  246 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~--------~~~~~~~---  246 (724)
                      .+-..++|+|..|+|||||++.+.....    .+...++.+.+. ....+.+.+........        .++....   
T Consensus       155 ~~GqrigI~G~nG~GKSTLL~~Ia~~~~----~d~gvi~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~  230 (434)
T PRK05922        155 GKGQRIGVFSEPGSGKSSLLSTIAKGSK----STINVIALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVI  230 (434)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHhccCC----CCceEEEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHH
Confidence            3445799999999999999999987542    233344434332 23334444443332221        1111101   


Q ss_pred             -HHHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          247 -YHRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       247 -~~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                       ...+-.+.++++ +++++|+++||+-..
T Consensus       231 a~~~a~tiAEyfrd~G~~VLl~~DslTR~  259 (434)
T PRK05922        231 AGRAAMTIAEYFRDQGHRVLFIMDSLSRW  259 (434)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHH
Confidence             111233444542 479999999999543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	724
2omx_A	462	Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX		5e-06
2omu_A	462	Crystal Structure Of Inla G194s+s Y369s/hec1 Comple		6e-06
2omt_A	462	Crystal Structure Of Inla G194s+sHEC1 COMPLEX Lengt		6e-06
2omy_A	461	Crystal Structure Of Inla S192n/hec1 Complex Length		7e-06
2omv_A	461	Crystal Structure Of Inla S192n Y369s/hec1 Complex		7e-06
1o6s_A	466	Internalin (Listeria Monocytogenes) E-Cadherin (Hum		7e-06
2omz_A	466	Crystal Structure Of Inla Y369a/hec1 Complex Length		8e-06
3sfz_A	1249	Crystal Structure Of Full-Length Murine Apaf-1 Leng		3e-04
1z6t_A	591	Structure Of The Apoptotic Protease-activating Fact		5e-04

>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX Length = 462

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 175 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 233
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 234 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 279
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 280 AGLTALTNLELNENQLEDISPISNLKN 306

>pdb|2OMU|A Chain A, Crystal Structure Of Inla G194s+s Y369s/hec1 Complex Length = 462

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 175 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 233
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 234 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 279
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 280 AGLTALTNLELNENQLEDISPISNLKN 306

>pdb|2OMT|A Chain A, Crystal Structure Of Inla G194s+sHEC1 COMPLEX Length = 462

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 175 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 233
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 234 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 279
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 280 AGLTALTNLELNENQLEDISPISNLKN 306

>pdb|2OMY|A Chain A, Crystal Structure Of Inla S192n/hec1 Complex Length = 461

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 174 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 232
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 233 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 278
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 279 AGLTALTNLELNENQLEDISPISNLKN 305

>pdb|2OMV|A Chain A, Crystal Structure Of Inla S192n Y369s/hec1 Complex Length = 461

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 174 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 232
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 233 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 278
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 279 AGLTALTNLELNENQLEDISPISNLKN 305

>pdb|1O6S|A Chain A, Internalin (Listeria Monocytogenes) E-Cadherin (Human) Recognition Complex Length = 466

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 179 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 237
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 238 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 283
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 284 AGLTALTNLELNENQLEDISPISNLKN 310

>pdb|2OMZ|A Chain A, Crystal Structure Of Inla Y369a/hec1 Complex Length = 466

Iteration: 1
 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 46/147 (31%), Positives = 78/147 (53%), Gaps = 15/147 (10%)
Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ LD +  + S + S L +L NL++L     ++ DI  +G L  L+ LSL G ++K + 
Sbjct: 178 LERLDISSNKVSDI-SVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIG 236
Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  LT L  LDL+N + +  +AP  +S L++L EL +G              ++++ L
Sbjct: 237 -TLASLTNLTDLDLAN-NQISNLAP--LSGLTKLTELKLG----------ANQISNISPL 282
Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSLGN 723
            GL+ LT LE++    E +  I +L N
Sbjct: 283 AGLTALTNLELNENQLEDISPISNLKN 309

>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1 Length = 1249

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 60/254 (23%), Positives = 104/254 (40%), Gaps = 44/254 (17%)
Query: 161 IFNSRKKIFQDVIEALKDDKLN----IIGVCGMGGVGKTTLVKQIAK--QVMEDNVFDKV 214
           IF +RKK+   + + L   KLN     + + GM G GK+ L  +  +   ++E      V
Sbjct: 125 IFVTRKKLVHAIQQKLW--KLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGV 182
Query: 215 VMAEITKNPDA---QKIQGELASDLGMNFDSNDLIYHR-------AKQLCQ--RLKKEKR 262
               I K   +    K+Q     +L M  D  +    R       AK   +   L+K  R
Sbjct: 183 HWVSIGKQDKSGLLMKLQ-----NLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPR 237
Query: 263 VLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWI 322
            L+ILD++W    L                    +C I+LT+R + +    M  + +  +
Sbjct: 238 SLLILDDVWDPWVLKAF---------------DNQCQILLTTRDKSVTDSVMGPKHVVPV 282
Query: 323 DA-LSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWK 381
           ++ L  E+ L++    V  + K  D    A  I+ +C G P+ +S +   L++  P  W 
Sbjct: 283 ESGLGREKGLEILSLFV--NMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRD-FPNRWA 339
Query: 382 DALNKLTSSNLREI 395
             L +L +   + I
Sbjct: 340 YYLRQLQNKQFKRI 353

>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1 Bound To Adp Length = 591

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 54/248 (21%), Positives = 103/248 (41%), Gaps = 32/248 (12%)
Query: 161 IFNSRKKIFQDVIEALKDDK--LNIIGVCGMGGVGKTTLVKQIAK-QVMEDNVFDKVVMA 217
           +F +RKK+   + + L   K     + + GM G GK+ L  +  +   + +  F   V  
Sbjct: 125 VFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHW 184
Query: 218 EITKNPDAQKIQGELASDLGMNFDSNDLIYHR-------AKQLCQ--RLKKEKRVLIILD 268
                 D   +  +L  +L    D ++    R       AK   +   L+K  R L+ILD
Sbjct: 185 VSVGKQDKSGLLMKL-QNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILD 243
Query: 269 NIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWID-ALSE 327
           ++W    L                    +C I+LT+R + +    M  + +  ++ +L +
Sbjct: 244 DVWDSWVLKAFD---------------SQCQILLTTRDKSVTDSVMGPKYVVPVESSLGK 288
Query: 328 EEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKL 387
           E+ L++    V  + K +D    A  I+ +C G P+ +S +   L++  P  W+  L +L
Sbjct: 289 EKGLEILSLFV--NMKKADLPEQAHSIIKECKGSPLVVSLIGALLRD-FPNRWEYYLKQL 345
Query: 388 TSSNLREI 395
            +   + I
Sbjct: 346 QNKQFKRI 353

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	724
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-52
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-49
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	1e-35
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	2e-28
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	3e-18
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	1e-16
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	5e-14
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	1e-13
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-09
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	4e-18
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	1e-17
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-12
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-10
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	4e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-13
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-10
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-10
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-07
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-05
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-13
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-10
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	4e-10
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	1e-09
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-07
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	2e-05
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	1e-12
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	6e-09
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	1e-12
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-11
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	5e-10
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	9e-10
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	1e-09
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	1e-08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-05
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	9e-12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	4e-11
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	1e-10
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	2e-09
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	4e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	2e-12
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-08
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-07
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	3e-12
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	1e-11
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	2e-09
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	5e-07
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-12
1o6v_A	466	Internalin A; bacterial infection, extracellular r	3e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	4e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	6e-11
1o6v_A	466	Internalin A; bacterial infection, extracellular r	8e-09
1o6v_A	466	Internalin A; bacterial infection, extracellular r	4e-07
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	1e-11
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	5e-10
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	1e-08
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	3e-08
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	4e-08
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	3e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	2e-11
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	5e-10
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	1e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	9e-05
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-11
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	7e-11
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	8e-10
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-09
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	4e-09
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-08
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-07
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	5e-11
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	8e-09
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	1e-08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	8e-07
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	5e-11
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	9e-10
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-08
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	4e-08
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	6e-08
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	9e-07
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	5e-11
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-08
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	1e-06
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-04
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	6e-11
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	3e-10
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-07
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	1e-05
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	1e-10
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	2e-10
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	2e-10
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	2e-10
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-10
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	3e-10
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-09
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	9e-09
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-08
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-07
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	4e-04
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	3e-10
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	4e-10
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	3e-05
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	3e-10
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	4e-10
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	1e-09
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	1e-08
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	8e-06
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	4e-10
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	7e-09
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	1e-07
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	6e-04
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	4e-10
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	6e-09
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	1e-08
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	6e-06
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	4e-10
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	5e-10
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	5e-10
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	3e-08
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	5e-10
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	3e-09
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	6e-08
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	2e-04
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	5e-09
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	6e-05
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-04
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	2e-04
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	6e-09
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	5e-08
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	9e-07
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	1e-04
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	1e-08
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	1e-08
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	6e-05
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	1e-08
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	6e-08
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	2e-05
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	4e-04
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	1e-08
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	7e-08
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	2e-08
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-08
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-08
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	6e-08
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-07
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	5e-06
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-05
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	5e-05
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-04
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-04
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	6e-08
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	3e-07
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	4e-06
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	8e-08
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	2e-07
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	4e-07
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	1e-07
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	8e-06
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	3e-05
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	1e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	1e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	9e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	5e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	9e-06
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	3e-05
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	5e-04
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	1e-07
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	3e-07
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	2e-05
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	4e-07
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	4e-04
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	6e-07
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	3e-06
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	8e-07
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	1e-06
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	9e-05
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	1e-06
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	1e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	3e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	4e-06
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-05
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	6e-05
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	7e-05
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	7e-06
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	1e-05
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	1e-05
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	1e-05
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	1e-05
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	2e-05
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	3e-05
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	4e-05
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	5e-05
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	1e-04
3m19_A	251	Variable lymphocyte receptor A diversity region; a	8e-05
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	2e-04
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	8e-04

>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 =  189 bits (481), Expect = 2e-52
 Identities = 60/481 (12%), Positives = 133/481 (27%), Gaps = 68/481 (14%)

Query: 43  ERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPC 102
           E + ++  R +R+   +     Q  E+   +  +    +     + +  I+         
Sbjct: 42  ELISKMSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLL 101

Query: 103 FKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIF 162
              +     SR  L ++                 L++ NV       +RE          
Sbjct: 102 RPVVIAPQFSRQMLDRK-----------------LLLGNVPKQMTCYIRE---------- 134

Query: 163 NSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQ--VMEDNVFDKVVMAEIT 220
                     ++ + D     + + G  G GK+ +  Q   +   +    +D +V  + +
Sbjct: 135 -YHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS 193

Query: 221 KNPDA---------QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIW 271
                           +       L      +       + +C  L      L + D++ 
Sbjct: 194 GTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV 253

Query: 272 TKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEAL 331
                          +E  +     R   ++T+R  ++      + +   + +L  +E  
Sbjct: 254 Q--------------EETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECY 299

Query: 332 QLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSSN 391
              E              +  + +    G P  L     + + K+        NKL S  
Sbjct: 300 DFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRG 359

Query: 392 LREIHGMDADVYSPI----KLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRY 447
           L  +  +    Y  +    +   + L DE +S      +   G  I V      +     
Sbjct: 360 LVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDIC 419

Query: 448 DKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEA--KLHDVIHVVAASIAEE 505
                        E   + V   +  L     LL G        K+  +IH+    + + 
Sbjct: 420 SNE---------EEQLDDEVADRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDA 470

Query: 506 K 506
           +
Sbjct: 471 Q 471

>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 =  185 bits (470), Expect = 6e-49
 Identities = 100/602 (16%), Positives = 193/602 (32%), Gaps = 169/602 (28%)

Query: 70  FADVTEWLGKVEQFTQGYAKHIINDEDEVRKP--CFKGLSPNLMSRYKLSKRAVEDA--- 124
             DV +    +   ++    HII  +D V      F  L   L  + ++ ++ VE+    
Sbjct: 35  CKDVQDMPKSI--LSKEEIDHIIMSKDAVSGTLRLFWTL---LSKQEEMVQKFVEEVLRI 89

Query: 125 KYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKD-----------YNIFNSRKKIFQDVI 173
            Y    L +     +      P    R + + +D           YN+  SR + +  + 
Sbjct: 90  NYK--FLMSP----IKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV--SRLQPYLKLR 141

Query: 174 EALKDDKLN-IIGVCGMGGVGKTTLVKQIA-----KQVMEDNVFDKVVMAEITKNPDAQK 227
           +AL + +    + + G+ G GKT +   +      +  M+  +F  + +          +
Sbjct: 142 QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF-WLNLKNCNSPETVLE 200

Query: 228 IQGELASDLGMNF----DSNDLIYHRAKQLCQRL------KKEKRVLIILDNIWTKLELD 277
           +  +L   +  N+    D +  I  R   +   L      K  +  L++L N+      +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260

Query: 278 KIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCID-MNSQKMFWI------DALSEEEA 330
              +                C I+LT+R + +   D +++     I        L+ +E 
Sbjct: 261 AFNL---------------SCKILLTTRFKQV--TDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 331 LQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSS 390
             L  K +    +  D   L  E+       P  LS +A ++++   A W D    +   
Sbjct: 304 KSLLLKYLD--CRPQD---LPREV---LTTNPRRLSIIAESIRDG-LATW-DNWKHVNCD 353

Query: 391 NLREIHGMDADVYSPIKLSYDFLD-DEAKSLFLLCGLHREGRPIHVHYLLRY-------- 441
            L  I          I+ S + L+  E + +F    +      I    L           
Sbjct: 354 KLTTI----------IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403

Query: 442 ---VMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVI--- 495
              V+   +   L + +           + ++   LK          E+E  LH  I   
Sbjct: 404 VMVVVNKLHKYSL-VEKQPKES---TISIPSIYLELKVKL-------ENEYALHRSIVDH 452

Query: 496 ---------------------------HVVAASIAEEKLMFSIPNV-VDFEREMEETIQK 527
                                      H+      E   +F    V +DF R +E+ I+ 
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF--RMVFLDF-RFLEQKIRH 509

Query: 528 GPIAISLP------------YR----DIQELPERLEC------PQLKLFLLFAKYDSTLQ 565
              A +              Y+    D     ERL        P+++  L+ +KY   L+
Sbjct: 510 DSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569

Query: 566 IS 567
           I+
Sbjct: 570 IA 571

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 65.6 bits (159), Expect = 4e-11
 Identities = 97/639 (15%), Positives = 191/639 (29%), Gaps = 165/639 (25%)

Query: 152 EFGDMKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF 211
           E G+   Y      K I     +A  D+  +                K +  Q M  ++ 
Sbjct: 10  ETGEH-QY----QYKDILSVFEDAFVDN-FD---------------CKDV--QDMPKSIL 46

Query: 212 DKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQL--CQRLKKEKRVLIILDN 269
            K  +  I  + DA                          +L      K+E+ V   ++ 
Sbjct: 47  SKEEIDHIIMSKDAVS---------------------GTLRLFWTLLSKQEEMVQKFVEE 85

Query: 270 IWTKLELDKIGIPYGDVDE--KDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSE 327
           +   L ++     Y  +    K +   P   T +     RD L    N  ++F    +S 
Sbjct: 86  V---LRIN-----YKFLMSPIKTEQRQPSMMTRMYIE-QRDRLY---NDNQVFAKYNVSR 133

Query: 328 EEALQLFEKIVGESTKASDFRPLAEEIV----GKCGGLPVALSTVAN-ALKNKSP--AIW 380
            +    + K+        + RP A+ ++       G   VAL    +  ++ K      W
Sbjct: 134 LQ---PYLKL---RQALLELRP-AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 381 KDALNKLTSSNLREIHG---MDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHY 437
                 L   N         M   +   I  ++    D + ++ L     +         
Sbjct: 187 ------LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA-------E 233

Query: 438 LLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHV 497
           L R +    Y+  L +  NV   +A     +A   NL    LL     +    L      
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKA----WNAF--NLSCKILLTTRFKQVTDFL-SAATT 286

Query: 498 VAASIAEEKLMFSIP-------NVVDFEREM--EETIQKGPIAISLPYRDIQELPERLEC 548
              S+    +  +           +D   +    E +   P  +S+    I++     + 
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD- 345

Query: 549 PQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-----FSPLPSSLGRLINLQTL 603
              K  +   K  + ++ S         L VL+    R      S  P S    I    L
Sbjct: 346 -NWK-HVNCDKLTTIIESS---------LNVLEPAEYRKMFDRLSVFPPSA--HIPTILL 392

Query: 604 CL---DGWRLEDIAIVGQLKKLEILSLRGAEIK--------QLPLQIGQLTRL--QLLD- 649
            L   D  + + + +V +L K  ++  +  E          +L +++     L   ++D 
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH 452

Query: 650 --LSNCSSLVVIAPNVIS------------------KLSRLEELYMGDSFSQWDKVEGGS 689
             +        + P  +                   +++    +++   F +  K+   S
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE-QKIRHDS 511

Query: 690 NASLAELKGLSKLTTLE-----IDVRDAEMLRRIWSLGN 723
            A  A    L+ L  L+     I   D +  R + ++ +
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550

>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 =  141 bits (358), Expect = 1e-35
 Identities = 59/319 (18%), Positives = 123/319 (38%), Gaps = 34/319 (10%)

Query: 139 VSNVSHPPPPKMREFGDMKDYNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTT 196
           VS ++      + E G  +   +F +RKK+   + + L     +   + + GM G GK+ 
Sbjct: 103 VSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSV 162

Query: 197 LVKQIA--KQVMEDNVFDKVVMAEITKNPDAQKIQG--ELASDLGMNFDSNDLIYHRAKQ 252
           L  +      ++E      V    + K   +  +     L + L  +   +  +    ++
Sbjct: 163 LAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEE 222

Query: 253 LCQRLK-----KEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR 307
              RL+     K  R L+ILD++W    L                    +C I+LT+R +
Sbjct: 223 AKDRLRILMLRKHPRSLLILDDVWDSWVLKAFD---------------SQCQILLTTRDK 267

Query: 308 DLLCIDMNSQ-KMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS 366
            +    M  +  +    +L +E+ L++    V    K +D    A  I+ +C G P+ +S
Sbjct: 268 SVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNM--KKADLPEQAHSIIKECKGSPLVVS 325

Query: 367 TVANALKNKSPAIWKDALNKLTSSNLREIHGMDADVYSPI----KLSYDFLDDEAKSLFL 422
            +   L++  P  W+  L +L +   + I    +  Y  +     +S + L ++ K  + 
Sbjct: 326 LIGALLRDF-PNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYT 384

Query: 423 LCGLHREGRPIHVHYLLRY 441
              + ++   +    L   
Sbjct: 385 DLSILQKDVKVPTKVLCIL 403

>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 =  121 bits (305), Expect = 2e-28
 Identities = 90/617 (14%), Positives = 193/617 (31%), Gaps = 110/617 (17%)

Query: 43  ERVEELGQRRKRVKILVDQATEQGYEIFADVTEWLGKVEQFTQGYAKHIINDEDEVRKPC 102
           E+V+    + +R   L+     +    +            F          D   +    
Sbjct: 41  EKVKSQATQYQRAAALIKMILNKDNCAY----------ISFYNALLHEGYKDLAAL---- 86

Query: 103 FKGLSPNLMSRYKLSKRAVEDAKYAEHLLATGSLLIVSNVSHPPPPKMREFGDMKDYNIF 162
            +   P + S             +   +L  G +        P  P            IF
Sbjct: 87  LQSGLPLVSSSSGKDTDG-GITSFVRTVLCEGGV--------PQRPV-----------IF 126

Query: 163 NSRKKIFQDVIEAL--KDDKLNIIGVCGMGGVGKTTLVKQIAKQ--VMEDNVFDKVVMAE 218
            +RKK+   + + L   + +   + + GM G GK+ L  +  +   ++E      V    
Sbjct: 127 VTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS 186

Query: 219 ITKNPDAQ--KIQGELASDLGMNFDSNDLIYHRAKQLCQRLK-----KEKRVLIILDNIW 271
           I K   +        L   L      +  +    ++   RL+     K  R L+ILD++W
Sbjct: 187 IGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW 246

Query: 272 TKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWI-DALSEEEA 330
               L                    +C I+LT+R + +    M  + +  +   L  E+ 
Sbjct: 247 DPWVLKAFD---------------NQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKG 291

Query: 331 LQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSS 390
           L++    V    K  D    A  I+ +C G P+ +S +   L++  P  W   L +L + 
Sbjct: 292 LEILSLFVN--MKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDF-PNRWAYYLRQLQNK 348

Query: 391 NLREIHGMDA----DVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYL-------- 438
             + I    +     +   + +S + L ++ K  +    + ++   +    L        
Sbjct: 349 QFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLET 408

Query: 439 --LRYVMGLRYDKGLGLFRN------VYTL-----EAARNRVDA--------LIDNLKAS 477
             +  ++    +K L LF N       Y L     +    +  +        ++   +  
Sbjct: 409 EEVEDILQEFVNKSL-LFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVTQFQRY 467

Query: 478 CLLLDGDAEDEAKLHDVIHVVAASIAEEKLMFSIPNVVDFEREMEETIQKGPIAISLP-- 535
                   + E  ++    +    +A   +   +  ++     ++   +    A  +   
Sbjct: 468 YQPHTLSPDQEDCMYWYNFLAYH-MASANMHKELCALMFSLDWIKAKTELVGPAHLIHEF 526

Query: 536 --YRDIQELPERLECPQLKLFLLF-------AKYDSTLQISDHFFEGTEELKVLDFTGIR 586
             YR I +  +   C   + FL           + + +Q+     E +E  +       +
Sbjct: 527 VAYRHILDEKDCAVCENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYRQAKLQAKQ 586

Query: 587 FSPLPSSLGRLINLQTL 603
                      IN +T+
Sbjct: 587 EGDTGRLYLEWINKKTI 603

>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 = 85.0 bits (211), Expect = 4e-18
 Identities = 35/191 (18%), Positives = 61/191 (31%), Gaps = 28/191 (14%)

Query: 533 SLPYRDIQELPERLECPQLKLFLLFAKYDSTLQ-ISDHFFEGTEE-LKVLDFTGIRFSPL 590
                D                 +  +    L+  +D   + T+     L+   +     
Sbjct: 37  RHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPGRVALELRSVPLPQF 96

Query: 591 PSSLGRLINLQTLCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD 649
           P    RL +LQ + +D   L ++   + Q   LE L+L    ++ LP  I  L RL+ L 
Sbjct: 97  PDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPLRALPASIASLNRLRELS 156

Query: 650 LSNCSSLVVI--------APNVISKLSRLEELYMGDSFSQWDKVEGGSNASL----AELK 697
           +  C  L  +        A      L  L+ L +                 +    A + 
Sbjct: 157 IRACPELTELPEPLASTDASGEHQGLVNLQSLRL-------------EWTGIRSLPASIA 203

Query: 698 GLSKLTTLEID 708
            L  L +L+I 
Sbjct: 204 NLQNLKSLKIR 214

>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 = 83.8 bits (208), Expect = 1e-17
 Identities = 39/155 (25%), Positives = 66/155 (42%), Gaps = 26/155 (16%)

Query: 577 LKVLDFTGI-RFSPLPSSLGR---------LINLQTLCLDGWRLEDI-AIVGQLKKLEIL 625
           L+ L        + LP  L           L+NLQ+L L+   +  + A +  L+ L+ L
Sbjct: 152 LRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSL 211

Query: 626 SLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV 685
            +R + +  L   I  L +L+ LDL  C++L    P +    + L+ L + D        
Sbjct: 212 KIRNSPLSALGPAIHHLPKLEELDLRGCTALRNY-PPIFGGRAPLKRLILKD-------- 262

Query: 686 EGGSNASLAEL-KGLSKLTTLEI-DVRDAEMLRRI 718
                ++L  L   + +LT LE  D+R    L R+
Sbjct: 263 ----CSNLLTLPLDIHRLTQLEKLDLRGCVNLSRL 293

>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 = 67.3 bits (165), Expect = 3e-12
 Identities = 19/118 (16%), Positives = 37/118 (31%), Gaps = 7/118 (5%)

Query: 564 LQISDHFFEGTEELKVLDFTGI-RFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
           +  S H    +   + L F G     P    L +         + W              
Sbjct: 1   MGSSHHHHHHSSGRENLYFQGSTALRPYHDVLSQWQRHYNADRNRWHS--AWRQANSNNP 58

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQL--LDLSNCSSLVVIAPNVISKLSRLEELYMGDS 678
           +I +  G  +K     +   T+     L+L +   L    P+   +LS L+ + +  +
Sbjct: 59  QIETRTGRALKATADLLEDATQPGRVALELRSV-PLPQF-PDQAFRLSHLQHMTIDAA 114

>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 = 61.9 bits (151), Expect = 2e-10
 Identities = 23/83 (27%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 577 LKVLDFTGI-RFSPLPSSLGRLINLQTLCL-DGWRLEDI-AIVGQLKKLEILSLRG-AEI 632
           L+ LD  G       P   G    L+ L L D   L  +   + +L +LE L LRG   +
Sbjct: 231 LEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNL 290

Query: 633 KQLPLQIGQLTRLQLLDLSNCSS 655
            +LP  I QL    ++ +     
Sbjct: 291 SRLPSLIAQLPANCIILVPPHLQ 313

>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 = 42.2 bits (100), Expect = 4e-04
 Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 3/63 (4%)

Query: 577 LKVLDFTGI-RFSPLPSSLGRLINLQTLCLDG-WRLEDI-AIVGQLKKLEILSLRGAEIK 633
           LK L          LP  + RL  L+ L L G   L  + +++ QL    I+ +      
Sbjct: 255 LKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILVPPHLQA 314

Query: 634 QLP 636
           QL 
Sbjct: 315 QLD 317

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 72.2 bits (177), Expect = 3e-13
 Identities = 24/173 (13%), Positives = 57/173 (32%), Gaps = 6/173 (3%)

Query: 537 RDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGR 596
           +   +  +RL    L L     +      I        ++ ++ + T  R + +  ++ R
Sbjct: 389 KMFLDYDQRLNLSDL-LQDAINRNPEMKPIKKDSRISLKDTQIGNLTN-RITFISKAIQR 446

Query: 597 LINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSL 656
           L  LQ +           I   +   +  S    + +   L    L  L  ++L NC ++
Sbjct: 447 LTKLQIIYFANSPFTYDNI--AVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNM 504

Query: 657 VVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
             + P+ +  L  L+ L +         +++        +     K+    + 
Sbjct: 505 TQL-PDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMG 556

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 63.7 bits (155), Expect = 1e-10
 Identities = 18/129 (13%), Positives = 35/129 (27%), Gaps = 16/129 (12%)

Query: 565 QISDHFFEGTEELKVLD-----FTGI---RFSPLPSSLGRLINLQTLCLDGWRLEDI--- 613
           +     F     +  +       T I      P   +      L T+ L   +L  +   
Sbjct: 687 KFPTELFATGSPISTIILSNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDD 746

Query: 614 AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV-----IAPNVISKLS 668
                L  L  + +        P Q    ++L+   + +             P  I+   
Sbjct: 747 FRATTLPYLSNMDVSYNCFSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCP 806

Query: 669 RLEELYMGD 677
            L +L +G 
Sbjct: 807 SLIQLQIGS 815

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 63.4 bits (154), Expect = 2e-10
 Identities = 25/152 (16%), Positives = 57/152 (37%), Gaps = 15/152 (9%)

Query: 539 IQELPERL-ECPQLK-LFL-------LFAKYDSTLQISDHFFEGTEELKVLDFTG--IRF 587
           + +LP+ L + P+L+ L +                +++D    G + +++       +  
Sbjct: 504 MTQLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPK-IQIFYMGYNNLEE 562

Query: 588 SPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTR-LQ 646
            P  +SL +++ L  L     ++  +   G   KL  L L   +I+++P      T  ++
Sbjct: 563 FPASASLQKMVKLGLLDCVHNKVRHLEAFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVE 622

Query: 647 LLDLSNCSSLVVIAPNV-ISKLSRLEELYMGD 677
            L  S+   L  I        +  +  +    
Sbjct: 623 GLGFSHN-KLKYIPNIFNAKSVYVMGSVDFSY 653

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 53.7 bits (129), Expect = 2e-07
 Identities = 19/122 (15%), Positives = 46/122 (37%), Gaps = 11/122 (9%)

Query: 566 ISDHFFEGT-EELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--------AIV 616
           +SD F   T   L  +D +   FS  P+       L+   +   R  +           +
Sbjct: 743 LSDDFRATTLPYLSNMDVSYNCFSSFPTQPLNSSQLKAFGIRHQRDAEGNRILRQWPTGI 802

Query: 617 GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
                L  L +   +I+++  ++    +L +LD+++  ++ +   +V   +     + + 
Sbjct: 803 TTCPSLIQLQIGSNDIRKVDEKL--TPQLYILDIADNPNISIDVTSVCPYIEAGMYVLLY 860

Query: 677 DS 678
           D 
Sbjct: 861 DK 862

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 46.8 bits (111), Expect = 3e-05
 Identities = 23/174 (13%), Positives = 53/174 (30%), Gaps = 43/174 (24%)

Query: 577 LKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLEDIA--------------------- 614
           +  L   G      +P ++G+L  L+ L                                
Sbjct: 325 VTGLSLAGFGAKGRVPDAIGQLTELKVLSFGTHSETVSGRLFGDEELTPDMSEERKHRIR 384

Query: 615 ------IVGQLKKLEILSLRGAEIKQLP----LQIGQLTRLQLLDLSNCSSLVVIAPNVI 664
                  +   ++L +  L    I + P    ++      L+   + N ++ +      I
Sbjct: 385 MHYKKMFLDYDQRLNLSDLLQDAINRNPEMKPIKKDSRISLKDTQIGNLTNRITFISKAI 444

Query: 665 SKLSRLEELYMGD-SFSQWDKVEGGSNASL----------AELKGLSKLTTLEI 707
            +L++L+ +Y  +  F+  +      +A+                L  LT +E+
Sbjct: 445 QRLTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVEL 498

>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 = 71.6 bits (176), Expect = 5e-13
 Identities = 19/135 (14%), Positives = 49/135 (36%), Gaps = 9/135 (6%)

Query: 576 ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRL--EDIAIVGQLKKLEILSLRGAEIK 633
           +   +       + +  ++ RL  L+   +       E+I    + +  E         K
Sbjct: 184 KDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQ----YK 239

Query: 634 QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNAS 692
              L+   L  L  +++ NC +L  + P  +  L  ++ + +        ++++     +
Sbjct: 240 TEDLKWDNLKDLTDVEVYNCPNLTKL-PTFLKALPEMQLINVACNRGISGEQLKDDWQ-A 297

Query: 693 LAELKGLSKLTTLEI 707
           LA+     K+  + I
Sbjct: 298 LADAPVGEKIQIIYI 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 = 63.1 bits (154), Expect = 2e-10
 Identities = 18/142 (12%), Positives = 43/142 (30%), Gaps = 16/142 (11%)

Query: 577 LKVLDFTGIRFSPLPSSL-GRLINLQTLCLDGWRLEDIAI---VGQLKKLEILSLRG--- 629
           L  L+    + + +P++  G    ++ L     +L+ I        +  +  +       
Sbjct: 355 LASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLKYIPNIFDAKSVSVMSAIDFSYNEI 414

Query: 630 -----AEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQWD 683
                     L     +   +  ++LSN   +      + S  S L  + +     ++  
Sbjct: 415 GSVDGKNFDPLDPTPFKGINVSSINLSNN-QISKFPKELFSTGSPLSSINLMGNMLTEIP 473

Query: 684 KVEGGSNASLAELKGLSKLTTL 705
           K            K    LT++
Sbjct: 474 KNSLKD--ENENFKNTYLLTSI 493

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 62.4 bits (152), Expect = 4e-10
 Identities = 17/146 (11%), Positives = 49/146 (33%), Gaps = 22/146 (15%)

Query: 576 ELKVLD-----FTGIRFSPL----PSSLGRLINLQTLCLDGWRLEDIAI---VGQLKKLE 623
           E+++++                   +       +Q + +    L+   +   + ++KKL 
Sbjct: 274 EMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVETSLQKMKKLG 333

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQW 682
           +L     +++      G   +L  L+L+    +  I  N      ++E L          
Sbjct: 334 MLECLYNQLEGKLPAFGSEIKLASLNLAYN-QITEIPANFCGFTEQVENLSFAHNKLK-- 390

Query: 683 DKVEGGSNASLAELKGLSKLTTLEID 708
                    ++ + K +S ++ ++  
Sbjct: 391 ------YIPNIFDAKSVSVMSAIDFS 410

>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 = 60.8 bits (148), Expect = 1e-09
 Identities = 19/128 (14%), Positives = 34/128 (26%), Gaps = 16/128 (12%)

Query: 566 ISDHFFEGTEELKVLD-----FTGI---RFSPLPSSLGRLINLQTLCLDGWRLEDI---A 614
                F     L  ++      T I          +      L ++ L   +L  +    
Sbjct: 448 FPKELFSTGSPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDF 507

Query: 615 IVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV-----IAPNVISKLSR 669
               L  L  + L      + P Q    + L+   + N             P  I+    
Sbjct: 508 RATTLPYLVGIDLSYNSFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGITLCPS 567

Query: 670 LEELYMGD 677
           L +L +G 
Sbjct: 568 LTQLQIGS 575

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 52.0 bits (125), Expect = 5e-07
 Identities = 19/137 (13%), Positives = 44/137 (32%), Gaps = 14/137 (10%)

Query: 566 ISDHFFEGT-EELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--------AIV 616
           +SD F   T   L  +D +   FS  P+       L+   +   R              +
Sbjct: 503 LSDDFRATTLPYLVGIDLSYNSFSKFPTQPLNSSTLKGFGIRNQRDAQGNRTLREWPEGI 562

Query: 617 GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
                L  L +   +I+++  +I     + +LD+ +    + I  + +          + 
Sbjct: 563 TLCPSLTQLQIGSNDIRKVNEKI--TPNISVLDIKDN-PNISIDLSYVCPYIEAGMYML- 618

Query: 677 DSFSQWDKVEGGSNASL 693
             + +   + G     +
Sbjct: 619 -FYDKTQDIRGCDALDI 634

>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 = 47.0 bits (112), Expect = 2e-05
 Identities = 17/165 (10%), Positives = 36/165 (21%), Gaps = 47/165 (28%)

Query: 576 ELKVLD-----FTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAI--------------- 615
           EL+VL               P  +   ++ +         +   +               
Sbjct: 106 ELEVLALGSHGEKVNERLFGPKGISANMSDEQKQKMRMHYQKTFVDYDPREDFSDLIKDC 165

Query: 616 -------------VGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPN 662
                             K   +      I  +   + +LT+L+   + N    V     
Sbjct: 166 INSDPQQKSIKKSSRITLKDTQIGQLSNNITFVSKAVMRLTKLRQFYMGNS-PFVAENIC 224

Query: 663 VISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEI 707
              +    E      +                +   L  LT +E+
Sbjct: 225 EAWENENSEYAQQYKTED-------------LKWDNLKDLTDVEV 256

>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 = 68.1 bits (167), Expect = 1e-12
 Identities = 30/148 (20%), Positives = 54/148 (36%), Gaps = 12/148 (8%)

Query: 562 STLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG---Q 618
           S          GT  LK LD +      + S+   L  L+ L      L+ ++       
Sbjct: 65  SFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLS 124

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L+ L  L +     +     I   L+ L++L ++  S      P++ ++L  L  L +  
Sbjct: 125 LRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDL-- 182

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTL 705
           S  Q +++   +         LS L  L
Sbjct: 183 SQCQLEQLSPTA------FNSLSSLQVL 204

>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 = 56.9 bits (138), Expect = 6e-09
 Identities = 27/138 (19%), Positives = 43/138 (31%), Gaps = 13/138 (9%)

Query: 576 ELKVLDFTGIRFSPLPSS-LGRLINLQTLCLDGWRLEDIAIVGQ----LKKLEILSLRGA 630
               L+    +   LP     +L  L  L L    L       Q       L+ L L   
Sbjct: 29  SATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFN 88

Query: 631 EIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN 690
            +  +      L +L+ LD  + +   +   +V   L  L  L +  S +       G  
Sbjct: 89  GVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDI--SHTHTRVAFNGI- 145

Query: 691 ASLAELKGLSKLTTLEID 708
                  GLS L  L++ 
Sbjct: 146 -----FNGLSSLEVLKMA 158

>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 = 70.0 bits (172), Expect = 1e-12
 Identities = 39/173 (22%), Positives = 63/173 (36%), Gaps = 13/173 (7%)

Query: 539 IQELPERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTG--IRFSPL-PSS 593
            + L +      P L   L        L++     E  E L+ LD +   I  S      
Sbjct: 313 FENLCQISASNFPSLT-HLSIKGNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQ 371

Query: 594 LGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ--IGQLTRLQLLD 649
           L  L +LQ+L L       +      +  +LE+L L    +K    Q     L  L++L+
Sbjct: 372 LRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLN 431

Query: 650 LSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKL 702
           LS+   L + +  +   L  L+ L +    + + K       SL  L  L  L
Sbjct: 432 LSHS-LLDISSEQLFDGLPALQHLNL--QGNHFPKGNIQKTNSLQTLGRLEIL 481

>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 = 66.2 bits (162), Expect = 2e-11
 Identities = 29/146 (19%), Positives = 55/146 (37%), Gaps = 11/146 (7%)

Query: 565 QISDHFFEGTEE--LKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI-AIVGQLK 620
            IS   FEG  E  ++ ++     F  +  ++      LQ L L    L ++ + +  L 
Sbjct: 242 DISPAVFEGLCEMSVESINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLS 301

Query: 621 KLEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
            L+ L L   + + L  +       L  L +   +  + +    +  L  L EL +  S 
Sbjct: 302 TLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELDL--SH 359

Query: 680 SQWDKVEGGSNASLAELKGLSKLTTL 705
              +  +  +      L+ LS L +L
Sbjct: 360 DDIETSDCCNLQ----LRNLSHLQSL 381

>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 = 61.6 bits (150), Expect = 5e-10
 Identities = 32/153 (20%), Positives = 46/153 (30%), Gaps = 21/153 (13%)

Query: 565 QISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQ---- 618
            +          L  L   G   R       L  L NL+ L L    +E           
Sbjct: 315 NLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRN 374

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L  L+ L+L   E   L  +   +  +L+LLDL+     V  A +    L  L+ L +  
Sbjct: 375 LSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNLHLLKVLNLSH 434

Query: 678 ---SFSQWDKVEGGSNASLAELKGLSKLTTLEI 707
                S                 GL  L  L +
Sbjct: 435 SLLDISSEQ-----------LFDGLPALQHLNL 456

>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 = 60.8 bits (148), Expect = 9e-10
 Identities = 31/166 (18%), Positives = 64/166 (38%), Gaps = 26/166 (15%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPL----PSSLGRLINLQTLCLDGWRLEDIA--IVGQL 619
            S+  F+G   L+ L+  G  F        +SL  L  L+ L L    L  I       L
Sbjct: 440 SSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSSIDQHAFTSL 499

Query: 620 KKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-- 677
           K +  + L    +    ++     +   L+L++ + + +I P+++  LS+   + +    
Sbjct: 500 KMMNHVDLSHNRLTSSSIEALSHLKGIYLNLAS-NHISIILPSLLPILSQQRTINLRQNP 558

Query: 678 --------SFSQW-----DKVEGGSN---ASLAELKGLSKLTTLEI 707
                    F +W      K+E   +    +   L+G+  L+ + +
Sbjct: 559 LDCTCSNIYFLEWYKENMQKLEDTEDTLCENPPLLRGVR-LSDVTL 603

>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 = 60.4 bits (147), Expect = 1e-09
 Identities = 18/138 (13%), Positives = 43/138 (31%), Gaps = 6/138 (4%)

Query: 543 PERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSL---GRLIN 599
           P   +    +        +  +          + L +  F  +    +  ++      ++
Sbjct: 196 PGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDMDDEDISPAVFEGLCEMS 255

Query: 600 LQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV 657
           ++++ L      +I          L+ L L    + +LP  +  L+ L+ L LS      
Sbjct: 256 VESINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSAN-KFE 314

Query: 658 VIAPNVISKLSRLEELYM 675
            +     S    L  L +
Sbjct: 315 NLCQISASNFPSLTHLSI 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 = 56.9 bits (138), Expect = 1e-08
 Identities = 23/114 (20%), Positives = 40/114 (35%), Gaps = 5/114 (4%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
            I +  F+    L  L  T      +   +L     L+ L      +  I    +   K 
Sbjct: 71  WIHEDTFQSQHRLDTLVLTANPLIFMAETALSGPKALKHLFFIQTGISSIDFIPLHNQKT 130

Query: 622 LEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
           LE L L    I  + L       +L++LD  N  ++  ++   +S L +   L 
Sbjct: 131 LESLYLGSNHISSIKLPKGFPTEKLKVLDFQNN-AIHYLSKEDMSSLQQATNLS 183

>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 = 49.6 bits (119), Expect = 3e-06
 Identities = 24/135 (17%), Positives = 44/135 (32%), Gaps = 14/135 (10%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAE 631
            E  K  +   +  + +P +L    + + L      L  I      +L  L  L L   +
Sbjct: 11  KEVNKTYNCENLGLNEIPGTLPN--STECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQ 68

Query: 632 IKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN 690
           I  +         RL  L L+    L+ +A   +S    L+ L+     +    ++    
Sbjct: 69  IYWIHEDTFQSQHRLDTLVLTAN-PLIFMAETALSGPKALKHLFF--IQTGISSIDFIP- 124

Query: 691 ASLAELKGLSKLTTL 705
                L     L +L
Sbjct: 125 -----LHNQKTLESL 134

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 46.5 bits (111), Expect = 2e-05
 Identities = 27/165 (16%), Positives = 42/165 (25%), Gaps = 26/165 (15%)

Query: 566 ISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
           I        + L+ L      I    LP        L+ L      +  +    +  L++
Sbjct: 120 IDFIPLHNQKTLESLYLGSNHISSIKLPK-GFPTEKLKVLDFQNNAIHYLSKEDMSSLQQ 178

Query: 622 LEILSLR--GAEIKQLPLQIGQLTRLQLLDLSNCS-SLVVIAPNVISKLSRLEELYMGD- 677
              LSL   G +I  +          Q L+       LV+      S +  L      D 
Sbjct: 179 ATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDM 238

Query: 678 --SFSQWDKVEGGSNASLAEL---------------KGLSKLTTL 705
                     EG    S+  +                  S L  L
Sbjct: 239 DDEDISPAVFEGLCEMSVESINLQKHYFFNISSNTFHCFSGLQEL 283

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 68.3 bits (168), Expect = 2e-12
 Identities = 32/181 (17%), Positives = 63/181 (34%), Gaps = 26/181 (14%)

Query: 532 ISLPYRDIQELPERLECPQLK-LFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSP 589
           + +    +  +        L+ L L      +  QI+D        +L  L     + + 
Sbjct: 49  LVVAGEKVASIQGIEYLTNLEYLNL------NGNQITDISPLSNLVKLTNLYIGTNKITD 102

Query: 590 LPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD 649
           + + L  L NL+ L L+   + DI+ +  L K+  L+L           +  +T L  L 
Sbjct: 103 ISA-LQNLTNLRELYLNEDNISDISPLANLTKMYSLNLGANHNLSDLSPLSNMTGLNYLT 161

Query: 650 LSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEI 707
           ++    +  + P  I+ L+ L  L +              N    ++ L  L+ L     
Sbjct: 162 VTES-KVKDVTP--IANLTDLYSLSLNY------------NQIEDISPLASLTSLHYFTA 206

Query: 708 D 708
            
Sbjct: 207 Y 207

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 67.6 bits (166), Expect = 3e-12
 Identities = 25/136 (18%), Positives = 54/136 (39%), Gaps = 19/136 (13%)

Query: 575 EELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQ 634
            E           + + +    L ++  L + G ++  I  +  L  LE L+L G +I  
Sbjct: 22  AEGIRAVLQKASVTDVVT-QEELESITKLVVAGEKVASIQGIEYLTNLEYLNLNGNQITD 80

Query: 635 LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN--AS 692
           +   +  L +L  L +     +  I+   +  L+ L ELY+ +            +  + 
Sbjct: 81  IS-PLSNLVKLTNLYIGTN-KITDISA--LQNLTNLRELYLNE------------DNISD 124

Query: 693 LAELKGLSKLTTLEID 708
           ++ L  L+K+ +L + 
Sbjct: 125 ISPLANLTKMYSLNLG 140

>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 = 66.0 bits (162), Expect = 9e-12
 Identities = 34/147 (23%), Positives = 57/147 (38%), Gaps = 18/147 (12%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           QI+D         L  L     + + L   L  L  L  L +   ++ DI  V  L KL+
Sbjct: 210 QITDITPVANMTRLNSLKIGNNKITDLSP-LANLSQLTWLEIGTNQISDINAVKDLTKLK 268

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
           +L++   +I  +   +  L++L  L L+N   L      VI  L+ L  L++        
Sbjct: 269 MLNVGSNQISDIS-VLNNLSQLNSLFLNNNQ-LGNEDMEVIGGLTNLTTLFLSQ------ 320

Query: 684 KVEGGSN--ASLAELKGLSKLTTLEID 708
                 N    +  L  LSK+ + +  
Sbjct: 321 ------NHITDIRPLASLSKMDSADFA 341

>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 = 64.1 bits (157), Expect = 4e-11
 Identities = 30/134 (22%), Positives = 57/134 (42%), Gaps = 19/134 (14%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L  L  T  +   +   +  L +L +L L+  ++EDI+ +  L  L   +    +I  + 
Sbjct: 157 LNYLTVTESKVKDVTP-IANLTDLYSLSLNYNQIEDISPLASLTSLHYFTAYVNQITDIT 215

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNA--SLA 694
             +  +TRL  L + N   +  ++P  ++ LS+L  L +G             N    + 
Sbjct: 216 P-VANMTRLNSLKIGNN-KITDLSP--LANLSQLTWLEIGT------------NQISDIN 259

Query: 695 ELKGLSKLTTLEID 708
            +K L+KL  L + 
Sbjct: 260 AVKDLTKLKMLNVG 273

>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 = 62.6 bits (153), Expect = 1e-10
 Identities = 27/145 (18%), Positives = 65/145 (44%), Gaps = 14/145 (9%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           QI D         L        + + +   +  +  L +L +   ++ D++ +  L +L 
Sbjct: 188 QIEDISPLASLTSLHYFTAYVNQITDITP-VANMTRLNSLKIGNNKITDLSPLANLSQLT 246

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
            L +   +I  +   +  LT+L++L++ +   +  I+   ++ LS+L  L++ ++     
Sbjct: 247 WLEIGTNQISDIN-AVKDLTKLKMLNVGSN-QISDISV--LNNLSQLNSLFLNNN----- 297

Query: 684 KVEGGSNASLAELKGLSKLTTLEID 708
           ++    N  +  + GL+ LTTL + 
Sbjct: 298 QL---GNEDMEVIGGLTNLTTLFLS 319

>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 = 59.1 bits (144), Expect = 2e-09
 Identities = 26/115 (22%), Positives = 52/115 (45%), Gaps = 6/115 (5%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           +I+D        +L  L+    + S + + +  L  L+ L +   ++ DI+++  L +L 
Sbjct: 232 KITDLSPLANLSQLTWLEIGTNQISDINA-VKDLTKLKMLNVGSNQISDISVLNNLSQLN 290

Query: 624 ILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L L   ++    +  IG LT L  L LS    +  I P  ++ LS+++     +
Sbjct: 291 SLFLNNNQLGNEDMEVIGGLTNLTTLFLSQN-HITDIRP--LASLSKMDSADFAN 342

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 48.7 bits (117), Expect = 4e-06
 Identities = 21/109 (19%), Positives = 36/109 (33%), Gaps = 14/109 (12%)

Query: 600 LQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVI 659
             TL      +  I     L +     L+ A +  +     +L  +  L ++    +  I
Sbjct: 2   AATLATLPAPINQIFPDADLAEGIRAVLQKASVTDVV-TQEELESITKLVVAGE-KVASI 59

Query: 660 APNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
               I  L+ LE L +  +              ++ L  L KLT L I 
Sbjct: 60  QG--IEYLTNLEYLNLNGN----------QITDISPLSNLVKLTNLYIG 96

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 68.1 bits (167), Expect = 2e-12
 Identities = 19/115 (16%), Positives = 35/115 (30%), Gaps = 4/115 (3%)

Query: 565 QISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
            + D        ++ LD     I              L+ L L    + D+       KL
Sbjct: 134 MLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVVFAKL 193

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           + L L   ++  +  +      +  + L N   LV+I    +     LE   +  
Sbjct: 194 KTLDLSSNKLAFMGPEFQSAAGVTWISLRNN-KLVLI-EKALRFSQNLEHFDLRG 246

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 56.5 bits (137), Expect = 1e-08
 Identities = 21/128 (16%), Positives = 42/128 (32%), Gaps = 19/128 (14%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           Q      +    +K LD +G   S +  + L     L+ L L    L +   +  L  L 
Sbjct: 24  QALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLR 83

Query: 624 ILSLRGAEIKQLP-----------------LQIGQLTRLQLLDLSNCSSLVVIAPNVISK 666
            L L    +++L                  +   +    + + L+N   + ++       
Sbjct: 84  TLDLNNNYVQELLVGPSIETLHAANNNISRVSCSRGQGKKNIYLANN-KITMLRDLDEGC 142

Query: 667 LSRLEELY 674
            SR++ L 
Sbjct: 143 RSRVQYLD 150

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 53.1 bits (128), Expect = 1e-07
 Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 16/97 (16%)

Query: 615 IVGQLKKLEILSLRGAEIKQLPLQIGQ-LTRLQLLDLSNCSSLVVIAPNVISKLSRLEEL 673
           I     + +I  +  + +KQ    + Q    ++ LDLS    L  I+   ++  ++LE L
Sbjct: 5   IKQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGN-PLSQISAADLAPFTKLELL 63

Query: 674 YMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
            +             SN      +L+ LS L TL+++
Sbjct: 64  NL------------SSNVLYETLDLESLSTLRTLDLN 88

>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 = 65.4 bits (160), Expect = 3e-12
 Identities = 23/132 (17%), Positives = 51/132 (38%), Gaps = 15/132 (11%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L  +    I  + L + +    N++ L ++     +   +  L  LE L + G ++    
Sbjct: 46  LTYITLANINVTDL-TGIEYAHNIKDLTINNIHATNYNPISGLSNLERLRIMGKDVTSDK 104

Query: 637 LQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAE 695
           +  +  LT L LLD+S+  +        I+ L ++  + +              N ++ +
Sbjct: 105 IPNLSGLTSLTLLDISHS-AHDDSILTKINTLPKVNSIDL------------SYNGAITD 151

Query: 696 LKGLSKLTTLEI 707
           +  L  L  L+ 
Sbjct: 152 IMPLKTLPELKS 163

>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 = 63.4 bits (155), Expect = 1e-11
 Identities = 30/148 (20%), Positives = 53/148 (35%), Gaps = 17/148 (11%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAI--VGQLKK 621
            ++D    E    +K L    I  +   + +  L NL+ L + G  +    I  +  L  
Sbjct: 55  NVTDLTGIEYAHNIKDLTINNIHATNY-NPISGLSNLERLRIMGKDVTSDKIPNLSGLTS 113

Query: 622 LEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
           L +L +  +      L  I  L ++  +DLS   ++  I P  +  L  L+ L +   F 
Sbjct: 114 LTLLDISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIMP--LKTLPELKSLNI--QFD 169

Query: 681 QWDKVEGGSNASLAELKGLSKLTTLEID 708
                 G        ++   KL  L   
Sbjct: 170 GVHDYRG--------IEDFPKLNQLYAF 189

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 56.9 bits (138), Expect = 2e-09
 Identities = 16/116 (13%), Positives = 44/116 (37%), Gaps = 10/116 (8%)

Query: 593 SLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN 652
           +  ++ +L  + L    + D+  +     ++ L++           I  L+ L+ L +  
Sbjct: 39  TEAQMNSLTYITLANINVTDLTGIEYAHNIKDLTINNIHATNYN-PISGLSNLERLRIMG 97

Query: 653 CSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
              +       +S L+ L  L +  S           ++ L ++  L K+ ++++ 
Sbjct: 98  K-DVTSDKIPNLSGLTSLTLLDISHS--------AHDDSILTKINTLPKVNSIDLS 144

>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 = 50.0 bits (120), Expect = 5e-07
 Identities = 20/118 (16%), Positives = 41/118 (34%), Gaps = 9/118 (7%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLEDIAI--VGQLK 620
             ++ +   G   L+ L   G   +     +L  L +L  L +     +D  +  +  L 
Sbjct: 77  HATNYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLP 136

Query: 621 KLEILSLRG-AEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           K+  + L     I  +   +  L  L+ L++     +       I    +L +LY   
Sbjct: 137 KVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFD-GVHDYRG--IEDFPKLNQLYAFS 190

>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 = 68.5 bits (168), Expect = 3e-12
 Identities = 29/140 (20%), Positives = 51/140 (36%), Gaps = 19/140 (13%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGA 630
               +++  L    +    +   +  L NL  +     +L DI  +  L KL  + +   
Sbjct: 42  QTDLDQVTTLQADRLGIKSI-DGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNN 100

Query: 631 EIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN 690
           +I  +   +  LT L  L L N   +  I P  +  L+ L  L +             SN
Sbjct: 101 QIADIT-PLANLTNLTGLTLFNN-QITDIDP--LKNLTNLNRLEL------------SSN 144

Query: 691 --ASLAELKGLSKLTTLEID 708
             + ++ L GL+ L  L   
Sbjct: 145 TISDISALSGLTSLQQLSFG 164

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 65.4 bits (160), Expect = 3e-11
 Identities = 28/147 (19%), Positives = 52/147 (35%), Gaps = 20/147 (13%)

Query: 565 QISDHF-FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            I+  F      E           +   S    L  + TL  D   ++ I  V  L  L 
Sbjct: 13  PINQIFTDTALAEKMKTVLGKTNVTDTVS-QTDLDQVTTLQADRLGIKSIDGVEYLNNLT 71

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
            ++    ++  +   +  LT+L  + ++N   +  I P  ++ L+ L  L + +      
Sbjct: 72  QINFSNNQLTDIT-PLKNLTKLVDILMNNN-QIADITP--LANLTNLTGLTLFN------ 121

Query: 684 KVEGGSN--ASLAELKGLSKLTTLEID 708
                 N    +  LK L+ L  LE+ 
Sbjct: 122 ------NQITDIDPLKNLTNLNRLELS 142

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 65.0 bits (159), Expect = 4e-11
 Identities = 36/157 (22%), Positives = 64/157 (40%), Gaps = 18/157 (11%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           Q+ D         L  LD    + S L   L  L  L  L L   ++ +I+ +  L  L 
Sbjct: 232 QLKDIGTLASLTNLTDLDLANNQISNLAP-LSGLTKLTELKLGANQISNISPLAGLTALT 290

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD------ 677
            L L   +++ +   I  L  L  L L    ++  I+P  +S L++L+ L+  +      
Sbjct: 291 NLELNENQLEDIS-PISNLKNLTYLTLYFN-NISDISP--VSSLTKLQRLFFYNNKVSDV 346

Query: 678 -SFSQWDKVEG---GSN--ASLAELKGLSKLTTLEID 708
            S +    +     G N  + L  L  L+++T L ++
Sbjct: 347 SSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLN 383

>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 = 64.2 bits (157), Expect = 6e-11
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 21/147 (14%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            ISD     G   L+ L F        P  L  L  L+ L +   ++ DI+++ +L  LE
Sbjct: 145 TISDISALSGLTSLQQLSFGNQVTDLKP--LANLTTLERLDISSNKVSDISVLAKLTNLE 202

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
            L     +I  +   +G LT L  L L+      +     ++ L+ L +L + +      
Sbjct: 203 SLIATNNQISDIT-PLGILTNLDELSLNGNQ---LKDIGTLASLTNLTDLDLAN------ 252

Query: 684 KVEGGSN--ASLAELKGLSKLTTLEID 708
                 N  ++LA L GL+KLT L++ 
Sbjct: 253 ------NQISNLAPLSGLTKLTELKLG 273

>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 = 57.7 bits (140), Expect = 8e-09
 Identities = 26/114 (22%), Positives = 48/114 (42%), Gaps = 6/114 (5%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           QIS+     G   L  L+    +   +   +  L NL  L L    + DI+ V  L KL+
Sbjct: 276 QISNISPLAGLTALTNLELNENQLEDISP-ISNLKNLTYLTLYFNNISDISPVSSLTKLQ 334

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L     ++  +   +  LT +  L   +   +  + P  ++ L+R+ +L + D
Sbjct: 335 RLFFYNNKVSDVS-SLANLTNINWLSAGHNQ-ISDLTP--LANLTRITQLGLND 384

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 52.3 bits (126), Expect = 4e-07
 Identities = 26/137 (18%), Positives = 45/137 (32%), Gaps = 9/137 (6%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRL 597
           ++++        L    L         ISD        +L+ L F   + S + S L  L
Sbjct: 299 LEDISPISNLKNLTYLTL-----YFNNISDISPVSSLTKLQRLFFYNNKVSDVSS-LANL 352

Query: 598 INLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV 657
            N+  L     ++ D+  +  L ++  L L        P+       +     +   +L 
Sbjct: 353 TNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGAL- 411

Query: 658 VIAPNVISKLSRLEELY 674
            IAP  IS      E  
Sbjct: 412 -IAPATISDGGSYTEPD 427

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 66.9 bits (164), Expect = 1e-11
 Identities = 26/138 (18%), Positives = 50/138 (36%), Gaps = 15/138 (10%)

Query: 577 LKVLDFTGIRFS----PLPSSLGRLINLQTLCLDGWRLE-DIAIVGQLKKLEILSLRGAE 631
           +  +D +    +     + SSL  L  L++L L    +   ++       L  L L    
Sbjct: 52  VTSIDLSSKPLNVGFSAVSSSLLSLTGLESLFLSNSHINGSVSGFKCSASLTSLDLSRNS 111

Query: 632 IK-QLP--LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQWDKVEG 687
           +   +     +G  + L+ L++S+ +       +   KL+ LE L +   S S      G
Sbjct: 112 LSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKVSGGLKLNSLEVLDLSANSIS------G 165

Query: 688 GSNASLAELKGLSKLTTL 705
            +        G  +L  L
Sbjct: 166 ANVVGWVLSDGCGELKHL 183

>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 = 61.8 bits (151), Expect = 5e-10
 Identities = 25/151 (16%), Positives = 48/151 (31%), Gaps = 36/151 (23%)

Query: 562 STLQISDHFFEGT-------EELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDG------ 607
             L +S + F            L+ LD +G + S     ++     L+ L +        
Sbjct: 203 EFLDVSSNNFSTGIPFLGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFVGP 262

Query: 608 ---WRLEDI----------------AIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQL 647
                L+ +                 + G    L  L L G      +P   G  + L+ 
Sbjct: 263 IPPLPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLES 322

Query: 648 LDLSNCSSLV-VIAPNVISKLSRLEELYMGD 677
           L LS+  +    +  + + K+  L+ L +  
Sbjct: 323 LALSSN-NFSGELPMDTLLKMRGLKVLDLSF 352

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 57.2 bits (139), Expect = 1e-08
 Identities = 35/189 (18%), Positives = 58/189 (30%), Gaps = 35/189 (18%)

Query: 541 ELPERLECPQLK-LFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLI 598
           ++   L+   L+ L L          +     +G  ELK L  +G + S  +   + R +
Sbjct: 143 KVSGGLKLNSLEVLDLSANSISGANVVGWVLSDGCGELKHLAISGNKISGDVD--VSRCV 200

Query: 599 NLQTLCLDGWRLE-DIAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLS----- 651
           NL+ L +        I  +G    L+ L + G ++       I   T L+LL++S     
Sbjct: 201 NLEFLDVSSNNFSTGIPFLGDCSALQHLDISGNKLSGDFSRAISTCTELKLLNISSNQFV 260

Query: 652 ------NCSSLVV-----------IAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNASL 693
                    SL             I   +      L  L +    F       G      
Sbjct: 261 GPIPPLPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFY------GAVPPFF 314

Query: 694 AELKGLSKL 702
                L  L
Sbjct: 315 GSCSLLESL 323

>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 = 56.1 bits (136), Expect = 3e-08
 Identities = 29/175 (16%), Positives = 54/175 (30%), Gaps = 47/175 (26%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFS-PLPSSLGR--LINLQTLCLDGWRLE-DI-AIVGQL 619
           ++ +     +  L  LD +   FS P+  +L +     LQ L L        I   +   
Sbjct: 358 ELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNGFTGKIPPTLSNC 417

Query: 620 KKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLS-------------NCSSLVVIA----- 660
            +L  L L    +   +P  +G L++L+ L L                 +L  +      
Sbjct: 418 SELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFND 477

Query: 661 -----PNVISKLSRLEELYMG-----DSFSQWDKVEGGSNASLAELKGLSKLTTL 705
                P+ +S  + L  + +          +W             +  L  L  L
Sbjct: 478 LTGEIPSGLSNCTNLNWISLSNNRLTGEIPKW-------------IGRLENLAIL 519

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 55.7 bits (135), Expect = 4e-08
 Identities = 30/164 (18%), Positives = 50/164 (30%), Gaps = 35/164 (21%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKL 622
           I          L+ L       +  +PS L    NL  + L   RL       +G+L+ L
Sbjct: 458 IPQELMYVKT-LETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENL 516

Query: 623 EILSLR-----GAEIKQLPLQIGQLTRLQLLDLS-------------NCSSLVVI----- 659
            IL L      G     +P ++G    L  LDL+               S  +       
Sbjct: 517 AILKLSNNSFSG----NIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAG 572

Query: 660 -APNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKL 702
                I      +E +   +  ++   +G  +  L  L   +  
Sbjct: 573 KRYVYIKNDGMKKECHGAGNLLEF---QGIRSEQLNRLSTRNPC 613

>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 = 46.4 bits (111), Expect = 3e-05
 Identities = 18/84 (21%), Positives = 31/84 (36%), Gaps = 12/84 (14%)

Query: 577 LKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLE-DI-AIVGQLKKLEIL-----SLR 628
               + T   +      +     ++  L +    L   I   +G +  L IL      + 
Sbjct: 610 RNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDIS 669

Query: 629 GAEIKQLPLQIGQLTRLQLLDLSN 652
           G  I   P ++G L  L +LDLS+
Sbjct: 670 G-SI---PDEVGDLRGLNILDLSS 689

>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 = 65.8 bits (161), Expect = 2e-11
 Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 4/120 (3%)

Query: 562 STLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI---AIVGQ 618
           S          GT  LK LD +      + S+   L  L+ L      L+ +   ++   
Sbjct: 360 SFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLS 419

Query: 619 LKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L+ L  L +     +         L+ L++L ++  S      P++ ++L  L  L +  
Sbjct: 420 LRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQ 479

>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 = 62.0 bits (151), Expect = 5e-10
 Identities = 28/105 (26%), Positives = 37/105 (35%), Gaps = 5/105 (4%)

Query: 577 LKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIK 633
            K LD +      L   S      LQ L L    ++ I       L  L  L L G  I+
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQ 89

Query: 634 QLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L L     L+ LQ L      +L  +    I  L  L+EL +  
Sbjct: 90  SLALGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAH 133

>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 = 32/152 (21%), Positives = 56/152 (36%), Gaps = 12/152 (7%)

Query: 566 ISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
           + +      + LK L+     I+   LP     L NL+ L L   +++ I    +  L +
Sbjct: 115 LENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQ 174

Query: 622 LEI----LSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM-G 676
           + +    L L    +  +     +  RL  L L N    + +    I  L+ LE   +  
Sbjct: 175 MPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVL 234

Query: 677 DSFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
             F     +E    ++   L+GL  LT  E  
Sbjct: 235 GEFRNEGNLEKFDKSA---LEGLCNLTIEEFR 263

>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 = 57.0 bits (138), Expect = 1e-08
 Identities = 24/115 (20%), Positives = 44/115 (38%), Gaps = 6/115 (5%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLEDI---AIVGQLKK 621
                F     L  LD +              L +L+ L + G   ++     I  +L+ 
Sbjct: 412 SEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRN 471

Query: 622 LEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
           L  L L   +++QL P     L+ LQ+L++S+  +   +       L+ L+ L  
Sbjct: 472 LTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHN-NFFSLDTFPYKCLNSLQVLDY 525

>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 = 56.2 bits (136), Expect = 3e-08
 Identities = 29/172 (16%), Positives = 51/172 (29%), Gaps = 20/172 (11%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLI 598
           I+ + +       +   L        +         + LK L FT  +     S +  L 
Sbjct: 294 IERVKDFSYNFGWQHLEL-----VNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVD-LP 347

Query: 599 NLQTLCLDGWRLEDIAIV----GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCS 654
           +L+ L L    L               L+ L L    +  +      L +L+ LD  + +
Sbjct: 348 SLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSN 407

Query: 655 SLVVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNASLAELKGLSKLTTL 705
              +   +V   L  L  L +              +   +    GLS L  L
Sbjct: 408 LKQMSEFSVFLSLRNLIYLDISHTHTR-------VAFNGI--FNGLSSLEVL 450

>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 = 55.4 bits (134), Expect = 4e-08
 Identities = 29/118 (24%), Positives = 44/118 (37%), Gaps = 7/118 (5%)

Query: 566 ISDHFFEGTEELKVLDFTGIRF--SPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
             +  F G   L+VL   G  F  + LP     L NL  L L   +LE +       L  
Sbjct: 436 AFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSS 495

Query: 622 LEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKL-SRLEELYMGD 677
           L++L++       L       L  LQ+LD S  + ++      +    S L  L +  
Sbjct: 496 LQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSL-NHIMTSKKQELQHFPSSLAFLNLTQ 552

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 47.7 bits (114), Expect = 1e-05
 Identities = 22/153 (14%), Positives = 39/153 (25%), Gaps = 28/153 (18%)

Query: 553 LFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-------PLPSSLGRLINLQTLCL 605
             L+  ++ +   +        E L  L     R +        +      L N+ +  L
Sbjct: 230 HRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSL 289

Query: 606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLP--------------------LQIGQLTRL 645
               +E +         + L L   +  Q P                         L  L
Sbjct: 290 VSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSL 349

Query: 646 QLLDLSNCS-SLVVIAPNVISKLSRLEELYMGD 677
           + LDLS    S            + L+ L +  
Sbjct: 350 EFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSF 382

>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 = 44.6 bits (106), Expect = 9e-05
 Identities = 20/86 (23%), Positives = 26/86 (30%), Gaps = 12/86 (13%)

Query: 622 LEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SF 679
            + L L    ++ L          LQ+LDLS C  +  I       LS L  L +     
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLILTGNPI 88

Query: 680 SQWDKVEGGSNASLAELKGLSKLTTL 705
                             GLS L  L
Sbjct: 89  Q-------SLALGA--FSGLSSLQKL 105

>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 = 65.4 bits (160), Expect = 3e-11
 Identities = 29/127 (22%), Positives = 50/127 (39%), Gaps = 15/127 (11%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFS---PLPSSLGRLINLQTLCLDGWRLEDI--AIVGQL 619
           Q++ + F     L+ L    +        PS    L NL  L L    + +I   ++  L
Sbjct: 444 QLTRNSFALVPSLQRLMLRRVALKNVDSSPSPFQPLRNLTILDLSNNNIANINDDMLEGL 503

Query: 620 KKLEILSLRGAEIKQL---------PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL 670
           +KLEIL L+   + +L            +  L+ L +L+L +      I   V   L  L
Sbjct: 504 EKLEILDLQHNNLARLWKHANPGGPIYFLKGLSHLHILNLESN-GFDEIPVEVFKDLFEL 562

Query: 671 EELYMGD 677
           + + +G 
Sbjct: 563 KIIDLGL 569

>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 = 64.6 bits (158), Expect = 7e-11
 Identities = 31/147 (21%), Positives = 53/147 (36%), Gaps = 12/147 (8%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
           Q+SD  F     L  L         +  +   +  NL TL L    L         QL+ 
Sbjct: 87  QLSDKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLEN 146

Query: 622 LEILSLRGAEIKQLP---LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS 678
           L+ L L   +I+ L    L I   + L+ L+LS+   +   +P     + RL  L++ + 
Sbjct: 147 LQELLLSNNKIQALKSEELDIFANSSLKKLELSSNQ-IKEFSPGCFHAIGRLFGLFLNNV 205

Query: 679 FSQWDKVEGGSNASLAELKGLSKLTTL 705
                ++       L      + +  L
Sbjct: 206 -----QLGPSLTEKLCLELANTSIRNL 227

>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 = 61.2 bits (149), Expect = 8e-10
 Identities = 28/117 (23%), Positives = 44/117 (37%), Gaps = 8/117 (6%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDG---WRLEDIAIVGQLKK 621
           Q+ D        L  L    +R  P  ++  R   L +L +      +LE       L  
Sbjct: 18  QVPDDLPTNITVL-NLTHNQLRRLP-AANFTRYSQLTSLDVGFNTISKLEPELCQK-LPM 74

Query: 622 LEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L++L+L+  E+ QL  +     T L  L L +  S+  I  N   K   L  L +  
Sbjct: 75  LKVLNLQHNELSQLSDKTFAFCTNLTELHLMSN-SIQKIKNNPFVKQKNLITLDLSH 130

>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 = 60.4 bits (147), Expect = 1e-09
 Identities = 30/154 (19%), Positives = 52/154 (33%), Gaps = 18/154 (11%)

Query: 565 QISDHFFEGTEELKVLDFTG--IRFSPLPSSLGR---LINLQTLCLDGWRLEDI--AIVG 617
            I  + F G   LK L  +        L +          L  L L   ++  I      
Sbjct: 343 GIKSNMFTGLINLKYLSLSNSFTSLRTLTNETFVSLAHSPLHILNLTKNKISKIESDAFS 402

Query: 618 QLKKLEILSLRGAEIKQL--PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
            L  LE+L L   EI Q     +   L  +  + LS     + +  N  + +  L+ L +
Sbjct: 403 WLGHLEVLDLGLNEIGQELTGQEWRGLENIFEIYLSYNK-YLQLTRNSFALVPSLQRLML 461

Query: 676 GD-SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
              +           ++S +  + L  LT L++ 
Sbjct: 462 RRVALK-------NVDSSPSPFQPLRNLTILDLS 488

>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 = 58.9 bits (143), Expect = 4e-09
 Identities = 31/151 (20%), Positives = 54/151 (35%), Gaps = 17/151 (11%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDG---WRLEDIAIVGQLK 620
           ++     +    LKVL+      S L   +     NL  L L      ++++     + K
Sbjct: 63  KLEPELCQKLPMLKVLNLQHNELSQLSDKTFAFCTNLTELHLMSNSIQKIKNNPF-VKQK 121

Query: 621 KLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVIS--KLSRLEELYMGD 677
            L  L L    +    L    QL  LQ L LSN   +  +    +     S L++L +  
Sbjct: 122 NLITLDLSHNGLSSTKLGTQVQLENLQELLLSNN-KIQALKSEELDIFANSSLKKLEL-- 178

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
           S +Q  +   G          + +L  L ++
Sbjct: 179 SSNQIKEFSPGC------FHAIGRLFGLFLN 203

>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 = 57.3 bits (139), Expect = 1e-08
 Identities = 29/125 (23%), Positives = 49/125 (39%), Gaps = 14/125 (11%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPL---------PSSLGRLINLQTLCLDGWRLEDI--A 614
           I+D   EG E+L++LD      + L            L  L +L  L L+    ++I   
Sbjct: 495 INDDMLEGLEKLEILDLQHNNLARLWKHANPGGPIYFLKGLSHLHILNLESNGFDEIPVE 554

Query: 615 IVGQLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISK-LSRLEE 672
           +   L +L+I+ L    +  LP  +      L+ L+L   + +  +   V       L E
Sbjct: 555 VFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQK-NLITSVEKKVFGPAFRNLTE 613

Query: 673 LYMGD 677
           L M  
Sbjct: 614 LDMRF 618

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 56.9 bits (138), Expect = 2e-08
 Identities = 29/152 (19%), Positives = 57/152 (37%), Gaps = 17/152 (11%)

Query: 562 STLQISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRL-----EDIA 614
             L+  +        LK L+ +   I+    P     +  L  L L+  +L     E + 
Sbjct: 158 QALKSEELDIFANSSLKKLELSSNQIKEFS-PGCFHAIGRLFGLFLNNVQLGPSLTEKLC 216

Query: 615 IVGQLKKLEILSLRGAEIKQLP---LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE 671
           +      +  LSL  +++           + T L +LDLS  + L V+  +  + L +LE
Sbjct: 217 LELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNN-LNVVGNDSFAWLPQLE 275

Query: 672 ELYMGDSFSQWDKVEGGSNASLAELKGLSKLT 703
             ++  +      ++   + SL  L  +  L 
Sbjct: 276 YFFLEYN-----NIQHLFSHSLHGLFNVRYLN 302

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 56.9 bits (138), Expect = 2e-08
 Identities = 28/149 (18%), Positives = 55/149 (36%), Gaps = 16/149 (10%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDIAIVGQ----- 618
           +I D  F+  + L+ L+        +  +    LINL+ L L         +  +     
Sbjct: 319 KIDDFSFQWLKCLEHLNMEDNDIPGIKSNMFTGLINLKYLSLSNSFTSLRTLTNETFVSL 378

Query: 619 -LKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
               L IL+L   +I ++       L  L++LDL        +       L  + E+Y+ 
Sbjct: 379 AHSPLHILNLTKNKISKIESDAFSWLGHLEVLDLGLNEIGQELTGQEWRGLENIFEIYL- 437

Query: 677 DSFSQWDKVEGGSNASLAELKGLSKLTTL 705
            S++++ ++   S         +  L  L
Sbjct: 438 -SYNKYLQLTRNS------FALVPSLQRL 459

>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 = 53.1 bits (128), Expect = 2e-07
 Identities = 25/131 (19%), Positives = 43/131 (32%), Gaps = 16/131 (12%)

Query: 563 TLQISDHFFEGTE--ELKVLDFTGIRFSPLPSSLG---RLINLQTLCLDGWRLEDI--AI 615
              +++          ++ L  +  + S   ++     +  NL  L L    L  +    
Sbjct: 208 GPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNNLNVVGNDS 267

Query: 616 VGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSN--------CSSLVVIAPNVISK 666
              L +LE   L    I+ L    +  L  ++ L+L           +SL  I       
Sbjct: 268 FAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQW 327

Query: 667 LSRLEELYMGD 677
           L  LE L M D
Sbjct: 328 LKCLEHLNMED 338

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 44.6 bits (106), Expect = 1e-04
 Identities = 16/106 (15%), Positives = 45/106 (42%), Gaps = 8/106 (7%)

Query: 598 INLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSL 656
           ++ +       +L  +        + +L+L   ++++L      + ++L  LD+    ++
Sbjct: 4   VSHEVADCSHLKLTQV-PDDLPTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFN-TI 61

Query: 657 VVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKL 702
             + P +  KL  L+ L +  +     ++   S+ + A    L++L
Sbjct: 62  SKLEPELCQKLPMLKVLNLQHN-----ELSQLSDKTFAFCTNLTEL 102

>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 = 64.7 bits (158), Expect = 5e-11
 Identities = 31/141 (21%), Positives = 53/141 (37%), Gaps = 7/141 (4%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
            I          L+VL     R + +   +   L +L+ L L    L  +  +  G L  
Sbjct: 40  YIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSS 99

Query: 622 LEILSLRGAEIKQLPLQ--IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
           L+ L+L G   + L +      LT LQ L + N  +   I     + L+ L EL +    
Sbjct: 100 LKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEI--KA 157

Query: 680 SQWDKVEGGSNASLAELKGLS 700
                 +  S  S+ ++  L+
Sbjct: 158 LSLRNYQSQSLKSIRDIHHLT 178

>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 = 57.8 bits (140), Expect = 8e-09
 Identities = 20/135 (14%), Positives = 48/135 (35%), Gaps = 21/135 (15%)

Query: 562 STLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKK 621
            ++Q +       + L  LD +   F P+P S      ++ L L    +  +      + 
Sbjct: 374 RSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSSTGIRVVK-TCIPQT 432

Query: 622 LEILSLRGAEIKQLPLQIGQLTRLQL-------------------LDLSNCSSLVVIAPN 662
           LE+L +    +    L + +L  L +                   + +S    L  +   
Sbjct: 433 LEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMKISRN-QLKSVPDG 491

Query: 663 VISKLSRLEELYMGD 677
           +  +L+ L+++++  
Sbjct: 492 IFDRLTSLQKIWLHT 506

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 57.0 bits (138), Expect = 1e-08
 Identities = 30/150 (20%), Positives = 51/150 (34%), Gaps = 26/150 (17%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPL----PSSLGRLINLQTLCLDGWRLEDIAIVG--- 617
            +   F +  + L+ LD +            +  G   +LQTL L    L  +   G   
Sbjct: 324 LVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEIL 383

Query: 618 -QLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
             LK L  L +       +P       +++ L+LS+   + V+   +      LE L + 
Sbjct: 384 LTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSST-GIRVVKTCI---PQTLEVLDV- 438

Query: 677 DSFSQWDKVEGGSNASLAEL-KGLSKLTTL 705
                       SN +L      L +L  L
Sbjct: 439 ------------SNNNLDSFSLFLPRLQEL 456

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 51.3 bits (123), Expect = 8e-07
 Identities = 27/168 (16%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 545 RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLC 604
                +L   L +    S ++  D    G   L   + +          +   + ++ L 
Sbjct: 237 DESFNELLKLLRYILELSEVEFDDCTLNG---LGDFNPSESDVVSELGKV-ETVTIRRLH 292

Query: 605 LDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQIGQ-LTRLQLLDLSNC--SSLVVI 659
           +  + L      +   L+K++ +++  +++  +P    Q L  L+ LDLS        + 
Sbjct: 293 IPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLK 352

Query: 660 APNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEI 707
                     L+ L +  S +    ++         L  L  LT+L+I
Sbjct: 353 NSACKGAWPSLQTLVL--SQNHLRSMQKTGEI----LLTLKNLTSLDI 394

>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 = 64.7 bits (158), Expect = 5e-11
 Identities = 25/117 (21%), Positives = 40/117 (34%), Gaps = 6/117 (5%)

Query: 566 ISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
             D  F G   L  L   G   + + L +      NL  L L   +LE I   +   L +
Sbjct: 439 DFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHR 498

Query: 622 LEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L++L++    +  L      QL  L  LD S    +      +      L    + +
Sbjct: 499 LQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFN-RIETSKGILQHFPKSLAFFNLTN 554

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 60.8 bits (148), Expect = 9e-10
 Identities = 32/148 (21%), Positives = 51/148 (34%), Gaps = 12/148 (8%)

Query: 562 STLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA---IVGQ 618
           S      +   GT  L+ LD +      + ++   L  LQ L      L+ +        
Sbjct: 363 SFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLS 422

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L+KL  L +     K     I   LT L  L ++  S       NV +  + L  L +  
Sbjct: 423 LEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDL-- 480

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTL 705
           S  Q +++  G          L +L  L
Sbjct: 481 SKCQLEQISWGV------FDTLHRLQLL 502

>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 = 56.2 bits (136), Expect = 3e-08
 Identities = 26/116 (22%), Positives = 44/116 (37%), Gaps = 6/116 (5%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDG---WRLEDIAIVGQLK 620
            +  + F    EL+ LD +      +   +   L +L  L L G         +  G L 
Sbjct: 46  ILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSG-LT 104

Query: 621 KLEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
            LE L     ++  L    IGQL  L+ L++++        P   S L+ L  + +
Sbjct: 105 SLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDL 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 = 55.8 bits (135), Expect = 4e-08
 Identities = 28/152 (18%), Positives = 49/152 (32%), Gaps = 12/152 (7%)

Query: 566 ISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
           +          LK L+     I    LP+    L NL  + L    ++ I    +  L++
Sbjct: 119 LESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRE 178

Query: 622 L----EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM-G 676
                  L +    I  +  Q  Q  +L  L L    +   I    +  L+ L    +  
Sbjct: 179 NPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLIL 238

Query: 677 DSFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
             F     +E    +    ++GL  +T  E  
Sbjct: 239 GEFKDERNLEIFEPSI---MEGLCDVTIDEFR 267

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 55.0 bits (133), Expect = 6e-08
 Identities = 28/198 (14%), Positives = 63/198 (31%), Gaps = 41/198 (20%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLG--- 595
           I+ L +  +  + +   +        Q+          LK L  T  + S     +    
Sbjct: 297 IKYLEDVPKHFKWQSLSI-----IRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPS 351

Query: 596 ----------------------RLINLQTLCLDGWRLEDI-AIVGQLKKLEILSLRGAEI 632
                                    +L+ L L       + A    L++L+ L  + + +
Sbjct: 352 LSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTL 411

Query: 633 KQLPLQ--IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN 690
           K++        L +L  LD+S   +  +    +   L+ L  L M  +       +  + 
Sbjct: 412 KRVTEFSAFLSLEKLLYLDISYT-NTKIDFDGIFLGLTSLNTLKMAGN-----SFKDNTL 465

Query: 691 ASLAELKGLSKLTTLEID 708
           +++      + LT L++ 
Sbjct: 466 SNV--FANTTNLTFLDLS 481

>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 = 9e-07
 Identities = 33/160 (20%), Positives = 52/160 (32%), Gaps = 25/160 (15%)

Query: 566 ISDHFFEGTEELKVLDFTGIR---FSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
                 EG  ++ + +F       FS        L N+  + L G  ++ +  V +  K 
Sbjct: 250 FEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKW 309

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD---SF 679
           + LS+   ++KQ P     L  L+ L L+     +         L  L  L +     SF
Sbjct: 310 QSLSIIRCQLKQFPTL--DLPFLKSLTLTMNKGSI---SFKKVALPSLSYLDLSRNALSF 364

Query: 680 SQWDKVEGGSNASLAEL--------------KGLSKLTTL 705
           S           SL  L               GL +L  L
Sbjct: 365 SGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHL 404

>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 = 64.5 bits (157), Expect = 5e-11
 Identities = 19/115 (16%), Positives = 35/115 (30%), Gaps = 4/115 (3%)

Query: 565 QISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
            + D        ++ LD     I              L+ L L    + D+       KL
Sbjct: 134 MLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVVFAKL 193

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           + L L   ++  +  +      +  + L N   LV+I    +     LE   +  
Sbjct: 194 KTLDLSSNKLAFMGPEFQSAAGVTWISLRNN-KLVLI-EKALRFSQNLEHFDLRG 246

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 56.8 bits (137), Expect = 2e-08
 Identities = 21/128 (16%), Positives = 42/128 (32%), Gaps = 19/128 (14%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           Q      +    +K LD +G   S +  + L     L+ L L    L +   +  L  L 
Sbjct: 24  QALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLDLESLSTLR 83

Query: 624 ILSLRGAEIKQLP-----------------LQIGQLTRLQLLDLSNCSSLVVIAPNVISK 666
            L L    +++L                  +   +    + + L+N   + ++       
Sbjct: 84  TLDLNNNYVQELLVGPSIETLHAANNNISRVSCSRGQGKKNIYLANN-KITMLRDLDEGC 142

Query: 667 LSRLEELY 674
            SR++ L 
Sbjct: 143 RSRVQYLD 150

>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 = 50.6 bits (121), Expect = 1e-06
 Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 16/97 (16%)

Query: 615 IVGQLKKLEILSLRGAEIKQLPLQIGQ-LTRLQLLDLSNCSSLVVIAPNVISKLSRLEEL 673
           I     + +I  +  + +KQ    + Q    ++ LDLS    L  I+   ++  ++LE L
Sbjct: 5   IKQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGN-PLSQISAADLAPFTKLELL 63

Query: 674 YMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
            +             SN      +L+ LS L TL+++
Sbjct: 64  NL------------SSNVLYETLDLESLSTLRTLDLN 88

>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 = 43.3 bits (102), Expect = 2e-04
 Identities = 28/175 (16%), Positives = 55/175 (31%), Gaps = 27/175 (15%)

Query: 545 RLECPQLKLFLLFAKYDSTLQ------ISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRL 597
              C  L+ F    +   T+       ++    E      +  +       LP+    RL
Sbjct: 248 GFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRL 307

Query: 598 INLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV 657
           I L+                  K+  +LS +G+E ++L  +     R + +D        
Sbjct: 308 IALK-----------------RKEHALLSGQGSETERLECERENQARQREIDALKE-QYR 349

Query: 658 VIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA 712
            +   V  +      L         D+       + AEL G  +    +I+++ A
Sbjct: 350 TVIDQVTLRKQAKITLEQ--KKKALDEQVSNGRRAHAELDGTLQQAVGQIELQHA 402

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 63.9 bits (156), Expect = 6e-11
 Identities = 21/157 (13%), Positives = 53/157 (33%), Gaps = 15/157 (9%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
           ++     +   ++++L+   ++   + + +      +Q L +    +  +   +   +  
Sbjct: 59  KLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPL 118

Query: 622 LEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD--- 677
           L +L L   ++  LP  I     +L  L +SN  +L  I  +     + L+ L +     
Sbjct: 119 LTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNN-NLERIEDDTFQATTSLQNLQLSSNRL 177

Query: 678 ------SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
                             N  L+ L     +  L+  
Sbjct: 178 THVDLSLIPSLFHANVSYN-LLSTLAIPIAVEELDAS 213

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 62.0 bits (151), Expect = 3e-10
 Identities = 25/115 (21%), Positives = 43/115 (37%), Gaps = 8/115 (6%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLKKL 622
            +         EL +L       +     L     L  + L    LE I      ++++L
Sbjct: 219 VVRGPVNV---ELTILKLQHNNLTDTAW-LLNYPGLVEVDLSYNELEKIMYHPFVKMQRL 274

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           E L +    +  L L    +  L++LDLS+   L+ +      +  RLE LY+  
Sbjct: 275 ERLYISNNRLVALNLYGQPIPTLKVLDLSHN-HLLHV-ERNQPQFDRLENLYLDH 327

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 53.1 bits (128), Expect = 2e-07
 Identities = 24/147 (16%), Positives = 45/147 (30%), Gaps = 24/147 (16%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGR-LINLQTLCLDGWRLEDIAIVGQLKKLE 623
            +    F  T +L  L  +      +     +   +LQ L L   RL  + +   +  L 
Sbjct: 131 SLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVDL-SLIPSLF 189

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
             ++    +  L         ++ LD S+  S+ V+   V      L  L +        
Sbjct: 190 HANVSYNLLSTLA----IPIAVEELDASHN-SINVVRGPV---NVELTILKLQH------ 235

Query: 684 KVEGGSN--ASLAELKGLSKLTTLEID 708
                 N     A L     L  +++ 
Sbjct: 236 ------NNLTDTAWLLNYPGLVEVDLS 256

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 47.0 bits (112), Expect = 1e-05
 Identities = 15/91 (16%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L   +I++ + + +++LP  +     +++LL+L++   +  I     +    +++LYM  
Sbjct: 44  LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQ-IEEIDTYAFAYAHTIQKLYM-- 100

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
            F+    +           + +  LT L ++
Sbjct: 101 GFNAIRYLPPHV------FQNVPLLTVLVLE 125

>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 = 62.8 bits (153), Expect = 1e-10
 Identities = 31/151 (20%), Positives = 56/151 (37%), Gaps = 22/151 (14%)

Query: 566 ISDHFFEGTEELKVLDFTGI-RFSPLPS-SLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           I  + F     L  LD   + +   +   +   L NL+ L L    ++D+  +  L  LE
Sbjct: 162 IPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDMPNLTPLVGLE 221

Query: 624 ILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW 682
            L + G    ++       L+ L+ L + N   + +I  N    L+ L EL +       
Sbjct: 222 ELEMSGNHFPEIRPGSFHGLSSLKKLWVMNS-QVSLIERNAFDGLASLVELNL------- 273

Query: 683 DKVEGGSNASLAEL-----KGLSKLTTLEID 708
                 ++ +L+ L       L  L  L + 
Sbjct: 274 ------AHNNLSSLPHDLFTPLRYLVELHLH 298

>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 = 62.8 bits (153), Expect = 2e-10
 Identities = 36/151 (23%), Positives = 49/151 (32%), Gaps = 20/151 (13%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI---AIVGQLK 620
            I    F     L+VL         +   +   L +L TL L    L  I   A    L 
Sbjct: 89  MIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEY-LS 147

Query: 621 KLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
           KL  L LR   I+ +P     ++  L  LDL     L  I+      L  L+ L +G   
Sbjct: 148 KLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGM-- 205

Query: 680 SQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
                          +  L  L  L  LE+ 
Sbjct: 206 ----------CNIKDMPNLTPLVGLEELEMS 226

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 62.8 bits (153), Expect = 2e-10
 Identities = 38/151 (25%), Positives = 56/151 (37%), Gaps = 20/151 (13%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI---AIVGQLK 620
            I  + F+    L++L  +      +   +   L NL TL L   RL  I   A V  L 
Sbjct: 78  IIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVY-LS 136

Query: 621 KLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
           KL+ L LR   I+ +P     ++  L+ LDL     L  I+      LS L  L +    
Sbjct: 137 KLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAM-- 194

Query: 680 SQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
                          +  L  L KL  L++ 
Sbjct: 195 ----------CNLREIPNLTPLIKLDELDLS 215

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 62.5 bits (152), Expect = 2e-10
 Identities = 34/150 (22%), Positives = 51/150 (34%), Gaps = 20/150 (13%)

Query: 566 ISDHFFEGTEELKVLDFTGI-RFSPLPS-SLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           I  + F     L+ LD   + R S +   +   L NL+ L L    L +I  +  L KL+
Sbjct: 151 IPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLD 210

Query: 624 ILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW 682
            L L G  +  +       L  LQ L +     + VI  N    L  L E+ +       
Sbjct: 211 ELDLSGNHLSAIRPGSFQGLMHLQKLWMIQS-QIQVIERNAFDNLQSLVEINL------- 262

Query: 683 DKVEGGSNA--SLAE--LKGLSKLTTLEID 708
                  N    L       L  L  + + 
Sbjct: 263 -----AHNNLTLLPHDLFTPLHHLERIHLH 287

>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 = 62.8 bits (153), Expect = 2e-10
 Identities = 34/179 (18%), Positives = 68/179 (37%), Gaps = 10/179 (5%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLI 598
                  ++ P L+   L     S          GT  LK LD +      + S+   L 
Sbjct: 337 GGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLE 396

Query: 599 NLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCS 654
            L+ L      L+ ++       L+ L  L +     +     I   L+ L++L ++  S
Sbjct: 397 QLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNS 456

Query: 655 SLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLS----KLTTLEIDV 709
                 P++ ++L  L  L +  S  Q +++   +  SL+ L+ L+    +L ++   +
Sbjct: 457 FQENFLPDIFTELRNLTFLDL--SQCQLEQLSPTAFNSLSSLQVLNMASNQLKSVPDGI 513

>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 = 62.4 bits (152), Expect = 3e-10
 Identities = 33/177 (18%), Positives = 54/177 (30%), Gaps = 18/177 (10%)

Query: 533 SLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS 592
           SL    I+ + +       +   L        +         + LK L FT  +     S
Sbjct: 288 SLVSVTIERVKDFSYNFGWQHLEL-----VNCKFGQFPTLKLKSLKRLTFTSNKGGNAFS 342

Query: 593 SLGRLINLQTLCLDGWRLEDIAIV----GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL 648
            +  L +L+ L L    L               L+ L L    +  +      L +L+ L
Sbjct: 343 EVD-LPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHL 401

Query: 649 DLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTL 705
           D  + +   +   +V   L  L  L +  S +       G         GLS L  L
Sbjct: 402 DFQHSNLKQMSEFSVFLSLRNLIYLDI--SHTHTRVAFNGI------FNGLSSLEVL 450

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 58.6 bits (142), Expect = 4e-09
 Identities = 29/105 (27%), Positives = 38/105 (36%), Gaps = 5/105 (4%)

Query: 577 LKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIK 633
            K LD +      L S S      LQ L L    ++ I       L  L  L L G  I+
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQ 89

Query: 634 QLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L L     L+ LQ L      +L  +    I  L  L+EL +  
Sbjct: 90  SLALGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAH 133

>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 = 57.4 bits (139), Expect = 9e-09
 Identities = 38/186 (20%), Positives = 65/186 (34%), Gaps = 26/186 (13%)

Query: 539 IQELPERL--ECPQLK-LFLLFAKYDSTLQ-ISDHFFEGTEELKVLDFTG--IRFSPLPS 592
           IQ L          L+ L       ++ L  + +      + LK L+     I+   LP 
Sbjct: 88  IQSLALGAFSGLSSLQKLVA----VETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPE 143

Query: 593 SLGRLINLQTLCLDGWRL-----EDIAIVGQLKKLEI-LSLRGAEIKQLPLQIGQLTRLQ 646
               L NL+ L L   ++      D+ ++ Q+  L + L L    +  +     +  RL 
Sbjct: 144 YFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLH 203

Query: 647 LLDLSNCSSLVVIAPNVISKLSRLEELY----MGDSFSQWDKVEGGSNASLAELKGLSKL 702
            L L N    + +    I  L+ LE          +    +K +  +      L+GL  L
Sbjct: 204 KLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSA------LEGLCNL 257

Query: 703 TTLEID 708
           T  E  
Sbjct: 258 TIEEFR 263

>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 = 56.3 bits (136), Expect = 2e-08
 Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 6/116 (5%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
            I D  ++    L  L  TG     L   +   L +LQ L      L  +    +G LK 
Sbjct: 66  TIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKT 125

Query: 622 LEILSLRGAEIKQLPL--QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
           L+ L++    I+   L      LT L+ LDLS+   +  I    +  L ++  L +
Sbjct: 126 LKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSN-KIQSIYCTDLRVLHQMPLLNL 180

>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 = 4e-07
 Identities = 23/114 (20%), Positives = 50/114 (43%), Gaps = 8/114 (7%)

Query: 570 FFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDI---AIVGQLKKLEI 624
            F     L  LD +    R +        L +L+ L + G   ++     I  +L+ L  
Sbjct: 416 VFLSLRNLIYLDISHTHTRVAF-NGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTF 474

Query: 625 LSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L L   +++QL       L+ LQ+L++++   L  +   +  +L+ L+++++  
Sbjct: 475 LDLSQCQLEQLSPTAFNSLSSLQVLNMASNQ-LKSVPDGIFDRLTSLQKIWLHT 527

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 42.8 bits (101), Expect = 4e-04
 Identities = 21/85 (24%), Positives = 31/85 (36%), Gaps = 10/85 (11%)

Query: 622 LEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
            + L L    ++ L          LQ+LDLS C  +  I       LS L  L +  + +
Sbjct: 30  TKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRC-EIQTIEDGAYQSLSHLSTLIL--TGN 86

Query: 681 QWDKVEGGSNASLAELKGLSKLTTL 705
               +  G+        GLS L  L
Sbjct: 87  PIQSLALGA------FSGLSSLQKL 105

>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 = 62.3 bits (151), Expect = 3e-10
 Identities = 21/157 (13%), Positives = 53/157 (33%), Gaps = 15/157 (9%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
           ++     +   ++++L+   ++   + + +      +Q L +    +  +   +   +  
Sbjct: 65  KLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPL 124

Query: 622 LEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD--- 677
           L +L L   ++  LP  I     +L  L +SN  +L  I  +     + L+ L +     
Sbjct: 125 LTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNN-NLERIEDDTFQATTSLQNLQLSSNRL 183

Query: 678 ------SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
                             N  L+ L     +  L+  
Sbjct: 184 THVDLSLIPSLFHANVSYN-LLSTLAIPIAVEELDAS 219

>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 = 62.3 bits (151), Expect = 4e-10
 Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 8/115 (6%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLKKL 622
            +          L +L       +     L     L  + L    LE I      ++++L
Sbjct: 225 VVRGPVNVE---LTILKLQHNNLTDTAW-LLNYPGLVEVDLSYNELEKIMYHPFVKMQRL 280

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           E L +    +  L L    +  L++LDLS+   L V       +  RLE LY+  
Sbjct: 281 ERLYISNNRLVALNLYGQPIPTLKVLDLSHNHLLHV--ERNQPQFDRLENLYLDH 333

>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 = 46.5 bits (110), Expect = 3e-05
 Identities = 15/91 (16%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L   +I++ + + +++LP  +     +++LL+L++   +  I     +    +++LYM  
Sbjct: 50  LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQ-IEEIDTYAFAYAHTIQKLYM-- 106

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
            F+    +           + +  LT L ++
Sbjct: 107 GFNAIRYLPPHV------FQNVPLLTVLVLE 131

>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 = 62.0 bits (151), Expect = 3e-10
 Identities = 32/148 (21%), Positives = 57/148 (38%), Gaps = 13/148 (8%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIAIV--GQLKK 621
            + D+ F+    LK L+        +   +   L +L+ L L+   L  I       L  
Sbjct: 118 ILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHG 177

Query: 622 LEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
           L +L LR   I  +      +L RL++L++S+   L  + PN +  L+ L  L +     
Sbjct: 178 LIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLN-LTSLSITH--C 234

Query: 681 QWDKVEGGSNASLAELKGLSKLTTLEID 708
               V   +      ++ L  L  L + 
Sbjct: 235 NLTAVPYLA------VRHLVYLRFLNLS 256

>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 = 61.7 bits (150), Expect = 4e-10
 Identities = 38/153 (24%), Positives = 62/153 (40%), Gaps = 11/153 (7%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
            I          L VL    +  + +   S  RL  L+ L +  W   D           
Sbjct: 166 SIPTEALSHLHGLIVLRLRHLNINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLN 225

Query: 622 LEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
           L  LS+    +  +P L +  L  L+ L+LS  + +  I  +++ +L RL+E+ +     
Sbjct: 226 LTSLSITHCNLTAVPYLAVRHLVYLRFLNLSY-NPISTIEGSMLHELLRLQEIQL--VGG 282

Query: 681 QWDKVEGGSNASLAELKGLS----KLTTLEIDV 709
           Q   VE  +   L  L+ L+    +LTTLE  V
Sbjct: 283 QLAVVEPYAFRGLNYLRVLNVSGNQLTTLEESV 315

>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 = 59.7 bits (145), Expect = 1e-09
 Identities = 30/149 (20%), Positives = 52/149 (34%), Gaps = 15/149 (10%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
            +    F     L+ L     R   +P      L NL  L +   ++  +   +   L  
Sbjct: 70  AVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYN 129

Query: 622 LEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SF 679
           L+ L +   ++  +  +    L  L+ L L  C +L  I    +S L  L  L +   + 
Sbjct: 130 LKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKC-NLTSIPTEALSHLHGLIVLRLRHLNI 188

Query: 680 SQWDKVEGGSNASLAELKGLSKLTTLEID 708
           +    +   S       K L +L  LEI 
Sbjct: 189 N---AIRDYS------FKRLYRLKVLEIS 208

>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 = 57.0 bits (138), Expect = 1e-08
 Identities = 32/141 (22%), Positives = 55/141 (39%), Gaps = 21/141 (14%)

Query: 576 ELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKKLEILSLRGAEI 632
           E ++LD    R   L         +L+ L L+   +  +       L  L  L LR   +
Sbjct: 33  ETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRL 92

Query: 633 KQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN- 690
           K +PL +   L+ L  LD+S    +V++   +   L  L+ L +GD            N 
Sbjct: 93  KLIPLGVFTGLSNLTKLDISENK-IVILLDYMFQDLYNLKSLEVGD------------ND 139

Query: 691 -ASLAE--LKGLSKLTTLEID 708
              ++     GL+ L  L ++
Sbjct: 140 LVYISHRAFSGLNSLEQLTLE 160

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 47.8 bits (114), Expect = 8e-06
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI---AIVGQLK 620
            +          L+ L+ +    S +    L  L+ LQ + L G +L  +   A  G L 
Sbjct: 238 AVPYLAVRHLVYLRFLNLSYNPISTIEGSMLHELLRLQEIQLVGGQLAVVEPYAFRG-LN 296

Query: 621 KLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSN 652
            L +L++ G ++  L   +   +  L+ L L +
Sbjct: 297 YLRVLNVSGNQLTTLEESVFHSVGNLETLILDS 329

>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 = 62.0 bits (150), Expect = 4e-10
 Identities = 36/178 (20%), Positives = 74/178 (41%), Gaps = 24/178 (13%)

Query: 530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFS 588
           I  +L  + + +   + E   +   +      +   I      +    +  L   G + +
Sbjct: 24  IKDNLKKKSVTDAVTQNELNSIDQIIA-----NNSDIKSVQGIQYLPNVTKLFLNGNKLT 78

Query: 589 PLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL 648
            +   L  L NL  L LD  +++D++ +  LKKL+ LSL    I  +   +  L +L+ L
Sbjct: 79  DI-KPLTNLKNLGWLFLDENKIKDLSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESL 136

Query: 649 DLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE 706
            L N   +  I    +S+L++L+ L +              +  ++++  L+ LT L+
Sbjct: 137 YLGNN-KITDITV--LSRLTKLDTLSL-------------EDNQISDIVPLAGLTKLQ 178

>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 = 58.2 bits (140), Expect = 7e-09
 Identities = 23/117 (19%), Positives = 45/117 (38%), Gaps = 14/117 (11%)

Query: 592 SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLS 651
                        L    + D     +L  ++ +    ++IK +   I  L  +  L L+
Sbjct: 15  FPDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLN 73

Query: 652 NCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
               L  I P  ++ L  L  L++ ++     K++      L+ LK L KL +L ++
Sbjct: 74  GN-KLTDIKP--LTNLKNLGWLFLDEN-----KIK-----DLSSLKDLKKLKSLSLE 117

>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 = 54.0 bits (129), Expect = 1e-07
 Identities = 30/112 (26%), Positives = 54/112 (48%), Gaps = 6/112 (5%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           +I D    +  ++LK L       S + + L  L  L++L L   ++ DI ++ +L KL+
Sbjct: 98  KIKDLSSLKDLKKLKSLSLEHNGISDI-NGLVHLPQLESLYLGNNKITDITVLSRLTKLD 156

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
            LSL   +I  +   +  LT+LQ L LS    +  +    ++ L  L+ L +
Sbjct: 157 TLSLEDNQISDIV-PLAGLTKLQNLYLSKN-HISDLRA--LAGLKNLDVLEL 204

>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 = 42.0 bits (98), Expect = 6e-04
 Identities = 13/107 (12%), Positives = 34/107 (31%), Gaps = 17/107 (15%)

Query: 600 LQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVI 659
           +         ++ I       +    +L+   +     Q  +L  +  +  +N   +  +
Sbjct: 1   MGETITVSTPIKQIFPDDAFAETIKDNLKKKSVTDAVTQ-NELNSIDQIIANNS-DIKSV 58

Query: 660 APNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE 706
               I  L  + +L++             +   L ++K L+ L  L 
Sbjct: 59  QG--IQYLPNVTKLFL-------------NGNKLTDIKPLTNLKNLG 90

>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 = 60.5 bits (147), Expect = 4e-10
 Identities = 36/178 (20%), Positives = 73/178 (41%), Gaps = 24/178 (13%)

Query: 530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFS 588
           I  +L  + + +   + E   +   +          I      +    +  L   G + +
Sbjct: 27  IKDNLKKKSVTDAVTQNELNSIDQIIANNS-----DIKSVQGIQYLPNVTKLFLNGNKLT 81

Query: 589 PLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL 648
            +   L  L NL  L LD  +++D++ +  LKKL+ LSL    I  +   +  L +L+ L
Sbjct: 82  DI-KPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESL 139

Query: 649 DLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE 706
            L N   +  I    +S+L++L+ L +              +  ++++  L+ LT L+
Sbjct: 140 YLGNN-KITDITV--LSRLTKLDTLSL-------------EDNQISDIVPLAGLTKLQ 181

>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 = 57.0 bits (138), Expect = 6e-09
 Identities = 34/147 (23%), Positives = 59/147 (40%), Gaps = 20/147 (13%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            ++D         +  +         +   +  L N+  L L+G +L DI  +  LK L 
Sbjct: 35  SVTDAVTQNELNSIDQIIANNSDIKSV-QGIQYLPNVTKLFLNGNKLTDIKPLANLKNLG 93

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
            L L   ++K L   +  L +L+ L L +   +  I    +  L +LE LY+G+      
Sbjct: 94  WLFLDENKVKDLS-SLKDLKKLKSLSLEHNG-ISDING--LVHLPQLESLYLGN------ 143

Query: 684 KVEGGSN--ASLAELKGLSKLTTLEID 708
                 N    +  L  L+KL TL ++
Sbjct: 144 ------NKITDITVLSRLTKLDTLSLE 164

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A Length = 291

 Score = 55.8 bits (135), Expect = 1e-08
 Identities = 24/119 (20%), Positives = 43/119 (36%), Gaps = 18/119 (15%)

Query: 592 SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLS 651
            S           L    + D     +L  ++ +    ++IK +   I  L  +  L L+
Sbjct: 18  FSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLN 76

Query: 652 NCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
               L  I P  ++ L  L  L++ +            N    L+ LK L KL +L ++
Sbjct: 77  GN-KLTDIKP--LANLKNLGWLFLDE------------NKVKDLSSLKDLKKLKSLSLE 120

>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 = 47.7 bits (114), Expect = 6e-06
 Identities = 29/114 (25%), Positives = 47/114 (41%), Gaps = 4/114 (3%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            ISD +      +L+ L     + + + + L RL  L TL L+  ++ DI  +  L KL+
Sbjct: 123 GISDINGLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQ 181

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L L    I  L   +  L  L +L+L +    +    N  S L     +   D
Sbjct: 182 NLYLSKNHISDLR-ALAGLKNLDVLELFSQ-ECLNKPINHQSNLVVPNTVKNTD 233

>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 = 61.7 bits (149), Expect = 4e-10
 Identities = 35/182 (19%), Positives = 66/182 (36%), Gaps = 22/182 (12%)

Query: 536 YRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-- 593
            +++QEL    +   L + LL    D  L       +    LK +D     +     S  
Sbjct: 371 CKELQELEPENKWCLLTIILLMRALD-PLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKF 429

Query: 594 -------LGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQ 646
                       +++ L L    L  +  + QL  +  L L    ++ LP  +  L  L+
Sbjct: 430 LLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLE 489

Query: 647 LLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNASLAELKGLSKLTTL 705
           +L  S+  +L  +    ++ L RL+EL + +    Q   ++         L    +L  L
Sbjct: 490 VLQASDN-ALENVDG--VANLPRLQELLLCNNRLQQSAAIQ--------PLVSCPRLVLL 538

Query: 706 EI 707
            +
Sbjct: 539 NL 540

>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 = 61.7 bits (149), Expect = 5e-10
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 4/101 (3%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           +  LD +  R   LP +L  L  L+ L      LE++  V  L +L+ L L    ++Q  
Sbjct: 465 VTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSA 524

Query: 637 --LQIGQLTRLQLLDLSN--CSSLVVIAPNVISKLSRLEEL 673
               +    RL LL+L          I   +   L  +  +
Sbjct: 525 AIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSI 565

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A Length = 290

 Score = 60.1 bits (146), Expect = 5e-10
 Identities = 33/134 (24%), Positives = 52/134 (38%), Gaps = 8/134 (5%)

Query: 577 LKVLDFTGIRFSPLPSS-LGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQL 635
             +L  +         + L     L  L LD   L  + + G L  L  L L   +++ L
Sbjct: 33  TTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVDGTLPVLGTLDLSHNQLQSL 92

Query: 636 PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAE 695
           PL    L  L +LD+S    L  +    +  L  L+ELY+    ++   +  G      +
Sbjct: 93  PLLGQTLPALTVLDVSFN-RLTSLPLGALRGLGELQELYLKG--NELKTLPPGLLTPTPK 149

Query: 696 LKGLS----KLTTL 705
           L+ LS     LT L
Sbjct: 150 LEKLSLANNNLTEL 163

>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 = 54.7 bits (132), Expect = 3e-08
 Identities = 27/108 (25%), Positives = 48/108 (44%), Gaps = 4/108 (3%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLKKLEILSLR 628
                 L  LD +  +   LP     L  L  L +   RL  +    +  L +L+ L L+
Sbjct: 73  DGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLK 132

Query: 629 GAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
           G E+K LP  +     +L+ L L+N ++L  +   +++ L  L+ L +
Sbjct: 133 GNELKTLPPGLLTPTPKLEKLSLAN-NNLTELPAGLLNGLENLDTLLL 179

>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 = 60.5 bits (147), Expect = 5e-10
 Identities = 33/176 (18%), Positives = 69/176 (39%), Gaps = 24/176 (13%)

Query: 532 ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSPL 590
           +S     +  +        L    L        QI+D    +   ++  L+ +G     +
Sbjct: 46  LSAFGTGVTTIEGVQYLNNLIGLEL-----KDNQITDLAPLKNLTKITELELSGNPLKNV 100

Query: 591 PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDL 650
            S++  L +++TL L   ++ D+  +  L  L++L L   +I  +   +  LT LQ L +
Sbjct: 101 -SAIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLYLDLNQITNIS-PLAGLTNLQYLSI 158

Query: 651 SNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE 706
            N   +  + P  ++ LS+L  L                +  ++++  L+ L  L 
Sbjct: 159 GNA-QVSDLTP--LANLSKLTTLKA-------------DDNKISDISPLASLPNLI 198

>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 = 58.2 bits (141), Expect = 3e-09
 Identities = 31/157 (19%), Positives = 55/157 (35%), Gaps = 18/157 (11%)

Query: 565 QISDHF-FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            I+  F          +       +    +   L  + TL   G  +  I  V  L  L 
Sbjct: 8   AINVIFPDPALANAIKIAAGKSNVTDT-VTQADLDGITTLSAFGTGVTTIEGVQYLNNLI 66

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD-SFSQW 682
            L L+  +I  L   +  LT++  L+LS    L  ++   I+ L  ++ L +     +  
Sbjct: 67  GLELKDNQITDLA-PLKNLTKITELELSGN-PLKNVSA--IAGLQSIKTLDLTSTQITDV 122

Query: 683 DKVEG---------GSNA--SLAELKGLSKLTTLEID 708
             + G           N   +++ L GL+ L  L I 
Sbjct: 123 TPLAGLSNLQVLYLDLNQITNISPLAGLTNLQYLSIG 159

>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 = 53.9 bits (130), Expect = 6e-08
 Identities = 27/114 (23%), Positives = 49/114 (42%), Gaps = 6/114 (5%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           QI+D     G   L+VL     + + + S L  L NLQ L +   ++ D+  +  L KL 
Sbjct: 118 QITDVTPLAGLSNLQVLYLDLNQITNI-SPLAGLTNLQYLSIGNAQVSDLTPLANLSKLT 176

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            L     +I  +   +  L  L  + L N   +  ++P  ++  S L  + + +
Sbjct: 177 TLKADDNKISDIS-PLASLPNLIEVHLKNN-QISDVSP--LANTSNLFIVTLTN 226

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 Length = 308

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 4/102 (3%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           Q+SD        +L  L     + S + S L  L NL  + L   ++ D++ +     L 
Sbjct: 162 QVSDLTPLANLSKLTTLKADDNKISDI-SPLASLPNLIEVHLKNNQISDVSPLANTSNLF 220

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVIS 665
           I++L    I   P  +     L + ++    S   IAP  IS
Sbjct: 221 IVTLTNQTITNQP--VFYNNNLVVPNVVKGPSGAPIAPATIS 260

>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 = 58.1 bits (141), Expect = 5e-09
 Identities = 38/193 (19%), Positives = 64/193 (33%), Gaps = 43/193 (22%)

Query: 534 LPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD--HFFEGTEELKVLDFTGIRFSPLP 591
           L    +  LPE    P L+  +      S   +++     +  + L V +      S LP
Sbjct: 78  LNNLGLSSLPE--LPPHLESLVA-----SCNSLTELPELPQSLKSLLVDNNNLKALSDLP 130

Query: 592 SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD-- 649
                   L+ L +   +LE +  +     L+I+ +    +K+LP     L  +   +  
Sbjct: 131 P------LLEYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQ 184

Query: 650 ------LSNCSSLVVIA------PNVISKLSRLEELYMGDSFSQWDKVEGGSN--ASLAE 695
                 L N   L  I         +      LE +  G+            N    L E
Sbjct: 185 LEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGN------------NILEELPE 232

Query: 696 LKGLSKLTTLEID 708
           L+ L  LTT+  D
Sbjct: 233 LQNLPFLTTIYAD 245

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 55.8 bits (135), Expect = 2e-08
 Identities = 23/137 (16%), Positives = 46/137 (33%), Gaps = 16/137 (11%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRL 597
           +++LP+    P L+            Q+ +    +    L  +         LP      
Sbjct: 165 LKKLPDLP--PSLEFIAA-----GNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPL-- 215

Query: 598 INLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLV 657
            +L+++      LE++  +  L  L  +      +K LP     L  L + D    + L 
Sbjct: 216 -SLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYL-TDL- 272

Query: 658 VIAPNVISKLSRLEELY 674
              P +   L+ L+   
Sbjct: 273 ---PELPQSLTFLDVSE 286

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 46.9 bits (112), Expect = 2e-05
 Identities = 22/138 (15%), Positives = 49/138 (35%), Gaps = 22/138 (15%)

Query: 533 SLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS 592
              +  + ELP  L    L          S+ +I     +    L+ L+ +  +   LP+
Sbjct: 286 ENIFSGLSELPPNLY--YLNA--------SSNEIR-SLCDLPPSLEELNVSNNKLIELPA 334

Query: 593 SLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN 652
                  L+ L      L ++      + L+ L +    +++ P     +  L++   S+
Sbjct: 335 LPP---RLERLIASFNHLAEVP--ELPQNLKQLHVEYNPLREFPDIPESVEDLRM--NSH 387

Query: 653 CSSLVVIAPNVISKLSRL 670
            + +    P +   L +L
Sbjct: 388 LAEV----PELPQNLKQL 401

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 46.1 bits (110), Expect = 3e-05
 Identities = 28/132 (21%), Positives = 48/132 (36%), Gaps = 18/132 (13%)

Query: 539 IQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLI 598
           ++ LP+    P L+   +         ++D   E  + L  LD +   FS L        
Sbjct: 249 LKTLPD--LPPSLEALNV-----RDNYLTD-LPELPQSLTFLDVSENIFSGLSELPP--- 297

Query: 599 NLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV 658
           NL  L      +  +        LE L++   ++ +LP    +L R   L  S    L  
Sbjct: 298 NLYYLNASSNEIRSL--CDLPPSLEELNVSNNKLIELPALPPRLER---LIASFN-HLAE 351

Query: 659 IAPNVISKLSRL 670
           + P +   L +L
Sbjct: 352 V-PELPQNLKQL 362

>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 = 45.0 bits (107), Expect = 6e-05
 Identities = 12/98 (12%), Positives = 28/98 (28%), Gaps = 10/98 (10%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           LK L          P     + +L+        L ++      + L+ L +    +++ P
Sbjct: 359 LKQLHVEYNPLREFPDIPESVEDLRMNS----HLAEVP--ELPQNLKQLHVETNPLREFP 412

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
                +  L++                     +LE+  
Sbjct: 413 DIPESVEDLRMNSERVVD----PYEFAHETTDKLEDDV 446

>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 = 43.8 bits (104), Expect = 2e-04
 Identities = 26/161 (16%), Positives = 43/161 (26%), Gaps = 41/161 (25%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQL---------------KK 621
           L+         + +P     + +           E  A  G                 ++
Sbjct: 13  LQEPLRHSSNLTEMPVEAENVKSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQ 72

Query: 622 LEILSLRGAEIKQLPLQIGQLTRLQLLD---------LSNCSSLVV--IAPNVISKL-SR 669
              L L    +  LP     L  L               +  SL+V       +S L   
Sbjct: 73  AHELELNNLGLSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPL 132

Query: 670 LEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
           LE L + +            N    L EL+  S L  +++D
Sbjct: 133 LEYLGVSN------------NQLEKLPELQNSSFLKIIDVD 161

>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 = 43.8 bits (104), Expect = 2e-04
 Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 10/97 (10%)

Query: 575 EELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQ 634
             L  L+ +      L        +L+ L +   +L ++       +LE L      + +
Sbjct: 297 PNLYYLNASSNEIRSLCDLPP---SLEELNVSNNKLIELP--ALPPRLERLIASFNHLAE 351

Query: 635 LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE 671
           +P     L +   L +     L    P++   +  L 
Sbjct: 352 VPELPQNLKQ---LHVEYN-PLREF-PDIPESVEDLR 383

>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 = 57.3 bits (139), Expect = 6e-09
 Identities = 25/150 (16%), Positives = 55/150 (36%), Gaps = 9/150 (6%)

Query: 562 STLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQL 619
            +  I +  F+G ++L  +       + +P  L    +L  L LDG ++  +  A +  L
Sbjct: 158 KSSGIENGAFQGMKKLSYIRIADTNITTIPQGL--PPSLTELHLDGNKITKVDAASLKGL 215

Query: 620 KKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS 678
             L  L L    I  +          L+ L L+N   LV + P  ++    ++ +Y+ + 
Sbjct: 216 NNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNN-KLVKV-PGGLADHKYIQVVYLHN- 272

Query: 679 FSQWDKVEGGSNASLAELKGLSKLTTLEID 708
            +    +              +  + + + 
Sbjct: 273 -NNISAIGSNDFCPPGYNTKKASYSGVSLF 301

>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 = 54.6 bits (132), Expect = 5e-08
 Identities = 32/161 (19%), Positives = 62/161 (38%), Gaps = 21/161 (13%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEI 624
           I D  F+  + L  L     + S + P +   L+ L+ L L   +L+++      K L+ 
Sbjct: 67  IKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELP-EKMPKTLQE 125

Query: 625 LSLRGAEIKQLPLQI-GQLTRLQLLDLS-NCSSLVVIAPNVISKLSRLEELYMGDSFSQW 682
           L +   EI ++   +   L ++ +++L  N      I       + +L  + +  + +  
Sbjct: 126 LRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRI--ADTNI 183

Query: 683 DKVEGGSNASLAEL---------------KGLSKLTTLEID 708
             +  G   SL EL               KGL+ L  L + 
Sbjct: 184 TTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLS 224

>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 = 50.4 bits (121), Expect = 9e-07
 Identities = 24/148 (16%), Positives = 49/148 (33%), Gaps = 15/148 (10%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLKKL 622
            I         EL  LD   I      +SL  L NL  L L    +  +    +     L
Sbjct: 185 TIPQGLPPSLTEL-HLDGNKITKVD-AASLKGLNNLAKLGLSFNSISAVDNGSLANTPHL 242

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSN-----CSSLVVIAPNVISKLSRLEELYMGD 677
             L L   ++ ++P  +     +Q++ L N       S     P   +K +    + +  
Sbjct: 243 RELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFS 302

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTL 705
           +  Q+ +++  +       + +     +
Sbjct: 303 NPVQYWEIQPST------FRCVYVRAAV 324

>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 = 43.5 bits (103), Expect = 1e-04
 Identities = 13/98 (13%), Positives = 28/98 (28%), Gaps = 11/98 (11%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--------AIVG 617
           + +     T  L+ L     +   +P  L     +Q + L    +  I            
Sbjct: 231 VDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNT 290

Query: 618 QLKKLEILSLRGAEIKQLPLQIG---QLTRLQLLDLSN 652
           +      +SL    ++   +Q      +     + L N
Sbjct: 291 KKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQLGN 328

>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 = 56.2 bits (136), Expect = 1e-08
 Identities = 34/151 (22%), Positives = 47/151 (31%), Gaps = 21/151 (13%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKKL 622
           +    F G   L  L         L       L  LQ L L    L+ +       L  L
Sbjct: 96  VDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNL 155

Query: 623 EILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ 681
             L L G  I  +P +    L  L  L L     +  + P+    L RL  LY+      
Sbjct: 156 THLFLHGNRISSVPERAFRGLHSLDRLLLHQNR-VAHVHPHAFRDLGRLMTLYL------ 208

Query: 682 WDKVEGGSNA--SLAE--LKGLSKLTTLEID 708
                  +N   +L    L  L  L  L ++
Sbjct: 209 ------FANNLSALPTEALAPLRALQYLRLN 233

>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 = 56.2 bits (136), Expect = 1e-08
 Identities = 27/149 (18%), Positives = 52/149 (34%), Gaps = 14/149 (9%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDG-WRLEDIA--IVGQLK 620
            +    F     L +L       + + + +   L  L+ L L    +L  +       L 
Sbjct: 46  HVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLG 105

Query: 621 KLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
           +L  L L    +++L   +   L  LQ L L + + L  +  +    L  L  L++    
Sbjct: 106 RLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNA-LQALPDDTFRDLGNLTHLFL--HG 162

Query: 680 SQWDKVEGGSNASLAELKGLSKLTTLEID 708
           ++   V   +       +GL  L  L + 
Sbjct: 163 NRISSVPERA------FRGLHSLDRLLLH 185

>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 = 44.6 bits (106), Expect = 6e-05
 Identities = 27/126 (21%), Positives = 47/126 (37%), Gaps = 13/126 (10%)

Query: 586 RFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQI-GQL 642
               +P  +      Q + L G R+  +  A     + L IL L    + ++       L
Sbjct: 22  GLQAVPVGI--PAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGL 79

Query: 643 TRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKL 702
             L+ LDLS+ + L  + P     L RL  L++        ++  G        +GL+ L
Sbjct: 80  ALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL--DRCGLQELGPGL------FRGLAAL 131

Query: 703 TTLEID 708
             L + 
Sbjct: 132 QYLYLQ 137

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 55.8 bits (135), Expect = 1e-08
 Identities = 27/126 (21%), Positives = 51/126 (40%), Gaps = 16/126 (12%)

Query: 592 SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLS 651
                L N     L    + D+    +L  ++  +   + I+ L   +   T L+ L LS
Sbjct: 13  FPDPGLANAVKQNLGKQSVTDLVSQKELSGVQNFNGDNSNIQSLA-GMQFFTNLKELHLS 71

Query: 652 NCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL----------KGLSK 701
           +   +  ++P  +  L++LEEL +  + ++   + G  +A L+ L            L  
Sbjct: 72  HN-QISDLSP--LKDLTKLEELSV--NRNRLKNLNGIPSACLSRLFLDNNELRDTDSLIH 126

Query: 702 LTTLEI 707
           L  LEI
Sbjct: 127 LKNLEI 132

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 53.5 bits (129), Expect = 6e-08
 Identities = 30/167 (17%), Positives = 59/167 (35%), Gaps = 39/167 (23%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
            ++D    +    ++  +        L + +    NL+ L L   ++ D++ +  L KLE
Sbjct: 30  SVTDLVSQKELSGVQNFNGDNSNIQSL-AGMQFFTNLKELHLSHNQISDLSPLKDLTKLE 88

Query: 624 ILSLRGAEIKQL-PLQ-------------------IGQLTRLQLLDLSNCSSLVVIAPNV 663
            LS+    +K L  +                    +  L  L++L + N   L  I    
Sbjct: 89  ELSVNRNRLKNLNGIPSACLSRLFLDNNELRDTDSLIHLKNLEILSIRNN-KLKSIVM-- 145

Query: 664 ISKLSRLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
           +  LS+LE L +              N   +   L  L K+  +++ 
Sbjct: 146 LGFLSKLEVLDLHG------------NEITNTGGLTRLKKVNWIDLT 180

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 21/111 (18%), Positives = 42/111 (37%), Gaps = 4/111 (3%)

Query: 565 QISD-HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLE 623
           ++ D       + L++L     +   +   LG L  L+ L L G  + +   + +LKK+ 
Sbjct: 117 ELRDTDSLIHLKNLEILSIRNNKLKSI-VMLGFLSKLEVLDLHGNEITNTGGLTRLKKVN 175

Query: 624 ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
            + L G +    P++      L + +         I+P  IS      +  
Sbjct: 176 WIDLTGQKCVNEPVKY--QPELYITNTVKDPDGRWISPYYISNGGSYVDGC 224

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 41.5 bits (98), Expect = 4e-04
 Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 18/102 (17%)

Query: 609 RLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLS 668
            +  +     L      +L    +  L     +L+ +Q  +  N  ++  +A   +   +
Sbjct: 8   PINQVFPDPGLANAVKQNLGKQSVTDLV-SQKELSGVQNFNGDNS-NIQSLAG--MQFFT 63

Query: 669 RLEELYMGDSFSQWDKVEGGSN--ASLAELKGLSKLTTLEID 708
            L+EL++              N  + L+ LK L+KL  L ++
Sbjct: 64  NLKELHL------------SHNQISDLSPLKDLTKLEELSVN 93

>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 = 56.7 bits (137), Expect = 1e-08
 Identities = 36/149 (24%), Positives = 58/149 (38%), Gaps = 13/149 (8%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKK 621
            IS+   +    L+ L  T    + +   S   L +L+ L L    L ++  +    L  
Sbjct: 66  YISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSS 125

Query: 622 LEILSLRGAEIKQLPLQI--GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF 679
           L  L+L G   K L        LT+LQ+L + N  +   I     + L+ LEEL +    
Sbjct: 126 LTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDA-- 183

Query: 680 SQWDKVEGGSNASLAELKGLSKLTTLEID 708
           S     E  S      LK +  ++ L + 
Sbjct: 184 SDLQSYEPKS------LKSIQNVSHLILH 206

>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 = 54.0 bits (130), Expect = 7e-08
 Identities = 13/123 (10%), Positives = 40/123 (32%), Gaps = 12/123 (9%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIAIV-------- 616
                 +  + +  L     +   L    +    +++ L L    L+             
Sbjct: 189 YEPKSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETN 248

Query: 617 --GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
              +      + +    + Q+   + Q++ L  L+ S    L  +   +  +L+ L++++
Sbjct: 249 SLIKKFTFRNVKITDESLFQVMKLLNQISGLLELEFSRN-QLKSVPDGIFDRLTSLQKIW 307

Query: 675 MGD 677
           +  
Sbjct: 308 LHT 310

>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 = 55.4 bits (134), Expect = 2e-08
 Identities = 30/108 (27%), Positives = 40/108 (37%), Gaps = 8/108 (7%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGA 630
           T+ L  L F  +R      S      LQ L L    ++ I   G    L  L  L L G 
Sbjct: 30  TKNLD-LSFNPLRHLG-SYSFFSFPELQVLDLSRCEIQTIE-DGAYQSLSHLSTLILTGN 86

Query: 631 EIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            I+ L L     L+ LQ L      +L  +    I  L  L+EL +  
Sbjct: 87  PIQSLALGAFSGLSSLQKLVAVET-NLASLENFPIGHLKTLKELNVAH 133

>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 = 56.0 bits (135), Expect = 4e-08
 Identities = 24/112 (21%), Positives = 40/112 (35%), Gaps = 12/112 (10%)

Query: 577 LKVLDFTGIRFSPLP--SSLGRLINLQTLCLDG---WRLEDIAIVGQLKKLEILSLRGAE 631
             ++  +  R   L     L R+ +LQ L L+              +   LE L L    
Sbjct: 403 ANLIHLSENRLENLDILYFLLRVPHLQILILNQNRFSSCSGDQTPSENPSLEQLFLGENM 462

Query: 632 IKQLPLQ------IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           ++              L+ LQ+L L++   L  + P V S L+ L  L +  
Sbjct: 463 LQLAWETELCWDVFEGLSHLQVLYLNHN-YLNSLPPGVFSHLTALRGLSLNS 513

>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 = 56.0 bits (135), Expect = 4e-08
 Identities = 23/119 (19%), Positives = 41/119 (34%), Gaps = 7/119 (5%)

Query: 565 QISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLK 620
            ++   F   E+L++L+        +    +   L NL+ L L   ++  +       L 
Sbjct: 38  TVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLF 97

Query: 621 KLEILSLRGAEIKQLPLQ---IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
            L  L L    +    L+      L  L  LDLS      +       KL+ L+ +   
Sbjct: 98  HLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFS 156

>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 = 55.2 bits (133), Expect = 6e-08
 Identities = 36/180 (20%), Positives = 65/180 (36%), Gaps = 15/180 (8%)

Query: 539 IQELPERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LG 595
           I+ +         QL+  L      + L I    F     L++LD    +   L      
Sbjct: 36  IRTVTASSFPFLEQLQ-LLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQ 94

Query: 596 RLINLQTLCLDGWRLEDIAIVGQ----LKKLEILSLRGAEIKQLPLQ--IGQLTRLQLLD 649
            L +L  L L    L D  +       LK L  L L   +I+ L L    G+L  L+ +D
Sbjct: 95  GLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSID 154

Query: 650 LSNCSSLVVIAPNVISKLS--RLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEI 707
            S+   + ++  + +  L    L    +  + S + +V       +   + +  L  L++
Sbjct: 155 FSSN-QIFLVCEHELEPLQGKTLSFFSL-AANSLYSRVSVDWGKCMNPFRNMV-LEILDV 211

>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 = 53.7 bits (129), Expect = 2e-07
 Identities = 27/145 (18%), Positives = 60/145 (41%), Gaps = 11/145 (7%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEIL 625
           I D  F+  E+L+ LD      +    ++  + ++  + L G +L  +  +       ++
Sbjct: 353 IQDQTFKFLEKLQTLDLRDNALT----TIHFIPSIPDIFLSGNKLVTLPKINL--TANLI 406

Query: 626 SLRGAEIKQLPLQ--IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD 683
            L    ++ L +   + ++  LQ+L L+             S+   LE+L++G++  Q  
Sbjct: 407 HLSENRLENLDILYFLLRVPHLQILILNQNRFSSCSGDQTPSENPSLEQLFLGENMLQL- 465

Query: 684 KVEGGSNASLAELKGLSKLTTLEID 708
                +       +GLS L  L ++
Sbjct: 466 --AWETELCWDVFEGLSHLQVLYLN 488

>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 = 49.0 bits (117), Expect = 5e-06
 Identities = 23/162 (14%), Positives = 55/162 (33%), Gaps = 15/162 (9%)

Query: 550 QLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSL---GRLINLQTLCLD 606
              + +     ++  +           +    F          +        +++ L L 
Sbjct: 215 GWTVDITGNFSNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAGLARSSVRHLDLS 274

Query: 607 GWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNV 663
              +  +   +   LK L++L+L   +I ++  +    L  LQ+L+LS    L  +  + 
Sbjct: 275 HGFVFSLNSRVFETLKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYN-LLGELYSSN 333

Query: 664 ISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTL 705
              L ++  + +    +    ++  +       K L KL TL
Sbjct: 334 FYGLPKVAYIDL--QKNHIAIIQDQT------FKFLEKLQTL 367

>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 = 46.7 bits (111), Expect = 2e-05
 Identities = 24/119 (20%), Positives = 43/119 (36%), Gaps = 13/119 (10%)

Query: 567 SDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG------- 617
             +F      L++L              +     +L+ L L    L+             
Sbjct: 418 ILYFLLRVPHLQILILNQNRFSSCSGDQTPSENPSLEQLFLGENMLQLAWETELCWDVFE 477

Query: 618 QLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM 675
            L  L++L L    +  LP  +   LT L+ L L++   L V++ N +   + LE L +
Sbjct: 478 GLSHLQVLYLNHNYLNSLPPGVFSHLTALRGLSLNSN-RLTVLSHNDL--PANLEILDI 533

>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 = 45.6 bits (108), Expect = 5e-05
 Identities = 27/147 (18%), Positives = 53/147 (36%), Gaps = 19/147 (12%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
           +I+D  F G + L+VL+ +      L S +   L  +  + L    +  I       L+K
Sbjct: 304 KIADEAFYGLDNLQVLNLSYNLLGELYSSNFYGLPKVAYIDLQKNHIAIIQDQTFKFLEK 363

Query: 622 LEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ 681
           L+ L LR   +  +      +  +  + LS              KL  L ++ +  +   
Sbjct: 364 LQTLDLRDNALTTIHF----IPSIPDIFLSGN------------KLVTLPKINLTANLIH 407

Query: 682 WDKVEGGSNASLAELKGLSKLTTLEID 708
             +    +   L  L  +  L  L ++
Sbjct: 408 LSENRLENLDILYFLLRVPHLQILILN 434

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 27/121 (22%), Positives = 44/121 (36%), Gaps = 5/121 (4%)

Query: 533 SLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP- 591
           S            LE  QL L     +     ++    FEG   L+VL       + LP 
Sbjct: 440 SCSGDQTPSENPSLE--QLFLGENMLQLAWETELCWDVFEGLSHLQVLYLNHNYLNSLPP 497

Query: 592 SSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLS 651
                L  L+ L L+  RL  ++       LEIL +   ++      +     L +LD++
Sbjct: 498 GVFSHLTALRGLSLNSNRLTVLSHNDLPANLEILDISRNQLLAPNPDV--FVSLSVLDIT 555

Query: 652 N 652
           +
Sbjct: 556 H 556

>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 = 4e-04
 Identities = 20/91 (21%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 619 LKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           L   E L L    I+ +       L +LQLL+L +  + + I       L  L  L +  
Sbjct: 23  LNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDL-- 80

Query: 678 SFSQWDKVEGGSNASLAELKGLSKLTTLEID 708
             S+   +   +       +GL  L  L + 
Sbjct: 81  GSSKIYFLHPDA------FQGLFHLFELRLY 105

>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 = 54.7 bits (132), Expect = 6e-08
 Identities = 24/158 (15%), Positives = 47/158 (29%), Gaps = 26/158 (16%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEI 624
           +++         L  L+      + +   +     L  L     +      V    +L  
Sbjct: 117 KLTKLDVSQNPLLTYLNCARNTLTEID--VSHNTQLTELDCHLNKKITKLDVTPQTQLTT 174

Query: 625 LSLRGAEIKQLPLQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRLEELYMGDSFSQW 682
           L     +I +L   + Q   L  L+      + L       +++  +L  L    S ++ 
Sbjct: 175 LDCSFNKITELD--VSQNKLLNRLNCDTNNITKL------DLNQNIQLTFLDC--SSNKL 224

Query: 683 DKVEGGSNASLAEL------------KGLSKLTTLEID 708
            +++      L                 LSKLTTL   
Sbjct: 225 TEIDVTPLTQLTYFDCSVNPLTELDVSTLSKLTTLHCI 262

>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 = 52.4 bits (126), Expect = 3e-07
 Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 11/119 (9%)

Query: 591 PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDL 650
             S  +L  L +L      + D+  + +L  L  L      I  L L   Q T L  L  
Sbjct: 35  TISEEQLATLTSLDCHNSSITDMTGIEKLTGLTKLICTSNNITTLDL--SQNTNLTYLAC 92

Query: 651 SNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLS--KLTTLEI 707
            +   L  +    ++ L++L  L      ++  K++   N  L  L   +   LT +++
Sbjct: 93  DSN-KLTNLD---VTPLTKLTYLNC--DTNKLTKLDVSQNPLLTYL-NCARNTLTEIDV 144

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 25/132 (18%), Positives = 43/132 (32%), Gaps = 25/132 (18%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L  L         +   L     L     +G R      V    +L +L  + A I +L 
Sbjct: 256 LTTLHCIQTDLLEID--LTHNTQLIYFQAEGCRKIKELDVTHNTQLYLLDCQAAGITELD 313

Query: 637 LQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLA 694
             + Q  +L  L L+N   + L       +S  ++L+ L                NA + 
Sbjct: 314 --LSQNPKLVYLYLNNTELTEL----D--VSHNTKLKSLSC-------------VNAHIQ 352

Query: 695 ELKGLSKLTTLE 706
           +   + K+  L 
Sbjct: 353 DFSSVGKIPALN 364

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 53.7 bits (130), Expect = 8e-08
 Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 5/81 (6%)

Query: 577 LKVLDFTGI-RFS-PLPSSLGRLINLQTLCLDGWRLE-DI-AIVGQLKKLEILSLRGAEI 632
           L  L   GI     P+P ++ +L  L  L +    +   I   + Q+K L  L      +
Sbjct: 78  LNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNAL 137

Query: 633 K-QLPLQIGQLTRLQLLDLSN 652
              LP  I  L  L  +    
Sbjct: 138 SGTLPPSISSLPNLVGITFDG 158

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 52.5 bits (127), Expect = 2e-07
 Identities = 28/134 (20%), Positives = 52/134 (38%), Gaps = 30/134 (22%)

Query: 582 FTGIRFSPLPSSLGRLINLQTLCLDGWRLE-DIAI---VGQLKKLEILSLRGAEIKQL-- 635
           + G+    L  +  +   +  L L G  L     I   +  L  L  L + G  I  L  
Sbjct: 38  WLGV----LCDTDTQTYRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGG--INNLVG 91

Query: 636 --PLQIGQLTRLQLLDLSNCS---SLVVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGS 689
             P  I +LT+L  L +++ +   ++    P+ +S++  L  L     + S       G+
Sbjct: 92  PIPPAIAKLTQLHYLYITHTNVSGAI----PDFLSQIKTLVTLDFSYNALS-------GT 140

Query: 690 -NASLAELKGLSKL 702
              S++ L  L  +
Sbjct: 141 LPPSISSLPNLVGI 154

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 51.4 bits (124), Expect = 4e-07
 Identities = 23/79 (29%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 577 LKVLDFTGIRFS-PLPSSLGRLINLQTLCLDGWRLE-DIAIVGQLKKLEILSLRGAEIK- 633
           L  +D +            G   N Q + L    L  D+  VG  K L  L LR   I  
Sbjct: 199 LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYG 258

Query: 634 QLPLQIGQLTRLQLLDLSN 652
            LP  + QL  L  L++S 
Sbjct: 259 TLPQGLTQLKFLHSLNVSF 277

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 53.5 bits (129), Expect = 1e-07
 Identities = 29/163 (17%), Positives = 57/163 (34%), Gaps = 17/163 (10%)

Query: 551 LKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRL 610
           LKL  L         I     E   EL  LD   I+       L R   L  L L   ++
Sbjct: 172 LKLNYLRISEAKLTGIPKDLPETLNELH-LDHNKIQAIE-LEDLLRYSKLYRLGLGHNQI 229

Query: 611 EDIA--IVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVIS--- 665
             I    +  L  L  L L   ++ ++P  +  L  LQ++ L   +++  +  N      
Sbjct: 230 RMIENGSLSFLPTLRELHLDNNKLSRVPAGLPDLKLLQVVYLHT-NNITKVGVNDFCPVG 288

Query: 666 ---KLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTL 705
              K +    + + ++   + +V+  +       + ++    +
Sbjct: 289 FGVKRAYYNGISLFNNPVPYWEVQPAT------FRCVTDRLAI 325

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 47.7 bits (114), Expect = 8e-06
 Identities = 21/121 (17%), Positives = 40/121 (33%), Gaps = 10/121 (8%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI-AIVGQLKKLE 623
           I         +L  L     +   + + SL  L  L+ L LD  +L  + A +  LK L+
Sbjct: 208 IELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNKLSRVPAGLPDLKLLQ 267

Query: 624 ILSLRGAEIKQLP-------LQIGQLTRLQLLDLS-NCSSLVVIAPNVISKLSRLEELYM 675
           ++ L    I ++            +      + L  N      + P     ++    +  
Sbjct: 268 VVYLHTNNITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQF 327

Query: 676 G 676
           G
Sbjct: 328 G 328

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 45.8 bits (109), Expect = 3e-05
 Identities = 26/147 (17%), Positives = 54/147 (36%), Gaps = 18/147 (12%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIA--IVGQLKKLE 623
           I +  F    +L+ L  +      +P +L    +L  L +   R+  +   +   L+ + 
Sbjct: 93  IHEKAFSPLRKLQKLYISKNHLVEIPPNL--PSSLVELRIHDNRIRKVPKGVFSGLRNMN 150

Query: 624 ILSLRGAEIKQLPLQIGQLT--RLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ 681
            + + G  ++    + G     +L  L +S    L  I  ++      L EL++    ++
Sbjct: 151 CIEMGGNPLENSGFEPGAFDGLKLNYLRISEA-KLTGIPKDL---PETLNELHLDH--NK 204

Query: 682 WDKVEGGSNASLAELKGLSKLTTLEID 708
              +E         L   SKL  L + 
Sbjct: 205 IQAIELED------LLRYSKLYRLGLG 225

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A Length = 198

 Score = 51.6 bits (124), Expect = 1e-07
 Identities = 32/139 (23%), Positives = 53/139 (38%), Gaps = 24/139 (17%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIK 633
             E   L         + ++L  L   + L L    +E I+ +  ++ L ILSL    IK
Sbjct: 24  EAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRILSLGRNLIK 83

Query: 634 QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLS------RLEELYMGDSF-SQWDKVE 686
           ++         L+ L +S          N I+ LS       L  LYM ++  + W +++
Sbjct: 84  KIENLDAVADTLEELWISY---------NQIASLSGIEKLVNLRVLYMSNNKITNWGEID 134

Query: 687 GGSNASLAELKGLSKLTTL 705
                   +L  L KL  L
Sbjct: 135 --------KLAALDKLEDL 145

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 53.7 bits (129), Expect = 1e-07
 Identities = 20/95 (21%), Positives = 35/95 (36%), Gaps = 9/95 (9%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
             VL+      + LP  L    ++ TL +    L  +       +L  L + G ++  LP
Sbjct: 42  NAVLNVGESGLTTLPDCLPA--HITTLVIPDNNLTSLP--ALPPELRTLEVSGNQLTSLP 97

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE 671
           +    L  L +      + L    P + S L +L 
Sbjct: 98  VLPPGLLELSIFSNPL-THL----PALPSGLCKLW 127

>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 = 51.4 bits (123), Expect = 9e-07
 Identities = 24/148 (16%), Positives = 45/148 (30%), Gaps = 7/148 (4%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           LK L  +G R + LP        L+ L + G RL  +        L  LS+   ++ +LP
Sbjct: 223 LKELIVSGNRLTSLPVLPS---ELKELMVSGNRLTSLP--MLPSGLLSLSVYRNQLTRLP 277

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEG-GSNASLAE 695
             +  L+    ++L     L       + +++                        +L  
Sbjct: 278 ESLIHLSSETTVNLEGN-PLSERTLQALREITSAPGYSGPIIRFDMAGASAPRETRALHL 336

Query: 696 LKGLSKLTTLEIDVRDAEMLRRIWSLGN 723
                 +   E +   A+         N
Sbjct: 337 AAADWLVPAREGEPAPADRWHMFGQEDN 364

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 48.7 bits (116), Expect = 5e-06
 Identities = 34/160 (21%), Positives = 59/160 (36%), Gaps = 34/160 (21%)

Query: 533 SLPYRDIQELPERLECPQLK-LFLLFAKYDSTLQISD--HFFEGTEELKVLDFTGIRFSP 589
            +P  ++  LP     P+L+ L +      S  Q++       G  EL +          
Sbjct: 67  VIPDNNLTSLPALP--PELRTLEV------SGNQLTSLPVLPPGLLELSIFSNPLTHLPA 118

Query: 590 LPSSLGRLI--------------NLQTLCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQ 634
           LPS L +L                LQ L +   +L  + A+  +L KL   + +   +  
Sbjct: 119 LPSGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQLASLPALPSELCKLWAYNNQ---LTS 175

Query: 635 LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
           LP+    L     L +S+   L  + P + S+L +L    
Sbjct: 176 LPMLPSGLQE---LSVSDN-QLASL-PTLPSELYKLWAYN 210

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 48.0 bits (114), Expect = 9e-06
 Identities = 20/120 (16%), Positives = 37/120 (30%), Gaps = 28/120 (23%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L+ L  +  + + LP+    L  L        RL  +        L+ L + G  +  LP
Sbjct: 183 LQELSVSDNQLASLPTLPSELYKLWAYNN---RLTSLP--ALPSGLKELIVSGNRLTSLP 237

Query: 637 LQIGQLTRLQL-----------------LDLSNC--SSLVVIAPNVISKLSRLEELYMGD 677
           +   +L  L +                 L +     + L    P  +  LS    + +  
Sbjct: 238 VLPSELKELMVSGNRLTSLPMLPSGLLSLSVYRNQLTRL----PESLIHLSSETTVNLEG 293

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 25/114 (21%), Positives = 40/114 (35%), Gaps = 26/114 (22%)

Query: 575 EELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIVGQLKKLEI--------- 624
             L  L   G + + LP        LQ L +   +L  + A+  +L KL           
Sbjct: 121 SGLCKLWIFGNQLTSLPVLPP---GLQELSVSDNQLASLPALPSELCKLWAYNNQLTSLP 177

Query: 625 --------LSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL 670
                   LS+   ++  LP    +L +L   +    +SL    P + S L  L
Sbjct: 178 MLPSGLQELSVSDNQLASLPTLPSELYKLWAYNN-RLTSL----PALPSGLKEL 226

>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 = 42.6 bits (100), Expect = 5e-04
 Identities = 30/145 (20%), Positives = 46/145 (31%), Gaps = 13/145 (8%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L  L     + + LP SL  L +  T+ L+G  L +  +               EI   P
Sbjct: 263 LLSLSVYRNQLTRLPESLIHLSSETTVNLEGNPLSERTL-----------QALREITSAP 311

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
              G + R  +   S       +       L    E        +W       NA  A  
Sbjct: 312 GYSGPIIRFDMAGASAPRETRALHLAAADWLVPAREGEP-APADRWHMFGQEDNAD-AFS 369

Query: 697 KGLSKLTTLEIDVRDAEMLRRIWSL 721
             L +L+  E  ++DA    +I S 
Sbjct: 370 LFLDRLSETENFIKDAGFKAQISSW 394

>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 = 53.6 bits (129), Expect = 1e-07
 Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 6/107 (5%)

Query: 577 LKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGAEI 632
           +  +D +    + L   S  RL +LQ L ++      +        L  L IL L   + 
Sbjct: 32  VNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQF 91

Query: 633 KQLPLQI-GQLTRLQLLDLSNCS-SLVVIAPNVISKLSRLEELYMGD 677
            QL       L  L++L L+ C+    V++ N    L+ LE L + D
Sbjct: 92  LQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRD 138

>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 = 52.4 bits (126), Expect = 3e-07
 Identities = 27/122 (22%), Positives = 48/122 (39%), Gaps = 7/122 (5%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKKL 622
           +    F    +L+ L       + +   +   L +L  L L    L  I   +   L KL
Sbjct: 290 LLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKL 349

Query: 623 EILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ 681
           E+L L    I+ L  Q    L  L+ L L     L  +   +  +L+ L+++++    + 
Sbjct: 350 EVLDLSYNHIRALGDQSFLGLPNLKELALDTN-QLKSVPDGIFDRLTSLQKIWLHT--NP 406

Query: 682 WD 683
           WD
Sbjct: 407 WD 408

>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 = 46.7 bits (111), Expect = 2e-05
 Identities = 31/147 (21%), Positives = 51/147 (34%), Gaps = 10/147 (6%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTLCLDGWRLEDIAIVG----QLKKLEIL 625
           F G   L +L     +F  L +     L NL+ L L    L+   + G     L  LE+L
Sbjct: 75  FRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEML 134

Query: 626 SLRGAEIKQLPLQI--GQLTRLQLLDLSNCSSLVVIAPNVISKL--SRLEELYMGDSFSQ 681
            LR   IK++        + R  +LDL+  + +  I    +          L +     Q
Sbjct: 135 VLRDNNIKKIQPASFFLNMRRFHVLDLTF-NKVKSICEEDLLNFQGKHFTLLRLSSITLQ 193

Query: 682 WDKVEGGSNASLAELKGLSKLTTLEID 708
                             + +TTL++ 
Sbjct: 194 DMNEYWLGWEKCGNPFKNTSITTLDLS 220

>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 = 51.8 bits (124), Expect = 4e-07
 Identities = 28/147 (19%), Positives = 54/147 (36%), Gaps = 9/147 (6%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDG----WRLEDIAIVGQLK 620
           I+   F+    L+ L  +      LP       +    L +        +E  + VG   
Sbjct: 95  INPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSF 154

Query: 621 KLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
           +  IL L    I+++       T+L  L+LS+ ++L  +  +V    S    L +  S +
Sbjct: 155 ESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDI--SRT 212

Query: 681 QWDKVEGGSNASLAELK--GLSKLTTL 705
           +   +      +L +L+      L  L
Sbjct: 213 RIHSLPSYGLENLKKLRARSTYNLKKL 239

>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 = 42.1 bits (99), Expect = 4e-04
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 622 LEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS 680
              L     +++ +          L+ +++S    L VI  +V S L +L E+ +  + +
Sbjct: 32  AIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKA-N 90

Query: 681 QWDKVEGGSNASLAELKGLSKLTTLEID 708
               +   +       + L  L  L I 
Sbjct: 91  NLLYINPEA------FQNLPNLQYLLIS 112

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 51.4 bits (123), Expect = 6e-07
 Identities = 24/116 (20%), Positives = 44/116 (37%), Gaps = 8/116 (6%)

Query: 567 SDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKKLE 623
           ++        L  L  +    + + S +   + NL+ L L    L  +   +   L+ LE
Sbjct: 56  AEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALE 115

Query: 624 ILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVI---SKLSRLEELYM 675
           +L L    I  +       + +LQ L LS    +      +I   +KL +L  L +
Sbjct: 116 VLLLYNNHIVVVDRNAFEDMAQLQKLYLSQN-QISRFPVELIKDGNKLPKLMLLDL 170

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 48.7 bits (116), Expect = 3e-06
 Identities = 26/117 (22%), Positives = 46/117 (39%), Gaps = 8/117 (6%)

Query: 565 QISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDIA--IVGQLKK 621
            IS   F     L+ LD +      L       L  L+ L L    +  +       + +
Sbjct: 78  FISSEAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQ 137

Query: 622 LEILSLRGAEIKQLPLQI----GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
           L+ L L   +I + P+++     +L +L LLDLS+ + L  +    + KL    +  
Sbjct: 138 LQKLYLSQNQISRFPVELIKDGNKLPKLMLLDLSS-NKLKKLPLTDLQKLPAWVKNG 193

>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 = 51.4 bits (123), Expect = 8e-07
 Identities = 27/132 (20%), Positives = 43/132 (32%), Gaps = 6/132 (4%)

Query: 552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRL 610
            L +     D       + +E    + + +FT      +      ++     L      L
Sbjct: 277 ALSIHQVVSDVFGFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDFSNNLL 336

Query: 611 EDIA--IVGQLKKLEILSLRGAEIKQLPLQIG---QLTRLQLLDLSNCSSLVVIAPNVIS 665
            D      G L +LE L L+  ++K+L        Q+  LQ LD+S  S          S
Sbjct: 337 TDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCS 396

Query: 666 KLSRLEELYMGD 677
               L  L M  
Sbjct: 397 WTKSLLSLNMSS 408

>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 = 50.6 bits (121), Expect = 1e-06
 Identities = 21/118 (17%), Positives = 50/118 (42%), Gaps = 3/118 (2%)

Query: 562 STLQISDHFFEGTEELKVLDFTG--IRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQL 619
             L          + L+ LD +   + +           +L +L +    L D       
Sbjct: 361 KELSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIFRCLP 420

Query: 620 KKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            ++++L L   +IK +P Q+ +L  LQ L++++   L  +   +  +L+ L+++++  
Sbjct: 421 PRIKVLDLHSNKIKSIPKQVVKLEALQELNVASN-QLKSVPDGIFDRLTSLQKIWLHT 477

>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 = 44.5 bits (105), Expect = 9e-05
 Identities = 17/105 (16%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG---QLKKLEILSL 627
           F+  +EL+ LD +  +   +       +NL+ L L     + + I      + +L+ L L
Sbjct: 65  FKFNQELEYLDLSHNKLVKISC--HPTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGL 122

Query: 628 RGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE 671
               +++  +  I  L   ++L +   +      P  +   +   
Sbjct: 123 STTHLEKSSVLPIAHLNISKVLLVLGETYGEKEDPEGLQDFNTES 167

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens} Length = 220

 Score = 49.3 bits (118), Expect = 1e-06
 Identities = 18/108 (16%), Positives = 39/108 (36%), Gaps = 7/108 (6%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGA 630
           T EL+ L+              +L  L+ +     ++ DI   G       +  + L   
Sbjct: 34  TAELR-LNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIE-EGAFEGASGVNEILLTSN 91

Query: 631 EIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
            ++ +  ++   L  L+ L L +   +  +  +    LS +  L + D
Sbjct: 92  RLENVQHKMFKGLESLKTLMLRSN-RITCVGNDSFIGLSSVRLLSLYD 138

>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 = 48.9 bits (117), Expect = 1e-06
 Identities = 30/141 (21%), Positives = 58/141 (41%), Gaps = 20/141 (14%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGA 630
             E++ L+   I+  P P +      L+ + L   ++ ++A       L+ L  L L G 
Sbjct: 34  ITEIR-LEQNTIKVIP-PGAFSPYKKLRRIDLSNNQISELA-PDAFQGLRSLNSLVLYGN 90

Query: 631 EIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGS 689
           +I +LP  +   L  LQLL L+  + +  +  +    L  L  L + D+  Q        
Sbjct: 91  KITELPKSLFEGLFSLQLLLLNA-NKINCLRVDAFQDLHNLNLLSLYDNKLQ-------- 141

Query: 690 NASLAE--LKGLSKLTTLEID 708
             ++A+     L  + T+ + 
Sbjct: 142 --TIAKGTFSPLRAIQTMHLA 160

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 49.6 bits (118), Expect = 3e-06
 Identities = 19/111 (17%), Positives = 37/111 (33%), Gaps = 9/111 (8%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIVGQLKKLE----ILSLRGAE 631
           L+VL     + + LP       +L+ L +    LE + A+  +    E        R   
Sbjct: 162 LEVLSVRNNQLTFLPELPE---SLEALDVSTNLLESLPAVPVRNHHSEETEIFFRCRENR 218

Query: 632 IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW 682
           I  +P  I  L     + L +   L       +S+ +   + +    +   
Sbjct: 219 ITHIPENILSLDPTCTIILEDN-PLSSRIRESLSQQTAQPDYHGPRIYFSM 268

>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 = 26/99 (26%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           LK LD    + + LP        L+ +  D  +L  +        LE+LS+R  ++  LP
Sbjct: 122 LKHLDVDNNQLTMLPELPA---LLEYINADNNQLTMLP--ELPTSLEVLSVRNNQLTFLP 176

Query: 637 LQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRLEEL 673
                L     LD+S     SL    P V  +    EE 
Sbjct: 177 ELPESLEA---LDVSTNLLESL----PAVPVRNHHSEET 208

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 46.9 bits (111), Expect = 2e-05
 Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 13/101 (12%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           + VL+ T      LP       +L+ L     RL  +        L+ L +   ++  LP
Sbjct: 82  ITVLEITQNALISLPELPA---SLEYLDACDNRLSTLP--ELPASLKHLDVDNNQLTMLP 136

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
                L     ++  N   L ++        + LE L + +
Sbjct: 137 ELPALLEY---INADNN-QLTMLP----ELPTSLEVLSVRN 169

>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 = 19/97 (19%), Positives = 33/97 (34%), Gaps = 15/97 (15%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQL 635
              L    +  S LP +L     +  L +    L  +  +   L+ L+    R   +  L
Sbjct: 61  FSELQLNRLNLSSLPDNLPP--QITVLEITQNALISLPELPASLEYLDACDNR---LSTL 115

Query: 636 PLQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRL 670
           P     L     LD+ N   + L    P + + L  +
Sbjct: 116 PELPASLKH---LDVDNNQLTML----PELPALLEYI 145

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 45.0 bits (106), Expect = 7e-05
 Identities = 22/130 (16%), Positives = 43/130 (33%), Gaps = 12/130 (9%)

Query: 546 LECPQLKLFLL--FAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSL--GRLINLQ 601
           +  P    F L   + Y++       +F   ++ +     G   +   S L    +    
Sbjct: 3   IMLPINNNFSLSQNSFYNTISGTYADYFSAWDKWEKQALPGENRNEAVSLLKECLINQFS 62

Query: 602 TLCLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIA 660
            L L+   L  +   +    ++ +L +    +  LP     L  L   D    S+L    
Sbjct: 63  ELQLNRLNLSSLPDNLPP--QITVLEITQNALISLPELPASLEYLDACDN-RLSTL---- 115

Query: 661 PNVISKLSRL 670
           P + + L  L
Sbjct: 116 PELPASLKHL 125

>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 = 46.9 bits (112), Expect = 7e-06
 Identities = 26/143 (18%), Positives = 55/143 (38%), Gaps = 13/143 (9%)

Query: 576 ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI---AIVGQLKKLEILSLRG-AE 631
           + +    T      +PS      + QTL L    L  I   A    L  +  + +     
Sbjct: 12  QEEDFRVTCKDIQRIPSLP---PSTQTLKLIETHLRTIPSHAFSN-LPNISRIYVSIDVT 67

Query: 632 IKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD----SFSQWDKVE 686
           ++QL       L+++  +++ N  +L  I P+ + +L  L+ L + +     F    KV 
Sbjct: 68  LQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFLGIFNTGLKMFPDLTKVY 127

Query: 687 GGSNASLAELKGLSKLTTLEIDV 709
                 + E+     +T++ ++ 
Sbjct: 128 STDIFFILEITDNPYMTSIPVNA 150

>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 = 46.5 bits (111), Expect = 1e-05
 Identities = 30/151 (19%), Positives = 46/151 (30%), Gaps = 22/151 (14%)

Query: 566 ISDHFFEGTEELKVLD--FTGIRFSPLPSSLGRLINLQTLCL-DGWRLEDI---AIVGQL 619
           I     +    LK L    TG++  P  + +        L + D   +  I   A  G  
Sbjct: 96  IDPDALKELPLLKFLGIFNTGLKMFPDLTKVYSTDIFFILEITDNPYMTSIPVNAFQGLC 155

Query: 620 KKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKL-SRLEELYMGDS 678
            +   L L       +       T+L  + L+    L VI  +    + S    L +   
Sbjct: 156 NETLTLKLYNNGFTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLDV--- 212

Query: 679 FSQWDKVEGGSNASLAEL--KGLSKLTTLEI 707
                     S  S+  L  KGL  L  L  
Sbjct: 213 ----------SQTSVTALPSKGLEHLKELIA 233

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A Length = 149

 Score = 45.1 bits (107), Expect = 1e-05
 Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 6/116 (5%)

Query: 563 TLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
            L++ +      +EL VLD +      L         L+ L      L  IA + +L KL
Sbjct: 8   HLELRNRTPSDVKEL-VLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKL 66

Query: 623 EILSLRGAEIKQL-PLQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRLEELYM 675
           + L L    +     +   +   L  L+LS      L  I P  + KL  L+ L +
Sbjct: 67  KKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEP--LKKLENLKSLDL 120

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 34/167 (20%), Positives = 54/167 (32%), Gaps = 26/167 (15%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCL------DGWRLEDIAIVGQ 618
           +++        LKVL              +     L TL L          L       +
Sbjct: 140 LAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLK 199

Query: 619 LKKLEILSLRGAEIKQLPLQIGQL----TRLQLLDLSNCSSLVVIAPNVISKLSRLEELY 674
              L++L+LR A ++        L     +LQ LDLS+ S             S+L  L 
Sbjct: 200 FPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLN 259

Query: 675 MGDSFSQWDKVEGGSNASLAEL-------------KGLSKLTTLEID 708
           +  SF+   +V  G  A L+ L               L ++  L + 
Sbjct: 260 L--SFTGLKQVPKGLPAKLSVLDLSYNRLDRNPSPDELPQVGNLSLK 304

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri} Length = 270

 Score = 46.5 bits (111), Expect = 1e-05
 Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 618 QLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMG 676
           +L KL +L L   +++ LP  I  +L  L+ L +++   L  +   V  +L  L EL + 
Sbjct: 59  RLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDN-KLQALPIGVFDQLVNLAELRLD 117

Query: 677 DSFSQWDKVEGGSNASLAELKGLS----KLTTLEIDV 709
              +Q   +      SL +L  LS    +L +L   V
Sbjct: 118 R--NQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGV 152

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A Length = 168

 Score = 44.7 bits (106), Expect = 2e-05
 Identities = 27/118 (22%), Positives = 47/118 (39%), Gaps = 6/118 (5%)

Query: 563 TLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKL 622
            L++ +       EL VLD        +       +NL+ L L    L  ++ + +L KL
Sbjct: 15  HLELRNRTPAAVREL-VLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKL 73

Query: 623 EILSLRGAEIKQL-PLQIGQLTRLQLLDLSNC--SSLVVIAPNVISKLSRLEELYMGD 677
           + L L    I     +   +L  L  L+LS      +  + P  + KL  L+ L + +
Sbjct: 74  KKLELSENRIFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEP--LKKLECLKSLDLFN 129

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A Length = 168

 Score = 44.3 bits (105), Expect = 3e-05
 Identities = 26/111 (23%), Positives = 42/111 (37%), Gaps = 14/111 (12%)

Query: 599 NLQTLCLDGWRLEDIAIVG---QLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSS 655
            ++ L LD  +  D  I G   +   LE LSL    +  +   + +L +L+ L+LS    
Sbjct: 25  AVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVS-NLPKLPKLKKLELSENR- 82

Query: 656 LVVIAPNVISKLSRLEELYMGD-SFSQWDKVEGGSNASLAELKGLSKLTTL 705
           +      +  KL  L  L +                 +L  LK L  L +L
Sbjct: 83  IFGGLDMLAEKLPNLTHLNLSGNKLKDIS--------TLEPLKKLECLKSL 125

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B* Length = 592

 Score = 46.1 bits (109), Expect = 4e-05
 Identities = 29/171 (16%), Positives = 48/171 (28%), Gaps = 21/171 (12%)

Query: 548 CPQLKLFLLFAKYDSTLQISD----HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL 603
              L++  L        +IS             L  +         L        NL+  
Sbjct: 191 NTSLEV--LNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEF 248

Query: 604 CL-----DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVV 658
           C      D    E    +   +KL  L L      ++P+      +++ LDL        
Sbjct: 249 CGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETE 308

Query: 659 IAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL-KGLSKLTTLEID 708
               +I K   LE L   +            +  L  L +   +L  L I+
Sbjct: 309 DHCTLIQKCPNLEVLETRNVI---------GDRGLEVLAQYCKQLKRLRIE 350

>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 Length = 336

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 5/106 (4%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED---IAIVGQLKKLEILSLRGAEIK 633
           +              +       +Q + L    +E      I+ Q  KL+ LSL G  + 
Sbjct: 72  VIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLS 131

Query: 634 QLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISK-LSRLEELYMGD 677
              +  + + + L  L+LS CS     A   +    SRL+EL +  
Sbjct: 132 DPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSW 177

>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 Length = 336

 Score = 43.7 bits (103), Expect = 1e-04
 Identities = 30/134 (22%), Positives = 49/134 (36%), Gaps = 10/134 (7%)

Query: 599 NLQTLCLDGWR--LED---IAIVGQLKKLEILSLRG-AEIKQLPLQ-IGQLTRLQLLDLS 651
            +  L L G+R  L+      +V +   L  L L     +K    Q   QL  LQ L LS
Sbjct: 196 TITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLS 255

Query: 652 NCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELK-GLSKLTTLEIDVR 710
            C  ++      + ++  L+ L +       D        +L  L+   S  TT+     
Sbjct: 256 RCYDIIPETLLELGEIPTLKTLQVFGIVP--DGTLQLLKEALPHLQINCSHFTTIARPTI 313

Query: 711 DAEMLRRIWSLGNR 724
             +  + IW +  R
Sbjct: 314 GNKKNQEIWGIKCR 327

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A Length = 251

 Score = 43.9 bits (104), Expect = 8e-05
 Identities = 30/107 (28%), Positives = 50/107 (46%), Gaps = 6/107 (5%)

Query: 574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAE 631
           TE+L  L  TG+      ++   L  L  L LD  +L+ +   +   L +L  L L   +
Sbjct: 37  TEKLD-LQSTGLATLS-DATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQ 94

Query: 632 IKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD 677
           +  LPL +   LT+L  L L   + L  +   V  +L++L+EL +  
Sbjct: 95  LASLPLGVFDHLTQLDKLYLGG-NQLKSLPSGVFDRLTKLKELRLNT 140

>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 = 43.3 bits (102), Expect = 2e-04
 Identities = 29/149 (19%), Positives = 52/149 (34%), Gaps = 8/149 (5%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI---AIVGQLKKLEILSL 627
           F   ++L+ LD +  R   +      + +L+ L L     + +      G L KL  L L
Sbjct: 96  FLFNQDLEYLDVSHNRLQNISC--CPMASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGL 153

Query: 628 RGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEG 687
             A+ +QL L    +  L L  +        I       L       +   F        
Sbjct: 154 SAAKFRQLDL--LPVAHLHLSCILLDLVSYHIKGGETESLQIPNTTVLHLVFHPNSLFSV 211

Query: 688 GSNASLAELKGLSKLTTLEIDVRDAEMLR 716
             N S+  L  L  L+ ++++  + + L 
Sbjct: 212 QVNMSVNALGHLQ-LSNIKLNDENCQRLM 239

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A Length = 272

 Score = 41.2 bits (97), Expect = 8e-04
 Identities = 33/140 (23%), Positives = 57/140 (40%), Gaps = 9/140 (6%)

Query: 571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGA 630
                 +  +         +   +  L N++ L L G +L DI+ + +L  L  L L G 
Sbjct: 37  QNELNSIDQIIANNSDIKSVQG-IQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGN 95

Query: 631 EIKQLPLQI-GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGS 689
           +++ LP  +  +LT L+ L L   + L  +   V  KL+ L  L +    +Q   +  G 
Sbjct: 96  QLQSLPNGVFDKLTNLKELVLVE-NQLQSLPDGVFDKLTNLTYLNLAH--NQLQSLPKGV 152

Query: 690 NASLAELKGLS----KLTTL 705
              L  L  L     +L +L
Sbjct: 153 FDKLTNLTELDLSYNQLQSL 172

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	724
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.68
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.68
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.68
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.67
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.67
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.67
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.67
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.67
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.66
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.66
2fna_A	357	Conserved hypothetical protein; structural genomic	99.65
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.64
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.64
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.62
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.62
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.62
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.62
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.62
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.6
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.6
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.59
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.59
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.59
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.58
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.57
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.57
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.57
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.57
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.56
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.56
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.56
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.56
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.56
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.56
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.55
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.55
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.55
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.55
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.55
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.55
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.54
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.54
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.54
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.54
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.52
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.52
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.52
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.52
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.51
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.51
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.51
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.5
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.5
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.5
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.5
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.5
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.5
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.5
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.49
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.49
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.49
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.49
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.48
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.48
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.48
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.48
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.48
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.48
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.47
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.47
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.47
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.47
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.47
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.47
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.47
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.46
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.46
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.45
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.45
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.45
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.44
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.43
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.43
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.42
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.42
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.42
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.41
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.41
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.41
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.41
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.4
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.4
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.4
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.4
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.4
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.4
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.4
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.4
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.39
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.39
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.39
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.39
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.39
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.38
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.37
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.37
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.37
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.36
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.34
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.34
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.34
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.34
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.33
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.33
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.32
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.32
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.32
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.31
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.3
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.3
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.3
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.29
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.29
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.29
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.27
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.26
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.26
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.25
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.25
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.23
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.22
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.22
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.22
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.21
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.2
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.16
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	99.13
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	99.13
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.11
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.11
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.1
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.04
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.03
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.95
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.93
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.88
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.84
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.83
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.79
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.78
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.77
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.76
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.64
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.62
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.61
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.59
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.59
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.57
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.55
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.54
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.54
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	98.52
3pvs_A	447	Replication-associated recombination protein A; ma	98.52
3bos_A	242	Putative DNA replication factor; P-loop containing	98.5
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.49
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.47
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.44
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.42
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.42
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.4
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.4
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.4
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.37
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.34
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.34
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.33
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.32
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.3
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.3
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.29
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.28
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.26
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.25
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	98.24
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.23
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.22
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.21
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.21
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.16
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.16
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.15
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.11
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.1
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.09
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.09
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.04
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.01
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.98
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.94
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.92
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.88
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.84
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.84
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.83
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.8
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.79
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.77
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.76
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.72
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.7
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.69
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.69
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.65
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.65
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.65
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.52
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.51
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.42
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.42
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.23
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.19
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.18
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.1
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.98
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.97
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.9
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.82
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.76
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.71
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.7
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.69
3io5_A	333	Recombination and repair protein; storage dimer, i	96.54
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.53
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.5
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.5
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.48
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.47
2qgz_A	308	Helicase loader, putative primosome component; str	96.43
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.39
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.37
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.37
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.22
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.2
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.2
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.19
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	96.15
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.04
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.04
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.98
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.93
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.93
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	95.88
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.8
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.8
3co5_A	143	Putative two-component system transcriptional RES	95.71
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.7
3ice_A	422	Transcription termination factor RHO; transcriptio	95.69
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.49
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.49
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.45
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.38
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	95.36
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.3
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.29
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.25
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	95.24
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.24
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.19
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.18
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.1
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.05
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.05
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.03
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.02
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.94
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.93
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.91
2xxa_A	433	Signal recognition particle protein; protein trans	94.91
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.9
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	94.87
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	94.86
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.86
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.83
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.78
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.78
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.77
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	94.76
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.75
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.69
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.67
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	94.64
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.64
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.63
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	94.62
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.58
1via_A	175	Shikimate kinase; structural genomics, transferase	94.56
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.56
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.55
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.55
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.54
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.53
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.53
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.5
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.49
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.48
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.47
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.44
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	94.44
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.44
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.43
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.42
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	94.41
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	94.4
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	94.38
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	94.35
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.35
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.35
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.34
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.34
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.29
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	94.28
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.26
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.26
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.25
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.24
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.23
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.23
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.21
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.21
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.21
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.2
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.18
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	94.17
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.16
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	94.16
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	94.12
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	94.11
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.04
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.04
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.04
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	94.03
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	94.02
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.02
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.01
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.0
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.96
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.96
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.94
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.94
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.92
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.88
2vli_A	183	Antibiotic resistance protein; transferase, tunica	93.86
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.86
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.86
3fwy_A	314	Light-independent protochlorophyllide reductase I	93.85
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.79
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	93.79
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.78
1tue_A	212	Replication protein E1; helicase, replication, E1E	93.77
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	93.77
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.76
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	93.76
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.73
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.73
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.72
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	93.7
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.66
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.64
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	93.64
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	93.63
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.63
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.61
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.61
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	93.56
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.56
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.53
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.48
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	93.46
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.41
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.34
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.32
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.28
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.25
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.24
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	93.24
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.23
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.19
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	93.16
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.15
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	93.14
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.13
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	93.11
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.09
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.01
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.98
3end_A	307	Light-independent protochlorophyllide reductase ir	92.95
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.95
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.92
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	92.87
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	92.87
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	92.84
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.82
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	92.8
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	92.79
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.77
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	92.75
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.75
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	92.74
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.62
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	92.6
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.57
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	92.55
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	92.52
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	92.47
2og2_A	359	Putative signal recognition particle receptor; nuc	92.46
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	92.46
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.43
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	92.41
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.41
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.41
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.38
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.36
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.29
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.28
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	92.26
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	92.15
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	92.13
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	92.12
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.11
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	92.04
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.03
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	92.01
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	91.96
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.93
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.9
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	91.86
1b0u_A	262	Histidine permease; ABC transporter, transport pro	91.86
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.81
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	91.77
1sgw_A	214	Putative ABC transporter; structural genomics, P p	91.72
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	91.72
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.72
1g6h_A	257	High-affinity branched-chain amino acid transport	91.7
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	91.64
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.64
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.59
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	91.53
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.51
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	91.45
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	91.43
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	91.43
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.42
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	91.4
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.39
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	91.34
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	91.33
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.3
2ghi_A	260	Transport protein; multidrug resistance protein, M	91.28
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.24
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.2
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.18
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	91.17
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	91.16
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.11
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	91.1
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	91.08
2ged_A	193	SR-beta, signal recognition particle receptor beta	91.08
2wji_A	165	Ferrous iron transport protein B homolog; membrane	91.06
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.06
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	91.02
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	90.92
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	90.89
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	90.79
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.74
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.69
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	90.68
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.59
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	90.53
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	90.47
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	90.46
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	90.44
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	90.37
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	90.27
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	90.26
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.26
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	90.14
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	90.12
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.02
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	89.95
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	89.94
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	89.89
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	89.89
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	89.85
1nrj_B	218	SR-beta, signal recognition particle receptor beta	89.83
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	89.81
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	89.8

>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=8.2e-48  Score=431.89  Aligned_cols=310  Identities=13%  Similarity=0.135  Sum_probs=241.1

Q ss_pred             cchHHHHHHHHHHhcCC---CccEEEEEcCCCCcHHHHHHHHHH--HHhhccCCCeEEEEEEecCC--ChHHHHHHHHHh
Q 004895          163 NSRKKIFQDVIEALKDD---KLNIIGVCGMGGVGKTTLVKQIAK--QVMEDNVFDKVVMAEITKNP--DAQKIQGELASD  235 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~~~---~~~vi~I~G~gGiGKTtLa~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~  235 (724)
                      +||++++++|.++|...   ..++|+|+||||+||||||+++|+  +.+.+.+|++++||++++.+  +..+++..|+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            39999999999999733   679999999999999999999998  46677899999999999985  789999999999


Q ss_pred             hCCCCC---C----CchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccc
Q 004895          236 LGMNFD---S----NDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD  308 (724)
Q Consensus       236 l~~~~~---~----~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~  308 (724)
                      ++....   .    ..........+.+.+.+++|+||||||||+..++ .+    +         ..+||+||||||++.
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~----~---------~~~gs~ilvTTR~~~  276 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RW----A---------QELRLRCLVTTRDVE  276 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HH----H---------HHTTCEEEEEESBGG
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cc----c---------ccCCCEEEEEcCCHH
Confidence            986521   1    1112334567777776434999999999998755 21    1         226899999999999


Q ss_pred             hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHHHHh
Q 004895          309 LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLT  388 (724)
Q Consensus       309 v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~~l~  388 (724)
                      ++.........|++++|+++|+|+||.+.++....++.+++++++|+++|+|+||||+++|+.++.++   |+.+ +.+.
T Consensus       277 v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~---w~~~-~~l~  352 (549)
T 2a5y_B          277 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT---FEKM-AQLN  352 (549)
T ss_dssp             GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS---HHHH-HHHH
T ss_pred             HHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccch---HHHH-HHhH
Confidence            87432224467999999999999999999876544467788999999999999999999999998764   4333 3332


Q ss_pred             cCccccccCCCcccchhhHhhhhhcHHHHHHHHH-----------hhccCCCCCcccHHHHHHHHhhccccccc--cccc
Q 004895          389 SSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFL-----------LCGLHREGRPIHVHYLLRYVMGLRYDKGL--GLFR  455 (724)
Q Consensus       389 ~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~-----------~~s~fp~~~~i~~~~Li~~W~~~~~~~~~--g~i~  455 (724)
                      ......   ...++..++.+||+.||+++|.||+           |||+||+++.|+    +++|+      |+  ||+.
T Consensus       353 ~~l~~~---~~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~------a~~~G~i~  419 (549)
T 2a5y_B          353 NKLESR---GLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWS------CVIPVDIC  419 (549)
T ss_dssp             HHHHHH---CSSTTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHH------HHSCC---
T ss_pred             HHhhcc---cHHHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeee------eeccceec
Confidence            221111   2456899999999999999999999           999999999999    78999      88  8886


Q ss_pred             cc---ccHHHHHHHHHHHHHHHHhhcccccC--CCCCcchhhHHHHHHHHHHhhhcc
Q 004895          456 NV---YTLEAARNRVDALIDNLKASCLLLDG--DAEDEAKLHDVIHVVAASIAEEKL  507 (724)
Q Consensus       456 ~~---~~~~~~~~~~~~~~~~L~~~~ll~~~--~~~~~~~mHdlv~d~a~~~~~~~~  507 (724)
                      ..   .+.+++.    +++++|+++||++..  +...+|+|||+||+||++++.+++
T Consensus       420 ~~~~~~~~~~~~----~~l~~L~~rsLl~~~~~~~~~~~~mHdlv~~~a~~~~~~~~  472 (549)
T 2a5y_B          420 SNEEEQLDDEVA----DRLKRLSKRGALLSGKRMPVLTFKIDHIIHMFLKHVVDAQT  472 (549)
T ss_dssp             ----CCCTHHHH----HHHHHTTTBSSCSEEECSSSCEEECCHHHHHHHHTTSCTHH
T ss_pred             cCCCCCCHHHHH----HHHHHHHHcCCeeEecCCCceEEEeChHHHHHHHHHHHHHH
Confidence            42   2333332    278889999999854  234679999999999999988765

>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=2.2e-38  Score=358.54  Aligned_cols=284  Identities=17%  Similarity=0.201  Sum_probs=222.8

Q ss_pred             ccchHHHHHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe-EEEEEEecCCChHHHHHHHHHhhCC-
Q 004895          162 FNSRKKIFQDVIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK-VVMAEITKNPDAQKIQGELASDLGM-  238 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~l~~~i~~~l~~-  238 (724)
                      .+||++++++|.++|.+ +..++|+|+||||+||||||+++|++.+.+.+|+. ++|+++++.++...++..|++.++. 
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i  209 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI  209 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhc
Confidence            38999999999999874 56899999999999999999999998777778986 9999999999988888888775421 


Q ss_pred             --CC----CC-Cc---hhHHHHHHHHHHHh--cCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecc
Q 004895          239 --NF----DS-ND---LIYHRAKQLCQRLK--KEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS  306 (724)
Q Consensus       239 --~~----~~-~~---~~~~~~~~l~~~l~--~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~  306 (724)
                        ..    +. ..   ........+.+.+.  .++|+||||||||+...|+.+              . +||+||||||+
T Consensus       210 ~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f--------------~-pGSRILVTTRd  274 (1221)
T 1vt4_I          210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF--------------N-LSCKILLTTRF  274 (1221)
T ss_dssp             CSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHH--------------H-SSCCEEEECSC
T ss_pred             CcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhh--------------C-CCeEEEEeccC
Confidence              11    10 01   11233445555541  368999999999998888764              1 48999999999


Q ss_pred             cchhhhhcCCCceEecC------CCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCC--CHH
Q 004895          307 RDLLCIDMNSQKMFWID------ALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNK--SPA  378 (724)
Q Consensus       307 ~~v~~~~~~~~~~~~l~------~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~--~~~  378 (724)
                      +.++.. +.....|.++      +|+++|||+||.+..+..     ..++..+|   |+|+||||+++|+.|+.+  +..
T Consensus       275 ~~Va~~-l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~-----~eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~e  345 (1221)
T 1vt4_I          275 KQVTDF-LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR-----PQDLPREV---LTTNPRRLSIIAESIRDGLATWD  345 (1221)
T ss_dssp             SHHHHH-HHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCC-----TTTHHHHH---CCCCHHHHHHHHHHHHHSCSSHH
T ss_pred             hHHHHh-cCCCeEEEecCccccCCcCHHHHHHHHHHHcCCC-----HHHHHHHH---hCCCHHHHHHHHHHHhCCCCCHH
Confidence            988632 2222356666      999999999999985432     23444444   999999999999999966  677


Q ss_pred             HHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHH-HHHHHhhccCCCCCcccHHHHHHHHhhccccccccccccc
Q 004895          379 IWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEA-KSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNV  457 (724)
Q Consensus       379 ~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~-k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~  457 (724)
                      +|+..              ....+..+|.+||+.||++. |+||++||+||+++.|+.+.++.+|+      ++|.    
T Consensus       346 eW~~~--------------~~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~------aeGe----  401 (1221)
T 1vt4_I          346 NWKHV--------------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF------DVIK----  401 (1221)
T ss_dssp             HHHHC--------------SCHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHC------SSCS----
T ss_pred             HHhcC--------------ChhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhc------CCCH----
Confidence            88642              13568999999999999999 99999999999999999999999999      7761    


Q ss_pred             ccHHHHHHHHHHHHHHHHhhcccccCCCCCcchhhHHHHHHHH
Q 004895          458 YTLEAARNRVDALIDNLKASCLLLDGDAEDEAKLHDVIHVVAA  500 (724)
Q Consensus       458 ~~~~~~~~~~~~~~~~L~~~~ll~~~~~~~~~~mHdlv~d~a~  500 (724)
                         ++    ..+++++|+++||++..+....|+|||++++++.
T Consensus       402 ---ed----Ae~~L~eLvdRSLLq~d~~~~rYrMHDLllELr~  437 (1221)
T 1vt4_I          402 ---SD----VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV  437 (1221)
T ss_dssp             ---HH----HHHHHHHHHTSSSSSBCSSSSEEBCCCHHHHHHH
T ss_pred             ---HH----HHHHHHHHHhhCCEEEeCCCCEEEehHHHHHHhc
Confidence               12    4457888999999987555678999999999653

>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=3.7e-38  Score=390.79  Aligned_cols=315  Identities=19%  Similarity=0.272  Sum_probs=246.5

Q ss_pred             CcccccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhh-cc-CCCeEEEEEEecCCC--hHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVME-DN-VFDKVVMAEITKNPD--AQKIQ  229 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~-~F~~~~wv~vs~~~~--~~~l~  229 (724)
                      |.....|+||++++++|.+.|.  ++..++|+|+||||+||||||+++|++.+. .. +|+.++|+++++..+  ....+
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~  199 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKL  199 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHH
T ss_pred             CCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHH
Confidence            5556779999999999999985  467899999999999999999999998643 23 557789999998654  33446


Q ss_pred             HHHHHhhCCCCC----CCchhHHHHHHHHHHHhc-CCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          230 GELASDLGMNFD----SNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       230 ~~i~~~l~~~~~----~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      ..++..++....    ...........+...+.. ++|+||||||||+..+|..+               .+||+|||||
T Consensus       200 ~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~---------------~~~~~ilvTt  264 (1249)
T 3sfz_A          200 QNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF---------------DNQCQILLTT  264 (1249)
T ss_dssp             HHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT---------------CSSCEEEEEE
T ss_pred             HHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh---------------cCCCEEEEEc
Confidence            667777764321    112234455555555542 24999999999998776653               3588999999


Q ss_pred             cccchhhhhcCCCceEecCC-CCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHH
Q 004895          305 RSRDLLCIDMNSQKMFWIDA-LSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDA  383 (724)
Q Consensus       305 R~~~v~~~~~~~~~~~~l~~-L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~  383 (724)
                      |++.++.........+.+++ |+++|+++||...++..  .+.+++++++|+++|+|+||||+++|+.|+.+. ..|+..
T Consensus       265 R~~~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~--~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~  341 (1249)
T 3sfz_A          265 RDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMK--KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYY  341 (1249)
T ss_dssp             SSTTTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSC--STTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHH
T ss_pred             CCHHHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCC--hhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHH
Confidence            99998644456667899996 99999999999988543  345577899999999999999999999999665 579999


Q ss_pred             HHHHhcCcccccc----CCCcccchhhHhhhhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhccccccccccccccc
Q 004895          384 LNKLTSSNLREIH----GMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYT  459 (724)
Q Consensus       384 ~~~l~~~~~~~~~----~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~  459 (724)
                      ++.+.......+.    .....+..+|.+||+.||+++|.||+|||+||+++.|+.+.++.+|.      +++       
T Consensus       342 l~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~------~~~-------  408 (1249)
T 3sfz_A          342 LRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWD------LET-------  408 (1249)
T ss_dssp             HHHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHT------CCH-------
T ss_pred             HHHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhC------CCH-------
Confidence            9888765533321    11246899999999999999999999999999999999999999998      442       


Q ss_pred             HHHHHHHHHHHHHHHHhhcccccCC--CCCcchhhHHHHHHHHHHhhhc
Q 004895          460 LEAARNRVDALIDNLKASCLLLDGD--AEDEAKLHDVIHVVAASIAEEK  506 (724)
Q Consensus       460 ~~~~~~~~~~~~~~L~~~~ll~~~~--~~~~~~mHdlv~d~a~~~~~~~  506 (724)
                       ++    +.+++++|+++||++...  ...+|+|||+||+|++..+.++
T Consensus       409 -~~----~~~~l~~L~~~sl~~~~~~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          409 -EE----VEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             -HH----HHHHHHHHHHTTSCEEEESSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             -HH----HHHHHHHHHhccceEEecCCCceEEEecHHHHHHHHhhhhHH
Confidence             23    345678888899997542  2336999999999999997765

>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=6.4e-35  Score=332.25  Aligned_cols=310  Identities=19%  Similarity=0.303  Sum_probs=232.8

Q ss_pred             CcccccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhh-ccCC-CeEEEEEEecCCChHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVME-DNVF-DKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F-~~~~wv~vs~~~~~~~l~~~  231 (724)
                      |.....|+||+.++++|.++|.  .+..++|+|+||||+||||||.+++++... ..+| +.++|+++++. +...++..
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~  198 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMK  198 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHH
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHH
Confidence            3345679999999999999987  356789999999999999999999987654 5668 58999999876 33344444


Q ss_pred             H---HHhhCCC----CCCCchhHHHHHHHHHHHhcC-CcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          232 L---ASDLGMN----FDSNDLIYHRAKQLCQRLKKE-KRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       232 i---~~~l~~~----~~~~~~~~~~~~~l~~~l~~~-kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      +   +..++..    .............+...+... +++||||||+|+...++.+               ..+++||||
T Consensus       199 l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~l---------------~~~~~ilvT  263 (591)
T 1z6t_A          199 LQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAF---------------DSQCQILLT  263 (591)
T ss_dssp             HHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHTT---------------CSSCEEEEE
T ss_pred             HHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHHh---------------cCCCeEEEE
Confidence            3   4455421    111222344556666666542 6899999999987655432               357899999


Q ss_pred             ecccchhhhhcCCCceEec---CCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHH
Q 004895          304 SRSRDLLCIDMNSQKMFWI---DALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIW  380 (724)
Q Consensus       304 tR~~~v~~~~~~~~~~~~l---~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w  380 (724)
                      ||+..++....  ...+++   ++|+.+|+++||...++..  .+...+.+++|+++|+|+||||.++|+.++.+. ..|
T Consensus       264 sR~~~~~~~~~--~~~~~v~~l~~L~~~ea~~L~~~~~~~~--~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-~~w  338 (591)
T 1z6t_A          264 TRDKSVTDSVM--GPKYVVPVESSLGKEKGLEILSLFVNMK--KADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRW  338 (591)
T ss_dssp             ESCGGGGTTCC--SCEEEEECCSSCCHHHHHHHHHHHHTSC--GGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-TCH
T ss_pred             CCCcHHHHhcC--CCceEeecCCCCCHHHHHHHHHHHhCCC--cccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-hhH
Confidence            99998753212  234444   5899999999999998742  223356889999999999999999999998653 469


Q ss_pred             HHHHHHHhcCccccc----cCCCcccchhhHhhhhhcHHHHHHHHHhhccCCCCCcccHHHHHHHHhhcccccccccccc
Q 004895          381 KDALNKLTSSNLREI----HGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRN  456 (724)
Q Consensus       381 ~~~~~~l~~~~~~~~----~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~  456 (724)
                      ..+++.+.......+    ......+..++..||+.||++.|.||++||+||+++.|+.+.++.+|.      ++     
T Consensus       339 ~~~l~~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~------~~-----  407 (591)
T 1z6t_A          339 EYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWD------ME-----  407 (591)
T ss_dssp             HHHHHHHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHT------CC-----
T ss_pred             HHHHHHHHHhHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhc------cC-----
Confidence            888888775542221    112357889999999999999999999999999999999999999997      32     


Q ss_pred             cccHHHHHHHHHHHHHHHHhhcccccC--CCCCcchhhHHHHHHHHHHhh
Q 004895          457 VYTLEAARNRVDALIDNLKASCLLLDG--DAEDEAKLHDVIHVVAASIAE  504 (724)
Q Consensus       457 ~~~~~~~~~~~~~~~~~L~~~~ll~~~--~~~~~~~mHdlv~d~a~~~~~  504 (724)
                         .++    +.++++.|+++||++..  +....|+||+++|++++....
T Consensus       408 ---~~~----~~~~l~~L~~~~Ll~~~~~~~~~~~~~H~lv~~~~~~~~~  450 (591)
T 1z6t_A          408 ---TEE----VEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNC  450 (591)
T ss_dssp             ---HHH----HHHHHHHHHHTTSSEEEEETTEEEEECCHHHHHHHHHHTG
T ss_pred             ---HHH----HHHHHHHHHhCcCeEEecCCCccEEEEcHHHHHHHHhhhh
Confidence               122    34578888899999743  233479999999999998843

>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=99.68  E-value=4.3e-16  Score=159.79  Aligned_cols=105  Identities=26%  Similarity=0.368  Sum_probs=50.8

Q ss_pred             CCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEc
Q 004895          573 GTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLD  649 (724)
Q Consensus       573 ~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~  649 (724)
                      .+++|+.|++++|.+..+|..+..+++|++|++++|.++.+  ..+..+++|++|++++|.++.+|.. +..+++|++|+
T Consensus        75 ~l~~L~~L~Ls~N~l~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~  154 (290)
T 1p9a_G           75 TLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLS  154 (290)
T ss_dssp             CCTTCCEEECCSSCCSSCCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEE
T ss_pred             CCCcCCEEECCCCcCCcCchhhccCCCCCEEECCCCcCcccCHHHHcCCCCCCEEECCCCCCCccChhhcccccCCCEEE
Confidence            44445555555555555554444555555555555554441  2344555555555555555544433 34445555555


Q ss_pred             cCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          650 LSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       650 l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +++ +.+..+|+..+..+++|++|++++|
T Consensus       155 L~~-N~l~~l~~~~~~~l~~L~~L~L~~N  182 (290)
T 1p9a_G          155 LAN-NNLTELPAGLLNGLENLDTLLLQEN  182 (290)
T ss_dssp             CTT-SCCSCCCTTTTTTCTTCCEEECCSS
T ss_pred             CCC-CcCCccCHHHhcCcCCCCEEECCCC
Confidence            554 2344444444444555555555444

>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=99.68  E-value=2.9e-16  Score=164.14  Aligned_cols=182  Identities=21%  Similarity=0.301  Sum_probs=116.5

Q ss_pred             ccCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccC-------
Q 004895          526 QKGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGR-------  596 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~-------  596 (724)
                      ..++++|++++|.+..+|... .+++|+.|.+..  +....+|.. +.++++|++|++++|.+. .+|..++.       
T Consensus       103 l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~--n~l~~lp~~-l~~l~~L~~L~L~~n~~~~~~p~~~~~~~~~~~~  179 (328)
T 4fcg_A          103 LSHLQHMTIDAAGLMELPDTMQQFAGLETLTLAR--NPLRALPAS-IASLNRLRELSIRACPELTELPEPLASTDASGEH  179 (328)
T ss_dssp             GTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEES--CCCCCCCGG-GGGCTTCCEEEEEEETTCCCCCSCSEEEC-CCCE
T ss_pred             CCCCCEEECCCCCccchhHHHhccCCCCEEECCC--CccccCcHH-HhcCcCCCEEECCCCCCccccChhHhhccchhhh
Confidence            356777777777776666533 567777777732  233345443 666777777777775544 56665543       


Q ss_pred             --CCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEE
Q 004895          597 --LINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEEL  673 (724)
Q Consensus       597 --l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L  673 (724)
                        +.+|++|+|++|.++. |..++.+++|++|++++|.++.+|..+..+++|++|++++|+....+|. .++.+++|++|
T Consensus       180 ~~l~~L~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~-~~~~l~~L~~L  258 (328)
T 4fcg_A          180 QGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPP-IFGGRAPLKRL  258 (328)
T ss_dssp             EESTTCCEEEEEEECCCCCCGGGGGCTTCCEEEEESSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCC-CTTCCCCCCEE
T ss_pred             ccCCCCCEEECcCCCcCcchHhhcCCCCCCEEEccCCCCCcCchhhccCCCCCEEECcCCcchhhhHH-HhcCCCCCCEE
Confidence              7777777777777666 4567777777777777777777777777777777777777655554443 46777777777


Q ss_pred             EccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc-cccccccc
Q 004895          674 YMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD-AEMLRRIW  719 (724)
Q Consensus       674 ~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~-~~~lp~~~  719 (724)
                      ++++|..     .+..+   ..+.++++|+.|++++|. ...+|..+
T Consensus       259 ~L~~n~~-----~~~~p---~~~~~l~~L~~L~L~~n~~~~~iP~~l  297 (328)
T 4fcg_A          259 ILKDCSN-----LLTLP---LDIHRLTQLEKLDLRGCVNLSRLPSLI  297 (328)
T ss_dssp             ECTTCTT-----CCBCC---TTGGGCTTCCEEECTTCTTCCCCCGGG
T ss_pred             ECCCCCc-----hhhcc---hhhhcCCCCCEEeCCCCCchhhccHHH
Confidence            7776532     22222   235567778888888765 34455443

>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=5e-16  Score=159.18  Aligned_cols=150  Identities=23%  Similarity=0.333  Sum_probs=84.8

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCc-CCCC-CccccCCCCCc
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-FSPL-PSSLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~-~~~l-p~~i~~l~~L~  601 (724)
                      +.++++|++++|.+..++.  ...+++|+.|.+  ..+....+....|.++++|+.|++++|. +..+ |..+..+.+|+
T Consensus        31 ~~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l--~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~~~~~~~~~~l~~L~  108 (285)
T 1ozn_A           31 PAASQRIFLHGNRISHVPAASFRACRNLTILWL--HSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLH  108 (285)
T ss_dssp             CTTCSEEECTTSCCCEECTTTTTTCTTCCEEEC--CSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCC
T ss_pred             CCCceEEEeeCCcCCccCHHHcccCCCCCEEEC--CCCccceeCHhhcCCccCCCEEeCCCCCCccccCHHHhcCCcCCC
Confidence            4456666666666655542  224566666666  2223334444445566666666666665 5544 44556666666


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +|++++|.++.  +..+..+++|++|++++|.++.+|.. +..+++|++|++++ +.+..+++..+..+++|++|++++|
T Consensus       109 ~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~-n~l~~~~~~~~~~l~~L~~L~l~~n  187 (285)
T 1ozn_A          109 TLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHG-NRISSVPERAFRGLHSLDRLLLHQN  187 (285)
T ss_dssp             EEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             EEECCCCcCCEECHhHhhCCcCCCEEECCCCcccccCHhHhccCCCccEEECCC-CcccccCHHHhcCccccCEEECCCC
Confidence            66666666555  23455666666666666666655443 55566666666665 3445555544555666666666554

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.67  E-value=2.5e-15  Score=158.82  Aligned_cols=292  Identities=15%  Similarity=0.124  Sum_probs=177.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC------ChHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP------DAQKIQ  229 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~------~~~~l~  229 (724)
                      +.....|+||+++++.|.+++..+  +++.|+|++|+|||||++++++..      + ++|+++....      +...+.
T Consensus         8 ~~~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~------~-~~~~~~~~~~~~~~~~~~~~~~   78 (350)
T 2qen_A            8 KTRREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER------P-GILIDCRELYAERGHITREELI   78 (350)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS------S-EEEEEHHHHHHTTTCBCHHHHH
T ss_pred             CCChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc------C-cEEEEeecccccccCCCHHHHH
Confidence            344567999999999999988654  799999999999999999998764      1 6788776542      566677


Q ss_pred             HHHHHhhCC-----------------CCCC-CchhHHHHHHHHHHHhcCCcEEEEEccccccccc---------cccccc
Q 004895          230 GELASDLGM-----------------NFDS-NDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL---------DKIGIP  282 (724)
Q Consensus       230 ~~i~~~l~~-----------------~~~~-~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~---------~~l~~~  282 (724)
                      ..+.+.+..                 ..+. ..........+.......++++|||||++....+         ..+...
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            777665542                 0000 0112223333333333223899999999775431         112111


Q ss_pred             cCCCCcCCCCCCCCCcEEEEEecccchhhh----------hc-CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHH
Q 004895          283 YGDVDEKDKNDDPRRCTIILTSRSRDLLCI----------DM-NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLA  351 (724)
Q Consensus       283 ~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~----------~~-~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~  351 (724)
                      . .        ...+.++|+|++.......          .. .....+++.+|+.+|+.+++.+.+....... -.+.+
T Consensus       159 ~-~--------~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~-~~~~~  228 (350)
T 2qen_A          159 Y-D--------SLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV-PENEI  228 (350)
T ss_dssp             H-H--------HCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHH
T ss_pred             H-H--------hcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCC-CHHHH
Confidence            1 1        1246789999876532110          01 1124799999999999999988653221111 24678


Q ss_pred             HHHHHHhCCchhHHHHHHHHhcC-CCHHHHH-HHHHHHhcCccccccCCCcccchhhHhhhhhc---HHHHHHHHHhhcc
Q 004895          352 EEIVGKCGGLPVALSTVANALKN-KSPAIWK-DALNKLTSSNLREIHGMDADVYSPIKLSYDFL---DDEAKSLFLLCGL  426 (724)
Q Consensus       352 ~~I~~~c~GlPLai~~~~~~l~~-~~~~~w~-~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L---~~~~k~cf~~~s~  426 (724)
                      .+|++.|+|+|+++..++..+.. .+...+. ...+.               +...+...+..+   ++..+..+..+|.
T Consensus       229 ~~i~~~tgG~P~~l~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~l~~l~~~~~~~~~~l~~la~  293 (350)
T 2qen_A          229 EEAVELLDGIPGWLVVFGVEYLRNGDFGRAMKRTLEV---------------AKGLIMGELEELRRRSPRYVDILRAIAL  293 (350)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCHHHHHHHHHHH---------------HHHHHHHHHHHHHHHCHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHhccccHhHHHHHHHHH---------------HHHHHHHHHHHHHhCChhHHHHHHHHHh
Confidence            89999999999999998876432 2222221 11111               111222223333   6888999999987


Q ss_pred             CCCCCcccHHHHHHHHhhcccccccccccccccHHHHHHHHHHHHHHHHhhcccccCCCCCcch-hhHHHHHHHH
Q 004895          427 HREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAK-LHDVIHVVAA  500 (724)
Q Consensus       427 fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~~~~~~~~~-mHdlv~d~a~  500 (724)
                         + ..+...+....-     .+.|   + .+.    ..+..+++.|.+.+++...+  +.|. .|++++++.+
T Consensus       294 ---g-~~~~~~l~~~~~-----~~~~---~-~~~----~~~~~~l~~L~~~gli~~~~--~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          294 ---G-YNRWSLIRDYLA-----VKGT---K-IPE----PRLYALLENLKKMNWIVEED--NTYKIADPVVATVLR  349 (350)
T ss_dssp             ---T-CCSHHHHHHHHH-----HTTC---C-CCH----HHHHHHHHHHHHTTSEEEET--TEEEESSHHHHHHHT
T ss_pred             ---C-CCCHHHHHHHHH-----HHhC---C-CCH----HHHHHHHHHHHhCCCEEecC--CEEEEecHHHHHHHc
Confidence               2 345566655432     0111   0 112    22345677888899986542  3455 4889888754

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.67  E-value=8.8e-16  Score=155.94  Aligned_cols=178  Identities=24%  Similarity=0.353  Sum_probs=140.8

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|++|++++|.+..+|. .+..+.+|++
T Consensus        36 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l--~~n~l~~i~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~  113 (270)
T 2o6q_A           36 PADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYL--NDNKLQTLPAGIFKELKNLETLWVTDNKLQALPIGVFDQLVNLAE  113 (270)
T ss_dssp             CTTCSEEECCSSCCSCCCTTSSSSCTTCCEEEC--CSSCCSCCCTTTTSSCTTCCEEECCSSCCCCCCTTTTTTCSSCCE
T ss_pred             CCCCCEEECcCCCCCeeCHHHhcCCCCCCEEEC--CCCccCeeChhhhcCCCCCCEEECCCCcCCcCCHhHcccccCCCE
Confidence            5678899999998887764  337889999998  4445567777778889999999999999987765 4688899999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |++++|.++..  ..++.+++|++|++++|.++.+|.. +..+++|++|++++ +.+..+++..+..+++|++|++++|.
T Consensus       114 L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~-n~l~~~~~~~~~~l~~L~~L~L~~N~  192 (270)
T 2o6q_A          114 LRLDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFDKLTSLKELRLYN-NQLKRVPEGAFDKLTELKTLKLDNNQ  192 (270)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EECCCCccCeeCHHHhCcCcCCCEEECCCCcCCccCHhHccCCcccceeEecC-CcCcEeChhHhccCCCcCEEECCCCc
Confidence            99999988873  4578899999999999999888776 78899999999988 46777887778889999999998864


Q ss_pred             CccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          680 SQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       680 ~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      .     .+..+   ..+..+++|+.|++++|.+..
T Consensus       193 l-----~~~~~---~~~~~l~~L~~L~l~~N~~~c  219 (270)
T 2o6q_A          193 L-----KRVPE---GAFDSLEKLKMLQLQENPWDC  219 (270)
T ss_dssp             C-----SCCCT---TTTTTCTTCCEEECCSSCBCC
T ss_pred             C-----CcCCH---HHhccccCCCEEEecCCCeeC
Confidence            3     21111   235677889999999987643

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.67  E-value=1e-15  Score=155.47  Aligned_cols=182  Identities=21%  Similarity=0.335  Sum_probs=147.0

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEEEc
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTLCL  605 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L~L  605 (724)
                      ...+.+.++++.+..+|.... ++++.|.+  ..+....++...|.++++|++|++++|.+..+|.. +..+++|++|++
T Consensus        16 ~~~~~l~~~~~~l~~ip~~~~-~~l~~L~l--~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l   92 (270)
T 2o6q_A           16 NNKNSVDCSSKKLTAIPSNIP-ADTKKLDL--QSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWV   92 (270)
T ss_dssp             TTTTEEECTTSCCSSCCSCCC-TTCSEEEC--CSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEEC
T ss_pred             CCCCEEEccCCCCCccCCCCC-CCCCEEEC--cCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEEC
Confidence            356788898888888886443 68999999  44455667777788999999999999999988765 478999999999


Q ss_pred             CCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcc
Q 004895          606 DGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW  682 (724)
Q Consensus       606 ~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~  682 (724)
                      ++|.++.+  ..+..+++|++|++++|.++.+|.. +..+++|++|++++ +.+..+++..++.+++|++|++++|..  
T Consensus        93 ~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~-n~l~~~~~~~~~~l~~L~~L~L~~n~l--  169 (270)
T 2o6q_A           93 TDNKLQALPIGVFDQLVNLAELRLDRNQLKSLPPRVFDSLTKLTYLSLGY-NELQSLPKGVFDKLTSLKELRLYNNQL--  169 (270)
T ss_dssp             CSSCCCCCCTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCCCCCTTTTTTCTTCCEEECCSSCC--
T ss_pred             CCCcCCcCCHhHcccccCCCEEECCCCccCeeCHHHhCcCcCCCEEECCC-CcCCccCHhHccCCcccceeEecCCcC--
Confidence            99998883  4678999999999999999988654 78999999999999 467888887789999999999998743  


Q ss_pred             ccccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          683 DKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       683 ~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                         .+..+   ..+.++++|+.|+++.|.++.+|...+
T Consensus       170 ---~~~~~---~~~~~l~~L~~L~L~~N~l~~~~~~~~  201 (270)
T 2o6q_A          170 ---KRVPE---GAFDKLTELKTLKLDNNQLKRVPEGAF  201 (270)
T ss_dssp             ---SCCCT---TTTTTCTTCCEEECCSSCCSCCCTTTT
T ss_pred             ---cEeCh---hHhccCCCcCEEECCCCcCCcCCHHHh
Confidence               21111   235678899999999999988887543

>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=99.67  E-value=1.1e-15  Score=156.77  Aligned_cols=173  Identities=24%  Similarity=0.308  Sum_probs=148.4

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++.+++.+|.+..++....+++|+.|.+  +.+....++.  +.++++|+.|++++|.+..+|. ++.+.+|++|++
T Consensus        45 l~~L~~L~l~~~~i~~~~~~~~l~~L~~L~L--~~n~l~~~~~--l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~L  119 (291)
T 1h6t_A           45 LNSIDQIIANNSDIKSVQGIQYLPNVTKLFL--NGNKLTDIKP--LANLKNLGWLFLDENKVKDLSS-LKDLKKLKSLSL  119 (291)
T ss_dssp             HHTCCEEECTTSCCCCCTTGGGCTTCCEEEC--CSSCCCCCGG--GTTCTTCCEEECCSSCCCCGGG-GTTCTTCCEEEC
T ss_pred             cCcccEEEccCCCcccChhHhcCCCCCEEEc--cCCccCCCcc--cccCCCCCEEECCCCcCCCChh-hccCCCCCEEEC
Confidence            4689999999999998887778999999999  3344455554  8899999999999999998765 899999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++.++.+..+++|++|++++|.++.+ ..+..+++|++|++++| .+..+++  +..+++|++|++++|..     
T Consensus       120 ~~n~i~~~~~l~~l~~L~~L~l~~n~l~~~-~~l~~l~~L~~L~L~~N-~l~~~~~--l~~l~~L~~L~L~~N~i-----  190 (291)
T 1h6t_A          120 EHNGISDINGLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDN-QISDIVP--LAGLTKLQNLYLSKNHI-----  190 (291)
T ss_dssp             TTSCCCCCGGGGGCTTCCEEECCSSCCCCC-GGGGGCTTCSEEECCSS-CCCCCGG--GTTCTTCCEEECCSSCC-----
T ss_pred             CCCcCCCChhhcCCCCCCEEEccCCcCCcc-hhhccCCCCCEEEccCC-ccccchh--hcCCCccCEEECCCCcC-----
Confidence            999999988899999999999999999988 56999999999999995 6777766  89999999999999742     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      ++     +..+.++++|+.|++++|.+...|.
T Consensus       191 ~~-----l~~l~~l~~L~~L~l~~n~i~~~~~  217 (291)
T 1h6t_A          191 SD-----LRALAGLKNLDVLELFSQECLNKPI  217 (291)
T ss_dssp             CB-----CGGGTTCTTCSEEEEEEEEEECCCE
T ss_pred             CC-----ChhhccCCCCCEEECcCCcccCCcc
Confidence            21     2357889999999999998866554

>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=99.67  E-value=1.6e-15  Score=157.08  Aligned_cols=175  Identities=21%  Similarity=0.307  Sum_probs=121.4

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|++++|.+..++....+++|+.|.+.  .+....++  .+..+++|+.|++++|.+..+|. +..+++|++|++
T Consensus        62 l~~L~~L~L~~n~i~~~~~~~~l~~L~~L~L~--~n~l~~~~--~~~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l  136 (308)
T 1h6u_A           62 LNNLIGLELKDNQITDLAPLKNLTKITELELS--GNPLKNVS--AIAGLQSIKTLDLTSTQITDVTP-LAGLSNLQVLYL  136 (308)
T ss_dssp             CTTCCEEECCSSCCCCCGGGTTCCSCCEEECC--SCCCSCCG--GGTTCTTCCEEECTTSCCCCCGG-GTTCTTCCEEEC
T ss_pred             cCCCCEEEccCCcCCCChhHccCCCCCEEEcc--CCcCCCch--hhcCCCCCCEEECCCCCCCCchh-hcCCCCCCEEEC
Confidence            45677777777777666655567777777773  22233333  36677777777777777777654 777777777777


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++..+.++.+++|++|++++|.++.+|. +..+++|++|++++| .+..+++  +..+++|++|++++|..     
T Consensus       137 ~~n~l~~~~~l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n-~l~~~~~--l~~l~~L~~L~L~~N~l-----  207 (308)
T 1h6u_A          137 DLNQITNISPLAGLTNLQYLSIGNAQVSDLTP-LANLSKLTTLKADDN-KISDISP--LASLPNLIEVHLKNNQI-----  207 (308)
T ss_dssp             CSSCCCCCGGGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCCGG--GGGCTTCCEEECTTSCC-----
T ss_pred             CCCccCcCccccCCCCccEEEccCCcCCCChh-hcCCCCCCEEECCCC-ccCcChh--hcCCCCCCEEEccCCcc-----
Confidence            77777775557777778888887777777766 777777888888773 4566654  67778888888777632     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      .+     +..+..+++|+.|++++|.+...|..+
T Consensus       208 ~~-----~~~l~~l~~L~~L~l~~N~i~~~~~~~  236 (308)
T 1h6u_A          208 SD-----VSPLANTSNLFIVTLTNQTITNQPVFY  236 (308)
T ss_dssp             CB-----CGGGTTCTTCCEEEEEEEEEECCCEEC
T ss_pred             Cc-----cccccCCCCCCEEEccCCeeecCCeee
Confidence            21     113677888889999888887766543

>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=99.66  E-value=1.4e-15  Score=152.63  Aligned_cols=177  Identities=22%  Similarity=0.327  Sum_probs=141.8

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEc
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCL  605 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L  605 (724)
                      ...++++++++.+..+|.... ++++.|.+  ..+....++...|.++++|++|++++|.+..++ ..+..+.+|++|+|
T Consensus        14 ~~~~~l~~~~~~l~~~p~~~~-~~l~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L   90 (251)
T 3m19_A           14 EGKKEVDCQGKSLDSVPSGIP-ADTEKLDL--QSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGL   90 (251)
T ss_dssp             GGGTEEECTTCCCSSCCSCCC-TTCCEEEC--TTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEEC
T ss_pred             CCCeEEecCCCCccccCCCCC-CCCCEEEc--cCCCcCccCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEEC
Confidence            355678888888888886554 68999988  445556667777889999999999999998664 45788999999999


Q ss_pred             CCcccCC-c-ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcc
Q 004895          606 DGWRLED-I-AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW  682 (724)
Q Consensus       606 ~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~  682 (724)
                      ++|.++. + ..+..+++|++|++++|.++.+|.. +..+++|++|++++ +.+..+++..++.+++|++|++++|..  
T Consensus        91 ~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~-N~l~~~~~~~~~~l~~L~~L~L~~N~l--  167 (251)
T 3m19_A           91 ANNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNT-NQLQSIPAGAFDKLTNLQTLSLSTNQL--  167 (251)
T ss_dssp             TTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCCCCCTTTTTTCTTCCEEECCSSCC--
T ss_pred             CCCcccccChhHhcccCCCCEEEcCCCcCCCcChhHhccCCcccEEECcC-CcCCccCHHHcCcCcCCCEEECCCCcC--
Confidence            9999888 3 4678999999999999999988776 58899999999998 577888887788999999999998743  


Q ss_pred             ccccCCccchHHhhcCCCCCcEEEeeccccccc
Q 004895          683 DKVEGGSNASLAELKGLSKLTTLEIDVRDAEML  715 (724)
Q Consensus       683 ~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~l  715 (724)
                         .+..+   ..+.++++|+.|++++|.+..-
T Consensus       168 ---~~~~~---~~~~~l~~L~~L~l~~N~~~c~  194 (251)
T 3m19_A          168 ---QSVPH---GAFDRLGKLQTITLFGNQFDCS  194 (251)
T ss_dssp             ---SCCCT---TTTTTCTTCCEEECCSCCBCTT
T ss_pred             ---CccCH---HHHhCCCCCCEEEeeCCceeCC
Confidence               22112   3456778899999999987553

>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=99.66  E-value=6.4e-16  Score=161.55  Aligned_cols=183  Identities=21%  Similarity=0.296  Sum_probs=149.7

Q ss_pred             ccCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhh--------hcCCCCceEEEcCCCcCCCCCccccC
Q 004895          526 QKGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHF--------FEGTEELKVLDFTGIRFSPLPSSLGR  596 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~--------~~~l~~L~~L~l~~~~~~~lp~~i~~  596 (724)
                      ..++++|++++|.+..+|... .+++|+.|.+. .+.....+|..+        |.++++|++|++++|.+..+|..+++
T Consensus       126 l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L~L~-~n~~~~~~p~~~~~~~~~~~~~~l~~L~~L~L~~n~l~~lp~~l~~  204 (328)
T 4fcg_A          126 FAGLETLTLARNPLRALPASIASLNRLRELSIR-ACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIAN  204 (328)
T ss_dssp             GTTCSEEEEESCCCCCCCGGGGGCTTCCEEEEE-EETTCCCCCSCSEEEC-CCCEEESTTCCEEEEEEECCCCCCGGGGG
T ss_pred             cCCCCEEECCCCccccCcHHHhcCcCCCEEECC-CCCCccccChhHhhccchhhhccCCCCCEEECcCCCcCcchHhhcC
Confidence            578999999999999888654 78999999994 333444455433        44699999999999999999999999


Q ss_pred             CCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEE
Q 004895          597 LINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELY  674 (724)
Q Consensus       597 l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~  674 (724)
                      +.+|++|+|++|.++. |+.++.+++|++|++++|.+. .+|..+..+++|++|++++|+.+..+|.. ++.+++|++|+
T Consensus       205 l~~L~~L~L~~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~~~~~~p~~-~~~l~~L~~L~  283 (328)
T 4fcg_A          205 LQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLD-IHRLTQLEKLD  283 (328)
T ss_dssp             CTTCCEEEEESSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEECTTCTTCCBCCTT-GGGCTTCCEEE
T ss_pred             CCCCCEEEccCCCCCcCchhhccCCCCCEEECcCCcchhhhHHHhcCCCCCCEEECCCCCchhhcchh-hhcCCCCCEEe
Confidence            9999999999999988 678999999999999998655 78889999999999999998877777654 89999999999


Q ss_pred             ccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      +++|.     ..+..|   ..+.+|++|+.+.+..+.+..++..
T Consensus       284 L~~n~-----~~~~iP---~~l~~L~~L~~l~l~~~~~~~l~~~  319 (328)
T 4fcg_A          284 LRGCV-----NLSRLP---SLIAQLPANCIILVPPHLQAQLDQH  319 (328)
T ss_dssp             CTTCT-----TCCCCC---GGGGGSCTTCEEECCGGGSCC----
T ss_pred             CCCCC-----chhhcc---HHHhhccCceEEeCCHHHHHHHhhh
Confidence            99974     333444   3456778899999998877666644

>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=99.65  E-value=6.5e-15  Score=155.98  Aligned_cols=293  Identities=14%  Similarity=0.133  Sum_probs=171.0

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-----CChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-----PDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~l~~~  231 (724)
                      .....|+||+++++.|.+ +..   +++.|+|++|+|||||++.+++....     ..+|+++...     .+...+...
T Consensus        10 ~~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~   80 (357)
T 2fna_A           10 DNRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNL-----PYIYLDLRKFEERNYISYKDFLLE   80 (357)
T ss_dssp             CSGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTC-----CEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             CCHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCC-----CEEEEEchhhccccCCCHHHHHHH
Confidence            345678999999999999 765   69999999999999999999987642     2678887653     344555555


Q ss_pred             HHHhhC--------------C----CCCCC--ch-----hHHHHHHHHHHHhc-C-CcEEEEEcccccccc-----cccc
Q 004895          232 LASDLG--------------M----NFDSN--DL-----IYHRAKQLCQRLKK-E-KRVLIILDNIWTKLE-----LDKI  279 (724)
Q Consensus       232 i~~~l~--------------~----~~~~~--~~-----~~~~~~~l~~~l~~-~-kr~LlVlDdv~~~~~-----~~~l  279 (724)
                      +.+.+.              .    ..+..  ..     .......+.+.+.. . ++++|||||++....     +..+
T Consensus        81 l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~  160 (357)
T 2fna_A           81 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  160 (357)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHH
Confidence            444331              0    00000  00     00112334444432 1 489999999976432     2111


Q ss_pred             ccccCCCCcCCCCCCCCCcEEEEEecccchhhh----------hcC-CCceEecCCCCHHHHHHHHHHHhCCCCCCCCch
Q 004895          280 GIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCI----------DMN-SQKMFWIDALSEEEALQLFEKIVGESTKASDFR  348 (724)
Q Consensus       280 ~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~----------~~~-~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~  348 (724)
                      ...+..        ...+.++|+|++.......          ..+ ....+.+.+|+.+|+.+++...+.......+  
T Consensus       161 l~~~~~--------~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~--  230 (357)
T 2fna_A          161 LAYAYD--------NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK--  230 (357)
T ss_dssp             HHHHHH--------HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC--
T ss_pred             HHHHHH--------cCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCC--
Confidence            111111        1246789999987542110          011 1257999999999999999886532111111  


Q ss_pred             hHHHHHHHHhCCchhHHHHHHHHhcC-CCHHHHHH-HHHHHhcCccccccCCCcccchhhHhhh---hhcHHHHHHHHHh
Q 004895          349 PLAEEIVGKCGGLPVALSTVANALKN-KSPAIWKD-ALNKLTSSNLREIHGMDADVYSPIKLSY---DFLDDEAKSLFLL  423 (724)
Q Consensus       349 ~~~~~I~~~c~GlPLai~~~~~~l~~-~~~~~w~~-~~~~l~~~~~~~~~~~~~~i~~~l~~sy---~~L~~~~k~cf~~  423 (724)
                      +. ..|++.|+|+|+++..++..+.. .+...|.. +.+...           ..+..-+...+   ..||+..+..+..
T Consensus       231 ~~-~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~~~l~~~~~~~l~~  298 (357)
T 2fna_A          231 DY-EVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAK-----------KLILKEFENFLHGREIARKRYLNIMRT  298 (357)
T ss_dssp             CH-HHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHH-----------HHHHHHHHHHHTTCGGGHHHHHHHHHH
T ss_pred             cH-HHHHHHhCCCHHHHHHHHHHHccccchHHHHHHHHHHHH-----------HHHHHHHHHHhhccccccHHHHHHHHH
Confidence            12 78999999999999999887642 23333321 111100           00111111111   1789999999999


Q ss_pred             hccCCCCCcccHHHHHHHHhhcccccccccccccccHHHHHHHHHHHHHHHHhhcccccCCCCCcch-hhHHHHHHH
Q 004895          424 CGLHREGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGDAEDEAK-LHDVIHVVA  499 (724)
Q Consensus       424 ~s~fp~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~~~~~~~~~-mHdlv~d~a  499 (724)
                      +|.   + . +...+....-     ...|.   ..+.    ..+..+++.|.+.+++...+  ..|+ .|++++++.
T Consensus       299 la~---g-~-~~~~l~~~~~-----~~~g~---~~~~----~~~~~~L~~L~~~gli~~~~--~~y~f~~~~~~~~l  356 (357)
T 2fna_A          299 LSK---C-G-KWSDVKRALE-----LEEGI---EISD----SEIYNYLTQLTKHSWIIKEG--EKYCPSEPLISLAF  356 (357)
T ss_dssp             HTT---C-B-CHHHHHHHHH-----HHHCS---CCCH----HHHHHHHHHHHHTTSEEESS--SCEEESSHHHHHHT
T ss_pred             HHc---C-C-CHHHHHHHHH-----HhcCC---CCCH----HHHHHHHHHHHhCCCEEecC--CEEEecCHHHHHhh
Confidence            998   2 2 4555543210     00110   0011    22445678888899987543  3466 589998864

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.64  E-value=3.6e-15  Score=154.40  Aligned_cols=173  Identities=18%  Similarity=0.279  Sum_probs=149.0

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|++.++.+..++....+++|+.|.+  +.+....++.  +.++++|+.|++++|.+..+| .++.+.+|++|++
T Consensus        40 l~~L~~L~l~~~~i~~l~~~~~l~~L~~L~L--~~n~i~~~~~--~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~L~l  114 (308)
T 1h6u_A           40 LDGITTLSAFGTGVTTIEGVQYLNNLIGLEL--KDNQITDLAP--LKNLTKITELELSGNPLKNVS-AIAGLQSIKTLDL  114 (308)
T ss_dssp             HHTCCEEECTTSCCCCCTTGGGCTTCCEEEC--CSSCCCCCGG--GTTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEEC
T ss_pred             cCCcCEEEeeCCCccCchhhhccCCCCEEEc--cCCcCCCChh--HccCCCCCEEEccCCcCCCch-hhcCCCCCCEEEC
Confidence            4689999999999988887678999999999  3344555555  889999999999999999886 6899999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++.++.+..+++|++|++++|.++.+|. +..+++|++|++++| .+..+++  +..+++|++|++++|..     
T Consensus       115 ~~n~l~~~~~l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n-~l~~~~~--l~~l~~L~~L~l~~n~l-----  185 (308)
T 1h6u_A          115 TSTQITDVTPLAGLSNLQVLYLDLNQITNISP-LAGLTNLQYLSIGNA-QVSDLTP--LANLSKLTTLKADDNKI-----  185 (308)
T ss_dssp             TTSCCCCCGGGTTCTTCCEEECCSSCCCCCGG-GGGCTTCCEEECCSS-CCCCCGG--GTTCTTCCEEECCSSCC-----
T ss_pred             CCCCCCCchhhcCCCCCCEEECCCCccCcCcc-ccCCCCccEEEccCC-cCCCChh--hcCCCCCCEEECCCCcc-----
Confidence            99999997779999999999999999998877 899999999999995 6777765  89999999999998743     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .+     +..+..+++|+.|+++.|.+..++.
T Consensus       186 ~~-----~~~l~~l~~L~~L~L~~N~l~~~~~  212 (308)
T 1h6u_A          186 SD-----ISPLASLPNLIEVHLKNNQISDVSP  212 (308)
T ss_dssp             CC-----CGGGGGCTTCCEEECTTSCCCBCGG
T ss_pred             Cc-----ChhhcCCCCCCEEEccCCccCcccc
Confidence            21     1227788999999999999988875

>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=4.1e-15  Score=151.11  Aligned_cols=176  Identities=23%  Similarity=0.290  Sum_probs=137.8

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~  604 (724)
                      ..+++.+.+.++.+..++....+++|+.|.+.  .+....++  .+.++++|++|++++|.+..+|. .++.+.+|++|+
T Consensus        40 l~~L~~L~l~~~~i~~~~~l~~l~~L~~L~l~--~n~l~~~~--~l~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~  115 (272)
T 3rfs_A           40 LNSIDQIIANNSDIKSVQGIQYLPNVRYLALG--GNKLHDIS--ALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELV  115 (272)
T ss_dssp             HTTCCEEECTTSCCCCCTTGGGCTTCCEEECT--TSCCCCCG--GGTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEE
T ss_pred             ccceeeeeeCCCCcccccccccCCCCcEEECC--CCCCCCch--hhcCCCCCCEEECCCCccCccChhHhcCCcCCCEEE
Confidence            46888999998888888776788999999983  33333333  47788999999999999987765 468899999999


Q ss_pred             cCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          605 LDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       605 L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      +++|.++..  ..++.+++|++|++++|.++.+|.. +..+++|++|++++| .+..+++..++.+++|++|++++|.. 
T Consensus       116 L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~L~~N~l-  193 (272)
T 3rfs_A          116 LVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYN-QLQSLPEGVFDKLTQLKDLRLYQNQL-  193 (272)
T ss_dssp             CTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSCC-
T ss_pred             CCCCcCCccCHHHhccCCCCCEEECCCCccCccCHHHhccCccCCEEECCCC-CcCccCHHHhcCCccCCEEECCCCcC-
Confidence            999998873  3478899999999999998888765 578999999999984 67778877778899999999988642 


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                          .+..+   ..+.++++|+.|+++.|.+..
T Consensus       194 ----~~~~~---~~~~~l~~L~~L~l~~N~~~~  219 (272)
T 3rfs_A          194 ----KSVPD---GVFDRLTSLQYIWLHDNPWDC  219 (272)
T ss_dssp             ----SCCCT---TTTTTCTTCCEEECCSSCBCC
T ss_pred             ----CccCH---HHHhCCcCCCEEEccCCCccc
Confidence                22222   235677889999999887643

>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=99.62  E-value=3.4e-15  Score=163.56  Aligned_cols=183  Identities=23%  Similarity=0.280  Sum_probs=108.1

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|+.|++++|.+..+|. .+..+.+|++
T Consensus        74 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L--s~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  151 (452)
T 3zyi_A           74 PSNTRYLNLMENNIQMIQADTFRHLHHLEVLQL--GRNSIRQIEVGAFNGLASLNTLELFDNWLTVIPSGAFEYLSKLRE  151 (452)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEEC--CSSCCCEECTTTTTTCTTCCEEECCSSCCSBCCTTTSSSCTTCCE
T ss_pred             CCCccEEECcCCcCceECHHHcCCCCCCCEEEC--CCCccCCcChhhccCcccCCEEECCCCcCCccChhhhcccCCCCE
Confidence            4566677777776655532  225666677666  3333444555556666666666666666665544 3556666666


Q ss_pred             EEcCCcccCCc--c-------------------------cccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCC
Q 004895          603 LCLDGWRLEDI--A-------------------------IVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSS  655 (724)
Q Consensus       603 L~L~~~~l~~~--~-------------------------~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~  655 (724)
                      |+|++|.++.+  .                         .+..+++|++|++++|.++.+| .+..+++|++|++++ +.
T Consensus       152 L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~L~Ls~-N~  229 (452)
T 3zyi_A          152 LWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDMP-NLTPLVGLEELEMSG-NH  229 (452)
T ss_dssp             EECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCCSSCC-CCTTCTTCCEEECTT-SC
T ss_pred             EECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCcccccc-cccccccccEEECcC-Cc
Confidence            66666665541  1                         2445555555555555555554 255566666666666 34


Q ss_pred             CcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          656 LVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       656 l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      +..+++..+..+++|+.|++++|..     .+.   ....+.++++|+.|++++|.++.+|...+
T Consensus       230 l~~~~~~~~~~l~~L~~L~L~~n~l-----~~~---~~~~~~~l~~L~~L~L~~N~l~~~~~~~~  286 (452)
T 3zyi_A          230 FPEIRPGSFHGLSSLKKLWVMNSQV-----SLI---ERNAFDGLASLVELNLAHNNLSSLPHDLF  286 (452)
T ss_dssp             CSEECGGGGTTCTTCCEEECTTSCC-----CEE---CTTTTTTCTTCCEEECCSSCCSCCCTTSS
T ss_pred             CcccCcccccCccCCCEEEeCCCcC-----ceE---CHHHhcCCCCCCEEECCCCcCCccChHHh
Confidence            5555555666667777777666532     111   12345667788888888888887776543

>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=99.62  E-value=4.2e-15  Score=167.37  Aligned_cols=173  Identities=24%  Similarity=0.309  Sum_probs=148.6

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ...++.|.+.+|.+..++....+++|+.|.+  +.+....+++  +..+++|+.|+|++|.+..+| .++.+.+|++|+|
T Consensus        42 L~~L~~L~l~~n~i~~l~~l~~l~~L~~L~L--s~N~l~~~~~--l~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~L  116 (605)
T 1m9s_A           42 LNSIDQIIANNSDIKSVQGIQYLPNVTKLFL--NGNKLTDIKP--LTNLKNLGWLFLDENKIKDLS-SLKDLKKLKSLSL  116 (605)
T ss_dssp             HTTCCCCBCTTCCCCCCTTGGGCTTCCEEEC--TTSCCCCCGG--GGGCTTCCEEECCSSCCCCCT-TSTTCTTCCEEEC
T ss_pred             CCCCCEEECcCCCCCCChHHccCCCCCEEEe--eCCCCCCChh--hccCCCCCEEECcCCCCCCCh-hhccCCCCCEEEe
Confidence            5688999999999998887778999999999  3444555555  789999999999999999877 6899999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.+..++.+..|++|+.|+|++|.++.+ ..+..|++|++|+|++| .+..+++  +..|++|+.|++++|.+     
T Consensus       117 s~N~l~~l~~l~~l~~L~~L~Ls~N~l~~l-~~l~~l~~L~~L~Ls~N-~l~~~~~--l~~l~~L~~L~Ls~N~i-----  187 (605)
T 1m9s_A          117 EHNGISDINGLVHLPQLESLYLGNNKITDI-TVLSRLTKLDTLSLEDN-QISDIVP--LAGLTKLQNLYLSKNHI-----  187 (605)
T ss_dssp             TTSCCCCCGGGGGCTTCSEEECCSSCCCCC-GGGGSCTTCSEEECCSS-CCCCCGG--GTTCTTCCEEECCSSCC-----
T ss_pred             cCCCCCCCccccCCCccCEEECCCCccCCc-hhhcccCCCCEEECcCC-cCCCchh--hccCCCCCEEECcCCCC-----
Confidence            999999988899999999999999999988 56999999999999995 5677766  89999999999999742     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .+     +..+..|++|+.|+++.|.+...|.
T Consensus       188 ~~-----l~~l~~l~~L~~L~L~~N~l~~~p~  214 (605)
T 1m9s_A          188 SD-----LRALAGLKNLDVLELFSQECLNKPI  214 (605)
T ss_dssp             CB-----CGGGTTCTTCSEEECCSEEEECCCC
T ss_pred             CC-----ChHHccCCCCCEEEccCCcCcCCcc
Confidence            21     2457889999999999998876554

>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=99.62  E-value=5.8e-15  Score=151.20  Aligned_cols=179  Identities=20%  Similarity=0.202  Sum_probs=147.1

Q ss_pred             ccCceEEeccCCCcccCC-Cc-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELP-ER-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~-~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~  602 (724)
                      ..++++|.+++|.+..++ .. ..+++|+.|.+. .+.....++...|.++++|+.|++++|.+..+ |..+..+.+|++
T Consensus        55 ~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~-~n~~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~  133 (285)
T 1ozn_A           55 CRNLTILWLHSNVLARIDAAAFTGLALLEQLDLS-DNAQLRSVDPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQY  133 (285)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTTTCTTCCEEECC-SCTTCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCE
T ss_pred             CCCCCEEECCCCccceeCHhhcCCccCCCEEeCC-CCCCccccCHHHhcCCcCCCEEECCCCcCCEECHhHhhCCcCCCE
Confidence            468999999999887763 32 368999999993 22225666667789999999999999999976 667899999999


Q ss_pred             EEcCCcccCC-c-ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLED-I-AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |++++|.++. + ..++.+++|++|++++|.++.+|.. +..+++|++|++++| .+...++..++.+++|+.|++++|.
T Consensus       134 L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~L~l~~n~  212 (285)
T 1ozn_A          134 LYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQN-RVAHVHPHAFRDLGRLMTLYLFANN  212 (285)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS-CCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             EECCCCcccccCHhHhccCCCccEEECCCCcccccCHHHhcCccccCEEECCCC-cccccCHhHccCcccccEeeCCCCc
Confidence            9999999988 3 4589999999999999999988875 889999999999994 5777767778999999999999974


Q ss_pred             CccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          680 SQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       680 ~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      .     .+.   ....+..+++|+.|++++|.+..
T Consensus       213 l-----~~~---~~~~~~~l~~L~~L~l~~N~~~c  239 (285)
T 1ozn_A          213 L-----SAL---PTEALAPLRALQYLRLNDNPWVC  239 (285)
T ss_dssp             C-----SCC---CHHHHTTCTTCCEEECCSSCEEC
T ss_pred             C-----CcC---CHHHcccCcccCEEeccCCCccC
Confidence            3     221   12346788999999999998753

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.62  E-value=3.6e-15  Score=162.84  Aligned_cols=183  Identities=22%  Similarity=0.286  Sum_probs=107.3

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +.+++.|.+++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|+.|++++|.+..+|. .+..+.+|++
T Consensus        63 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L--s~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  140 (440)
T 3zyj_A           63 STNTRLLNLHENQIQIIKVNSFKHLRHLEILQL--SRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPNGAFVYLSKLKE  140 (440)
T ss_dssp             CTTCSEEECCSCCCCEECTTTTSSCSSCCEEEC--CSSCCCEECGGGGTTCSSCCEEECCSSCCSSCCTTTSCSCSSCCE
T ss_pred             CCCCcEEEccCCcCCeeCHHHhhCCCCCCEEEC--CCCcCCccChhhccCCccCCEEECCCCcCCeeCHhHhhccccCce
Confidence            4566777777777766542  235677777777  3334445555566677777777777777766654 4666667777


Q ss_pred             EEcCCcccCCc--ccc-------------------------cCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCC
Q 004895          603 LCLDGWRLEDI--AIV-------------------------GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSS  655 (724)
Q Consensus       603 L~L~~~~l~~~--~~~-------------------------~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~  655 (724)
                      |+|++|.++.+  ..+                         .++++|++|++++|.++.+|. +..+++|++|++++| .
T Consensus       141 L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~Ls~N-~  218 (440)
T 3zyj_A          141 LWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPN-LTPLIKLDELDLSGN-H  218 (440)
T ss_dssp             EECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTSCCSSCCC-CTTCSSCCEEECTTS-C
T ss_pred             eeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCCcCccccc-cCCCcccCEEECCCC-c
Confidence            77776665542  234                         444555555555555555442 455555555555552 4


Q ss_pred             CcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          656 LVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       656 l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      +..+++..+..+++|+.|++++|....     .   ....+.++++|+.|+++.|.++.+|...+
T Consensus       219 l~~~~~~~~~~l~~L~~L~L~~n~l~~-----~---~~~~~~~l~~L~~L~L~~N~l~~~~~~~~  275 (440)
T 3zyj_A          219 LSAIRPGSFQGLMHLQKLWMIQSQIQV-----I---ERNAFDNLQSLVEINLAHNNLTLLPHDLF  275 (440)
T ss_dssp             CCEECTTTTTTCTTCCEEECTTCCCCE-----E---CTTSSTTCTTCCEEECTTSCCCCCCTTTT
T ss_pred             cCccChhhhccCccCCEEECCCCceeE-----E---ChhhhcCCCCCCEEECCCCCCCccChhHh
Confidence            444544555566666666665543211     1   12345567788888888888877776543

>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=99.62  E-value=3e-14  Score=154.15  Aligned_cols=298  Identities=15%  Similarity=0.095  Sum_probs=178.1

Q ss_pred             ccccchHHHHHHHHHHh-c----C--CCccEEEE--EcCCCCcHHHHHHHHHHHHhhc---cCCC-eEEEEEEecCCChH
Q 004895          160 NIFNSRKKIFQDVIEAL-K----D--DKLNIIGV--CGMGGVGKTTLVKQIAKQVMED---NVFD-KVVMAEITKNPDAQ  226 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L-~----~--~~~~vi~I--~G~gGiGKTtLa~~v~~~~~~~---~~F~-~~~wv~vs~~~~~~  226 (724)
                      ..|+||+++++.|.+++ .    .  ...+.+.|  +|++|+||||||+.+++.....   ..|+ .++|+++....+..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLY  101 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHH
Confidence            57899999999999888 4    2  34567777  9999999999999999887542   1233 36788877778889


Q ss_pred             HHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHh-cCCcEEEEEcccccccc--------ccccccccCCCCcCCCCCCC-
Q 004895          227 KIQGELASDLGMNFDSND-LIYHRAKQLCQRLK-KEKRVLIILDNIWTKLE--------LDKIGIPYGDVDEKDKNDDP-  295 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~--------~~~l~~~~~~~~~~~~~~~~-  295 (724)
                      .++..++.+++...+... ........+...+. .+++++|||||++....        +..+...+...     .... 
T Consensus       102 ~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~-----~~~~~  176 (412)
T 1w5s_A          102 TILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEI-----PSRDG  176 (412)
T ss_dssp             HHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHS-----CCTTS
T ss_pred             HHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhc-----ccCCC
Confidence            999999999976543211 12334455555553 35789999999987432        11111111110     0012 


Q ss_pred             -CCcEEEEEecccchhh--------hhcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHhC------
Q 004895          296 -RRCTIILTSRSRDLLC--------IDMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKCG------  359 (724)
Q Consensus       296 -~~s~ilvTtR~~~v~~--------~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c~------  359 (724)
                       ....+|+||+......        ........+.+++|+.++++++|...+.... ...--.+....|++.|+      
T Consensus       177 ~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  256 (412)
T 1w5s_A          177 VNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGD  256 (412)
T ss_dssp             CCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSC
T ss_pred             CceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhccCC
Confidence             4456888887654320        0011123499999999999999987653111 11122567889999999      


Q ss_pred             CchhHHHHHHHHh-c-----CC---CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhccCC--
Q 004895          360 GLPVALSTVANAL-K-----NK---SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHR--  428 (724)
Q Consensus       360 GlPLai~~~~~~l-~-----~~---~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp--  428 (724)
                      |.|..+..+.... .     +.   +...+..+......             ...+..++..||++.+.++..++.+.  
T Consensus       257 G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~-------------~~~~~~~l~~l~~~~~~~l~aia~l~~~  323 (412)
T 1w5s_A          257 GSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEA-------------ASIQTHELEALSIHELIILRLIAEATLG  323 (412)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC-------------------CCSSSSSCHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc-------------cchHHHHHHcCCHHHHHHHHHHHHHHhc
Confidence            9997655544322 1     11   23334333332100             23345567889999999999888653  


Q ss_pred             CCCcccHHHHHHHHhhcccccccccccccccHHHHHHHHHHHHHHHHhhccccc
Q 004895          429 EGRPIHVHYLLRYVMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD  482 (724)
Q Consensus       429 ~~~~i~~~~Li~~W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~  482 (724)
                      .+..++...+...+...-+ ...|. . ..+    ...+..+++.|...+++..
T Consensus       324 ~~~~~~~~~~~~~~~~~~~-~~~~~-~-~~~----~~~~~~~l~~L~~~gli~~  370 (412)
T 1w5s_A          324 GMEWINAGLLRQRYEDASL-TMYNV-K-PRG----YTQYHIYLKHLTSLGLVDA  370 (412)
T ss_dssp             TCSSBCHHHHHHHHHHHHH-HHSCC-C-CCC----HHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCccHHHHHHHHHHHHH-hhcCC-C-CCC----HHHHHHHHHHHHhCCCEEe
Confidence            2235666665554420000 01111 0 001    1234456788888999854

>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=8.5e-15  Score=150.09  Aligned_cols=182  Identities=21%  Similarity=0.254  Sum_probs=152.6

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++.+.+.++.+..+|.... ++++.|.+  +.+....++...|.++++|+.|++++|.+..+|.. +.+.+|++|++
T Consensus         9 l~~l~~l~~~~~~l~~ip~~~~-~~l~~L~L--~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~-~~l~~L~~L~L   84 (290)
T 1p9a_G            9 VASHLEVNCDKRNLTALPPDLP-KDTTILHL--SENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVD-GTLPVLGTLDL   84 (290)
T ss_dssp             STTCCEEECTTSCCSSCCSCCC-TTCCEEEC--TTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEECC-SCCTTCCEEEC
T ss_pred             cCCccEEECCCCCCCcCCCCCC-CCCCEEEc--CCCcCCccCHHHhhcCCCCCEEECCCCccCcccCC-CCCCcCCEEEC
Confidence            3578889999999998886553 78999999  44556667777799999999999999999987764 88999999999


Q ss_pred             CCcccCC-cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccc
Q 004895          606 DGWRLED-IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD  683 (724)
Q Consensus       606 ~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~  683 (724)
                      ++|.++. |..+..+++|++|++++|.++.+|. .+..+++|++|++++ +.+..+|+..+..+++|+.|++++|.... 
T Consensus        85 s~N~l~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~l~~-  162 (290)
T 1p9a_G           85 SHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKG-NELKTLPPGLLTPTPKLEKLSLANNNLTE-  162 (290)
T ss_dssp             CSSCCSSCCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTT-SCCCCCCTTTTTTCTTCCEEECTTSCCSC-
T ss_pred             CCCcCCcCchhhccCCCCCEEECCCCcCcccCHHHHcCCCCCCEEECCC-CCCCccChhhcccccCCCEEECCCCcCCc-
Confidence            9999988 5678899999999999999998875 589999999999999 57788888888999999999999975321 


Q ss_pred             cccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          684 KVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       684 ~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                          ..+   ..+.++++|+.|+++.|.++.+|..++
T Consensus       163 ----l~~---~~~~~l~~L~~L~L~~N~l~~ip~~~~  192 (290)
T 1p9a_G          163 ----LPA---GLLNGLENLDTLLLQENSLYTIPKGFF  192 (290)
T ss_dssp             ----CCT---TTTTTCTTCCEEECCSSCCCCCCTTTT
T ss_pred             ----cCH---HHhcCcCCCCEEECCCCcCCccChhhc
Confidence                111   235678899999999999999987665

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.60  E-value=4.3e-15  Score=151.02  Aligned_cols=170  Identities=19%  Similarity=0.279  Sum_probs=142.0

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L~  604 (724)
                      ..++++|++++|.+..++....+++|+.|.+  +.+....++...|.++++|++|++++|.+..+|.. ++.+.+|++|+
T Consensus        62 l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~  139 (272)
T 3rfs_A           62 LPNVRYLALGGNKLHDISALKELTNLTYLIL--TGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLN  139 (272)
T ss_dssp             CTTCCEEECTTSCCCCCGGGTTCTTCCEEEC--TTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEE
T ss_pred             CCCCcEEECCCCCCCCchhhcCCCCCCEEEC--CCCccCccChhHhcCCcCCCEEECCCCcCCccCHHHhccCCCCCEEE
Confidence            5789999999999988876668999999999  44556677888889999999999999999977654 78999999999


Q ss_pred             cCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          605 LDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       605 L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      +++|.++.+  ..++.+++|++|++++|.++.+|.. +..+++|++|++++| .+..+++..++.+++|++|++++|.. 
T Consensus       140 L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~~-  217 (272)
T 3rfs_A          140 LAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQN-QLKSVPDGVFDRLTSLQYIWLHDNPW-  217 (272)
T ss_dssp             CCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSCB-
T ss_pred             CCCCccCccCHHHhccCccCCEEECCCCCcCccCHHHhcCCccCCEEECCCC-cCCccCHHHHhCCcCCCEEEccCCCc-
Confidence            999999883  3478999999999999999988766 689999999999994 67788888789999999999998732 


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                          .          ..+++|+.|++..|.+.
T Consensus       218 ----~----------~~~~~l~~l~~~~n~~~  235 (272)
T 3rfs_A          218 ----D----------CTCPGIRYLSEWINKHS  235 (272)
T ss_dssp             ----C----------CCTTTTHHHHHHHHHTG
T ss_pred             ----c----------ccCcHHHHHHHHHHhCC
Confidence                1          12445666666666553

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.59  E-value=4.4e-15  Score=154.20  Aligned_cols=183  Identities=16%  Similarity=0.159  Sum_probs=101.7

Q ss_pred             cCceEEeccCCCcc---cCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCc
Q 004895          527 KGPIAISLPYRDIQ---ELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQ  601 (724)
Q Consensus       527 ~~~~~l~l~~~~~~---~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~  601 (724)
                      .++++|+++++.+.   .+|... .+++|+.|.+.+.+.....+|. .|.++++|++|++++|.+. .+|..++++++|+
T Consensus        50 ~~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n~l~~~~p~-~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~  128 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPP-AIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLV  128 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCG-GGGGCTTCSEEEEEEECCEEECCGGGGGCTTCC
T ss_pred             ceEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCCcccccCCh-hHhcCCCCCEEECcCCeeCCcCCHHHhCCCCCC
Confidence            35666666666664   244332 5666666666211222223332 3556666666666666665 5566666666666


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCC-CCCeEccCCCC----------------------C
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLT-RLQLLDLSNCS----------------------S  655 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~-~L~~L~l~~~~----------------------~  655 (724)
                      +|++++|.++.  |..++.+++|++|++++|.++ .+|..+..++ +|++|++++|.                      .
T Consensus       129 ~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~~~~~~~~~~l~L~~L~Ls~N~  208 (313)
T 1ogq_A          129 TLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNM  208 (313)
T ss_dssp             EEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCSEEECCSSE
T ss_pred             EEeCCCCccCCcCChHHhcCCCCCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeeeccCChHHhCCcccEEECcCCc
Confidence            66666666553  455666666666666666665 5566666665 66666666532                      2


Q ss_pred             CcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccc-cccccc
Q 004895          656 LVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE-MLRRIW  719 (724)
Q Consensus       656 l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~-~lp~~~  719 (724)
                      +...++..++.+++|++|++++|.     +.+    .+..+..+++|+.|+++.|.+. .+|..+
T Consensus       209 l~~~~~~~~~~l~~L~~L~L~~N~-----l~~----~~~~~~~l~~L~~L~Ls~N~l~~~~p~~l  264 (313)
T 1ogq_A          209 LEGDASVLFGSDKNTQKIHLAKNS-----LAF----DLGKVGLSKNLNGLDLRNNRIYGTLPQGL  264 (313)
T ss_dssp             EEECCGGGCCTTSCCSEEECCSSE-----ECC----BGGGCCCCTTCCEEECCSSCCEECCCGGG
T ss_pred             ccCcCCHHHhcCCCCCEEECCCCc-----eee----ecCcccccCCCCEEECcCCcccCcCChHH
Confidence            222333334444555555554432     111    1233566778888888888876 455443

>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=99.59  E-value=3.4e-15  Score=148.60  Aligned_cols=182  Identities=14%  Similarity=0.207  Sum_probs=148.2

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEeccccc-ccccchhhhcCCCCceEEEcCC-CcCCCCC-ccccCCCCC
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDS-TLQISDHFFEGTEELKVLDFTG-IRFSPLP-SSLGRLINL  600 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~-~~~~~~~~~~~l~~L~~L~l~~-~~~~~lp-~~i~~l~~L  600 (724)
                      +..+++|++++|.+..++..  ..+++|+.|.+  ..+. ...++...|.++++|+.|++++ |.+..+| ..+..+++|
T Consensus        30 ~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l--~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L  107 (239)
T 2xwt_C           30 PPSTQTLKLIETHLRTIPSHAFSNLPNISRIYV--SIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLL  107 (239)
T ss_dssp             CTTCCEEEEESCCCSEECTTTTTTCTTCCEEEE--ECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTC
T ss_pred             CCcccEEEEeCCcceEECHHHccCCCCCcEEeC--CCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCC
Confidence            46899999999999888752  37899999999  3333 5677777789999999999998 9999776 468899999


Q ss_pred             cEEEcCCcccCCcccccCCCCCc---EEEccCC-cCcccchh-hhcCCCCC-eEccCCCCCCcccChHHhhCCCCCcEEE
Q 004895          601 QTLCLDGWRLEDIAIVGQLKKLE---ILSLRGA-EIKQLPLQ-IGQLTRLQ-LLDLSNCSSLVVIAPNVISKLSRLEELY  674 (724)
Q Consensus       601 ~~L~L~~~~l~~~~~~~~l~~L~---~L~l~~~-~i~~lp~~-i~~l~~L~-~L~l~~~~~l~~~~~~~i~~l~~L~~L~  674 (724)
                      ++|++++|.++.++.++.+.+|+   +|++++| .++.+|.. +..+++|+ +|++++ +.+..+|+..+.. ++|++|+
T Consensus       108 ~~L~l~~n~l~~lp~~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~-n~l~~i~~~~~~~-~~L~~L~  185 (239)
T 2xwt_C          108 KFLGIFNTGLKMFPDLTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYN-NGFTSVQGYAFNG-TKLDAVY  185 (239)
T ss_dssp             CEEEEEEECCCSCCCCTTCCBCCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCS-CCCCEECTTTTTT-CEEEEEE
T ss_pred             CEEeCCCCCCccccccccccccccccEEECCCCcchhhcCcccccchhcceeEEEcCC-CCCcccCHhhcCC-CCCCEEE
Confidence            99999999998866688888888   9999999 99988775 88999999 999998 4677888765544 8999999


Q ss_pred             ccCCC-CccccccCCccchHHhhcCC-CCCcEEEeeccccccccccc
Q 004895          675 MGDSF-SQWDKVEGGSNASLAELKGL-SKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       675 l~~~~-~~~~~~~~~~~~~l~~L~~L-~~L~~L~l~~n~~~~lp~~~  719 (724)
                      +++|. ...     ..   ...+.++ ++|+.|+++.|.++.+|...
T Consensus       186 L~~n~~l~~-----i~---~~~~~~l~~~L~~L~l~~N~l~~l~~~~  224 (239)
T 2xwt_C          186 LNKNKYLTV-----ID---KDAFGGVYSGPSLLDVSQTSVTALPSKG  224 (239)
T ss_dssp             CTTCTTCCE-----EC---TTTTTTCSBCCSEEECTTCCCCCCCCTT
T ss_pred             cCCCCCccc-----CC---HHHhhccccCCcEEECCCCccccCChhH
Confidence            99873 221     11   1235567 89999999999999988763

>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=99.59  E-value=8.1e-15  Score=149.34  Aligned_cols=151  Identities=23%  Similarity=0.293  Sum_probs=118.9

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~  602 (724)
                      +..+++|++++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|+.|++++|.+..+| ..+..+.+|++
T Consensus        27 ~~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  104 (276)
T 2z62_A           27 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDL--SRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK  104 (276)
T ss_dssp             CTTCCEEECTTCCCCEECTTTTTTCTTCSEEEC--TTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCE
T ss_pred             CCCccEEECCCCcccccCHhHhccccCCcEEEC--CCCcCCccCHHHccCCcCCCEEECCCCccCccChhhhcCCccccE
Confidence            5678999999998877763  336889999998  344556677777888999999999999988654 67888999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcc--cchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCc----EEE
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQ--LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE----ELY  674 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~--lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~----~L~  674 (724)
                      |++++|.+...  ..++.+++|++|++++|.++.  +|..+..+++|++|++++ +.+..+++..+..+++|+    .|+
T Consensus       105 L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls~-N~l~~~~~~~~~~l~~L~~l~l~L~  183 (276)
T 2z62_A          105 LVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSS-NKIQSIYCTDLRVLHQMPLLNLSLD  183 (276)
T ss_dssp             EECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCS-SCCCEECGGGGHHHHTCTTCCEEEE
T ss_pred             EECCCCCccccCchhcccCCCCCEEECcCCccceecCchhhccCCCCCEEECCC-CCCCcCCHHHhhhhhhccccceeee
Confidence            99999988773  358889999999999998885  688899999999999998 456677665566555555    677


Q ss_pred             ccCCC
Q 004895          675 MGDSF  679 (724)
Q Consensus       675 l~~~~  679 (724)
                      +++|.
T Consensus       184 ls~n~  188 (276)
T 2z62_A          184 LSLNP  188 (276)
T ss_dssp             CCSSC
T ss_pred             cCCCc
Confidence            76654

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.58  E-value=9.1e-15  Score=151.78  Aligned_cols=179  Identities=16%  Similarity=0.207  Sum_probs=122.3

Q ss_pred             ccCceEEeccCCCcc-cCCCc-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCC-CCc
Q 004895          526 QKGPIAISLPYRDIQ-ELPER-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLI-NLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~-~~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~-~L~  601 (724)
                      ..++++|++++|.+. .+|.. ..+++|+.|.+  +.+......+..|..+++|++|++++|.+. .+|..++.+. +|+
T Consensus       100 l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~L--s~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~~L~  177 (313)
T 1ogq_A          100 LTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDF--SYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFT  177 (313)
T ss_dssp             CTTCSEEEEEEECCEEECCGGGGGCTTCCEEEC--CSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCC
T ss_pred             CCCCCEEECcCCeeCCcCCHHHhCCCCCCEEeC--CCCccCCcCChHHhcCCCCCeEECcCCcccCcCCHHHhhhhhcCc
Confidence            345666666666664 34432 25666666666  222233223334666777777777777776 6677777776 777


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +|++++|.++.  |..++.+. |++|++++|.++ ..|..+..+++|++|++++| .+...++. +..+++|++|++++|
T Consensus       178 ~L~L~~N~l~~~~~~~~~~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~~-~~~l~~L~~L~Ls~N  254 (313)
T 1ogq_A          178 SMTISRNRLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKN-SLAFDLGK-VGLSKNLNGLDLRNN  254 (313)
T ss_dssp             EEECCSSEEEEECCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEECCSS-EECCBGGG-CCCCTTCCEEECCSS
T ss_pred             EEECcCCeeeccCChHHhCCc-ccEEECcCCcccCcCCHHHhcCCCCCEEECCCC-ceeeecCc-ccccCCCCEEECcCC
Confidence            77777777664  45666665 788888887777 45667889999999999995 45555554 789999999999997


Q ss_pred             CCccccccCCccchHHhhcCCCCCcEEEeeccccc-cccc
Q 004895          679 FSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE-MLRR  717 (724)
Q Consensus       679 ~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~-~lp~  717 (724)
                      .     +.+..+   ..+.++++|+.|++++|.+. .+|.
T Consensus       255 ~-----l~~~~p---~~l~~l~~L~~L~Ls~N~l~~~ip~  286 (313)
T 1ogq_A          255 R-----IYGTLP---QGLTQLKFLHSLNVSFNNLCGEIPQ  286 (313)
T ss_dssp             C-----CEECCC---GGGGGCTTCCEEECCSSEEEEECCC
T ss_pred             c-----ccCcCC---hHHhcCcCCCEEECcCCcccccCCC
Confidence            4     333333   34667889999999999986 4554

>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=99.57  E-value=7e-15  Score=152.27  Aligned_cols=182  Identities=25%  Similarity=0.253  Sum_probs=97.9

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccc---------
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSL---------  594 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i---------  594 (724)
                      +.++++|.+++|.+..++..  ..+++|+.|.+..+...........+.++++|++|++++|.+..+|..+         
T Consensus        27 ~~~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~l~~~~~~l~~L~~L  106 (306)
T 2z66_A           27 PSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHL  106 (306)
T ss_dssp             CTTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHHHSCSCCCEEECCSCSEEEEEEEEETCTTCCEE
T ss_pred             CCCCCEEECCCCccCccCHhHhhccccCCEEECCCCccCcccCcccccccccccCEEECCCCccccChhhcCCCCCCCEE
Confidence            45677777777777766653  3667777777732221111110122334455555555555544444444         


Q ss_pred             ----------------cCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcc--cchhhhcCCCCCeEccCCCC
Q 004895          595 ----------------GRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQ--LPLQIGQLTRLQLLDLSNCS  654 (724)
Q Consensus       595 ----------------~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~--lp~~i~~l~~L~~L~l~~~~  654 (724)
                                      ..+.+|++|++++|.+..  +..+..+++|++|++++|.++.  +|..+..+++|++|++++| 
T Consensus       107 ~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n-  185 (306)
T 2z66_A          107 DFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQC-  185 (306)
T ss_dssp             ECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTS-
T ss_pred             ECCCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCEEECCCCccccccchhHHhhCcCCCEEECCCC-
Confidence                            444555555555554443  2335555555556665555543  4555566666666666663 


Q ss_pred             CCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccc
Q 004895          655 SLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       655 ~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                      .+..+++..++.+++|++|++++|..     .+..+   ..+..+++|+.|++++|.+...+
T Consensus       186 ~l~~~~~~~~~~l~~L~~L~L~~N~l-----~~~~~---~~~~~l~~L~~L~L~~N~l~~~~  239 (306)
T 2z66_A          186 QLEQLSPTAFNSLSSLQVLNMSHNNF-----FSLDT---FPYKCLNSLQVLDYSLNHIMTSK  239 (306)
T ss_dssp             CCCEECTTTTTTCTTCCEEECTTSCC-----SBCCS---GGGTTCTTCCEEECTTSCCCBCS
T ss_pred             CcCCcCHHHhcCCCCCCEEECCCCcc-----CccCh---hhccCcccCCEeECCCCCCcccC
Confidence            44555455566666666666666432     11111   23556777888888888776544

>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=99.57  E-value=2.5e-14  Score=156.76  Aligned_cols=150  Identities=22%  Similarity=0.231  Sum_probs=127.3

Q ss_pred             CceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcC
Q 004895          528 GPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLD  606 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~  606 (724)
                      ..+.+...+..+..+|... .++++.|.+  ..+....++...|.++++|+.|++++|.+..+ |..+..+.+|++|+|+
T Consensus        55 ~~~~v~c~~~~l~~iP~~~-~~~l~~L~L--~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~  131 (452)
T 3zyi_A           55 QFSKVVCTRRGLSEVPQGI-PSNTRYLNL--MENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELF  131 (452)
T ss_dssp             SSCEEECCSSCCSSCCSCC-CTTCSEEEC--CSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECC
T ss_pred             CCcEEEECCCCcCccCCCC-CCCccEEEC--cCCcCceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECC
Confidence            3456777777888888644 368999999  44556667777899999999999999999965 4789999999999999


Q ss_pred             CcccCC-c-ccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          607 GWRLED-I-AIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       607 ~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      +|.++. + ..+..+++|++|++++|.++.+|. .+.++++|++|++++|+.+..+++..+..+++|++|++++|..
T Consensus       132 ~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l  208 (452)
T 3zyi_A          132 DNWLTVIPSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNI  208 (452)
T ss_dssp             SSCCSBCCTTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCC
T ss_pred             CCcCCccChhhhcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCcc
Confidence            999988 3 458999999999999999998876 5889999999999998888888888889999999999988753

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.57  E-value=2.2e-14  Score=156.52  Aligned_cols=149  Identities=23%  Similarity=0.300  Sum_probs=127.4

Q ss_pred             ceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCC
Q 004895          529 PIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDG  607 (724)
Q Consensus       529 ~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~  607 (724)
                      .+.+...+..+..+|.... ++++.|.+  ..+....++...|.++++|+.|++++|.+..++ ..+..+.+|++|+|++
T Consensus        45 ~~~v~c~~~~l~~iP~~~~-~~l~~L~L--~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~  121 (440)
T 3zyj_A           45 FSKVICVRKNLREVPDGIS-TNTRLLNL--HENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFD  121 (440)
T ss_dssp             SCEEECCSCCCSSCCSCCC-TTCSEEEC--CSCCCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCS
T ss_pred             CCEEEeCCCCcCcCCCCCC-CCCcEEEc--cCCcCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCC
Confidence            4567777778888886543 78999999  445566677778999999999999999999764 6789999999999999


Q ss_pred             cccCCc--ccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          608 WRLEDI--AIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       608 ~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      |.++.+  ..+..+++|++|++++|.++.+|. .+.++++|++|++++|+.+..+++..+..+++|++|++++|..
T Consensus       122 n~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l  197 (440)
T 3zyj_A          122 NRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNL  197 (440)
T ss_dssp             SCCSSCCTTTSCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTSCC
T ss_pred             CcCCeeCHhHhhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCCcC
Confidence            999883  469999999999999999998876 5889999999999998888888887889999999999988753

>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=99.57  E-value=7.5e-15  Score=155.35  Aligned_cols=190  Identities=17%  Similarity=0.181  Sum_probs=91.0

Q ss_pred             CceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc--cccCCCCCcEE
Q 004895          528 GPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS--SLGRLINLQTL  603 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~--~i~~l~~L~~L  603 (724)
                      ++++|++++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|++|++++|.+..+|.  .+..+++|++|
T Consensus        77 ~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L--s~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~L~~L  154 (353)
T 2z80_A           77 NLQALVLTSNGINTIEEDSFSSLGSLEHLDL--SYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQIL  154 (353)
T ss_dssp             TCCEEECTTSCCCEECTTTTTTCTTCCEEEC--CSSCCSSCCHHHHTTCTTCSEEECTTCCCSSSCSSCSCTTCTTCCEE
T ss_pred             CCCEEECCCCccCccCHhhcCCCCCCCEEEC--CCCcCCcCCHhHhCCCccCCEEECCCCCCcccCchhhhccCCCCcEE
Confidence            44444444444433321  113444444444  2222333444444444455555555544444443  34444455555


Q ss_pred             EcCCcc-cCC--cccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          604 CLDGWR-LED--IAIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       604 ~L~~~~-l~~--~~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++++|. +..  +..++.+++|++|++++|.++.+ |..+..+++|++|++++| .+..+|...++.+++|++|++++|.
T Consensus       155 ~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n-~l~~~~~~~~~~~~~L~~L~L~~n~  233 (353)
T 2z80_A          155 RVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLILHMK-QHILLLEIFVDVTSSVECLELRDTD  233 (353)
T ss_dssp             EEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSEEEEEEEECS-CSTTHHHHHHHHTTTEEEEEEESCB
T ss_pred             ECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHhccccCCeecCCCC-ccccchhhhhhhcccccEEECCCCc
Confidence            554442 333  13344455555555555544433 444555555555555552 3344444334445666666666553


Q ss_pred             CccccccCC-------------------cc----chHHhhcCCCCCcEEEeecccccccccccc
Q 004895          680 SQWDKVEGG-------------------SN----ASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       680 ~~~~~~~~~-------------------~~----~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      .........                   ..    .....+.++++|+.|++++|.++.+|...+
T Consensus       234 l~~~~~~~l~~~~~~~~l~~l~L~~~~l~~~~l~~l~~~l~~l~~L~~L~Ls~N~l~~i~~~~~  297 (353)
T 2z80_A          234 LDTFHFSELSTGETNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLELEFSRNQLKSVPDGIF  297 (353)
T ss_dssp             CTTCCCC------CCCCCCEEEEESCBCCHHHHHHHHHHHHTCTTCCEEECCSSCCCCCCTTTT
T ss_pred             cccccccccccccccchhhccccccccccCcchhhhHHHHhcccCCCEEECCCCCCCccCHHHH
Confidence            221100000                   00    112346778899999999999998887653

>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=99.56  E-value=3e-14  Score=145.10  Aligned_cols=173  Identities=20%  Similarity=0.280  Sum_probs=129.6

Q ss_pred             EeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCccc
Q 004895          532 ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRL  610 (724)
Q Consensus       532 l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~~l  610 (724)
                      +.-.+.++..+|... .++|+.|.+  +.+....++...|.++++|++|++++|.+..+| ..+..+.+|++|++++|.+
T Consensus        12 ~~c~~~~l~~ip~~l-~~~l~~L~l--s~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l   88 (276)
T 2z62_A           12 YQCMELNFYKIPDNL-PFSTKNLDL--SFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPI   88 (276)
T ss_dssp             EECTTSCCSSCCSSS-CTTCCEEEC--TTCCCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCC
T ss_pred             EEecCCCccccCCCC-CCCccEEEC--CCCcccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCcc
Confidence            344455566677643 257999999  445566677767899999999999999999765 4789999999999999999


Q ss_pred             CC--cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccC-hHHhhCCCCCcEEEccCCCCcccccc
Q 004895          611 ED--IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIA-PNVISKLSRLEELYMGDSFSQWDKVE  686 (724)
Q Consensus       611 ~~--~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~-~~~i~~l~~L~~L~l~~~~~~~~~~~  686 (724)
                      +.  +..+..+++|++|++++|.++.++. .+..+++|++|++++| .+..+. |..++.+++|++|++++|..     .
T Consensus        89 ~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~l~~~~~~l~~L~~L~Ls~N~l-----~  162 (276)
T 2z62_A           89 QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNKI-----Q  162 (276)
T ss_dssp             CEECTTTTTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSS-CCCCCCCCGGGGGCTTCCEEECCSSCC-----C
T ss_pred             CccChhhhcCCccccEEECCCCCccccCchhcccCCCCCEEECcCC-ccceecCchhhccCCCCCEEECCCCCC-----C
Confidence            88  3679999999999999999998866 6899999999999995 555532 45689999999999999753     2


Q ss_pred             CCccchHHhhcCCCCCc-EEEeeccccc
Q 004895          687 GGSNASLAELKGLSKLT-TLEIDVRDAE  713 (724)
Q Consensus       687 ~~~~~~l~~L~~L~~L~-~L~l~~n~~~  713 (724)
                      +..+..+..+.+++.|. .|+++.|.++
T Consensus       163 ~~~~~~~~~l~~L~~l~l~L~ls~n~l~  190 (276)
T 2z62_A          163 SIYCTDLRVLHQMPLLNLSLDLSLNPMN  190 (276)
T ss_dssp             EECGGGGHHHHTCTTCCEEEECCSSCCC
T ss_pred             cCCHHHhhhhhhccccceeeecCCCccc
Confidence            22233444455444333 3444444333

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.56  E-value=9.4e-15  Score=147.47  Aligned_cols=168  Identities=20%  Similarity=0.232  Sum_probs=100.0

Q ss_pred             ceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCc
Q 004895          529 PIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       529 ~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~  608 (724)
                      +..+.+..+.+..++....+++|+.|.+.  .+....++  .+..+++|+.|++++|.+..+|. ++.+++|++|++++|
T Consensus        21 l~~l~l~~~~i~~~~~~~~l~~L~~L~l~--~n~i~~l~--~l~~l~~L~~L~L~~N~i~~~~~-l~~l~~L~~L~L~~N   95 (263)
T 1xeu_A           21 AVKQNLGKQSVTDLVSQKELSGVQNFNGD--NSNIQSLA--GMQFFTNLKELHLSHNQISDLSP-LKDLTKLEELSVNRN   95 (263)
T ss_dssp             HHHHHHTCSCTTSEECHHHHTTCSEEECT--TSCCCCCT--TGGGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSS
T ss_pred             HHHHHhcCCCcccccchhhcCcCcEEECc--CCCcccch--HHhhCCCCCEEECCCCccCCChh-hccCCCCCEEECCCC
Confidence            33444555555555444456666666662  22333333  25566677777777777666665 666777777777777


Q ss_pred             ccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCC
Q 004895          609 RLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGG  688 (724)
Q Consensus       609 ~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~  688 (724)
                      .++.++.+.. .+|++|++++|.++.+| .+..+++|++|++++ +.+..++  .++.+++|++|++++|.     +.+.
T Consensus        96 ~l~~l~~~~~-~~L~~L~L~~N~l~~~~-~l~~l~~L~~L~Ls~-N~i~~~~--~l~~l~~L~~L~L~~N~-----i~~~  165 (263)
T 1xeu_A           96 RLKNLNGIPS-ACLSRLFLDNNELRDTD-SLIHLKNLEILSIRN-NKLKSIV--MLGFLSKLEVLDLHGNE-----ITNT  165 (263)
T ss_dssp             CCSCCTTCCC-SSCCEEECCSSCCSBSG-GGTTCTTCCEEECTT-SCCCBCG--GGGGCTTCCEEECTTSC-----CCBC
T ss_pred             ccCCcCcccc-CcccEEEccCCccCCCh-hhcCcccccEEECCC-CcCCCCh--HHccCCCCCEEECCCCc-----Ccch
Confidence            6666444444 66777777777666654 366677777777766 3455553  25667777777776653     2111


Q ss_pred             ccchHHhhcCCCCCcEEEeecccccccc
Q 004895          689 SNASLAELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       689 ~~~~l~~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                           ..+..+++|+.|++++|.+...|
T Consensus       166 -----~~l~~l~~L~~L~l~~N~~~~~~  188 (263)
T 1xeu_A          166 -----GGLTRLKKVNWIDLTGQKCVNEP  188 (263)
T ss_dssp             -----TTSTTCCCCCEEEEEEEEEECCC
T ss_pred             -----HHhccCCCCCEEeCCCCcccCCc
Confidence                 34556666777777776665544

>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=99.56  E-value=9.2e-15  Score=151.37  Aligned_cols=178  Identities=20%  Similarity=0.284  Sum_probs=144.5

Q ss_pred             ccCceEEeccCCCcccCCCc-ccCCCccEEEEecccccccccch-hhhcCCCCceEEEcCCCcCCC-CCccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER-LECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSP-LPSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~-~~~~~Lr~L~l~~~~~~~~~~~~-~~~~~l~~L~~L~l~~~~~~~-lp~~i~~l~~L~~  602 (724)
                      ..++++|++++|.+..++.. ..+++|+.|.+  ..+....++. ..+..+++|++|++++|.+.. .|..+..+.+|++
T Consensus        77 ~~~L~~L~Ls~n~i~~l~~~~~~l~~L~~L~l--~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~  154 (306)
T 2z66_A           77 TTSLKYLDLSFNGVITMSSNFLGLEQLEHLDF--QHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEV  154 (306)
T ss_dssp             CSCCCEEECCSCSEEEEEEEEETCTTCCEEEC--TTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCE
T ss_pred             ccccCEEECCCCccccChhhcCCCCCCCEEEC--CCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCE
Confidence            56888999998888777643 37889999998  3344444544 568899999999999999984 5667899999999


Q ss_pred             EEcCCcccCC---cccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          603 LCLDGWRLED---IAIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       603 L~L~~~~l~~---~~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      |++++|.+..   +..+..+++|++|++++|.++.+ |..+..+++|++|++++ +.+..+++..+..+++|++|++++|
T Consensus       155 L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N  233 (306)
T 2z66_A          155 LKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSH-NNFFSLDTFPYKCLNSLQVLDYSLN  233 (306)
T ss_dssp             EECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTT-SCCSBCCSGGGTTCTTCCEEECTTS
T ss_pred             EECCCCccccccchhHHhhCcCCCEEECCCCCcCCcCHHHhcCCCCCCEEECCC-CccCccChhhccCcccCCEeECCCC
Confidence            9999999875   57899999999999999999977 66799999999999999 4677777767899999999999997


Q ss_pred             CCccccccCCccchHHhhcCC-CCCcEEEeecccccc
Q 004895          679 FSQWDKVEGGSNASLAELKGL-SKLTTLEIDVRDAEM  714 (724)
Q Consensus       679 ~~~~~~~~~~~~~~l~~L~~L-~~L~~L~l~~n~~~~  714 (724)
                      ..     .+..+   ..+..+ ++|+.|++++|.+..
T Consensus       234 ~l-----~~~~~---~~~~~~~~~L~~L~L~~N~~~~  262 (306)
T 2z66_A          234 HI-----MTSKK---QELQHFPSSLAFLNLTQNDFAC  262 (306)
T ss_dssp             CC-----CBCSS---SSCCCCCTTCCEEECTTCCEEC
T ss_pred             CC-----cccCH---HHHHhhhccCCEEEccCCCeec
Confidence            43     22222   234556 489999999998864

>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=99.56  E-value=4e-14  Score=148.24  Aligned_cols=64  Identities=19%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             cCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc
Q 004895          527 KGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS  592 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~  592 (724)
                      ..++.|.+++|.+..++.  ...+++|++|.+  +.+....+.+..|.++++|++|++++|.+..+|.
T Consensus        52 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~  117 (330)
T 1xku_A           52 PDTALLDLQNNKITEIKDGDFKNLKNLHTLIL--INNKISKISPGAFAPLVKLERLYLSKNQLKELPE  117 (330)
T ss_dssp             TTCCEEECCSSCCCCBCTTTTTTCTTCCEEEC--CSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCS
T ss_pred             CCCeEEECCCCcCCEeChhhhccCCCCCEEEC--CCCcCCeeCHHHhcCCCCCCEEECCCCcCCccCh
Confidence            455556666665555543  124555666655  2223333433445555555555555555554443

>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=99.56  E-value=8.7e-15  Score=154.84  Aligned_cols=180  Identities=19%  Similarity=0.245  Sum_probs=138.8

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|+.|.+  +.+....++...|.++++|++|++++|.+..+|.. ++.+++|++
T Consensus        51 ~~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~  128 (353)
T 2z80_A           51 TEAVKSLDLSNNRITYISNSDLQRCVNLQALVL--TSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTF  128 (353)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEEC--TTSCCCEECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCSE
T ss_pred             cccCcEEECCCCcCcccCHHHhccCCCCCEEEC--CCCccCccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCCE
Confidence            4578899999888887765  347888999988  34455566666788889999999999999888765 788999999


Q ss_pred             EEcCCcccCCc-c--cccCCCCCcEEEccCC-cCcccc-hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          603 LCLDGWRLEDI-A--IVGQLKKLEILSLRGA-EIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       603 L~L~~~~l~~~-~--~~~~l~~L~~L~l~~~-~i~~lp-~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      |++++|.++.+ .  .+..+++|++|++++| .+..+| ..+..+++|++|++++| .+...++..++.+++|++|++++
T Consensus       129 L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~l~~l~~L~~L~l~~  207 (353)
T 2z80_A          129 LNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDAS-DLQSYEPKSLKSIQNVSHLILHM  207 (353)
T ss_dssp             EECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEET-TCCEECTTTTTTCSEEEEEEEEC
T ss_pred             EECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCC-CcCccCHHHHhccccCCeecCCC
Confidence            99999988873 3  5888999999999998 577664 56888899999999884 56666666788899999999888


Q ss_pred             CCCccccccCCccchHHhhcCCCCCcEEEeecccccccc
Q 004895          678 SFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       678 ~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                      |..     . ..+.  ..+..+++|+.|+++.|.++.++
T Consensus       208 n~l-----~-~~~~--~~~~~~~~L~~L~L~~n~l~~~~  238 (353)
T 2z80_A          208 KQH-----I-LLLE--IFVDVTSSVECLELRDTDLDTFH  238 (353)
T ss_dssp             SCS-----T-THHH--HHHHHTTTEEEEEEESCBCTTCC
T ss_pred             Ccc-----c-cchh--hhhhhcccccEEECCCCcccccc
Confidence            642     1 1111  12345788999999999987765

>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=99.56  E-value=2.9e-14  Score=161.79  Aligned_cols=105  Identities=18%  Similarity=0.233  Sum_probs=48.6

Q ss_pred             cCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEE
Q 004895          527 KGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTL  603 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L  603 (724)
                      .+++.|++++|.+..++.  ...+++|+.|.+  +.+....+++..|.++++|++|++++|.+..+|.. ++++++|++|
T Consensus        75 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L  152 (597)
T 3oja_B           75 RQVELLNLNDLQIEEIDTYAFAYAHTIQKLYM--GFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTL  152 (597)
T ss_dssp             CCCSEEECTTSCCCEECTTTTTTCTTCCEEEC--CSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEE
T ss_pred             CCCcEEECCCCCCCCCChHHhcCCCCCCEEEC--CCCcCCCCCHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCCEE
Confidence            345555555555444432  124445555555  22223334444445555555555555555544443 2445555555


Q ss_pred             EcCCcccCC--cccccCCCCCcEEEccCCcCc
Q 004895          604 CLDGWRLED--IAIVGQLKKLEILSLRGAEIK  633 (724)
Q Consensus       604 ~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~  633 (724)
                      +|++|.++.  +..++.+++|++|++++|.++
T Consensus       153 ~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~  184 (597)
T 3oja_B          153 SMSNNNLERIEDDTFQATTSLQNLQLSSNRLT  184 (597)
T ss_dssp             ECCSSCCCBCCTTTTTTCTTCCEEECTTSCCS
T ss_pred             EeeCCcCCCCChhhhhcCCcCcEEECcCCCCC
Confidence            555554444  123444455555555444443

>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=99.55  E-value=6.1e-14  Score=146.82  Aligned_cols=177  Identities=15%  Similarity=0.211  Sum_probs=93.3

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC---CCCccccCCCCCcEE
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS---PLPSSLGRLINLQTL  603 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~---~lp~~i~~l~~L~~L  603 (724)
                      .++++|.+++|.+..+|.... ++|+.|.+  ..+....++...|.++++|+.|++++|.+.   ..|..+..+.+|++|
T Consensus       100 ~~L~~L~Ls~n~l~~l~~~~~-~~L~~L~l--~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L  176 (330)
T 1xku_A          100 VKLERLYLSKNQLKELPEKMP-KTLQELRV--HENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYI  176 (330)
T ss_dssp             TTCCEEECCSSCCSBCCSSCC-TTCCEEEC--CSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEE
T ss_pred             CCCCEEECCCCcCCccChhhc-ccccEEEC--CCCcccccCHhHhcCCccccEEECCCCcCCccCcChhhccCCCCcCEE
Confidence            455666666666655554332 55666655  223334455555666666666666666654   234455666666666


Q ss_pred             EcCCcccCCc-ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          604 CLDGWRLEDI-AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       604 ~L~~~~l~~~-~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      ++++|.++.+ ..+.  ++|++|++++|.++.+ |..+..+++|++|++++ +.+..+++..++.+++|++|++++|...
T Consensus       177 ~l~~n~l~~l~~~~~--~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~-n~l~~~~~~~~~~l~~L~~L~L~~N~l~  253 (330)
T 1xku_A          177 RIADTNITTIPQGLP--PSLTELHLDGNKITKVDAASLKGLNNLAKLGLSF-NSISAVDNGSLANTPHLRELHLNNNKLV  253 (330)
T ss_dssp             ECCSSCCCSCCSSCC--TTCSEEECTTSCCCEECTGGGTTCTTCCEEECCS-SCCCEECTTTGGGSTTCCEEECCSSCCS
T ss_pred             ECCCCccccCCcccc--ccCCEEECCCCcCCccCHHHhcCCCCCCEEECCC-CcCceeChhhccCCCCCCEEECCCCcCc
Confidence            6666655552 2221  4556666666655544 34455556666666655 3344444444555566666666554321


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                            ..+   ..+..+++|+.|++++|.++.+|..
T Consensus       254 ------~lp---~~l~~l~~L~~L~l~~N~i~~~~~~  281 (330)
T 1xku_A          254 ------KVP---GGLADHKYIQVVYLHNNNISAIGSN  281 (330)
T ss_dssp             ------SCC---TTTTTCSSCCEEECCSSCCCCCCTT
T ss_pred             ------cCC---hhhccCCCcCEEECCCCcCCccChh
Confidence                  111   1234455555666666655555543

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.55  E-value=2e-14  Score=139.65  Aligned_cols=164  Identities=20%  Similarity=0.305  Sum_probs=125.4

Q ss_pred             EEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEEEcCCcc
Q 004895          531 AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTLCLDGWR  609 (724)
Q Consensus       531 ~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L~L~~~~  609 (724)
                      .+...++.+..+|... .++|+.|.+  ..+....++...|.++++|++|++++|.+..+|.. +..+.+|++|++++|.
T Consensus        11 ~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           11 TVECYSQGRTSVPTGI-PAQTTYLDL--ETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQ   87 (208)
T ss_dssp             EEECCSSCCSSCCSCC-CTTCSEEEC--CSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EEEecCCCccCCCCCC-CCCCcEEEc--CCCccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCCc
Confidence            4566667777776543 468888888  33445567777788899999999999999877654 5789999999999999


Q ss_pred             cCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcccccc
Q 004895          610 LEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVE  686 (724)
Q Consensus       610 l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~  686 (724)
                      ++.+  ..+..+++|++|++++|.++.+|.. +..+++|++|++++ +.+..+++..+..+++|++|++++|..     .
T Consensus        88 l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~-N~l~~~~~~~~~~l~~L~~L~l~~N~~-----~  161 (208)
T 2o6s_A           88 LQSLPNGVFDKLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQ-NQLKSVPDGVFDRLTSLQYIWLHDNPW-----D  161 (208)
T ss_dssp             CCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSCCB-----C
T ss_pred             CCccCHhHhcCccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCC-CccceeCHHHhccCCCccEEEecCCCe-----e
Confidence            8873  3478899999999999999988765 68899999999998 467778877788899999999988632     1


Q ss_pred             CCccchHHhhcCCCCCcEEEeeccccc
Q 004895          687 GGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       687 ~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                                ..+++|+.|+++.|.++
T Consensus       162 ----------~~~~~l~~L~~~~n~~~  178 (208)
T 2o6s_A          162 ----------CTCPGIRYLSEWINKHS  178 (208)
T ss_dssp             ----------CCTTTTHHHHHHHHHCT
T ss_pred             ----------cCCCCHHHHHHHHHhCC
Confidence                      23345666666666554

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.55  E-value=4.8e-14  Score=151.35  Aligned_cols=39  Identities=31%  Similarity=0.380  Sum_probs=20.2

Q ss_pred             hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          639 IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       639 i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +..+++|++|++++| .+...++..++.+++|++|++++|
T Consensus       244 l~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n  282 (390)
T 3o6n_A          244 LLNYPGLVEVDLSYN-ELEKIMYHPFVKMQRLERLYISNN  282 (390)
T ss_dssp             GGGCTTCSEEECCSS-CCCEEESGGGTTCSSCCEEECCSS
T ss_pred             HcCCCCccEEECCCC-cCCCcChhHccccccCCEEECCCC
Confidence            444455555555552 344444444555566666665554

>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=99.55  E-value=2.7e-14  Score=137.46  Aligned_cols=130  Identities=19%  Similarity=0.245  Sum_probs=79.5

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcc-cchhhhcCCCCCe
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQ-LPLQIGQLTRLQL  647 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~-lp~~i~~l~~L~~  647 (724)
                      +..+++|+.|++++|.+..+| .+..+++|++|++++|.++.  +..++.+++|++|++++|.++. .|..+..+++|++
T Consensus        62 l~~l~~L~~L~l~~n~~~~~~-~l~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~Ls~n~i~~~~~~~l~~l~~L~~  140 (197)
T 4ezg_A           62 IEYAHNIKDLTINNIHATNYN-PISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSAHDDSILTKINTLPKVNS  140 (197)
T ss_dssp             GGGCTTCSEEEEESCCCSCCG-GGTTCTTCCEEEEECTTCBGGGSCCCTTCTTCCEEECCSSBCBGGGHHHHTTCSSCCE
T ss_pred             HhcCCCCCEEEccCCCCCcch-hhhcCCCCCEEEeECCccCcccChhhcCCCCCCEEEecCCccCcHhHHHHhhCCCCCE
Confidence            455666666666666555443 56666677777777776665  5666667777777777776663 4566667777777


Q ss_pred             EccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          648 LDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       648 L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      |++++|..+..++  .+..+++|++|++++|..     .+     +..+..+++|+.|++++|.+.
T Consensus       141 L~L~~n~~i~~~~--~l~~l~~L~~L~l~~n~i-----~~-----~~~l~~l~~L~~L~l~~N~i~  194 (197)
T 4ezg_A          141 IDLSYNGAITDIM--PLKTLPELKSLNIQFDGV-----HD-----YRGIEDFPKLNQLYAFSQTIG  194 (197)
T ss_dssp             EECCSCTBCCCCG--GGGGCSSCCEEECTTBCC-----CC-----CTTGGGCSSCCEEEECBC---
T ss_pred             EEccCCCCccccH--hhcCCCCCCEEECCCCCC-----cC-----hHHhccCCCCCEEEeeCcccC
Confidence            7777654355554  266777777777766532     11     124555667777777777654

>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=99.55  E-value=2.7e-14  Score=157.64  Aligned_cols=151  Identities=19%  Similarity=0.231  Sum_probs=119.3

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +..+++|++++|.+..++.  ...+++|+.|.+  +.+....+++..|.++++|+.|++++|.+..+|. .+.++.+|++
T Consensus        31 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L--~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  108 (477)
T 2id5_A           31 PTETRLLDLGKNRIKTLNQDEFASFPHLEELEL--NENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTK  108 (477)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEEC--TTSCCCEECTTTTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCCE
T ss_pred             CCCCcEEECCCCccceECHhHccCCCCCCEEEC--CCCccCEeChhhhhCCccCCEEECCCCcCCccCcccccCCCCCCE
Confidence            5678899999888877643  236888999988  3445556666678888999999999998888775 4688889999


Q ss_pred             EEcCCcccCC--cccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |+|++|.+..  +..+..+++|++|++++|.++.+ |..+..+++|++|++++| .+..+++..+..+++|+.|++.+|.
T Consensus       109 L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~~~l~~l~~L~~L~l~~n~  187 (477)
T 2id5_A          109 LDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKC-NLTSIPTEALSHLHGLIVLRLRHLN  187 (477)
T ss_dssp             EECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEESC-CCSSCCHHHHTTCTTCCEEEEESCC
T ss_pred             EECCCCccccCChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCCC-cCcccChhHhcccCCCcEEeCCCCc
Confidence            9999988877  35688888888999888888866 446888888888888884 6677777778888888888888764

>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=99.55  E-value=5.4e-14  Score=138.78  Aligned_cols=146  Identities=21%  Similarity=0.306  Sum_probs=126.6

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~~  608 (724)
                      ..++.+++.+..+|.... ++|+.|.+  +.+....+++..|.++++|+.|++++|.+..+|. .+..+.+|++|+|++|
T Consensus        22 ~~v~c~~~~l~~ip~~~~-~~L~~L~L--s~n~i~~~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N   98 (229)
T 3e6j_A           22 TTVDCRSKRHASVPAGIP-TNAQILYL--HDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTN   98 (229)
T ss_dssp             TEEECTTSCCSSCCSCCC-TTCSEEEC--CSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CEeEccCCCcCccCCCCC-CCCCEEEc--CCCccCccCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCC
Confidence            457778888888886543 88999999  4455666767778999999999999999998875 4689999999999999


Q ss_pred             ccCCc--ccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          609 RLEDI--AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       609 ~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      .++.+  ..+..+++|++|++++|.++.+|..+..+++|++|++++ +.+..+++..+..+++|+.|++.+|.
T Consensus        99 ~l~~l~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~l~~N~  170 (229)
T 3e6j_A           99 QLTVLPSAVFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQ-NQLKSIPHGAFDRLSSLTHAYLFGNP  170 (229)
T ss_dssp             CCCCCCTTTTTTCTTCCEEECCSSCCCSCCTTGGGCTTCSEEECCS-SCCCCCCTTTTTTCTTCCEEECTTSC
T ss_pred             cCCccChhHhCcchhhCeEeccCCcccccCcccccCCCCCEEECCC-CcCCccCHHHHhCCCCCCEEEeeCCC
Confidence            99883  347899999999999999999999999999999999999 57888888778999999999999875

>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=99.54  E-value=8.9e-14  Score=146.69  Aligned_cols=171  Identities=22%  Similarity=0.315  Sum_probs=122.3

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++++++.+|.+..++....+++|+.|.+.  .+....++.  +..+++|+.|++++|.+..+|. +..+++|++|++
T Consensus       176 l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~--~n~l~~~~~--~~~~~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~l  250 (347)
T 4fmz_A          176 LTDLYSLSLNYNQIEDISPLASLTSLHYFTAY--VNQITDITP--VANMTRLNSLKIGNNKITDLSP-LANLSQLTWLEI  250 (347)
T ss_dssp             CTTCSEEECTTSCCCCCGGGGGCTTCCEEECC--SSCCCCCGG--GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEEC
T ss_pred             CCCCCEEEccCCcccccccccCCCccceeecc--cCCCCCCch--hhcCCcCCEEEccCCccCCCcc-hhcCCCCCEEEC
Confidence            45777788887777777665567778887773  233333333  6677888888888888887766 778888888888


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++.++.+..+++|++|++++|.++.+| .+..+++|++|++++| .+...++..++.+++|++|++++|..     
T Consensus       251 ~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~-~~~~l~~L~~L~L~~n-~l~~~~~~~l~~l~~L~~L~L~~n~l-----  323 (347)
T 4fmz_A          251 GTNQISDINAVKDLTKLKMLNVGSNQISDIS-VLNNLSQLNSLFLNNN-QLGNEDMEVIGGLTNLTTLFLSQNHI-----  323 (347)
T ss_dssp             CSSCCCCCGGGTTCTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSS-CCCGGGHHHHHTCTTCSEEECCSSSC-----
T ss_pred             CCCccCCChhHhcCCCcCEEEccCCccCCCh-hhcCCCCCCEEECcCC-cCCCcChhHhhccccCCEEEccCCcc-----
Confidence            8888877777888888888888888887774 4778888888888885 45666666778888888888887642     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      .+.     ..+..+++|+.|++++|.++
T Consensus       324 ~~~-----~~~~~l~~L~~L~l~~N~i~  346 (347)
T 4fmz_A          324 TDI-----RPLASLSKMDSADFANQVIK  346 (347)
T ss_dssp             CCC-----GGGGGCTTCSEESSSCC---
T ss_pred             ccc-----cChhhhhccceeehhhhccc
Confidence            211     11566778888888888765

>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=99.54  E-value=6.5e-14  Score=140.43  Aligned_cols=151  Identities=23%  Similarity=0.382  Sum_probs=131.6

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +..++.|.+++|.+..++..  ..+++|+.|.+  +.+....++...|.++++|++|++++|.+..+|. .+..+.+|++
T Consensus        34 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  111 (251)
T 3m19_A           34 PADTEKLDLQSTGLATLSDATFRGLTKLTWLNL--DYNQLQTLSAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLDK  111 (251)
T ss_dssp             CTTCCEEECTTSCCCCCCTTTTTTCTTCCEEEC--TTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCE
T ss_pred             CCCCCEEEccCCCcCccCHhHhcCcccCCEEEC--CCCcCCccCHhHhccCCcCCEEECCCCcccccChhHhcccCCCCE
Confidence            56899999999999887642  47899999999  4455666777788999999999999999998764 5789999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |+|++|.++.+  ..+..+++|++|++++|.++.+|. .+..+++|++|++++ +.+..+++..+..+++|++|++++|.
T Consensus       112 L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~l~~N~  190 (251)
T 3m19_A          112 LYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLTNLQTLSLST-NQLQSVPHGAFDRLGKLQTITLFGNQ  190 (251)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSCC
T ss_pred             EEcCCCcCCCcChhHhccCCcccEEECcCCcCCccCHHHcCcCcCCCEEECCC-CcCCccCHHHHhCCCCCCEEEeeCCc
Confidence            99999999883  347899999999999999999987 589999999999999 57788888788999999999999975

>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=99.54  E-value=3.3e-14  Score=162.00  Aligned_cols=175  Identities=23%  Similarity=0.212  Sum_probs=108.5

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|++|.+  +.+....+++..|.++++|++|++++|.+..+ |..++++.+|++
T Consensus        31 ~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L--s~n~l~~i~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~  108 (606)
T 3vq2_A           31 PSSTKNIDLSFNPLKILKSYSFSNFSELQWLDL--SRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLEN  108 (606)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEEC--TTCCCCEECTTTTTTCTTCCEEECTTCCCCCCCTTSSTTCTTCCE
T ss_pred             CCCcCEEECCCCCcCEeChhhccCCccCcEEeC--CCCcccccCHHHhhchhhcCEeECCCCcccccChhhcCCcccCCE
Confidence            4567777777777766543  236677777777  33344455555667777777777777777755 666777777777


Q ss_pred             EEcCCcccCC-c-ccccCCCCCcEEEccCCcCc--ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCc----EEE
Q 004895          603 LCLDGWRLED-I-AIVGQLKKLEILSLRGAEIK--QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE----ELY  674 (724)
Q Consensus       603 L~L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~--~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~----~L~  674 (724)
                      |++++|.++. + ..++++++|++|++++|.++  .+|..++++++|++|++++| .+..+++..++.+++|+    +|+
T Consensus       109 L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~~l~~L~  187 (606)
T 3vq2_A          109 LVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYN-YIQTITVNDLQFLRENPQVNLSLD  187 (606)
T ss_dssp             EECTTSCCCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSS-CCCEECTTTTHHHHHCTTCCCEEE
T ss_pred             EEccCCccccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCC-cceecChhhhhhhhccccccceee
Confidence            7777777665 2 45777777777777777666  35677777777777777773 45555555555555544    677


Q ss_pred             ccCCCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      +++|....     ..+    ..-...+|+.|++++|.+
T Consensus       188 l~~n~l~~-----~~~----~~~~~~~L~~L~L~~n~~  216 (606)
T 3vq2_A          188 MSLNPIDF-----IQD----QAFQGIKLHELTLRGNFN  216 (606)
T ss_dssp             CTTCCCCE-----ECT----TTTTTCEEEEEEEESCCS
T ss_pred             ccCCCcce-----eCc----ccccCceeeeeeccCCcc
Confidence            76653211     111    111223677777777765

>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=99.54  E-value=7.1e-14  Score=143.32  Aligned_cols=168  Identities=24%  Similarity=0.319  Sum_probs=137.0

Q ss_pred             EeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccC
Q 004895          532 ISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLE  611 (724)
Q Consensus       532 l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~  611 (724)
                      +.+..+.+..+.....+++|+.|.+.  .+....++.  +..+++|+.|++++|.+..+|. ++.+.+|++|++++|.++
T Consensus        29 ~~l~~~~~~~~~~~~~l~~L~~L~l~--~~~i~~~~~--~~~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n~l~  103 (291)
T 1h6t_A           29 DNLKKKSVTDAVTQNELNSIDQIIAN--NSDIKSVQG--IQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVK  103 (291)
T ss_dssp             HHTTCSCTTSEECHHHHHTCCEEECT--TSCCCCCTT--GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC
T ss_pred             HHhcCCCcccccchhhcCcccEEEcc--CCCcccChh--HhcCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCCcCC
Confidence            34555555554444578899999993  334444443  7889999999999999998887 999999999999999999


Q ss_pred             CcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccc
Q 004895          612 DIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNA  691 (724)
Q Consensus       612 ~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~  691 (724)
                      .++.++.+++|++|++++|.++.+| .+..+++|++|++++| .+..+  ..++.+++|++|++++|..     .+.   
T Consensus       104 ~~~~l~~l~~L~~L~L~~n~i~~~~-~l~~l~~L~~L~l~~n-~l~~~--~~l~~l~~L~~L~L~~N~l-----~~~---  171 (291)
T 1h6t_A          104 DLSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNN-KITDI--TVLSRLTKLDTLSLEDNQI-----SDI---  171 (291)
T ss_dssp             CGGGGTTCTTCCEEECTTSCCCCCG-GGGGCTTCCEEECCSS-CCCCC--GGGGGCTTCSEEECCSSCC-----CCC---
T ss_pred             CChhhccCCCCCEEECCCCcCCCCh-hhcCCCCCCEEEccCC-cCCcc--hhhccCCCCCEEEccCCcc-----ccc---
Confidence            9888999999999999999999874 6899999999999995 56666  3489999999999998742     221   


Q ss_pred             hHHhhcCCCCCcEEEeecccccccccc
Q 004895          692 SLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       692 ~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                        ..+..+++|+.|+++.|.++.+|..
T Consensus       172 --~~l~~l~~L~~L~L~~N~i~~l~~l  196 (291)
T 1h6t_A          172 --VPLAGLTKLQNLYLSKNHISDLRAL  196 (291)
T ss_dssp             --GGGTTCTTCCEEECCSSCCCBCGGG
T ss_pred             --hhhcCCCccCEEECCCCcCCCChhh
Confidence              1277899999999999999888763

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.52  E-value=8e-14  Score=146.07  Aligned_cols=180  Identities=18%  Similarity=0.246  Sum_probs=99.3

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL  603 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L  603 (724)
                      +.+++.|++++|.+..++.  ...+++|+.|.+  ..+....+++..|.++++|++|++++|.+..+|..+.  .+|++|
T Consensus        53 ~~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~L  128 (332)
T 2ft3_A           53 SPDTTLLDLQNNDISELRKDDFKGLQHLYALVL--VNNKISKIHEKAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVEL  128 (332)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTTTCTTCCEEEC--CSSCCCEECGGGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCEE
T ss_pred             CCCCeEEECCCCcCCccCHhHhhCCCCCcEEEC--CCCccCccCHhHhhCcCCCCEEECCCCcCCccCcccc--ccCCEE
Confidence            3466777777777665532  235677777777  2333444544556666777777777666666555443  445555


Q ss_pred             EcCCcccCCc--ccccCCCCCcEEEccCCc----------------------------------------------Cccc
Q 004895          604 CLDGWRLEDI--AIVGQLKKLEILSLRGAE----------------------------------------------IKQL  635 (724)
Q Consensus       604 ~L~~~~l~~~--~~~~~l~~L~~L~l~~~~----------------------------------------------i~~l  635 (724)
                      ++++|.++..  ..+..+++|++|++++|.                                              ++.+
T Consensus       129 ~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~L~~L~l~~n~l~~l~~~~~~~L~~L~l~~n~i~~~  208 (332)
T 2ft3_A          129 RIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGLKLNYLRISEAKLTGIPKDLPETLNELHLDHNKIQAI  208 (332)
T ss_dssp             ECCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSCCCSCCBCCSSBCSSCCSSSCSSCSCCBCCSSCCCCC
T ss_pred             ECCCCccCccCHhHhCCCccCCEEECCCCccccCCCCcccccCCccCEEECcCCCCCccCccccCCCCEEECCCCcCCcc
Confidence            5555544441  224444444444444443                                              3333


Q ss_pred             c-hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          636 P-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       636 p-~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      | ..+..+++|++|++++ +.+..+++..++.+++|++|++++|...      ..+   ..+..+++|+.|+++.|.++.
T Consensus       209 ~~~~l~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~l~------~lp---~~l~~l~~L~~L~l~~N~l~~  278 (332)
T 2ft3_A          209 ELEDLLRYSKLYRLGLGH-NQIRMIENGSLSFLPTLRELHLDNNKLS------RVP---AGLPDLKLLQVVYLHTNNITK  278 (332)
T ss_dssp             CTTSSTTCTTCSCCBCCS-SCCCCCCTTGGGGCTTCCEEECCSSCCC------BCC---TTGGGCTTCCEEECCSSCCCB
T ss_pred             CHHHhcCCCCCCEEECCC-CcCCcCChhHhhCCCCCCEEECCCCcCe------ecC---hhhhcCccCCEEECCCCCCCc
Confidence            2 3355555566666655 3445555544566666666666655321      111   235566777888888887777


Q ss_pred             ccccc
Q 004895          715 LRRIW  719 (724)
Q Consensus       715 lp~~~  719 (724)
                      +|...
T Consensus       279 ~~~~~  283 (332)
T 2ft3_A          279 VGVND  283 (332)
T ss_dssp             CCTTS
T ss_pred             cChhH
Confidence            76543

>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=99.52  E-value=2.8e-13  Score=142.85  Aligned_cols=172  Identities=18%  Similarity=0.240  Sum_probs=93.9

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .++++|++++|.+..++....+++|++|.+.  .+....++  .+.++++|++|++++|.+..+|. +..+++|++|+++
T Consensus        66 ~~L~~L~l~~n~i~~~~~~~~l~~L~~L~L~--~n~i~~~~--~~~~l~~L~~L~l~~n~i~~~~~-~~~l~~L~~L~l~  140 (347)
T 4fmz_A           66 TNLEYLNLNGNQITDISPLSNLVKLTNLYIG--TNKITDIS--ALQNLTNLRELYLNEDNISDISP-LANLTKMYSLNLG  140 (347)
T ss_dssp             TTCCEEECCSSCCCCCGGGTTCTTCCEEECC--SSCCCCCG--GGTTCTTCSEEECTTSCCCCCGG-GTTCTTCCEEECT
T ss_pred             CCccEEEccCCccccchhhhcCCcCCEEEcc--CCcccCch--HHcCCCcCCEEECcCCcccCchh-hccCCceeEEECC
Confidence            4555555555555554443445555555552  12222222  24555555555555555555544 5555555555555


Q ss_pred             Ccc-cCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          607 GWR-LEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       607 ~~~-l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      +|. +..++.+..+++|++|++++|.+..++. +..+++|++|++++| .+..+++  +..+++|+.|++++|..     
T Consensus       141 ~n~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~-~~~l~~L~~L~l~~n-~l~~~~~--~~~l~~L~~L~l~~n~l-----  211 (347)
T 4fmz_A          141 ANHNLSDLSPLSNMTGLNYLTVTESKVKDVTP-IANLTDLYSLSLNYN-QIEDISP--LASLTSLHYFTAYVNQI-----  211 (347)
T ss_dssp             TCTTCCCCGGGTTCTTCCEEECCSSCCCCCGG-GGGCTTCSEEECTTS-CCCCCGG--GGGCTTCCEEECCSSCC-----
T ss_pred             CCCCcccccchhhCCCCcEEEecCCCcCCchh-hccCCCCCEEEccCC-ccccccc--ccCCCccceeecccCCC-----
Confidence            553 3334445555556666665555555544 555566666666553 3444433  45566666666655421     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .     .+..+..+++|+.|++++|.++.+|.
T Consensus       212 ~-----~~~~~~~~~~L~~L~l~~n~l~~~~~  238 (347)
T 4fmz_A          212 T-----DITPVANMTRLNSLKIGNNKITDLSP  238 (347)
T ss_dssp             C-----CCGGGGGCTTCCEEECCSSCCCCCGG
T ss_pred             C-----CCchhhcCCcCCEEEccCCccCCCcc
Confidence            1     11226677889999999998877775

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.52  E-value=8.3e-14  Score=145.95  Aligned_cols=129  Identities=17%  Similarity=0.216  Sum_probs=94.5

Q ss_pred             CceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCC
Q 004895          576 ELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSN  652 (724)
Q Consensus       576 ~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~  652 (724)
                      .|+.|++++|.+..+|..+.  .+|++|++++|.++.  +..+..+++|++|++++|.++.+|. .+..+++|++|++++
T Consensus       173 ~L~~L~l~~n~l~~l~~~~~--~~L~~L~l~~n~i~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~  250 (332)
T 2ft3_A          173 KLNYLRISEAKLTGIPKDLP--ETLNELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDN  250 (332)
T ss_dssp             CCSCCBCCSSBCSSCCSSSC--SSCSCCBCCSSCCCCCCTTSSTTCTTCSCCBCCSSCCCCCCTTGGGGCTTCCEEECCS
T ss_pred             ccCEEECcCCCCCccCcccc--CCCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCcCChhHhhCCCCCCEEECCC
Confidence            44444444444444444333  578888888888877  3678999999999999999998765 689999999999999


Q ss_pred             CCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhh---cCCCCCcEEEeeccccc
Q 004895          653 CSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL---KGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       653 ~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L---~~L~~L~~L~l~~n~~~  713 (724)
                      | .+..+|.. ++.+++|++|++++|....     .....+..+   ....+|+.|++++|.+.
T Consensus       251 N-~l~~lp~~-l~~l~~L~~L~l~~N~l~~-----~~~~~~~~~~~~~~~~~l~~L~l~~N~~~  307 (332)
T 2ft3_A          251 N-KLSRVPAG-LPDLKLLQVVYLHTNNITK-----VGVNDFCPVGFGVKRAYYNGISLFNNPVP  307 (332)
T ss_dssp             S-CCCBCCTT-GGGCTTCCEEECCSSCCCB-----CCTTSSSCSSCCSSSCCBSEEECCSSSSC
T ss_pred             C-cCeecChh-hhcCccCCEEECCCCCCCc-----cChhHccccccccccccccceEeecCccc
Confidence            4 67788765 8999999999999975322     112222211   12567899999999876

>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=99.52  E-value=8.5e-14  Score=136.42  Aligned_cols=146  Identities=22%  Similarity=0.336  Sum_probs=123.5

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      +.+...++.+..+|.... ++++.|.+  ..+....++...|.++++|+.|++++|.+..+ |..+..+.+|++|+|++|
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   90 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNLP-ETITEIRL--EQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGN   90 (220)
T ss_dssp             TEEECTTSCCSSCCSSCC-TTCCEEEC--CSSCCCEECTTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSS
T ss_pred             CEEEcCCCCcCcCCCccC-cCCCEEEC--CCCcCCCcCHhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCC
Confidence            457777888888886543 68999998  44556677777789999999999999999965 788999999999999999


Q ss_pred             ccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          609 RLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       609 ~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      .++.+  ..+..+++|++|++++|.++.+ |..+..+++|++|++++ +.+..+++..+..+++|++|++++|.
T Consensus        91 ~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~  163 (220)
T 2v9t_B           91 KITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYD-NKLQTIAKGTFSPLRAIQTMHLAQNP  163 (220)
T ss_dssp             CCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             cCCccCHhHccCCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCC-CcCCEECHHHHhCCCCCCEEEeCCCC
Confidence            99883  3478999999999999999977 45688999999999999 56788888778999999999999874

>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=1.1e-13  Score=133.16  Aligned_cols=146  Identities=16%  Similarity=0.182  Sum_probs=126.1

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC-CCccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP-LPSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~-lp~~i~~l~~L~~L~  604 (724)
                      ..+++++++++|.+..++....+++|+.|.+..+  ....++  .+..+++|++|++++|.+.. .|..++.+++|++|+
T Consensus        43 l~~L~~L~l~~n~i~~l~~l~~l~~L~~L~l~~n--~~~~~~--~l~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~  118 (197)
T 4ezg_A           43 MNSLTYITLANINVTDLTGIEYAHNIKDLTINNI--HATNYN--PISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLD  118 (197)
T ss_dssp             HHTCCEEEEESSCCSCCTTGGGCTTCSEEEEESC--CCSCCG--GGTTCTTCCEEEEECTTCBGGGSCCCTTCTTCCEEE
T ss_pred             cCCccEEeccCCCccChHHHhcCCCCCEEEccCC--CCCcch--hhhcCCCCCEEEeECCccCcccChhhcCCCCCCEEE
Confidence            4689999999999998887668999999999433  333332  47889999999999999984 688899999999999


Q ss_pred             cCCcccCC--cccccCCCCCcEEEccCCc-CcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          605 LDGWRLED--IAIVGQLKKLEILSLRGAE-IKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       605 L~~~~l~~--~~~~~~l~~L~~L~l~~~~-i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      +++|.++.  +..++.+++|++|++++|. ++.+| .+..+++|++|++++| .+..++  .+..+++|++|++++|.
T Consensus       119 Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n-~i~~~~--~l~~l~~L~~L~l~~N~  192 (197)
T 4ezg_A          119 ISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFD-GVHDYR--GIEDFPKLNQLYAFSQT  192 (197)
T ss_dssp             CCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTB-CCCCCT--TGGGCSSCCEEEECBC-
T ss_pred             ecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCC-CCcChH--HhccCCCCCEEEeeCcc
Confidence            99999987  6889999999999999997 88887 6999999999999995 566665  48999999999999864

>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=99.51  E-value=1.6e-13  Score=160.35  Aligned_cols=177  Identities=20%  Similarity=0.324  Sum_probs=126.0

Q ss_pred             ccCceEEeccCCCcc-cCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQ-ELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~-~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~~  602 (724)
                      ...+++|.+.+|.+. .+|... .+++|+.|.+  ..+......+..+..+++|++|++++|.+. .+|..++.+++|++
T Consensus       465 l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~L--~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~  542 (768)
T 3rgz_A          465 VKTLETLILDFNDLTGEIPSGLSNCTNLNWISL--SNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIW  542 (768)
T ss_dssp             CTTCCEEECCSSCCCSCCCGGGGGCTTCCEEEC--CSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCE
T ss_pred             CCCceEEEecCCcccCcCCHHHhcCCCCCEEEc--cCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCE
Confidence            456777777777765 344333 5777777777  233333333345677888888888888887 67888888888888


Q ss_pred             EEcCCcccCC--cc------------------------------------------------------------------
Q 004895          603 LCLDGWRLED--IA------------------------------------------------------------------  614 (724)
Q Consensus       603 L~L~~~~l~~--~~------------------------------------------------------------------  614 (724)
                      |++++|.+..  |.                                                                  
T Consensus       543 L~Ls~N~l~g~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g  622 (768)
T 3rgz_A          543 LDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGNLLEFQGIRSEQLNRLSTRNPCNITSRVYGG  622 (768)
T ss_dssp             EECCSSEEESBCCGGGGTTTTCBCCSTTCSCEEEEEECCSCCTTCCSSEEEEECTTCCGGGGGGGGGTCCSCTTSCEEEE
T ss_pred             EECCCCccCCcCChHHhcccchhhhhccccccccccccccccccccccccccccccccchhhhccccccccccccceecc
Confidence            8888876542  21                                                                  


Q ss_pred             ----cccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCc
Q 004895          615 ----IVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGS  689 (724)
Q Consensus       615 ----~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~  689 (724)
                          .++.+.+|++||+++|.++ .+|..++++++|+.|++++| .+....|..++.|++|+.|++++|.     +.+..
T Consensus       623 ~~~~~~~~l~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~Ls~N-~l~g~ip~~l~~L~~L~~LdLs~N~-----l~g~i  696 (768)
T 3rgz_A          623 HTSPTFDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHN-DISGSIPDEVGDLRGLNILDLSSNK-----LDGRI  696 (768)
T ss_dssp             ECCCSCSSSBCCCEEECCSSCCBSCCCGGGGGCTTCCEEECCSS-CCCSCCCGGGGGCTTCCEEECCSSC-----CEECC
T ss_pred             cCchhhhccccccEEECcCCcccccCCHHHhccccCCEEeCcCC-ccCCCCChHHhCCCCCCEEECCCCc-----ccCcC
Confidence                2344677888888888887 77888999999999999984 4554445568999999999998863     44444


Q ss_pred             cchHHhhcCCCCCcEEEeeccccc
Q 004895          690 NASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       690 ~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      |.   .+.++++|+.|++++|.+.
T Consensus       697 p~---~l~~l~~L~~L~ls~N~l~  717 (768)
T 3rgz_A          697 PQ---AMSALTMLTEIDLSNNNLS  717 (768)
T ss_dssp             CG---GGGGCCCCSEEECCSSEEE
T ss_pred             Ch---HHhCCCCCCEEECcCCccc
Confidence            54   4556778999999999763

>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=99.51  E-value=8.4e-14  Score=158.66  Aligned_cols=150  Identities=19%  Similarity=0.208  Sum_probs=121.9

Q ss_pred             ccCceEEeccCCCcccCCC-c-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE-R-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~-~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~  602 (724)
                      ..++++|++++|.+..++. . ..+++|++|.+  +.+....+++..|.++++|++|++++|.+..+| ..++++.+|++
T Consensus        55 l~~L~~L~Ls~n~l~~i~~~~~~~l~~L~~L~L--s~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  132 (606)
T 3vq2_A           55 FSELQWLDLSRCEIETIEDKAWHGLHHLSNLIL--TGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKK  132 (606)
T ss_dssp             CTTCCEEECTTCCCCEECTTTTTTCTTCCEEEC--TTCCCCCCCTTSSTTCTTCCEEECTTSCCCCSSSSCCTTCTTCCE
T ss_pred             CccCcEEeCCCCcccccCHHHhhchhhcCEeEC--CCCcccccChhhcCCcccCCEEEccCCccccccccccCCCCCCCE
Confidence            5789999999999988743 2 47899999999  445566676677899999999999999999776 68999999999


Q ss_pred             EEcCCcccCC---cccccCCCCCcEEEccCCcCcccc-hhhhcCCCCC----eEccCCCCCCcccChHHhhCCCCCcEEE
Q 004895          603 LCLDGWRLED---IAIVGQLKKLEILSLRGAEIKQLP-LQIGQLTRLQ----LLDLSNCSSLVVIAPNVISKLSRLEELY  674 (724)
Q Consensus       603 L~L~~~~l~~---~~~~~~l~~L~~L~l~~~~i~~lp-~~i~~l~~L~----~L~l~~~~~l~~~~~~~i~~l~~L~~L~  674 (724)
                      |++++|.+..   |..++++++|++|++++|.++.+| ..+..+++|+    +|++++ +.+..+++..+. ..+|+.|+
T Consensus       133 L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~~l~~L~l~~-n~l~~~~~~~~~-~~~L~~L~  210 (606)
T 3vq2_A          133 LNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSL-NPIDFIQDQAFQ-GIKLHELT  210 (606)
T ss_dssp             EECCSSCCCCCCCCGGGGTCTTCCEEECCSSCCCEECTTTTHHHHHCTTCCCEEECTT-CCCCEECTTTTT-TCEEEEEE
T ss_pred             EeCCCCcccceechHhHhhcCCCCEEEccCCcceecChhhhhhhhccccccceeeccC-CCcceeCccccc-Cceeeeee
Confidence            9999999874   678999999999999999999774 4466666554    799988 456777766443 34788888


Q ss_pred             ccCCC
Q 004895          675 MGDSF  679 (724)
Q Consensus       675 l~~~~  679 (724)
                      +++|.
T Consensus       211 L~~n~  215 (606)
T 3vq2_A          211 LRGNF  215 (606)
T ss_dssp             EESCC
T ss_pred             ccCCc
Confidence            87764

>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=99.50  E-value=9.6e-14  Score=129.88  Aligned_cols=140  Identities=22%  Similarity=0.199  Sum_probs=116.9

Q ss_pred             CCCCceEEEcCCCcCC--CCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcc-cchhhhcCCCCCeEc
Q 004895          573 GTEELKVLDFTGIRFS--PLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQ-LPLQIGQLTRLQLLD  649 (724)
Q Consensus       573 ~l~~L~~L~l~~~~~~--~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~-lp~~i~~l~~L~~L~  649 (724)
                      ..+.|+.|++++|.+.  .+|..+..+++|++|++++|.++.+..++.+++|++|++++|.++. +|..+..+++|++|+
T Consensus        22 ~~~~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           22 TPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLN  101 (168)
T ss_dssp             CTTSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESSCCCCCSSCCCCSSCCEEEEESCCCCSCCCHHHHHCTTCCEEE
T ss_pred             CcccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCCCCCChhhhccCCCCCEEECcCCcCchHHHHHHhhCCCCCEEe
Confidence            3478999999999998  8998899999999999999998888889999999999999999997 777788899999999


Q ss_pred             cCCCCCCcccCh-HHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          650 LSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       650 l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      +++| .+..++. ..++.+++|++|++++|.     +.+..+.....+..+++|+.|+++.|.+..+|..
T Consensus       102 Ls~N-~l~~~~~~~~l~~l~~L~~L~l~~N~-----l~~~~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~  165 (168)
T 2ell_A          102 LSGN-KLKDISTLEPLKKLECLKSLDLFNCE-----VTNLNDYRESVFKLLPQLTYLDGYDREDQEAPDS  165 (168)
T ss_dssp             CBSS-SCCSSGGGGGGSSCSCCCEEECCSSG-----GGTSTTHHHHHHTTCSSCCEETTEETTSCBCCSS
T ss_pred             ccCC-ccCcchhHHHHhcCCCCCEEEeeCCc-----CcchHHHHHHHHHhCccCcEecCCCCChhhcccc
Confidence            9995 6677653 568999999999999874     3222221224577889999999999999888864

>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=99.50  E-value=1.6e-13  Score=151.54  Aligned_cols=176  Identities=23%  Similarity=0.284  Sum_probs=141.3

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      +.+..+++.+..+|... .++++.|.+  +.+....++...|.++++|++|++++|.+..+ |..++++.+|++|+|++|
T Consensus        14 ~~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           14 RAVLCHRKRFVAVPEGI-PTETRLLDL--GKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSN   90 (477)
T ss_dssp             TEEECCSCCCSSCCSCC-CTTCSEEEC--CSSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             CEEEeCCCCcCcCCCCC-CCCCcEEEC--CCCccceECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCC
Confidence            45666777788888644 368999999  44556667777899999999999999999965 788999999999999999


Q ss_pred             ccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          609 RLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       609 ~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      .++.+  ..+.++++|++|++++|.+..+ |..+..+++|++|++++ +.+..+++..++.+++|++|++++|....   
T Consensus        91 ~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~-n~l~~~~~~~~~~l~~L~~L~l~~n~l~~---  166 (477)
T 2id5_A           91 RLKLIPLGVFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGD-NDLVYISHRAFSGLNSLEQLTLEKCNLTS---  166 (477)
T ss_dssp             CCCSCCTTSSTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECC-TTCCEECTTSSTTCTTCCEEEEESCCCSS---
T ss_pred             cCCccCcccccCCCCCCEEECCCCccccCChhHccccccCCEEECCC-CccceeChhhccCCCCCCEEECCCCcCcc---
Confidence            99883  4589999999999999999966 56799999999999999 56777777779999999999999974321   


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                        ..   ...+.++++|+.|+++.|.+..++.
T Consensus       167 --~~---~~~l~~l~~L~~L~l~~n~i~~~~~  193 (477)
T 2id5_A          167 --IP---TEALSHLHGLIVLRLRHLNINAIRD  193 (477)
T ss_dssp             --CC---HHHHTTCTTCCEEEEESCCCCEECT
T ss_pred             --cC---hhHhcccCCCcEEeCCCCcCcEeCh
Confidence              11   2335566777777777777666554

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.50  E-value=1.3e-13  Score=147.92  Aligned_cols=148  Identities=18%  Similarity=0.163  Sum_probs=98.9

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~  602 (724)
                      ..+++++++.++.+..+|..  ..+++|+.|.+  ..+....++...|.++++|+.|++++|.+..+| ..++.+++|++
T Consensus        44 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           44 LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNL--NDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTV  121 (390)
T ss_dssp             GCCCSEEEEESCEESEECTHHHHHCCCCSEEEC--TTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCE
T ss_pred             cCCceEEEecCCchhhCChhHhcccccCcEEEC--CCCcccccChhhccCCCCcCEEECCCCCCCcCCHHHhcCCCCCCE
Confidence            45677777777777777653  25677777777  333445555556777777777777777777553 44677777777


Q ss_pred             EEcCCcccCC-ccc-ccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLED-IAI-VGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~-~~~-~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |++++|.++. ++. ++.+++|++|++++|.++.+|+ .+..+++|++|++++| .+..++   ++.+++|+.|++++|.
T Consensus       122 L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n-~l~~~~---~~~l~~L~~L~l~~n~  197 (390)
T 3o6n_A          122 LVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSN-RLTHVD---LSLIPSLFHANVSYNL  197 (390)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSS-CCSBCC---GGGCTTCSEEECCSSC
T ss_pred             EECCCCccCcCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCC-cCCccc---cccccccceeeccccc
Confidence            7777777776 333 5677777777777777776643 4677777777777773 445543   4566777777776653

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.50  E-value=1.9e-14  Score=149.33  Aligned_cols=177  Identities=21%  Similarity=0.174  Sum_probs=134.7

Q ss_pred             ccCceEEeccCCCcc-cCCCc---ccCCCccEEEEecccccccccchhhhcCC-----CCceEEEcCCCcCCCCC-cccc
Q 004895          526 QKGPIAISLPYRDIQ-ELPER---LECPQLKLFLLFAKYDSTLQISDHFFEGT-----EELKVLDFTGIRFSPLP-SSLG  595 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~-~~~~~---~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l-----~~L~~L~l~~~~~~~lp-~~i~  595 (724)
                      ..++++|++++|.+. .+|..   ..+++|+.|.+.  .+....+| ..+..+     ++|++|++++|.+..+| ..++
T Consensus        94 l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls--~N~l~~~~-~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~  170 (312)
T 1wwl_A           94 ISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLR--NVSWATRD-AWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVR  170 (312)
T ss_dssp             TSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEE--SCBCSSSS-SHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCC
T ss_pred             cCCccEEEccCCcccchhHHHHHHhcCCCccEEEcc--CCCCcchh-HHHHHHHHhhcCCCcEEEeeCCCCccchHHHhc
Confidence            568999999999986 45654   468999999993  33444444 345555     89999999999999775 7899


Q ss_pred             CCCCCcEEEcCCcccCC----cccc--cCCCCCcEEEccCCcCcccc---hh-hhcCCCCCeEccCCCCCCcccCh-HHh
Q 004895          596 RLINLQTLCLDGWRLED----IAIV--GQLKKLEILSLRGAEIKQLP---LQ-IGQLTRLQLLDLSNCSSLVVIAP-NVI  664 (724)
Q Consensus       596 ~l~~L~~L~L~~~~l~~----~~~~--~~l~~L~~L~l~~~~i~~lp---~~-i~~l~~L~~L~l~~~~~l~~~~~-~~i  664 (724)
                      .+++|++|++++|.+..    ++.+  +.+++|++|++++|.++.+|   .. +..+++|++|++++| .+...++ ..+
T Consensus       171 ~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~~~~~~~~  249 (312)
T 1wwl_A          171 VFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHN-SLRDAAGAPSC  249 (312)
T ss_dssp             CCSSCCEEECCSCTTCHHHHHHHHSCTTSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTS-CCCSSCCCSCC
T ss_pred             cCCCCCEEECCCCCcCcchHHHHHHHhccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCC-cCCcccchhhh
Confidence            99999999999998654    3444  88999999999999998543   33 357899999999995 5555442 345


Q ss_pred             hCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          665 SKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       665 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      ..+++|++|++++|...      ..+..   +.  ++|+.|+++.|.++.+|.
T Consensus       250 ~~l~~L~~L~Ls~N~l~------~ip~~---~~--~~L~~L~Ls~N~l~~~p~  291 (312)
T 1wwl_A          250 DWPSQLNSLNLSFTGLK------QVPKG---LP--AKLSVLDLSYNRLDRNPS  291 (312)
T ss_dssp             CCCTTCCEEECTTSCCS------SCCSS---CC--SEEEEEECCSSCCCSCCC
T ss_pred             hhcCCCCEEECCCCccC------hhhhh---cc--CCceEEECCCCCCCCChh
Confidence            67899999999997532      12222   22  689999999999988876

>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=99.50  E-value=1.6e-13  Score=156.44  Aligned_cols=151  Identities=15%  Similarity=0.170  Sum_probs=126.0

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~  602 (724)
                      +..+++|++++|.+..++.  ...+++|++|++  +.+....+.+..|.++++|++|++++|.+..+ |..++.+.+|++
T Consensus        32 ~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L--s~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~  109 (606)
T 3t6q_A           32 PNSTECLEFSFNVLPTIQNTTFSRLINLTFLDL--TRCQIYWIHEDTFQSQHRLDTLVLTANPLIFMAETALSGPKALKH  109 (606)
T ss_dssp             CTTCCEEECTTCCCSEECTTTSTTCTTCSEEEC--TTCCCCEECTTTTTTCTTCCEEECTTCCCSEECTTTTSSCTTCCE
T ss_pred             CCcCcEEEccCCccCcCChhHhccCccceEEEC--CCCccceeChhhccCccccCeeeCCCCcccccChhhhcccccccE
Confidence            6789999999999988743  247899999999  44455566667789999999999999999854 778999999999


Q ss_pred             EEcCCcccCC--cccccCCCCCcEEEccCCcCcccc-hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCc--EEEccC
Q 004895          603 LCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE--ELYMGD  677 (724)
Q Consensus       603 L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp-~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~--~L~l~~  677 (724)
                      |++++|.++.  +..++++++|++|++++|.++.++ +.+..+++|++|++++ +.+..+++..++.+++|+  +|++++
T Consensus       110 L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~-n~l~~~~~~~~~~l~~L~~l~L~l~~  188 (606)
T 3t6q_A          110 LFFIQTGISSIDFIPLHNQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDFQN-NAIHYLSKEDMSSLQQATNLSLNLNG  188 (606)
T ss_dssp             EECTTSCCSCGGGSCCTTCTTCCEEECCSSCCCCCCCCTTCCCTTCCEEECCS-SCCCEECHHHHHTTTTCCSEEEECTT
T ss_pred             eeccccCcccCCcchhccCCcccEEECCCCcccccCcccccCCcccCEEEccc-CcccccChhhhhhhcccceeEEecCC
Confidence            9999999988  467899999999999999998763 3455599999999999 467788788889999999  888887


Q ss_pred             CC
Q 004895          678 SF  679 (724)
Q Consensus       678 ~~  679 (724)
                      |.
T Consensus       189 n~  190 (606)
T 3t6q_A          189 ND  190 (606)
T ss_dssp             CC
T ss_pred             Cc
Confidence            64

>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=99.50  E-value=1.3e-13  Score=135.05  Aligned_cols=146  Identities=17%  Similarity=0.305  Sum_probs=121.3

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEeccccccccc-chhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcCC
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQI-SDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDG  607 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~-~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~  607 (724)
                      +.++++++.+..+|... .+.++.|.+  +.+....+ +...|.++++|+.|++++|.+..+|. .+..+.+|++|+|++
T Consensus        14 ~~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           14 TTVDCSNQKLNKIPEHI-PQYTAELRL--NNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTS   90 (220)
T ss_dssp             TEEECCSSCCSSCCSCC-CTTCSEEEC--CSSCCCEECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS
T ss_pred             CEeEeCCCCcccCccCC-CCCCCEEEc--CCCcCCccCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCC
Confidence            47888889888888644 356788888  33444444 44568899999999999999997654 789999999999999


Q ss_pred             cccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          608 WRLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       608 ~~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |.++.+  ..+..+++|++|++++|.++.+ |..+..+++|++|++++ +.+..+++..+..+++|+.|++++|.
T Consensus        91 N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~  164 (220)
T 2v70_A           91 NRLENVQHKMFKGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYD-NQITTVAPGAFDTLHSLSTLNLLANP  164 (220)
T ss_dssp             SCCCCCCGGGGTTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTT-SCCCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             CccCccCHhHhcCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCC-CcCCEECHHHhcCCCCCCEEEecCcC
Confidence            999883  4589999999999999999977 56689999999999999 56788877789999999999999874

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.50  E-value=3.1e-14  Score=162.63  Aligned_cols=152  Identities=13%  Similarity=0.133  Sum_probs=114.3

Q ss_pred             cchhhhcCCCCceEEEcCCCcCCC------------------CCcccc--CCCCCcEEEcCCcccCC--cccccCCCCCc
Q 004895          566 ISDHFFEGTEELKVLDFTGIRFSP------------------LPSSLG--RLINLQTLCLDGWRLED--IAIVGQLKKLE  623 (724)
Q Consensus       566 ~~~~~~~~l~~L~~L~l~~~~~~~------------------lp~~i~--~l~~L~~L~L~~~~l~~--~~~~~~l~~L~  623 (724)
                      +|. .+.++++|++|++++|.+..                  +|..++  ++.+|++|+|++|.+..  |..++++++|+
T Consensus       198 ip~-~l~~l~~L~~L~Ls~n~l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~  276 (636)
T 4eco_A          198 VSK-AVMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQ  276 (636)
T ss_dssp             ECG-GGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSSCCTTTTTCSSCC
T ss_pred             CCH-HHhcccCCCEEECcCCccccccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCccChHHHhcCCCCC
Confidence            444 47889999999999999987                  999998  99999999999998766  67899999999


Q ss_pred             EEEccCCc-Cc--ccchhhhcC------CCCCeEccCCCCCCcccCh-HHhhCCCCCcEEEccCCCCc-ccc-cc-----
Q 004895          624 ILSLRGAE-IK--QLPLQIGQL------TRLQLLDLSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQ-WDK-VE-----  686 (724)
Q Consensus       624 ~L~l~~~~-i~--~lp~~i~~l------~~L~~L~l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~-~~~-~~-----  686 (724)
                      +|++++|. ++  .+|..++++      ++|++|++++| .+..+|. ..++.+++|++|++++|... ... +.     
T Consensus       277 ~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n-~l~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip~~~~l~~L  355 (636)
T 4eco_A          277 LINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYN-NLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGSEIKL  355 (636)
T ss_dssp             EEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSS-CCSSCCCHHHHTTCTTCCEEECCSCCCEEECCCCEEEEEE
T ss_pred             EEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCC-cCCccCchhhhccCCCCCEEeCcCCcCccchhhhCCCCCC
Confidence            99999997 88  489988887      89999999995 5667765 25899999999999887533 100 00     


Q ss_pred             ------C-CccchHHhhcCCCC-CcEEEeeccccccccccc
Q 004895          687 ------G-GSNASLAELKGLSK-LTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       687 ------~-~~~~~l~~L~~L~~-L~~L~l~~n~~~~lp~~~  719 (724)
                            + ........+.++++ |+.|+++.|.++.+|..+
T Consensus       356 ~~L~L~~N~l~~lp~~l~~l~~~L~~L~Ls~N~l~~lp~~~  396 (636)
T 4eco_A          356 ASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLKYIPNIF  396 (636)
T ss_dssp             SEEECCSSEEEECCTTSEEECTTCCEEECCSSCCSSCCSCC
T ss_pred             CEEECCCCccccccHhhhhhcccCcEEEccCCcCcccchhh
Confidence                  0 00011123455666 777777777777777643

>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=99.49  E-value=2.4e-13  Score=159.00  Aligned_cols=181  Identities=20%  Similarity=0.276  Sum_probs=117.1

Q ss_pred             cCceEEeccCCCcc-cCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCcEE
Q 004895          527 KGPIAISLPYRDIQ-ELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTL  603 (724)
Q Consensus       527 ~~~~~l~l~~~~~~-~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~~L  603 (724)
                      .+++.|.+.+|.+. .+|... .+++|+.|.+  ..+......+..+.++++|++|++++|.+. .+|..++.+++|++|
T Consensus       442 ~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L--~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L  519 (768)
T 3rgz_A          442 SKLRDLKLWLNMLEGEIPQELMYVKTLETLIL--DFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAIL  519 (768)
T ss_dssp             TTCCEEECCSSCCCSCCCGGGGGCTTCCEEEC--CSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEE
T ss_pred             CCCCEEECCCCcccCcCCHHHcCCCCceEEEe--cCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHhcCCCCCEE
Confidence            45666666666664 334332 4666777766  222333233344667777777777777777 667777777777777


Q ss_pred             EcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhh----------------------------------------
Q 004895          604 CLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIG----------------------------------------  640 (724)
Q Consensus       604 ~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~----------------------------------------  640 (724)
                      +|++|.+..  |..++.+++|++|++++|.++ .+|..+.                                        
T Consensus       520 ~L~~N~l~~~~p~~l~~l~~L~~L~Ls~N~l~g~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  599 (768)
T 3rgz_A          520 KLSNNSFSGNIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGNLLEFQGI  599 (768)
T ss_dssp             ECCSSCCEEECCGGGGGCTTCCEEECCSSEEESBCCGGGGTTTTCBCCSTTCSCEEEEEECCSCCTTCCSSEEEEECTTC
T ss_pred             ECCCCcccCcCCHHHcCCCCCCEEECCCCccCCcCChHHhcccchhhhhccccccccccccccccccccccccccccccc
Confidence            777777664  566777777777777777665 5554332                                        


Q ss_pred             ------------------------------cCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCcc
Q 004895          641 ------------------------------QLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSN  690 (724)
Q Consensus       641 ------------------------------~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~  690 (724)
                                                    .+++|+.|++++| .+....|..++.+++|+.|++++|.     +.+..|
T Consensus       600 ~~~~~~~l~~~~~~~l~~~~~~g~~~~~~~~l~~L~~LdLs~N-~l~g~ip~~l~~l~~L~~L~Ls~N~-----l~g~ip  673 (768)
T 3rgz_A          600 RSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYN-MLSGYIPKEIGSMPYLFILNLGHND-----ISGSIP  673 (768)
T ss_dssp             CGGGGGGGGGTCCSCTTSCEEEEECCCSCSSSBCCCEEECCSS-CCBSCCCGGGGGCTTCCEEECCSSC-----CCSCCC
T ss_pred             cchhhhccccccccccccceecccCchhhhccccccEEECcCC-cccccCCHHHhccccCCEEeCcCCc-----cCCCCC
Confidence                                          2456777777774 4444444557888888888888753     444455


Q ss_pred             chHHhhcCCCCCcEEEeeccccc-ccccc
Q 004895          691 ASLAELKGLSKLTTLEIDVRDAE-MLRRI  718 (724)
Q Consensus       691 ~~l~~L~~L~~L~~L~l~~n~~~-~lp~~  718 (724)
                      .   .+.+|++|+.|+++.|.++ .+|..
T Consensus       674 ~---~l~~L~~L~~LdLs~N~l~g~ip~~  699 (768)
T 3rgz_A          674 D---EVGDLRGLNILDLSSNKLDGRIPQA  699 (768)
T ss_dssp             G---GGGGCTTCCEEECCSSCCEECCCGG
T ss_pred             h---HHhCCCCCCEEECCCCcccCcCChH
Confidence            4   4556778999999999886 45544

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.49  E-value=1.1e-13  Score=156.55  Aligned_cols=151  Identities=23%  Similarity=0.282  Sum_probs=124.4

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~  602 (724)
                      +..+++|++++|.+..++.  ...+++|++|++  +.+....+++..|.++++|++|++++|.+..+| ..++.+.+|++
T Consensus        27 ~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L--s~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  104 (570)
T 2z63_A           27 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDL--SRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK  104 (570)
T ss_dssp             CSSCCEEECCSCCCCEECTTTTTTCSSCCEEEC--TTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCE
T ss_pred             cccccEEEccCCccCccChhHhhCCCCceEEEC--CCCcCCccCcccccCchhCCEEeCcCCcCCccCHhhhcCcccccc
Confidence            5689999999999987753  347899999999  344566677778899999999999999998664 68999999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcc--cchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC----cEEE
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQ--LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL----EELY  674 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~--lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L----~~L~  674 (724)
                      |++++|.++..  ..++++++|++|++++|.++.  +|..++++++|++|++++| .+..+++..++.+++|    +.|+
T Consensus       105 L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~~~~~L~  183 (570)
T 2z63_A          105 LVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSN-KIQSIYCTDLRVLHQMPLLNLSLD  183 (570)
T ss_dssp             EECTTSCCCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTS-CCCEECGGGGHHHHTCTTCCCEEE
T ss_pred             ccccccccccCCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcCC-ccceecHHHccchhccchhhhhcc
Confidence            99999998883  358999999999999998885  6899999999999999984 5667776667777777    6777


Q ss_pred             ccCCC
Q 004895          675 MGDSF  679 (724)
Q Consensus       675 l~~~~  679 (724)
                      +++|.
T Consensus       184 l~~n~  188 (570)
T 2z63_A          184 LSLNP  188 (570)
T ss_dssp             CTTCC
T ss_pred             cCCCC
Confidence            77654

>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=99.49  E-value=1.6e-13  Score=154.44  Aligned_cols=172  Identities=24%  Similarity=0.306  Sum_probs=139.3

Q ss_pred             ceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCc
Q 004895          529 PIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       529 ~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~  608 (724)
                      +.++.+..+.+..+.....+++|+.|.+  +.+....++  .+..+++|+.|+|++|.+..+|. ++.+.+|++|+|++|
T Consensus        23 l~~l~l~~~~i~~~~~~~~L~~L~~L~l--~~n~i~~l~--~l~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N   97 (605)
T 1m9s_A           23 TIKDNLKKKSVTDAVTQNELNSIDQIIA--NNSDIKSVQ--GIQYLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDEN   97 (605)
T ss_dssp             HHHHHTTCSCTTSEECHHHHTTCCCCBC--TTCCCCCCT--TGGGCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSS
T ss_pred             HHHHhccCCCcccccchhcCCCCCEEEC--cCCCCCCCh--HHccCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCC
Confidence            3344455555555555557889999988  333444454  37889999999999999998877 999999999999999


Q ss_pred             ccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCC
Q 004895          609 RLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGG  688 (724)
Q Consensus       609 ~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~  688 (724)
                      .+..++.++.+++|++|+|++|.++.+| .+..|++|+.|+|++| .+..+  ..++.|++|+.|++++|.+     .+.
T Consensus        98 ~l~~l~~l~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~Ls~N-~l~~l--~~l~~l~~L~~L~Ls~N~l-----~~~  168 (605)
T 1m9s_A           98 KIKDLSSLKDLKKLKSLSLEHNGISDIN-GLVHLPQLESLYLGNN-KITDI--TVLSRLTKLDTLSLEDNQI-----SDI  168 (605)
T ss_dssp             CCCCCTTSTTCTTCCEEECTTSCCCCCG-GGGGCTTCSEEECCSS-CCCCC--GGGGSCTTCSEEECCSSCC-----CCC
T ss_pred             CCCCChhhccCCCCCEEEecCCCCCCCc-cccCCCccCEEECCCC-ccCCc--hhhcccCCCCEEECcCCcC-----CCc
Confidence            9999889999999999999999999875 5999999999999995 56666  3489999999999999742     222


Q ss_pred             ccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          689 SNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       689 ~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      .     .+..+++|+.|+|+.|.+..+|...
T Consensus       169 ~-----~l~~l~~L~~L~Ls~N~i~~l~~l~  194 (605)
T 1m9s_A          169 V-----PLAGLTKLQNLYLSKNHISDLRALA  194 (605)
T ss_dssp             G-----GGTTCTTCCEEECCSSCCCBCGGGT
T ss_pred             h-----hhccCCCCCEEECcCCCCCCChHHc
Confidence            1     2778999999999999998887543

>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=99.49  E-value=1.1e-13  Score=137.52  Aligned_cols=173  Identities=15%  Similarity=0.087  Sum_probs=142.4

Q ss_pred             ccCceEEeccCCC-cccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCc-
Q 004895          526 QKGPIAISLPYRD-IQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQ-  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~-~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~-  601 (724)
                      ..++++|.+++|. +..++..  ..+++|+.|.+. +.+....++...|.++++|+.|++++|.+..+|. ++.+.+|+ 
T Consensus        54 l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~-~~n~l~~i~~~~f~~l~~L~~L~l~~n~l~~lp~-~~~l~~L~~  131 (239)
T 2xwt_C           54 LPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIR-NTRNLTYIDPDALKELPLLKFLGIFNTGLKMFPD-LTKVYSTDI  131 (239)
T ss_dssp             CTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEE-EETTCCEECTTSEECCTTCCEEEEEEECCCSCCC-CTTCCBCCS
T ss_pred             CCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECC-CCCCeeEcCHHHhCCCCCCCEEeCCCCCCccccc-ccccccccc
Confidence            4689999999997 8887643  478999999993 2255667777789999999999999999999987 88888888 


Q ss_pred             --EEEcCCc-ccCCc--ccccCCCCCc-EEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCC-CCCcEEE
Q 004895          602 --TLCLDGW-RLEDI--AIVGQLKKLE-ILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKL-SRLEELY  674 (724)
Q Consensus       602 --~L~L~~~-~l~~~--~~~~~l~~L~-~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l-~~L~~L~  674 (724)
                        +|++++| .++.+  ..+..+++|+ +|++++|.++.+|......++|++|++++|..+..+++..+..+ ++|+.|+
T Consensus       132 L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l~~i~~~~~~~~~L~~L~L~~n~~l~~i~~~~~~~l~~~L~~L~  211 (239)
T 2xwt_C          132 FFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSGPSLLD  211 (239)
T ss_dssp             EEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCCCEECTTTTTTCEEEEEECTTCTTCCEECTTTTTTCSBCCSEEE
T ss_pred             ccEEECCCCcchhhcCcccccchhcceeEEEcCCCCCcccCHhhcCCCCCCEEEcCCCCCcccCCHHHhhccccCCcEEE
Confidence              9999999 88883  4589999999 99999999999998866669999999999645888988888999 9999999


Q ss_pred             ccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                      +++|....      .+..     .+++|+.|.++.+.
T Consensus       212 l~~N~l~~------l~~~-----~~~~L~~L~l~~~~  237 (239)
T 2xwt_C          212 VSQTSVTA------LPSK-----GLEHLKELIARNTW  237 (239)
T ss_dssp             CTTCCCCC------CCCT-----TCTTCSEEECTTC-
T ss_pred             CCCCcccc------CChh-----HhccCceeeccCcc
Confidence            99864321      1111     56788999887653

>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=99.48  E-value=2.1e-13  Score=157.61  Aligned_cols=151  Identities=21%  Similarity=0.213  Sum_probs=126.9

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|++|.+  ..+....+++..|.++++|++|++++|.+..+|. .++++.+|++
T Consensus        24 ~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L--s~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~  101 (680)
T 1ziw_A           24 PTNITVLNLTHNQLRRLPAANFTRYSQLTSLDV--GFNTISKLEPELCQKLPMLKVLNLQHNELSQLSDKTFAFCTNLTE  101 (680)
T ss_dssp             CTTCSEEECCSSCCCCCCGGGGGGGTTCSEEEC--CSSCCCCCCTTHHHHCTTCCEEECCSSCCCCCCTTTTTTCTTCSE
T ss_pred             CCCCcEEECCCCCCCCcCHHHHhCCCcCcEEEC--CCCccCccCHHHHhcccCcCEEECCCCccCccChhhhccCCCCCE
Confidence            5789999999999988875  347899999999  3345566767778999999999999999998886 5999999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhh--CCCCCcEEEccC
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVIS--KLSRLEELYMGD  677 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~--~l~~L~~L~l~~  677 (724)
                      |++++|.++.+  ..++++++|++|++++|.++.. |..+.++++|++|++++| .+...++..++  .+++|++|++++
T Consensus       102 L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~~~~~~~~~L~~L~L~~  180 (680)
T 1ziw_A          102 LHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNN-KIQALKSEELDIFANSSLKKLELSS  180 (680)
T ss_dssp             EECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSS-CCCCBCHHHHGGGTTCEESEEECTT
T ss_pred             EECCCCccCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCC-cccccCHHHhhccccccccEEECCC
Confidence            99999998883  5799999999999999988865 556889999999999994 56777776554  568999999998


Q ss_pred             CC
Q 004895          678 SF  679 (724)
Q Consensus       678 ~~  679 (724)
                      |.
T Consensus       181 n~  182 (680)
T 1ziw_A          181 NQ  182 (680)
T ss_dssp             CC
T ss_pred             Cc
Confidence            74

>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=99.48  E-value=3.4e-13  Score=148.27  Aligned_cols=173  Identities=19%  Similarity=0.230  Sum_probs=100.9

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .+++.+++.++.+..++....+++|+.|++.  .+....+++  +.++++|++|++++|.+..+|. ++++++|++|+++
T Consensus        46 ~~l~~L~l~~~~i~~l~~~~~l~~L~~L~Ls--~n~l~~~~~--~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~L~  120 (466)
T 1o6v_A           46 DQVTTLQADRLGIKSIDGVEYLNNLTQINFS--NNQLTDITP--LKNLTKLVDILMNNNQIADITP-LANLTNLTGLTLF  120 (466)
T ss_dssp             HTCCEEECCSSCCCCCTTGGGCTTCCEEECC--SSCCCCCGG--GTTCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECC
T ss_pred             ccccEEecCCCCCccCcchhhhcCCCEEECC--CCccCCchh--hhccccCCEEECCCCccccChh-hcCCCCCCEEECC
Confidence            4666777776666666655566777777762  233334443  5666777777777777666655 6677777777777


Q ss_pred             CcccCCcccccCCCCCcEEEccCCcCcccch--------------------hhhcCCCCCeEccCCCCCCcccChHHhhC
Q 004895          607 GWRLEDIAIVGQLKKLEILSLRGAEIKQLPL--------------------QIGQLTRLQLLDLSNCSSLVVIAPNVISK  666 (724)
Q Consensus       607 ~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~--------------------~i~~l~~L~~L~l~~~~~l~~~~~~~i~~  666 (724)
                      +|.++..+.+..+++|++|++++|.++.+|.                    .+.++++|++|++++| .+..++.  +..
T Consensus       121 ~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~~~~~~~~~~~l~~L~~L~l~~n-~l~~~~~--l~~  197 (466)
T 1o6v_A          121 NNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSN-KVSDISV--LAK  197 (466)
T ss_dssp             SSCCCCCGGGTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSS-CCCCCGG--GGG
T ss_pred             CCCCCCChHHcCCCCCCEEECCCCccCCChhhccCCcccEeecCCcccCchhhccCCCCCEEECcCC-cCCCChh--hcc
Confidence            7766665446667777777777766665543                    1444455555555553 2333321  455


Q ss_pred             CCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          667 LSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       667 l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      +++|++|++++|..     .+     +..+..+++|+.|++++|.++.++.
T Consensus       198 l~~L~~L~l~~n~l-----~~-----~~~~~~l~~L~~L~l~~n~l~~~~~  238 (466)
T 1o6v_A          198 LTNLESLIATNNQI-----SD-----ITPLGILTNLDELSLNGNQLKDIGT  238 (466)
T ss_dssp             CTTCSEEECCSSCC-----CC-----CGGGGGCTTCCEEECCSSCCCCCGG
T ss_pred             CCCCCEEEecCCcc-----cc-----cccccccCCCCEEECCCCCcccchh
Confidence            55555555555421     11     1124456677777777777665543

>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=99.48  E-value=5.6e-13  Score=146.51  Aligned_cols=175  Identities=21%  Similarity=0.254  Sum_probs=135.0

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++.|++.+|.+..++....+++|+.|.+.  .+....++.  +.++++|+.|++++|.+..+|. +..+++|++|++
T Consensus       220 l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~--~n~l~~~~~--~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~L  294 (466)
T 1o6v_A          220 LTNLDELSLNGNQLKDIGTLASLTNLTDLDLA--NNQISNLAP--LSGLTKLTELKLGANQISNISP-LAGLTALTNLEL  294 (466)
T ss_dssp             CTTCCEEECCSSCCCCCGGGGGCTTCSEEECC--SSCCCCCGG--GTTCTTCSEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             cCCCCEEECCCCCcccchhhhcCCCCCEEECC--CCccccchh--hhcCCCCCEEECCCCccCcccc-ccCCCccCeEEc
Confidence            46788888888888777666678888888883  233333433  6788889999999988887766 788888999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++..+.++.+++|++|++++|.++.+++ +..+++|+.|++++| .+..++  .+..+++|+.|++++|.     +
T Consensus       295 ~~n~l~~~~~~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~~L~l~~n-~l~~~~--~l~~l~~L~~L~l~~n~-----l  365 (466)
T 1o6v_A          295 NENQLEDISPISNLKNLTYLTLYFNNISDISP-VSSLTKLQRLFFYNN-KVSDVS--SLANLTNINWLSAGHNQ-----I  365 (466)
T ss_dssp             CSSCCSCCGGGGGCTTCSEEECCSSCCSCCGG-GGGCTTCCEEECCSS-CCCCCG--GGTTCTTCCEEECCSSC-----C
T ss_pred             CCCcccCchhhcCCCCCCEEECcCCcCCCchh-hccCccCCEeECCCC-ccCCch--hhccCCCCCEEeCCCCc-----c
Confidence            99988886668888999999999998887765 788899999999885 566653  37889999999998864     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      .+..     .+..+++|+.|++++|.+..+|...
T Consensus       366 ~~~~-----~~~~l~~L~~L~l~~n~~~~~p~~~  394 (466)
T 1o6v_A          366 SDLT-----PLANLTRITQLGLNDQAWTNAPVNY  394 (466)
T ss_dssp             CBCG-----GGTTCTTCCEEECCCEEEECCCBCC
T ss_pred             Cccc-----hhhcCCCCCEEeccCCcccCCchhh
Confidence            2222     2678889999999999888766543

>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=99.48  E-value=1.5e-13  Score=150.63  Aligned_cols=186  Identities=20%  Similarity=0.225  Sum_probs=134.5

Q ss_pred             ccCceEEeccCCCcccC-CC-cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQEL-PE-RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~-~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..+ +. ...+++|+.|.+. .+.....++...|.++++|++|++++|.+..+ |..++++.+|++
T Consensus        29 ~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~-~n~~~~~i~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~  107 (455)
T 3v47_A           29 PAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVE-QQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEV  107 (455)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTSSCTTCCEEECC-CCSTTCEECTTTTTTCTTCCEEECTTCTTCEECTTTTTTCTTCCE
T ss_pred             CCccCEEEecCCccCcCChhHhccCccccEEECc-CCcccceECcccccccccCCEEeCCCCccCccChhhccCcccCCE
Confidence            57899999999999776 33 2478999999993 33233356677789999999999999999855 788999999999


Q ss_pred             EEcCCcccCC--ccc--ccCCCCCcEEEccCCcCccc-chh-hhcCCCCCeEccCCCCCCcccChHHhhCC--CCCcEEE
Q 004895          603 LCLDGWRLED--IAI--VGQLKKLEILSLRGAEIKQL-PLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKL--SRLEELY  674 (724)
Q Consensus       603 L~L~~~~l~~--~~~--~~~l~~L~~L~l~~~~i~~l-p~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l--~~L~~L~  674 (724)
                      |++++|.++.  +..  ++.+++|++|++++|.++.+ |.. +.++++|++|++++| .+...++..++.+  .+|+.|+
T Consensus       108 L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~l~~l~~~~L~~L~  186 (455)
T 3v47_A          108 LTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFN-KVKSICEEDLLNFQGKHFTLLR  186 (455)
T ss_dssp             EECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGGGCTTCCEEECTTC-CBSCCCTTTSGGGTTCEEEEEE
T ss_pred             EeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccCCCCcccEEeCCCC-cccccChhhhhccccccccccc
Confidence            9999999987  444  89999999999999999877 555 889999999999995 5566666556655  5677777


Q ss_pred             ccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      +++|.................+..+++|+.|++++|.+.
T Consensus       187 l~~n~l~~~~~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~  225 (455)
T 3v47_A          187 LSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFK  225 (455)
T ss_dssp             CTTCBCTTCSTTCTTHHHHCCTTTTCEEEEEECTTSCCC
T ss_pred             cccCcccccchhhccccccccccccceeeeEecCCCccc
Confidence            776542211000000111122334566777777777653

>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=99.48  E-value=2.6e-13  Score=155.32  Aligned_cols=174  Identities=20%  Similarity=0.286  Sum_probs=118.3

Q ss_pred             CCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcCCcccCC-c
Q 004895          536 YRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLED-I  613 (724)
Q Consensus       536 ~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~~~l~~-~  613 (724)
                      +.+++.+|..+. ++++.|++  +.+....+++..|.++++|++|+|++|.+..+|+ .|.++.+|++|+|++|.++. +
T Consensus        40 ~~~l~~vP~~lp-~~~~~LdL--s~N~i~~l~~~~f~~l~~L~~L~Ls~N~i~~i~~~~f~~L~~L~~L~Ls~N~l~~l~  116 (635)
T 4g8a_A           40 ELNFYKIPDNLP-FSTKNLDL--SFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLA  116 (635)
T ss_dssp             TSCCSSCCSSSC-TTCCEEEC--TTSCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEEC
T ss_pred             CCCcCccCCCCC-cCCCEEEe--eCCCCCCCCHHHHhCCCCCCEEECCCCcCCCcChhHhcCCCCCCEEEccCCcCCCCC
Confidence            335566665332 46788887  4455666777778888888888888888887654 57788888888888888777 3


Q ss_pred             -ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCccc-ChHHhhCCCCCcEEEccCCCCccccccCCcc
Q 004895          614 -AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVI-APNVISKLSRLEELYMGDSFSQWDKVEGGSN  690 (724)
Q Consensus       614 -~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~-~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~  690 (724)
                       ..|++|++|++|++++|.++.+|.. ++++++|++|++++| .+..+ .+..++.+++|++|++++|.     +.+..+
T Consensus       117 ~~~f~~L~~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N-~l~~~~~~~~~~~l~~L~~L~L~~N~-----l~~~~~  190 (635)
T 4g8a_A          117 LGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNK-----IQSIYC  190 (635)
T ss_dssp             GGGGTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSS-CCCCCCCCGGGGGCTTCCEEECCSSC-----CCEECG
T ss_pred             HHHhcCCCCCCEEECCCCcCCCCChhhhhcCcccCeeccccC-ccccCCCchhhccchhhhhhcccCcc-----cccccc
Confidence             4578888888888888888877654 778888888888874 44433 24456778888888887753     333334


Q ss_pred             chHHhhcCCCCC-cEEEeecccccccccc
Q 004895          691 ASLAELKGLSKL-TTLEIDVRDAEMLRRI  718 (724)
Q Consensus       691 ~~l~~L~~L~~L-~~L~l~~n~~~~lp~~  718 (724)
                      ..+..+.+++.+ ..++++.|.++.++..
T Consensus       191 ~~l~~L~~l~~~~~~~~ls~n~l~~i~~~  219 (635)
T 4g8a_A          191 TDLRVLHQMPLLNLSLDLSLNPMNFIQPG  219 (635)
T ss_dssp             GGGHHHHTCTTCCCEEECTTCCCCEECTT
T ss_pred             ccccchhhhhhhhhhhhcccCcccccCcc
Confidence            455556555433 3677777766655543

>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=99.48  E-value=2.1e-13  Score=154.74  Aligned_cols=147  Identities=19%  Similarity=0.179  Sum_probs=90.3

Q ss_pred             ccCceEEeccCCCcccCCCcc--cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~--~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      ..+++.+++.++.+..+|...  .+++|++|.+  +.+....+++..|.++++|++|++++|.+..+|+ .++++++|++
T Consensus        50 l~~l~~l~l~~~~l~~lp~~~~~~l~~L~~L~L--~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  127 (597)
T 3oja_B           50 LNNQKIVTFKNSTMRKLPAALLDSFRQVELLNL--NDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTV  127 (597)
T ss_dssp             GCCCSEEEESSCEESEECTHHHHHCCCCSEEEC--TTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCE
T ss_pred             CCCceEEEeeCCCCCCcCHHHHccCCCCcEEEC--CCCCCCCCChHHhcCCCCCCEEECCCCcCCCCCHHHHcCCCCCCE
Confidence            355666666666666665432  4666777766  3333445555556666777777777776665543 4566777777


Q ss_pred             EEcCCcccCC-ccc-ccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          603 LCLDGWRLED-IAI-VGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       603 L~L~~~~l~~-~~~-~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      |+|++|.++. |+. ++++++|++|++++|.++.+|+ .+..+++|++|++++| .+..++   ++.+++|+.|++++|
T Consensus       128 L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N-~l~~~~---~~~l~~L~~L~l~~n  202 (597)
T 3oja_B          128 LVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSN-RLTHVD---LSLIPSLFHANVSYN  202 (597)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECTTS-CCSBCC---GGGCTTCSEEECCSS
T ss_pred             EEeeCCCCCCCCHHHhccCCCCCEEEeeCCcCCCCChhhhhcCCcCcEEECcCC-CCCCcC---hhhhhhhhhhhcccC
Confidence            7777776666 322 4666777777777776665543 4666677777777663 444443   355666666666665

>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=99.47  E-value=8.8e-14  Score=156.48  Aligned_cols=179  Identities=21%  Similarity=0.260  Sum_probs=138.8

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~  602 (724)
                      +..+++|++++|.+..++.  ...+++|++|.+  +.+....+++..|.++++|++|++++|.+..+|.. ++++.+|++
T Consensus        25 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L--s~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~  102 (549)
T 2z81_A           25 TAAMKSLDLSFNKITYIGHGDLRACANLQVLIL--KSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKY  102 (549)
T ss_dssp             CTTCCEEECCSSCCCEECSSTTSSCTTCCEEEC--TTSCCCEECTTTTTTCTTCCEEECTTSCCCSCCHHHHTTCTTCCE
T ss_pred             CCCccEEECcCCccCccChhhhhcCCcccEEEC--CCCCcCccChhhccccccCCEEECCCCccCccCHHHhccCCCCcE
Confidence            4678999999998877642  247889999998  44455566767788899999999999999877664 889999999


Q ss_pred             EEcCCcccCC---cccccCCCCCcEEEccCCc-Ccccc-hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          603 LCLDGWRLED---IAIVGQLKKLEILSLRGAE-IKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       603 L~L~~~~l~~---~~~~~~l~~L~~L~l~~~~-i~~lp-~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      |++++|.++.   +..++++++|++|++++|. +..+| ..+..+++|++|++++| .+....+..++.+++|++|+++.
T Consensus       103 L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n-~l~~~~~~~l~~l~~L~~L~l~~  181 (549)
T 2z81_A          103 LNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKAL-SLRNYQSQSLKSIRDIHHLTLHL  181 (549)
T ss_dssp             EECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEET-TCCEECTTTTTTCSEEEEEEEEC
T ss_pred             EECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeeeccCC-cccccChhhhhccccCceEeccc
Confidence            9999998874   4678899999999999986 66776 46888999999999884 45665566688899999999887


Q ss_pred             CCCccccccCCccchHHhhcCCCCCcEEEeeccccccc
Q 004895          678 SFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEML  715 (724)
Q Consensus       678 ~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~l  715 (724)
                      |...      ..+..  .+..+++|+.|+++.|.+..+
T Consensus       182 n~~~------~~~~~--~~~~l~~L~~L~L~~n~l~~~  211 (549)
T 2z81_A          182 SESA------FLLEI--FADILSSVRYLELRDTNLARF  211 (549)
T ss_dssp             SBST------THHHH--HHHSTTTBSEEEEESCBCTTC
T ss_pred             Cccc------ccchh--hHhhcccccEEEccCCccccc
Confidence            6321      11111  234688999999999998775

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.47  E-value=1.8e-13  Score=145.01  Aligned_cols=172  Identities=19%  Similarity=0.206  Sum_probs=111.6

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhc-CCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCC
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFE-GTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDG  607 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~-~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~  607 (724)
                      +.+..+++.+..+|... .+.++.|.+  +.+....++...|. ++++|+.|+|++|.+..+| ..+..+.+|++|+|++
T Consensus        21 ~~l~c~~~~l~~iP~~~-~~~l~~L~L--s~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~   97 (361)
T 2xot_A           21 NILSCSKQQLPNVPQSL-PSYTALLDL--SHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSS   97 (361)
T ss_dssp             TEEECCSSCCSSCCSSC-CTTCSEEEC--CSSCCCEECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS
T ss_pred             CEEEeCCCCcCccCccC-CCCCCEEEC--CCCCCCccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECCC
Confidence            45667777777776533 245777777  34455556666665 7777888888888777654 4577777888888888


Q ss_pred             cccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHh---hCCCCCcEEEccCCCCc
Q 004895          608 WRLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVI---SKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       608 ~~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i---~~l~~L~~L~l~~~~~~  681 (724)
                      |.++.+  ..+..+++|++|+|++|.++.+ |..+..+++|++|+|++ +.+..+|+..+   ..+++|+.|++++|.+ 
T Consensus        98 N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~-N~l~~l~~~~~~~~~~l~~L~~L~L~~N~l-  175 (361)
T 2xot_A           98 NHLHTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQ-NQISRFPVELIKDGNKLPKLMLLDLSSNKL-  175 (361)
T ss_dssp             SCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS-SCCCSCCGGGTC----CTTCCEEECCSSCC-
T ss_pred             CcCCcCCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCC-CcCCeeCHHHhcCcccCCcCCEEECCCCCC-
Confidence            777763  3477777888888888877766 45577777888888877 45667766544   5677788888777532 


Q ss_pred             cccccCCccchHHhhcCCCC--CcEEEeeccccc
Q 004895          682 WDKVEGGSNASLAELKGLSK--LTTLEIDVRDAE  713 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~--L~~L~l~~n~~~  713 (724)
                          .....   ..+..+++  |+.|++++|.+.
T Consensus       176 ----~~l~~---~~~~~l~~~~l~~l~l~~N~~~  202 (361)
T 2xot_A          176 ----KKLPL---TDLQKLPAWVKNGLYLHNNPLE  202 (361)
T ss_dssp             ----CCCCH---HHHHHSCHHHHTTEECCSSCEE
T ss_pred             ----CccCH---HHhhhccHhhcceEEecCCCcc
Confidence                22112   22333443  356777777653

>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=99.47  E-value=2.5e-13  Score=133.01  Aligned_cols=143  Identities=17%  Similarity=0.237  Sum_probs=118.2

Q ss_pred             cccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccc
Q 004895          560 YDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLP  636 (724)
Q Consensus       560 ~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp  636 (724)
                      ......+|...   .+.|+.|++++|.+..+|. .+..+.+|++|+|++|.++.  +..+..+++|++|+|++|.++.+|
T Consensus        20 ~~~l~~iP~~l---~~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~   96 (220)
T 2v9t_B           20 GKGLTEIPTNL---PETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELP   96 (220)
T ss_dssp             TSCCSSCCSSC---CTTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSSCCCCCC
T ss_pred             CCCcCcCCCcc---CcCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCCcCCccC
Confidence            34445566543   2689999999999997765 78999999999999999988  478999999999999999999998


Q ss_pred             hh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          637 LQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       637 ~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      .. +..+++|++|++++ +.+..+++..+..+++|++|++++|.+     .+..+   ..+..+++|+.|++++|.+..
T Consensus        97 ~~~f~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~l-----~~~~~---~~~~~l~~L~~L~L~~N~~~c  166 (220)
T 2v9t_B           97 KSLFEGLFSLQLLLLNA-NKINCLRVDAFQDLHNLNLLSLYDNKL-----QTIAK---GTFSPLRAIQTMHLAQNPFIC  166 (220)
T ss_dssp             TTTTTTCTTCCEEECCS-SCCCCCCTTTTTTCTTCCEEECCSSCC-----SCCCT---TTTTTCTTCCEEECCSSCEEC
T ss_pred             HhHccCCCCCCEEECCC-CCCCEeCHHHcCCCCCCCEEECCCCcC-----CEECH---HHHhCCCCCCEEEeCCCCcCC
Confidence            87 58899999999999 578888888899999999999999753     22222   245678899999999998643

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.47  E-value=1.7e-13  Score=151.18  Aligned_cols=175  Identities=14%  Similarity=0.139  Sum_probs=77.5

Q ss_pred             CceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc------------
Q 004895          528 GPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS------------  593 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~------------  593 (724)
                      ++++|++++|.+..++.  ...+++|++|.+.  .+.....++  |..+++|++|++++|.+..+|..            
T Consensus        35 ~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls--~N~l~~~~~--l~~l~~L~~L~Ls~N~l~~l~~~~~L~~L~L~~N~  110 (487)
T 3oja_A           35 NVKELDLSGNPLSQISAADLAPFTKLELLNLS--SNVLYETLD--LESLSTLRTLDLNNNYVQELLVGPSIETLHAANNN  110 (487)
T ss_dssp             GCCEEECCSSCCCCCCGGGGTTCTTCCEEECT--TSCCEEEEE--CTTCTTCCEEECCSSEEEEEEECTTCCEEECCSSC
T ss_pred             CccEEEeeCCcCCCCCHHHHhCCCCCCEEEee--CCCCCCCcc--cccCCCCCEEEecCCcCCCCCCCCCcCEEECcCCc
Confidence            55566666665555432  1245556666552  222222222  44455555555555544332211            


Q ss_pred             -----ccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCccc-chhhh-cCCCCCeEccCCCCCCcccChHHh
Q 004895          594 -----LGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQL-PLQIG-QLTRLQLLDLSNCSSLVVIAPNVI  664 (724)
Q Consensus       594 -----i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~l-p~~i~-~l~~L~~L~l~~~~~l~~~~~~~i  664 (724)
                           ...+++|++|+|++|.++.  +..++.+++|++|++++|.++.+ |..+. .+++|++|++++| .+..+++  .
T Consensus       111 l~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~l~~~l~~L~~L~Ls~N-~l~~~~~--~  187 (487)
T 3oja_A          111 ISRVSCSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYN-FIYDVKG--Q  187 (487)
T ss_dssp             CCCEEECCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECTTS-CCCEEEC--C
T ss_pred             CCCCCccccCCCCEEECCCCCCCCCCchhhcCCCCCCEEECCCCCCCCcChHHHhhhCCcccEEecCCC-ccccccc--c
Confidence                 0123444555555554444  23444555555555555555432 33333 4455555555552 2333332  2


Q ss_pred             hCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          665 SKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       665 ~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      ..+++|++|++++|.+     ++. +   ..+..+++|+.|++++|.+..+|..
T Consensus       188 ~~l~~L~~L~Ls~N~l-----~~~-~---~~~~~l~~L~~L~Ls~N~l~~lp~~  232 (487)
T 3oja_A          188 VVFAKLKTLDLSSNKL-----AFM-G---PEFQSAAGVTWISLRNNKLVLIEKA  232 (487)
T ss_dssp             CCCTTCCEEECCSSCC-----CEE-C---GGGGGGTTCSEEECTTSCCCEECTT
T ss_pred             ccCCCCCEEECCCCCC-----CCC-C---HhHcCCCCccEEEecCCcCcccchh
Confidence            3345555555544321     110 1   1233445555555555555555543

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.47  E-value=6.7e-13  Score=144.98  Aligned_cols=172  Identities=15%  Similarity=0.140  Sum_probs=104.3

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|++++|.+..+|....+++|+.|.+.  .+....++   +..+++|++|++++|.+..+|  ++.+++|++|++
T Consensus        41 l~~L~~L~Ls~n~l~~~~~l~~l~~L~~L~Ls--~n~l~~~~---~~~l~~L~~L~Ls~N~l~~~~--~~~l~~L~~L~L  113 (457)
T 3bz5_A           41 LATLTSLDCHNSSITDMTGIEKLTGLTKLICT--SNNITTLD---LSQNTNLTYLACDSNKLTNLD--VTPLTKLTYLNC  113 (457)
T ss_dssp             HTTCCEEECCSSCCCCCTTGGGCTTCSEEECC--SSCCSCCC---CTTCTTCSEEECCSSCCSCCC--CTTCTTCCEEEC
T ss_pred             cCCCCEEEccCCCcccChhhcccCCCCEEEcc--CCcCCeEc---cccCCCCCEEECcCCCCceee--cCCCCcCCEEEC
Confidence            35667777777776666654566777777773  22233332   556667777777777766654  666777777777


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccc--
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWD--  683 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~--  683 (724)
                      ++|.++.++ ++.+++|++|++++|.++.+|  ++.+++|++|++++|..+..++   ++.+++|++|++++|.....  
T Consensus       114 ~~N~l~~l~-~~~l~~L~~L~l~~N~l~~l~--l~~l~~L~~L~l~~n~~~~~~~---~~~l~~L~~L~ls~n~l~~l~l  187 (457)
T 3bz5_A          114 DTNKLTKLD-VSQNPLLTYLNCARNTLTEID--VSHNTQLTELDCHLNKKITKLD---VTPQTQLTTLDCSFNKITELDV  187 (457)
T ss_dssp             CSSCCSCCC-CTTCTTCCEEECTTSCCSCCC--CTTCTTCCEEECTTCSCCCCCC---CTTCTTCCEEECCSSCCCCCCC
T ss_pred             CCCcCCeec-CCCCCcCCEEECCCCccceec--cccCCcCCEEECCCCCcccccc---cccCCcCCEEECCCCccceecc
Confidence            777666643 666667777777777666654  5566666666666654444331   45555555555555432110  


Q ss_pred             --------------cccCCccchHHhhcCCCCCcEEEeecccccccc
Q 004895          684 --------------KVEGGSNASLAELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       684 --------------~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                                    .+++     + .+..+++|+.|+++.|.++.+|
T Consensus       188 ~~l~~L~~L~l~~N~l~~-----~-~l~~l~~L~~L~Ls~N~l~~ip  228 (457)
T 3bz5_A          188 SQNKLLNRLNCDTNNITK-----L-DLNQNIQLTFLDCSSNKLTEID  228 (457)
T ss_dssp             TTCTTCCEEECCSSCCSC-----C-CCTTCTTCSEEECCSSCCSCCC
T ss_pred             ccCCCCCEEECcCCcCCe-----e-ccccCCCCCEEECcCCcccccC
Confidence                          0111     1 3566788888888888887776

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.47  E-value=4.3e-13  Score=153.12  Aligned_cols=184  Identities=16%  Similarity=0.145  Sum_probs=110.3

Q ss_pred             ceEEeccCCCcccCCCccc---CCCccEEEEecccccccccchhhhc-------CCCCceEEEcCCCcCCCCCcccc-CC
Q 004895          529 PIAISLPYRDIQELPERLE---CPQLKLFLLFAKYDSTLQISDHFFE-------GTEELKVLDFTGIRFSPLPSSLG-RL  597 (724)
Q Consensus       529 ~~~l~l~~~~~~~~~~~~~---~~~Lr~L~l~~~~~~~~~~~~~~~~-------~l~~L~~L~l~~~~~~~lp~~i~-~l  597 (724)
                      +++|++++|.+..+|....   +++|+.|.+.  .+......+..+.       .+.+|+.|++++|.+..+|..+. .+
T Consensus       379 L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls--~N~l~~~~p~~l~~~~~~~~~~~~L~~L~Ls~N~l~~lp~~~~~~l  456 (636)
T 4eco_A          379 VENLSFAHNKLKYIPNIFDAKSVSVMSAIDFS--YNEIGSVDGKNFDPLDPTPFKGINVSSINLSNNQISKFPKELFSTG  456 (636)
T ss_dssp             CCEEECCSSCCSSCCSCCCTTCSSCEEEEECC--SSCTTTTTTCSSCTTCSSCCCCCCEEEEECCSSCCCSCCTHHHHTT
T ss_pred             CcEEEccCCcCcccchhhhhcccCccCEEECc--CCcCCCcchhhhcccccccccCCCCCEEECcCCccCcCCHHHHccC
Confidence            7777777777776665432   3367777762  2222222222233       45677777777777777766543 46


Q ss_pred             CCCcEEEcCCcccCC-cccc-c-------CCCCCcEEEccCCcCcccchhhh--cCCCCCeEccCCCCCCcccChHHhhC
Q 004895          598 INLQTLCLDGWRLED-IAIV-G-------QLKKLEILSLRGAEIKQLPLQIG--QLTRLQLLDLSNCSSLVVIAPNVISK  666 (724)
Q Consensus       598 ~~L~~L~L~~~~l~~-~~~~-~-------~l~~L~~L~l~~~~i~~lp~~i~--~l~~L~~L~l~~~~~l~~~~~~~i~~  666 (724)
                      ++|++|+|++|.++. |..+ .       ++++|++|++++|.++.+|..+.  .+++|++|++++| .+..+|.. ++.
T Consensus       457 ~~L~~L~Ls~N~l~~i~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N-~l~~ip~~-~~~  534 (636)
T 4eco_A          457 SPLSSINLMGNMLTEIPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYN-SFSKFPTQ-PLN  534 (636)
T ss_dssp             CCCSEEECCSSCCSBCCSSSSEETTEECTTGGGCCEEECCSSCCCBCCGGGSTTTCTTCCEEECCSS-CCSSCCCG-GGG
T ss_pred             CCCCEEECCCCCCCCcCHHHhccccccccccCCccEEECcCCcCCccChhhhhccCCCcCEEECCCC-CCCCcChh-hhc
Confidence            777777777777665 2222 1       22377777777777777777765  7777777777773 45555443 667


Q ss_pred             CCCCcEEEccCCCC-ccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          667 LSRLEELYMGDSFS-QWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       667 l~~L~~L~l~~~~~-~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                      +++|++|++++|.. ..+.+.+..+.   .+.++++|+.|+++.|.+..+|..+
T Consensus       535 l~~L~~L~Ls~N~~ls~N~l~~~~p~---~l~~l~~L~~L~Ls~N~l~~ip~~~  585 (636)
T 4eco_A          535 SSTLKGFGIRNQRDAQGNRTLREWPE---GITLCPSLTQLQIGSNDIRKVNEKI  585 (636)
T ss_dssp             CSSCCEEECCSCBCTTCCBCCCCCCT---TGGGCSSCCEEECCSSCCCBCCSCC
T ss_pred             CCCCCEEECCCCcccccCcccccChH---HHhcCCCCCEEECCCCcCCccCHhH
Confidence            77777777755421 11223333332   3345667777777777777776643

>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=99.47  E-value=4.5e-13  Score=146.90  Aligned_cols=31  Identities=16%  Similarity=0.246  Sum_probs=21.8

Q ss_pred             ccCceEEeccCCCcccC-CC--cccCCCccEEEE
Q 004895          526 QKGPIAISLPYRDIQEL-PE--RLECPQLKLFLL  556 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~-~~--~~~~~~Lr~L~l  556 (724)
                      ..++++|.+++|.+..+ |.  ...+++|+.|.+
T Consensus       128 l~~L~~L~L~~n~l~~~~~~~~~~~l~~L~~L~L  161 (455)
T 3v47_A          128 LTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDL  161 (455)
T ss_dssp             CTTCCEEECCSSBCCSCCCCGGGGGCTTCCEEEC
T ss_pred             cccCCEEECCCCccCccCcccccCCCCcccEEeC
Confidence            45778888888877666 33  236778888887

>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=99.46  E-value=1.6e-13  Score=154.31  Aligned_cols=149  Identities=17%  Similarity=0.210  Sum_probs=81.9

Q ss_pred             cCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC--CCccccCCCCCcE
Q 004895          527 KGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP--LPSSLGRLINLQT  602 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~--lp~~i~~l~~L~~  602 (724)
                      .++++|.+++|.+..++.  ...+++|++|++  +.+....+++..|.++++|++|++++|.+..  .|..++++.+|++
T Consensus        50 ~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L--s~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~  127 (549)
T 2z81_A           50 ANLQVLILKSSRINTIEGDAFYSLGSLEHLDL--SDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQT  127 (549)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEEC--TTSCCCSCCHHHHTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCE
T ss_pred             CcccEEECCCCCcCccChhhccccccCCEEEC--CCCccCccCHHHhccCCCCcEEECCCCcccccchhhhhhccCCccE
Confidence            455666666665555432  224556666666  3333444555555666666666666666652  3455566666666


Q ss_pred             EEcCCcc-cCC-c-ccccCCCCCcEEEccCCcCcc-cchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          603 LCLDGWR-LED-I-AIVGQLKKLEILSLRGAEIKQ-LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       603 L~L~~~~-l~~-~-~~~~~l~~L~~L~l~~~~i~~-lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      |++++|. +.. + ..++.+++|++|++++|.++. .|..+..+++|++|+++.| ....+|...++.+++|++|++++|
T Consensus       128 L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~l~~n-~~~~~~~~~~~~l~~L~~L~L~~n  206 (549)
T 2z81_A          128 LRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTLHLS-ESAFLLEIFADILSSVRYLELRDT  206 (549)
T ss_dssp             EEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCSEEEEEEEECS-BSTTHHHHHHHSTTTBSEEEEESC
T ss_pred             EECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhhccccCceEecccC-cccccchhhHhhcccccEEEccCC
Confidence            6666665 333 2 345666666666666665553 4555666666666666553 334444433445666666666654

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.46  E-value=2.6e-13  Score=136.87  Aligned_cols=144  Identities=24%  Similarity=0.290  Sum_probs=125.6

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|++.+|.+..++....+++|+.|.+  +.+....++.  +.++++|+.|++++|.+..+|....  .+|++|++
T Consensus        40 l~~L~~L~l~~n~i~~l~~l~~l~~L~~L~L--~~N~i~~~~~--l~~l~~L~~L~L~~N~l~~l~~~~~--~~L~~L~L  113 (263)
T 1xeu_A           40 LSGVQNFNGDNSNIQSLAGMQFFTNLKELHL--SHNQISDLSP--LKDLTKLEELSVNRNRLKNLNGIPS--ACLSRLFL  113 (263)
T ss_dssp             HTTCSEEECTTSCCCCCTTGGGCTTCCEEEC--CSSCCCCCGG--GTTCSSCCEEECCSSCCSCCTTCCC--SSCCEEEC
T ss_pred             cCcCcEEECcCCCcccchHHhhCCCCCEEEC--CCCccCCChh--hccCCCCCEEECCCCccCCcCcccc--CcccEEEc
Confidence            4789999999999999986668999999999  3445555665  8899999999999999998876444  99999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++|.++.++.++.+++|++|++++|.++.+| .+..+++|++|++++| .+...  ..+..+++|+.|++++|.
T Consensus       114 ~~N~l~~~~~l~~l~~L~~L~Ls~N~i~~~~-~l~~l~~L~~L~L~~N-~i~~~--~~l~~l~~L~~L~l~~N~  183 (263)
T 1xeu_A          114 DNNELRDTDSLIHLKNLEILSIRNNKLKSIV-MLGFLSKLEVLDLHGN-EITNT--GGLTRLKKVNWIDLTGQK  183 (263)
T ss_dssp             CSSCCSBSGGGTTCTTCCEEECTTSCCCBCG-GGGGCTTCCEEECTTS-CCCBC--TTSTTCCCCCEEEEEEEE
T ss_pred             cCCccCCChhhcCcccccEEECCCCcCCCCh-HHccCCCCCEEECCCC-cCcch--HHhccCCCCCEEeCCCCc
Confidence            9999999888999999999999999999987 6999999999999995 56666  348999999999999864

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.45  E-value=3.6e-13  Score=156.98  Aligned_cols=133  Identities=11%  Similarity=0.106  Sum_probs=68.8

Q ss_pred             ceEEEcCCCcCCCCCccccCCCC--CcEEEcCCcccCC-cccc----c--CCCCCcEEEccCCcCcccchhhh-cCCCCC
Q 004895          577 LKVLDFTGIRFSPLPSSLGRLIN--LQTLCLDGWRLED-IAIV----G--QLKKLEILSLRGAEIKQLPLQIG-QLTRLQ  646 (724)
Q Consensus       577 L~~L~l~~~~~~~lp~~i~~l~~--L~~L~L~~~~l~~-~~~~----~--~l~~L~~L~l~~~~i~~lp~~i~-~l~~L~  646 (724)
                      |+.|++++|.+..+|..++.+..  |++|+|++|.+.. ++.+    +  .+.+|++|++++|.++.+|..+. .+++|+
T Consensus       621 L~~L~Ls~N~L~~lp~~~~~~~~~~L~~L~Ls~N~l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~L~~lp~~~~~~l~~L~  700 (876)
T 4ecn_A          621 VEGLGFSHNKLKYIPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPIS  700 (876)
T ss_dssp             CCEEECCSSCCCSCCSCCCTTCSSCEEEEECCSSCTTTTSSSCSSCTTTCCCCCEEEEECCSSCCCSCCHHHHHTTCCCS
T ss_pred             CCEEECcCCCCCcCchhhhccccCCCCEEECcCCcCCCccccchhhhccccCCCcCEEEccCCcCCccCHHHHccCCCCC
Confidence            44444444444444444433322  4444444444433 1111    1  22356666666666666666543 566666


Q ss_pred             eEccCCCCCCcccChHHhhC-------CCCCcEEEccCCCCccccccCCccchHHhhc--CCCCCcEEEeeccccccccc
Q 004895          647 LLDLSNCSSLVVIAPNVISK-------LSRLEELYMGDSFSQWDKVEGGSNASLAELK--GLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       647 ~L~l~~~~~l~~~~~~~i~~-------l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~--~L~~L~~L~l~~n~~~~lp~  717 (724)
                      +|++++| .+..+|+..+..       |++|++|++++|.+.      ..+   ..+.  .+++|+.|+++.|.+..+|.
T Consensus       701 ~L~Ls~N-~L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~L~------~lp---~~l~~~~l~~L~~L~Ls~N~L~~lp~  770 (876)
T 4ecn_A          701 TIILSNN-LMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLT------SLS---DDFRATTLPYLSNMDVSYNCFSSFPT  770 (876)
T ss_dssp             EEECCSC-CCSCCCTTSSSCTTSCCTTGGGCCEEECCSSCCC------CCC---GGGSTTTCTTCCEEECCSSCCSSCCC
T ss_pred             EEECCCC-cCCccChHHhccccccccccCCccEEECCCCCCc------cch---HHhhhccCCCcCEEEeCCCCCCccch
Confidence            6666663 444555432221       226666666665321      111   2333  67788888888888877775


Q ss_pred             cc
Q 004895          718 IW  719 (724)
Q Consensus       718 ~~  719 (724)
                      .+
T Consensus       771 ~l  772 (876)
T 4ecn_A          771 QP  772 (876)
T ss_dssp             GG
T ss_pred             hh
Confidence            54

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.45  E-value=6.9e-13  Score=154.63  Aligned_cols=185  Identities=10%  Similarity=0.066  Sum_probs=97.8

Q ss_pred             cC-ceEEeccCCCcccCCCccc---CCCccEEEEecccccccccchhh---hc--CCCCceEEEcCCCcCCCCCcccc-C
Q 004895          527 KG-PIAISLPYRDIQELPERLE---CPQLKLFLLFAKYDSTLQISDHF---FE--GTEELKVLDFTGIRFSPLPSSLG-R  596 (724)
Q Consensus       527 ~~-~~~l~l~~~~~~~~~~~~~---~~~Lr~L~l~~~~~~~~~~~~~~---~~--~l~~L~~L~l~~~~~~~lp~~i~-~  596 (724)
                      .+ ++.|++++|.+..+|....   .++|+.|.+..+  .....++.+   +.  .+.+|+.|++++|.+..+|..+. .
T Consensus       618 ~~~L~~L~Ls~N~L~~lp~~~~~~~~~~L~~L~Ls~N--~l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~L~~lp~~~~~~  695 (876)
T 4ecn_A          618 TDQVEGLGFSHNKLKYIPNIFNAKSVYVMGSVDFSYN--KIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFAT  695 (876)
T ss_dssp             CTTCCEEECCSSCCCSCCSCCCTTCSSCEEEEECCSS--CTTTTSSSCSSCTTTCCCCCEEEEECCSSCCCSCCHHHHHT
T ss_pred             cccCCEEECcCCCCCcCchhhhccccCCCCEEECcCC--cCCCccccchhhhccccCCCcCEEEccCCcCCccCHHHHcc
Confidence            44 8888888888777765432   234677766322  111111110   11  22356666666666666665543 5


Q ss_pred             CCCCcEEEcCCcccCC-ccccc--------CCCCCcEEEccCCcCcccchhhh--cCCCCCeEccCCCCCCcccChHHhh
Q 004895          597 LINLQTLCLDGWRLED-IAIVG--------QLKKLEILSLRGAEIKQLPLQIG--QLTRLQLLDLSNCSSLVVIAPNVIS  665 (724)
Q Consensus       597 l~~L~~L~L~~~~l~~-~~~~~--------~l~~L~~L~l~~~~i~~lp~~i~--~l~~L~~L~l~~~~~l~~~~~~~i~  665 (724)
                      +++|++|+|++|.++. |..+.        ++++|++|+|++|.++.+|..+.  .+++|++|++++| .+..+|.. ++
T Consensus       696 l~~L~~L~Ls~N~L~~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~L~~lp~~l~~~~l~~L~~L~Ls~N-~L~~lp~~-l~  773 (876)
T 4ecn_A          696 GSPISTIILSNNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYN-CFSSFPTQ-PL  773 (876)
T ss_dssp             TCCCSEEECCSCCCSCCCTTSSSCTTSCCTTGGGCCEEECCSSCCCCCCGGGSTTTCTTCCEEECCSS-CCSSCCCG-GG
T ss_pred             CCCCCEEECCCCcCCccChHHhccccccccccCCccEEECCCCCCccchHHhhhccCCCcCEEEeCCC-CCCccchh-hh
Confidence            6666666666666555 22222        22366666666666666666655  6666666666663 44445433 55


Q ss_pred             CCCCCcEEEccCCCC-ccccccCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          666 KLSRLEELYMGDSFS-QWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       666 ~l~~L~~L~l~~~~~-~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      .+++|+.|++++|.. ..+.+.+..+   ..+.++++|+.|++++|.+..+|..
T Consensus       774 ~L~~L~~L~Ls~N~~ls~N~l~~~ip---~~l~~L~~L~~L~Ls~N~L~~Ip~~  824 (876)
T 4ecn_A          774 NSSQLKAFGIRHQRDAEGNRILRQWP---TGITTCPSLIQLQIGSNDIRKVDEK  824 (876)
T ss_dssp             GCTTCCEEECCCCBCTTCCBCCCCCC---TTGGGCSSCCEEECCSSCCCBCCSC
T ss_pred             cCCCCCEEECCCCCCcccccccccCh---HHHhcCCCCCEEECCCCCCCccCHh
Confidence            666666666655321 1111222222   2333455666666666666656554

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.45  E-value=2.4e-13  Score=140.96  Aligned_cols=173  Identities=18%  Similarity=0.149  Sum_probs=113.1

Q ss_pred             ccCceEEeccCCCcccCCCcc-cC-----CCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC---CCccc--
Q 004895          526 QKGPIAISLPYRDIQELPERL-EC-----PQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP---LPSSL--  594 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~-----~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~---lp~~i--  594 (724)
                      ..++++|++++|.+..+|... .+     ++|+.|.+  +.+....++...|.++++|+.|++++|.+..   +|..+  
T Consensus       120 l~~L~~L~Ls~N~l~~~~~~~~~l~~~~~~~L~~L~L--~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~  197 (312)
T 1wwl_A          120 GPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSI--AQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCP  197 (312)
T ss_dssp             SCCCSEEEEESCBCSSSSSHHHHHHTTCCTTCCEEEE--ESCSCCCCCTTTCCCCSSCCEEECCSCTTCHHHHHHHHSCT
T ss_pred             CCCccEEEccCCCCcchhHHHHHHHHhhcCCCcEEEe--eCCCCccchHHHhccCCCCCEEECCCCCcCcchHHHHHHHh
Confidence            456777788777776665432 22     77888877  3344555665667777888888888877652   34444  


Q ss_pred             cCCCCCcEEEcCCcccCCc-----ccccCCCCCcEEEccCCcCcccc--hhhhcCCCCCeEccCCCCCCcccChHHhhCC
Q 004895          595 GRLINLQTLCLDGWRLEDI-----AIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQLLDLSNCSSLVVIAPNVISKL  667 (724)
Q Consensus       595 ~~l~~L~~L~L~~~~l~~~-----~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l  667 (724)
                      +.+.+|++|++++|.++.+     ..+..+++|++|++++|.++..+  ..+..+++|++|++++| .++.+|.. +.  
T Consensus       198 ~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~Ls~N-~l~~ip~~-~~--  273 (312)
T 1wwl_A          198 LKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFT-GLKQVPKG-LP--  273 (312)
T ss_dssp             TSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTSCCCSSCCCSCCCCCTTCCEEECTTS-CCSSCCSS-CC--
T ss_pred             ccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCCcCCcccchhhhhhcCCCCEEECCCC-ccChhhhh-cc--
Confidence            6777888888888877742     22356678888888888777544  34556777888888773 45666553 33  


Q ss_pred             CCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          668 SRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       668 ~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      ++|++|++++|.     +++. +    .+..+++|+.|++++|.++.
T Consensus       274 ~~L~~L~Ls~N~-----l~~~-p----~~~~l~~L~~L~L~~N~l~~  310 (312)
T 1wwl_A          274 AKLSVLDLSYNR-----LDRN-P----SPDELPQVGNLSLKGNPFLD  310 (312)
T ss_dssp             SEEEEEECCSSC-----CCSC-C----CTTTSCEEEEEECTTCTTTC
T ss_pred             CCceEEECCCCC-----CCCC-h----hHhhCCCCCEEeccCCCCCC
Confidence            678888887753     2221 1    25566777888888777653

>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=99.44  E-value=6.3e-13  Score=153.59  Aligned_cols=179  Identities=19%  Similarity=0.200  Sum_probs=144.7

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      +.++.+++.+..+|.... ++++.|.+  +.+....++...|.++++|++|++++|.+..+ |..++++.+|++|+|++|
T Consensus         7 ~~~~cs~~~L~~ip~~~~-~~l~~L~L--s~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n   83 (680)
T 1ziw_A            7 EVADCSHLKLTQVPDDLP-TNITVLNL--THNQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQHN   83 (680)
T ss_dssp             SEEECCSSCCSSCCSCSC-TTCSEEEC--CSSCCCCCCGGGGGGGTTCSEEECCSSCCCCCCTTHHHHCTTCCEEECCSS
T ss_pred             CeeECCCCCccccccccC-CCCcEEEC--CCCCCCCcCHHHHhCCCcCcEEECCCCccCccCHHHHhcccCcCEEECCCC
Confidence            356777788888886543 78999999  44556677887899999999999999999965 678899999999999999


Q ss_pred             ccCC-cc-cccCCCCCcEEEccCCcCcccc-hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          609 RLED-IA-IVGQLKKLEILSLRGAEIKQLP-LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       609 ~l~~-~~-~~~~l~~L~~L~l~~~~i~~lp-~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      .++. ++ .++++++|++|++++|.++.+| ..++++++|++|++++| .+...++..++++++|++|++++|.     +
T Consensus        84 ~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n-~l~~~~~~~~~~l~~L~~L~L~~n~-----l  157 (680)
T 1ziw_A           84 ELSQLSDKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKNLITLDLSHN-GLSSTKLGTQVQLENLQELLLSNNK-----I  157 (680)
T ss_dssp             CCCCCCTTTTTTCTTCSEEECCSSCCCCCCSCTTTTCTTCCEEECCSS-CCSCCCCCSSSCCTTCCEEECCSSC-----C
T ss_pred             ccCccChhhhccCCCCCEEECCCCccCccChhHccccCCCCEEECCCC-cccccCchhhcccccCCEEEccCCc-----c
Confidence            9988 33 5999999999999999999886 56999999999999995 5666777778999999999999874     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      .+..+..+. ...+++|+.|+++.|.++.++..
T Consensus       158 ~~~~~~~~~-~~~~~~L~~L~L~~n~l~~~~~~  189 (680)
T 1ziw_A          158 QALKSEELD-IFANSSLKKLELSSNQIKEFSPG  189 (680)
T ss_dssp             CCBCHHHHG-GGTTCEESEEECTTCCCCCBCTT
T ss_pred             cccCHHHhh-ccccccccEEECCCCcccccChh
Confidence            222222222 23467899999999988776543

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.43  E-value=6.5e-13  Score=130.06  Aligned_cols=148  Identities=15%  Similarity=0.198  Sum_probs=119.3

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC--ccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEc
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP--SSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSL  627 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp--~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l  627 (724)
                      +++.+  +.+....+|..+   ...++.|++++|.+..++  ..+..+.+|++|+|++|.++.+  ..+..+++|++|++
T Consensus        14 ~~l~~--s~n~l~~iP~~~---~~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~L   88 (220)
T 2v70_A           14 TTVDC--SNQKLNKIPEHI---PQYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILL   88 (220)
T ss_dssp             TEEEC--CSSCCSSCCSCC---CTTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEEC
T ss_pred             CEeEe--CCCCcccCccCC---CCCCCEEEcCCCcCCccCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEEC
Confidence            45555  334455566543   346789999999999763  3488999999999999999883  47999999999999


Q ss_pred             cCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEE
Q 004895          628 RGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE  706 (724)
Q Consensus       628 ~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~  706 (724)
                      ++|.++.+|.. +..+++|++|++++ +.+..+++..+..+++|++|++++|.     +.+..+   ..+..+++|+.|+
T Consensus        89 s~N~l~~~~~~~~~~l~~L~~L~Ls~-N~l~~~~~~~~~~l~~L~~L~L~~N~-----l~~~~~---~~~~~l~~L~~L~  159 (220)
T 2v70_A           89 TSNRLENVQHKMFKGLESLKTLMLRS-NRITCVGNDSFIGLSSVRLLSLYDNQ-----ITTVAP---GAFDTLHSLSTLN  159 (220)
T ss_dssp             CSSCCCCCCGGGGTTCSSCCEEECTT-SCCCCBCTTSSTTCTTCSEEECTTSC-----CCCBCT---TTTTTCTTCCEEE
T ss_pred             CCCccCccCHhHhcCCcCCCEEECCC-CcCCeECHhHcCCCccCCEEECCCCc-----CCEECH---HHhcCCCCCCEEE
Confidence            99999988765 88999999999999 56788877789999999999999974     332222   3466788999999


Q ss_pred             eeccccc
Q 004895          707 IDVRDAE  713 (724)
Q Consensus       707 l~~n~~~  713 (724)
                      +++|.+.
T Consensus       160 L~~N~l~  166 (220)
T 2v70_A          160 LLANPFN  166 (220)
T ss_dssp             CCSCCEE
T ss_pred             ecCcCCc
Confidence            9999875

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.43  E-value=1.1e-12  Score=148.28  Aligned_cols=182  Identities=20%  Similarity=0.268  Sum_probs=142.2

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      +.+.-++.++..+|... .++++.|++  +.+....++...|.++++|++|++++|.+..+ |..++++.+|++|+|++|
T Consensus        10 ~~~~c~~~~l~~ip~~l-~~~l~~L~L--s~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n   86 (570)
T 2z63_A           10 ITYQCMELNFYKIPDNL-PFSTKNLDL--SFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGN   86 (570)
T ss_dssp             TEEECCSSCCSSCCSSS-CSSCCEEEC--CSCCCCEECTTTTTTCSSCCEEECTTCCCCEECTTTTTTCTTCCEEECTTC
T ss_pred             cEEEeCCCCccccCCCc-cccccEEEc--cCCccCccChhHhhCCCCceEEECCCCcCCccCcccccCchhCCEEeCcCC
Confidence            34555556677777643 367999999  44555667777789999999999999999976 457899999999999999


Q ss_pred             ccCC--cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCccc-ChHHhhCCCCCcEEEccCCCCcccc
Q 004895          609 RLED--IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVI-APNVISKLSRLEELYMGDSFSQWDK  684 (724)
Q Consensus       609 ~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~-~~~~i~~l~~L~~L~l~~~~~~~~~  684 (724)
                      .++.  +..++++++|++|++++|.++.+|. .++++++|++|++++| .+..+ .|..++++++|++|++++|.     
T Consensus        87 ~l~~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n-~l~~~~lp~~~~~l~~L~~L~l~~n~-----  160 (570)
T 2z63_A           87 PIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHN-LIQSFKLPEYFSNLTNLEHLDLSSNK-----  160 (570)
T ss_dssp             CCCEECTTTTTTCTTCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSS-CCCCCCCCGGGGGCTTCCEEECTTSC-----
T ss_pred             cCCccCHhhhcCccccccccccccccccCCCccccccccccEEecCCC-ccceecChhhhcccCCCCEEeCcCCc-----
Confidence            9988  3679999999999999999998876 5999999999999995 45542 24568999999999999874     


Q ss_pred             ccCCccchHHhhcCCCCC-cEEEeecccccccccccc
Q 004895          685 VEGGSNASLAELKGLSKL-TTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       685 ~~~~~~~~l~~L~~L~~L-~~L~l~~n~~~~lp~~~~  720 (724)
                      +.+..+..+..+.+|+.+ ..|+++.|.+..++...+
T Consensus       161 l~~~~~~~~~~l~~L~~~~~~L~l~~n~l~~~~~~~~  197 (570)
T 2z63_A          161 IQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAF  197 (570)
T ss_dssp             CCEECGGGGHHHHTCTTCCCEEECTTCCCCEECTTTT
T ss_pred             cceecHHHccchhccchhhhhcccCCCCceecCHHHh
Confidence            333334456666666444 689999998877765443

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.42  E-value=5e-13  Score=141.60  Aligned_cols=151  Identities=22%  Similarity=0.297  Sum_probs=130.6

Q ss_pred             ccCceEEeccCCCcccCCCcc---cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCc
Q 004895          526 QKGPIAISLPYRDIQELPERL---ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~---~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~  601 (724)
                      +..+++|++++|.+..++...   .+++|+.|.+  +.+....++...|.++++|+.|+|++|.+..+|. .+..+.+|+
T Consensus        38 ~~~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L--~~N~i~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~  115 (361)
T 2xot_A           38 PSYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLL--SHNHLNFISSEAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALE  115 (361)
T ss_dssp             CTTCSEEECCSSCCCEECTTSSSSCCTTCCEEEC--CSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCC
T ss_pred             CCCCCEEECCCCCCCccChhhhhhcccccCEEEC--CCCcCCccChhhccCCCCCCEEECCCCcCCcCCHHHhCCCcCCC
Confidence            567899999999998876542   7899999999  4556677777789999999999999999997755 689999999


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchhh----hcCCCCCeEccCCCCCCcccChHHhhCCCC--CcEE
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQI----GQLTRLQLLDLSNCSSLVVIAPNVISKLSR--LEEL  673 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~i----~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~--L~~L  673 (724)
                      +|+|++|.++.  +..+..+++|++|+|++|.++.+|..+    ..+++|++|+|++ +.+..+|+..+..+++  |+.|
T Consensus       116 ~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~~l~~L~~L~L~~-N~l~~l~~~~~~~l~~~~l~~l  194 (361)
T 2xot_A          116 VLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQISRFPVELIKDGNKLPKLMLLDLSS-NKLKKLPLTDLQKLPAWVKNGL  194 (361)
T ss_dssp             EEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCSCCGGGTC----CTTCCEEECCS-SCCCCCCHHHHHHSCHHHHTTE
T ss_pred             EEECCCCcccEECHHHhCCcccCCEEECCCCcCCeeCHHHhcCcccCCcCCEEECCC-CCCCccCHHHhhhccHhhcceE
Confidence            99999999987  467999999999999999999999876    6799999999999 6788999888899987  4899


Q ss_pred             EccCCC
Q 004895          674 YMGDSF  679 (724)
Q Consensus       674 ~l~~~~  679 (724)
                      ++.+|.
T Consensus       195 ~l~~N~  200 (361)
T 2xot_A          195 YLHNNP  200 (361)
T ss_dssp             ECCSSC
T ss_pred             EecCCC
Confidence            999875

>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=99.42  E-value=7.1e-13  Score=150.93  Aligned_cols=22  Identities=5%  Similarity=0.138  Sum_probs=14.1

Q ss_pred             hhcCCCCCcEEEeecccccccc
Q 004895          695 ELKGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       695 ~L~~L~~L~~L~l~~n~~~~lp  716 (724)
                      .+.++++|+.|+++.|.+...+
T Consensus       495 ~~~~l~~L~~L~Ls~N~l~~~~  516 (606)
T 3t6q_A          495 AFTSLKMMNHVDLSHNRLTSSS  516 (606)
T ss_dssp             TTTTCTTCCEEECCSSCCCGGG
T ss_pred             hhccccCCCEEECCCCccCcCC
Confidence            3456667777777777665544

>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=99.42  E-value=1.3e-12  Score=128.81  Aligned_cols=148  Identities=19%  Similarity=0.268  Sum_probs=118.9

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEcc
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLR  628 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~  628 (724)
                      +++.+  .......+|...   .++|++|++++|.+..+ |..+..+.+|++|+|++|.++.+  ..+..+++|++|+++
T Consensus        22 ~~v~c--~~~~l~~ip~~~---~~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls   96 (229)
T 3e6j_A           22 TTVDC--RSKRHASVPAGI---PTNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLG   96 (229)
T ss_dssp             TEEEC--TTSCCSSCCSCC---CTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECC
T ss_pred             CEeEc--cCCCcCccCCCC---CCCCCEEEcCCCccCccCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECC
Confidence            34444  334455566533   37899999999999976 67889999999999999999883  457899999999999


Q ss_pred             CCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEe
Q 004895          629 GAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEI  707 (724)
Q Consensus       629 ~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l  707 (724)
                      +|.++.+|.. +..+++|++|++++ +.+..+|.. +..+++|++|++++|.+     .+..+   ..+..+++|+.|++
T Consensus        97 ~N~l~~l~~~~~~~l~~L~~L~Ls~-N~l~~lp~~-~~~l~~L~~L~L~~N~l-----~~~~~---~~~~~l~~L~~L~l  166 (229)
T 3e6j_A           97 TNQLTVLPSAVFDRLVHLKELFMCC-NKLTELPRG-IERLTHLTHLALDQNQL-----KSIPH---GAFDRLSSLTHAYL  166 (229)
T ss_dssp             SSCCCCCCTTTTTTCTTCCEEECCS-SCCCSCCTT-GGGCTTCSEEECCSSCC-----CCCCT---TTTTTCTTCCEEEC
T ss_pred             CCcCCccChhHhCcchhhCeEeccC-CcccccCcc-cccCCCCCEEECCCCcC-----CccCH---HHHhCCCCCCEEEe
Confidence            9999999776 68999999999999 567788765 79999999999999743     22111   34677889999999


Q ss_pred             ecccccc
Q 004895          708 DVRDAEM  714 (724)
Q Consensus       708 ~~n~~~~  714 (724)
                      ++|.+..
T Consensus       167 ~~N~~~c  173 (229)
T 3e6j_A          167 FGNPWDC  173 (229)
T ss_dssp             TTSCBCT
T ss_pred             eCCCccC
Confidence            9998754

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.41  E-value=2.3e-11  Score=130.14  Aligned_cols=297  Identities=15%  Similarity=0.135  Sum_probs=178.3

Q ss_pred             ccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc---C-CCeEEEEEEecCCChHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN---V-FDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---~-F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      ..++||+++++.+..++.    ....+.+.|+|++|+||||+|+.+++......   . --.++|+++....+...++..
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            678999999999999884    34567899999999999999999999874321   1 123678888888888899999


Q ss_pred             HHHhhCCCCCCCch-hHHHHHHHHHHHh-cCCcEEEEEccccccccc----cccccccCCCCcCCCCCC-CCCcEEEEEe
Q 004895          232 LASDLGMNFDSNDL-IYHRAKQLCQRLK-KEKRVLIILDNIWTKLEL----DKIGIPYGDVDEKDKNDD-PRRCTIILTS  304 (724)
Q Consensus       232 i~~~l~~~~~~~~~-~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~~----~~l~~~~~~~~~~~~~~~-~~~s~ilvTt  304 (724)
                      ++.+++...+.... .......+...+. .+++.+|||||++.....    +.+...+...    .... ..+..+|+||
T Consensus        99 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~----~~~~~~~~~~~I~~t  174 (387)
T 2v1u_A           99 IAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRIN----QELGDRVWVSLVGIT  174 (387)
T ss_dssp             HHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGG----GCC-----CEEEEEC
T ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhch----hhcCCCceEEEEEEE
Confidence            99999765432221 2334555666664 346899999999765321    1121111100    0001 3456788888


Q ss_pred             cccchh----hhhcCC--CceEecCCCCHHHHHHHHHHHhCCC-CCCCCchhHHHHHHHHhC---Cchh-HHHHHHHHhc
Q 004895          305 RSRDLL----CIDMNS--QKMFWIDALSEEEALQLFEKIVGES-TKASDFRPLAEEIVGKCG---GLPV-ALSTVANALK  373 (724)
Q Consensus       305 R~~~v~----~~~~~~--~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~l~~~~~~I~~~c~---GlPL-ai~~~~~~l~  373 (724)
                      +.....    ......  ...+.+++++.++..+++.+.+... ....--++..+.+++.++   |.|. ++.++.....
T Consensus       175 ~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~  254 (387)
T 2v1u_A          175 NSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGE  254 (387)
T ss_dssp             SCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             CCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            765321    111111  2478999999999999999886420 111112456788999998   9994 3333322221


Q ss_pred             -----C--C-CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhc-cCCCCCcccHHHHHHHHhh
Q 004895          374 -----N--K-SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCG-LHREGRPIHVHYLLRYVMG  444 (724)
Q Consensus       374 -----~--~-~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s-~fp~~~~i~~~~Li~~W~~  444 (724)
                           +  . +.+.+..++....              ...+..++..||++.+..+..++ ++.....+....+.+....
T Consensus       255 ~a~~~~~~~i~~~~v~~a~~~~~--------------~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~  320 (387)
T 2v1u_A          255 IAERRREERVRREHVYSARAEIE--------------RDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKE  320 (387)
T ss_dssp             HHHHTTCSCBCHHHHHHHHHHHH--------------HHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHH
T ss_pred             HHHHcCCCCcCHHHHHHHHHHHh--------------hchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHH
Confidence                 1  1 5666666665432              12356678889988887776665 4432225555544443320


Q ss_pred             cccccccccccccccHHHHHHHHHHHHHHHHhhccccc
Q 004895          445 LRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD  482 (724)
Q Consensus       445 ~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~  482 (724)
                        ..+..| ... .    +...+.++++.|...|++..
T Consensus       321 --~~~~~~-~~~-~----~~~~~~~~l~~L~~~gli~~  350 (387)
T 2v1u_A          321 --LTSTLG-LEH-V----TLRRVSGIISELDMLGIVKS  350 (387)
T ss_dssp             --HHHHTT-CCC-C----CHHHHHHHHHHHHHTTSEEE
T ss_pred             --HHHhcC-CCC-C----CHHHHHHHHHHHHhCCCeEE
Confidence              000112 111 1    12344567788888888864

>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=99.41  E-value=7e-13  Score=148.00  Aligned_cols=143  Identities=15%  Similarity=0.170  Sum_probs=120.0

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      ++++++++.+..+|.... ++|+.|.+  +.+....+++..|.++++|++|++++|.+..+ |..++++.+|++|+|++|
T Consensus         3 ~~l~ls~n~l~~ip~~~~-~~L~~L~L--s~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N   79 (520)
T 2z7x_B            3 FLVDRSKNGLIHVPKDLS-QKTTILNI--SQNYISELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSHN   79 (520)
T ss_dssp             CEEECTTSCCSSCCCSCC-TTCSEEEC--CSSCCCCCCHHHHTTCTTCCEEECCSSCCCEEEGGGGTTCTTCCEEECCSS
T ss_pred             ceEecCCCCccccccccc-ccccEEEC--CCCcccccChhhccccccccEEecCCCccCCcChHHhhcccCCCEEecCCC
Confidence            578899999998887655 89999999  44556677777899999999999999999966 778999999999999999


Q ss_pred             ccCCcccccCCCCCcEEEccCCcCcc--cchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC--cEEEccCCCC
Q 004895          609 RLEDIAIVGQLKKLEILSLRGAEIKQ--LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL--EELYMGDSFS  680 (724)
Q Consensus       609 ~l~~~~~~~~l~~L~~L~l~~~~i~~--lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L--~~L~l~~~~~  680 (724)
                      .++.++.. .+++|++|++++|.++.  +|..++++++|++|++++| .+..   ..++.+++|  ++|++++|..
T Consensus        80 ~l~~lp~~-~l~~L~~L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n-~l~~---~~~~~l~~L~L~~L~l~~n~l  150 (520)
T 2z7x_B           80 KLVKISCH-PTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTT-HLEK---SSVLPIAHLNISKVLLVLGET  150 (520)
T ss_dssp             CCCEEECC-CCCCCSEEECCSSCCSSCCCCGGGGGCTTCCEEEEEES-SCCG---GGGGGGTTSCEEEEEEEECTT
T ss_pred             ceeecCcc-ccCCccEEeccCCccccccchhhhccCCcceEEEecCc-ccch---hhccccccceeeEEEeecccc
Confidence            99885444 89999999999999985  5789999999999999995 4444   336778888  9999988743

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.41  E-value=6.1e-13  Score=138.27  Aligned_cols=175  Identities=14%  Similarity=0.161  Sum_probs=106.7

Q ss_pred             cCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcC-----------------
Q 004895          527 KGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRF-----------------  587 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~-----------------  587 (724)
                      .++++|++++|.+..++.  ...+++|+.|.+.  .+....+++  +..+++|++|++++|.+                 
T Consensus        34 ~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls--~n~l~~~~~--~~~l~~L~~L~Ls~n~l~~l~~~~~L~~L~l~~n  109 (317)
T 3o53_A           34 WNVKELDLSGNPLSQISAADLAPFTKLELLNLS--SNVLYETLD--LESLSTLRTLDLNNNYVQELLVGPSIETLHAANN  109 (317)
T ss_dssp             GGCSEEECTTSCCCCCCHHHHTTCTTCCEEECT--TSCCEEEEE--ETTCTTCCEEECCSSEEEEEEECTTCCEEECCSS
T ss_pred             CCCCEEECcCCccCcCCHHHhhCCCcCCEEECC--CCcCCcchh--hhhcCCCCEEECcCCccccccCCCCcCEEECCCC
Confidence            355556665555554432  1245555555552  222222222  44555555555555544                 


Q ss_pred             --CCCCccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccc-hhh-hcCCCCCeEccCCCCCCcccCh
Q 004895          588 --SPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLP-LQI-GQLTRLQLLDLSNCSSLVVIAP  661 (724)
Q Consensus       588 --~~lp~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp-~~i-~~l~~L~~L~l~~~~~l~~~~~  661 (724)
                        ..+|.  ..+.+|++|++++|.++..  ..++.+++|++|++++|.++.++ ..+ ..+++|++|++++| .+..++.
T Consensus       110 ~l~~~~~--~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N-~l~~~~~  186 (317)
T 3o53_A          110 NISRVSC--SRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYN-FIYDVKG  186 (317)
T ss_dssp             CCSEEEE--CCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECTTS-CCCEEEC
T ss_pred             ccCCcCc--cccCCCCEEECCCCCCCCccchhhhccCCCCEEECCCCCCCcccHHHHhhccCcCCEEECCCC-cCccccc
Confidence              43332  2356677777777777762  46777788888888888777653 344 36788888888874 4565543


Q ss_pred             HHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccc
Q 004895          662 NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       662 ~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                        ...+++|++|++++|..     .+ .+   ..+..+++|+.|++++|.++.+|..+
T Consensus       187 --~~~l~~L~~L~Ls~N~l-----~~-l~---~~~~~l~~L~~L~L~~N~l~~l~~~~  233 (317)
T 3o53_A          187 --QVVFAKLKTLDLSSNKL-----AF-MG---PEFQSAAGVTWISLRNNKLVLIEKAL  233 (317)
T ss_dssp             --CCCCTTCCEEECCSSCC-----CE-EC---GGGGGGTTCSEEECTTSCCCEECTTC
T ss_pred             --ccccccCCEEECCCCcC-----Cc-ch---hhhcccCcccEEECcCCcccchhhHh
Confidence              34578888888887642     21 11   23566788999999999998888654

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.41  E-value=6.5e-13  Score=137.64  Aligned_cols=179  Identities=16%  Similarity=0.060  Sum_probs=115.3

Q ss_pred             cCceEEeccCCCcccC-CCc---ccCCCccEEEEeccccccc--ccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCC
Q 004895          527 KGPIAISLPYRDIQEL-PER---LECPQLKLFLLFAKYDSTL--QISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLIN  599 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~-~~~---~~~~~Lr~L~l~~~~~~~~--~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~  599 (724)
                      .++++|++++|.+... |..   ..+++|++|.+..+.....  .++...+..+++|++|++++|.+..+| ..++.+++
T Consensus        91 ~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~  170 (310)
T 4glp_A           91 SRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFPA  170 (310)
T ss_dssp             SCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCCCTTSCCCCTT
T ss_pred             CceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCCCcchhhHHHhccCCC
Confidence            4588888888877543 333   4577888888843221110  011223446788888888888887554 57778888


Q ss_pred             CcEEEcCCcccCC---c---ccccCCCCCcEEEccCCcCcccchh----hhcCCCCCeEccCCCCCCcccChHHhhCC--
Q 004895          600 LQTLCLDGWRLED---I---AIVGQLKKLEILSLRGAEIKQLPLQ----IGQLTRLQLLDLSNCSSLVVIAPNVISKL--  667 (724)
Q Consensus       600 L~~L~L~~~~l~~---~---~~~~~l~~L~~L~l~~~~i~~lp~~----i~~l~~L~~L~l~~~~~l~~~~~~~i~~l--  667 (724)
                      |++|+|++|.+..   .   ..++.+++|++|++++|.++.+|..    +..+++|++|++++| .+....|..++.+  
T Consensus       171 L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~l~~~l~~L~~L~Ls~N-~l~~~~p~~~~~~~~  249 (310)
T 4glp_A          171 LTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETPTGVCAALAAAGVQPHSLDLSHN-SLRATVNPSAPRCMW  249 (310)
T ss_dssp             CCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCCHHHHHHHHHHHTCCCSSEECTTS-CCCCCCCSCCSSCCC
T ss_pred             CCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCCCCCchHHHHHHHHhcCCCCCEEECCCC-CCCccchhhHHhccC
Confidence            8888888887543   1   2236778888888888888766553    467788888888884 4555523335555  


Q ss_pred             -CCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          668 -SRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       668 -~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                       ++|++|++++|...      ..+..+     .++|+.|+++.|.++.+|.
T Consensus       250 ~~~L~~L~Ls~N~l~------~lp~~~-----~~~L~~L~Ls~N~l~~~~~  289 (310)
T 4glp_A          250 SSALNSLNLSFAGLE------QVPKGL-----PAKLRVLDLSSNRLNRAPQ  289 (310)
T ss_dssp             CTTCCCEECCSSCCC------SCCSCC-----CSCCSCEECCSCCCCSCCC
T ss_pred             cCcCCEEECCCCCCC------chhhhh-----cCCCCEEECCCCcCCCCch
Confidence             58888888876432      112211     1577777777777776654

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.40  E-value=2.1e-13  Score=141.39  Aligned_cols=187  Identities=13%  Similarity=0.037  Sum_probs=137.6

Q ss_pred             cCceEEeccCCCccc-----CCCcccCCCccEEEEecccccccccchhhh-cCCCCceEEEcCCCcCCC-CC----cccc
Q 004895          527 KGPIAISLPYRDIQE-----LPERLECPQLKLFLLFAKYDSTLQISDHFF-EGTEELKVLDFTGIRFSP-LP----SSLG  595 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~-----~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~-~~l~~L~~L~l~~~~~~~-lp----~~i~  595 (724)
                      ..++++.+....+..     +.....+++|+.|.+..+ .-....+..++ ..+++|+.|++++|.+.. .|    ..+.
T Consensus        64 ~~l~~l~l~~~~~~~~~~~~~~~~~~~~~L~~L~l~~n-~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~~~~  142 (310)
T 4glp_A           64 LRVRRLTVGAAQVPAQLLVGALRVLAYSRLKELTLEDL-KITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQW  142 (310)
T ss_dssp             CCCCEEEECSCCCBHHHHHHHHHHHHHSCCCEEEEESC-CCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHHHTT
T ss_pred             cceeEEEEeCCcCCHHHHHHHHHhcccCceeEEEeeCC-EeccchhhhhhhccCCCCCEEEeecccccchhhhhHHHHhh
Confidence            356777777665532     222335678999999322 22233444333 889999999999999984 33    3456


Q ss_pred             CCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcc---cchh--hhcCCCCCeEccCCCCCCcccChH---Hhh
Q 004895          596 RLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQ---LPLQ--IGQLTRLQLLDLSNCSSLVVIAPN---VIS  665 (724)
Q Consensus       596 ~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~---lp~~--i~~l~~L~~L~l~~~~~l~~~~~~---~i~  665 (724)
                      .+++|++|+|++|.+..  +..++.+++|++|++++|.+..   +|..  +..+++|++|++++| .++.++..   .++
T Consensus       143 ~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N-~l~~l~~~~~~l~~  221 (310)
T 4glp_A          143 LKPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNT-GMETPTGVCAALAA  221 (310)
T ss_dssp             BCSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSS-CCCCHHHHHHHHHH
T ss_pred             hccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCC-CCCchHHHHHHHHh
Confidence            79999999999999987  3678999999999999998764   4433  478999999999995 56555432   357


Q ss_pred             CCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccccc
Q 004895          666 KLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       666 ~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      .+++|++|++++|.     +.+..+..+..+..+++|+.|+++.|.++.+|..++
T Consensus       222 ~l~~L~~L~Ls~N~-----l~~~~p~~~~~~~~~~~L~~L~Ls~N~l~~lp~~~~  271 (310)
T 4glp_A          222 AGVQPHSLDLSHNS-----LRATVNPSAPRCMWSSALNSLNLSFAGLEQVPKGLP  271 (310)
T ss_dssp             HTCCCSSEECTTSC-----CCCCCCSCCSSCCCCTTCCCEECCSSCCCSCCSCCC
T ss_pred             cCCCCCEEECCCCC-----CCccchhhHHhccCcCcCCEEECCCCCCCchhhhhc
Confidence            89999999999974     343334455566666899999999999999987653

>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=99.40  E-value=2.3e-12  Score=145.27  Aligned_cols=103  Identities=23%  Similarity=0.261  Sum_probs=57.0

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL  603 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L  603 (724)
                      +.++++|++++|.+..++.  ...+++|+.|.+  +.+....+++..|.++++|++|++++|.+..+|..  .+.+|++|
T Consensus        51 ~~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~L--s~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~L~~L  126 (562)
T 3a79_B           51 PPRTKALSLSQNSISELRMPDISFLSELRVLRL--SHNRIRSLDFHVFLFNQDLEYLDVSHNRLQNISCC--PMASLRHL  126 (562)
T ss_dssp             CTTCCEEECCSSCCCCCCGGGTTTCTTCCEEEC--CSCCCCEECTTTTTTCTTCCEEECTTSCCCEECSC--CCTTCSEE
T ss_pred             CCCcCEEECCCCCccccChhhhccCCCccEEEC--CCCCCCcCCHHHhCCCCCCCEEECCCCcCCccCcc--ccccCCEE
Confidence            3456666666666655542  235666666666  23334444445556666666666666666655544  55556666


Q ss_pred             EcCCcccCC---cccccCCCCCcEEEccCCcC
Q 004895          604 CLDGWRLED---IAIVGQLKKLEILSLRGAEI  632 (724)
Q Consensus       604 ~L~~~~l~~---~~~~~~l~~L~~L~l~~~~i  632 (724)
                      ++++|.++.   |..++++++|++|++++|.+
T Consensus       127 ~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n~l  158 (562)
T 3a79_B          127 DLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKF  158 (562)
T ss_dssp             ECCSSCCSBCCCCGGGGGCTTCCEEEEECSBC
T ss_pred             ECCCCCccccCchHhhcccCcccEEecCCCcc
Confidence            666655544   13455555555555555543

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.40  E-value=6.6e-13  Score=121.40  Aligned_cols=129  Identities=22%  Similarity=0.195  Sum_probs=98.2

Q ss_pred             CCCceEEEcCCCcCC--CCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcc-cchhhhcCCCCCeEcc
Q 004895          574 TEELKVLDFTGIRFS--PLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQ-LPLQIGQLTRLQLLDL  650 (724)
Q Consensus       574 l~~L~~L~l~~~~~~--~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~-lp~~i~~l~~L~~L~l  650 (724)
                      .++|+.|++++|.+.  .+|..++.+++|++|++++|.++....++.+++|++|++++|.++. +|..+..+++|++|++
T Consensus        16 ~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l   95 (149)
T 2je0_A           16 PSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNL   95 (149)
T ss_dssp             GGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCCCCTTCCCCTTCCEEECCSSCCCSCTHHHHHHCTTCCEEEC
T ss_pred             CccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCCCchhhhcCCCCCEEECCCCcccchHHHHhhhCCCCCEEEC
Confidence            467888888888888  7888888888999999998888877778888899999999998886 7777778889999999


Q ss_pred             CCCCCCcccC-hHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEee
Q 004895          651 SNCSSLVVIA-PNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID  708 (724)
Q Consensus       651 ~~~~~l~~~~-~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~  708 (724)
                      ++| .+..++ +..++.+++|++|++++|.     +.+..+.....+..+++|+.|+++
T Consensus        96 s~N-~i~~~~~~~~~~~l~~L~~L~l~~N~-----l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           96 SGN-KIKDLSTIEPLKKLENLKSLDLFNCE-----VTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             TTS-CCCSHHHHGGGGGCTTCCEEECTTCG-----GGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             CCC-cCCChHHHHHHhhCCCCCEEeCcCCc-----ccchHHHHHHHHHHCCCcccccCC
Confidence            884 466653 2457888899999988863     222222112345667788888765

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.40  E-value=9.3e-13  Score=155.61  Aligned_cols=181  Identities=20%  Similarity=0.235  Sum_probs=139.0

Q ss_pred             ccCceEEeccCCCcccCCC--cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPE--RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~--~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~  602 (724)
                      +.++++|++++|.+..++.  ...+++|+.|++ ..+.....+++..|.++++|++|+|++|.+..+ |..++++.+|++
T Consensus        23 p~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdL-s~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L~~  101 (844)
T 3j0a_A           23 LNTTERLLLSFNYIRTVTASSFPFLEQLQLLEL-GSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFE  101 (844)
T ss_dssp             CTTCCEEEEESCCCCEECSSSCSSCCSCSEEEE-CTTCCCCEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSCCC
T ss_pred             CCCcCEEECCCCcCCccChhHCcccccCeEEeC-CCCCCccccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCcccCE
Confidence            6789999999999877642  347899999999 333345567677789999999999999999855 889999999999


Q ss_pred             EEcCCcccCC--ccc--ccCCCCCcEEEccCCcCccc--chhhhcCCCCCeEccCCCCCCcccChHHhhCC--CCCcEEE
Q 004895          603 LCLDGWRLED--IAI--VGQLKKLEILSLRGAEIKQL--PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKL--SRLEELY  674 (724)
Q Consensus       603 L~L~~~~l~~--~~~--~~~l~~L~~L~l~~~~i~~l--p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l--~~L~~L~  674 (724)
                      |+|++|.++.  +..  ++++++|++|++++|.++.+  |..++++++|++|++++| .+....+..++.+  ++|+.|+
T Consensus       102 L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N-~i~~~~~~~l~~l~~~~L~~L~  180 (844)
T 3j0a_A          102 LRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSN-QIFLVCEHELEPLQGKTLSFFS  180 (844)
T ss_dssp             EECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESS-CCCCCCSGGGHHHHHCSSCCCE
T ss_pred             eeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCC-cCCeeCHHHcccccCCccceEE
Confidence            9999999886  443  89999999999999998865  357899999999999984 5556555567777  8999999


Q ss_pred             ccCCCCccccccCCccchHHhhc---CCCCCcEEEeeccccc
Q 004895          675 MGDSFSQWDKVEGGSNASLAELK---GLSKLTTLEIDVRDAE  713 (724)
Q Consensus       675 l~~~~~~~~~~~~~~~~~l~~L~---~L~~L~~L~l~~n~~~  713 (724)
                      ++.|...     +..+..+..+.   ...+|+.|+++.|.+.
T Consensus       181 L~~n~l~-----~~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~  217 (844)
T 3j0a_A          181 LAANSLY-----SRVSVDWGKCMNPFRNMVLEILDVSGNGWT  217 (844)
T ss_dssp             ECCSBSC-----CCCCCCCCSSSCTTTTCCBSEEBCSSCCSS
T ss_pred             CCCCccc-----cccccchhhcCCccccCceeEEecCCCcCc
Confidence            9887432     22222222211   1125999999999764

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.40  E-value=3.4e-12  Score=139.39  Aligned_cols=166  Identities=16%  Similarity=0.139  Sum_probs=99.3

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .++++|++++|.+..++ ...+++|+.|.+..  +....++   +.++++|++|++++|.+..+|  ++.+++|++|+++
T Consensus        64 ~~L~~L~Ls~n~l~~~~-~~~l~~L~~L~Ls~--N~l~~~~---~~~l~~L~~L~L~~N~l~~l~--~~~l~~L~~L~l~  135 (457)
T 3bz5_A           64 TGLTKLICTSNNITTLD-LSQNTNLTYLACDS--NKLTNLD---VTPLTKLTYLNCDTNKLTKLD--VSQNPLLTYLNCA  135 (457)
T ss_dssp             TTCSEEECCSSCCSCCC-CTTCTTCSEEECCS--SCCSCCC---CTTCTTCCEEECCSSCCSCCC--CTTCTTCCEEECT
T ss_pred             CCCCEEEccCCcCCeEc-cccCCCCCEEECcC--CCCceee---cCCCCcCCEEECCCCcCCeec--CCCCCcCCEEECC
Confidence            45555666555555543 33455555555521  2222222   444555555555555555443  4445555555555


Q ss_pred             CcccCCcc---------------------cccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhh
Q 004895          607 GWRLEDIA---------------------IVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVIS  665 (724)
Q Consensus       607 ~~~l~~~~---------------------~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~  665 (724)
                      +|.++.++                     .++.+++|++|++++|.++.+|  +..+++|+.|++++| .+..++   ++
T Consensus       136 ~N~l~~l~l~~l~~L~~L~l~~n~~~~~~~~~~l~~L~~L~ls~n~l~~l~--l~~l~~L~~L~l~~N-~l~~~~---l~  209 (457)
T 3bz5_A          136 RNTLTEIDVSHNTQLTELDCHLNKKITKLDVTPQTQLTTLDCSFNKITELD--VSQNKLLNRLNCDTN-NITKLD---LN  209 (457)
T ss_dssp             TSCCSCCCCTTCTTCCEEECTTCSCCCCCCCTTCTTCCEEECCSSCCCCCC--CTTCTTCCEEECCSS-CCSCCC---CT
T ss_pred             CCccceeccccCCcCCEEECCCCCcccccccccCCcCCEEECCCCccceec--cccCCCCCEEECcCC-cCCeec---cc
Confidence            55443321                     3556677777777777777766  667777777777773 455552   67


Q ss_pred             CCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          666 KLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       666 ~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .+++|++|++++|.     +.+     +. +..+++|+.|+++.|.++.+|.
T Consensus       210 ~l~~L~~L~Ls~N~-----l~~-----ip-~~~l~~L~~L~l~~N~l~~~~~  250 (457)
T 3bz5_A          210 QNIQLTFLDCSSNK-----LTE-----ID-VTPLTQLTYFDCSVNPLTELDV  250 (457)
T ss_dssp             TCTTCSEEECCSSC-----CSC-----CC-CTTCTTCSEEECCSSCCSCCCC
T ss_pred             cCCCCCEEECcCCc-----ccc-----cC-ccccCCCCEEEeeCCcCCCcCH
Confidence            77888888887753     332     11 6678999999999999887763

>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=99.40  E-value=3.2e-11  Score=128.89  Aligned_cols=295  Identities=15%  Similarity=0.130  Sum_probs=174.1

Q ss_pred             cccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC-CCeEEEEEEecCCChHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV-FDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      +..|+||+++++.+.+++.    ....+.+.|+|++|+||||||+.+++....... -..++|+++....+...++..++
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~   98 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQIDTPYRVLADLL   98 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHHCSHHHHHHHHT
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCCCCHHHHHHHHH
Confidence            3678999999999999886    345678999999999999999999998754311 12467888777777888888888


Q ss_pred             HhhCCCCCCCc-hhHHHHHHHHHHHhc-CCcEEEEEcccccccc------ccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          234 SDLGMNFDSND-LIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE------LDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       234 ~~l~~~~~~~~-~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      ..++....... ........+.+.+.. +++.+||||+++....      +..+......      . ...+..+|+||+
T Consensus        99 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~------~-~~~~~~~I~~~~  171 (386)
T 2qby_A           99 ESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSE------V-NKSKISFIGITN  171 (386)
T ss_dssp             TTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHS------C-CC--EEEEEEES
T ss_pred             HHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhh------c-CCCeEEEEEEEC
Confidence            88876533221 123344555555543 3489999999976432      1111111100      0 123556777887


Q ss_pred             ccchh-----hh-hcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHhC---CchhHH-HHHHHHhc-
Q 004895          306 SRDLL-----CI-DMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKCG---GLPVAL-STVANALK-  373 (724)
Q Consensus       306 ~~~v~-----~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c~---GlPLai-~~~~~~l~-  373 (724)
                      .....     .. .......+.+++++.++..+++.+.+.... ...-..+..+.+++.++   |.|..+ .++..... 
T Consensus       172 ~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~  251 (386)
T 2qby_A          172 DVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEI  251 (386)
T ss_dssp             CGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            65421     00 011124899999999999999998764111 11222567788888888   999844 33322221 


Q ss_pred             ----C--C-CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhccCCC-C-CcccHHHHHHHHhh
Q 004895          374 ----N--K-SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHRE-G-RPIHVHYLLRYVMG  444 (724)
Q Consensus       374 ----~--~-~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp~-~-~~i~~~~Li~~W~~  444 (724)
                          +  . +.+.+..++....              ...+...+..||+..+..+..++..-+ + ..+....+.+... 
T Consensus       252 a~~~~~~~i~~~~v~~a~~~~~--------------~~~~~~~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~-  316 (386)
T 2qby_A          252 AERMKDTKVKEEYVYMAKEEIE--------------RDRVRDIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYL-  316 (386)
T ss_dssp             HHHTTCSSCCHHHHHHHHHHHH--------------HHHHHHHHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHH-
T ss_pred             HHhcCCCccCHHHHHHHHHHHh--------------hchHHHHHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHH-
Confidence                1  1 5555555554421              134566777888888877776663211 1 1344444433222 


Q ss_pred             cccccccccccccccHHHHHHHHHHHHHHHHhhccccc
Q 004895          445 LRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLD  482 (724)
Q Consensus       445 ~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~  482 (724)
                       ..++..| +.. .    ....+..+++.|...+++..
T Consensus       317 -~~~~~~g-~~~-~----~~~~~~~~l~~L~~~gli~~  347 (386)
T 2qby_A          317 -NICKKLG-VEA-V----TQRRVSDIINELDMVGILTA  347 (386)
T ss_dssp             -HHHHHHT-CCC-C----CHHHHHHHHHHHHHHTSEEE
T ss_pred             -HHHHhcC-CCC-C----CHHHHHHHHHHHHhCCCEEE
Confidence             0000111 000 0    11334556777888898853

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.40  E-value=7.8e-13  Score=156.28  Aligned_cols=173  Identities=17%  Similarity=0.183  Sum_probs=137.3

Q ss_pred             EEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CC-CccccCCCCCcEEEcCCc
Q 004895          531 AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PL-PSSLGRLINLQTLCLDGW  608 (724)
Q Consensus       531 ~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~l-p~~i~~l~~L~~L~L~~~  608 (724)
                      ..+.++++++.+|.  -.++++.|++  +.+....+++..|.++++|++|++++|... .+ |..++++.+|++|+|++|
T Consensus         8 ~~dcs~~~L~~vP~--lp~~l~~LdL--s~N~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N   83 (844)
T 3j0a_A            8 IAFYRFCNLTQVPQ--VLNTTERLLL--SFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSS   83 (844)
T ss_dssp             EEEESCCCSSCCCS--SCTTCCEEEE--ESCCCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTC
T ss_pred             EEEccCCCCCCCCC--CCCCcCEEEC--CCCcCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCC
Confidence            45566778888887  5689999999  344556666667899999999999999544 55 778999999999999999


Q ss_pred             ccCC--cccccCCCCCcEEEccCCcCcc-cchh--hhcCCCCCeEccCCCCCCccc-ChHHhhCCCCCcEEEccCCCCcc
Q 004895          609 RLED--IAIVGQLKKLEILSLRGAEIKQ-LPLQ--IGQLTRLQLLDLSNCSSLVVI-APNVISKLSRLEELYMGDSFSQW  682 (724)
Q Consensus       609 ~l~~--~~~~~~l~~L~~L~l~~~~i~~-lp~~--i~~l~~L~~L~l~~~~~l~~~-~~~~i~~l~~L~~L~l~~~~~~~  682 (724)
                      .+..  |..++++++|++|++++|.++. +|..  +.++++|++|++++|. +... ++..+++|++|++|++++|.   
T Consensus        84 ~l~~~~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~-l~~~~~~~~~~~L~~L~~L~Ls~N~---  159 (844)
T 3j0a_A           84 KIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQ-IRSLYLHPSFGKLNSLKSIDFSSNQ---  159 (844)
T ss_dssp             CCCEECTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCC-CCCCCCCGGGGTCSSCCEEEEESSC---
T ss_pred             cCcccCHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCc-ccccccchhHhhCCCCCEEECCCCc---
Confidence            9887  5789999999999999999884 5665  8999999999999954 4444 34568999999999999864   


Q ss_pred             ccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          683 DKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       683 ~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                        +.+..+..+..+.. ++|+.|+++.|.+..
T Consensus       160 --i~~~~~~~l~~l~~-~~L~~L~L~~n~l~~  188 (844)
T 3j0a_A          160 --IFLVCEHELEPLQG-KTLSFFSLAANSLYS  188 (844)
T ss_dssp             --CCCCCSGGGHHHHH-CSSCCCEECCSBSCC
T ss_pred             --CCeeCHHHcccccC-CccceEECCCCcccc
Confidence              33333444554433 689999999998654

>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=99.40  E-value=2.9e-13  Score=141.99  Aligned_cols=176  Identities=20%  Similarity=0.200  Sum_probs=116.2

Q ss_pred             ccCceEEeccCCCccc--CCCc-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCC-cCC--CCCccccCCCC
Q 004895          526 QKGPIAISLPYRDIQE--LPER-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGI-RFS--PLPSSLGRLIN  599 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~--~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~~~--~lp~~i~~l~~  599 (724)
                      ..++++|++++|.+..  ++.. ..+++|+.|.+..  +.........+..+++|+.|++++| .++  .+|..+..+++
T Consensus        92 ~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~--~~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~  169 (336)
T 2ast_B           92 PFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEG--LRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSR  169 (336)
T ss_dssp             CBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTT--CBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTT
T ss_pred             CCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcC--cccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhcCCC
Confidence            3577778887776643  3322 2577888888732  2233223334666788888888887 566  35666777888


Q ss_pred             CcEEEcCCc-ccCC---cccccCCC-CCcEEEccCCc--C--cccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC
Q 004895          600 LQTLCLDGW-RLED---IAIVGQLK-KLEILSLRGAE--I--KQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL  670 (724)
Q Consensus       600 L~~L~L~~~-~l~~---~~~~~~l~-~L~~L~l~~~~--i--~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L  670 (724)
                      |++|++++| .++.   +..+..++ +|++|++++|.  +  ..+|..+.++++|++|++++|..++...+..++.+++|
T Consensus       170 L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L  249 (336)
T 2ast_B          170 LDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYL  249 (336)
T ss_dssp             CCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTC
T ss_pred             CCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHHHHhCCCCC
Confidence            888888888 6764   34567777 88888888873  4  35677777788888888888654544333457778888


Q ss_pred             cEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecc
Q 004895          671 EELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVR  710 (724)
Q Consensus       671 ~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n  710 (724)
                      ++|++++|.       +..+..+..+.++++|+.|++++|
T Consensus       250 ~~L~l~~~~-------~~~~~~~~~l~~~~~L~~L~l~~~  282 (336)
T 2ast_B          250 QHLSLSRCY-------DIIPETLLELGEIPTLKTLQVFGI  282 (336)
T ss_dssp             CEEECTTCT-------TCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             CEeeCCCCC-------CCCHHHHHHHhcCCCCCEEeccCc
Confidence            888887763       112334455667778888888776

>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=99.39  E-value=1.8e-11  Score=130.81  Aligned_cols=244  Identities=15%  Similarity=0.065  Sum_probs=159.2

Q ss_pred             ccccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc----C--CCeEEEEEEecCC-ChHHH
Q 004895          160 NIFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----V--FDKVVMAEITKNP-DAQKI  228 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~--F~~~~wv~vs~~~-~~~~l  228 (724)
                      ..++||+++++.+.+++.    ....+.+.|+|++|+||||||+.+++......    .  ...++|++++... +...+
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            678999999999987765    34567899999999999999999999864321    1  2347788887777 88888


Q ss_pred             HHHHHHhh-CCCCCCC-chhHHHHHHHHHHHhcCCcEEEEEcccccccc--cccc-ccccCCCCcCCCCCCCCCcEEEEE
Q 004895          229 QGELASDL-GMNFDSN-DLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKI-GIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       229 ~~~i~~~l-~~~~~~~-~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l-~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      +..++..+ +...... .........+...+.. ++.+|||||++....  +... ...+..        ...+..||+|
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~-~~~vlilDEi~~l~~~~~~~~~l~~l~~--------~~~~~~iI~~  170 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRN-IRAIIYLDEVDTLVKRRGGDIVLYQLLR--------SDANISVIMI  170 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSS-SCEEEEEETTHHHHHSTTSHHHHHHHHT--------SSSCEEEEEE
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhcc-CCCEEEEECHHHhccCCCCceeHHHHhc--------CCcceEEEEE
Confidence            88988887 3322211 1123445566666654 445999999976532  1121 112211        1157789999


Q ss_pred             ecccch----h-hhhcCCCceEecCCCCHHHHHHHHHHHhCC-CCCCCCchhHHHHHHHHhC---Cchh-HHHHHHHHhc
Q 004895          304 SRSRDL----L-CIDMNSQKMFWIDALSEEEALQLFEKIVGE-STKASDFRPLAEEIVGKCG---GLPV-ALSTVANALK  373 (724)
Q Consensus       304 tR~~~v----~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~-~~~~~~l~~~~~~I~~~c~---GlPL-ai~~~~~~l~  373 (724)
                      |+....    . .........+.+++++.++..++|...+.. .....--++..+.|++.|+   |.|. |+..+-....
T Consensus       171 t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~  250 (384)
T 2qby_B          171 SNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQ  250 (384)
T ss_dssp             CSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             ECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Confidence            887532    1 111111238999999999999999998641 1111122467788999998   9887 4444333321


Q ss_pred             ---C--C-CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhcc
Q 004895          374 ---N--K-SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGL  426 (724)
Q Consensus       374 ---~--~-~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~  426 (724)
                         +  . +.+.+..+++...              ...+..++..|+++.+..+..++.
T Consensus       251 ~a~~~~~i~~~~v~~~~~~~~--------------~~~~~~~~~~l~~~~~~~l~al~~  295 (384)
T 2qby_B          251 LASGGGIIRKEHVDKAIVDYE--------------QERLIEAVKALPFHYKLALRSLIE  295 (384)
T ss_dssp             HTTSSSCCCHHHHHHHHHHHH--------------HHHHHHHHHSSCHHHHHHHHHHHT
T ss_pred             HhcCCCccCHHHHHHHHHHHh--------------cchHHHHHHcCCHHHHHHHHHHHH
Confidence               1  2 6677777666532              134667788899888888777766

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.39  E-value=9.3e-13  Score=127.85  Aligned_cols=156  Identities=20%  Similarity=0.267  Sum_probs=127.1

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~  602 (724)
                      +.++++|++.+|.+..++..  ..+++|+.|.+  ..+....++...|.++++|++|++++|.+..+|.. +..+.+|++
T Consensus        27 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l--~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~  104 (208)
T 2o6s_A           27 PAQTTYLDLETNSLKSLPNGVFDELTSLTQLYL--GGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLKE  104 (208)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEEC--CSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCE
T ss_pred             CCCCcEEEcCCCccCcCChhhhcccccCcEEEC--CCCccCccChhhcCCCCCcCEEECCCCcCCccCHhHhcCccCCCE
Confidence            56899999999999888753  37899999999  34456677888889999999999999999988764 689999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |++++|.++..  ..+..+++|++|++++|.++.+|.. +..+++|++|++++|..        .+.+++|+.|+++.| 
T Consensus       105 L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~--------~~~~~~l~~L~~~~n-  175 (208)
T 2o6s_A          105 LALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPW--------DCTCPGIRYLSEWIN-  175 (208)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCCB--------CCCTTTTHHHHHHHH-
T ss_pred             EEcCCCcCcccCHhHhccCCcCCEEECCCCccceeCHHHhccCCCccEEEecCCCe--------ecCCCCHHHHHHHHH-
Confidence            99999999883  3478999999999999999988776 78899999999999532        245678888887764 


Q ss_pred             CccccccCCccchHHhh
Q 004895          680 SQWDKVEGGSNASLAEL  696 (724)
Q Consensus       680 ~~~~~~~~~~~~~l~~L  696 (724)
                          .+.|..+..++.+
T Consensus       176 ----~~~g~ip~~~~~l  188 (208)
T 2o6s_A          176 ----KHSGVVRNSAGSV  188 (208)
T ss_dssp             ----HCTTTBBCTTSSB
T ss_pred             ----hCCceeeccCccc
Confidence                3555555554443

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.39  E-value=2.5e-12  Score=143.18  Aligned_cols=157  Identities=17%  Similarity=0.177  Sum_probs=85.9

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .+++.|++++|.+..+|  ..+++|+.|.+  +.+....+|.  +.+  +|+.|++++|.++.+|.   .+.+|++|+|+
T Consensus        80 ~~L~~L~Ls~N~l~~ip--~~l~~L~~L~L--s~N~l~~ip~--l~~--~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls  148 (571)
T 3cvr_A           80 PQITVLEITQNALISLP--ELPASLEYLDA--CDNRLSTLPE--LPA--SLKHLDVDNNQLTMLPE---LPALLEYINAD  148 (571)
T ss_dssp             TTCSEEECCSSCCSCCC--CCCTTCCEEEC--CSSCCSCCCC--CCT--TCCEEECCSSCCSCCCC---CCTTCCEEECC
T ss_pred             CCCCEEECcCCCCcccc--cccCCCCEEEc--cCCCCCCcch--hhc--CCCEEECCCCcCCCCCC---cCccccEEeCC
Confidence            45666666666666555  23556666666  2223333443  222  56666666666666655   45666666666


Q ss_pred             CcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC-------cEEEccCCC
Q 004895          607 GWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL-------EELYMGDSF  679 (724)
Q Consensus       607 ~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L-------~~L~l~~~~  679 (724)
                      +|.++.++.  .+++|++|++++|.++.+|. +.  ++|++|++++ +.++.+|.  +..  +|       +.|++++|.
T Consensus       149 ~N~l~~lp~--~l~~L~~L~Ls~N~L~~lp~-l~--~~L~~L~Ls~-N~L~~lp~--~~~--~L~~~~~~L~~L~Ls~N~  218 (571)
T 3cvr_A          149 NNQLTMLPE--LPTSLEVLSVRNNQLTFLPE-LP--ESLEALDVST-NLLESLPA--VPV--RNHHSEETEIFFRCRENR  218 (571)
T ss_dssp             SSCCSCCCC--CCTTCCEEECCSSCCSCCCC-CC--TTCCEEECCS-SCCSSCCC--CC----------CCEEEECCSSC
T ss_pred             CCccCcCCC--cCCCcCEEECCCCCCCCcch-hh--CCCCEEECcC-CCCCchhh--HHH--hhhcccccceEEecCCCc
Confidence            666665333  45566666666666666665 44  6666666666 34555544  332  44       666666653


Q ss_pred             CccccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          680 SQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       680 ~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      +     + ..+.   .+.++++|+.|++++|.++
T Consensus       219 l-----~-~lp~---~l~~l~~L~~L~L~~N~l~  243 (571)
T 3cvr_A          219 I-----T-HIPE---NILSLDPTCTIILEDNPLS  243 (571)
T ss_dssp             C-----C-CCCG---GGGGSCTTEEEECCSSSCC
T ss_pred             c-----e-ecCH---HHhcCCCCCEEEeeCCcCC
Confidence            2     1 1122   2334666777777777664

>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=99.39  E-value=9.8e-13  Score=123.97  Aligned_cols=135  Identities=16%  Similarity=0.233  Sum_probs=91.9

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCC-CCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhh-hcCCCCCeE
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLI-NLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQI-GQLTRLQLL  648 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~-~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i-~~l~~L~~L  648 (724)
                      +.++..|+.|++++|.+..+|. +..+. +|++|++++|.++.++.++.+++|++|++++|.++.+|+.+ ..+++|++|
T Consensus        15 ~~~~~~L~~L~l~~n~l~~i~~-~~~~~~~L~~L~Ls~N~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L   93 (176)
T 1a9n_A           15 YTNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNNRICRIGEGLDQALPDLTEL   93 (176)
T ss_dssp             EECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCSSCCCEECCCCCCSSCCEEECCSSCCCEECSCHHHHCTTCCEE
T ss_pred             cCCcCCceEEEeeCCCCchhHH-hhhcCCCCCEEECCCCCCCcccccccCCCCCEEECCCCcccccCcchhhcCCCCCEE
Confidence            4456777888888887777754 44444 78888888887777777777888888888888887777654 778888888


Q ss_pred             ccCCCCCCcccCh-HHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          649 DLSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       649 ~l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ++++| .+..+|. ..++.+++|++|++++|..     ..........+..+++|+.|+++.|..
T Consensus        94 ~L~~N-~i~~~~~~~~l~~l~~L~~L~l~~N~i-----~~~~~~~~~~~~~l~~L~~Ld~~~n~~  152 (176)
T 1a9n_A           94 ILTNN-SLVELGDLDPLASLKSLTYLCILRNPV-----TNKKHYRLYVIYKVPQVRVLDFQKVKL  152 (176)
T ss_dssp             ECCSC-CCCCGGGGGGGGGCTTCCEEECCSSGG-----GGSTTHHHHHHHHCTTCSEETTEECCH
T ss_pred             ECCCC-cCCcchhhHhhhcCCCCCEEEecCCCC-----CCcHhHHHHHHHHCCccceeCCCcCCH
Confidence            88774 4566554 2467788888888877642     111111112355667788888877764

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.39  E-value=2.7e-13  Score=140.95  Aligned_cols=168  Identities=17%  Similarity=0.138  Sum_probs=102.9

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~  604 (724)
                      ..++++|++++|.+..++.   .++|+.|.+.  .+....++.   ..+++|+.|++++|.+..++ ..++.+.+|++|+
T Consensus        79 l~~L~~L~Ls~n~l~~l~~---~~~L~~L~l~--~n~l~~~~~---~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~  150 (317)
T 3o53_A           79 LSTLRTLDLNNNYVQELLV---GPSIETLHAA--NNNISRVSC---SRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLD  150 (317)
T ss_dssp             CTTCCEEECCSSEEEEEEE---CTTCCEEECC--SSCCSEEEE---CCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEE
T ss_pred             cCCCCEEECcCCccccccC---CCCcCEEECC--CCccCCcCc---cccCCCCEEECCCCCCCCccchhhhccCCCCEEE
Confidence            3567777777777665542   3677777772  233333332   23566777777777777553 3566677777777


Q ss_pred             cCCcccCC--cccc-cCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          605 LDGWRLED--IAIV-GQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       605 L~~~~l~~--~~~~-~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      +++|.++.  +..+ ..+++|++|++++|.++.+|.. ..+++|++|++++ +.+..+|+. +..+++|++|++++|...
T Consensus       151 Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~-~~l~~L~~L~Ls~-N~l~~l~~~-~~~l~~L~~L~L~~N~l~  227 (317)
T 3o53_A          151 LKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQ-VVFAKLKTLDLSS-NKLAFMGPE-FQSAAGVTWISLRNNKLV  227 (317)
T ss_dssp             CTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCEEECC-CCCTTCCEEECCS-SCCCEECGG-GGGGTTCSEEECTTSCCC
T ss_pred             CCCCCCCcccHHHHhhccCcCCEEECCCCcCcccccc-cccccCCEEECCC-CcCCcchhh-hcccCcccEEECcCCccc
Confidence            77777665  2333 3567777777777777766543 3467777777777 355666655 667777777777765321


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      .      .+   ..+..+++|+.|++++|.+.
T Consensus       228 ~------l~---~~~~~l~~L~~L~l~~N~~~  250 (317)
T 3o53_A          228 L------IE---KALRFSQNLEHFDLRGNGFH  250 (317)
T ss_dssp             E------EC---TTCCCCTTCCEEECTTCCCB
T ss_pred             c------hh---hHhhcCCCCCEEEccCCCcc
Confidence            1      11   23455667777777777665

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.38  E-value=7.8e-13  Score=152.67  Aligned_cols=153  Identities=16%  Similarity=0.196  Sum_probs=98.2

Q ss_pred             ccCceEEeccCCCcccCCCc-ccCCCccEEEEecc--cccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER-LECPQLKLFLLFAK--YDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~-~~~~~Lr~L~l~~~--~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~  602 (724)
                      ...++++++..+.+...+.. ....+|+.+.+...  ......++...|..+..|+.|+|++|.+..+|..++++.+|++
T Consensus       172 ~~~~~~l~L~~n~~~~~~~~~l~~l~Ls~~~i~~~~~~~n~~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~l~~L~~  251 (727)
T 4b8c_D          172 TPLTPKIELFANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTR  251 (727)
T ss_dssp             --------------------------------------------------CCCCCCEEECTTSCCSCCCGGGGGCCSCSC
T ss_pred             CCccceEEeeCCCCCcchhhHhhcCccCcccccCccccccceecChhhhccCCCCcEEECCCCCCCCCChhhcCCCCCCE
Confidence            45678888888877665432 24444555544211  1112235667788999999999999999999999999999999


Q ss_pred             EEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          603 LCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       603 L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      |+|++|.++. |..+++|++|++|+|++|.++.+|..++.|++|++|+|++| .+..+|.. |+.|++|++|++++|.+
T Consensus       252 L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N-~l~~lp~~-~~~l~~L~~L~L~~N~l  328 (727)
T 4b8c_D          252 LYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDN-MVTTLPWE-FGNLCNLQFLGVEGNPL  328 (727)
T ss_dssp             CBCTTSCCSCCCGGGGGGTTCCEEECTTSCCSSCCSSGGGGTTCSEEECCSS-CCCCCCSS-TTSCTTCCCEECTTSCC
T ss_pred             EEeeCCcCcccChhhhCCCCCCEEeCcCCcCCccChhhcCCCCCCEEECCCC-CCCccChh-hhcCCCccEEeCCCCcc
Confidence            9999999988 67899999999999999999999999999999999999994 67888765 89999999999999753

>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=99.37  E-value=7.3e-13  Score=138.92  Aligned_cols=176  Identities=19%  Similarity=0.289  Sum_probs=138.3

Q ss_pred             cCceEEeccCCCcccCC-CcccCCCccEEEEeccccccc-ccchhhhcCCCCceEEEcCCCcCC-CCCccccCCCCCcEE
Q 004895          527 KGPIAISLPYRDIQELP-ERLECPQLKLFLLFAKYDSTL-QISDHFFEGTEELKVLDFTGIRFS-PLPSSLGRLINLQTL  603 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~-~~~~~~~Lr~L~l~~~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~-~lp~~i~~l~~L~~L  603 (724)
                      .+++.+.+.+|.+...+ ....+++|+.|.+..+  ... ......+.++++|+.|++++|.+. ..|..++.+++|++|
T Consensus        70 ~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~--~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L  147 (336)
T 2ast_B           70 QGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNS--VIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRL  147 (336)
T ss_dssp             TTCSEEECTTCEECSCCCSCCCCBCCCEEECTTC--EECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEE
T ss_pred             ccceEEEcCCccccccchhhccCCCCCEEEccCC--CcCHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEE
Confidence            67889999988876553 4457899999999332  222 213456889999999999999988 678889999999999


Q ss_pred             EcCCc-ccCC---cccccCCCCCcEEEccCC-cCcc--cchhhhcCC-CCCeEccCCCC-CCc-ccChHHhhCCCCCcEE
Q 004895          604 CLDGW-RLED---IAIVGQLKKLEILSLRGA-EIKQ--LPLQIGQLT-RLQLLDLSNCS-SLV-VIAPNVISKLSRLEEL  673 (724)
Q Consensus       604 ~L~~~-~l~~---~~~~~~l~~L~~L~l~~~-~i~~--lp~~i~~l~-~L~~L~l~~~~-~l~-~~~~~~i~~l~~L~~L  673 (724)
                      ++++| .++.   +..+..+++|++|++++| .++.  +|..+..++ +|++|++++|. .+. ...+..++.+++|++|
T Consensus       148 ~L~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L  227 (336)
T 2ast_B          148 NLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHL  227 (336)
T ss_dssp             ECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEE
T ss_pred             ECCCCCCCCHHHHHHHHhcCCCCCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEE
Confidence            99999 6775   355889999999999999 9984  788899999 99999999974 343 2234457899999999


Q ss_pred             EccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          674 YMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       674 ~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                      ++++|..    ++   ...+..+.++++|+.|++++|.
T Consensus       228 ~l~~~~~----l~---~~~~~~l~~l~~L~~L~l~~~~  258 (336)
T 2ast_B          228 DLSDSVM----LK---NDCFQEFFQLNYLQHLSLSRCY  258 (336)
T ss_dssp             ECTTCTT----CC---GGGGGGGGGCTTCCEEECTTCT
T ss_pred             eCCCCCc----CC---HHHHHHHhCCCCCCEeeCCCCC
Confidence            9999742    11   1234466778999999999985

>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=99.37  E-value=1.5e-12  Score=146.76  Aligned_cols=145  Identities=21%  Similarity=0.260  Sum_probs=120.8

Q ss_pred             CceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcC
Q 004895          528 GPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLD  606 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~  606 (724)
                      ..+++++++++++.+|.... ++|+.|.+  +.+....+++..|.++++|++|++++|.+..+ |..++.+.+|++|+|+
T Consensus        32 ~~~~l~ls~~~L~~ip~~~~-~~L~~L~L--s~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls  108 (562)
T 3a79_B           32 LESMVDYSNRNLTHVPKDLP-PRTKALSL--SQNSISELRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVS  108 (562)
T ss_dssp             -CCEEECTTSCCCSCCTTSC-TTCCEEEC--CSSCCCCCCGGGTTTCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECT
T ss_pred             CCcEEEcCCCCCccCCCCCC-CCcCEEEC--CCCCccccChhhhccCCCccEEECCCCCCCcCCHHHhCCCCCCCEEECC
Confidence            44889999999999987553 89999999  45556677777899999999999999999966 6789999999999999


Q ss_pred             CcccCCcccccCCCCCcEEEccCCcCcccc--hhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC--cEEEccCCCC
Q 004895          607 GWRLEDIAIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL--EELYMGDSFS  680 (724)
Q Consensus       607 ~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L--~~L~l~~~~~  680 (724)
                      +|.++.++.. .+++|++|++++|.++.+|  ..++++++|++|++++| .+....   ++.+++|  ++|++++|..
T Consensus       109 ~N~l~~lp~~-~l~~L~~L~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n-~l~~~~---~~~l~~L~L~~L~L~~n~l  181 (562)
T 3a79_B          109 HNRLQNISCC-PMASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGLSAA-KFRQLD---LLPVAHLHLSCILLDLVSY  181 (562)
T ss_dssp             TSCCCEECSC-CCTTCSEEECCSSCCSBCCCCGGGGGCTTCCEEEEECS-BCCTTT---TGGGTTSCEEEEEEEESSC
T ss_pred             CCcCCccCcc-ccccCCEEECCCCCccccCchHhhcccCcccEEecCCC-ccccCc---hhhhhhceeeEEEeecccc
Confidence            9999985444 8999999999999999764  78999999999999994 455432   4555666  9999998753

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.37  E-value=3.1e-12  Score=142.34  Aligned_cols=166  Identities=19%  Similarity=0.240  Sum_probs=89.7

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .+++.|++++|.+..+|... +++|+.|.+  +.+....+|    ..+++|+.|++++|.++.+|. ++.  +|++|+|+
T Consensus        59 ~~L~~L~Ls~n~L~~lp~~l-~~~L~~L~L--s~N~l~~ip----~~l~~L~~L~Ls~N~l~~ip~-l~~--~L~~L~Ls  128 (571)
T 3cvr_A           59 NQFSELQLNRLNLSSLPDNL-PPQITVLEI--TQNALISLP----ELPASLEYLDACDNRLSTLPE-LPA--SLKHLDVD  128 (571)
T ss_dssp             TTCSEEECCSSCCSCCCSCC-CTTCSEEEC--CSSCCSCCC----CCCTTCCEEECCSSCCSCCCC-CCT--TCCEEECC
T ss_pred             CCccEEEeCCCCCCccCHhH-cCCCCEEEC--cCCCCcccc----cccCCCCEEEccCCCCCCcch-hhc--CCCEEECC
Confidence            35666666666666665433 356666666  222333444    234666666666666666665 444  66666666


Q ss_pred             CcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcccccc
Q 004895          607 GWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVE  686 (724)
Q Consensus       607 ~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~  686 (724)
                      +|.++.++.  .+++|++|++++|.++.+|.   .+++|++|++++| .+..+|.  ++  ++|+.|++++|.+..    
T Consensus       129 ~N~l~~lp~--~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~Ls~N-~L~~lp~--l~--~~L~~L~Ls~N~L~~----  194 (571)
T 3cvr_A          129 NNQLTMLPE--LPALLEYINADNNQLTMLPE---LPTSLEVLSVRNN-QLTFLPE--LP--ESLEALDVSTNLLES----  194 (571)
T ss_dssp             SSCCSCCCC--CCTTCCEEECCSSCCSCCCC---CCTTCCEEECCSS-CCSCCCC--CC--TTCCEEECCSSCCSS----
T ss_pred             CCcCCCCCC--cCccccEEeCCCCccCcCCC---cCCCcCEEECCCC-CCCCcch--hh--CCCCEEECcCCCCCc----
Confidence            666666333  55666666666666666665   4566666666663 4555544  33  666666666653221    


Q ss_pred             CCccchHH-hh-cCCCCCcEEEeeccccccccccc
Q 004895          687 GGSNASLA-EL-KGLSKLTTLEIDVRDAEMLRRIW  719 (724)
Q Consensus       687 ~~~~~~l~-~L-~~L~~L~~L~l~~n~~~~lp~~~  719 (724)
                        .+. +. .| ...+.|+.|++++|.++.+|..+
T Consensus       195 --lp~-~~~~L~~~~~~L~~L~Ls~N~l~~lp~~l  226 (571)
T 3cvr_A          195 --LPA-VPVRNHHSEETEIFFRCRENRITHIPENI  226 (571)
T ss_dssp             --CCC-CC--------CCEEEECCSSCCCCCCGGG
T ss_pred             --hhh-HHHhhhcccccceEEecCCCcceecCHHH
Confidence              111 11 11 11122366666666666666543

>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=99.36  E-value=5.1e-12  Score=142.44  Aligned_cols=99  Identities=18%  Similarity=0.226  Sum_probs=68.1

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      +.+++.|.+++|.+..+|.  .+++|++|++.  .+....+|.    .+++|+.|++++|.++.+|.   .+.+|++|++
T Consensus        60 ~~~L~~L~L~~N~l~~lp~--~l~~L~~L~Ls--~N~l~~lp~----~l~~L~~L~Ls~N~l~~l~~---~l~~L~~L~L  128 (622)
T 3g06_A           60 PAHITTLVIPDNNLTSLPA--LPPELRTLEVS--GNQLTSLPV----LPPGLLELSIFSNPLTHLPA---LPSGLCKLWI  128 (622)
T ss_dssp             CTTCSEEEECSCCCSCCCC--CCTTCCEEEEC--SCCCSCCCC----CCTTCCEEEECSCCCCCCCC---CCTTCCEEEC
T ss_pred             CCCCcEEEecCCCCCCCCC--cCCCCCEEEcC--CCcCCcCCC----CCCCCCEEECcCCcCCCCCC---CCCCcCEEEC
Confidence            4577778888777777766  56778888773  333444554    56778888888887777776   4667777777


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccch
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPL  637 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~  637 (724)
                      ++|.++.++.  .+++|++|++++|.++.+|.
T Consensus       129 ~~N~l~~lp~--~l~~L~~L~Ls~N~l~~l~~  158 (622)
T 3g06_A          129 FGNQLTSLPV--LPPGLQELSVSDNQLASLPA  158 (622)
T ss_dssp             CSSCCSCCCC--CCTTCCEEECCSSCCSCCCC
T ss_pred             CCCCCCcCCC--CCCCCCEEECcCCcCCCcCC
Confidence            7777766432  24677777887777776654

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.34  E-value=2.2e-12  Score=117.83  Aligned_cols=104  Identities=28%  Similarity=0.391  Sum_probs=79.5

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-c-ccccCCCCCcEEEccCCcCcccc--hhhhcCCCCC
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-I-AIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQ  646 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~  646 (724)
                      +..+++|+.|++++|.+..+ ..++.+++|++|++++|.++. + ..++.+++|++|++++|.++.+|  ..+..+++|+
T Consensus        38 ~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~ls~N~i~~~~~~~~~~~l~~L~  116 (149)
T 2je0_A           38 TDEFEELEFLSTINVGLTSI-ANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLK  116 (149)
T ss_dssp             CTTCTTCCEEECTTSCCCCC-TTCCCCTTCCEEECCSSCCCSCTHHHHHHCTTCCEEECTTSCCCSHHHHGGGGGCTTCC
T ss_pred             HhhcCCCcEEECcCCCCCCc-hhhhcCCCCCEEECCCCcccchHHHHhhhCCCCCEEECCCCcCCChHHHHHHhhCCCCC
Confidence            56677888888888888776 667788888888888888776 4 44556888888888888888765  6788888888


Q ss_pred             eEccCCCCCCcccCh---HHhhCCCCCcEEEcc
Q 004895          647 LLDLSNCSSLVVIAP---NVISKLSRLEELYMG  676 (724)
Q Consensus       647 ~L~l~~~~~l~~~~~---~~i~~l~~L~~L~l~  676 (724)
                      +|++++| .+...++   ..++.+++|+.|+++
T Consensus       117 ~L~l~~N-~l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A          117 SLDLFNC-EVTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             EEECTTC-GGGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             EEeCcCC-cccchHHHHHHHHHHCCCcccccCC
Confidence            8888884 5666665   567888888888764

>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=99.34  E-value=3.5e-12  Score=145.86  Aligned_cols=151  Identities=23%  Similarity=0.290  Sum_probs=127.3

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQT  602 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~  602 (724)
                      |..+++|++++|.++.++..  ..+++|+.|++  +.+....+++..|.++++|++|+|++|++..+|. .+.++.+|++
T Consensus        51 p~~~~~LdLs~N~i~~l~~~~f~~l~~L~~L~L--s~N~i~~i~~~~f~~L~~L~~L~Ls~N~l~~l~~~~f~~L~~L~~  128 (635)
T 4g8a_A           51 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDL--SRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK  128 (635)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEEC--TTCCCCEECTTTTTTCTTCCEEECTTCCCCEECGGGGTTCTTCCE
T ss_pred             CcCCCEEEeeCCCCCCCCHHHHhCCCCCCEEEC--CCCcCCCcChhHhcCCCCCCEEEccCCcCCCCCHHHhcCCCCCCE
Confidence            67899999999999988743  47999999999  4556777888889999999999999999998875 5899999999


Q ss_pred             EEcCCcccCCc--ccccCCCCCcEEEccCCcCcc--cchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCc----EEE
Q 004895          603 LCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQ--LPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE----ELY  674 (724)
Q Consensus       603 L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~--lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~----~L~  674 (724)
                      |+|++|.++.+  ..++++++|++|++++|.++.  +|..+..+++|++|++++ +.+..+++..+..+.+++    .++
T Consensus       129 L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~l~~L~~l~~~~~~~~  207 (635)
T 4g8a_A          129 LVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSS-NKIQSIYCTDLRVLHQMPLLNLSLD  207 (635)
T ss_dssp             EECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCS-SCCCEECGGGGHHHHTCTTCCCEEE
T ss_pred             EECCCCcCCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhcccC-ccccccccccccchhhhhhhhhhhh
Confidence            99999999884  458999999999999999874  578899999999999999 567777776666655543    566


Q ss_pred             ccCCC
Q 004895          675 MGDSF  679 (724)
Q Consensus       675 l~~~~  679 (724)
                      ++.|.
T Consensus       208 ls~n~  212 (635)
T 4g8a_A          208 LSLNP  212 (635)
T ss_dssp             CTTCC
T ss_pred             cccCc
Confidence            66553

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.34  E-value=3.1e-12  Score=141.04  Aligned_cols=168  Identities=16%  Similarity=0.122  Sum_probs=114.6

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLC  604 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~  604 (724)
                      ..++++|++++|.+..++.   .++|+.|.+.  .+....++.   ..+++|+.|++++|.+..+ |..++.+++|++|+
T Consensus        79 l~~L~~L~Ls~N~l~~l~~---~~~L~~L~L~--~N~l~~~~~---~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~  150 (487)
T 3oja_A           79 LSTLRTLDLNNNYVQELLV---GPSIETLHAA--NNNISRVSC---SRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLD  150 (487)
T ss_dssp             CTTCCEEECCSSEEEEEEE---CTTCCEEECC--SSCCCCEEE---CCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEEE
T ss_pred             CCCCCEEEecCCcCCCCCC---CCCcCEEECc--CCcCCCCCc---cccCCCCEEECCCCCCCCCCchhhcCCCCCCEEE
Confidence            4577888888887766653   3778888772  333333333   2456788888888887755 55677788888888


Q ss_pred             cCCcccCC--ccccc-CCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCc
Q 004895          605 LDGWRLED--IAIVG-QLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQ  681 (724)
Q Consensus       605 L~~~~l~~--~~~~~-~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~  681 (724)
                      |++|.++.  |..+. .+++|++|++++|.++.+|. ...+++|++|++++ +.+..+|+. ++.+++|+.|++++|.+.
T Consensus       151 Ls~N~l~~~~~~~l~~~l~~L~~L~Ls~N~l~~~~~-~~~l~~L~~L~Ls~-N~l~~~~~~-~~~l~~L~~L~Ls~N~l~  227 (487)
T 3oja_A          151 LKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKG-QVVFAKLKTLDLSS-NKLAFMGPE-FQSAAGVTWISLRNNKLV  227 (487)
T ss_dssp             CTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCEEEC-CCCCTTCCEEECCS-SCCCEECGG-GGGGTTCSEEECTTSCCC
T ss_pred             CCCCCCCCcChHHHhhhCCcccEEecCCCccccccc-cccCCCCCEEECCC-CCCCCCCHh-HcCCCCccEEEecCCcCc
Confidence            88887776  34554 67788888888888777654 34577888888887 456677665 677888888888776422


Q ss_pred             cccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          682 WDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       682 ~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                           + .+   ..+..+++|+.|++++|.+.
T Consensus       228 -----~-lp---~~l~~l~~L~~L~l~~N~l~  250 (487)
T 3oja_A          228 -----L-IE---KALRFSQNLEHFDLRGNGFH  250 (487)
T ss_dssp             -----E-EC---TTCCCCTTCCEEECTTCCBC
T ss_pred             -----c-cc---hhhccCCCCCEEEcCCCCCc
Confidence                 1 11   23556677888888887765

>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=99.34  E-value=7.2e-12  Score=139.77  Aligned_cols=174  Identities=12%  Similarity=0.063  Sum_probs=118.1

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC---CCccccCCCCCcEE
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP---LPSSLGRLINLQTL  603 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~---lp~~i~~l~~L~~L  603 (724)
                      .+++.+.+++|.+...+....+++|+.|.+.  .+.........+.++++|+.|++++|.+..   +|..++.+++|++|
T Consensus       302 ~~L~~L~l~~n~l~~~~~~~~l~~L~~L~Ls--~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~l~~L~~L  379 (520)
T 2z7x_B          302 MNIKNFTVSGTRMVHMLCPSKISPFLHLDFS--NNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQL  379 (520)
T ss_dssp             CCCSEEEEESSCCCCCCCCSSCCCCCEEECC--SSCCCTTTTTTCCCCSSCCEEECCSSCCCBHHHHHHHHTTCTTCCEE
T ss_pred             CceeEEEcCCCccccccchhhCCcccEEEeE--CCccChhhhhhhccCCCCCEEEccCCccCccccchHHHhhCCCCCEE
Confidence            3577777777776555432467778888882  233333333446778888888888888874   45667788888888


Q ss_pred             EcCCcccCC-cc--cccCCCCCcEEEccCCcCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          604 CLDGWRLED-IA--IVGQLKKLEILSLRGAEIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       604 ~L~~~~l~~-~~--~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++++|.++. ++  .+..+++|++|++++|.++ .+|..+.  ++|++|++++| .+..+|.. +..+++|++|++++|.
T Consensus       380 ~Ls~N~l~~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~l~--~~L~~L~Ls~N-~l~~ip~~-~~~l~~L~~L~L~~N~  455 (520)
T 2z7x_B          380 DISQNSVSYDEKKGDCSWTKSLLSLNMSSNILTDTIFRCLP--PRIKVLDLHSN-KIKSIPKQ-VVKLEALQELNVASNQ  455 (520)
T ss_dssp             ECCSSCCBCCGGGCSCCCCTTCCEEECCSSCCCGGGGGSCC--TTCCEEECCSS-CCCCCCGG-GGGCTTCCEEECCSSC
T ss_pred             ECCCCcCCcccccchhccCccCCEEECcCCCCCcchhhhhc--ccCCEEECCCC-cccccchh-hhcCCCCCEEECCCCc
Confidence            888888776 32  3677788888888888775 4455443  67888888884 56677665 5688888888888864


Q ss_pred             CccccccCCccchHHhhcCCCCCcEEEeecccccc
Q 004895          680 SQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       680 ~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      ...      .+..  .+..+++|+.|++++|.+..
T Consensus       456 l~~------l~~~--~~~~l~~L~~L~l~~N~~~c  482 (520)
T 2z7x_B          456 LKS------VPDG--IFDRLTSLQKIWLHTNPWDC  482 (520)
T ss_dssp             CCC------CCTT--TTTTCTTCCEEECCSSCBCC
T ss_pred             CCc------cCHH--HhccCCcccEEECcCCCCcc
Confidence            321      1111  35667788888888887654

>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=99.33  E-value=1.5e-10  Score=123.97  Aligned_cols=319  Identities=12%  Similarity=0.110  Sum_probs=188.6

Q ss_pred             ccccchHHHHHHHHHHhcC----CCcc--EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALKD----DKLN--IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~----~~~~--vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ..++||+++++.+..++..    ....  .+.|+|++|+||||||+.+++....... ..++|++++...+...+...++
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT-ARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCC-CEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcC-eeEEEEeCccCCCHHHHHHHHH
Confidence            5688999999999988863    3334  8999999999999999999988754211 2467788777778889999999


Q ss_pred             HhhCCCCCCCc-hhHHHHHHHHHHHh-cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          234 SDLGMNFDSND-LIYHRAKQLCQRLK-KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       234 ~~l~~~~~~~~-~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      ..++...+... ........+...+. .+++.+|||||++...  .+..+...+....    .....+..||++|+....
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~----~~~~~~~~iI~~~~~~~~  171 (389)
T 1fnn_A           96 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEAD----KLGAFRIALVIVGHNDAV  171 (389)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHH----HHSSCCEEEEEEESSTHH
T ss_pred             HHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCC----CCCcCCEEEEEEECCchH
Confidence            98876543221 12334444544443 2568999999997652  2222211111100    000136678888876633


Q ss_pred             hhh------hcCCCceEecCCCCHHHHHHHHHHHhCCCC-CCCCchhHHHHHHHHh---------CCchhHHHHHHHHhc
Q 004895          310 LCI------DMNSQKMFWIDALSEEEALQLFEKIVGEST-KASDFRPLAEEIVGKC---------GGLPVALSTVANALK  373 (724)
Q Consensus       310 ~~~------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~-~~~~l~~~~~~I~~~c---------~GlPLai~~~~~~l~  373 (724)
                      ...      ..-....+.+++++.++..+++...+.... ...--++..+.|++.+         +|.|..+..+.....
T Consensus       172 ~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~  251 (389)
T 1fnn_A          172 LNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSA  251 (389)
T ss_dssp             HHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHH
T ss_pred             HHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHH
Confidence            110      001123699999999999999998864211 1122256788999999         788755443333221


Q ss_pred             ------CC---CHHHHHHHHHHHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhhccCC---CCCcccHHHHHHH
Q 004895          374 ------NK---SPAIWKDALNKLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLCGLHR---EGRPIHVHYLLRY  441 (724)
Q Consensus       374 ------~~---~~~~w~~~~~~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~s~fp---~~~~i~~~~Li~~  441 (724)
                            +.   +.+....+.....              ...+...+..||++.+.++..++.+.   .+..+....+...
T Consensus       252 ~~a~~~~~~~i~~~~v~~~~~~~~--------------~~~~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~  317 (389)
T 1fnn_A          252 YAAQQNGRKHIAPEDVRKSSKEVL--------------FGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEES  317 (389)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHS--------------CCCCHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHH
T ss_pred             HHHHHhCCCCcCHHHHHHHHHHHh--------------hhhHHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHH
Confidence                  11   3333433333321              22345567889988888888777654   2214666666655


Q ss_pred             HhhcccccccccccccccHHHHHHHHHHHHHHHHhhcccccCC------CCCc-------chhhHHHHHHHHHHhhh
Q 004895          442 VMGLRYDKGLGLFRNVYTLEAARNRVDALIDNLKASCLLLDGD------AEDE-------AKLHDVIHVVAASIAEE  505 (724)
Q Consensus       442 W~~~~~~~~~g~i~~~~~~~~~~~~~~~~~~~L~~~~ll~~~~------~~~~-------~~mHdlv~d~a~~~~~~  505 (724)
                      +...  .+..|. .. .    ....+..+++.|...+++....      ..+.       +..|+++..+...+..+
T Consensus       318 ~~~~--~~~~~~-~~-~----~~~~~~~~l~~L~~~gli~~~~~~~~~g~~g~~~~~~l~~~~~~v~~~~~~~~~~~  386 (389)
T 1fnn_A          318 YKIV--CEEYGE-RP-R----VHSQLWSYLNDLREKGIVETRQNKRGEGVRGRTTLISIGTEPLDTLEAVITKLIKE  386 (389)
T ss_dssp             HHHH--HHHTTC-CC-C----CHHHHHHHHHHHHHTTSSEEEEC---------CEEEECCSSCHHHHHHHHHHHHHH
T ss_pred             HHHH--HHHcCC-CC-C----CHHHHHHHHHHHHhCCCeEEeeeccCCCCCCceeEEEeCCCHHHHHHHHHHHHHHH
Confidence            5400  001121 00 0    1234567888899999986421      1111       23567777666554433

>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=99.33  E-value=5e-12  Score=120.89  Aligned_cols=122  Identities=18%  Similarity=0.199  Sum_probs=92.8

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc--ccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEc
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS--LGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSL  627 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~--i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l  627 (724)
                      +++.+  +.+....+|...+   ..|+.|++++|.+..+|..  ++.+.+|++|+|++|.++.  +..+..+++|++|++
T Consensus        11 ~~l~~--s~~~l~~ip~~~~---~~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L   85 (192)
T 1w8a_A           11 TTVDC--TGRGLKEIPRDIP---LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQL   85 (192)
T ss_dssp             TEEEC--TTSCCSSCCSCCC---TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEEC
T ss_pred             CEEEc--CCCCcCcCccCCC---CCCCEEECCCCcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEEC
Confidence            45555  3344455665432   3788888888888877653  7888888888888888877  357888888888888


Q ss_pred             cCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          628 RGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       628 ~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++|.++.+|.. +..+++|++|++++ +.+..+++..++.+++|++|++++|.
T Consensus        86 s~N~l~~~~~~~~~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (192)
T 1w8a_A           86 GENKIKEISNKMFLGLHQLKTLNLYD-NQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CSCCCCEECSSSSTTCTTCCEEECCS-SCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             CCCcCCccCHHHhcCCCCCCEEECCC-CcCCeeCHHHhhcCCCCCEEEeCCCC
Confidence            88888877654 77888888888888 46677767778888888888888864

>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=99.32  E-value=1.6e-12  Score=122.54  Aligned_cols=127  Identities=17%  Similarity=0.122  Sum_probs=87.5

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-ccc-ccCCCCCcE
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAI-VGQLKKLEI  624 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~-~~~l~~L~~  624 (724)
                      .+++|+.|.+.  .+....++ .+....++|++|++++|.+..+ ..++.+++|++|++++|.++. ++. ++.+++|++
T Consensus        17 ~~~~L~~L~l~--~n~l~~i~-~~~~~~~~L~~L~Ls~N~l~~~-~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~   92 (176)
T 1a9n_A           17 NAVRDRELDLR--GYKIPVIE-NLGATLDQFDAIDFSDNEIRKL-DGFPLLRRLKTLLVNNNRICRIGEGLDQALPDLTE   92 (176)
T ss_dssp             CTTSCEEEECT--TSCCCSCC-CGGGGTTCCSEEECCSSCCCEE-CCCCCCSSCCEEECCSSCCCEECSCHHHHCTTCCE
T ss_pred             CcCCceEEEee--CCCCchhH-HhhhcCCCCCEEECCCCCCCcc-cccccCCCCCEEECCCCcccccCcchhhcCCCCCE
Confidence            45555555552  22222332 2223334788888888888766 567788888888888888777 333 478888888


Q ss_pred             EEccCCcCcccch--hhhcCCCCCeEccCCCCCCcccChH---HhhCCCCCcEEEccCC
Q 004895          625 LSLRGAEIKQLPL--QIGQLTRLQLLDLSNCSSLVVIAPN---VISKLSRLEELYMGDS  678 (724)
Q Consensus       625 L~l~~~~i~~lp~--~i~~l~~L~~L~l~~~~~l~~~~~~---~i~~l~~L~~L~l~~~  678 (724)
                      |++++|.++.+|.  .+..+++|++|++++| .+...|..   .++.+++|+.|+++.|
T Consensus        93 L~L~~N~i~~~~~~~~l~~l~~L~~L~l~~N-~i~~~~~~~~~~~~~l~~L~~Ld~~~n  150 (176)
T 1a9n_A           93 LILTNNSLVELGDLDPLASLKSLTYLCILRN-PVTNKKHYRLYVIYKVPQVRVLDFQKV  150 (176)
T ss_dssp             EECCSCCCCCGGGGGGGGGCTTCCEEECCSS-GGGGSTTHHHHHHHHCTTCSEETTEEC
T ss_pred             EECCCCcCCcchhhHhhhcCCCCCEEEecCC-CCCCcHhHHHHHHHHCCccceeCCCcC
Confidence            8888888887776  6788888888888884 45566543   4778888888887765

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.32  E-value=9.5e-12  Score=118.94  Aligned_cols=122  Identities=19%  Similarity=0.307  Sum_probs=101.2

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccC
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRG  629 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~  629 (724)
                      +++.+  +.+....+|...   .+.|+.|++++|.+..+|..+..+.+|++|+|++|.++.+  ..+..+++|++|++++
T Consensus        13 ~~l~~--~~~~l~~ip~~~---~~~l~~L~L~~n~i~~ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~   87 (193)
T 2wfh_A           13 TVVRC--SNKGLKVLPKGI---PRDVTELYLDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSY   87 (193)
T ss_dssp             TEEEC--TTSCCSSCCSCC---CTTCCEEECCSSCCCSCCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS
T ss_pred             CEEEc--CCCCCCcCCCCC---CCCCCEEECCCCcCchhHHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCC
Confidence            34444  344455666543   3579999999999999999999999999999999999883  5689999999999999


Q ss_pred             CcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          630 AEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       630 ~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      |.++.+|+ .+..+++|++|++++ +.+..+++..+..+++|+.|++++|.
T Consensus        88 N~l~~i~~~~f~~l~~L~~L~L~~-N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (193)
T 2wfh_A           88 NRLRCIPPRTFDGLKSLRLLSLHG-NDISVVPEGAFNDLSALSHLAIGANP  137 (193)
T ss_dssp             SCCCBCCTTTTTTCTTCCEEECCS-SCCCBCCTTTTTTCTTCCEEECCSSC
T ss_pred             CccCEeCHHHhCCCCCCCEEECCC-CCCCeeChhhhhcCccccEEEeCCCC
Confidence            99998865 588999999999999 56788888778899999999999874

>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=99.32  E-value=6e-12  Score=117.56  Aligned_cols=106  Identities=25%  Similarity=0.345  Sum_probs=64.4

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-c-ccccCCCCCcEEEccCCcCcccc--hhhhcCCCCC
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-I-AIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQ  646 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~  646 (724)
                      +..+++|++|++++|.+..+ ..++.+++|++|++++|.++. + ..+..+++|++|++++|.++.+|  ..+..+++|+
T Consensus        45 ~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~l~~l~~L~  123 (168)
T 2ell_A           45 TAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSENRIFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLK  123 (168)
T ss_dssp             CGGGGGCCEEEEESSCCCCC-SSCCCCSSCCEEEEESCCCCSCCCHHHHHCTTCCEEECBSSSCCSSGGGGGGSSCSCCC
T ss_pred             HHhCCCCCEEeCcCCCCCCh-hhhccCCCCCEEECcCCcCchHHHHHHhhCCCCCEEeccCCccCcchhHHHHhcCCCCC
Confidence            34555666666666666655 556666666666666666655 3 33444666666666666666654  4566666666


Q ss_pred             eEccCCCCCCcccCh---HHhhCCCCCcEEEccCC
Q 004895          647 LLDLSNCSSLVVIAP---NVISKLSRLEELYMGDS  678 (724)
Q Consensus       647 ~L~l~~~~~l~~~~~---~~i~~l~~L~~L~l~~~  678 (724)
                      +|++++| .+...++   ..+..+++|++|++.+|
T Consensus       124 ~L~l~~N-~l~~~~~~~~~~~~~l~~L~~L~l~~n  157 (168)
T 2ell_A          124 SLDLFNC-EVTNLNDYRESVFKLLPQLTYLDGYDR  157 (168)
T ss_dssp             EEECCSS-GGGTSTTHHHHHHTTCSSCCEETTEET
T ss_pred             EEEeeCC-cCcchHHHHHHHHHhCccCcEecCCCC
Confidence            6666663 4455554   34666666666666665

>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=99.31  E-value=2.5e-11  Score=136.78  Aligned_cols=29  Identities=14%  Similarity=0.139  Sum_probs=19.8

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEE
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLL  556 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l  556 (724)
                      +.+++.|++++|.+..+|.  .+++|+.|.+
T Consensus        80 l~~L~~L~Ls~N~l~~lp~--~l~~L~~L~L  108 (622)
T 3g06_A           80 PPELRTLEVSGNQLTSLPV--LPPGLLELSI  108 (622)
T ss_dssp             CTTCCEEEECSCCCSCCCC--CCTTCCEEEE
T ss_pred             CCCCCEEEcCCCcCCcCCC--CCCCCCEEEC
Confidence            4567777777777766665  5567777776

>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=99.30  E-value=5.4e-11  Score=116.48  Aligned_cols=189  Identities=11%  Similarity=0.094  Sum_probs=118.4

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .....++||++.++.+.+++.....+.+.|+|++|+|||++|+.+++.......-...+.++.+...+...+...+....
T Consensus        14 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (226)
T 2chg_A           14 RTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVRHKIKEFA   93 (226)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTCHHHHHHHHHHHH
T ss_pred             CCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccChHHHHHHHHHHh
Confidence            34567889999999999998866655699999999999999999998864321112234444443333332222211111


Q ss_pred             CCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccchh-hhh
Q 004895          237 GMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-CID  313 (724)
Q Consensus       237 ~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-~~~  313 (724)
                      ....                ...+++.+||+||++...  ..+.+...+..        ...++.+|+||+..... ...
T Consensus        94 ~~~~----------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~--------~~~~~~~i~~~~~~~~~~~~l  149 (226)
T 2chg_A           94 RTAP----------------IGGAPFKIIFLDEADALTADAQAALRRTMEM--------YSKSCRFILSCNYVSRIIEPI  149 (226)
T ss_dssp             TSCC----------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSCHHH
T ss_pred             cccC----------------CCccCceEEEEeChhhcCHHHHHHHHHHHHh--------cCCCCeEEEEeCChhhcCHHH
Confidence            1000                012467999999997653  22333222222        34567888888765421 111


Q ss_pred             cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHH
Q 004895          314 MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVAN  370 (724)
Q Consensus       314 ~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~  370 (724)
                      ......+.+.+++.++..+++.+.+...... --++..+.|++.++|.|..+..+..
T Consensus       150 ~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~l~~~l~  205 (226)
T 2chg_A          150 QSRCAVFRFKPVPKEAMKKRLLEICEKEGVK-ITEDGLEALIYISGGDFRKAINALQ  205 (226)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHhCceeecCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            2234489999999999999999887422211 1146778899999999986554433

>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=99.30  E-value=5.5e-11  Score=118.17  Aligned_cols=200  Identities=13%  Similarity=0.165  Sum_probs=118.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      +.....++||+.+++.+..++..+. .+.+.|+|++|+||||+|+.+++.......+...      ....... ...+..
T Consensus        19 p~~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~------~~~~~~~-~~~~~~   91 (250)
T 1njg_A           19 PQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITAT------PCGVCDN-CREIEQ   91 (250)
T ss_dssp             CCSGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSS------CCSCSHH-HHHHHT
T ss_pred             CccHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC------CCcccHH-HHHHhc
Confidence            3345678999999999999887543 4588999999999999999999887542211000      0000000 011110


Q ss_pred             hhCCC-----CCCCchhHHHHHHHHHHHh----cCCcEEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          235 DLGMN-----FDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       235 ~l~~~-----~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      .....     ..... .......+.+.+.    .+++.+||+||++..  ..++.+...+..        ...+..+|+|
T Consensus        92 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~--------~~~~~~~i~~  162 (250)
T 1njg_A           92 GRFVDLIEIDAASRT-KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE--------PPEHVKFLLA  162 (250)
T ss_dssp             TCCSSEEEEETTCGG-GHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHS--------CCTTEEEEEE
T ss_pred             cCCcceEEecCcccc-cHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhc--------CCCceEEEEE
Confidence            00000     00000 1111222222221    246799999999764  234444333322        3456788888


Q ss_pred             ecccchh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          304 SRSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       304 tR~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      |+..... .........+++++++.++..+++.+.+...... --++..+.|++.|+|.|..+..+...+
T Consensus       163 t~~~~~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~~~~~~~~~~~  231 (250)
T 1njg_A          163 TTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLTDQA  231 (250)
T ss_dssp             ESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             eCChHhCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            8765422 1112334689999999999999999887532211 124678899999999999987766544

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.30  E-value=1e-11  Score=118.75  Aligned_cols=121  Identities=23%  Similarity=0.339  Sum_probs=100.4

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~  608 (724)
                      +.+.++++.+..+|... .++|+.|.+  +.+....++ ..|.++++|+.|++++|.+..+| ..+..+.+|++|+|++|
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   88 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGI-PRDVTELYL--DGNQFTLVP-KELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYN   88 (193)
T ss_dssp             TEEECTTSCCSSCCSCC-CTTCCEEEC--CSSCCCSCC-GGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CEEEcCCCCCCcCCCCC-CCCCCEEEC--CCCcCchhH-HHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCC
Confidence            46788888888888654 468999998  344455666 46889999999999999999775 46899999999999999


Q ss_pred             ccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCC
Q 004895          609 RLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCS  654 (724)
Q Consensus       609 ~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~  654 (724)
                      .++.+  ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.
T Consensus        89 ~l~~i~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (193)
T 2wfh_A           89 RLRCIPPRTFDGLKSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGANP  137 (193)
T ss_dssp             CCCBCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSC
T ss_pred             ccCEeCHHHhCCCCCCCEEECCCCCCCeeChhhhhcCccccEEEeCCCC
Confidence            98883  4689999999999999999988875 7889999999999853

>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=99.29  E-value=3.2e-11  Score=131.53  Aligned_cols=138  Identities=16%  Similarity=0.233  Sum_probs=79.1

Q ss_pred             cCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          527 KGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      .+++++++++|.+..++..  .++|++|.+.  .+....+|  .|.++++|++|++++|.+..+|..+   .+|++|+++
T Consensus       111 ~~L~~L~l~~n~l~~l~~~--~~~L~~L~L~--~n~l~~lp--~~~~l~~L~~L~l~~N~l~~lp~~~---~~L~~L~L~  181 (454)
T 1jl5_A          111 QSLKSLLVDNNNLKALSDL--PPLLEYLGVS--NNQLEKLP--ELQNSSFLKIIDVDNNSLKKLPDLP---PSLEFIAAG  181 (454)
T ss_dssp             TTCCEEECCSSCCSCCCSC--CTTCCEEECC--SSCCSSCC--CCTTCTTCCEEECCSSCCSCCCCCC---TTCCEEECC
T ss_pred             CCCcEEECCCCccCcccCC--CCCCCEEECc--CCCCCCCc--ccCCCCCCCEEECCCCcCcccCCCc---ccccEEECc
Confidence            4555555555555544432  1456666662  22333344  2566666666666666666665433   366666666


Q ss_pred             CcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          607 GWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       607 ~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      +|.++.++.++.+++|++|++++|.++.+|...   .+|++|++++| .+..+|.  ++.+++|++|++++|.
T Consensus       182 ~n~l~~l~~~~~l~~L~~L~l~~N~l~~l~~~~---~~L~~L~l~~n-~l~~lp~--~~~l~~L~~L~l~~N~  248 (454)
T 1jl5_A          182 NNQLEELPELQNLPFLTAIYADNNSLKKLPDLP---LSLESIVAGNN-ILEELPE--LQNLPFLTTIYADNNL  248 (454)
T ss_dssp             SSCCSSCCCCTTCTTCCEEECCSSCCSSCCCCC---TTCCEEECCSS-CCSSCCC--CTTCTTCCEEECCSSC
T ss_pred             CCcCCcCccccCCCCCCEEECCCCcCCcCCCCc---CcccEEECcCC-cCCcccc--cCCCCCCCEEECCCCc
Confidence            666666545666666666666666666555432   35666666663 3445542  5666666666666653

>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=99.29  E-value=9.4e-12  Score=139.17  Aligned_cols=99  Identities=25%  Similarity=0.295  Sum_probs=65.5

Q ss_pred             ceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCC
Q 004895          577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSS  655 (724)
Q Consensus       577 L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~  655 (724)
                      |++|++++|.++.+|. ++.+.+|++|+|++|.++. |..++.+++|++|+|++|.++.+| .++.+++|++|++++ +.
T Consensus       443 L~~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~  519 (567)
T 1dce_A          443 VRVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCN-NR  519 (567)
T ss_dssp             CSEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCS-SC
T ss_pred             ceEEEecCCCCCCCcC-ccccccCcEeecCcccccccchhhhcCCCCCEEECCCCCCCCCc-ccCCCCCCcEEECCC-CC
Confidence            6666666666666665 6666677777777766666 456666777777777777666666 666677777777766 34


Q ss_pred             CcccC-hHHhhCCCCCcEEEccCC
Q 004895          656 LVVIA-PNVISKLSRLEELYMGDS  678 (724)
Q Consensus       656 l~~~~-~~~i~~l~~L~~L~l~~~  678 (724)
                      +..++ |..++.|++|+.|++++|
T Consensus       520 l~~~~~p~~l~~l~~L~~L~L~~N  543 (567)
T 1dce_A          520 LQQSAAIQPLVSCPRLVLLNLQGN  543 (567)
T ss_dssp             CCSSSTTGGGGGCTTCCEEECTTS
T ss_pred             CCCCCCcHHHhcCCCCCEEEecCC
Confidence            55553 444666777777777665

>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=99.29  E-value=2.7e-11  Score=132.19  Aligned_cols=165  Identities=22%  Similarity=0.242  Sum_probs=125.2

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      +.+++++++++|.+..+|..  .++|+.|.+.  .+....++.    ..++|++|++++|.+..+| .++++.+|++|++
T Consensus        90 ~~~L~~L~l~~n~l~~lp~~--~~~L~~L~l~--~n~l~~l~~----~~~~L~~L~L~~n~l~~lp-~~~~l~~L~~L~l  160 (454)
T 1jl5_A           90 PPHLESLVASCNSLTELPEL--PQSLKSLLVD--NNNLKALSD----LPPLLEYLGVSNNQLEKLP-ELQNSSFLKIIDV  160 (454)
T ss_dssp             CTTCSEEECCSSCCSSCCCC--CTTCCEEECC--SSCCSCCCS----CCTTCCEEECCSSCCSSCC-CCTTCTTCCEEEC
T ss_pred             cCCCCEEEccCCcCCccccc--cCCCcEEECC--CCccCcccC----CCCCCCEEECcCCCCCCCc-ccCCCCCCCEEEC
Confidence            46889999999998888753  4789999983  333333332    1268999999999999998 5999999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.++.++..  +.+|++|++++|.++.+| .++.+++|++|++++| .+..+|.    ..++|++|++++|....   
T Consensus       161 ~~N~l~~lp~~--~~~L~~L~L~~n~l~~l~-~~~~l~~L~~L~l~~N-~l~~l~~----~~~~L~~L~l~~n~l~~---  229 (454)
T 1jl5_A          161 DNNSLKKLPDL--PPSLEFIAAGNNQLEELP-ELQNLPFLTAIYADNN-SLKKLPD----LPLSLESIVAGNNILEE---  229 (454)
T ss_dssp             CSSCCSCCCCC--CTTCCEEECCSSCCSSCC-CCTTCTTCCEEECCSS-CCSSCCC----CCTTCCEEECCSSCCSS---
T ss_pred             CCCcCcccCCC--cccccEEECcCCcCCcCc-cccCCCCCCEEECCCC-cCCcCCC----CcCcccEEECcCCcCCc---
Confidence            99998874322  358999999999999988 6999999999999995 5666653    23689999999874321   


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                         .+    .+.++++|+.|+++.|.++.+|.
T Consensus       230 ---lp----~~~~l~~L~~L~l~~N~l~~l~~  254 (454)
T 1jl5_A          230 ---LP----ELQNLPFLTTIYADNNLLKTLPD  254 (454)
T ss_dssp             ---CC----CCTTCTTCCEEECCSSCCSSCCS
T ss_pred             ---cc----ccCCCCCCCEEECCCCcCCcccc
Confidence               11    25567777777777777766654

>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=99.27  E-value=1.1e-11  Score=118.51  Aligned_cols=122  Identities=20%  Similarity=0.322  Sum_probs=102.9

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccch-hhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCC
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISD-HFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDG  607 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~-~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~  607 (724)
                      +.+.++++.+..+|.... ++++.|.+  +.+....++. ..|..+++|++|++++|.+..+ |..+..+.+|++|+|++
T Consensus        11 ~~l~~s~~~l~~ip~~~~-~~l~~L~l--~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~   87 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIP-LHTTELLL--NDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGE   87 (192)
T ss_dssp             TEEECTTSCCSSCCSCCC-TTCSEEEC--CSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS
T ss_pred             CEEEcCCCCcCcCccCCC-CCCCEEEC--CCCcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCC
Confidence            678899999988887543 48999999  3444555554 3588999999999999999966 77899999999999999


Q ss_pred             cccCCc--ccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCC
Q 004895          608 WRLEDI--AIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCS  654 (724)
Q Consensus       608 ~~l~~~--~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~  654 (724)
                      |.++.+  ..+..+++|++|++++|.++.+ |..+..+++|++|++++|.
T Consensus        88 N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (192)
T 1w8a_A           88 NKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             CcCCccCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCC
Confidence            999883  4589999999999999999966 6679999999999999954

>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=99.26  E-value=5.9e-12  Score=132.74  Aligned_cols=154  Identities=17%  Similarity=0.139  Sum_probs=105.4

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCce-EEEcCCCcCCCC-CccccCCCCCc
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELK-VLDFTGIRFSPL-PSSLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~-~L~l~~~~~~~l-p~~i~~l~~L~  601 (724)
                      +.++++|.+++|.++.+|..  ..+++|+.|.+. .+.....++...|.+++.|. .+.+++|++..+ |..+..+++|+
T Consensus        29 ~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls-~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~L~  107 (350)
T 4ay9_X           29 PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEIS-QNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQ  107 (350)
T ss_dssp             CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEE-CCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCC
T ss_pred             CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECc-CCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhccccc
Confidence            46788888888888888753  368888888883 22222345555666666654 355556666655 44566777777


Q ss_pred             EEEcCCcccCCc---------------------------ccccCC-CCCcEEEccCCcCcccchhhhcCCCCCeEccCCC
Q 004895          602 TLCLDGWRLEDI---------------------------AIVGQL-KKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNC  653 (724)
Q Consensus       602 ~L~L~~~~l~~~---------------------------~~~~~l-~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~  653 (724)
                      +|++++|.++.+                           ..+..+ ..|++|++++|.++.+|..+....+|+.|++.++
T Consensus       108 ~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~i~~i~~~~f~~~~L~~l~l~~~  187 (350)
T 4ay9_X          108 YLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDN  187 (350)
T ss_dssp             EEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEECTTSSTTEEEEEEECTTC
T ss_pred             cccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhccccccccCCChhhccccchhHHhhccC
Confidence            777776665431                           122333 3577788888888888877777778888888777


Q ss_pred             CCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          654 SSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       654 ~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      +.++.+|+..+..+++|++|++++|.+
T Consensus       188 n~l~~i~~~~f~~l~~L~~LdLs~N~l  214 (350)
T 4ay9_X          188 NNLEELPNDVFHGASGPVILDISRTRI  214 (350)
T ss_dssp             TTCCCCCTTTTTTEECCSEEECTTSCC
T ss_pred             CcccCCCHHHhccCcccchhhcCCCCc
Confidence            778888877778888888888887643

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.26  E-value=6.2e-12  Score=145.17  Aligned_cols=114  Identities=24%  Similarity=0.295  Sum_probs=78.1

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEE
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEIL  625 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L  625 (724)
                      .+++|+.|.+  +.+....++...+ ++++|+.|+|++|.+..+|..|++|.+|++|+|++|.++. |..++.|.+|++|
T Consensus       222 ~l~~L~~L~L--s~n~l~~l~~~~~-~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L  298 (727)
T 4b8c_D          222 DDQLWHALDL--SNLQIFNISANIF-KYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYF  298 (727)
T ss_dssp             CCCCCCEEEC--TTSCCSCCCGGGG-GCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCSSCCSSGGGGTTCSEE
T ss_pred             cCCCCcEEEC--CCCCCCCCChhhc-CCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCCccChhhcCCCCCCEE
Confidence            4566777776  3333445555544 6777777777777777777777777777777777777766 5667777777777


Q ss_pred             EccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHh
Q 004895          626 SLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVI  664 (724)
Q Consensus       626 ~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i  664 (724)
                      +|++|.++.+|..|++|++|++|+|++| .+...+|..+
T Consensus       299 ~L~~N~l~~lp~~~~~l~~L~~L~L~~N-~l~~~~p~~~  336 (727)
T 4b8c_D          299 YFFDNMVTTLPWEFGNLCNLQFLGVEGN-PLEKQFLKIL  336 (727)
T ss_dssp             ECCSSCCCCCCSSTTSCTTCCCEECTTS-CCCSHHHHHH
T ss_pred             ECCCCCCCccChhhhcCCCccEEeCCCC-ccCCCChHHH
Confidence            7777777777777777777777777773 4554444444

>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=99.25  E-value=5.2e-12  Score=135.15  Aligned_cols=184  Identities=13%  Similarity=0.112  Sum_probs=120.7

Q ss_pred             ccCceEEeccCCCccc-----CCCc-ccCCCccEEEEecccccccccc----hhhhcCC---------CCceEEEcCCCc
Q 004895          526 QKGPIAISLPYRDIQE-----LPER-LECPQLKLFLLFAKYDSTLQIS----DHFFEGT---------EELKVLDFTGIR  586 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~-----~~~~-~~~~~Lr~L~l~~~~~~~~~~~----~~~~~~l---------~~L~~L~l~~~~  586 (724)
                      ..++++|++++|.+..     ++.. ..+++|+.|.+..+  ......    ...+..+         ++|+.|++++|.
T Consensus        93 ~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n--~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n~  170 (386)
T 2ca6_A           93 CPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNN--GLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNR  170 (386)
T ss_dssp             CTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSS--CCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSC
T ss_pred             CCcccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCC--CCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECCCCC
Confidence            4678888888887754     3322 25788888888322  222111    1123333         788888888888


Q ss_pred             CC--CCC---ccccCCCCCcEEEcCCcccCC------cc-cccCCCCCcEEEccCCcC-----cccchhhhcCCCCCeEc
Q 004895          587 FS--PLP---SSLGRLINLQTLCLDGWRLED------IA-IVGQLKKLEILSLRGAEI-----KQLPLQIGQLTRLQLLD  649 (724)
Q Consensus       587 ~~--~lp---~~i~~l~~L~~L~L~~~~l~~------~~-~~~~l~~L~~L~l~~~~i-----~~lp~~i~~l~~L~~L~  649 (724)
                      +.  .+|   ..+..+++|++|++++|.++.      .+ .+..+++|++|++++|.+     ..+|..+..+++|++|+
T Consensus       171 l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~~l~~~~~L~~L~  250 (386)
T 2ca6_A          171 LENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELG  250 (386)
T ss_dssp             CTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEE
T ss_pred             CCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHHHHccCCCcCEEE
Confidence            86  344   466778888888888888772      23 777888888888888887     46778888888888888


Q ss_pred             cCCCCCCccc----ChHHh--hCCCCCcEEEccCCCCccccccCCccchHHhh-cCCCCCcEEEeecccccccc
Q 004895          650 LSNCSSLVVI----APNVI--SKLSRLEELYMGDSFSQWDKVEGGSNASLAEL-KGLSKLTTLEIDVRDAEMLR  716 (724)
Q Consensus       650 l~~~~~l~~~----~~~~i--~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L-~~L~~L~~L~l~~n~~~~lp  716 (724)
                      +++|. +...    .+..+  +.+++|++|++++|.+...    ........+ .++++|+.|++++|.++...
T Consensus       251 L~~n~-i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~~----g~~~l~~~l~~~l~~L~~L~l~~N~l~~~~  319 (386)
T 2ca6_A          251 LNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNEIELD----AVRTLKTVIDEKMPDLLFLELNGNRFSEED  319 (386)
T ss_dssp             CTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHH----HHHHHHHHHHHHCTTCCEEECTTSBSCTTS
T ss_pred             CCCCC-CchhhHHHHHHHHhhccCCCeEEEECcCCcCCHH----HHHHHHHHHHhcCCCceEEEccCCcCCcch
Confidence            88854 4433    12334  3488888888888643211    000122333 45788888998888876544

>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=99.25  E-value=4e-12  Score=136.04  Aligned_cols=180  Identities=19%  Similarity=0.247  Sum_probs=106.1

Q ss_pred             ccCceEEeccCCCcccC----CCc--------ccCCCccEEEEecccccccc----cchhhhcCCCCceEEEcCCCcCCC
Q 004895          526 QKGPIAISLPYRDIQEL----PER--------LECPQLKLFLLFAKYDSTLQ----ISDHFFEGTEELKVLDFTGIRFSP  589 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~----~~~--------~~~~~Lr~L~l~~~~~~~~~----~~~~~~~~l~~L~~L~l~~~~~~~  589 (724)
                      ..++++|++++|.+..+    |..        ..+++|+.|.+..+  ....    .....+..+++|+.|++++|.+..
T Consensus        59 ~~~L~~L~Ls~~~~~~l~~~~~~~~~~l~~~l~~~~~L~~L~Ls~n--~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~  136 (386)
T 2ca6_A           59 KKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDN--AFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGP  136 (386)
T ss_dssp             CTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSC--CCCTTTHHHHHHHHHHCTTCCEEECCSSCCHH
T ss_pred             CCCccEEeCcccccCccccchhHHHHHHHHHHhhCCcccEEECCCC--cCCHHHHHHHHHHHHhCCCCCEEECcCCCCCH
Confidence            35677777776654433    211        25677777777322  2222    122345667777777777777752


Q ss_pred             -----CCccccCC---------CCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCc------ccchhhhcCC
Q 004895          590 -----LPSSLGRL---------INLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIK------QLPLQIGQLT  643 (724)
Q Consensus       590 -----lp~~i~~l---------~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~------~lp~~i~~l~  643 (724)
                           ++..+..+         ++|++|++++|.++.  .    ..+..+++|++|++++|.++      -+|..+.+++
T Consensus       137 ~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~  216 (386)
T 2ca6_A          137 QAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQ  216 (386)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCT
T ss_pred             HHHHHHHHHHHHHhhhhhcccCCCCcEEECCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCC
Confidence                 23333344         677777777777763  2    35566777777777777776      2233667777


Q ss_pred             CCCeEccCCCCCC-----cccChHHhhCCCCCcEEEccCCCCccccccCCccc-hHHhhc--CCCCCcEEEeecccccc
Q 004895          644 RLQLLDLSNCSSL-----VVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNA-SLAELK--GLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       644 ~L~~L~l~~~~~l-----~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~-~l~~L~--~L~~L~~L~l~~n~~~~  714 (724)
                      +|++|++++|. +     ..+ +..+..+++|++|++++|.+     .+.... ....+.  ++++|+.|++++|.++.
T Consensus       217 ~L~~L~Ls~n~-l~~~g~~~l-~~~l~~~~~L~~L~L~~n~i-----~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~  288 (386)
T 2ca6_A          217 ELKVLDLQDNT-FTHLGSSAL-AIALKSWPNLRELGLNDCLL-----SARGAAAVVDAFSKLENIGLQTLRLQYNEIEL  288 (386)
T ss_dssp             TCCEEECCSSC-CHHHHHHHH-HHHGGGCTTCCEEECTTCCC-----CHHHHHHHHHHHHTCSSCCCCEEECCSSCCBH
T ss_pred             CccEEECcCCC-CCcHHHHHH-HHHHccCCCcCEEECCCCCC-----chhhHHHHHHHHhhccCCCeEEEECcCCcCCH
Confidence            77777777743 4     223 33467777777777777632     111111 122342  36777777777777765

>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=99.23  E-value=2.5e-11  Score=127.89  Aligned_cols=187  Identities=18%  Similarity=0.135  Sum_probs=136.6

Q ss_pred             EEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCC-CCCc-cccCCCCCcE-EEcCC
Q 004895          531 AISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFS-PLPS-SLGRLINLQT-LCLDG  607 (724)
Q Consensus       531 ~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~-~lp~-~i~~l~~L~~-L~L~~  607 (724)
                      .+.-++++++++|..+ .++++.|.+  ..+....++...|.++++|++|+|++|.+. .+|. .+.++.+|.. +.+++
T Consensus        13 ~v~C~~~~Lt~iP~~l-~~~l~~L~L--s~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~   89 (350)
T 4ay9_X           13 VFLCQESKVTEIPSDL-PRNAIELRF--VLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKA   89 (350)
T ss_dssp             EEEEESTTCCSCCTTC-CTTCSEEEE--ESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEE
T ss_pred             EEEecCCCCCccCcCc-CCCCCEEEc--cCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccC
Confidence            4556677888888655 468999999  445677888888999999999999999986 4554 5788888775 56677


Q ss_pred             cccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCC-CCcEEEccCCCCccc
Q 004895          608 WRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLS-RLEELYMGDSFSQWD  683 (724)
Q Consensus       608 ~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~-~L~~L~l~~~~~~~~  683 (724)
                      |.++.  +..+..+++|++|++++|.++.+|.. +....++..|++.+++.+..+++..+..+. .|+.|++++|.+...
T Consensus        90 N~l~~l~~~~f~~l~~L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~i~~i  169 (350)
T 4ay9_X           90 NNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEI  169 (350)
T ss_dssp             TTCCEECTTSBCCCTTCCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEE
T ss_pred             CcccccCchhhhhccccccccccccccccCCchhhcccchhhhhhhccccccccccccchhhcchhhhhhccccccccCC
Confidence            88887  36789999999999999999987653 455667778888776777777766556654 577888877653211


Q ss_pred             c---ccC-----------CccchH--HhhcCCCCCcEEEeecccccccccccc
Q 004895          684 K---VEG-----------GSNASL--AELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       684 ~---~~~-----------~~~~~l--~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      .   +.+           ..-..+  ..+.++++|+.|+++.|.++.+|...+
T Consensus       170 ~~~~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~l~~lp~~~~  222 (350)
T 4ay9_X          170 HNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGL  222 (350)
T ss_dssp             CTTSSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSCCCCCCSSSC
T ss_pred             ChhhccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCCcCccChhhh
Confidence            0   000           000011  235678899999999999999987654

>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=99.22  E-value=3.4e-11  Score=134.69  Aligned_cols=104  Identities=25%  Similarity=0.275  Sum_probs=90.6

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCccc--chhhhcCCCCCeE
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQL--PLQIGQLTRLQLL  648 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~l--p~~i~~l~~L~~L  648 (724)
                      |.++++|+.|++++|.+..+|..++.+++|++|+|++|.++.++.++.+++|++|++++|.++.+  |..++.+++|++|
T Consensus       459 ~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~l~~l~~L~~L~Ls~N~l~~~~~p~~l~~l~~L~~L  538 (567)
T 1dce_A          459 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLL  538 (567)
T ss_dssp             GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGGGTTCSSCCEEECCSSCCCSSSTTGGGGGCTTCCEE
T ss_pred             ccccccCcEeecCcccccccchhhhcCCCCCEEECCCCCCCCCcccCCCCCCcEEECCCCCCCCCCCcHHHhcCCCCCEE
Confidence            67788999999999999999999999999999999999999977999999999999999999988  8899999999999


Q ss_pred             ccCCCCCCcccChH---HhhCCCCCcEEEc
Q 004895          649 DLSNCSSLVVIAPN---VISKLSRLEELYM  675 (724)
Q Consensus       649 ~l~~~~~l~~~~~~---~i~~l~~L~~L~l  675 (724)
                      ++++ +.+...|+.   .+..+++|+.|++
T Consensus       539 ~L~~-N~l~~~~~~~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          539 NLQG-NSLCQEEGIQERLAEMLPSVSSILT  567 (567)
T ss_dssp             ECTT-SGGGGSSSCTTHHHHHCTTCSEEEC
T ss_pred             EecC-CcCCCCccHHHHHHHHCcccCccCC
Confidence            9999 456666542   2345778887753

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.22  E-value=2e-11  Score=104.64  Aligned_cols=75  Identities=13%  Similarity=0.211  Sum_probs=61.0

Q ss_pred             hhHhHhhHhhhhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHHHHHHHHhh
Q 004895           15 EGTKTLSEPIIGRMSYVLKCQSYIDGLKERVEELGQRRKRVKILVDQATEQG-YEIFADVTEWLGKVEQFTQGYAKHIIN   93 (724)
Q Consensus        15 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~i~~~l~~a~~~~-~~~~~~v~~Wl~~l~~~~~~~~ed~ld   93 (724)
                      .+.+++.+.+.+++.       .+.++++++++|+++|..|+++|.+|++++ ...++.++.|+++||+++|| +||++|
T Consensus         5 ~ll~KL~~ll~~E~~-------l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD-~ED~iD   76 (115)
T 3qfl_A            5 NLIPKLGELLTEEFK-------LHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYV-IEDVVD   76 (115)
T ss_dssp             SHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHH-HHHHHH
T ss_pred             HHHHHHHHHHHHHHH-------HHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHH-HHHHHH
Confidence            344444445555444       378999999999999999999999999874 23589999999999999999 999999


Q ss_pred             hhcc
Q 004895           94 DEDE   97 (724)
Q Consensus        94 ~~~~   97 (724)
                      ++..
T Consensus        77 ~f~~   80 (115)
T 3qfl_A           77 KFLV   80 (115)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8753

>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=99.22  E-value=7.3e-13  Score=127.51  Aligned_cols=137  Identities=21%  Similarity=0.237  Sum_probs=97.3

Q ss_pred             hhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeE
Q 004895          570 FFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLL  648 (724)
Q Consensus       570 ~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L  648 (724)
                      .+..+++|++|++++|.+..+| .++.+.+|++|++++|.++. |..++.+++|++|++++|.++.+| .+..+++|++|
T Consensus        43 ~~~~l~~L~~L~ls~n~l~~l~-~~~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~~L~L~~N~l~~l~-~~~~l~~L~~L  120 (198)
T 1ds9_A           43 TLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLS-GIEKLVNLRVL  120 (198)
T ss_dssp             HHHHTTTCSEEECSEEEESCCC-CHHHHTTCCEEEEEEEEECSCSSHHHHHHHCSEEEEEEEECCCHH-HHHHHHHSSEE
T ss_pred             HHhcCCCCCEEECCCCCCcccc-ccccCCCCCEEECCCCCcccccchhhcCCcCCEEECcCCcCCcCC-ccccCCCCCEE
Confidence            5677888888888888888887 78888888888888888877 455666788888888888888877 58888888888


Q ss_pred             ccCCCCCCcccCh-HHhhCCCCCcEEEccCCCCccccccCC---ccchHHhhcCCCCCcEEEeecccc
Q 004895          649 DLSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQWDKVEGG---SNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       649 ~l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~~~~~~~~---~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ++++| .+..+++ ..+..+++|++|++++|..... ....   .......+..+++|+.|+  ++.+
T Consensus       121 ~l~~N-~i~~~~~~~~l~~l~~L~~L~l~~N~l~~~-~~~~~~~~~~~~~~~~~l~~L~~Ld--~~~i  184 (198)
T 1ds9_A          121 YMSNN-KITNWGEIDKLAALDKLEDLLLAGNPLYND-YKENNATSEYRIEVVKRLPNLKKLD--GMPV  184 (198)
T ss_dssp             EESEE-ECCCHHHHHHHTTTTTCSEEEECSCHHHHH-HHTTTTHHHHHHHHHHHCSSCSEEC--CGGG
T ss_pred             ECCCC-cCCchhHHHHHhcCCCCCEEEecCCccccc-cccccchHHHHHHHHHhCCCcEEEC--Cccc
Confidence            88884 5565543 4578888888888887632110 0000   001112356777888876  4444

>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=2.7e-11  Score=128.36  Aligned_cols=132  Identities=23%  Similarity=0.257  Sum_probs=63.5

Q ss_pred             CCceEEEcCCCcCCCCCc-c----ccC-CCCCcEEEcCCcccCC------cccccCCC-CCcEEEccCCcCcccc-h---
Q 004895          575 EELKVLDFTGIRFSPLPS-S----LGR-LINLQTLCLDGWRLED------IAIVGQLK-KLEILSLRGAEIKQLP-L---  637 (724)
Q Consensus       575 ~~L~~L~l~~~~~~~lp~-~----i~~-l~~L~~L~L~~~~l~~------~~~~~~l~-~L~~L~l~~~~i~~lp-~---  637 (724)
                      ++|+.|++++|.+...+. .    +.. ..+|++|+|++|.++.      +..+..++ +|++|++++|.++..+ .   
T Consensus       109 ~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~  188 (362)
T 3goz_A          109 FTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQILAAIPANVNSLNLRGNNLASKNCAELA  188 (362)
T ss_dssp             TTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHH
T ss_pred             CCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHHHhcCCccccEeeecCCCCchhhHHHHH
Confidence            556666666666553322 2    222 2356666666665553      12233343 5666666666555332 2   


Q ss_pred             -hhhcC-CCCCeEccCCCCCCcc-----cChHHhhC-CCCCcEEEccCCCCccccccCCccchH-HhhcCCCCCcEEEee
Q 004895          638 -QIGQL-TRLQLLDLSNCSSLVV-----IAPNVISK-LSRLEELYMGDSFSQWDKVEGGSNASL-AELKGLSKLTTLEID  708 (724)
Q Consensus       638 -~i~~l-~~L~~L~l~~~~~l~~-----~~~~~i~~-l~~L~~L~l~~~~~~~~~~~~~~~~~l-~~L~~L~~L~~L~l~  708 (724)
                       .+..+ ++|++|++++| .+..     ++. .+.. .++|++|++++|..     .+.....+ ..+..+++|+.|+++
T Consensus       189 ~~l~~~~~~L~~L~Ls~N-~i~~~~~~~l~~-~l~~~~~~L~~L~Ls~N~l-----~~~~~~~l~~~~~~l~~L~~L~L~  261 (362)
T 3goz_A          189 KFLASIPASVTSLDLSAN-LLGLKSYAELAY-IFSSIPNHVVSLNLCLNCL-----HGPSLENLKLLKDSLKHLQTVYLD  261 (362)
T ss_dssp             HHHHTSCTTCCEEECTTS-CGGGSCHHHHHH-HHHHSCTTCCEEECCSSCC-----CCCCHHHHHHTTTTTTTCSEEEEE
T ss_pred             HHHHhCCCCCCEEECCCC-CCChhHHHHHHH-HHhcCCCCceEEECcCCCC-----CcHHHHHHHHHHhcCCCccEEEec
Confidence             22333 36666666663 3333     221 2333 34666666666432     21112222 223556667777777


Q ss_pred             ccccc
Q 004895          709 VRDAE  713 (724)
Q Consensus       709 ~n~~~  713 (724)
                      +|.+.
T Consensus       262 ~n~l~  266 (362)
T 3goz_A          262 YDIVK  266 (362)
T ss_dssp             HHHHT
T ss_pred             cCCcc
Confidence            77633

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.20  E-value=1e-10  Score=110.08  Aligned_cols=122  Identities=19%  Similarity=0.363  Sum_probs=92.3

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc-cccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEcc
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS-SLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLR  628 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~-~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~  628 (724)
                      +.+.+  ..+....+|...   .+.|+.|++++|.+..+|. .++.+.+|++|++++|.++.+  ..++.+++|++|+++
T Consensus        10 ~~l~~--~~~~l~~~p~~~---~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~   84 (177)
T 2o6r_A           10 TEIRC--NSKGLTSVPTGI---PSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLH   84 (177)
T ss_dssp             TEEEC--CSSCCSSCCTTC---CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECC
T ss_pred             CEEEe--cCCCCccCCCCC---CCCCcEEEeCCCcccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECC
Confidence            44555  333344555432   3678889999988887765 457888899999999888873  346888899999999


Q ss_pred             CCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          629 GAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       629 ~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      +|.++.+|.. +..+++|++|++++ +.+..+|+..+..+++|++|++++|.
T Consensus        85 ~N~l~~~~~~~~~~l~~L~~L~l~~-N~l~~~~~~~~~~l~~L~~L~l~~N~  135 (177)
T 2o6r_A           85 ENKLQSLPNGVFDKLTQLKELALDT-NQLKSVPDGIFDRLTSLQKIWLHTNP  135 (177)
T ss_dssp             SSCCCCCCTTTTTTCTTCCEEECCS-SCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CCCccccCHHHhhCCcccCEEECcC-CcceEeCHHHhcCCcccCEEEecCCC
Confidence            9988888765 57888999999988 46777877767888889999888864

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.16  E-value=2.1e-10  Score=107.97  Aligned_cols=122  Identities=20%  Similarity=0.315  Sum_probs=103.2

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEEEcCCc
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTLCLDGW  608 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L~L~~~  608 (724)
                      +.+.+.++.+..+|... .++|+.|.+  +.+....++...|.++++|++|++++|.+..+|.. +..+.+|++|++++|
T Consensus        10 ~~l~~~~~~l~~~p~~~-~~~l~~L~l--~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N   86 (177)
T 2o6r_A           10 TEIRCNSKGLTSVPTGI-PSSATRLEL--ESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHEN   86 (177)
T ss_dssp             TEEECCSSCCSSCCTTC-CTTCSEEEC--CSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CEEEecCCCCccCCCCC-CCCCcEEEe--CCCcccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCCC
Confidence            46778888888887543 478999999  34445677777889999999999999999988764 689999999999999


Q ss_pred             ccCC-c-ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCC
Q 004895          609 RLED-I-AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCS  654 (724)
Q Consensus       609 ~l~~-~-~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~  654 (724)
                      .++. + ..+..+++|++|++++|.++.+|.. +..+++|++|++++|.
T Consensus        87 ~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~  135 (177)
T 2o6r_A           87 KLQSLPNGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNP  135 (177)
T ss_dssp             CCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CccccCHHHhhCCcccCEEECcCCcceEeCHHHhcCCcccCEEEecCCC
Confidence            9988 3 3478999999999999999999887 4789999999999954

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=99.13  E-value=1.7e-10  Score=108.19  Aligned_cols=99  Identities=21%  Similarity=0.413  Sum_probs=67.7

Q ss_pred             eEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCC
Q 004895          578 KVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCS  654 (724)
Q Consensus       578 ~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~  654 (724)
                      +.++++++.+..+|..+.  .+|++|+|++|.++.  +..++.+++|++|+|++|.++.+|.. +..+++|++|++++ +
T Consensus        15 ~~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           15 TLVNCQNIRLASVPAGIP--TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLND-N   91 (174)
T ss_dssp             SEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCS-S
T ss_pred             cEEEeCCCCCCccCCCcC--CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCC-C
Confidence            566777777777776554  667777777777666  24567777777777777777777665 46677777777776 4


Q ss_pred             CCcccChHHhhCCCCCcEEEccCCC
Q 004895          655 SLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       655 ~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      .+..+|+..++.+++|++|++++|.
T Consensus        92 ~l~~l~~~~~~~l~~L~~L~L~~N~  116 (174)
T 2r9u_A           92 HLKSIPRGAFDNLKSLTHIYLYNNP  116 (174)
T ss_dssp             CCCCCCTTTTTTCTTCSEEECCSSC
T ss_pred             ccceeCHHHhccccCCCEEEeCCCC
Confidence            5666666556777777777777653

>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=99.13  E-value=1.5e-10  Score=108.02  Aligned_cols=100  Identities=21%  Similarity=0.358  Sum_probs=78.5

Q ss_pred             ceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCC
Q 004895          577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNC  653 (724)
Q Consensus       577 L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~  653 (724)
                      .+.++++++.+..+|..+.  .+|++|+|++|.++.  +..+..+++|++|++++|.++.+|.. +..+++|++|++++ 
T Consensus        11 ~~~l~~s~n~l~~ip~~~~--~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~-   87 (170)
T 3g39_A           11 GTTVDCSGKSLASVPTGIP--TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLND-   87 (170)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCS-
T ss_pred             CCEEEeCCCCcCccCccCC--CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCC-
Confidence            4678888888888887664  778888888888877  35578888888888888888888766 47888888888888 


Q ss_pred             CCCcccChHHhhCCCCCcEEEccCCC
Q 004895          654 SSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       654 ~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      +.+..+++..++.+++|++|++++|.
T Consensus        88 N~l~~~~~~~~~~l~~L~~L~L~~N~  113 (170)
T 3g39_A           88 NQLKSIPRGAFDNLKSLTHIWLLNNP  113 (170)
T ss_dssp             SCCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CccCEeCHHHhcCCCCCCEEEeCCCC
Confidence            56777777767888888888888864

>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=99.11  E-value=5.3e-10  Score=116.27  Aligned_cols=192  Identities=14%  Similarity=0.135  Sum_probs=118.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      |.....++||+..++.+..++..+..+.+.|+|++|+||||+|+.+++..........+++++.+...+...+ +++++.
T Consensus        17 p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~   95 (323)
T 1sxj_B           17 PQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVV-RNQIKH   95 (323)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHH-HTHHHH
T ss_pred             CCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccccChHHH-HHHHHH
Confidence            4445678999999999999988766656999999999999999999998643211112444544433332222 222221


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccchh-hh
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-CI  312 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-~~  312 (724)
                      +.....              .+..+++.++|+||++...  .++.+...+..        ...++.+|+||+...-. ..
T Consensus        96 ~~~~~~--------------~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~--------~~~~~~~il~~~~~~~l~~~  153 (323)
T 1sxj_B           96 FAQKKL--------------HLPPGKHKIVILDEADSMTAGAQQALRRTMEL--------YSNSTRFAFACNQSNKIIEP  153 (323)
T ss_dssp             HHHBCC--------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHH--------TTTTEEEEEEESCGGGSCHH
T ss_pred             HHhccc--------------cCCCCCceEEEEECcccCCHHHHHHHHHHHhc--------cCCCceEEEEeCChhhchhH
Confidence            110000              0002458999999997642  23333222222        33567788888664321 11


Q ss_pred             hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH-HHHHHHH
Q 004895          313 DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA-LSTVANA  371 (724)
Q Consensus       313 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa-i~~~~~~  371 (724)
                      .......+.+.+++.++..+++...+...... --++....|++.|+|.|.. +..+...
T Consensus       154 l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~r~a~~~l~~~  212 (323)
T 1sxj_B          154 LQSQCAILRYSKLSDEDVLKRLLQIIKLEDVK-YTNDGLEAIIFTAEGDMRQAINNLQST  212 (323)
T ss_dssp             HHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHhhceEEeecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            12334589999999999999999876422111 1146778999999999954 4444433

>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=3.1e-11  Score=127.83  Aligned_cols=180  Identities=15%  Similarity=0.172  Sum_probs=129.8

Q ss_pred             cCceEEeccCCCcccCCCc------ccC-CCccEEEEecccccccccchhh----hcC-CCCceEEEcCCCcCC-----C
Q 004895          527 KGPIAISLPYRDIQELPER------LEC-PQLKLFLLFAKYDSTLQISDHF----FEG-TEELKVLDFTGIRFS-----P  589 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~~~~------~~~-~~Lr~L~l~~~~~~~~~~~~~~----~~~-l~~L~~L~l~~~~~~-----~  589 (724)
                      .++++|++++|.+......      ..+ ++|+.|.+.  .+.....+...    +.. .+.|+.|++++|.+.     .
T Consensus        80 ~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls--~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~  157 (362)
T 3goz_A           80 ANVTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLG--WNDFSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDE  157 (362)
T ss_dssp             TTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECC--SSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHH
T ss_pred             CCccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECc--CCcCCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHH
Confidence            6899999999988655422      133 799999993  33344444333    344 369999999999988     3


Q ss_pred             CCccccCCC-CCcEEEcCCcccCC--cc----cccCC-CCCcEEEccCCcCcc-----cchhhhcC-CCCCeEccCCCCC
Q 004895          590 LPSSLGRLI-NLQTLCLDGWRLED--IA----IVGQL-KKLEILSLRGAEIKQ-----LPLQIGQL-TRLQLLDLSNCSS  655 (724)
Q Consensus       590 lp~~i~~l~-~L~~L~L~~~~l~~--~~----~~~~l-~~L~~L~l~~~~i~~-----lp~~i~~l-~~L~~L~l~~~~~  655 (724)
                      ++..+..+. +|++|+|++|.++.  +.    .+..+ ++|++|++++|.++.     +|..+..+ ++|++|++++| .
T Consensus       158 l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~N-~  236 (362)
T 3goz_A          158 LIQILAAIPANVNSLNLRGNNLASKNCAELAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCLN-C  236 (362)
T ss_dssp             HHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCSS-C
T ss_pred             HHHHHhcCCccccEeeecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcCC-C
Confidence            455556666 99999999999876  22    34555 599999999999887     77777774 59999999995 5


Q ss_pred             CcccCh----HHhhCCCCCcEEEccCCCCccccccCCccc----hHHhhcCCCCCcEEEeecccccc
Q 004895          656 LVVIAP----NVISKLSRLEELYMGDSFSQWDKVEGGSNA----SLAELKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       656 l~~~~~----~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~----~l~~L~~L~~L~~L~l~~n~~~~  714 (724)
                      +...++    ..+..+++|++|++++|.     +......    ....+.++++|+.|++++|.+..
T Consensus       237 l~~~~~~~l~~~~~~l~~L~~L~L~~n~-----l~~i~~~~~~~l~~~~~~l~~L~~LdL~~N~l~~  298 (362)
T 3goz_A          237 LHGPSLENLKLLKDSLKHLQTVYLDYDI-----VKNMSKEQCKALGAAFPNIQKIILVDKNGKEIHP  298 (362)
T ss_dssp             CCCCCHHHHHHTTTTTTTCSEEEEEHHH-----HTTCCHHHHHHHHTTSTTCCEEEEECTTSCBCCG
T ss_pred             CCcHHHHHHHHHHhcCCCccEEEeccCC-----ccccCHHHHHHHHHHhccCCceEEEecCCCcCCC
Confidence            666554    234678999999999863     1111122    22356678899999999998754

>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=99.10  E-value=3.2e-12  Score=122.94  Aligned_cols=132  Identities=18%  Similarity=0.214  Sum_probs=108.0

Q ss_pred             CcccCCCc-ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccc
Q 004895          538 DIQELPER-LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIV  616 (724)
Q Consensus       538 ~~~~~~~~-~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~  616 (724)
                      .++.+|.. ..+++|+.|.+.  .+....++  .+.++++|+.|++++|.+..+|..+..+++|++|++++|.++.++.+
T Consensus        36 ~l~~l~~~~~~l~~L~~L~ls--~n~l~~l~--~~~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~~L~L~~N~l~~l~~~  111 (198)
T 1ds9_A           36 PIEKMDATLSTLKACKHLALS--TNNIEKIS--SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLSGI  111 (198)
T ss_dssp             TCCCCHHHHHHTTTCSEEECS--EEEESCCC--CHHHHTTCCEEEEEEEEECSCSSHHHHHHHCSEEEEEEEECCCHHHH
T ss_pred             cHhhhhHHHhcCCCCCEEECC--CCCCcccc--ccccCCCCCEEECCCCCcccccchhhcCCcCCEEECcCCcCCcCCcc
Confidence            33444432 368899999993  33444565  57889999999999999999999888899999999999999997789


Q ss_pred             cCCCCCcEEEccCCcCcccch--hhhcCCCCCeEccCCCCCCcccCh----------HHhhCCCCCcEEE
Q 004895          617 GQLKKLEILSLRGAEIKQLPL--QIGQLTRLQLLDLSNCSSLVVIAP----------NVISKLSRLEELY  674 (724)
Q Consensus       617 ~~l~~L~~L~l~~~~i~~lp~--~i~~l~~L~~L~l~~~~~l~~~~~----------~~i~~l~~L~~L~  674 (724)
                      +.+++|++|++++|.++.+|.  .+..+++|++|++++| .+...+|          ..+..+++|+.|+
T Consensus       112 ~~l~~L~~L~l~~N~i~~~~~~~~l~~l~~L~~L~l~~N-~l~~~~~~~~~~~~~~~~~~~~l~~L~~Ld  180 (198)
T 1ds9_A          112 EKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLLAGN-PLYNDYKENNATSEYRIEVVKRLPNLKKLD  180 (198)
T ss_dssp             HHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEEECSC-HHHHHHHTTTTHHHHHHHHHHHCSSCSEEC
T ss_pred             ccCCCCCEEECCCCcCCchhHHHHHhcCCCCCEEEecCC-ccccccccccchHHHHHHHHHhCCCcEEEC
Confidence            999999999999999998865  7899999999999995 4433322          2478999999997

>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=99.04  E-value=9.6e-11  Score=128.44  Aligned_cols=180  Identities=16%  Similarity=0.125  Sum_probs=90.8

Q ss_pred             cCceEEeccCCCcccC-C-Ccc-cCC----CccEEEEeccccccc----ccchhhhcCCCCceEEEcCCCcCCC-CCccc
Q 004895          527 KGPIAISLPYRDIQEL-P-ERL-ECP----QLKLFLLFAKYDSTL----QISDHFFEGTEELKVLDFTGIRFSP-LPSSL  594 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~-~-~~~-~~~----~Lr~L~l~~~~~~~~----~~~~~~~~~l~~L~~L~l~~~~~~~-lp~~i  594 (724)
                      .++++|++++|.+... + ... .++    +|++|.+..+  ...    ......+..+++|+.|++++|.+.. .+..+
T Consensus        56 ~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~L~~n--~i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l  133 (461)
T 1z7x_W           56 PALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNC--CLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLL  133 (461)
T ss_dssp             TTCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTS--CCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHH
T ss_pred             CCcCEEeCCCCcCChHHHHHHHHHHhhCCCceeEEEccCC--CCCHHHHHHHHHHHccCCceeEEECCCCcCchHHHHHH
Confidence            4566666666655321 0 000 122    4666666222  111    1223345566666666666666542 12222


Q ss_pred             c-----CCCCCcEEEcCCcccCC------cccccCCCCCcEEEccCCcCccc-chhhh-----cCCCCCeEccCCCCCCc
Q 004895          595 G-----RLINLQTLCLDGWRLED------IAIVGQLKKLEILSLRGAEIKQL-PLQIG-----QLTRLQLLDLSNCSSLV  657 (724)
Q Consensus       595 ~-----~l~~L~~L~L~~~~l~~------~~~~~~l~~L~~L~l~~~~i~~l-p~~i~-----~l~~L~~L~l~~~~~l~  657 (724)
                      .     ...+|++|++++|.++.      +..+..+++|++|++++|.++.. +..+.     .+++|++|++++| .+.
T Consensus       134 ~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n-~l~  212 (461)
T 1z7x_W          134 CEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESC-GVT  212 (461)
T ss_dssp             HHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTS-CCB
T ss_pred             HHHHhcCCCcceEEECCCCCCCHHHHHHHHHHHhhCCCCCEEECcCCCcchHHHHHHHHHHhcCCCCceEEEccCC-CCc
Confidence            1     23456666666666554      23445566677777776665532 22222     2456777777664 333


Q ss_pred             cc----ChHHhhCCCCCcEEEccCCCCccccccCCccchH-Hh-hcCCCCCcEEEeecccccc
Q 004895          658 VI----APNVISKLSRLEELYMGDSFSQWDKVEGGSNASL-AE-LKGLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       658 ~~----~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l-~~-L~~L~~L~~L~l~~n~~~~  714 (724)
                      ..    .+..+..+++|++|++++|.....     ....+ .. ...+++|+.|+++.|.++.
T Consensus       213 ~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~-----~~~~l~~~~~~~~~~L~~L~L~~n~l~~  270 (461)
T 1z7x_W          213 SDNCRDLCGIVASKASLRELALGSNKLGDV-----GMAELCPGLLHPSSRLRTLWIWECGITA  270 (461)
T ss_dssp             TTHHHHHHHHHHHCTTCCEEECCSSBCHHH-----HHHHHHHHHTSTTCCCCEEECTTSCCCH
T ss_pred             HHHHHHHHHHHHhCCCccEEeccCCcCChH-----HHHHHHHHHhcCCCCceEEECcCCCCCH
Confidence            32    133456677777777776532111     00011 11 1246788888888887765

>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=99.03  E-value=1.1e-10  Score=128.03  Aligned_cols=137  Identities=20%  Similarity=0.204  Sum_probs=70.2

Q ss_pred             hcCCCCceEEEcCCCcCCCC------CccccCCCCCcEEEcCCcccCC------cccccCCCCCcEEEccCCcCccc-ch
Q 004895          571 FEGTEELKVLDFTGIRFSPL------PSSLGRLINLQTLCLDGWRLED------IAIVGQLKKLEILSLRGAEIKQL-PL  637 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~l------p~~i~~l~~L~~L~L~~~~l~~------~~~~~~l~~L~~L~l~~~~i~~l-p~  637 (724)
                      +..+++|+.|++++|.+...      +.....+.+|++|++++|.++.      +..+..+++|++|++++|.++.. +.
T Consensus       223 l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~  302 (461)
T 1z7x_W          223 VASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGAR  302 (461)
T ss_dssp             HHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHH
T ss_pred             HHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcCCCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHHH
Confidence            44556666666666655421      1112245566666666666554      23344566666666666655422 11


Q ss_pred             hhhc-----CCCCCeEccCCCCCCccc----ChHHhhCCCCCcEEEccCCCCccccccCCccchH-HhhcC-CCCCcEEE
Q 004895          638 QIGQ-----LTRLQLLDLSNCSSLVVI----APNVISKLSRLEELYMGDSFSQWDKVEGGSNASL-AELKG-LSKLTTLE  706 (724)
Q Consensus       638 ~i~~-----l~~L~~L~l~~~~~l~~~----~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l-~~L~~-L~~L~~L~  706 (724)
                      .+..     .++|++|++++|. +...    .+..+..+++|++|++++|..     .+.....+ ..+.. .++|+.|+
T Consensus       303 ~l~~~l~~~~~~L~~L~L~~n~-l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i-----~~~~~~~l~~~l~~~~~~L~~L~  376 (461)
T 1z7x_W          303 LLCETLLEPGCQLESLWVKSCS-FTAACCSHFSSVLAQNRFLLELQISNNRL-----EDAGVRELCQGLGQPGSVLRVLW  376 (461)
T ss_dssp             HHHHHHTSTTCCCCEEECTTSC-CBGGGHHHHHHHHHHCSSCCEEECCSSBC-----HHHHHHHHHHHHTSTTCCCCEEE
T ss_pred             HHHHHhccCCccceeeEcCCCC-CchHHHHHHHHHHhhCCCccEEEccCCcc-----ccccHHHHHHHHcCCCCceEEEE
Confidence            2221     2466666666643 3322    123355667777777766532     11111112 12222 56788888


Q ss_pred             eeccccc
Q 004895          707 IDVRDAE  713 (724)
Q Consensus       707 l~~n~~~  713 (724)
                      +++|.++
T Consensus       377 L~~n~i~  383 (461)
T 1z7x_W          377 LADCDVS  383 (461)
T ss_dssp             CTTSCCC
T ss_pred             CCCCCCC
Confidence            8888776

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.95  E-value=2.7e-09  Score=99.89  Aligned_cols=79  Identities=25%  Similarity=0.405  Sum_probs=54.3

Q ss_pred             CCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCcccCCc-c-cccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEcc
Q 004895          575 EELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI-A-IVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDL  650 (724)
Q Consensus       575 ~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~~l~~~-~-~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l  650 (724)
                      +.|++|++++|.+..+ |..+..+.+|++|+|++|.++.+ + .+..+++|++|+|++|.++.+|.. +..+++|++|++
T Consensus        33 ~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L  112 (174)
T 2r9u_A           33 TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYL  112 (174)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEEC
T ss_pred             CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccceeCHHHhccccCCCEEEe
Confidence            5667777777777755 45667777777777777777662 2 356777777777777777777665 667777777777


Q ss_pred             CCC
Q 004895          651 SNC  653 (724)
Q Consensus       651 ~~~  653 (724)
                      ++|
T Consensus       113 ~~N  115 (174)
T 2r9u_A          113 YNN  115 (174)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            773

>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=98.93  E-value=2.9e-09  Score=110.79  Aligned_cols=189  Identities=14%  Similarity=0.109  Sum_probs=115.2

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .....++|+++.++.+..++..+..+.+.|+|++|+||||+|+.+++.......-...+.++.+...+...+ +..+   
T Consensus        22 ~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~---   97 (327)
T 1iqp_A           22 QRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDERGINVI-REKV---   97 (327)
T ss_dssp             CSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCHHHHHTT-HHHH---
T ss_pred             CCHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccccCchHHH-HHHH---
Confidence            345668899999999999988776666999999999999999999998643211011333333221111111 0000   


Q ss_pred             CCCCCCCchhHHHHHHHHHH--HhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccchh-h
Q 004895          237 GMNFDSNDLIYHRAKQLCQR--LKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL-C  311 (724)
Q Consensus       237 ~~~~~~~~~~~~~~~~l~~~--l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~-~  311 (724)
                                    ......  +..+++.++|+||++...  .++.+...+..        ...++++|+||...... .
T Consensus        98 --------------~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~--------~~~~~~~i~~~~~~~~l~~  155 (327)
T 1iqp_A           98 --------------KEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEM--------FSSNVRFILSCNYSSKIIE  155 (327)
T ss_dssp             --------------HHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSCH
T ss_pred             --------------HHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHh--------cCCCCeEEEEeCCccccCH
Confidence                          000000  111467899999997652  23333222222        33567888888765321 1


Q ss_pred             hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          312 IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       312 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      ........+.+.+++.++..+++...+...... --++..+.|++.++|.|..+..+...+
T Consensus       156 ~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~g~~r~~~~~l~~~  215 (327)
T 1iqp_A          156 PIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIAEGDMRRAINILQAA  215 (327)
T ss_dssp             HHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            111223478999999999999999877532211 114677899999999998665544433

>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=98.88  E-value=6.8e-09  Score=96.77  Aligned_cols=79  Identities=28%  Similarity=0.382  Sum_probs=51.4

Q ss_pred             CCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEcc
Q 004895          575 EELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDL  650 (724)
Q Consensus       575 ~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l  650 (724)
                      +.|+.|++++|.+..+ |..+..+.+|++|+|++|.++.+  ..+..+++|++|+|++|.++.+|.. +..+++|++|++
T Consensus        30 ~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L  109 (170)
T 3g39_A           30 TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWL  109 (170)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEEC
T ss_pred             CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccCEeCHHHhcCCCCCCEEEe
Confidence            4566666666666655 44566667777777777766662  2356667777777777777766654 666777777777


Q ss_pred             CCC
Q 004895          651 SNC  653 (724)
Q Consensus       651 ~~~  653 (724)
                      ++|
T Consensus       110 ~~N  112 (170)
T 3g39_A          110 LNN  112 (170)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            663

>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=98.84  E-value=7.4e-09  Score=107.89  Aligned_cols=162  Identities=19%  Similarity=0.175  Sum_probs=118.2

Q ss_pred             CCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCccc-------CC-------
Q 004895          548 CPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRL-------ED-------  612 (724)
Q Consensus       548 ~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~~l-------~~-------  612 (724)
                      |++|+.|.+  .. ....+++..|.++++|+.|++++|.+..++ ..+..+.++.++.+..+..       ..       
T Consensus       100 ~~~L~~l~L--~~-~i~~I~~~aF~~~~~L~~l~l~~n~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~  176 (329)
T 3sb4_A          100 KQTLEKVIL--SE-KIKNIEDAAFKGCDNLKICQIRKKTAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGE  176 (329)
T ss_dssp             CTTCCC-CB--CT-TCCEECTTTTTTCTTCCEEEBCCSSCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESC
T ss_pred             cCCCcEEEC--Cc-cccchhHHHhhcCcccceEEcCCCCccccchhhhcCCCceEEecCcchhhhhcccccccccccccc
Confidence            788888888  22 556677788888888999998888876553 3455566666665544110       00       


Q ss_pred             ------------------------c-----------------ccc-cCCCCCcEEEccCCcCcccchh-hhcCCCCCeEc
Q 004895          613 ------------------------I-----------------AIV-GQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLD  649 (724)
Q Consensus       613 ------------------------~-----------------~~~-~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~  649 (724)
                                              +                 ..+ ..+++|++|++++|.++.+|.. +..+++|+.|+
T Consensus       177 ~L~~~i~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n~i~~I~~~aF~~~~~L~~l~  256 (329)
T 3sb4_A          177 PLETTIQVGAMGKLEDEIMKAGLQPRDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKTNATTIPDFTFAQKKYLLKIK  256 (329)
T ss_dssp             CCEEEEEECTTCCHHHHHHHTTCCGGGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTBCCCEECTTTTTTCTTCCEEE
T ss_pred             ccceeEEecCCCcHHHHHhhcccCccccceEEEeeeecHHHHHHHHHhcCCCeEEECCCCCcceecHhhhhCCCCCCEEE
Confidence                                    0                 000 1378999999999999999876 88999999999


Q ss_pred             cCCCCCCcccChHHhhCCCCCc-EEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecccccccccccccCC
Q 004895          650 LSNCSSLVVIAPNVISKLSRLE-ELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSLGN  723 (724)
Q Consensus       650 l~~~~~l~~~~~~~i~~l~~L~-~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~~~n  723 (724)
                      ++++  +..+++..+..+++|+ .+.+..+      +...   .-..+.++++|+.|+++.|.++.++...|.++
T Consensus       257 l~~n--i~~I~~~aF~~~~~L~~~l~l~~~------l~~I---~~~aF~~c~~L~~l~l~~n~i~~I~~~aF~~~  320 (329)
T 3sb4_A          257 LPHN--LKTIGQRVFSNCGRLAGTLELPAS------VTAI---EFGAFMGCDNLRYVLATGDKITTLGDELFGNG  320 (329)
T ss_dssp             CCTT--CCEECTTTTTTCTTCCEEEEECTT------CCEE---CTTTTTTCTTEEEEEECSSCCCEECTTTTCTT
T ss_pred             CCcc--cceehHHHhhCChhccEEEEEccc------ceEE---chhhhhCCccCCEEEeCCCccCccchhhhcCC
Confidence            9983  8889999999999999 9998763      1111   11356688899999999999999998877654

>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=98.83  E-value=3.9e-08  Score=101.84  Aligned_cols=187  Identities=12%  Similarity=0.135  Sum_probs=114.6

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      |.....++|++..++.+.+++..+..+.+.++|++|+|||++|+.+++.......-..++.++.+...+...+.      
T Consensus        13 p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~------   86 (319)
T 2chq_A           13 PRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVR------   86 (319)
T ss_dssp             CSSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTCTTTSS------
T ss_pred             CCCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccChHHHH------
Confidence            34456788999999999998876665568999999999999999999986321100113344443322111110      


Q ss_pred             hCCCCCCCchhHHHHHHHHHH--HhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccch-h
Q 004895          236 LGMNFDSNDLIYHRAKQLCQR--LKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL-L  310 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~--l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v-~  310 (724)
                                  .........  +..+++.++|+|+++...  ..+.+...+..        ...++.+|+||....- .
T Consensus        87 ------------~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~--------~~~~~~~i~~~~~~~~l~  146 (319)
T 2chq_A           87 ------------HKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEM--------YSKSCRFILSCNYVSRII  146 (319)
T ss_dssp             ------------HHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSS--------SSSSEEEEEEESCGGGSC
T ss_pred             ------------HHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHh--------cCCCCeEEEEeCChhhcc
Confidence                        011111100  012467899999997652  23333333322        3456778877765432 1


Q ss_pred             hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          311 CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       311 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                      ..-......+.+.+++.++..+++...+...... --++....|++.++|.+..+....
T Consensus       147 ~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~-i~~~~l~~l~~~~~G~~r~~~~~l  204 (319)
T 2chq_A          147 EPIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK-ITEDGLEALIYISGGDFRKAINAL  204 (319)
T ss_dssp             HHHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCC-BCHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             hHHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            1112334589999999999999999887533221 124577889999999998654433

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.79  E-value=1.1e-07  Score=96.80  Aligned_cols=174  Identities=9%  Similarity=0.077  Sum_probs=105.8

Q ss_pred             cccchHHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC---C-C-eEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV---F-D-KVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---F-~-~~~wv~vs~~~~~~~l~~~  231 (724)
                      .+.||++++++|...|.    .+..+.+.|+|++|+|||++++.|++.......   . + .++++++....+...++..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHH
Confidence            36799999999987775    567788999999999999999999999864221   1 1 2556666677788899999


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHH--hcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRL--KKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l--~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                      |++++................++..+  ..+++++++||+++....-+.+...+.+    ......+ ..||.++...+.
T Consensus       101 I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~----~~~~~s~-~~vI~i~n~~d~  175 (318)
T 3te6_A          101 IWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKW----ISSKNSK-LSIICVGGHNVT  175 (318)
T ss_dssp             HHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHH----HHCSSCC-EEEEEECCSSCC
T ss_pred             HHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhc----ccccCCc-EEEEEEecCccc
Confidence            99999543211111223334444443  2357899999999765421111111100    0000112 224444433322


Q ss_pred             hhh-------hcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          310 LCI-------DMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       310 ~~~-------~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                      ...       ..-....+.+++++.+|..+++.+++.
T Consensus       176 ~~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          176 IREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             CHHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHH
T ss_pred             chhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHH
Confidence            100       011125789999999999999999874

>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=98.78  E-value=1.5e-08  Score=106.40  Aligned_cols=88  Identities=23%  Similarity=0.145  Sum_probs=51.3

Q ss_pred             ccccchhhhcCCCCceEEEcCC-CcCCCCC-ccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh
Q 004895          563 TLQISDHFFEGTEELKVLDFTG-IRFSPLP-SSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ  638 (724)
Q Consensus       563 ~~~~~~~~~~~l~~L~~L~l~~-~~~~~lp-~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~  638 (724)
                      ...+|.  +..+++|+.|+|++ |.+..+| ..|+.|.+|++|+|++|.++.  +..|.+|++|++|+|++|.++.+|..
T Consensus        21 l~~ip~--l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~   98 (347)
T 2ifg_A           21 LDSLHH--LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWK   98 (347)
T ss_dssp             CTTTTT--SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCST
T ss_pred             CCccCC--CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCccceeCHH
Confidence            344454  55566666666664 6666554 346666666666666666655  23456666666666666666666555


Q ss_pred             hhcCCCCCeEccCC
Q 004895          639 IGQLTRLQLLDLSN  652 (724)
Q Consensus       639 i~~l~~L~~L~l~~  652 (724)
                      +.....|+.|++.+
T Consensus        99 ~~~~~~L~~l~l~~  112 (347)
T 2ifg_A           99 TVQGLSLQELVLSG  112 (347)
T ss_dssp             TTCSCCCCEEECCS
T ss_pred             HcccCCceEEEeeC
Confidence            43333366666665

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.77  E-value=2.4e-09  Score=113.24  Aligned_cols=180  Identities=14%  Similarity=0.037  Sum_probs=110.4

Q ss_pred             ccCceEEeccCCCcccCC-----Ccc--cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCC-Cccc---
Q 004895          526 QKGPIAISLPYRDIQELP-----ERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPL-PSSL---  594 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~-----~~~--~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i---  594 (724)
                      ...++.+++++|.+....     ..+  .+++|+.|++..+. -.......+...+++|+.|+|++|.+... ...+   
T Consensus        71 ~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~-l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~  149 (372)
T 3un9_A           71 LSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQ-LDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDL  149 (372)
T ss_dssp             HTTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCC-CCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHH
T ss_pred             HhhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCC-CCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHH
Confidence            568899999999875421     111  23688898883222 11112223344566889999999988732 1222   


Q ss_pred             --cCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCcc-----cchhhhcCCCCCeEccCCCCCCcccC-
Q 004895          595 --GRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQ-----LPLQIGQLTRLQLLDLSNCSSLVVIA-  660 (724)
Q Consensus       595 --~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~-----lp~~i~~l~~L~~L~l~~~~~l~~~~-  660 (724)
                        ....+|++|+|++|.++.  .    ..+..+++|++|+|++|.++.     ++..+...++|++|++++| .++... 
T Consensus       150 L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~l~~~g~~~L~~~L~~~~~L~~L~Ls~N-~i~~~g~  228 (372)
T 3un9_A          150 LLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYN-GAGDTAA  228 (372)
T ss_dssp             HHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSSCHHHHHHHHHHHGGGCSCCCEEECCSS-CCCHHHH
T ss_pred             HHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCCCCcHHHHHHHHHHhcCCCcCeEECCCC-CCCHHHH
Confidence              245789999999998765  1    345678889999999998763     3566777889999999985 444322 


Q ss_pred             ---hHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCC--CcEEE--eecccc
Q 004895          661 ---PNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSK--LTTLE--IDVRDA  712 (724)
Q Consensus       661 ---~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~--L~~L~--l~~n~~  712 (724)
                         ...+...++|++|++++|.+     +......+..+.....  |+.+.  +..+.+
T Consensus       229 ~~l~~~L~~~~~L~~L~Ls~N~i-----~~~g~~~L~~~~~~~~~~L~~l~~ll~~~~~  282 (372)
T 3un9_A          229 LALARAAREHPSLELLHLYFNEL-----SSEGRQVLRDLGGAAEGGARVVVSLTEGTAV  282 (372)
T ss_dssp             HHHHHHHHHCSSCCEEECTTSSC-----CHHHHHHHHHCC------CEEECCCC----C
T ss_pred             HHHHHHHHhCCCCCEEeccCCCC-----CHHHHHHHHHHhcCCCccchhhHhhhcCCcc
Confidence               22355678899999988743     2222223444443332  66666  555554

>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=98.76  E-value=1.3e-07  Score=100.28  Aligned_cols=195  Identities=13%  Similarity=0.162  Sum_probs=111.6

Q ss_pred             ccccccchHHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          158 DYNIFNSRKKIFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      ....++||+..++.+..++..+. ...+.|+|++|+||||+|+.+++.......+..       ..+..-.-...+....
T Consensus        14 ~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~-------~~~~~~~~~~~~~~~~   86 (373)
T 1jr3_A           14 TFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA-------TPCGVCDNCREIEQGR   86 (373)
T ss_dssp             STTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS-------SCCSSSHHHHHHHTSC
T ss_pred             chhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC-------CCCcccHHHHHHhccC
Confidence            34568999999999999887544 357889999999999999999987743211100       0000000011111100


Q ss_pred             CCC-----CCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          237 GMN-----FDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       237 ~~~-----~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      ...     ..... ..+....+.+.+.    .+++.++|+||++...  ..+.+...+..        ...+..+|++|.
T Consensus        87 ~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~--------~~~~~~~Il~~~  157 (373)
T 1jr3_A           87 FVDLIEIDAASRT-KVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEE--------PPEHVKFLLATT  157 (373)
T ss_dssp             CSSCEEEETTCSC-CSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHS--------CCSSEEEEEEES
T ss_pred             CCceEEecccccC-CHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhc--------CCCceEEEEEeC
Confidence            000     00000 0011222333322    2457899999997642  23333222222        234566777766


Q ss_pred             ccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          306 SRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       306 ~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                      ... +..........+++.+++.++..+++.+.+...... --.+....|++.++|.|..+..+.
T Consensus       158 ~~~~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~-~~~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          158 DPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIA-HEPRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             CGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC-BCHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             ChHhCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHCCCCHHHHHHHH
Confidence            443 211112334689999999999999998876422111 114567889999999998776554

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.64  E-value=1.4e-07  Score=89.48  Aligned_cols=153  Identities=16%  Similarity=0.230  Sum_probs=87.6

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC-----CCeEEEEEEecCCChHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV-----FDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-----F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ...++||+++++.+.+.+.....+.+.|+|++|+|||++|+.+++.......     ...+++++++.      +    .
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~----~   90 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA------L----V   90 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH------H----H
T ss_pred             ccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHH------H----h
Confidence            4568899999999999988766678899999999999999999998754211     12244444321      1    1


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHH-hcCCcEEEEEccccccc---------cccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRL-KKEKRVLIILDNIWTKL---------ELDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l-~~~kr~LlVlDdv~~~~---------~~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      ..  ..  ...........+...+ ..+++.+|||||++...         .+..+...+.         ...+..+|+|
T Consensus        91 ~~--~~--~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~~---------~~~~~~~i~~  157 (195)
T 1jbk_A           91 AG--AK--YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL---------ARGELHCVGA  157 (195)
T ss_dssp             TT--TC--SHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH---------HTTSCCEEEE
T ss_pred             cc--CC--ccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHhh---------ccCCeEEEEe
Confidence            00  00  0000111222333333 23567899999997642         1111111111         1234456666


Q ss_pred             ecccch------hhhhcCCCceEecCCCCHHHHHHHH
Q 004895          304 SRSRDL------LCIDMNSQKMFWIDALSEEEALQLF  334 (724)
Q Consensus       304 tR~~~v------~~~~~~~~~~~~l~~L~~~e~~~Lf  334 (724)
                      |.....      ..........+.+.+++.++..+++
T Consensus       158 ~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          158 TTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             CCHHHHHHHHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence            665431      1111223346889999988876654

>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=98.62  E-value=4.3e-08  Score=110.94  Aligned_cols=150  Identities=14%  Similarity=0.096  Sum_probs=82.2

Q ss_pred             ccCceEEeccCCCcccCCC-----c-ccCCCccEEEEeccccc--ccccchhhhcCCCCceEEEcCCCcCCCCCccccCC
Q 004895          526 QKGPIAISLPYRDIQELPE-----R-LECPQLKLFLLFAKYDS--TLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRL  597 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~-----~-~~~~~Lr~L~l~~~~~~--~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l  597 (724)
                      ..++++|++.+|.+.....     . ..+++|++|.+..+...  ........+.++++|+.|++++|.+..+|..+..+
T Consensus       163 ~~~L~~L~L~~~~~~~~~~~~l~~~~~~~~~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~~l~~~~~~~  242 (592)
T 3ogk_B          163 CRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAA  242 (592)
T ss_dssp             CTTCSEEECTTCEEECCCSHHHHHHHHHCCCCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECSSCBGGGGHHHHHHC
T ss_pred             CCCCCEEECccccccCcchhHHHHHHhcCCCccEEEeeccCCCccCHHHHHHHHhhCCCCcEEeccCccHHHHHHHHhhh
Confidence            4677888888776533211     1 25677888877322211  01122334566788888888888777777777777


Q ss_pred             CCCcEEEcCCcccC----C-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCccc-ChHHhhCCCCCc
Q 004895          598 INLQTLCLDGWRLE----D-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVI-APNVISKLSRLE  671 (724)
Q Consensus       598 ~~L~~L~L~~~~l~----~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~-~~~~i~~l~~L~  671 (724)
                      ++|++|+++.+...    . +..+..+++|+.|+++++....+|..+..+++|++|++++|. +... +...+..+++|+
T Consensus       243 ~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~~~-l~~~~~~~~~~~~~~L~  321 (592)
T 3ogk_B          243 ANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYAL-LETEDHCTLIQKCPNLE  321 (592)
T ss_dssp             TTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGGGGCCEEEETTCC-CCHHHHHHHHTTCTTCC
T ss_pred             hHHHhhcccccccccchHHHHHHhhccccccccCccccchhHHHHHHhhcCCCcEEecCCCc-CCHHHHHHHHHhCcCCC
Confidence            77777777643211    0 234455555555555554444555555555555555555543 2211 112234555555


Q ss_pred             EEEcc
Q 004895          672 ELYMG  676 (724)
Q Consensus       672 ~L~l~  676 (724)
                      +|++.
T Consensus       322 ~L~L~  326 (592)
T 3ogk_B          322 VLETR  326 (592)
T ss_dssp             EEEEE
T ss_pred             EEecc
Confidence            55544

>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=98.61  E-value=2.1e-08  Score=113.46  Aligned_cols=125  Identities=16%  Similarity=0.121  Sum_probs=69.1

Q ss_pred             cCceEEeccCCCcccC-CCcc--cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC-----CCccccCCC
Q 004895          527 KGPIAISLPYRDIQEL-PERL--ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP-----LPSSLGRLI  598 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~-~~~~--~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~-----lp~~i~~l~  598 (724)
                      .++++|.+.++.+... +...  .+++|++|.+..+...........+.++++|++|++++|.+..     ++.....++
T Consensus       105 ~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~~~~  184 (594)
T 2p1m_B          105 TWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDTYT  184 (594)
T ss_dssp             TTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCEEEEHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCTTCC
T ss_pred             CCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcCCCCHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhhcCC
Confidence            4677777776655321 1111  4677777777432111111123344567777777777776552     222223556


Q ss_pred             CCcEEEcCCcc--cCC--c-ccccCCCCCcEEEccCC-cCcccchhhhcCCCCCeEccC
Q 004895          599 NLQTLCLDGWR--LED--I-AIVGQLKKLEILSLRGA-EIKQLPLQIGQLTRLQLLDLS  651 (724)
Q Consensus       599 ~L~~L~L~~~~--l~~--~-~~~~~l~~L~~L~l~~~-~i~~lp~~i~~l~~L~~L~l~  651 (724)
                      +|++|++++|.  +..  + ..+..+++|++|++++| .+..+|..+.++++|++|+++
T Consensus       185 ~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~l~  243 (594)
T 2p1m_B          185 SLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTG  243 (594)
T ss_dssp             CCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHHHHHCTTCSEEECS
T ss_pred             cCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHHHhcCCcceEcccc
Confidence            77777777775  221  1 12344677777777776 444555556666666666543

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.59  E-value=1.3e-08  Score=107.42  Aligned_cols=103  Identities=17%  Similarity=0.172  Sum_probs=45.1

Q ss_pred             CCceEEEcCCCcCCC--CCccccCCCCCcEEEcCCcccCC--cccc-----cCCCCCcEEEccCCcCcc-----cchhhh
Q 004895          575 EELKVLDFTGIRFSP--LPSSLGRLINLQTLCLDGWRLED--IAIV-----GQLKKLEILSLRGAEIKQ-----LPLQIG  640 (724)
Q Consensus       575 ~~L~~L~l~~~~~~~--lp~~i~~l~~L~~L~L~~~~l~~--~~~~-----~~l~~L~~L~l~~~~i~~-----lp~~i~  640 (724)
                      +.|+.|+|++|.+..  +..-...+.+|++|+|++|.++.  ...+     ...++|++|+|++|.++.     ++..+.
T Consensus       101 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~  180 (372)
T 3un9_A          101 HALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLA  180 (372)
T ss_dssp             SCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHH
T ss_pred             CCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHh
Confidence            455555555555441  11111223445555555555543  1111     123455555555555432     233344


Q ss_pred             cCCCCCeEccCCCCCCcccC----hHHhhCCCCCcEEEccCC
Q 004895          641 QLTRLQLLDLSNCSSLVVIA----PNVISKLSRLEELYMGDS  678 (724)
Q Consensus       641 ~l~~L~~L~l~~~~~l~~~~----~~~i~~l~~L~~L~l~~~  678 (724)
                      .+++|++|+|++| .+....    ...+..+++|++|++++|
T Consensus       181 ~~~~L~~L~Ls~N-~l~~~g~~~L~~~L~~~~~L~~L~Ls~N  221 (372)
T 3un9_A          181 GNTSVTHLSLLHT-GLGDEGLELLAAQLDRNRQLQELNVAYN  221 (372)
T ss_dssp             TCSSCCEEECTTS-SCHHHHHHHHHHHGGGCSCCCEEECCSS
T ss_pred             cCCCcCEEeCCCC-CCCcHHHHHHHHHHhcCCCcCeEECCCC
Confidence            4555555555553 232211    122344455555555554

>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=98.59  E-value=2.1e-07  Score=97.80  Aligned_cols=197  Identities=13%  Similarity=0.109  Sum_probs=113.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC-CeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF-DKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|+++.++.+..++..+..+.+.|+|++|+||||+|+.+++.......+ ..+..++.+.......+. +.+.
T Consensus        33 p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  111 (353)
T 1sxj_D           33 PKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR-EKVK  111 (353)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHT-THHH
T ss_pred             CCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHH-HHHH
Confidence            44456788999999999999887655558999999999999999999986421111 123444444433333221 2111


Q ss_pred             hhC-CCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hh
Q 004895          235 DLG-MNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LL  310 (724)
Q Consensus       235 ~l~-~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~  310 (724)
                      .+. ....... ..     .......+++-+|++|++....  ..+.+...+..        .....++|++|.... +.
T Consensus       112 ~~~~~~~~~~~-~~-----~~~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~--------~~~~~~~il~~~~~~~l~  177 (353)
T 1sxj_D          112 NFARLTVSKPS-KH-----DLENYPCPPYKIIILDEADSMTADAQSALRRTMET--------YSGVTRFCLICNYVTRII  177 (353)
T ss_dssp             HHHHSCCCCCC-TT-----HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSC
T ss_pred             HHhhhcccccc-hh-----hcccCCCCCceEEEEECCCccCHHHHHHHHHHHHh--------cCCCceEEEEeCchhhCc
Confidence            111 0000000 00     0001112355799999986542  22222222221        223456777665443 21


Q ss_pred             hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          311 CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       311 ~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      .........+.+.+++.++....+.+.+...... --++..+.|++.++|.|..+..+
T Consensus       178 ~~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~-i~~~~l~~l~~~~~G~~r~~~~~  234 (353)
T 1sxj_D          178 DPLASQCSKFRFKALDASNAIDRLRFISEQENVK-CDDGVLERILDISAGDLRRGITL  234 (353)
T ss_dssp             HHHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHTSSCHHHHHHH
T ss_pred             chhhccCceEEeCCCCHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            1111223478999999999999999877432211 12567889999999999865443

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.57  E-value=9.8e-08  Score=99.99  Aligned_cols=180  Identities=13%  Similarity=0.122  Sum_probs=111.1

Q ss_pred             ccCceEEeccCCCcc--c-------CCC-cccCCCccEEEEeccccc---c----cccchhhhcCCCCceEEEcCCCcCC
Q 004895          526 QKGPIAISLPYRDIQ--E-------LPE-RLECPQLKLFLLFAKYDS---T----LQISDHFFEGTEELKVLDFTGIRFS  588 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~--~-------~~~-~~~~~~Lr~L~l~~~~~~---~----~~~~~~~~~~l~~L~~L~l~~~~~~  588 (724)
                      +..++.|.+......  .       +.. ...+++|++|.+......   .    ..-....+..+++|+.|++++|.-.
T Consensus       106 ~~~v~~L~lg~~~~~~~~~~~~~~~L~~s~~~l~~L~~L~l~~~~~e~~~is~~~~~~L~~ll~~~P~L~~L~L~g~~~l  185 (362)
T 2ra8_A          106 LPSLKQITIGXWGYEGEDCSDIADGIVENKEKFAHFEGLFWGDIDFEEQEISWIEQVDLSPVLDAMPLLNNLKIKGTNNL  185 (362)
T ss_dssp             GGGCSEEEECCCCSSSCCSHHHHHHHHTTHHHHTTCSEEEECCCCTTTCCGGGCBCCBCHHHHHTCTTCCEEEEECCBTC
T ss_pred             chhcceEEEcccccCCCcHHHHHHHHHHhhhhcchhhheeecCcchhhcccccccccCHHHHHhcCCCCcEEEEeCCCCc
Confidence            456777777644432  1       111 124689999988321111   0    0113356788899999999988433


Q ss_pred             CCCccccCCCCCcEEEcCCcccCC--ccccc--CCCCCcEEEccCC--c------Ccccchhh--hcCCCCCeEccCCCC
Q 004895          589 PLPSSLGRLINLQTLCLDGWRLED--IAIVG--QLKKLEILSLRGA--E------IKQLPLQI--GQLTRLQLLDLSNCS  654 (724)
Q Consensus       589 ~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~--~l~~L~~L~l~~~--~------i~~lp~~i--~~l~~L~~L~l~~~~  654 (724)
                      .+|. +. +.+|++|+|..|.+..  ...++  .+++|++|+|+.+  .      +..+...+  ..+++|++|.+.+|.
T Consensus       186 ~l~~-~~-~~~L~~L~L~~~~l~~~~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~  263 (362)
T 2ra8_A          186 SIGK-KP-RPNLKSLEIISGGLPDSVVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAE  263 (362)
T ss_dssp             BCCS-CB-CTTCSEEEEECSBCCHHHHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCT
T ss_pred             eecc-cc-CCCCcEEEEecCCCChHHHHHHHHccCCCCcEEEEeccccccccchhHHHHHHHHhcCCCCCcCEEeCCCCC
Confidence            5554 43 8899999999888765  34444  7899999998632  1      22222222  357899999998865


Q ss_pred             CCcccChHHh---hCCCCCcEEEccCCCCccccccCCccch-HHhhcCCCCCcEEEeeccccc
Q 004895          655 SLVVIAPNVI---SKLSRLEELYMGDSFSQWDKVEGGSNAS-LAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       655 ~l~~~~~~~i---~~l~~L~~L~l~~~~~~~~~~~~~~~~~-l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      .....+ ..+   +.+++|++|+++.|..     .+..... ...+.++++|+.|+++.|.++
T Consensus       264 i~~~~~-~~la~a~~~~~L~~LdLs~n~L-----~d~G~~~L~~~L~~l~~L~~L~L~~n~i~  320 (362)
T 2ra8_A          264 EQNVVV-EMFLESDILPQLETMDISAGVL-----TDEGARLLLDHVDKIKHLKFINMKYNYLS  320 (362)
T ss_dssp             THHHHH-HHHHHCSSGGGCSEEECCSSCC-----BHHHHHHHHTTHHHHTTCSEEECCSBBCC
T ss_pred             CchHHH-HHHHhCccCCCCCEEECCCCCC-----ChHHHHHHHhhcccCCcceEEECCCCcCC
Confidence            322221 222   3578999999987642     2111112 223466789999999988764

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.55  E-value=1.2e-07  Score=99.58  Aligned_cols=101  Identities=17%  Similarity=0.131  Sum_probs=73.5

Q ss_pred             EEeccCC-CcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCc
Q 004895          531 AISLPYR-DIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGW  608 (724)
Q Consensus       531 ~l~l~~~-~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~  608 (724)
                      .+..+++ .+..+|....+++|+.|.+ .+.+....++...|.++++|+.|+|++|.+..+| ..|.+|.+|++|+|++|
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 GLRCTRDGALDSLHHLPGAENLTELYI-ENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFN   90 (347)
T ss_dssp             CEECCSSCCCTTTTTSCSCSCCSEEEC-CSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSS
T ss_pred             EEEcCCCCCCCccCCCCCCCCeeEEEc-cCCCCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCC
Confidence            3556666 6777777335677888888 2235666777777888888888888888888654 46788888888888888


Q ss_pred             ccCC-ccc-ccCCCCCcEEEccCCcCc
Q 004895          609 RLED-IAI-VGQLKKLEILSLRGAEIK  633 (724)
Q Consensus       609 ~l~~-~~~-~~~l~~L~~L~l~~~~i~  633 (724)
                      .++. |+. +..+. |++|+|.+|.+.
T Consensus        91 ~l~~~~~~~~~~~~-L~~l~l~~N~~~  116 (347)
T 2ifg_A           91 ALESLSWKTVQGLS-LQELVLSGNPLH  116 (347)
T ss_dssp             CCSCCCSTTTCSCC-CCEEECCSSCCC
T ss_pred             ccceeCHHHcccCC-ceEEEeeCCCcc
Confidence            8877 333 44444 888888888776

>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=98.54  E-value=9.6e-08  Score=108.05  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=23.8

Q ss_pred             CCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--c-ccccCCCCCcEEEcc
Q 004895          574 TEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--I-AIVGQLKKLEILSLR  628 (724)
Q Consensus       574 l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~-~~~~~l~~L~~L~l~  628 (724)
                      +++|+.|+++++....+|..+..+++|++|+|++|.+..  + ..+..+++|++|+++
T Consensus       269 ~~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~  326 (592)
T 3ogk_B          269 PRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCPNLEVLETR  326 (592)
T ss_dssp             CTTCCEEEETTCCTTTGGGGGGGGGGCCEEEETTCCCCHHHHHHHHTTCTTCCEEEEE
T ss_pred             cccccccCccccchhHHHHHHhhcCCCcEEecCCCcCCHHHHHHHHHhCcCCCEEecc
Confidence            334444444443333344444444555555555554333  1 223444444444444

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.54  E-value=1.8e-06  Score=87.58  Aligned_cols=184  Identities=20%  Similarity=0.188  Sum_probs=105.8

Q ss_pred             ccccccchHHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALKD-------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....++|.++.++.|.+.+..             ....-+.|+|++|+|||+||+.+++.....     .+.+..+.-..
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~-----~~~v~~~~~~~   89 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNAT-----FIRVVGSELVK   89 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCE-----EEEEEGGGGCC
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehHHHHH
Confidence            456788999999988877641             345678999999999999999999876321     33333322111


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc------------c-ccccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL------------E-LDKIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~------------~-~~~l~~~~~~~~~~~~  291 (724)
                                    .... . .......+.......++.+|+|||++...            . ...+...+..   ...
T Consensus        90 --------------~~~~-~-~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~---~~~  150 (285)
T 3h4m_A           90 --------------KFIG-E-GASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAE---MDG  150 (285)
T ss_dssp             --------------CSTT-H-HHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHH---HHT
T ss_pred             --------------hccc-h-HHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHH---hhC
Confidence                          0101 0 12233344444444567899999996531            0 0111000000   000


Q ss_pred             CCCCCCcEEEEEecccchhh-hhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC-chhHHH
Q 004895          292 NDDPRRCTIILTSRSRDLLC-IDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG-LPVALS  366 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~-~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G-lPLai~  366 (724)
                      .....+..||.||....... ...   .....+.++..+.++..++|+..+.......+  .....+++.+.| .|-.+.
T Consensus       151 ~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~--~~~~~l~~~~~g~~~~~i~  228 (285)
T 3h4m_A          151 FDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAED--VNLEEIAKMTEGCVGAELK  228 (285)
T ss_dssp             TCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHHCTTCCHHHHH
T ss_pred             CCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCc--CCHHHHHHHcCCCCHHHHH
Confidence            01234567788887554321 101   22347899999999999999988764322221  125677888877 444444


Q ss_pred             H
Q 004895          367 T  367 (724)
Q Consensus       367 ~  367 (724)
                      .
T Consensus       229 ~  229 (285)
T 3h4m_A          229 A  229 (285)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=98.52  E-value=3e-06  Score=87.68  Aligned_cols=184  Identities=16%  Similarity=0.113  Sum_probs=108.0

Q ss_pred             ccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          158 DYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ....|+|++..+..+..++.     ......+.|+|++|+|||++|+.+++....     ..++++.+......++.   
T Consensus        10 ~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~~~-----~~~~~~~~~~~~~~~l~---   81 (324)
T 1hqc_A           10 TLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGV-----NLRVTSGPAIEKPGDLA---   81 (324)
T ss_dssp             STTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHHTC-----CEEEECTTTCCSHHHHH---
T ss_pred             cHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEeccccCChHHHH---
Confidence            45678999999888887765     234467889999999999999999987632     23445443332222221   


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhc--CCcEEEEEcccccccc--ccccccccCC-----CCcCCCC-----CCCCCc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKK--EKRVLIILDNIWTKLE--LDKIGIPYGD-----VDEKDKN-----DDPRRC  298 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~--~kr~LlVlDdv~~~~~--~~~l~~~~~~-----~~~~~~~-----~~~~~s  298 (724)
                                            ..+..  .++.+|+|||+.....  ...+...+..     +......     ....+.
T Consensus        82 ----------------------~~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~  139 (324)
T 1hqc_A           82 ----------------------AILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF  139 (324)
T ss_dssp             ----------------------HHHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCC
T ss_pred             ----------------------HHHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCE
Confidence                                  11111  3457888999865421  1111000000     0000000     001235


Q ss_pred             EEEEEecccchh-hhhcCC-CceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHh
Q 004895          299 TIILTSRSRDLL-CIDMNS-QKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANAL  372 (724)
Q Consensus       299 ~ilvTtR~~~v~-~~~~~~-~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l  372 (724)
                      .+|.||...... ...... ...+.+.+++.+|..+++.+.+...... --++..+.|++.++|.|..+..+...+
T Consensus       140 ~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~-~~~~~~~~l~~~~~G~~r~l~~~l~~~  214 (324)
T 1hqc_A          140 TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR-ITEEAALEIGRRSRGTMRVAKRLFRRV  214 (324)
T ss_dssp             EEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCC-CCHHHHHHHHHHSCSCHHHHHHHHHHH
T ss_pred             EEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            566666644321 111112 2578999999999999999887532221 225678899999999998877665544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.52  E-value=2.4e-06  Score=91.96  Aligned_cols=179  Identities=17%  Similarity=0.203  Sum_probs=108.2

Q ss_pred             CcccccccchHHHH---HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHH
Q 004895          156 MKDYNIFNSRKKIF---QDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGE  231 (724)
Q Consensus       156 ~~~~~~~~gR~~~~---~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~  231 (724)
                      +.....++|.+..+   ..+...+..+..+.+.|+|++|+||||+|+.+++.....       ++.++.. ....++ +.
T Consensus        22 P~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~~~-------f~~l~a~~~~~~~i-r~   93 (447)
T 3pvs_A           22 PENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYANAD-------VERISAVTSGVKEI-RE   93 (447)
T ss_dssp             CCSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTTCE-------EEEEETTTCCHHHH-HH
T ss_pred             CCCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhCCC-------eEEEEeccCCHHHH-HH
Confidence            44566788999888   677777777777889999999999999999999876321       3333322 222222 11


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEE-Eecccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIIL-TSRSRD  308 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilv-TtR~~~  308 (724)
                      ++.                 ........+++.+|++|++....  ..+.+...+.          .....+|. ||.+..
T Consensus        94 ~~~-----------------~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le----------~~~v~lI~att~n~~  146 (447)
T 3pvs_A           94 AIE-----------------RARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIE----------DGTITFIGATTENPS  146 (447)
T ss_dssp             HHH-----------------HHHHHHHTTCCEEEEEETTTCC------CCHHHHH----------TTSCEEEEEESSCGG
T ss_pred             HHH-----------------HHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHh----------cCceEEEecCCCCcc
Confidence            111                 11111223578999999997652  2333322221          12234444 444432


Q ss_pred             --hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCC------CCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          309 --LLCIDMNSQKMFWIDALSEEEALQLFEKIVGEST------KASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       309 --v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~------~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                        +..........+.+.+++.++...++.+.+....      ...--++..+.|++.++|.+-.+..+.
T Consensus       147 ~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~L  215 (447)
T 3pvs_A          147 FELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNTL  215 (447)
T ss_dssp             GSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHHH
T ss_pred             cccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHHH
Confidence              1111233445889999999999999998874311      111124677889999999887654443

>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=98.50  E-value=4e-07  Score=89.84  Aligned_cols=176  Identities=14%  Similarity=0.158  Sum_probs=103.6

Q ss_pred             cccccch---HHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          159 YNIFNSR---KKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       159 ~~~~~gR---~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      ...|+|+   +..++.+..+......+.+.|+|++|+||||||+.+++.....  ...+.|++++...+.      +.+ 
T Consensus        27 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~--~~~~~~~~~~~~~~~------~~~-   97 (242)
T 3bos_A           27 FTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL--ERRSFYIPLGIHASI------STA-   97 (242)
T ss_dssp             TTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEEEGGGGGGS------CGG-
T ss_pred             hhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEHHHHHHH------HHH-
Confidence            3455652   3566666666655567789999999999999999999987653  234667766432110      000 


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----ccccccccCCCCcCCCCCCCCCcEEEEEecccch--
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL--  309 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v--  309 (724)
                                       ....+  .++.+||+||++....    .+.+...+...      ......++|+||+...-  
T Consensus        98 -----------------~~~~~--~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~------~~~~~~~ii~~~~~~~~~~  152 (242)
T 3bos_A           98 -----------------LLEGL--EQFDLICIDDVDAVAGHPLWEEAIFDLYNRV------AEQKRGSLIVSASASPMEA  152 (242)
T ss_dssp             -----------------GGTTG--GGSSEEEEETGGGGTTCHHHHHHHHHHHHHH------HHHCSCEEEEEESSCTTTT
T ss_pred             -----------------HHHhc--cCCCEEEEeccccccCCHHHHHHHHHHHHHH------HHcCCCeEEEEcCCCHHHH
Confidence                             00111  2457999999976522    11221111000      01112247777774431  


Q ss_pred             ----hhh--hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          310 ----LCI--DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       310 ----~~~--~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                          ...  .......+.+++++.++..+++.+.+..... .--++..+.|++.++|.+-.+..+.
T Consensus       153 ~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~-~~~~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          153 GFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGL-QLPEDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             TCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTC-CCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHccCCHHHHHHHH
Confidence                000  0111268999999999999999988742211 1225678889999999887665443

>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=98.49  E-value=4.8e-06  Score=83.81  Aligned_cols=199  Identities=17%  Similarity=0.131  Sum_probs=103.7

Q ss_pred             cccchHHHHHHHHH-------Hhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          161 IFNSRKKIFQDVIE-------ALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       161 ~~~gR~~~~~~l~~-------~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      .++|....++++++       .+.   ......+.|+|++|+|||++|+.+++....    . .+.++.+...       
T Consensus        34 ~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~----~-~~~i~~~~~~-------  101 (272)
T 1d2n_A           34 GIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNF----P-FIKICSPDKM-------  101 (272)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTC----S-EEEEECGGGC-------
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCC----C-EEEEeCHHHh-------
Confidence            34565555444444       232   345678899999999999999999997532    1 2233332210       


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------------ccccccccCCCCcCCCCCCCCCc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------------LDKIGIPYGDVDEKDKNDDPRRC  298 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------------~~~l~~~~~~~~~~~~~~~~~~s  298 (724)
                           .+.   ...........+.......++.+|+|||++....            ++.+...+..     ........
T Consensus       102 -----~g~---~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~-----~~~~~~~~  168 (272)
T 1d2n_A          102 -----IGF---SETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKK-----APPQGRKL  168 (272)
T ss_dssp             -----TTC---CHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTC-----CCSTTCEE
T ss_pred             -----cCC---chHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcC-----ccCCCCCE
Confidence                 110   0000111222333333335689999999965310            1111111110     00012234


Q ss_pred             EEEEEecccchhhh---hcCCCceEecCCCCH-HHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC------chhHHHHH
Q 004895          299 TIILTSRSRDLLCI---DMNSQKMFWIDALSE-EEALQLFEKIVGESTKASDFRPLAEEIVGKCGG------LPVALSTV  368 (724)
Q Consensus       299 ~ilvTtR~~~v~~~---~~~~~~~~~l~~L~~-~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G------lPLai~~~  368 (724)
                      .||.||........   ...-...+.+++++. ++...++.+...      --.+....|++.+.|      .+-++.++
T Consensus       169 ~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~~~------~~~~~~~~l~~~~~g~~~~g~ir~l~~~l  242 (272)
T 1d2n_A          169 LIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLGN------FKDKERTTIAQQVKGKKVWIGIKKLLMLI  242 (272)
T ss_dssp             EEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHHTC------SCHHHHHHHHHHHTTSEEEECHHHHHHHH
T ss_pred             EEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHhcCC------CCHHHHHHHHHHhcCCCccccHHHHHHHH
Confidence            46666766533211   111245788999988 666666665321      114567889999988      34444444


Q ss_pred             HHHhcCCCHHHHHHHHHHHhcC
Q 004895          369 ANALKNKSPAIWKDALNKLTSS  390 (724)
Q Consensus       369 ~~~l~~~~~~~w~~~~~~l~~~  390 (724)
                      -..........+..+++.+...
T Consensus       243 ~~a~~~~~~~~~~~~~~~l~~~  264 (272)
T 1d2n_A          243 EMSLQMDPEYRVRKFLALLREE  264 (272)
T ss_dssp             HHHTTSCGGGHHHHHHHHHHHT
T ss_pred             HHHhhhchHHHHHHHHHHHHHc
Confidence            3333333556677777665543

>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=98.47  E-value=4e-07  Score=94.68  Aligned_cols=167  Identities=13%  Similarity=0.114  Sum_probs=119.4

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcC-------C--------
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRF-------S--------  588 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~-------~--------  588 (724)
                      ..+++.+.+.. .+..++..  ..|++|+.|.+  ..+....+++..|.++..+..+.+.....       .        
T Consensus       100 ~~~L~~l~L~~-~i~~I~~~aF~~~~~L~~l~l--~~n~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~  176 (329)
T 3sb4_A          100 KQTLEKVILSE-KIKNIEDAAFKGCDNLKICQI--RKKTAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGE  176 (329)
T ss_dssp             CTTCCC-CBCT-TCCEECTTTTTTCTTCCEEEB--CCSSCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESC
T ss_pred             cCCCcEEECCc-cccchhHHHhhcCcccceEEc--CCCCccccchhhhcCCCceEEecCcchhhhhcccccccccccccc
Confidence            35777888876 77777643  37899999998  34444567777777777777776654211       0        


Q ss_pred             ------------CCCc----------cc------------------cCCCCCcEEEcCCcccCCc--ccccCCCCCcEEE
Q 004895          589 ------------PLPS----------SL------------------GRLINLQTLCLDGWRLEDI--AIVGQLKKLEILS  626 (724)
Q Consensus       589 ------------~lp~----------~i------------------~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~  626 (724)
                                  .+|.          .+                  ..+.+|++|+|++|.++.+  ..|.++.+|+.|+
T Consensus       177 ~L~~~i~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~l~~~~~~L~~l~L~~n~i~~I~~~aF~~~~~L~~l~  256 (329)
T 3sb4_A          177 PLETTIQVGAMGKLEDEIMKAGLQPRDINFLTIEGKLDNADFKLIRDYMPNLVSLDISKTNATTIPDFTFAQKKYLLKIK  256 (329)
T ss_dssp             CCEEEEEECTTCCHHHHHHHTTCCGGGCSEEEEEECCCHHHHHHHHHHCTTCCEEECTTBCCCEECTTTTTTCTTCCEEE
T ss_pred             ccceeEEecCCCcHHHHHhhcccCccccceEEEeeeecHHHHHHHHHhcCCCeEEECCCCCcceecHhhhhCCCCCCEEE
Confidence                        0000          00                  1378999999999998884  5699999999999


Q ss_pred             ccCCcCcccchh-hhcCCCCC-eEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcE
Q 004895          627 LRGAEIKQLPLQ-IGQLTRLQ-LLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTT  704 (724)
Q Consensus       627 l~~~~i~~lp~~-i~~l~~L~-~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~  704 (724)
                      +..| ++.++.. +..+++|+ .+.+.+  .+..+++..+..|++|+.|++.++..     .....   ..+.++++|+.
T Consensus       257 l~~n-i~~I~~~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~L~~l~l~~n~i-----~~I~~---~aF~~~~~L~~  325 (329)
T 3sb4_A          257 LPHN-LKTIGQRVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDNLRYVLATGDKI-----TTLGD---ELFGNGVPSKL  325 (329)
T ss_dssp             CCTT-CCEECTTTTTTCTTCCEEEEECT--TCCEECTTTTTTCTTEEEEEECSSCC-----CEECT---TTTCTTCCCCE
T ss_pred             CCcc-cceehHHHhhCChhccEEEEEcc--cceEEchhhhhCCccCCEEEeCCCcc-----Cccch---hhhcCCcchhh
Confidence            9997 8888765 88999999 999987  67888888899999999999976532     21111   24566777877


Q ss_pred             EE
Q 004895          705 LE  706 (724)
Q Consensus       705 L~  706 (724)
                      +.
T Consensus       326 ly  327 (329)
T 3sb4_A          326 IY  327 (329)
T ss_dssp             EE
T ss_pred             hc
Confidence            65

>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=98.44  E-value=1.3e-06  Score=96.45  Aligned_cols=194  Identities=11%  Similarity=0.076  Sum_probs=110.7

Q ss_pred             CcccccccchHHHHHHHHHHhcC-----------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD-----------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~-----------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      |.....++|+++.++.+.+++..                 +..+.+.|+|++|+||||+|+.+++...    + .++.++
T Consensus        35 P~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~----~-~~i~in  109 (516)
T 1sxj_A           35 PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG----Y-DILEQN  109 (516)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTT----C-EEEEEC
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcC----C-CEEEEe
Confidence            45567789999999999999863                 1347899999999999999999998772    1 244555


Q ss_pred             EecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-----ccccccccCCCCcCCCCC
Q 004895          219 ITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       219 vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~~  293 (724)
                      ++...... +....+........-.........   .....+++.+||+|+++....     +..+...+          
T Consensus       110 ~s~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~---~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l----------  175 (516)
T 1sxj_A          110 ASDVRSKT-LLNAGVKNALDNMSVVGYFKHNEE---AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFC----------  175 (516)
T ss_dssp             TTSCCCHH-HHHHTGGGGTTBCCSTTTTTC-------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHH----------
T ss_pred             CCCcchHH-HHHHHHHHHhccccHHHHHhhhhh---hhhccCCCeEEEEECCCccchhhHHHHHHHHHHH----------
Confidence            55544433 223322222111000000000000   001125679999999976532     12221111          


Q ss_pred             CCCCcEEEEEecccch--hhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch-hHHHHHH
Q 004895          294 DPRRCTIILTSRSRDL--LCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP-VALSTVA  369 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~v--~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~~~  369 (724)
                      ...+..||+++.....  ..........+.+++++.++..+++.+.+......- -++....|++.++|.+ -++..+.
T Consensus       176 ~~~~~~iIli~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i-~~~~l~~la~~s~GdiR~~i~~L~  253 (516)
T 1sxj_A          176 RKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKL-DPNVIDRLIQTTRGDIRQVINLLS  253 (516)
T ss_dssp             HHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCC-CTTHHHHHHHHTTTCHHHHHHHHT
T ss_pred             HhcCCCEEEEEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHcCCcHHHHHHHHH
Confidence            1123335555544321  111123345789999999999999988764221111 1346788999999954 4555543

>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=98.42  E-value=1.1e-05  Score=84.69  Aligned_cols=187  Identities=12%  Similarity=0.098  Sum_probs=106.5

Q ss_pred             ccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          158 DYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ....++|.+..++.|.+.+.            ....+.+.|+|++|+|||+||+.+++....     ..+.++++.-.. 
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~-----~~~~i~~~~l~~-  155 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQSGA-----TFFSISASSLTS-  155 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHTTC-----EEEEEEGGGGCC-
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHcCC-----eEEEEehHHhhc-
Confidence            34568899999888887763            134568899999999999999999886532     234455442211 


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~  292 (724)
                                   .... . .......+.......++.+|+||+++....             ...+...+...    ..
T Consensus       156 -------------~~~g-~-~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~----~~  216 (357)
T 3d8b_A          156 -------------KWVG-E-GEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGA----TT  216 (357)
T ss_dssp             -------------SSTT-H-HHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC-------
T ss_pred             -------------cccc-h-HHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcc----cc
Confidence                         0000 0 122233344444445679999999954311             11111111000    00


Q ss_pred             CCCCCcEEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC-chhHHHHHH
Q 004895          293 DDPRRCTIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG-LPVALSTVA  369 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G-lPLai~~~~  369 (724)
                      ....+..||.||......  .........+.+...+.++..+++...+...... --.+....|++.+.| .|-.|..+.
T Consensus       217 ~~~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~-l~~~~l~~la~~t~G~s~~dl~~l~  295 (357)
T 3d8b_A          217 SSEDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCC-LSEEEIEQIVQQSDAFSGADMTQLC  295 (357)
T ss_dssp             -CCCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC-CCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             cCCCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC-ccHHHHHHHHHHcCCCCHHHHHHHH
Confidence            012345566666543221  1111223467888999999999998877432211 124567889999988 455555554


Q ss_pred             H
Q 004895          370 N  370 (724)
Q Consensus       370 ~  370 (724)
                      .
T Consensus       296 ~  296 (357)
T 3d8b_A          296 R  296 (357)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.42  E-value=9.5e-06  Score=81.04  Aligned_cols=178  Identities=13%  Similarity=0.134  Sum_probs=97.0

Q ss_pred             cccccchHHHHHHHHHHhc---C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          159 YNIFNSRKKIFQDVIEALK---D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ...++|.+..++.+.+.+.   .         ...+-+.|+|++|+|||++|+.+++....     ..+.++.+.-.+. 
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~-----~~~~~~~~~~~~~-   78 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQV-----PFLAMAGAEFVEV-   78 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTC-----CEEEEETTTTSSS-
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCC-----CEEEechHHHHhh-
Confidence            4557788877776655432   1         23456889999999999999999987642     1334444322110 


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc-------------cc----cccccccCCCCcC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL-------------EL----DKIGIPYGDVDEK  289 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~-------------~~----~~l~~~~~~~~~~  289 (724)
                                   .. .. .......+........+.+|+|||++...             ..    ..+...+..    
T Consensus        79 -------------~~-~~-~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~----  139 (262)
T 2qz4_A           79 -------------IG-GL-GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDG----  139 (262)
T ss_dssp             -------------ST-TH-HHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHT----
T ss_pred             -------------cc-Ch-hHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhC----
Confidence                         00 00 12223334444444567999999997541             00    111111100    


Q ss_pred             CCCCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          290 DKNDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       290 ~~~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                        .....+..||.||......... .   .....+.++..+.++-.+++...+...............+++.+.|.+-
T Consensus       140 --~~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~  215 (262)
T 2qz4_A          140 --MGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSG  215 (262)
T ss_dssp             --CCTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCH
T ss_pred             --cCCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCH
Confidence              0122355677777554321111 1   2235778999999999999998775322222212234678888887654

>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=98.40  E-value=1.7e-06  Score=90.78  Aligned_cols=200  Identities=11%  Similarity=0.106  Sum_probs=108.5

Q ss_pred             CcccccccchHHHHHHHHHHh-cCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCe-----------------
Q 004895          156 MKDYNIFNSRKKIFQDVIEAL-KDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDK-----------------  213 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L-~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~-----------------  213 (724)
                      |.....++|++..++.+..++ ..++.+.+.|+|+.|+||||+|+.++........    ++.                 
T Consensus        10 P~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~   89 (354)
T 1sxj_E           10 PKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVS   89 (354)
T ss_dssp             CCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEE
T ss_pred             CCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeecccccccceeeeec
Confidence            344567889999999999888 6555444899999999999999999986421110    000                 


Q ss_pred             ---EEEEEEecCC-ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCC
Q 004895          214 ---VVMAEITKNP-DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVD  287 (724)
Q Consensus       214 ---~~wv~vs~~~-~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~  287 (724)
                         .+.+..+... ......++++..+.....-..    .. .+ ..+. .++-++|||++...+.  .+.+...+..  
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~----~~-~l-s~l~-~~~~vlilDE~~~L~~~~~~~L~~~le~--  160 (354)
T 1sxj_E           90 SPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDF----QD-SK-DGLA-HRYKCVIINEANSLTKDAQAALRRTMEK--  160 (354)
T ss_dssp             CSSEEEECCC----CCHHHHHHHHHHHTTTTC-------------------CCEEEEEECTTSSCHHHHHHHHHHHHH--
T ss_pred             ccceEEecHhhcCCcchHHHHHHHHHHHHhccccc----cc-cc-cccC-CCCeEEEEeCccccCHHHHHHHHHHHHh--
Confidence               1111111100 000012223332211110000    00 00 0011 3567999999976421  1222222211  


Q ss_pred             cCCCCCCCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHH
Q 004895          288 EKDKNDDPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       288 ~~~~~~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~  366 (724)
                            ...++.+|++|.... +...-......+++.+++.++..+.+.+.+......-+-++....|++.++|.+..+.
T Consensus       161 ------~~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~i~~~~~G~~r~a~  234 (354)
T 1sxj_E          161 ------YSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSL  234 (354)
T ss_dssp             ------STTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHHHH
T ss_pred             ------hcCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCCHHHHH
Confidence                  223567777776543 2222223447899999999999999998774221110003567889999999987665


Q ss_pred             HHHH
Q 004895          367 TVAN  370 (724)
Q Consensus       367 ~~~~  370 (724)
                      .+..
T Consensus       235 ~~l~  238 (354)
T 1sxj_E          235 LMLE  238 (354)
T ss_dssp             HHHT
T ss_pred             HHHH
Confidence            4443

>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=98.40  E-value=1.8e-07  Score=105.81  Aligned_cols=129  Identities=20%  Similarity=0.202  Sum_probs=91.0

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCC-cCCC--CCccccCCCCCcEEEcCCcccCC--cccc----c
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGI-RFSP--LPSSLGRLINLQTLCLDGWRLED--IAIV----G  617 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~~~~--lp~~i~~l~~L~~L~L~~~~l~~--~~~~----~  617 (724)
                      .+++|+.|.+..+. -....+..+...+++|+.|++++| .+..  ++..+.++++|++|+|++|.++.  +..+    .
T Consensus       103 ~~~~L~~L~L~~~~-~~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~  181 (594)
T 2p1m_B          103 SYTWLEEIRLKRMV-VTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPD  181 (594)
T ss_dssp             HCTTCCEEEEESCB-CCHHHHHHHHHHCTTCCEEEEESCEEEEHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCT
T ss_pred             hCCCCCeEEeeCcE-EcHHHHHHHHHhCCCCcEEeCCCcCCCCHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhh
Confidence            57899999994332 222223333336899999999999 5553  55555689999999999998765  2223    3


Q ss_pred             CCCCCcEEEccCCc--Cc--ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          618 QLKKLEILSLRGAE--IK--QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       618 ~l~~L~~L~l~~~~--i~--~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      .+++|++|++++|.  ++  .++.-+.++++|++|++++|..+..+ +..+..+++|++|++..
T Consensus       182 ~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l-~~~~~~~~~L~~L~l~~  244 (594)
T 2p1m_B          182 TYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKL-ATLLQRAPQLEELGTGG  244 (594)
T ss_dssp             TCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHH-HHHHHHCTTCSEEECSB
T ss_pred             cCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHH-HHHHhcCCcceEccccc
Confidence            67799999999986  33  33444567899999999998665554 34567777777777544

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.40  E-value=2.1e-05  Score=81.11  Aligned_cols=188  Identities=15%  Similarity=0.136  Sum_probs=106.6

Q ss_pred             cccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....+.|.++.++.|.+.+.            ....+-+.|+|++|+|||+||+.+++....    ...+.++.+.-.+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~----~~~~~i~~~~l~~   84 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANN----STFFSISSSDLVS   84 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHTTS----CEEEEEECCSSCC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHcCC----CcEEEEEhHHHHh
Confidence            345667788888777776552            123467899999999999999999987621    1123333332111


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc-------------cccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL-------------DKIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~-------------~~l~~~~~~~~~~~~  291 (724)
                                    .....  .......+.......++.+|+||+++....-             ..+...+..+     
T Consensus        85 --------------~~~g~--~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~-----  143 (322)
T 1xwi_A           85 --------------KWLGE--SEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGV-----  143 (322)
T ss_dssp             --------------SSCCS--CHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCS-----
T ss_pred             --------------hhhhH--HHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcc-----
Confidence                          11111  1233444555444467899999999754110             0110001000     


Q ss_pred             CCCCCCcEEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHHH
Q 004895          292 NDDPRRCTIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALSTV  368 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~~  368 (724)
                      .....+..||.||......  .........+.++..+.++-.+++...+....... -......|++.+.|+ +-.|..+
T Consensus       144 ~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l  222 (322)
T 1xwi_A          144 GVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSL-TEADFRELGRKTDGYSGADISII  222 (322)
T ss_dssp             SSCCTTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCC-CHHHHHHHHHTCTTCCHHHHHHH
T ss_pred             cccCCCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHH
Confidence            0023445566666544321  11112335788888999999999998875332111 245678899999887 4445554


Q ss_pred             HH
Q 004895          369 AN  370 (724)
Q Consensus       369 ~~  370 (724)
                      ..
T Consensus       223 ~~  224 (322)
T 1xwi_A          223 VR  224 (322)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=98.37  E-value=1.1e-05  Score=83.19  Aligned_cols=187  Identities=15%  Similarity=0.148  Sum_probs=108.7

Q ss_pred             CcccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      ......++|.++.++.|.+.+.            ....+-+.|+|++|+|||+||+.+++.....     .+.++.+   
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~~~~-----~~~v~~~---   85 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSS---   85 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHHTCE-----EEEEEHH---
T ss_pred             CCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHHCCC-----EEEEchH---
Confidence            3446678899999998888762            1124578999999999999999999876321     2333322   


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKD  290 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~  290 (724)
                         ++    ...    ....  .......+.......++.+|+||++.....             ...+...+...    
T Consensus        86 ---~l----~~~----~~g~--~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~----  148 (322)
T 3eie_A           86 ---DL----VSK----WMGE--SEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGV----  148 (322)
T ss_dssp             ---HH----HTT----TGGG--HHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGG----
T ss_pred             ---HH----hhc----ccch--HHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccc----
Confidence               11    110    0001  223344455555556779999999975421             11111111000    


Q ss_pred             CCCCCCCcEEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHH
Q 004895          291 KNDDPRRCTIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALST  367 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~  367 (724)
                       .....+..||.||......  .........+.++..+.++-.++|+..+......- -......|++.+.|. +-.|..
T Consensus       149 -~~~~~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~-~~~~l~~la~~t~g~sg~di~~  226 (322)
T 3eie_A          149 -GNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVL-TKEDYRTLGAMTEGYSGSDIAV  226 (322)
T ss_dssp             -GTSCCCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCC-CHHHHHHHHHTTTTCCHHHHHH
T ss_pred             -cccCCceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCC-CHHHHHHHHHHcCCCCHHHHHH
Confidence             0023455666677654321  11112235678888999999999999876432211 245678899998874 444444


Q ss_pred             HH
Q 004895          368 VA  369 (724)
Q Consensus       368 ~~  369 (724)
                      +.
T Consensus       227 l~  228 (322)
T 3eie_A          227 VV  228 (322)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=98.34  E-value=4.6e-06  Score=86.97  Aligned_cols=182  Identities=12%  Similarity=0.122  Sum_probs=105.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-eEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-KVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.+..++.|..++..++.+.+.++|+.|+||||+|+.+++..... .+. .+..++.+...+...+. +++.
T Consensus        21 p~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~-~~~~~~~~~~~~~~~~~~~ir-~~i~   98 (340)
T 1sxj_C           21 PETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGK-NYSNMVLELNASDDRGIDVVR-NQIK   98 (340)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTT-SHHHHEEEECTTSCCSHHHHH-THHH
T ss_pred             CCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCC-CccceEEEEcCcccccHHHHH-HHHH
Confidence            44456678999999998888877766558999999999999999999986432 111 12333333222222211 1111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHH--hcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-h
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRL--KKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-L  309 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l--~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v  309 (724)
                      .+                 .+..  ..+.+-++|+|++....  ..+.+...+..        ....+.+|++|.... +
T Consensus        99 ~~-----------------~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~--------~~~~~~~il~~n~~~~i  153 (340)
T 1sxj_C           99 DF-----------------ASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIER--------YTKNTRFCVLANYAHKL  153 (340)
T ss_dssp             HH-----------------HHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGS
T ss_pred             HH-----------------HhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhc--------CCCCeEEEEEecCcccc
Confidence            11                 0000  01246799999996542  22222211111        223456666665432 2


Q ss_pred             hhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          310 LCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       310 ~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ...-......+.+.+++.++..+.+.+.+...... --++..+.|++.++|.+--+
T Consensus       154 ~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~-i~~~~~~~i~~~s~G~~r~~  208 (340)
T 1sxj_C          154 TPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLK-LSPNAEKALIELSNGDMRRV  208 (340)
T ss_dssp             CHHHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCC-BCHHHHHHHHHHHTTCHHHH
T ss_pred             chhHHhhceeEeccCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHH
Confidence            11112334578999999999999888876322111 11456788999999988643

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.34  E-value=3.4e-06  Score=89.84  Aligned_cols=178  Identities=11%  Similarity=0.142  Sum_probs=116.9

Q ss_pred             ccCceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCcc-ccCCCCCcEE
Q 004895          526 QKGPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSS-LGRLINLQTL  603 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~-i~~l~~L~~L  603 (724)
                      ..+++.+.+..|.+..++... .+.+|+++.+.   .....+....|.++++|+.+++..+ +..++.. +.+ .+|+.+
T Consensus       179 c~~L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp---~~l~~I~~~aF~~~~~L~~l~l~~~-l~~I~~~aF~~-~~L~~i  253 (401)
T 4fdw_A          179 CYNLKKADLSKTKITKLPASTFVYAGIEEVLLP---VTLKEIGSQAFLKTSQLKTIEIPEN-VSTIGQEAFRE-SGITTV  253 (401)
T ss_dssp             CTTCCEEECTTSCCSEECTTTTTTCCCSEEECC---TTCCEECTTTTTTCTTCCCEECCTT-CCEECTTTTTT-CCCSEE
T ss_pred             cccCCeeecCCCcceEechhhEeecccCEEEeC---CchheehhhHhhCCCCCCEEecCCC-ccCcccccccc-CCccEE
Confidence            456778888777777765432 56788888772   2355677777888888888888764 4555443 333 677888


Q ss_pred             EcCCcccCC--cccccCCCCCcEEEccCCcCc-----ccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEc
Q 004895          604 CLDGWRLED--IAIVGQLKKLEILSLRGAEIK-----QLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYM  675 (724)
Q Consensus       604 ~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-----~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l  675 (724)
                      .+.. .++.  ...|.++.+|+.+++.++.+.     .++. .+..+++|+.+.+..  .+..++...+..|++|+.+.+
T Consensus       254 ~lp~-~i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~~--~i~~I~~~aF~~c~~L~~l~l  330 (401)
T 4fdw_A          254 KLPN-GVTNIASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIPE--SIRILGQGLLGGNRKVTQLTI  330 (401)
T ss_dssp             EEET-TCCEECTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCCT--TCCEECTTTTTTCCSCCEEEE
T ss_pred             EeCC-CccEEChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeCC--ceEEEhhhhhcCCCCccEEEE
Confidence            7743 3444  256778888888888776554     4543 477788888888874  467777777788888888887


Q ss_pred             cCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccccccccc
Q 004895          676 GDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSL  721 (724)
Q Consensus       676 ~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~~  721 (724)
                      ..+      +...   .-..+.++ +|+.+.+..|....++...|.
T Consensus       331 p~~------l~~I---~~~aF~~~-~L~~l~l~~n~~~~l~~~~F~  366 (401)
T 4fdw_A          331 PAN------VTQI---NFSAFNNT-GIKEVKVEGTTPPQVFEKVWY  366 (401)
T ss_dssp             CTT------CCEE---CTTSSSSS-CCCEEEECCSSCCBCCCSSCC
T ss_pred             Ccc------ccEE---cHHhCCCC-CCCEEEEcCCCCccccccccc
Confidence            553      1111   11234556 778888877776666555443

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.33  E-value=5.4e-06  Score=86.40  Aligned_cols=184  Identities=14%  Similarity=0.141  Sum_probs=105.3

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      +.....++|++..++.+..++.     ......+.|+|++|+|||++|+.+++....     ..+.++.+......++  
T Consensus        25 p~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~~~-----~~~~~~~~~~~~~~~~--   97 (338)
T 3pfi_A           25 PSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEMSA-----NIKTTAAPMIEKSGDL--   97 (338)
T ss_dssp             CCSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHTTC-----CEEEEEGGGCCSHHHH--
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHhCC-----CeEEecchhccchhHH--
Confidence            3456778999999998888875     234457899999999999999999876532     1233433322211111  


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCc----------CCCCCCCCCc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDE----------KDKNDDPRRC  298 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~----------~~~~~~~~~s  298 (724)
                                          ......  ..+..+|+||++....  ....+...+.....          .......++.
T Consensus        98 --------------------~~~~~~--~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~  155 (338)
T 3pfi_A           98 --------------------AAILTN--LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKF  155 (338)
T ss_dssp             --------------------HHHHHT--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCC
T ss_pred             --------------------HHHHHh--ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCe
Confidence                                111111  1356789999987642  11111111000000          0000011235


Q ss_pred             EEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHH
Q 004895          299 TIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVA  369 (724)
Q Consensus       299 ~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~  369 (724)
                      .+|.+|......  .........+.+.+++.++...++.+.+...... --.+..+.|++.+.|.|-.+..+.
T Consensus       156 ~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~-~~~~~~~~l~~~~~G~~r~l~~~l  227 (338)
T 3pfi_A          156 TLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKT-CEEKAALEIAKRSRSTPRIALRLL  227 (338)
T ss_dssp             EEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCE-ECHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             EEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHHCcCHHHHHHHH
Confidence            566666553321  1111223689999999999999999887532211 124677889999999996554433

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.32  E-value=9.1e-06  Score=85.73  Aligned_cols=196  Identities=10%  Similarity=0.090  Sum_probs=102.5

Q ss_pred             cccccchHHHHHH---HHHHhcCCCc--cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec----CCChHHHH
Q 004895          159 YNIFNSRKKIFQD---VIEALKDDKL--NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK----NPDAQKIQ  229 (724)
Q Consensus       159 ~~~~~gR~~~~~~---l~~~L~~~~~--~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~~~~l~  229 (724)
                      ...|+|++..+..   +.+.+..+..  +.+.|+|++|+|||++|+.+++.......   .+.+....    .....+.+
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~---~~~~~~~~~~~~~~~~~~~~  119 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTP---FTAIAGSEIFSLEMSKTEAL  119 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCC---EEEEEGGGGSCSSSCHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCC---cccccchhhhhcccchhHHH
Confidence            5678999988666   4444444433  58999999999999999999998753211   22222221    22333333


Q ss_pred             HHHHHh-hCCC---------------------------CCC-----CchhHHHHHHHHHH-HhcCC----cEEEEEcccc
Q 004895          230 GELASD-LGMN---------------------------FDS-----NDLIYHRAKQLCQR-LKKEK----RVLIILDNIW  271 (724)
Q Consensus       230 ~~i~~~-l~~~---------------------------~~~-----~~~~~~~~~~l~~~-l~~~k----r~LlVlDdv~  271 (724)
                      ...... ++..                           ...     .............. ...++    +.+|+||++.
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi~  199 (368)
T 3uk6_A          120 TQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVH  199 (368)
T ss_dssp             HHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESGG
T ss_pred             HHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhcc
Confidence            333322 1100                           000     00011111111111 11233    3599999997


Q ss_pred             ccc--cccccccccCCCCcCCCCCCCCCcEEEEEecc-------------cchhhhhcCCCceEecCCCCHHHHHHHHHH
Q 004895          272 TKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS-------------RDLLCIDMNSQKMFWIDALSEEEALQLFEK  336 (724)
Q Consensus       272 ~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~-------------~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~  336 (724)
                      ...  ..+.+...+..        .... .++++|..             ..+..........+.+++++.++..+++.+
T Consensus       200 ~l~~~~~~~L~~~le~--------~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~  270 (368)
T 3uk6_A          200 MLDIESFSFLNRALES--------DMAP-VLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRI  270 (368)
T ss_dssp             GSBHHHHHHHHHHTTC--------TTCC-EEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHH
T ss_pred             ccChHHHHHHHHHhhC--------cCCC-eeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHH
Confidence            652  12222222211        1112 34444431             111111122334689999999999999998


Q ss_pred             HhCCCCCCCCchhHHHHHHHHhC-CchhHHHH
Q 004895          337 IVGESTKASDFRPLAEEIVGKCG-GLPVALST  367 (724)
Q Consensus       337 ~~~~~~~~~~l~~~~~~I~~~c~-GlPLai~~  367 (724)
                      .+...... --.+....|++.+. |.|..+..
T Consensus       271 ~~~~~~~~-~~~~~l~~l~~~~~~G~~r~~~~  301 (368)
T 3uk6_A          271 RCEEEDVE-MSEDAYTVLTRIGLETSLRYAIQ  301 (368)
T ss_dssp             HHHHTTCC-BCHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHcCCC-CCHHHHHHHHHHhcCCCHHHHHH
Confidence            87532211 12467788999987 77765543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.30  E-value=2.4e-06  Score=87.82  Aligned_cols=154  Identities=13%  Similarity=0.154  Sum_probs=86.2

Q ss_pred             cccchHHHHHHHHHHhc---------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          161 IFNSRKKIFQDVIEALK---------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~---------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      .++|.+..++.+.+.+.               ......+.|+|++|+|||++|+.+++...........-++.++.    
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~----  107 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTR----  107 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECG----
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcH----
Confidence            46788887777765543               23345789999999999999999999876533222222333321    


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc-----------ccccccccccCCCCcCCCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK-----------LELDKIGIPYGDVDEKDKNDD  294 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~-----------~~~~~l~~~~~~~~~~~~~~~  294 (724)
                      .+        +.......  .......+...   .+..+|+||+++..           .....+...+..        .
T Consensus       108 ~~--------l~~~~~g~--~~~~~~~~~~~---~~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~--------~  166 (309)
T 3syl_A          108 DD--------LVGQYIGH--TAPKTKEVLKR---AMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMEN--------N  166 (309)
T ss_dssp             GG--------TCCSSTTC--HHHHHHHHHHH---HTTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHH--------C
T ss_pred             HH--------hhhhcccc--cHHHHHHHHHh---cCCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhc--------C
Confidence            11        11111111  11112222222   23469999999743           111222222222        3


Q ss_pred             CCCcEEEEEecccchh-------hhhcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          295 PRRCTIILTSRSRDLL-------CIDMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       295 ~~~s~ilvTtR~~~v~-------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                      ..+..||+||......       .........+.+++++.++..+++.+.+.
T Consensus       167 ~~~~~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          167 RDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             TTTCEEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHH
Confidence            3456777777543210       01011226889999999999999988764

>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=98.30  E-value=3.3e-06  Score=87.47  Aligned_cols=178  Identities=12%  Similarity=0.078  Sum_probs=102.9

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|+++.++.+..++..+.. .++.+.|++|+|||++|+.+++....     .++.++.+.. ....+ +..+.
T Consensus        22 P~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~-----~~~~i~~~~~-~~~~i-~~~~~   94 (324)
T 3u61_B           22 PSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNA-----DMMFVNGSDC-KIDFV-RGPLT   94 (324)
T ss_dssp             CCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTE-----EEEEEETTTC-CHHHH-HTHHH
T ss_pred             CCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCC-----CEEEEccccc-CHHHH-HHHHH
Confidence            44567789999999999999875543 57788888999999999999887632     2445554332 22221 11111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHH-hcCCcEEEEEccccccc---cccccccccCCCCcCCCCCCCCCcEEEEEecccchh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRL-KKEKRVLIILDNIWTKL---ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL  310 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l-~~~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~  310 (724)
                      ..                 .... ..+++.++++||+....   ..+.+...+..        ...++.+|+||....-.
T Consensus        95 ~~-----------------~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~--------~~~~~~iI~~~n~~~~l  149 (324)
T 3u61_B           95 NF-----------------ASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEA--------YSSNCSIIITANNIDGI  149 (324)
T ss_dssp             HH-----------------HHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHH--------HGGGCEEEEEESSGGGS
T ss_pred             HH-----------------HhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHh--------CCCCcEEEEEeCCcccc
Confidence            11                 0000 01367899999997653   22222221111        12356777777664321


Q ss_pred             -hhhcCCCceEecCCCCHHHHHHHHHH-------HhCCCCCCCCch-hHHHHHHHHhCCchhHHH
Q 004895          311 -CIDMNSQKMFWIDALSEEEALQLFEK-------IVGESTKASDFR-PLAEEIVGKCGGLPVALS  366 (724)
Q Consensus       311 -~~~~~~~~~~~l~~L~~~e~~~Lf~~-------~~~~~~~~~~l~-~~~~~I~~~c~GlPLai~  366 (724)
                       ..-......+.+++++.++-.+++..       .+......- -+ +....|++.++|.+..+.
T Consensus       150 ~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~-~~~~~~~~l~~~~~gd~R~a~  213 (324)
T 3u61_B          150 IKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAI-ADMKVVAALVKKNFPDFRKTI  213 (324)
T ss_dssp             CTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCB-SCHHHHHHHHHHTCSCTTHHH
T ss_pred             CHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCC-CcHHHHHHHHHhCCCCHHHHH
Confidence             11111235789999998885444332       222111111 13 678889999988876543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.29  E-value=3.7e-05  Score=81.63  Aligned_cols=187  Identities=14%  Similarity=0.123  Sum_probs=104.7

Q ss_pred             CcccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      +.....++|.+..++.|.+.+.            ....+-+.|+|++|+|||+||+.+++....     ..+.++++.-.
T Consensus       111 ~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~~~-----~~~~v~~~~l~  185 (389)
T 3vfd_A          111 AVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNA-----TFFNISAASLT  185 (389)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEECSCCC-
T ss_pred             CCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhhcC-----cEEEeeHHHhh
Confidence            4456778999999999988773            123468899999999999999999876532     13344433221


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKD  290 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~  290 (724)
                      +  ..            ...  .......+........+.+|+||+++....             ...+...+...    
T Consensus       186 ~--~~------------~g~--~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~----  245 (389)
T 3vfd_A          186 S--KY------------VGE--GEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGV----  245 (389)
T ss_dssp             ----------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHH----
T ss_pred             c--cc------------cch--HHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcc----
Confidence            1  00            000  112233344444445668999999965410             00110000000    


Q ss_pred             CCCCCCCcEEEEEecccchh-h-hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHH
Q 004895          291 KNDDPRRCTIILTSRSRDLL-C-IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALST  367 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~  367 (724)
                      .........||.||...... . ........+.+...+.++-.+++...+...... -..+....|++.+.|..- +|..
T Consensus       246 ~~~~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~-l~~~~~~~la~~~~g~~~~~l~~  324 (389)
T 3vfd_A          246 QSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSP-LTQKELAQLARMTDGYSGSDLTA  324 (389)
T ss_dssp             C-----CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCC-SCHHHHHHHHHHTTTCCHHHHHH
T ss_pred             cccCCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCCHHHHHH
Confidence            00012334566666543321 1 111222468889999999999999887543221 124567889999988654 5544


Q ss_pred             H
Q 004895          368 V  368 (724)
Q Consensus       368 ~  368 (724)
                      +
T Consensus       325 L  325 (389)
T 3vfd_A          325 L  325 (389)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.28  E-value=6.2e-06  Score=88.88  Aligned_cols=185  Identities=12%  Similarity=0.163  Sum_probs=104.6

Q ss_pred             ccccc-chH--HHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          159 YNIFN-SRK--KIFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       159 ~~~~~-gR~--~~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ...|+ |..  .....+........ ...+.|+|++|+||||||+.+++.......-..+++++.+      ++..++..
T Consensus       104 fd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~------~~~~~~~~  177 (440)
T 2z4s_A          104 FENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE------KFLNDLVD  177 (440)
T ss_dssp             GGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH------HHHHHHHH
T ss_pred             hhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH------HHHHHHHH
Confidence            44555 532  23334444433332 6678999999999999999999987543111235566543      23344444


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----ccccccccCCCCcCCCCCCCCCcEEEEEecccchh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL  310 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~  310 (724)
                      .+...         ....+...+. .+..+|+|||++....    .+.+...+...       ...|..||+||....-.
T Consensus       178 ~~~~~---------~~~~~~~~~~-~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l-------~~~~~~iIitt~~~~~~  240 (440)
T 2z4s_A          178 SMKEG---------KLNEFREKYR-KKVDILLIDDVQFLIGKTGVQTELFHTFNEL-------HDSGKQIVICSDREPQK  240 (440)
T ss_dssp             HHHTT---------CHHHHHHHHT-TTCSEEEEECGGGGSSCHHHHHHHHHHHHHH-------HTTTCEEEEEESSCGGG
T ss_pred             HHHcc---------cHHHHHHHhc-CCCCEEEEeCcccccCChHHHHHHHHHHHHH-------HHCCCeEEEEECCCHHH
Confidence            33211         0112233332 2567999999976532    12221111100       12466788888764210


Q ss_pred             --------hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          311 --------CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       311 --------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                              .........+.+++++.++..+++.+.+...... --++....|++.++|.+-.+.-
T Consensus       241 l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~-i~~e~l~~la~~~~gn~R~l~~  304 (440)
T 2z4s_A          241 LSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGE-LPEEVLNFVAENVDDNLRRLRG  304 (440)
T ss_dssp             CSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCC-CCTTHHHHHHHHCCSCHHHHHH
T ss_pred             HHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHhcCCCHHHHHH
Confidence                    1112223578899999999999999887421111 1135678899999998865543

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.26  E-value=5.3e-05  Score=77.18  Aligned_cols=187  Identities=12%  Similarity=0.115  Sum_probs=103.5

Q ss_pred             cccccccchHHHHHHHHHHhcC------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALKD------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....++|.+..++.+.+.+..            ...+.+.|+|++|+||||+|+.+++....     ..+.++++.-..
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~~~-----~~~~i~~~~l~~   92 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATECSA-----TFLNISAASLTS   92 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHTTC-----EEEEEESTTTSS
T ss_pred             CCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHhCC-----CeEEeeHHHHhh
Confidence            3456788999999888877631            23568899999999999999999986632     123344332111


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccccc-------------ccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELD-------------KIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~-------------~l~~~~~~~~~~~~  291 (724)
                                    .....  .......+.......++.+|+||++.....-.             .+...+..   ...
T Consensus        93 --------------~~~~~--~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~---~~~  153 (297)
T 3b9p_A           93 --------------KYVGD--GEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDG---LPG  153 (297)
T ss_dssp             --------------SSCSC--HHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHH---CC-
T ss_pred             --------------cccch--HHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhc---ccc
Confidence                          11111  12233334444444577999999996542100             01000000   000


Q ss_pred             CCCCCCcEEEEEecccchh-h-hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHH
Q 004895          292 NDDPRRCTIILTSRSRDLL-C-IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTV  368 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~-~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~  368 (724)
                      .....+..||.||...... . ........+.++..+.++-..++...+...... --.+....|++.+.|.+- ++..+
T Consensus       154 ~~~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~-~~~~~~~~la~~~~g~~~~~l~~l  232 (297)
T 3b9p_A          154 NPDGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSP-LDTEALRRLAKITDGYSGSDLTAL  232 (297)
T ss_dssp             -----CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCC-SCHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             cCCCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHcCCCCHHHHHHH
Confidence            0012345566677654321 1 101222467777888888888888776432211 114567789999998875 44443

>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=98.25  E-value=2.9e-05  Score=81.15  Aligned_cols=185  Identities=15%  Similarity=0.154  Sum_probs=104.6

Q ss_pred             ccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          158 DYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ....++|.+..++.|.+.+.            ....+-|.|+|++|+|||+||+.+++.....     .+.++.+     
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~~~~-----~~~v~~~-----  118 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANST-----FFSVSSS-----  118 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHHTCE-----EEEEEHH-----
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCC-----EEEeeHH-----
Confidence            35567898888888887762            1123458899999999999999999987421     2333322     


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~  292 (724)
                       ++    ....    ...  .......+.......++.+|+||+++....             ...+...+..+     .
T Consensus       119 -~l----~~~~----~g~--~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~-----~  182 (355)
T 2qp9_X          119 -DL----VSKW----MGE--SEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGV-----G  182 (355)
T ss_dssp             -HH----HSCC---------CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHC-----C
T ss_pred             -HH----hhhh----cch--HHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcc-----c
Confidence             11    1111    011  122334444444445789999999975421             11111111000     0


Q ss_pred             CCCCCcEEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHHHH
Q 004895          293 DDPRRCTIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALSTVA  369 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~~~  369 (724)
                      ....+..||.||......  .........+.+...+.++-.+++...+......- -......|++.+.|. |-.|..+.
T Consensus       183 ~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~-~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          183 NDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVL-TKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             ---CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCC-CHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             ccCCCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCC-CHHHHHHHHHHcCCCCHHHHHHHH
Confidence            012345566666554321  11113335778889999999999998875432111 144678899999884 44454443

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=98.24  E-value=8.8e-07  Score=81.49  Aligned_cols=82  Identities=16%  Similarity=0.215  Sum_probs=40.1

Q ss_pred             CceEEEcCCCcCCC-CCccccCCCCCcEEEcCCcc-cCC--cccccCC----CCCcEEEccCC-cCccc-chhhhcCCCC
Q 004895          576 ELKVLDFTGIRFSP-LPSSLGRLINLQTLCLDGWR-LED--IAIVGQL----KKLEILSLRGA-EIKQL-PLQIGQLTRL  645 (724)
Q Consensus       576 ~L~~L~l~~~~~~~-lp~~i~~l~~L~~L~L~~~~-l~~--~~~~~~l----~~L~~L~l~~~-~i~~l-p~~i~~l~~L  645 (724)
                      .|+.||+++|.++. -...+..+++|++|+|++|. +++  +..++.+    ++|++|++++| .|+.- -..+.++++|
T Consensus        62 ~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~L  141 (176)
T 3e4g_A           62 KIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRNL  141 (176)
T ss_dssp             CEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTTC
T ss_pred             eEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCCC
Confidence            46666666666552 12334555666666666653 444  3444433    24555555555 34411 1223445555


Q ss_pred             CeEccCCCCCCc
Q 004895          646 QLLDLSNCSSLV  657 (724)
Q Consensus       646 ~~L~l~~~~~l~  657 (724)
                      ++|++++|..++
T Consensus       142 ~~L~L~~c~~It  153 (176)
T 3e4g_A          142 KYLFLSDLPGVK  153 (176)
T ss_dssp             CEEEEESCTTCC
T ss_pred             CEEECCCCCCCC
Confidence            555555554433

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.23  E-value=1.6e-05  Score=82.82  Aligned_cols=180  Identities=12%  Similarity=0.138  Sum_probs=105.8

Q ss_pred             cccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      .....+.|-++.+++|.+.+.             -...+-|.++|++|+|||.||+.+++.....     .+.++.+.-.
T Consensus       145 v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l~  219 (405)
T 4b4t_J          145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK-----FIRVSGAELV  219 (405)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCE-----EEEEEGGGGS
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCC-----ceEEEhHHhh
Confidence            445667788887777766543             1234678899999999999999999987542     3344433221


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc------------c-ccccccCCCCcCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL------------D-KIGIPYGDVDEKD  290 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~------------~-~l~~~~~~~~~~~  290 (724)
                      +              ...++  .......++.......+++|++|+++....-            . .+...+   ...+
T Consensus       220 s--------------k~vGe--se~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL---~~lD  280 (405)
T 4b4t_J          220 Q--------------KYIGE--GSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELL---NQLD  280 (405)
T ss_dssp             C--------------SSTTH--HHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHH---HHHH
T ss_pred             c--------------cccch--HHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHH---Hhhh
Confidence            1              11111  2334455555555567899999999754110            0 000000   0011


Q ss_pred             CCCCCCCcEEEEEecccchhh---h-hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          291 KNDDPRRCTIILTSRSRDLLC---I-DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~~---~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ......+..||.||.......   . .......+.++.-+.++-.++|+.+.......++.  ....|++.+.|+-
T Consensus       281 g~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dv--dl~~lA~~t~G~S  354 (405)
T 4b4t_J          281 GFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGI--NLRKVAEKMNGCS  354 (405)
T ss_dssp             TTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSC--CHHHHHHHCCSCC
T ss_pred             ccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccC--CHHHHHHHCCCCC
Confidence            122445566777777665421   1 12344688888888888889998877543222221  1467888888754

>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=98.22  E-value=2.8e-05  Score=80.63  Aligned_cols=171  Identities=11%  Similarity=0.142  Sum_probs=102.4

Q ss_pred             hHHHHHHHHHHhcCCC-ccEEEEEcCCCCcHHHHHHHHHHHHhhcc--------------------CCCeEEEEEEe---
Q 004895          165 RKKIFQDVIEALKDDK-LNIIGVCGMGGVGKTTLVKQIAKQVMEDN--------------------VFDKVVMAEIT---  220 (724)
Q Consensus       165 R~~~~~~l~~~L~~~~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------------------~F~~~~wv~vs---  220 (724)
                      .++..+.+...+..++ ...+.++|+.|+|||++|+.+++......                    |+| ..++...   
T Consensus         7 ~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~   85 (334)
T 1a5t_A            7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKGK   85 (334)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTTC
T ss_pred             hHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccccC
Confidence            3555667777776655 45789999999999999999999864321                    122 2233221   


Q ss_pred             cCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCc
Q 004895          221 KNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRC  298 (724)
Q Consensus       221 ~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s  298 (724)
                      ....+++ .+++.+.+....                 ..+++-++|+|+++...  ..+.+...+..        ...++
T Consensus        86 ~~~~i~~-ir~l~~~~~~~~-----------------~~~~~kvviIdead~l~~~a~naLLk~lEe--------p~~~~  139 (334)
T 1a5t_A           86 NTLGVDA-VREVTEKLNEHA-----------------RLGGAKVVWVTDAALLTDAAANALLKTLEE--------PPAET  139 (334)
T ss_dssp             SSBCHHH-HHHHHHHTTSCC-----------------TTSSCEEEEESCGGGBCHHHHHHHHHHHTS--------CCTTE
T ss_pred             CCCCHHH-HHHHHHHHhhcc-----------------ccCCcEEEEECchhhcCHHHHHHHHHHhcC--------CCCCe
Confidence            1112221 122222221110                 02467899999997653  22333222222        33456


Q ss_pred             EEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          299 TIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       299 ~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      .+|++|.... +...-.+....+.+.++++++..+.+.+...      --++.+..+++.++|.|..+..+
T Consensus       140 ~~Il~t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~~------~~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          140 WFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT------MSQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             EEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC------CCHHHHHHHHHHTTTCHHHHHHT
T ss_pred             EEEEEeCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhcC------CCHHHHHHHHHHcCCCHHHHHHH
Confidence            6666666543 3222234456899999999999999988751      11456688999999999766443

>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=98.21  E-value=4.4e-05  Score=82.32  Aligned_cols=187  Identities=17%  Similarity=0.177  Sum_probs=104.0

Q ss_pred             cccccccchHHHHHHHHHHhc------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....++|.+..++.|.+.+.            ....+-+.|+|++|+|||+||+.+++....      .-++.++..  
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~~------~~~~~v~~~--  202 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANN------STFFSISSS--  202 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHCCS------SEEEEECCC--
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHcCC------CCEEEEeHH--
Confidence            345668899988888887662            123467899999999999999999987621      123333322  


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------c----cccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------L----DKIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~----~~l~~~~~~~~~~~~  291 (724)
                        ++....   .+..   .    .....+.......++.+|+||++.....         .    ..+...+..   .  
T Consensus       203 --~l~~~~---~g~~---~----~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~---~--  265 (444)
T 2zan_A          203 --DLVSKW---LGES---E----KLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQG---V--  265 (444)
T ss_dssp             --------------C---C----CTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTC---S--
T ss_pred             --HHHhhh---cchH---H----HHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhC---c--
Confidence              111111   1110   1    1223344444445789999999975411         0    111111110   0  


Q ss_pred             CCCCCCcEEEEEecccchh--hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHHH
Q 004895          292 NDDPRRCTIILTSRSRDLL--CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALSTV  368 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~--~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~~  368 (724)
                      .....+..||.||......  .........+.++..+.++-..+|...+....... -......|++.+.|+ +-.|..+
T Consensus       266 ~~~~~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l-~~~~l~~la~~t~G~sgadl~~l  344 (444)
T 2zan_A          266 GVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSL-TEADFQELGRKTDGYSGADISII  344 (444)
T ss_dssp             SCCCSSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEEC-CHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             ccCCCCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCC-CHHHHHHHHHHcCCCCHHHHHHH
Confidence            0023456677677654322  11112234777888888888899988875332111 135677899999884 4444444


Q ss_pred             H
Q 004895          369 A  369 (724)
Q Consensus       369 ~  369 (724)
                      .
T Consensus       345 ~  345 (444)
T 2zan_A          345 V  345 (444)
T ss_dssp             H
T ss_pred             H
Confidence            3

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.21  E-value=8.9e-06  Score=86.62  Aligned_cols=143  Identities=13%  Similarity=0.133  Sum_probs=86.0

Q ss_pred             CceEEeccCCCcccCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcC
Q 004895          528 GPIAISLPYRDIQELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLD  606 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~  606 (724)
                      +++.+.+..+ +..++... ...+|+++.+.   .....+....|.++.+|+.+++++|.+..+|.......+|+.+.|.
T Consensus       136 ~L~~i~l~~~-i~~I~~~aF~~~~L~~i~lp---~~l~~I~~~aF~~c~~L~~l~l~~n~l~~I~~~aF~~~~L~~l~lp  211 (401)
T 4fdw_A          136 QIAKVVLNEG-LKSIGDMAFFNSTVQEIVFP---STLEQLKEDIFYYCYNLKKADLSKTKITKLPASTFVYAGIEEVLLP  211 (401)
T ss_dssp             CCSEEECCTT-CCEECTTTTTTCCCCEEECC---TTCCEECSSTTTTCTTCCEEECTTSCCSEECTTTTTTCCCSEEECC
T ss_pred             CccEEEeCCC-ccEECHHhcCCCCceEEEeC---CCccEehHHHhhCcccCCeeecCCCcceEechhhEeecccCEEEeC
Confidence            4555555433 44443221 22357777762   1445566677888888888888888888777655556778888886


Q ss_pred             CcccCC--cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          607 GWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       607 ~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      .+ ++.  ...+.++.+|+.+++..+ ++.++.....-.+|+.+.+..  .+..++...+..+++|+.+.+.++
T Consensus       212 ~~-l~~I~~~aF~~~~~L~~l~l~~~-l~~I~~~aF~~~~L~~i~lp~--~i~~I~~~aF~~c~~L~~l~l~~~  281 (401)
T 4fdw_A          212 VT-LKEIGSQAFLKTSQLKTIEIPEN-VSTIGQEAFRESGITTVKLPN--GVTNIASRAFYYCPELAEVTTYGS  281 (401)
T ss_dssp             TT-CCEECTTTTTTCTTCCCEECCTT-CCEECTTTTTTCCCSEEEEET--TCCEECTTTTTTCTTCCEEEEESS
T ss_pred             Cc-hheehhhHhhCCCCCCEEecCCC-ccCccccccccCCccEEEeCC--CccEEChhHhhCCCCCCEEEeCCc
Confidence            44 444  245677777777777653 455544322225566666643  345555555666666666665543

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.16  E-value=5.1e-06  Score=78.05  Aligned_cols=50  Identities=24%  Similarity=0.306  Sum_probs=43.4

Q ss_pred             ccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          158 DYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ....++||+++++.+.+.+.....+.+.|+|++|+|||++|+.+++....
T Consensus        20 ~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~   69 (187)
T 2p65_A           20 KLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQ   69 (187)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHT
T ss_pred             ccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            34568899999999999988766778899999999999999999998743

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.16  E-value=1.4e-05  Score=86.94  Aligned_cols=152  Identities=18%  Similarity=0.249  Sum_probs=87.2

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----Ce-EEEEEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DK-VVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~-~~wv~vs~~~~~~~l~~~  231 (724)
                      .....++||++++..+++.+......-+.|+|++|+|||++|+.+++........    +. ++.++++.          
T Consensus       177 ~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~----------  246 (468)
T 3pxg_A          177 DSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMGT----------  246 (468)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC--------------
T ss_pred             CCCCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCCc----------
Confidence            3456789999999999999876555667899999999999999999987432111    11 22333320          


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccch--
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL--  309 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v--  309 (724)
                         .    ....  .......+...+...++.+|++|  ...+..+.+...+          .....++|.+|.....  
T Consensus       247 ---~----~~g~--~e~~~~~~~~~~~~~~~~iLfiD--~~~~a~~~L~~~L----------~~g~v~vI~at~~~e~~~  305 (468)
T 3pxg_A          247 ---K----YRGE--FEDRLKKVMDEIRQAGNIILFID--AAIDASNILKPSL----------ARGELQCIGATTLDEYRK  305 (468)
T ss_dssp             ---------------CTTHHHHHHHHHTCCCCEEEEC--C--------CCCT----------TSSSCEEEEECCTTTTHH
T ss_pred             ---c----ccch--HHHHHHHHHHHHHhcCCeEEEEe--CchhHHHHHHHhh----------cCCCEEEEecCCHHHHHH
Confidence               0    0000  01122344444444567899999  1112212222222          2234556666655431  


Q ss_pred             ----hhhhcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          310 ----LCIDMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       310 ----~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                          ..........+.+++.+.++..+++...+.
T Consensus       306 ~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~~  339 (468)
T 3pxg_A          306 YIEKDAALERRFQPIQVDQPSVDESIQILQGLRD  339 (468)
T ss_dssp             HHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTT
T ss_pred             HhhcCHHHHHhCccceeCCCCHHHHHHHHHHHHH
Confidence                111122334799999999999999998764

>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=98.15  E-value=6.9e-05  Score=76.41  Aligned_cols=178  Identities=13%  Similarity=0.206  Sum_probs=101.0

Q ss_pred             ccccccchHHHHHHHHHHhcC-------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALKD-------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~-------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....++|.+..++.|.+++..             ...+.+.|+|++|+|||+||+.+++....     ..+.++      
T Consensus        13 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~-----~~i~v~------   81 (301)
T 3cf0_A           13 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQA-----NFISIK------   81 (301)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTC-----EEEEEC------
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCC-----CEEEEE------
Confidence            345678888887777766531             34567899999999999999999987632     122232      


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------------ccccccccCCCCc
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------------LDKIGIPYGDVDE  288 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------------~~~l~~~~~~~~~  288 (724)
                      ..++....   .+..       ......+........+.+|+||++.....                ...+...+..   
T Consensus        82 ~~~l~~~~---~g~~-------~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~---  148 (301)
T 3cf0_A           82 GPELLTMW---FGES-------EANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDG---  148 (301)
T ss_dssp             HHHHHHHH---HTTC-------TTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHS---
T ss_pred             hHHHHhhh---cCch-------HHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhc---
Confidence            22333222   1211       11233344444445679999999964310                0111111100   


Q ss_pred             CCCCCCCCCcEEEEEecccchh-hhhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          289 KDKNDDPRRCTIILTSRSRDLL-CIDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       289 ~~~~~~~~~s~ilvTtR~~~v~-~~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                         .....+..||.||...... ....   .....+.++..+.++-.+++...+.......+.  ....+++.+.|.|-+
T Consensus       149 ---~~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~--~~~~la~~~~g~sg~  223 (301)
T 3cf0_A          149 ---MSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV--DLEFLAKMTNGFSGA  223 (301)
T ss_dssp             ---SCTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSC--CHHHHHHTCSSCCHH
T ss_pred             ---ccCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccc--hHHHHHHHcCCCCHH
Confidence               0123456677777655322 1111   223578899999999999998887533222211  134667777777644

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.11  E-value=4.1e-05  Score=81.13  Aligned_cols=181  Identities=14%  Similarity=0.121  Sum_probs=102.9

Q ss_pred             CcccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      ......+.|-++.++.|.+.+.             -...+-|.++|++|+|||.||+.+++.....     .+.++.+.-
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~-----f~~v~~s~l  251 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNAT-----FLKLAAPQL  251 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGG
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCC-----EEEEehhhh
Confidence            3445667788888888776643             1245688999999999999999999987542     334443321


Q ss_pred             CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------------cc-ccccccCCCCcC
Q 004895          223 PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------------LD-KIGIPYGDVDEK  289 (724)
Q Consensus       223 ~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------------~~-~l~~~~~~~~~~  289 (724)
                      .              ....+.  .......++.......+++|++|+++....            .. .+...+   ...
T Consensus       252 ~--------------~~~vGe--se~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL---~~l  312 (434)
T 4b4t_M          252 V--------------QMYIGE--GAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELL---NQL  312 (434)
T ss_dssp             C--------------SSCSSH--HHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHH---HHH
T ss_pred             h--------------hcccch--HHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHH---HHh
Confidence            1              111111  223344444444445789999999864310            00 000000   011


Q ss_pred             CCCCCCCCcEEEEEecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          290 DKNDDPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       290 ~~~~~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      +......+..||.||........+.    .....+.++.-+.++-.++|+.+.......++..  ...|++.+.|+-
T Consensus       313 dg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvd--l~~lA~~t~G~s  387 (434)
T 4b4t_M          313 DGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDIN--WQELARSTDEFN  387 (434)
T ss_dssp             TTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCC--HHHHHHHCSSCC
T ss_pred             hccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCC--HHHHHHhCCCCC
Confidence            1112334556777777665431111    2234678888888888888887764322222211  467788887753

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.10  E-value=8.7e-05  Score=78.69  Aligned_cols=179  Identities=16%  Similarity=0.206  Sum_probs=102.6

Q ss_pred             ccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+.|-++.++.|.+.+.             -...+-|.++|++|+|||+||+.+++.....     .+.++.+.-.+
T Consensus       179 ~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~-----~~~v~~s~l~s  253 (437)
T 4b4t_L          179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGAN-----FIFSPASGIVD  253 (437)
T ss_dssp             CSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGTCC
T ss_pred             ChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC-----EEEEehhhhcc
Confidence            34566788877777766543             1245788999999999999999999987542     33444443211


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--------cc-----ccccccCCCCcCCC
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--------LD-----KIGIPYGDVDEKDK  291 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--------~~-----~l~~~~~~~~~~~~  291 (724)
                                    .....  .......++.......+++|++|+++....        .+     .+...+.   ..+.
T Consensus       254 --------------k~~Ge--se~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~---~lDg  314 (437)
T 4b4t_L          254 --------------KYIGE--SARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLT---QMDG  314 (437)
T ss_dssp             --------------SSSSH--HHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHH---HHHS
T ss_pred             --------------ccchH--HHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHH---Hhhc
Confidence                          11111  223344455555556889999999975311        00     0000000   0111


Q ss_pred             CCCCCCcEEEEEecccchhhhh-cC---CCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          292 NDDPRRCTIILTSRSRDLLCID-MN---SQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       292 ~~~~~~s~ilvTtR~~~v~~~~-~~---~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      .....+..||.||........+ ..   -...+.++.-+.++-.++|+.+.......++..  ...|++.+.|+-
T Consensus       315 ~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~d--l~~lA~~t~G~s  387 (437)
T 4b4t_L          315 FDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFD--FEAAVKMSDGFN  387 (437)
T ss_dssp             SSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCC--HHHHHHTCCSCC
T ss_pred             ccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccC--HHHHHHhCCCCC
Confidence            1234456778787765532111 11   234677877788888888887765332222211  467788887754

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.09  E-value=3.8e-05  Score=81.17  Aligned_cols=178  Identities=14%  Similarity=0.106  Sum_probs=102.9

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|-++.+++|.+.+.             -...+-|.++|++|+|||+||+.+++.....     .+.++.+.-.  
T Consensus       208 ~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~-----fi~vs~s~L~--  280 (467)
T 4b4t_H          208 YSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDAT-----FIRVIGSELV--  280 (467)
T ss_dssp             CSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCE-----EEEEEGGGGC--
T ss_pred             HHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCC-----eEEEEhHHhh--
Confidence            3456788888777766542             1346788999999999999999999987542     3344433211  


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccccc-------------ccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELD-------------KIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~-------------~l~~~~~~~~~~~~~  292 (724)
                                  .....+  .......++.......+++|++|+++....-.             .+...+   ...+..
T Consensus       281 ------------sk~vGe--sek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL---~~lDg~  343 (467)
T 4b4t_H          281 ------------QKYVGE--GARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELI---TQLDGF  343 (467)
T ss_dssp             ------------CCSSSH--HHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHH---HHHHSS
T ss_pred             ------------cccCCH--HHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHH---HHhhcc
Confidence                        111111  22344455555555678999999996541100             000000   001111


Q ss_pred             CCCCCcEEEEEecccchh---hh-hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          293 DDPRRCTIILTSRSRDLL---CI-DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~---~~-~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ....+..||.||......   .. .......+.++.-+.++-.++|+.++.......+..  ...|++.|.|+-
T Consensus       344 ~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvd--l~~LA~~T~GfS  415 (467)
T 4b4t_H          344 DPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIR--WELISRLCPNST  415 (467)
T ss_dssp             CCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCC--HHHHHHHCCSCC
T ss_pred             CCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCC--HHHHHHHCCCCC
Confidence            234455667777655432   11 113346788888888888889988775433222221  467888888754

>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=98.09  E-value=3.6e-05  Score=79.57  Aligned_cols=167  Identities=14%  Similarity=0.131  Sum_probs=93.5

Q ss_pred             HHHHHHHhcCC--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchh
Q 004895          169 FQDVIEALKDD--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLI  246 (724)
Q Consensus       169 ~~~l~~~L~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~  246 (724)
                      ...+......+  ....+.|+|++|+||||||+.+++..... . ..+++++++      ++...+...+...       
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-~-~~~~~i~~~------~~~~~~~~~~~~~-------   87 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-G-YRVIYSSAD------DFAQAMVEHLKKG-------   87 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-T-CCEEEEEHH------HHHHHHHHHHHHT-------
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-C-CEEEEEEHH------HHHHHHHHHHHcC-------
Confidence            34444444433  34678899999999999999999987543 1 224566543      3333333332110       


Q ss_pred             HHHHHHHHHHHhcCCcEEEEEcccccccc---c-cccccccCCCCcCCCCCCCCCcEEEEEecccch-----h---hhhc
Q 004895          247 YHRAKQLCQRLKKEKRVLIILDNIWTKLE---L-DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL-----L---CIDM  314 (724)
Q Consensus       247 ~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---~-~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v-----~---~~~~  314 (724)
                        ....+...+.  +..+|++||+.....   + +.+...+...       ...+..||+||....-     .   ....
T Consensus        88 --~~~~~~~~~~--~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~-------~~~~~~iii~~~~~~~~l~~l~~~L~sR~  156 (324)
T 1l8q_A           88 --TINEFRNMYK--SVDLLLLDDVQFLSGKERTQIEFFHIFNTL-------YLLEKQIILASDRHPQKLDGVSDRLVSRF  156 (324)
T ss_dssp             --CHHHHHHHHH--TCSEEEEECGGGGTTCHHHHHHHHHHHHHH-------HHTTCEEEEEESSCGGGCTTSCHHHHHHH
T ss_pred             --cHHHHHHHhc--CCCEEEEcCcccccCChHHHHHHHHHHHHH-------HHCCCeEEEEecCChHHHHHhhhHhhhcc
Confidence              1112223332  357999999976432   1 1221111100       1235568888764421     0   0111


Q ss_pred             CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          315 NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       315 ~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      .....+.+++ +.++..+++.+.+...... --++....|++.+ |.+-.
T Consensus       157 ~~~~~i~l~~-~~~e~~~il~~~~~~~~~~-l~~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          157 EGGILVEIEL-DNKTRFKIIKEKLKEFNLE-LRKEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             HTSEEEECCC-CHHHHHHHHHHHHHHTTCC-CCHHHHHHHHHHC-SSHHH
T ss_pred             cCceEEEeCC-CHHHHHHHHHHHHHhcCCC-CCHHHHHHHHHhC-CCHHH
Confidence            2225689999 9999999999887522111 1146677888888 76643

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.04  E-value=0.00011  Score=76.88  Aligned_cols=180  Identities=13%  Similarity=0.122  Sum_probs=102.0

Q ss_pred             cccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      .....+.|-++.+++|.+.+.             -...+-|.++|++|+|||.||+.+++.....     .+.++.+.- 
T Consensus       179 v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~-----fi~v~~s~l-  252 (437)
T 4b4t_I          179 ESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSAT-----FLRIVGSEL-  252 (437)
T ss_dssp             CCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCE-----EEEEESGGG-
T ss_pred             CcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCC-----EEEEEHHHh-
Confidence            445566788887777766543             1235779999999999999999999987642     233333321 


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccccc-------------ccccccCCCCcCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELD-------------KIGIPYGDVDEKD  290 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~-------------~l~~~~~~~~~~~  290 (724)
                                   ......+  .......++.......+++|++|+++....-.             .+...+   ...+
T Consensus       253 -------------~sk~vGe--sek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL---~~lD  314 (437)
T 4b4t_I          253 -------------IQKYLGD--GPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELL---NQLD  314 (437)
T ss_dssp             -------------CCSSSSH--HHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHH---HHHH
T ss_pred             -------------hhccCch--HHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHH---HHhh
Confidence                         1111111  23344455555555678999999997531100             000000   0001


Q ss_pred             CCCCCCCcEEEEEecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          291 KNDDPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ......+..||.||-.......+.    .....+.++.-+.++-.++|+.+.......++.  ....|++.+.|+-
T Consensus       315 g~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dv--dl~~LA~~T~GfS  388 (437)
T 4b4t_I          315 GFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDV--NLETLVTTKDDLS  388 (437)
T ss_dssp             HCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCC--CHHHHHHHCCSCC
T ss_pred             CcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcC--CHHHHHHhCCCCC
Confidence            112344556777777665431111    122457777778888888998877533222221  1457778887754

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.01  E-value=0.00013  Score=77.21  Aligned_cols=180  Identities=15%  Similarity=0.166  Sum_probs=98.6

Q ss_pred             cccccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP  223 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~  223 (724)
                      .....+.|-++.++.|.+.+.             -...+-+.++|++|+|||+||+.+++.....     .+.++.++-.
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~-----~~~v~~~~l~  243 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAA-----FIRVNGSEFV  243 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCE-----EEEEEGGGTC
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCC-----eEEEecchhh
Confidence            345567788888887776553             1245678999999999999999999987532     3444444321


Q ss_pred             ChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--------cc----c-cccccCCCCcCC
Q 004895          224 DAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--------LD----K-IGIPYGDVDEKD  290 (724)
Q Consensus       224 ~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--------~~----~-l~~~~~~~~~~~  290 (724)
                      +              ...+.  ....+..++.......++++++|+++....        .+    . +...+.   ..+
T Consensus       244 ~--------------~~~Ge--~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~---~ld  304 (428)
T 4b4t_K          244 H--------------KYLGE--GPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLT---QMD  304 (428)
T ss_dssp             C--------------SSCSH--HHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHH---HHH
T ss_pred             c--------------cccch--hHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHH---Hhh
Confidence            1              11111  223344555555556789999999964310        00    0 000000   011


Q ss_pred             CCCCCCCcEEEEEecccchh-hhhc---CCCceEecCCCCHHH-HHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          291 KNDDPRRCTIILTSRSRDLL-CIDM---NSQKMFWIDALSEEE-ALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~-~~~~---~~~~~~~l~~L~~~e-~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      ......+..||.||...... ....   .....+.++.++..+ -..+|+.+.......++.  ....|++.+.|+-
T Consensus       305 g~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~--dl~~lA~~t~G~s  379 (428)
T 4b4t_K          305 GFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEA--DLDSLIIRNDSLS  379 (428)
T ss_dssp             HSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTC--CHHHHHHHTTTCC
T ss_pred             CCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCccc--CHHHHHHHCCCCC
Confidence            11234456677777765532 1111   222467777675544 445666665432222221  1467788887754

>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=97.98  E-value=3.8e-06  Score=77.20  Aligned_cols=82  Identities=13%  Similarity=0.181  Sum_probs=62.4

Q ss_pred             CCCcEEEcCCcccCC--cccccCCCCCcEEEccCC-cCccc-chhhhcC----CCCCeEccCCCCCCcccChHHhhCCCC
Q 004895          598 INLQTLCLDGWRLED--IAIVGQLKKLEILSLRGA-EIKQL-PLQIGQL----TRLQLLDLSNCSSLVVIAPNVISKLSR  669 (724)
Q Consensus       598 ~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~-~i~~l-p~~i~~l----~~L~~L~l~~~~~l~~~~~~~i~~l~~  669 (724)
                      .+|++|++++|.+++  +..+..+++|++|+|++| .|+.- -..+..+    ++|++|++++|..++..--..+.++++
T Consensus        61 ~~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~  140 (176)
T 3e4g_A           61 YKIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRN  140 (176)
T ss_dssp             CCEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTT
T ss_pred             ceEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCC
Confidence            468999999998876  577888999999999998 57631 2334443    369999999988776644445778899


Q ss_pred             CcEEEccCCC
Q 004895          670 LEELYMGDSF  679 (724)
Q Consensus       670 L~~L~l~~~~  679 (724)
                      |++|++++|.
T Consensus       141 L~~L~L~~c~  150 (176)
T 3e4g_A          141 LKYLFLSDLP  150 (176)
T ss_dssp             CCEEEEESCT
T ss_pred             CCEEECCCCC
Confidence            9999998874

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.94  E-value=6.7e-06  Score=77.39  Aligned_cols=109  Identities=16%  Similarity=0.152  Sum_probs=65.7

Q ss_pred             hhhcCCCCceEEEcCCC-cCC-----CCCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCcc--
Q 004895          569 HFFEGTEELKVLDFTGI-RFS-----PLPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQ--  634 (724)
Q Consensus       569 ~~~~~l~~L~~L~l~~~-~~~-----~lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~--  634 (724)
                      ..+...+.|+.|+|++| .+.     .+...+....+|++|+|++|.+..  .    ..+...++|++|+|++|.|..  
T Consensus        30 ~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~i~~~g  109 (185)
T 1io0_A           30 RIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSG  109 (185)
T ss_dssp             HHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHH
T ss_pred             HHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCcCCHHH
Confidence            44666778888888887 765     234455666778888888887765  1    334455677777777777663  


Q ss_pred             ---cchhhhcCCCCCeEcc--CCCCCCcccC----hHHhhCCCCCcEEEccCC
Q 004895          635 ---LPLQIGQLTRLQLLDL--SNCSSLVVIA----PNVISKLSRLEELYMGDS  678 (724)
Q Consensus       635 ---lp~~i~~l~~L~~L~l--~~~~~l~~~~----~~~i~~l~~L~~L~l~~~  678 (724)
                         +...+...++|++|++  ++| .+....    ...+...++|++|++++|
T Consensus       110 ~~~l~~~L~~n~~L~~L~L~~~~N-~i~~~g~~~l~~~L~~n~~L~~L~L~~n  161 (185)
T 1io0_A          110 ILALVEALQSNTSLIELRIDNQSQ-PLGNNVEMEIANMLEKNTTLLKFGYHFT  161 (185)
T ss_dssp             HHHHHHGGGGCSSCCEEECCCCSS-CCCHHHHHHHHHHHHHCSSCCEEECCCS
T ss_pred             HHHHHHHHHhCCCceEEEecCCCC-CCCHHHHHHHHHHHHhCCCcCEEeccCC
Confidence               3445556666777777  442 332211    122344455666666554

>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=97.92  E-value=4.7e-05  Score=89.34  Aligned_cols=179  Identities=15%  Similarity=0.206  Sum_probs=96.5

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC---C-C-eEEEEEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV---F-D-KVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~---F-~-~~~wv~vs~~~~~~~l~~~  231 (724)
                      .....++||++++..+++.+......-+.++|++|+||||+|+.+++.......   . + .+++++++.-..       
T Consensus       167 ~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~-------  239 (854)
T 1qvr_A          167 GKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA-------  239 (854)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------
T ss_pred             CCCcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc-------
Confidence            445678999999999999987665566789999999999999999998743211   1 1 234444322110       


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhc-CCcEEEEEcccccccc-------ccc---cccccCCCCcCCCCCCCCCcEE
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE-------LDK---IGIPYGDVDEKDKNDDPRRCTI  300 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~-------~~~---l~~~~~~~~~~~~~~~~~~s~i  300 (724)
                           +..... . .......+...+.. +++.+|++|++.....       ++.   +...+          ...+..+
T Consensus       240 -----g~~~~g-~-~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l----------~~~~i~~  302 (854)
T 1qvr_A          240 -----GAKYRG-E-FEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL----------ARGELRL  302 (854)
T ss_dssp             ------------C-HHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH----------HTTCCCE
T ss_pred             -----cCccch-H-HHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHH----------hCCCeEE
Confidence                 000001 1 22233444444443 3679999999975421       111   11111          1123445


Q ss_pred             EEEecccch-----hhhhcCCCceEecCCCCHHHHHHHHHHHhCC---CCCCCCchhHHHHHHHHhC
Q 004895          301 ILTSRSRDL-----LCIDMNSQKMFWIDALSEEEALQLFEKIVGE---STKASDFRPLAEEIVGKCG  359 (724)
Q Consensus       301 lvTtR~~~v-----~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~---~~~~~~l~~~~~~I~~~c~  359 (724)
                      |.+|.....     ..........+.+++++.++..+++......   .....-..+....+++.+.
T Consensus       303 I~at~~~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~  369 (854)
T 1qvr_A          303 IGATTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSH  369 (854)
T ss_dssp             EEEECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHH
T ss_pred             EEecCchHHhhhccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHh
Confidence            555543321     1111223346899999999999999765421   1111112345566666663

>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=97.88  E-value=1.4e-05  Score=79.28  Aligned_cols=62  Identities=32%  Similarity=0.378  Sum_probs=37.6

Q ss_pred             cCCCCceEEEcCCCcCCCC---CccccCCCCCcEEEcCCcccCCcccccCCC--CCcEEEccCCcCc
Q 004895          572 EGTEELKVLDFTGIRFSPL---PSSLGRLINLQTLCLDGWRLEDIAIVGQLK--KLEILSLRGAEIK  633 (724)
Q Consensus       572 ~~l~~L~~L~l~~~~~~~l---p~~i~~l~~L~~L~L~~~~l~~~~~~~~l~--~L~~L~l~~~~i~  633 (724)
                      .+++.|+.|+|++|.+..+   |..+..+++|++|+|++|.++....+..+.  +|++|+|++|.+.
T Consensus       167 ~~l~~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          167 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLC  233 (267)
T ss_dssp             HHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSCCCSGGGGGGGTTSCCSEEECTTSTTG
T ss_pred             hhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCccCCchhhhhcccCCcceEEccCCcCc
Confidence            4566677777777776643   344556666666776666666544444443  6666666666554

>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=97.84  E-value=9.2e-05  Score=75.27  Aligned_cols=146  Identities=14%  Similarity=0.124  Sum_probs=88.2

Q ss_pred             chHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc--cCCCeEEEEEEec-CCChHHHHHHHHHhhCCCC
Q 004895          164 SRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED--NVFDKVVMAEITK-NPDAQKIQGELASDLGMNF  240 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~  240 (724)
                      |.++.++.|...+..++.+...++|+.|+||||+|+.+++.....  .+.+ +.+++.++ ..+++++ +++.+.+....
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~i-r~li~~~~~~p   78 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSP   78 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCC
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHHH-HHHHHHHhhcc
Confidence            345556677777776667789999999999999999998863211  2333 34555443 3333333 33444443211


Q ss_pred             CCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhhhhcCCC
Q 004895          241 DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLCIDMNSQ  317 (724)
Q Consensus       241 ~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~~~~~~~  317 (724)
                      .                 .+++-++|+|+++...  ..+.+...+..        ....+.+|++|.+.. +... ....
T Consensus        79 ~-----------------~~~~kvviIdead~lt~~a~naLLk~LEe--------p~~~t~fIl~t~~~~kl~~t-I~SR  132 (305)
T 2gno_A           79 E-----------------LYTRKYVIVHDCERMTQQAANAFLKALEE--------PPEYAVIVLNTRRWHYLLPT-IKSR  132 (305)
T ss_dssp             S-----------------SSSSEEEEETTGGGBCHHHHHHTHHHHHS--------CCTTEEEEEEESCGGGSCHH-HHTT
T ss_pred             c-----------------cCCceEEEeccHHHhCHHHHHHHHHHHhC--------CCCCeEEEEEECChHhChHH-HHce
Confidence            0                 1456899999997653  33333322322        334566766665443 3222 2222


Q ss_pred             ceEecCCCCHHHHHHHHHHHh
Q 004895          318 KMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       318 ~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                       .+++.++++++..+.+.+.+
T Consensus       133 -~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          133 -VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             -SEEEECCCCHHHHHHHHHHH
T ss_pred             -eEeCCCCCHHHHHHHHHHHh
Confidence             89999999999999998876

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.84  E-value=8.6e-05  Score=86.08  Aligned_cols=152  Identities=19%  Similarity=0.272  Sum_probs=87.7

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCC----Ce-EEEEEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVF----DK-VVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F----~~-~~wv~vs~~~~~~~l~~~  231 (724)
                      .....++||+++++.+.+.+......-+.++|++|+|||++|+.+++........    ++ ++.++.            
T Consensus       177 ~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~------------  244 (758)
T 3pxi_A          177 DSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM------------  244 (758)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC--------------
T ss_pred             CCCCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc------------
Confidence            3456789999999999999876555668899999999999999999986321110    11 122222            


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccch--
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL--  309 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v--  309 (724)
                           +......  .......+.......++.+|++|.  ..+..+.+...+          .....++|.||.....  
T Consensus       245 -----g~~~~G~--~e~~l~~~~~~~~~~~~~iLfiD~--~~~~~~~L~~~l----------~~~~v~~I~at~~~~~~~  305 (758)
T 3pxi_A          245 -----GTKYRGE--FEDRLKKVMDEIRQAGNIILFIDA--AIDASNILKPSL----------ARGELQCIGATTLDEYRK  305 (758)
T ss_dssp             ---------------CTTHHHHHHHHHTCCCCEEEECC----------CCCT----------TSSSCEEEEECCTTTTHH
T ss_pred             -----cccccch--HHHHHHHHHHHHHhcCCEEEEEcC--chhHHHHHHHHH----------hcCCEEEEeCCChHHHHH
Confidence                 1110000  111233444444445778999991  111112222221          2334567766665441  


Q ss_pred             ----hhhhcCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          310 ----LCIDMNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       310 ----~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                          ..........+.+++.+.++..+++.....
T Consensus       306 ~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~  339 (758)
T 3pxi_A          306 YIEKDAALERRFQPIQVDQPSVDESIQILQGLRD  339 (758)
T ss_dssp             HHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTT
T ss_pred             HhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHH
Confidence                111112235799999999999999997654

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.83  E-value=0.00099  Score=66.01  Aligned_cols=181  Identities=15%  Similarity=0.120  Sum_probs=95.5

Q ss_pred             cccccccchHHHHHHHHHHh---cC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEAL---KD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L---~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....++|.+..++++.+.+   ..         ...+-+.|+|++|+||||+|+.+++....  .   .+.++.+.-.+
T Consensus         9 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~--~---~~~i~~~~~~~   83 (257)
T 1lv7_A            9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKV--P---FFTISGSDFVE   83 (257)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTC--C---EEEECSCSSTT
T ss_pred             CCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCC--C---EEEEeHHHHHH
Confidence            34566778887766665443   21         12345889999999999999999987632  1   23333222111


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc----------------cccccccCCCCc
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL----------------DKIGIPYGDVDE  288 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~----------------~~l~~~~~~~~~  288 (724)
                                    .....  .......+.+......+.++++|+++....-                ..+...+.    
T Consensus        84 --------------~~~~~--~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~----  143 (257)
T 1lv7_A           84 --------------MFVGV--GASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMD----  143 (257)
T ss_dssp             --------------SCCCC--CHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHH----
T ss_pred             --------------Hhhhh--hHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhh----
Confidence                          00011  1122333444444456789999999543110                00100000    


Q ss_pred             CCCCCCCCCcEEEEEecccchh-hhhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCC-chh
Q 004895          289 KDKNDDPRRCTIILTSRSRDLL-CIDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGG-LPV  363 (724)
Q Consensus       289 ~~~~~~~~~s~ilvTtR~~~v~-~~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~G-lPL  363 (724)
                        ......+..||.||...... ....   .....+.++..+.++-.++++.........++  .....++..+.| .+-
T Consensus       144 --~~~~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~--~~~~~la~~~~G~~~~  219 (257)
T 1lv7_A          144 --GFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPD--IDAAIIARGTPGFSGA  219 (257)
T ss_dssp             --TCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHTCTTCCHH
T ss_pred             --CcccCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCcc--ccHHHHHHHcCCCCHH
Confidence              00123345677777655421 1111   12346778888888888888877643221221  123457777777 554


Q ss_pred             HHH
Q 004895          364 ALS  366 (724)
Q Consensus       364 ai~  366 (724)
                      -+.
T Consensus       220 dl~  222 (257)
T 1lv7_A          220 DLA  222 (257)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=97.80  E-value=0.00023  Score=82.52  Aligned_cols=158  Identities=20%  Similarity=0.287  Sum_probs=93.8

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEE-EEEecCCChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVM-AEITKNPDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~w-v~vs~~~~~~~l~~~  231 (724)
                      .....++||++++..+++.|......-+.|+|++|+|||++|+.+++.......    .+..+| ++.+.      +   
T Consensus       183 ~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~------l---  253 (758)
T 1r6b_X          183 GGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS------L---  253 (758)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-----------
T ss_pred             CCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHH------H---
Confidence            345678999999999999998666667889999999999999999998643211    133332 21111      0   


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--------cc---cccccccCCCCcCCCCCCCCCcEE
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--------EL---DKIGIPYGDVDEKDKNDDPRRCTI  300 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--------~~---~~l~~~~~~~~~~~~~~~~~~s~i  300 (724)
                       .  .+.... .. .......+...+...++.+|++||+....        ..   ..+...+          ...+..+
T Consensus       254 -~--~~~~~~-g~-~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l----------~~~~~~~  318 (758)
T 1r6b_X          254 -L--AGTKYR-GD-FEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL----------SSGKIRV  318 (758)
T ss_dssp             ----CCCCCS-SC-HHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCS----------SSCCCEE
T ss_pred             -h--cccccc-ch-HHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHH----------hCCCeEE
Confidence             0  011111 11 23344455555554567999999997541        11   1121111          2234556


Q ss_pred             EEEecccchh------hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          301 ILTSRSRDLL------CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       301 lvTtR~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      |.+|......      .........+.+++.+.++..+++....
T Consensus       319 I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          319 IGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             EEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             EEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence            6666543210      0011223468899999999999988764

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.79  E-value=2.1e-05  Score=73.89  Aligned_cols=116  Identities=10%  Similarity=0.041  Sum_probs=84.8

Q ss_pred             ccccCCCCCcEEEcCCc-ccCC------cccccCCCCCcEEEccCCcCcc-----cchhhhcCCCCCeEccCCCCCCccc
Q 004895          592 SSLGRLINLQTLCLDGW-RLED------IAIVGQLKKLEILSLRGAEIKQ-----LPLQIGQLTRLQLLDLSNCSSLVVI  659 (724)
Q Consensus       592 ~~i~~l~~L~~L~L~~~-~l~~------~~~~~~l~~L~~L~l~~~~i~~-----lp~~i~~l~~L~~L~l~~~~~l~~~  659 (724)
                      ..+...++|++|+|++| .+..      ...+...++|++|+|++|.+..     +...+...++|++|+|++| .+...
T Consensus        30 ~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N-~i~~~  108 (185)
T 1io0_A           30 RIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESN-FISGS  108 (185)
T ss_dssp             HHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSS-CCCHH
T ss_pred             HHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCC-cCCHH
Confidence            44567889999999999 8875      1456778899999999998873     4556777789999999995 44432


Q ss_pred             ----ChHHhhCCCCCcEEEc--cCCCCccccccCCccc-hHHhhcCCCCCcEEEeeccccc
Q 004895          660 ----APNVISKLSRLEELYM--GDSFSQWDKVEGGSNA-SLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       660 ----~~~~i~~l~~L~~L~l--~~~~~~~~~~~~~~~~-~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                          ....+...++|++|++  ++|.+...     ... ....+...++|+.|++++|.+.
T Consensus       109 g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~-----g~~~l~~~L~~n~~L~~L~L~~n~i~  164 (185)
T 1io0_A          109 GILALVEALQSNTSLIELRIDNQSQPLGNN-----VEMEIANMLEKNTTLLKFGYHFTQQG  164 (185)
T ss_dssp             HHHHHHHGGGGCSSCCEEECCCCSSCCCHH-----HHHHHHHHHHHCSSCCEEECCCSSHH
T ss_pred             HHHHHHHHHHhCCCceEEEecCCCCCCCHH-----HHHHHHHHHHhCCCcCEEeccCCCCC
Confidence                1334677889999999  66543211     111 2234566789999999999874

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.77  E-value=3e-05  Score=81.01  Aligned_cols=19  Identities=21%  Similarity=0.200  Sum_probs=10.4

Q ss_pred             EecCCC-CHHHHHHHHHHHh
Q 004895          320 FWIDAL-SEEEALQLFEKIV  338 (724)
Q Consensus       320 ~~l~~L-~~~e~~~Lf~~~~  338 (724)
                      ...+.+ +.++|...|.+..
T Consensus        38 ~~~~~f~~~~~a~~~~~~l~   57 (362)
T 2ra8_A           38 TQVKNFSSAGEAEKAAGKLI   57 (362)
T ss_dssp             EEEEECSSHHHHHHHHHHHH
T ss_pred             EEeeeCCCHHHHHHHHHHHH
Confidence            333334 4677766666653

>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=97.76  E-value=0.00054  Score=74.35  Aligned_cols=180  Identities=12%  Similarity=0.139  Sum_probs=101.6

Q ss_pred             cccccchHHHHHHHHHHhc-------------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK-------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~-------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...++|.+..+++|.+.+.             .....-+.|+|++|+|||++|+.+++....     ..+.++++.    
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~-----~fv~vn~~~----  273 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGA-----FFFLINGPE----  273 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSS-----EEEEEEHHH----
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCC-----CEEEEEchH----
Confidence            4567899998888877764             134457889999999999999999876521     133444321    


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-------------ccccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-------------LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-------------~~~l~~~~~~~~~~~~~  292 (724)
                            +...+    .. . .......++.....+++.+|+||+++....             ...+...+..      .
T Consensus       274 ------l~~~~----~g-~-~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~------~  335 (489)
T 3hu3_A          274 ------IMSKL----AG-E-SESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDG------L  335 (489)
T ss_dssp             ------HHTSC----TT-H-HHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHH------S
T ss_pred             ------hhhhh----cc-h-hHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhc------c
Confidence                  11111    01 1 122233444444456789999999953311             0111111110      0


Q ss_pred             CCCCCcEEEEEecccchh-hh--h-cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCc-hhHHHH
Q 004895          293 DDPRRCTIILTSRSRDLL-CI--D-MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGL-PVALST  367 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~-~~--~-~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~Gl-PLai~~  367 (724)
                      ....+..||.||...... ..  . ......+.+...+.++-.++|..++.......+  ....++++.+.|+ +-.+..
T Consensus       336 ~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~--~~l~~la~~t~g~s~~dL~~  413 (489)
T 3hu3_A          336 KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADD--VDLEQVANETHGHVGADLAA  413 (489)
T ss_dssp             CTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTT--CCHHHHHHTCTTCCHHHHHH
T ss_pred             ccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcch--hhHHHHHHHccCCcHHHHHH
Confidence            023345666676655321 11  1 122346889999999999999988753322211  1245677777775 434443

>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=97.72  E-value=2.7e-05  Score=72.81  Aligned_cols=90  Identities=14%  Similarity=0.217  Sum_probs=53.1

Q ss_pred             hHHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC
Q 004895          165 RKKIFQDVIEALKD---DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD  241 (724)
Q Consensus       165 R~~~~~~l~~~L~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~  241 (724)
                      +++.++.+.+++.+   .....+.|+|++|+||||||+.+++.......+. +++++      ..++...+.........
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~-~~~~~------~~~~~~~~~~~~~~~~~   91 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR-GYFFD------TKDLIFRLKHLMDEGKD   91 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC-CCEEE------HHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe-EEEEE------HHHHHHHHHHHhcCchH
Confidence            44555555555432   3356899999999999999999999886332222 34443      33444444433321110


Q ss_pred             CCchhHHHHHHHHHHHhcCCcEEEEEccccc
Q 004895          242 SNDLIYHRAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       242 ~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                      .         .+...+.  +.-+|||||++.
T Consensus        92 ~---------~~~~~~~--~~~llilDE~~~  111 (180)
T 3ec2_A           92 T---------KFLKTVL--NSPVLVLDDLGS  111 (180)
T ss_dssp             S---------HHHHHHH--TCSEEEEETCSS
T ss_pred             H---------HHHHHhc--CCCEEEEeCCCC
Confidence            0         2223333  456999999973

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.70  E-value=2.6e-05  Score=70.10  Aligned_cols=45  Identities=13%  Similarity=0.135  Sum_probs=33.8

Q ss_pred             cccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++|+...+.++.+.+.  .....-|.|+|++|+|||++|+.+++..
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            46788888888887764  2233346799999999999999998764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.69  E-value=9.5e-05  Score=70.47  Aligned_cols=88  Identities=20%  Similarity=0.241  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHhcCC----CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC
Q 004895          166 KKIFQDVIEALKDD----KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD  241 (724)
Q Consensus       166 ~~~~~~l~~~L~~~----~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~  241 (724)
                      ...++.+.+++...    ....+.|+|++|+|||+||+.+++.....  ...++|++++      ++...+......   
T Consensus        35 ~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~--~~~~~~~~~~------~~~~~~~~~~~~---  103 (202)
T 2w58_A           35 IKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR--NVSSLIVYVP------ELFRELKHSLQD---  103 (202)
T ss_dssp             HHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT--TCCEEEEEHH------HHHHHHHHC------
T ss_pred             HHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc--CCeEEEEEhH------HHHHHHHHHhcc---
Confidence            34455555555422    12688999999999999999999987643  3346676653      444444433221   


Q ss_pred             CCchhHHHHHHHHHHHhcCCcEEEEEccccc
Q 004895          242 SNDLIYHRAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       242 ~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                       .. .    ..+...+.+  .-+|||||++.
T Consensus       104 -~~-~----~~~~~~~~~--~~~lilDei~~  126 (202)
T 2w58_A          104 -QT-M----NEKLDYIKK--VPVLMLDDLGA  126 (202)
T ss_dssp             -CC-C----HHHHHHHHH--SSEEEEEEECC
T ss_pred             -ch-H----HHHHHHhcC--CCEEEEcCCCC
Confidence             11 1    122333332  23999999965

>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=97.69  E-value=0.00082  Score=72.34  Aligned_cols=175  Identities=17%  Similarity=0.169  Sum_probs=97.0

Q ss_pred             cccccchHHHHHHHHHHh---cCC---------CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          159 YNIFNSRKKIFQDVIEAL---KDD---------KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L---~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ...++|.++.++++.+.+   ...         -.+-+.|+|++|+|||+||+.+++.....     .+.+++++.... 
T Consensus        15 f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~-----f~~is~~~~~~~-   88 (476)
T 2ce7_A           15 FKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVP-----FFHISGSDFVEL-   88 (476)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCC-----EEEEEGGGTTTC-
T ss_pred             HHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCC-----eeeCCHHHHHHH-
Confidence            456778887666665543   211         13458899999999999999999876421     334444332211 


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------------ccccccccCCCCcCC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------------LDKIGIPYGDVDEKD  290 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------------~~~l~~~~~~~~~~~  290 (724)
                                   ... . .......++.......+.+|+||++.....                ...+...+..     
T Consensus        89 -------------~~g-~-~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~-----  148 (476)
T 2ce7_A           89 -------------FVG-V-GAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDG-----  148 (476)
T ss_dssp             -------------CTT-H-HHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHH-----
T ss_pred             -------------Hhc-c-cHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhc-----
Confidence                         000 0 122233344444445789999999965311                1111111100     


Q ss_pred             CCCCCCCcEEEEEecccchhh-hhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          291 KNDDPRRCTIILTSRSRDLLC-IDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~~-~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                       .....+..||.||....... ...   .....+.++..+.++-.++++.++......++.  ....|++.+.|..
T Consensus       149 -~~~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v--~l~~la~~t~G~s  221 (476)
T 2ce7_A          149 -FDSKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDV--NLEIIAKRTPGFV  221 (476)
T ss_dssp             -SCGGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCC
T ss_pred             -cCCCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchh--hHHHHHHhcCCCc
Confidence             00223556777776654321 111   223477888888888888888777533222221  1455888888877

>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=97.65  E-value=5.3e-05  Score=75.91  Aligned_cols=175  Identities=15%  Similarity=0.192  Sum_probs=86.4

Q ss_pred             cccccchHHHHHHHHHHhc---C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          159 YNIFNSRKKIFQDVIEALK---D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ...++|.+..++.+.+.+.   .         ...+-+.|+|++|+|||+||+.+++....  .|   +.+..+.-.+. 
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~--~~---~~v~~~~~~~~-   83 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHV--PF---FSMGGSSFIEM-   83 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTC--CC---CCCCSCTTTTS-
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCC--CE---EEechHHHHHh-
Confidence            3456676665555554432   1         12334779999999999999999997643  12   11221111100 


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-----------------ccccccccCCCCcC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-----------------LDKIGIPYGDVDEK  289 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----------------~~~l~~~~~~~~~~  289 (724)
                              ..+.....       ...+.......++.+|+|||+.....                 +..+...+.     
T Consensus        84 --------~~~~~~~~-------~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~-----  143 (268)
T 2r62_A           84 --------FVGLGASR-------VRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMD-----  143 (268)
T ss_dssp             --------CSSSCSSS-------SSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTT-----
T ss_pred             --------hcchHHHH-------HHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhh-----
Confidence                    00110000       01122222234668999999965311                 111111111     


Q ss_pred             CCCC-CCCCcEEEEEecccchhh-hhc---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          290 DKND-DPRRCTIILTSRSRDLLC-IDM---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       290 ~~~~-~~~~s~ilvTtR~~~v~~-~~~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                       ... ......||.||....... ...   .....+.++..+.++-.+++...+......++.  ....|++.+.|.|
T Consensus       144 -~~~~~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~--~~~~la~~~~g~~  218 (268)
T 2r62_A          144 -GFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDV--NLQEVAKLTAGLA  218 (268)
T ss_dssp             -CSSCSCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSC--CTTTTTSSSCSSC
T ss_pred             -CcccCCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCcc--CHHHHHHHcCCCC
Confidence             001 112245666766554211 111   123567888899999999998876432211110  1223555666654

>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=97.65  E-value=6.2e-05  Score=74.56  Aligned_cols=79  Identities=25%  Similarity=0.323  Sum_probs=42.5

Q ss_pred             cCCCCCcEEEcCCcccCCcc----cccCCCCCcEEEccCCcCcccchhhhcCC--CCCeEccCCCCCCcccC------hH
Q 004895          595 GRLINLQTLCLDGWRLEDIA----IVGQLKKLEILSLRGAEIKQLPLQIGQLT--RLQLLDLSNCSSLVVIA------PN  662 (724)
Q Consensus       595 ~~l~~L~~L~L~~~~l~~~~----~~~~l~~L~~L~l~~~~i~~lp~~i~~l~--~L~~L~l~~~~~l~~~~------~~  662 (724)
                      .++++|++|+|++|.++.++    .+..+++|++|+|++|.++.+ ..+..+.  +|+.|+|.+|......|      ..
T Consensus       167 ~~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~i~~~-~~l~~l~~l~L~~L~L~~Npl~~~~~~~~~y~~~  245 (267)
T 3rw6_A          167 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSE-RELDKIKGLKLEELWLDGNSLCDTFRDQSTYISA  245 (267)
T ss_dssp             HHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSCCCSG-GGGGGGTTSCCSEEECTTSTTGGGCSSHHHHHHH
T ss_pred             hhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCccCCc-hhhhhcccCCcceEEccCCcCccccCcchhHHHH
Confidence            34566666777666666532    234666666666666666654 2234444  66666666643222222      12


Q ss_pred             HhhCCCCCcEEE
Q 004895          663 VISKLSRLEELY  674 (724)
Q Consensus       663 ~i~~l~~L~~L~  674 (724)
                      .+..+++|+.|+
T Consensus       246 il~~~P~L~~LD  257 (267)
T 3rw6_A          246 IRERFPKLLRLD  257 (267)
T ss_dssp             HHHHCTTCCEES
T ss_pred             HHHHCcccCeEC
Confidence            345566666554

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.65  E-value=0.00016  Score=74.01  Aligned_cols=105  Identities=18%  Similarity=0.279  Sum_probs=60.6

Q ss_pred             cccchHHHHHHHHHHhcCC---------CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKDD---------KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.+..++.+...+...         ....+.++|++|+|||++|+.+++.....  -...+.++++...... ....
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~--~~~~~~~~~~~~~~~~-~~~~   94 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKH-AVSR   94 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC--GGGEEEEEGGGCCSTT-HHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC--CcceEEeecccccccc-cHHH
Confidence            3568888887777766521         13579999999999999999999987432  1235566665543322 1112


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +   ++.........  ....+...+......+++||++...
T Consensus        95 l---~g~~~~~~~~~--~~~~~~~~~~~~~~~vl~lDEi~~l  131 (311)
T 4fcw_A           95 L---IGAPPGYVGYE--EGGQLTEAVRRRPYSVILFDAIEKA  131 (311)
T ss_dssp             H---HCCCTTSTTTT--TCCHHHHHHHHCSSEEEEEETGGGS
T ss_pred             h---cCCCCcccccc--ccchHHHHHHhCCCeEEEEeChhhc
Confidence            2   22221110000  0012333344345689999999765

>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=97.52  E-value=0.0016  Score=67.27  Aligned_cols=181  Identities=18%  Similarity=0.183  Sum_probs=95.7

Q ss_pred             CcccccccchHHHHHHHHHHhcC-----CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC--ChHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD-----DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP--DAQKI  228 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~-----~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l  228 (724)
                      +.....++|++..++.+...+..     .....+.|+|++|+||||||+.++......  |   .  ..+...  ...++
T Consensus        21 ~~~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~--~---~--~~sg~~~~~~~~l   93 (334)
T 1in4_A           21 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN--I---H--VTSGPVLVKQGDM   93 (334)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC--E---E--EEETTTCCSHHHH
T ss_pred             CccHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHhCCC--E---E--EEechHhcCHHHH
Confidence            34456678888877777655542     244678999999999999999999987431  1   1  112211  11111


Q ss_pred             HHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCc-----CCCC-----CCCC
Q 004895          229 QGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDE-----KDKN-----DDPR  296 (724)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~-----~~~~-----~~~~  296 (724)
                                            ..+...+  .++.++++|++....  ..+.+...+.....     ....     ....
T Consensus        94 ----------------------~~~~~~~--~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~  149 (334)
T 1in4_A           94 ----------------------AAILTSL--ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQ  149 (334)
T ss_dssp             ----------------------HHHHHHC--CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------C
T ss_pred             ----------------------HHHHHHc--cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCC
Confidence                                  1111111  234577788875432  11111000000000     0000     0001


Q ss_pred             CcEEE-EEecccchh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          297 RCTII-LTSRSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       297 ~s~il-vTtR~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ...++ .|++...+. .........+.+++.+.++..+++.+.+..... ..-.+.+..|++.+.|.|-.+..+
T Consensus       150 ~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~-~~~~~~~~~ia~~~~G~~R~a~~l  222 (334)
T 1in4_A          150 PFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV-EIEDAAAEMIAKRSRGTPRIAIRL  222 (334)
T ss_dssp             CCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC-CBCHHHHHHHHHTSTTCHHHHHHH
T ss_pred             CeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhcCCChHHHHHH
Confidence            12222 344433321 111122235889999999999999987642211 122567899999999999765433

>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=97.51  E-value=0.0005  Score=70.22  Aligned_cols=46  Identities=26%  Similarity=0.265  Sum_probs=36.7

Q ss_pred             cccchHHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALKD--------------DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|+++.++.+...+..              .....+.|+|++|+|||++|+.+++...
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~   75 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            467999888888776642              2345678999999999999999998773

>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=97.42  E-value=0.001  Score=75.88  Aligned_cols=176  Identities=11%  Similarity=0.125  Sum_probs=97.7

Q ss_pred             cccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|-++.+++|.+.+.    .         ...+-|.++|++|+|||+||+.+++.....     .+.++.++    
T Consensus       203 ~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~-----~~~v~~~~----  273 (806)
T 3cf2_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGPE----  273 (806)
T ss_dssp             GGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCE-----EEEEEHHH----
T ss_pred             hhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCe-----EEEEEhHH----
Confidence            3445566665555555432    1         235678999999999999999999876431     33444321    


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc-------------cccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL-------------DKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~-------------~~l~~~~~~~~~~~~~  292 (724)
                            +...    ....  .......+++......+++|+||+++....-             ..+...+.      ..
T Consensus       274 ------l~sk----~~ge--se~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~md------g~  335 (806)
T 3cf2_A          274 ------IMSK----LAGE--SESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMD------GL  335 (806)
T ss_dssp             ------HHSS----CTTH--HHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHH------HC
T ss_pred             ------hhcc----cchH--HHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHh------cc
Confidence                  1111    1111  2334445555555567899999999754210             01100000      00


Q ss_pred             CCCCCcEEEEEecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          293 DDPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      ....+..||.||..........    .-...++++.-+.++-.++|+.+........+.  ....|++++.|+--
T Consensus       336 ~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dv--dl~~lA~~T~Gfsg  408 (806)
T 3cf2_A          336 KQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDV--DLEQVANETHGHVG  408 (806)
T ss_dssp             CGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTC--CHHHHHHHCCSCCH
T ss_pred             cccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCccc--CHHHHHHhcCCCCH
Confidence            1223445666666554321111    233578888888888888988776532222221  25678888888753

>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=97.42  E-value=0.0013  Score=71.23  Aligned_cols=48  Identities=19%  Similarity=0.152  Sum_probs=36.6

Q ss_pred             cccccchHHHHHHHHHHh---cCC--CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          159 YNIFNSRKKIFQDVIEAL---KDD--KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L---~~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...++|.++.++.+...+   ..+  ..+-+.++|++|+|||++|+.+++...
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHHhC
Confidence            467889998877654443   332  235788999999999999999999875

>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=97.23  E-value=0.011  Score=58.20  Aligned_cols=151  Identities=16%  Similarity=0.169  Sum_probs=77.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCc
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKR  262 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr  262 (724)
                      -+.|+|++|+||||||+.++.....     ..+.++..      ++    ....     ... .......+.+......+
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~~~~-----~~i~~~~~------~~----~~~~-----~~~-~~~~i~~~~~~~~~~~~  109 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGEARV-----PFITASGS------DF----VEMF-----VGV-GAARVRDLFETAKRHAP  109 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHTTC-----CEEEEEHH------HH----HHSC-----TTH-HHHHHHHHHHHHTTSSS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCC-----CEEEeeHH------HH----HHHH-----hhH-HHHHHHHHHHHHHhcCC
Confidence            3899999999999999999987641     23333321      11    1110     000 11223334444333356


Q ss_pred             EEEEEcccccccc----------------ccccccccCCCCcCCCCCCCCCcEEEEEecccchhhhh-c---CCCceEec
Q 004895          263 VLIILDNIWTKLE----------------LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCID-M---NSQKMFWI  322 (724)
Q Consensus       263 ~LlVlDdv~~~~~----------------~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l  322 (724)
                      .++++|++.....                ...+...+..      ........++.||......... .   .....+.+
T Consensus       110 ~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g------~~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i  183 (254)
T 1ixz_A          110 CIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG------FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAI  183 (254)
T ss_dssp             EEEEEETHHHHHC---------CHHHHHHHHHHHHHHHT------CCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEEC
T ss_pred             eEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhC------CCCCCCEEEEEccCCchhCCHHHcCCCcCCeEEee
Confidence            8999999953210                0111111110      0012223455555555442111 1   23357788


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          323 DALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       323 ~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      +..+.++-.++++..+......++  .....|++.+.|.-
T Consensus       184 ~~p~~~~r~~il~~~~~~~~~~~~--~~~~~la~~~~G~~  221 (254)
T 1ixz_A          184 DAPDVKGREQILRIHARGKPLAED--VDLALLAKRTPGFV  221 (254)
T ss_dssp             CSCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHTCTTCC
T ss_pred             CCcCHHHHHHHHHHHHcCCCCCcc--cCHHHHHHHcCCCC
Confidence            888888888888877643211111  11345777776653

>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=97.19  E-value=0.00047  Score=68.77  Aligned_cols=61  Identities=11%  Similarity=0.118  Sum_probs=39.0

Q ss_pred             ccccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          160 NIFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      ..++|+...+..+.+.+.  .....-+.|+|++|+|||++|+.+++......  ...+.++++..
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~~~--~~~~~v~~~~~   68 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQ--GPFISLNCAAL   68 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTTTT--SCEEEEEGGGS
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCccC--CCeEEEecCCC
Confidence            456788888887776554  12234677999999999999999988653211  12455666543

>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=97.18  E-value=0.0017  Score=71.64  Aligned_cols=165  Identities=20%  Similarity=0.179  Sum_probs=77.3

Q ss_pred             cccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      .++|-++....+.+.+.      ......+.++|++|+||||||+.++......     ..-++++...+..++......
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l~~~-----~~~i~~~~~~~~~~~~g~~~~  156 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSLGRK-----FVRISLGGVRDESEIRGHRRT  156 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHHTCE-----EEEECCCC-------------
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhcCCC-----eEEEEecccchhhhhhhHHHH
Confidence            35676766666644432      2345689999999999999999999887421     223333332222222211111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------ccccccccCCCCcCCC-------CCCCCCcEEE
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------LDKIGIPYGDVDEKDK-------NDDPRRCTII  301 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------~~~l~~~~~~~~~~~~-------~~~~~~s~il  301 (724)
                      ..+...       ........... ...-+++||++.....      ...+...+........       ........||
T Consensus       157 ~ig~~~-------~~~~~~~~~a~-~~~~vl~lDEid~l~~~~~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI  228 (543)
T 3m6a_A          157 YVGAMP-------GRIIQGMKKAG-KLNPVFLLDEIDKMSSDFRGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFI  228 (543)
T ss_dssp             --------------CHHHHHHTTC-SSSEEEEEEESSSCC---------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEE
T ss_pred             HhccCc-------hHHHHHHHHhh-ccCCEEEEhhhhhhhhhhccCHHHHHHHHHhhhhcceeecccCCeeecccceEEE
Confidence            111100       01111111111 1334889999975421      1222111110000000       0001345667


Q ss_pred             EEecccchh-hhhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          302 LTSRSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       302 vTtR~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      .||...... .........+.+.+++.++-.+++..+.
T Consensus       229 ~ttN~~~~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          229 ATANNLATIPGPLRDRMEIINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             EECSSTTTSCHHHHHHEEEEECCCCCHHHHHHHHHHTH
T ss_pred             eccCccccCCHHHHhhcceeeeCCCCHHHHHHHHHHHH
Confidence            666654421 1111122478899999999888887754

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.10  E-value=0.027  Score=56.18  Aligned_cols=177  Identities=14%  Similarity=0.132  Sum_probs=90.3

Q ss_pred             cccccccchHHHHHHHHHHhc---C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          157 KDYNIFNSRKKIFQDVIEALK---D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~---~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      .....++|.++.+.++.+...   .         .-.+-+.|+|+.|+||||||+.++....     ...+.++.+    
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~-----~~~i~~~~~----  107 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEAR-----VPFITASGS----  107 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTT-----CCEEEEEHH----
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcC-----CCEEEecHH----
Confidence            335567787766555543321   1         0112388999999999999999998764     123333321    


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc------------c----cccccccCCCCc
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE------------L----DKIGIPYGDVDE  288 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~------------~----~~l~~~~~~~~~  288 (724)
                        ++    ....     ... .......+.+......+.++++|++.....            +    ..+...+..   
T Consensus       108 --~~----~~~~-----~~~-~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsg---  172 (278)
T 1iy2_A          108 --DF----VEMF-----VGV-GAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG---  172 (278)
T ss_dssp             --HH----HHST-----TTH-HHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTT---
T ss_pred             --HH----HHHH-----hhH-HHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhC---
Confidence              11    1110     000 112233344443334568999999953210            0    111111111   


Q ss_pred             CCCCCCCCCcEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          289 KDKNDDPRRCTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       289 ~~~~~~~~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                         ........++.||.........    ......+.++..+.++-.+++...+......++  .....+++.+.|..
T Consensus       173 ---g~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~--~~~~~la~~~~G~~  245 (278)
T 1iy2_A          173 ---FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED--VDLALLAKRTPGFV  245 (278)
T ss_dssp             ---CCTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHTCTTCC
T ss_pred             ---CCCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcc--cCHHHHHHHcCCCC
Confidence               0011223455555555442111    123457888888998888888877643221111  12345777777755

>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=96.98  E-value=0.0025  Score=73.90  Aligned_cols=102  Identities=18%  Similarity=0.257  Sum_probs=60.1

Q ss_pred             cccchHHHHHHHHHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.++.++.+...+..         .....+.++|++|+|||++|+.+++...     ...+.++++.......    
T Consensus       459 ~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~-----~~~~~i~~s~~~~~~~----  529 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHT----  529 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSC----
T ss_pred             hccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhc-----CCEEEEechhhcchhh----
Confidence            467888888887776641         1234789999999999999999998772     2345566654332100    


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +.+.+|....  .........+...+......+|+||++...
T Consensus       530 ~~~l~g~~~g--~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~  569 (758)
T 1r6b_X          530 VSRLIGAPPG--YVGFDQGGLLTDAVIKHPHAVLLLDEIEKA  569 (758)
T ss_dssp             CSSSCCCCSC--SHHHHHTTHHHHHHHHCSSEEEEEETGGGS
T ss_pred             HhhhcCCCCC--CcCccccchHHHHHHhCCCcEEEEeCcccc
Confidence            0111222111  111111223344444455789999999764

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.97  E-value=0.0017  Score=75.19  Aligned_cols=157  Identities=16%  Similarity=0.251  Sum_probs=83.2

Q ss_pred             ccccchHHHHHHHHHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALKD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      ..++|.+..++.+...+..         .....+.++|++|+|||++|+.+++.....  -...+.++++...+..... 
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~--~~~~i~i~~s~~~~~~~~~-  567 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD--EESMIRIDMSEYMEKHSTS-  567 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC--TTCEEEEEGGGGCSSCCCC-
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC--CcceEEEechhcccccccc-
Confidence            3477999988888777651         112368999999999999999999987421  2335666665432211000 


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCC---CCcCCCCCCCCCcEEEEEec
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGD---VDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~---~~~~~~~~~~~~s~ilvTtR  305 (724)
                                         ...+...+......+|+||++.....  ...+...+..   .............+||+||.
T Consensus       568 -------------------~~~l~~~~~~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn  628 (758)
T 3pxi_A          568 -------------------GGQLTEKVRRKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSN  628 (758)
T ss_dssp             ----------------------CHHHHHHCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEES
T ss_pred             -------------------cchhhHHHHhCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCC
Confidence                               01111222223446999999976521  1111111000   00000001224567888887


Q ss_pred             ccc-------------hhh-hhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          306 SRD-------------LLC-IDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       306 ~~~-------------v~~-~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      ...             ... ....-...+.+.+++.++..+++...+
T Consensus       629 ~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          629 VGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             SSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHH
T ss_pred             CChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHH
Confidence            321             000 001122578899999988888776653

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.90  E-value=0.0012  Score=67.24  Aligned_cols=45  Identities=11%  Similarity=0.183  Sum_probs=34.9

Q ss_pred             cccchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++|+...+.++.+.+.  .....-|.|+|.+|+|||++|+.+++..
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~   49 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACS   49 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHS
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhC
Confidence            46788888888777664  2333456799999999999999998864

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.82  E-value=0.01  Score=64.28  Aligned_cols=176  Identities=16%  Similarity=0.172  Sum_probs=90.8

Q ss_pred             ccccccchHHHHHHHHHH---hcCC---------CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          158 DYNIFNSRKKIFQDVIEA---LKDD---------KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~---L~~~---------~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ....++|.++.+.++.+.   +...         -.+-+.|+|++|+||||||+.++.....     ..+.++.+.-...
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~-----~~i~i~g~~~~~~  103 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARV-----PFITASGSDFVEM  103 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTC-----CEEEEEGGGGTSS
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCC-----CEEEEehhHHHHh
Confidence            345677877766655543   3221         1234899999999999999999987642     2344443321110


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------------ccccccccCCCCcC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------------LDKIGIPYGDVDEK  289 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------------~~~l~~~~~~~~~~  289 (724)
                                    .. .. .......+.+......+.++++|++.....                ...+...+..    
T Consensus       104 --------------~~-g~-~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg----  163 (499)
T 2dhr_A          104 --------------FV-GV-GAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG----  163 (499)
T ss_dssp             --------------CT-TH-HHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGG----
T ss_pred             --------------hh-hh-HHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcc----
Confidence                          00 00 111111222211112358999999964311                0111111110    


Q ss_pred             CCCCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          290 DKNDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       290 ~~~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                        ........|+.||......... .   .....+.++..+.++-.++++.++......++  .....|++.+.|+.
T Consensus       164 --~~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~d--v~l~~lA~~t~G~~  236 (499)
T 2dhr_A          164 --FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAED--VDLALLAKRTPGFV  236 (499)
T ss_dssp             --CCSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCS--STTHHHHTTSCSCC
T ss_pred             --cccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChH--HHHHHHHHhcCCCC
Confidence              0122344566666665442111 1   22347888888888888888877643221111  12456778888765

>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=96.76  E-value=0.0059  Score=59.62  Aligned_cols=92  Identities=14%  Similarity=0.092  Sum_probs=55.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHhhCCCC----------CCCch
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASDLGMNF----------DSNDL  245 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~----------~~~~~  245 (724)
                      .-.++.|+|++|+|||||+..++.......    .-..++|++....++..++ ..+++.++...          .....
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~~~  101 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERL-LAVAERYGLSGSDVLDNVAYARAFNT  101 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHH-HHHHHHcCCCHHHHhhCeEEEecCCH
Confidence            345999999999999999999988632211    1246888887765555444 34455555432          01110


Q ss_pred             --hHHHHHHHHHHHhcCCcEEEEEccccc
Q 004895          246 --IYHRAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       246 --~~~~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                        .......+...+...+.-+||+|.+..
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          102 DHQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence              111223344444445678999999854

>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=96.71  E-value=0.0053  Score=58.88  Aligned_cols=51  Identities=22%  Similarity=0.183  Sum_probs=36.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .-.++.|+|++|+||||||..++.  ..   -..++|++.....+...+. .+.+..
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~--~~---~~~v~~i~~~~~~~~~~~~-~~~~~~   69 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL--LS---GKKVAYVDTEGGFSPERLV-QMAETR   69 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH--HH---CSEEEEEESSCCCCHHHHH-HHHHTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--Hc---CCcEEEEECCCCCCHHHHH-HHHHhc
Confidence            345999999999999999999998  21   2458888877655655543 344433

>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=96.70  E-value=0.0014  Score=65.95  Aligned_cols=69  Identities=20%  Similarity=0.308  Sum_probs=44.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE--ecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI--TKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      .+++.|+|++|+|||+||.+++....     ..++|+++  .+..+.             ..  .. .......+.+.+.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~~G-----~~VlyIs~~~eE~v~~-------------~~--~~-le~~l~~i~~~l~  181 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEALG-----GKDKYATVRFGEPLSG-------------YN--TD-FNVFVDDIARAML  181 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHHHH-----TTSCCEEEEBSCSSTT-------------CB--CC-HHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhCC-----CCEEEEEecchhhhhh-------------hh--cC-HHHHHHHHHHHHh
Confidence            35678999999999999999988611     13567777  222111             00  11 3334455666665


Q ss_pred             cCCcEEEEEccccc
Q 004895          259 KEKRVLIILDNIWT  272 (724)
Q Consensus       259 ~~kr~LlVlDdv~~  272 (724)
                      + .+ +||+|++..
T Consensus       182 ~-~~-LLVIDsI~a  193 (331)
T 2vhj_A          182 Q-HR-VIVIDSLKN  193 (331)
T ss_dssp             H-CS-EEEEECCTT
T ss_pred             h-CC-EEEEecccc
Confidence            4 44 999999854

>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=96.54  E-value=0.0092  Score=59.77  Aligned_cols=85  Identities=8%  Similarity=0.138  Sum_probs=55.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLCQRL  257 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~~~l  257 (724)
                      ++-|.|++|+||||||.+++........=..++||+....++..     .+++++.+.+.     +...++....+.+.+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            78999999999999999998876542112458899887777653     36777765431     111222212333343


Q ss_pred             ---hcCCcEEEEEccccc
Q 004895          258 ---KKEKRVLIILDNIWT  272 (724)
Q Consensus       258 ---~~~kr~LlVlDdv~~  272 (724)
                         ..++.-++|+|-+..
T Consensus       105 ~~i~~~~~~lvVIDSI~a  122 (333)
T 3io5_A          105 DAIERGEKVVVFIDSLGN  122 (333)
T ss_dssp             HTCCTTCCEEEEEECSTT
T ss_pred             HHhhccCceEEEEecccc
Confidence               446788999999854

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.53  E-value=0.0082  Score=59.88  Aligned_cols=157  Identities=14%  Similarity=0.165  Sum_probs=79.7

Q ss_pred             cccccchHHHHHHHHHHhc----C---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK----D---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ...+.|-++.++.|.+.+.    .         .-.+-+.|+|++|+||||||+.++.....     ..+++..++-.+.
T Consensus         9 ~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~-----~~i~i~g~~l~~~   83 (274)
T 2x8a_A            9 WADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGL-----NFISVKGPELLNM   83 (274)
T ss_dssp             ---CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTC-----EEEEEETTTTCSS
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCC-----CEEEEEcHHHHhh
Confidence            4456677777666655432    0         11223899999999999999999986542     2344432221110


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccccc---------ccc-ccccCCCCcCCCCCCC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLEL---------DKI-GIPYGDVDEKDKNDDP  295 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~---------~~l-~~~~~~~~~~~~~~~~  295 (724)
                                    .  ..........+.+......++++++|++......         ..+ ...+..   .+.....
T Consensus        84 --------------~--~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~---Lsgg~~~  144 (274)
T 2x8a_A           84 --------------Y--VGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTE---MDGLEAR  144 (274)
T ss_dssp             --------------T--THHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC---------CTTHHHHHHHH---HHTCCST
T ss_pred             --------------h--hhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHh---hhccccc
Confidence                          0  0001122333444333346789999999643110         000 000000   0000012


Q ss_pred             CCcEEEEEecccchhhhh----cCCCceEecCCCCHHHHHHHHHHHhC
Q 004895          296 RRCTIILTSRSRDLLCID----MNSQKMFWIDALSEEEALQLFEKIVG  339 (724)
Q Consensus       296 ~~s~ilvTtR~~~v~~~~----~~~~~~~~l~~L~~~e~~~Lf~~~~~  339 (724)
                      ...-++.+|....+....    ..-...+.++..+.++-.++|+....
T Consensus       145 ~~~i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~  192 (274)
T 2x8a_A          145 QQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITK  192 (274)
T ss_dssp             TCEEEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTT
T ss_pred             CCEEEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHh
Confidence            234456666665543111    12345677888888888888887653

>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=96.50  E-value=0.014  Score=60.30  Aligned_cols=92  Identities=14%  Similarity=0.243  Sum_probs=57.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHhhCCCCC------------CC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASDLGMNFD------------SN  243 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~------------~~  243 (724)
                      .-.++.|+|++|+||||||.+++.......    .-..++|++....++...+. .+++.++....            ..
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~-~~~~~~g~~~~~~l~~l~~~~~~~~  199 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR-DIADRFNVDHDAVLDNVLYARAYTS  199 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCST
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHcCCCHHHHHhceeEeecCCH
Confidence            346899999999999999999988743211    12468999988877776654 44555554321            11


Q ss_pred             chhHHHHHHHHHHHhc--CCcEEEEEccccc
Q 004895          244 DLIYHRAKQLCQRLKK--EKRVLIILDNIWT  272 (724)
Q Consensus       244 ~~~~~~~~~l~~~l~~--~kr~LlVlDdv~~  272 (724)
                      .........+...+..  .+.-+||+|.+..
T Consensus       200 e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          200 EHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             THHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence            1111223334444444  4667999998843

>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=96.50  E-value=0.0088  Score=61.64  Aligned_cols=85  Identities=19%  Similarity=0.229  Sum_probs=54.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLCQ  255 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~~  255 (724)
                      -+++.|+|++|+||||||.+++.......  ..++|++....++..     .++.++...+.     .....+....+..
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~g--g~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~~  133 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKMG--GVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVDE  133 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHHH
Confidence            46999999999999999999998875421  347888776666543     45566554221     1112333333333


Q ss_pred             HHhcCCcEEEEEccccc
Q 004895          256 RLKKEKRVLIILDNIWT  272 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~~  272 (724)
                      .+...+.-++|+|.+..
T Consensus       134 l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          134 LVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             HHHTSCCSEEEEECTTT
T ss_pred             HhhhcCCCeEEehHhhh
Confidence            33334566899999844

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.48  E-value=0.0017  Score=65.66  Aligned_cols=27  Identities=22%  Similarity=0.320  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+.++|++|+|||+||+.+++...
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l~   61 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKMG   61 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            346788999999999999999999884

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.47  E-value=0.0029  Score=56.74  Aligned_cols=39  Identities=23%  Similarity=0.272  Sum_probs=29.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      ....+.|+|+.|+|||||++.++...... .+ .+++++..
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~-g~-~~~~~~~~   73 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEA-GK-NAAYIDAA   73 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTT-TC-CEEEEETT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhc-CC-cEEEEcHH
Confidence            55689999999999999999999987642 22 25666544

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.43  E-value=0.008  Score=61.06  Aligned_cols=54  Identities=15%  Similarity=0.278  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHhcCC---CccEEEEEcCCCCcHHHHHHHHHHHHh-hccCCCeEEEEEEe
Q 004895          165 RKKIFQDVIEALKDD---KLNIIGVCGMGGVGKTTLVKQIAKQVM-EDNVFDKVVMAEIT  220 (724)
Q Consensus       165 R~~~~~~l~~~L~~~---~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~~~~wv~vs  220 (724)
                      +...+..+.+++...   ....+.|+|++|+|||+||+.+++... .. . ..+++++++
T Consensus       133 ~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~-g-~~v~~~~~~  190 (308)
T 2qgz_A          133 RMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKK-G-VSTTLLHFP  190 (308)
T ss_dssp             HHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHS-C-CCEEEEEHH
T ss_pred             HHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhc-C-CcEEEEEHH
Confidence            444455555555431   246888999999999999999999876 43 2 235566543

>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=96.39  E-value=0.0087  Score=61.34  Aligned_cols=91  Identities=15%  Similarity=0.212  Sum_probs=56.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhcc---------CC-----CeEEEEEEecCCChHHHHHHHHHhhCCCCC----
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN---------VF-----DKVVMAEITKNPDAQKIQGELASDLGMNFD----  241 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~----  241 (724)
                      .-.++.|+|.+|+||||||.+++.......         ..     ..++|++....++..++. .+++.++....    
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~-~~~~~~g~~~~~~~~  175 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIM-QMAEHAGIDGQTVLD  175 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHH-HHHHHHTCCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHH-HHHHHcCCCHHHHhc
Confidence            346899999999999999999987642110         11     468999988877777665 44556654321    


Q ss_pred             -----CCchhH---HHHHHHHHHHhc-CCcEEEEEcccc
Q 004895          242 -----SNDLIY---HRAKQLCQRLKK-EKRVLIILDNIW  271 (724)
Q Consensus       242 -----~~~~~~---~~~~~l~~~l~~-~kr~LlVlDdv~  271 (724)
                           ......   .....+...+.+ .+.-+||+|.+.
T Consensus       176 ~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          176 NTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             TEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             CEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence                 001011   123344444444 456789999874

>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=96.37  E-value=0.012  Score=60.21  Aligned_cols=91  Identities=22%  Similarity=0.241  Sum_probs=58.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEEEEecCCChHHHHHHHHHhhCCCCC---------CCchhH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEITKNPDAQKIQGELASDLGMNFD---------SNDLIY  247 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~---------~~~~~~  247 (724)
                      -.++.|+|++|+||||||.+++........    -..++|++....++..++. .+++.++....         ......
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~-~~~~~~g~~~~~~~~~l~~~~~~~~~  185 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIE-NMAKALGLDIDNVMNNIYYIRAINTD  185 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHH-HHHHHhCCCHHHHhccEEEEeCCCHH
Confidence            468999999999999999999886432110    2468999988877776664 44566654321         010011


Q ss_pred             ---HHHHHHHHHHhc-CCcEEEEEccccc
Q 004895          248 ---HRAKQLCQRLKK-EKRVLIILDNIWT  272 (724)
Q Consensus       248 ---~~~~~l~~~l~~-~kr~LlVlDdv~~  272 (724)
                         .....+...+.. .+.-+||+|.+..
T Consensus       186 ~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          186 HQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             HHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence               223344444444 5677999999843

>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=96.37  E-value=0.0058  Score=71.57  Aligned_cols=60  Identities=20%  Similarity=0.365  Sum_probs=42.1

Q ss_pred             cccchHHHHHHHHHHhcC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          161 IFNSRKKIFQDVIEALKD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      .++|.+..++.+...+..         .....+.|+|++|+|||++|+.+++......  ...+.++++..
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~--~~~i~i~~~~~  627 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTE--EAMIRIDMTEY  627 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSG--GGEEEECTTTC
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCC--CcEEEEechhc
Confidence            467999888888776642         1125789999999999999999999874311  12455555543

>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=96.22  E-value=0.016  Score=60.11  Aligned_cols=85  Identities=20%  Similarity=0.183  Sum_probs=53.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLCQ  255 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~~  255 (724)
                      -.++.|.|.+|+||||||.+++......  -..++|++....++..     .++.++...+     ......+....+..
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~--g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~~  146 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKA--GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIMEL  146 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHC--CCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHHH
Confidence            4589999999999999999998876532  2368999988766543     2455554321     11112333333333


Q ss_pred             HHhcCCcEEEEEccccc
Q 004895          256 RLKKEKRVLIILDNIWT  272 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~~  272 (724)
                      .......-+||+|.+..
T Consensus       147 l~~~~~~~lVVIDsl~~  163 (366)
T 1xp8_A          147 LVRSGAIDVVVVDSVAA  163 (366)
T ss_dssp             HHTTTCCSEEEEECTTT
T ss_pred             HHhcCCCCEEEEeChHH
Confidence            33334456999999843

>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=96.20  E-value=0.017  Score=59.63  Aligned_cols=86  Identities=17%  Similarity=0.196  Sum_probs=53.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      .-+++.|+|++|+||||||.+++......  =..++|++....++..     .++.++...+.     .....+....+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~--g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~  132 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA--GGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  132 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT--TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC--CCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            34689999999999999999998776532  2358899887766542     35556644221     111222222222


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ......+.-+||+|.+..
T Consensus       133 ~l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          133 MLVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             HHHTTTCCSEEEEECGGG
T ss_pred             HHHhcCCCCEEEEcChHh
Confidence            222334567999999854

>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=96.20  E-value=0.0085  Score=68.37  Aligned_cols=95  Identities=14%  Similarity=0.232  Sum_probs=59.7

Q ss_pred             ccccccchHHHHHHHHHHhc----------C---CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          158 DYNIFNSRKKIFQDVIEALK----------D---DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~----------~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+.|-++.++.|.+.+.          .   ...+-+.++|++|.|||.+|+.+++.....       ++.++.   
T Consensus       475 ~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~-------f~~v~~---  544 (806)
T 3cf2_A          475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISIKG---  544 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCE-------EEECCH---
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCc-------eEEecc---
Confidence            34456677777777766543          0   123457899999999999999999876432       333321   


Q ss_pred             hHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          225 AQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       225 ~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                       .+    ++..    .-.+  .+..+..++..-+...+++|++|+++..
T Consensus       545 -~~----l~s~----~vGe--se~~vr~lF~~Ar~~~P~IifiDEiDsl  582 (806)
T 3cf2_A          545 -PE----LLTM----WFGE--SEANVREIFDKARQAAPCVLFFDELDSI  582 (806)
T ss_dssp             -HH----HHTT----TCSS--CHHHHHHHHHHHHTTCSEEEECSCGGGC
T ss_pred             -ch----hhcc----ccch--HHHHHHHHHHHHHHcCCceeechhhhHH
Confidence             12    2211    1112  2345566666666667899999999753

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=96.19  E-value=0.049  Score=56.22  Aligned_cols=159  Identities=9%  Similarity=-0.087  Sum_probs=95.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLK  258 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~  258 (724)
                      .-.++..++|+.|.||++.+..+.+..... .|+....+.+....++.++...                     +...=.
T Consensus        16 ~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~---------------------~~~~pl   73 (343)
T 1jr3_D           16 GLRAAYLLLGNDPLLLQESQDAVRQVAAAQ-GFEEHHTFSIDPNTDWNAIFSL---------------------CQAMSL   73 (343)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHHHHHHHH-TCCEEEEEECCTTCCHHHHHHH---------------------HHHHHH
T ss_pred             CCCcEEEEECCcHHHHHHHHHHHHHHHHhC-CCCeeEEEEecCCCCHHHHHHH---------------------hcCcCC
Confidence            446789999999999999999998876532 3433222233333333333221                     111111


Q ss_pred             cCCcEEEEEccccc-c--ccccccccccCCCCcCCCCCCCCCcEEEEEecc-------cchhhhhcCCCceEecCCCCHH
Q 004895          259 KEKRVLIILDNIWT-K--LELDKIGIPYGDVDEKDKNDDPRRCTIILTSRS-------RDLLCIDMNSQKMFWIDALSEE  328 (724)
Q Consensus       259 ~~kr~LlVlDdv~~-~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~-------~~v~~~~~~~~~~~~l~~L~~~  328 (724)
                      -+++-++|+|++.. .  ..++.+...+..        ...++.+|+++-.       ..+...-......++..+++.+
T Consensus        74 f~~~kvvii~~~~~kl~~~~~~aLl~~le~--------p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~  145 (343)
T 1jr3_D           74 FASRQTLLLLLPENGPNAAINEQLLTLTGL--------LHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQA  145 (343)
T ss_dssp             CCSCEEEEEECCSSCCCTTHHHHHHHHHTT--------CBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTT
T ss_pred             ccCCeEEEEECCCCCCChHHHHHHHHHHhc--------CCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHH
Confidence            24678899999865 2  334444333322        3346666666543       1222222344568999999999


Q ss_pred             HHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          329 EALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       329 e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      +....+.+.+....-.- -++.+..+++.++|.+..+...
T Consensus       146 ~l~~~l~~~~~~~g~~i-~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          146 QLPRWVAARAKQLNLEL-DDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             HHHHHHHHHHHHTTCEE-CHHHHHHHHHSSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCC-CHHHHHHHHHHhchHHHHHHHH
Confidence            99988888774322111 1467888999999988877543

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=96.15  E-value=0.021  Score=60.38  Aligned_cols=132  Identities=15%  Similarity=0.200  Sum_probs=83.8

Q ss_pred             ccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccch-hhhc
Q 004895          565 QISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPL-QIGQ  641 (724)
Q Consensus       565 ~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~-~i~~  641 (724)
                      .+....|.++..|+.+.+..+...--...+.++.+|+.+.+.. .++.+  ..|.++.+|+.+++..+ ++.++. .+..
T Consensus       255 ~i~~~aF~~c~~L~~i~lp~~~~~I~~~aF~~c~~L~~i~l~~-~i~~I~~~aF~~c~~L~~i~lp~~-v~~I~~~aF~~  332 (394)
T 4gt6_A          255 RIETHAFDSCAYLASVKMPDSVVSIGTGAFMNCPALQDIEFSS-RITELPESVFAGCISLKSIDIPEG-ITQILDDAFAG  332 (394)
T ss_dssp             EECTTTTTTCSSCCEEECCTTCCEECTTTTTTCTTCCEEECCT-TCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTTT
T ss_pred             EcccceeeecccccEEecccccceecCcccccccccccccCCC-cccccCceeecCCCCcCEEEeCCc-ccEehHhHhhC
Confidence            3445567788888888876543332234566778888888853 34442  46778888999988754 666654 4778


Q ss_pred             CCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          642 LTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       642 l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                      +.+|+.+.+..  .+..+....+.++++|+.+++.++.           ..+........|+.+.+..+.
T Consensus       333 C~~L~~i~ip~--sv~~I~~~aF~~C~~L~~i~~~~~~-----------~~~~~~~~~~~L~~i~i~~~~  389 (394)
T 4gt6_A          333 CEQLERIAIPS--SVTKIPESAFSNCTALNNIEYSGSR-----------SQWNAISTDSGLQNLPVAPGS  389 (394)
T ss_dssp             CTTCCEEEECT--TCCBCCGGGGTTCTTCCEEEESSCH-----------HHHHTCBCCCCC---------
T ss_pred             CCCCCEEEECc--ccCEEhHhHhhCCCCCCEEEECCce-----------eehhhhhccCCCCEEEeCCCC
Confidence            88999998875  4677777788899999998887642           122344555667777665443

>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=96.04  E-value=0.021  Score=59.09  Aligned_cols=86  Identities=19%  Similarity=0.222  Sum_probs=53.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      .-+++.|.|.+|+||||||.+++.......  ..++|++....++..     .++.++...+.     .....+....+.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~~~-----~a~~~g~~~~~l~i~~~~~~e~~~~~~~  134 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  134 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCccHH-----HHHHcCCChhheeeeCCCCHHHHHHHHH
Confidence            346899999999999999999988765432  358899987766633     24555543211     111222222222


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ......+.-+||+|.+..
T Consensus       135 ~l~~~~~~~lVVIDsl~~  152 (356)
T 1u94_A          135 ALARSGAVDVIVVDSVAA  152 (356)
T ss_dssp             HHHHHTCCSEEEEECGGG
T ss_pred             HHHhccCCCEEEEcCHHH
Confidence            222234556999999843

>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=96.04  E-value=0.02  Score=60.13  Aligned_cols=91  Identities=15%  Similarity=0.168  Sum_probs=55.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecCCChHHHHHHHHHhhCCCCC----------CCc--
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKNPDAQKIQGELASDLGMNFD----------SND--  244 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~----------~~~--  244 (724)
                      -.++.|+|++|+|||||+..++-......    .-..++|++....++...+ ..+++.++....          ...  
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl-~~~a~~~gl~~~~vleni~~~~~~~~~  256 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL-VSIAQRFGLDPDDALNNVAYARAYNAD  256 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHH-HHHHHHTTCCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHH-HHHHHHcCCChHhHhhcEEEeccCChH
Confidence            46999999999999999998764432211    1245889887776665544 446666664321          011  


Q ss_pred             hhHHHHHHHHHHHhcCCcEEEEEccccc
Q 004895          245 LIYHRAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       245 ~~~~~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                      ........+...+...+.-+||+|.+-.
T Consensus       257 ~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          257 HQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             HHHHHHHHHHHHHHhcCCceEEecchhh
Confidence            0112233344444445678999998743

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.98  E-value=0.028  Score=54.21  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=32.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      -.++.|+|++|+|||||++.++.......  ..++|+....  ...++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~--~~v~~~~~~~--~~~~~~~~   69 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAKGLRDG--DPCIYVTTEE--SRDSIIRQ   69 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHHT--CCEEEEESSS--CHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHCC--CeEEEEEccc--CHHHHHHH
Confidence            35899999999999999999997665322  2466665433  34444433

>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=95.93  E-value=0.028  Score=54.11  Aligned_cols=91  Identities=23%  Similarity=0.265  Sum_probs=52.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhc---c-CCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----------CCc-
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMED---N-VFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----------SND-  244 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----------~~~-  244 (724)
                      -.+++|+|+.|+|||||++.++......   . .-..++|+.......... +..+.+..+....           ... 
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER-IREIAQNRGLDPDEVLKHIYVARAFNSN  103 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH-HHHHHHHTTSCHHHHHHTEEEEECCSHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHH-HHHHHHHcCCCHHHHhhcEEEEecCChH
Confidence            4699999999999999999998754321   1 123478887655444333 3344444433211           010 


Q ss_pred             hhHHHHHHHHHHHh-----cCCcEEEEEccccc
Q 004895          245 LIYHRAKQLCQRLK-----KEKRVLIILDNIWT  272 (724)
Q Consensus       245 ~~~~~~~~l~~~l~-----~~kr~LlVlDdv~~  272 (724)
                      ........+...+.     ..++-++|+|..-.
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~  136 (231)
T 4a74_A          104 HQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTS  136 (231)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSSCEEEEEEETSSH
T ss_pred             HHHHHHHHHHHHHHHhcccCCceeEEEECChHH
Confidence            01111233333343     45678999998754

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.93  E-value=0.0086  Score=56.65  Aligned_cols=44  Identities=20%  Similarity=0.336  Sum_probs=35.0

Q ss_pred             chHHHHHHHHHHhcC---CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          164 SRKKIFQDVIEALKD---DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       164 gR~~~~~~l~~~L~~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .|++.++.+.+.+..   ....+|+|+|+.|+||||+++.+......
T Consensus         2 ~~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~   48 (201)
T 1rz3_A            2 ELRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (201)
T ss_dssp             CHHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            356677777777653   34579999999999999999999887654

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=95.88  E-value=0.07  Score=56.21  Aligned_cols=146  Identities=14%  Similarity=0.129  Sum_probs=78.3

Q ss_pred             CCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEc
Q 004895          548 CPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSL  627 (724)
Q Consensus       548 ~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l  627 (724)
                      +.+|+.+.+.   .....+....|.++..|..+.+..+...--...+..+..++.+....+.+.. ..+..+.+|+.+.+
T Consensus       229 ~~~l~~i~ip---~~~~~i~~~~f~~~~~l~~~~~~~~~~~i~~~~F~~~~~l~~~~~~~~~i~~-~~F~~~~~L~~i~l  304 (394)
T 4fs7_A          229 KTGVKNIIIP---DSFTELGKSVFYGCTDLESISIQNNKLRIGGSLFYNCSGLKKVIYGSVIVPE-KTFYGCSSLTEVKL  304 (394)
T ss_dssp             TCCCCEEEEC---TTCCEECSSTTTTCSSCCEEEECCTTCEECSCTTTTCTTCCEEEECSSEECT-TTTTTCTTCCEEEE
T ss_pred             cCCCceEEEC---CCceecccccccccccceeEEcCCCcceeeccccccccccceeccCceeecc-cccccccccccccc
Confidence            3455555552   1122344445666667777766655333223345555666666554433211 23556666777776


Q ss_pred             cCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEE
Q 004895          628 RGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE  706 (724)
Q Consensus       628 ~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~  706 (724)
                      ..+ ++.++. .+..+++|+.+.+..  .+..+....+.++++|+.+.+..+      +...   .-..+.++.+|+.+.
T Consensus       305 ~~~-i~~I~~~aF~~c~~L~~i~lp~--~v~~I~~~aF~~c~~L~~i~lp~~------l~~I---~~~aF~~C~~L~~i~  372 (394)
T 4fs7_A          305 LDS-VKFIGEEAFESCTSLVSIDLPY--LVEEIGKRSFRGCTSLSNINFPLS------LRKI---GANAFQGCINLKKVE  372 (394)
T ss_dssp             CTT-CCEECTTTTTTCTTCCEECCCT--TCCEECTTTTTTCTTCCEECCCTT------CCEE---CTTTBTTCTTCCEEE
T ss_pred             ccc-cceechhhhcCCCCCCEEEeCC--cccEEhHHhccCCCCCCEEEECcc------ccEe---hHHHhhCCCCCCEEE
Confidence            543 555543 366677777777754  355666666677777777766443      1100   112345566677766


Q ss_pred             eec
Q 004895          707 IDV  709 (724)
Q Consensus       707 l~~  709 (724)
                      +..
T Consensus       373 lp~  375 (394)
T 4fs7_A          373 LPK  375 (394)
T ss_dssp             EEG
T ss_pred             ECC
Confidence            653

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.80  E-value=0.01  Score=56.45  Aligned_cols=52  Identities=21%  Similarity=0.343  Sum_probs=36.8

Q ss_pred             HHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          167 KIFQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       167 ~~~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      +.+++|.+.+..  ....+|+|+|+.|+|||||++.+.......+  ....+|...
T Consensus         6 ~~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~~~g--~~~g~v~~d   59 (208)
T 3c8u_A            6 ALCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALSAQG--LPAEVVPMD   59 (208)
T ss_dssp             HHHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHHHTT--CCEEEEESG
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHhhcC--CceEEEecC
Confidence            455666666653  4567999999999999999999998876421  124455543

>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=95.80  E-value=0.031  Score=56.20  Aligned_cols=59  Identities=22%  Similarity=0.196  Sum_probs=37.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~  239 (724)
                      ...+++|+|++|+||||++..++.....+.. ..+..+.... .....+.+....+..+.+
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G-~~V~lv~~D~~r~~a~eqL~~~~~~~gl~  163 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKH-KKIAFITTDTYRIAAVEQLKTYAELLQAP  163 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTC-CCEEEEECCCSSTTHHHHHHHHHTTTTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CEEEEEecCcccchHHHHHHHHHHhcCCC
Confidence            4569999999999999999999988764222 2355555432 122333344444444443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=95.71  E-value=0.0036  Score=55.66  Aligned_cols=45  Identities=11%  Similarity=0.070  Sum_probs=31.7

Q ss_pred             cccchHHHHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++|+...++++.+.+..  ....-|.|+|++|+|||++|+.+++..
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~   51 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG   51 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC
Confidence            467888888777776541  223346799999999999999987643

>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=95.70  E-value=0.062  Score=56.81  Aligned_cols=29  Identities=34%  Similarity=0.499  Sum_probs=25.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ...+|.++|.+|+||||++..++.....+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~  127 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKR  127 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHC
Confidence            46799999999999999999999887653

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.69  E-value=0.018  Score=59.25  Aligned_cols=99  Identities=21%  Similarity=0.211  Sum_probs=55.0

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe-EEEEEEecCCChHHHHHHHHHhhCC-----CCCCC
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK-VVMAEITKNPDAQKIQGELASDLGM-----NFDSN  243 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~l~~~i~~~l~~-----~~~~~  243 (724)
                      +.++.+. -.+-..++|+|+.|+|||||++.+.+....+ +-+. ++++-+.+...  + ..++.+.+..     ..+++
T Consensus       163 raID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~-~~~v~~I~~lIGER~~--E-v~~~~~~~~~~vV~atadep  238 (422)
T 3ice_A          163 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN-HPDCVLMVLLIDERPE--E-VTEMQRLVKGEVVASTFDEP  238 (422)
T ss_dssp             HHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHH-CTTSEEEEEEESSCHH--H-HHHHHTTCSSEEEEECTTSC
T ss_pred             eeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhc-CCCeeEEEEEecCChH--H-HHHHHHHhCeEEEEeCCCCC
Confidence            3444443 2345689999999999999999998876542 2232 34566665432  1 2234444321     12222


Q ss_pred             chhHH----HHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          244 DLIYH----RAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       244 ~~~~~----~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      .....    .+-.+.+++. +++++||++||+...
T Consensus       239 ~~~r~~~a~~alt~AEyfrd~G~dVLil~DslTR~  273 (422)
T 3ice_A          239 ASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRL  273 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCEEEEEeCchHH
Confidence            21111    1111223332 479999999999543

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=95.49  E-value=0.022  Score=60.44  Aligned_cols=90  Identities=18%  Similarity=0.306  Sum_probs=52.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhC--------CCCCCCchhHH----
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLG--------MNFDSNDLIYH----  248 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~--------~~~~~~~~~~~----  248 (724)
                      ..++|+|..|+|||||++.+....... +-+.++++.+.+.. ...++..++...-.        ....+......    
T Consensus       152 q~~~i~G~sGvGKTtL~~~l~~~~~~~-~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~  230 (473)
T 1sky_E          152 GKIGLFGGAGVGKTVLIQELIHNIAQE-HGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVAL  230 (473)
T ss_dssp             CEEEEECCSSSCHHHHHHHHHHHHHHH-TCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEECCCCCCccHHHHHHHhhhhhc-cCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHH
Confidence            468999999999999999999886543 22445666666543 33445544543200        01111110111    


Q ss_pred             HHHHHHHHHh--cCCcEEEEEccccc
Q 004895          249 RAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       249 ~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                      ..-.+.+++.  +++++|+++||+..
T Consensus       231 ~~ltiAEyFrd~~G~~VLl~~D~itR  256 (473)
T 1sky_E          231 TGLTMAEYFRDEQGQDGLLFIDNIFR  256 (473)
T ss_dssp             HHHHHHHHHHHHSCCEEEEEEECTHH
T ss_pred             HHHHHHHHHHHhcCCcEEEEeccHHH
Confidence            1123444444  37899999999954

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.49  E-value=0.055  Score=55.06  Aligned_cols=51  Identities=18%  Similarity=0.238  Sum_probs=38.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -.++.|.|.+|+||||||.+++.....+.  ..++|++..  .+..++...+...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            45899999999999999999998765432  567787755  4566776666654

>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=95.45  E-value=0.084  Score=52.84  Aligned_cols=29  Identities=31%  Similarity=0.256  Sum_probs=25.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ....+|+|+|+.|+||||||+.+......
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            45679999999999999999999888764

>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=95.38  E-value=0.0099  Score=54.41  Aligned_cols=25  Identities=20%  Similarity=0.243  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|.|+.|+||||+|+.+.+...
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~~l~   26 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSKELK   26 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999988763

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=95.36  E-value=0.11  Score=66.91  Aligned_cols=79  Identities=20%  Similarity=0.268  Sum_probs=48.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      +-+.++|++|+|||++|+.+.....   .+ ..+.++.+...+...+++.+-..+........       .+..--..++
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~~~~---~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g-------~~~~P~~~gk 1336 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALRNSS---LY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKG-------LTLLPKSDIK 1336 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSCS---SC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTT-------EEEEEBSSSS
T ss_pred             CeEEEECCCCCCHHHHHHHHHhcCC---CC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCC-------ccccCCCCCc
Confidence            4567999999999999987765431   12 35567778777777776666655432210000       0000000257


Q ss_pred             cEEEEEcccc
Q 004895          262 RVLIILDNIW  271 (724)
Q Consensus       262 r~LlVlDdv~  271 (724)
                      +.++++||+.
T Consensus      1337 ~~VlFiDEin 1346 (2695)
T 4akg_A         1337 NLVLFCDEIN 1346 (2695)
T ss_dssp             CEEEEEETTT
T ss_pred             eEEEEecccc
Confidence            8999999974

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.30  E-value=0.021  Score=58.75  Aligned_cols=44  Identities=20%  Similarity=0.263  Sum_probs=36.0

Q ss_pred             cccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|+++.++.+...+..+.  -+.++|++|+|||+||+.+++...
T Consensus        28 ~i~g~~~~~~~l~~~l~~~~--~vll~G~pGtGKT~la~~la~~~~   71 (331)
T 2r44_A           28 VVVGQKYMINRLLIGICTGG--HILLEGVPGLAKTLSVNTLAKTMD   71 (331)
T ss_dssp             TCCSCHHHHHHHHHHHHHTC--CEEEESCCCHHHHHHHHHHHHHTT
T ss_pred             ceeCcHHHHHHHHHHHHcCC--eEEEECCCCCcHHHHHHHHHHHhC
Confidence            46789988888887776533  578999999999999999988663

>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=95.29  E-value=0.01  Score=54.70  Aligned_cols=25  Identities=20%  Similarity=0.316  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|+|++|+||||+|+.+.+...
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~   28 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            5789999999999999999988753

>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=95.25  E-value=0.094  Score=55.41  Aligned_cols=57  Identities=23%  Similarity=0.240  Sum_probs=36.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh--HHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA--QKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~l~~~i~~~l~~~  239 (724)
                      ...+|.++|++|+||||++..++.....++ . .+..++.. .+..  .+-+....+..+.+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G-~-kVllv~~D-~~r~~a~eqL~~~~~~~gv~  154 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRG-Y-KVGLVAAD-VYRPAAYDQLLQLGNQIGVQ  154 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTT-C-CEEEEEEC-CSCHHHHHHHHHHHHTTTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC-C-eEEEEecC-ccchhHHHHHHHHHHhcCCc
Confidence            367999999999999999999998886532 2 24444433 3332  23344445555543

>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=95.24  E-value=0.048  Score=57.08  Aligned_cols=124  Identities=15%  Similarity=0.156  Sum_probs=80.5

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEEEcCCcccCC--cccccCCCCCc
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTLCLDGWRLED--IAIVGQLKKLE  623 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~  623 (724)
                      .+.+|+.+.+.   .....+....|.++..|+.+.+..+ ++.++ ..+.++.+|+.+.+..+ +..  ...+.++.+|+
T Consensus       215 ~~~~l~~i~~~---~~~~~i~~~~f~~~~~L~~i~lp~~-v~~I~~~aF~~~~~l~~i~l~~~-i~~i~~~aF~~c~~L~  289 (379)
T 4h09_A          215 YGKNLKKITIT---SGVTTLGDGAFYGMKALDEIAIPKN-VTSIGSFLLQNCTALKTLNFYAK-VKTVPYLLCSGCSNLT  289 (379)
T ss_dssp             TCSSCSEEECC---TTCCEECTTTTTTCSSCCEEEECTT-CCEECTTTTTTCTTCCEEEECCC-CSEECTTTTTTCTTCC
T ss_pred             cccccceeeec---cceeEEccccccCCccceEEEcCCC-ccEeCccccceeehhcccccccc-ceeccccccccccccc
Confidence            34556665551   1233445556777777777777654 44432 34566777777777543 333  24567778888


Q ss_pred             EEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          624 ILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       624 ~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      .+.+.++.++.++.. +.++.+|+.+.+..  .+..+....+.++++|+.+.+..
T Consensus       290 ~i~l~~~~i~~I~~~aF~~c~~L~~i~lp~--~l~~I~~~aF~~C~~L~~i~ip~  342 (379)
T 4h09_A          290 KVVMDNSAIETLEPRVFMDCVKLSSVTLPT--ALKTIQVYAFKNCKALSTISYPK  342 (379)
T ss_dssp             EEEECCTTCCEECTTTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCCCCCCT
T ss_pred             cccccccccceehhhhhcCCCCCCEEEcCc--cccEEHHHHhhCCCCCCEEEECC
Confidence            888887777777544 77788888888865  36667666777888888777644

>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=95.24  E-value=0.072  Score=55.00  Aligned_cols=93  Identities=24%  Similarity=0.307  Sum_probs=53.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc--c-CC-CeEEEEEEecCCChHHHHHHHHHhhCCCCC----------C-C-
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED--N-VF-DKVVMAEITKNPDAQKIQGELASDLGMNFD----------S-N-  243 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~-~F-~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~----------~-~-  243 (724)
                      .-.++.|+|+.|+|||||+..++......  . .. ..++|++....+....+ ..+++..+....          . . 
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~~~~~~~v~~ni~~~~~~~~  208 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNRGLDPDEVLKHIYVARAFNS  208 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTTTCCHHHHGGGEEEEECCSH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHcCCCHHHHhhCEEEEecCCh
Confidence            45699999999999999999998875211  1 11 23588887665544433 345554433210          0 0 


Q ss_pred             chhHHHHHHHHHHHhc-----CCcEEEEEcccccc
Q 004895          244 DLIYHRAKQLCQRLKK-----EKRVLIILDNIWTK  273 (724)
Q Consensus       244 ~~~~~~~~~l~~~l~~-----~kr~LlVlDdv~~~  273 (724)
                      .........+...+..     .+.-+||+|.+-..
T Consensus       209 ~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          209 NHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             HHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             HHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence            0011222333333332     46789999998543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.19  E-value=0.013  Score=55.27  Aligned_cols=27  Identities=37%  Similarity=0.411  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+|.|+|+.|+||||+|+.+.....
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~   50 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLN   50 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            346899999999999999999998763

>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=95.18  E-value=0.011  Score=54.35  Aligned_cols=20  Identities=35%  Similarity=0.645  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQI  201 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v  201 (724)
                      .+|.|+|++|+||||+|+.+
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

>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=95.10  E-value=0.012  Score=60.94  Aligned_cols=51  Identities=18%  Similarity=0.232  Sum_probs=36.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.....++|.+..+..+...+......-+.|+|++|+|||++|+.+++...
T Consensus        20 ~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           20 VFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             CCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCc
Confidence            334556889888666554443332333488999999999999999998764

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.05  E-value=0.1  Score=50.65  Aligned_cols=39  Identities=18%  Similarity=0.220  Sum_probs=29.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      -.++.|.|++|+||||||.+++......  =..++|++...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~~~~~--~~~v~~~~~e~   61 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWNGLKM--GEPGIYVALEE   61 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHHHHHT--TCCEEEEESSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc--CCeEEEEEccC
Confidence            4589999999999999999887765432  23577877544

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.03  E-value=0.09  Score=55.66  Aligned_cols=101  Identities=22%  Similarity=0.321  Sum_probs=62.8

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhhCCC---------
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDLGMN---------  239 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l~~~---------  239 (724)
                      +.++.|. =.+-..++|+|..|+|||+|+..+.+.... .+-+.++++-+.+.. ...++.+++.+.-...         
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~~~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rtv  220 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVA  220 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHTTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEE
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhhHh-hCCCEEEEEECCCcchHHHHHHHHhhhccccccccCCceEE
Confidence            3455554 234458999999999999999999987643 334667788777654 3456666666542211         


Q ss_pred             -----CCCCchh----HHHHHHHHHHHh--cCCcEEEEEccccc
Q 004895          240 -----FDSNDLI----YHRAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       240 -----~~~~~~~----~~~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                           .+++...    ....-.+.+++.  +++++||++||+-.
T Consensus       221 vV~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~DsitR  264 (482)
T 2ck3_D          221 LVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFR  264 (482)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHH
Confidence                 1111101    112233445554  37999999999854

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.02  E-value=0.015  Score=54.07  Aligned_cols=26  Identities=38%  Similarity=0.456  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+.|.|+|+.|+||||+|+.+.+...
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~   30 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTK   30 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998763

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.94  E-value=0.014  Score=53.99  Aligned_cols=26  Identities=15%  Similarity=0.286  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -.+++|+|+.|+|||||++.+.....
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            35899999999999999999988653

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.93  E-value=0.024  Score=54.53  Aligned_cols=40  Identities=18%  Similarity=0.294  Sum_probs=30.5

Q ss_pred             HHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          168 IFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       168 ~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+.+...+......+|.|+|.+|+|||||+..+......
T Consensus        25 ~a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~~~   64 (226)
T 2hf9_A           25 LADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNLKD   64 (226)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            3444444444556789999999999999999999987643

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.91  E-value=0.014  Score=53.77  Aligned_cols=22  Identities=32%  Similarity=0.462  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .+|.|.|++|+||||+|+.+.+
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            4789999999999999999987

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.91  E-value=0.1  Score=55.35  Aligned_cols=90  Identities=22%  Similarity=0.276  Sum_probs=48.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCCCCC---CchhHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMNFDS---NDLIYHRAKQLCQ  255 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~l~~  255 (724)
                      ..++|.++|.+|+||||++..++.....+... .+.-+++.. .....+.+.......+.+.-.   .............
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~-kVllvd~D~~r~~a~~ql~~~~~~~~l~v~~~~~~~dp~~i~~~~l~  177 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKK-KVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALK  177 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEECCCSSTTHHHHHHHHHHHHTCEECCCCSSSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCC-eEEEEecCCCCccHHHHHHhhcccCCeeEEeCCCCCCHHHHHHHHHH
Confidence            46799999999999999999999988754122 355555542 223333333344444433111   1112233333444


Q ss_pred             HHhcCCcEEEEEccc
Q 004895          256 RLKKEKRVLIILDNI  270 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv  270 (724)
                      .+....-=++|+|-.
T Consensus       178 ~~~~~~~D~VIIDTp  192 (433)
T 2xxa_A          178 EAKLKFYDVLLVDTA  192 (433)
T ss_dssp             HHHHTTCSEEEEECC
T ss_pred             HHHhCCCCEEEEECC
Confidence            443222236666764

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.90  E-value=0.018  Score=54.41  Aligned_cols=27  Identities=30%  Similarity=0.500  Sum_probs=23.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+|+|+|+.|+||||+++.+....
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            455799999999999999999998766

>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=94.87  E-value=0.015  Score=54.25  Aligned_cols=25  Identities=32%  Similarity=0.454  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ...+++|+|+.|+|||||++.+...
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3468999999999999999999764

>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=94.86  E-value=0.019  Score=54.23  Aligned_cols=29  Identities=34%  Similarity=0.501  Sum_probs=25.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .....+|+|+|+.|+||||+++.+.....
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34567999999999999999999998876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.86  E-value=0.014  Score=53.59  Aligned_cols=25  Identities=36%  Similarity=0.444  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|+|+|+.|+||||+++.+.....
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~   29 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLN   29 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4799999999999999999988653

>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=94.83  E-value=0.35  Score=49.17  Aligned_cols=57  Identities=28%  Similarity=0.362  Sum_probs=37.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC--ChHHHHHHHHHhhCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP--DAQKIQGELASDLGM  238 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~l~~~i~~~l~~  238 (724)
                      ....+++|+|+.|+||||+++.++...+...  ..+.++. .+.+  ...+-+....+.++.
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~~~--g~V~l~g-~D~~r~~a~eql~~~~~~~gv  185 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKNHG--FSVVIAA-SDTFRAGAIEQLEEHAKRIGV  185 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEE-ECCSSTTHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcC--CEEEEEe-ecccccchHHHHHHHHHHcCc
Confidence            4567999999999999999999998876532  1244443 3332  233444555666654

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.78  E-value=0.018  Score=53.76  Aligned_cols=26  Identities=31%  Similarity=0.468  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+|.|.|+.|+||||+|+.+.+....
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~~l~~   27 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            47899999999999999999998763

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.78  E-value=0.021  Score=53.03  Aligned_cols=28  Identities=29%  Similarity=0.457  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+|.|+|++|+||||+++.++.....
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4568999999999999999999998764

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.77  E-value=0.015  Score=54.90  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=22.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|+|+.|+||||+|+.+....
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            4689999999999999999998876

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=94.76  E-value=0.58  Score=49.03  Aligned_cols=106  Identities=13%  Similarity=0.169  Sum_probs=76.1

Q ss_pred             ccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCc
Q 004895          594 LGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLE  671 (724)
Q Consensus       594 i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~  671 (724)
                      +..+.+|+.+.+..+...- ...+.++.+|+.+.+. +.++.++.. +..+.+|+.+.+..  .++.+....+..+++|+
T Consensus       261 F~~c~~L~~i~lp~~~~~I~~~aF~~c~~L~~i~l~-~~i~~I~~~aF~~c~~L~~i~lp~--~v~~I~~~aF~~C~~L~  337 (394)
T 4gt6_A          261 FDSCAYLASVKMPDSVVSIGTGAFMNCPALQDIEFS-SRITELPESVFAGCISLKSIDIPE--GITQILDDAFAGCEQLE  337 (394)
T ss_dssp             TTTCSSCCEEECCTTCCEECTTTTTTCTTCCEEECC-TTCCEECTTTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCC
T ss_pred             eeecccccEEecccccceecCcccccccccccccCC-CcccccCceeecCCCCcCEEEeCC--cccEehHhHhhCCCCCC
Confidence            4566778888876553222 2567788899999986 457777665 77889999999976  46778778889999999


Q ss_pred             EEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          672 ELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       672 ~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                      .+.+..+      +....   -..+.++++|+.+.+..+.
T Consensus       338 ~i~ip~s------v~~I~---~~aF~~C~~L~~i~~~~~~  368 (394)
T 4gt6_A          338 RIAIPSS------VTKIP---ESAFSNCTALNNIEYSGSR  368 (394)
T ss_dssp             EEEECTT------CCBCC---GGGGTTCTTCCEEEESSCH
T ss_pred             EEEECcc------cCEEh---HhHhhCCCCCCEEEECCce
Confidence            9988653      22111   1346678889999988764

>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=94.75  E-value=0.02  Score=53.45  Aligned_cols=25  Identities=36%  Similarity=0.428  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|.|++|+||||+|+.+....
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999998866

>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=94.69  E-value=0.02  Score=53.30  Aligned_cols=26  Identities=27%  Similarity=0.420  Sum_probs=23.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+|.|.|++|+||||+|+.+.+....
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~   29 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRK   29 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            57999999999999999999987753

>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=94.67  E-value=0.019  Score=53.13  Aligned_cols=26  Identities=46%  Similarity=0.492  Sum_probs=22.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|.|+|++|+||||+|+.+.+...
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~   36 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSG   36 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhC
Confidence            45788999999999999999988763

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=94.64  E-value=0.13  Score=54.03  Aligned_cols=61  Identities=18%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             ccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccC
Q 004895          614 AIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGD  677 (724)
Q Consensus       614 ~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~  677 (724)
                      ..+.++.+|+.+.+..+ +..++.. +..+.+|+.+.+..  .+..+....+..++.|+.+.+..
T Consensus       156 ~aF~~c~~L~~i~l~~~-~~~I~~~~F~~c~~L~~i~l~~--~~~~I~~~~F~~~~~L~~i~~~~  217 (394)
T 4fs7_A          156 EAFATCESLEYVSLPDS-METLHNGLFSGCGKLKSIKLPR--NLKIIRDYCFAECILLENMEFPN  217 (394)
T ss_dssp             TTTTTCTTCCEEECCTT-CCEECTTTTTTCTTCCBCCCCT--TCCEECTTTTTTCTTCCBCCCCT
T ss_pred             hhhcccCCCcEEecCCc-cceeccccccCCCCceEEEcCC--CceEeCchhhccccccceeecCC
Confidence            34667777888887654 3445443 66677788777765  35556555666777776665544

>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=94.64  E-value=0.026  Score=51.27  Aligned_cols=28  Identities=29%  Similarity=0.426  Sum_probs=24.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+++.|+|+.|+|||||+..+......
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~l~~   30 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAAAVR   30 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhhHh
Confidence            4579999999999999999999998764

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.63  E-value=0.021  Score=51.99  Aligned_cols=27  Identities=19%  Similarity=0.420  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+|+|.|+.|+||||+|+.+.....
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~~lg   32 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGLALK   32 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ccceEEEECCCCCCHHHHHHHHHHHhC
Confidence            457899999999999999999988764

>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=94.62  E-value=0.13  Score=53.66  Aligned_cols=109  Identities=15%  Similarity=0.234  Sum_probs=80.8

Q ss_pred             cchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hhc
Q 004895          566 ISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQ  641 (724)
Q Consensus       566 ~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~  641 (724)
                      +....+.....|..+.+..+ +..+ ...+..+.+|+.+.+..+ ++.  ...+.++.+|+.+.+.. .++.++.. +..
T Consensus       208 i~~~~f~~~~~l~~i~~~~~-~~~i~~~~f~~~~~L~~i~lp~~-v~~I~~~aF~~~~~l~~i~l~~-~i~~i~~~aF~~  284 (379)
T 4h09_A          208 VTAYGFSYGKNLKKITITSG-VTTLGDGAFYGMKALDEIAIPKN-VTSIGSFLLQNCTALKTLNFYA-KVKTVPYLLCSG  284 (379)
T ss_dssp             ECTTTTTTCSSCSEEECCTT-CCEECTTTTTTCSSCCEEEECTT-CCEECTTTTTTCTTCCEEEECC-CCSEECTTTTTT
T ss_pred             Eeecccccccccceeeeccc-eeEEccccccCCccceEEEcCCC-ccEeCccccceeehhccccccc-cceecccccccc
Confidence            33445667778888887654 3333 345677888999998765 444  25677888999999965 46677654 788


Q ss_pred             CCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          642 LTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       642 l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +++|+.+.+.+ +.+..++...+.++++|+.+.+..+
T Consensus       285 c~~L~~i~l~~-~~i~~I~~~aF~~c~~L~~i~lp~~  320 (379)
T 4h09_A          285 CSNLTKVVMDN-SAIETLEPRVFMDCVKLSSVTLPTA  320 (379)
T ss_dssp             CTTCCEEEECC-TTCCEECTTTTTTCTTCCEEECCTT
T ss_pred             ccccccccccc-cccceehhhhhcCCCCCCEEEcCcc
Confidence            99999999987 4677888888999999999998653

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.58  E-value=0.086  Score=65.71  Aligned_cols=85  Identities=19%  Similarity=0.192  Sum_probs=56.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      ..+++.|+|++|+|||+||.++.......  =..++|+++.+.++...     ++.++.+.+.     ....+.....+.
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~--G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~~ 1498 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD 1498 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTT--TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc--CCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHHH
Confidence            45799999999999999999998876542  23578888887766544     5556643211     111233344444


Q ss_pred             HHHhcCCcEEEEEcccc
Q 004895          255 QRLKKEKRVLIILDNIW  271 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~  271 (724)
                      ......+..+||+|.+.
T Consensus      1499 ~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1499 ALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHHTCCSEEEESCGG
T ss_pred             HHHhcCCCCEEEEcChh
Confidence            44455678899999994

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.56  E-value=0.019  Score=52.82  Aligned_cols=25  Identities=36%  Similarity=0.488  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..|.|+|++|+||||+|+.+.....
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l~   29 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDLD   29 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3689999999999999999998764

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.56  E-value=0.043  Score=56.03  Aligned_cols=42  Identities=26%  Similarity=0.453  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhc----CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          166 KKIFQDVIEALK----DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       166 ~~~~~~l~~~L~----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +...+.+++.+.    .+....|.|+|+.|+||||+++.++.....
T Consensus         5 ~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l~~   50 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINE   50 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHhCC
Confidence            444555555543    455667999999999999999999987653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.55  E-value=0.021  Score=56.15  Aligned_cols=25  Identities=28%  Similarity=0.239  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|+|+.|+||||||+.++....
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~~   26 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQETG   26 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcCC
Confidence            4789999999999999999988763

>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=94.55  E-value=0.034  Score=57.91  Aligned_cols=44  Identities=20%  Similarity=0.169  Sum_probs=35.1

Q ss_pred             ccchHHHHHHHHHHhc-------------C--CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK-------------D--DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~-------------~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++|.+..++.+...+.             .  .....+.++|++|+|||++|+.+++..
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~   75 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL   75 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc
Confidence            5788888888877762             1  134568899999999999999999876

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.54  E-value=0.16  Score=51.86  Aligned_cols=51  Identities=18%  Similarity=0.222  Sum_probs=37.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -.++.|.|.+|+||||||..++......  =..++|++.  .-+..++...++..
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~a~~--g~~Vl~fSl--Ems~~ql~~Rlls~   96 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSALND--DRGVAVFSL--EMSAEQLALRALSD   96 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHT--TCEEEEEES--SSCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHc--CCeEEEEeC--CCCHHHHHHHHHHH
Confidence            3589999999999999999999887642  134667655  45667777776554

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=94.53  E-value=0.092  Score=55.85  Aligned_cols=100  Identities=21%  Similarity=0.322  Sum_probs=63.5

Q ss_pred             HHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC-hHHHHHHHHHhhCCC----------
Q 004895          172 VIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD-AQKIQGELASDLGMN----------  239 (724)
Q Consensus       172 l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~l~~~i~~~l~~~----------  239 (724)
                      .++.|. =.+-..++|.|..|+|||+|+..+.+.... .+-+.++++-+.+... ..++.+++...-...          
T Consensus       155 vID~l~pigkGqr~gIfgg~GvGKT~L~~~l~~~~a~-~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rtv  233 (498)
T 1fx0_B          155 VVNLLAPYRRGGKIGLFGGAGVGKTVLIMELINNIAK-AHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKVA  233 (498)
T ss_dssp             THHHHSCCCTTCCEEEEECSSSSHHHHHHHHHHHTTT-TCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCEE
T ss_pred             EeeeecccccCCeEEeecCCCCCchHHHHHHHHHHHh-hCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccceE
Confidence            445444 234457899999999999999999987643 3457788888887653 556667776532111          


Q ss_pred             -----CCCCch----hHHHHHHHHHHHhc--CCcEEEEEccccc
Q 004895          240 -----FDSNDL----IYHRAKQLCQRLKK--EKRVLIILDNIWT  272 (724)
Q Consensus       240 -----~~~~~~----~~~~~~~l~~~l~~--~kr~LlVlDdv~~  272 (724)
                           .+++..    .....-.+.++++.  ++.+||++||+-.
T Consensus       234 vV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~DsitR  277 (498)
T 1fx0_B          234 LVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFR  277 (498)
T ss_dssp             EEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSHH
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHH
Confidence                 111110    01123344555653  7899999999854

>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=94.53  E-value=0.023  Score=52.16  Aligned_cols=25  Identities=28%  Similarity=0.542  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|+|+|+.|+||||+++.+....
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999998765

>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=94.50  E-value=0.024  Score=53.89  Aligned_cols=27  Identities=30%  Similarity=0.352  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+++|+|+.|+|||||++.+.....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            456899999999999999999987653

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.49  E-value=0.023  Score=53.55  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|+|.|+.|+||||+++.+.+...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            689999999999999999998764

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.48  E-value=0.027  Score=53.95  Aligned_cols=41  Identities=24%  Similarity=0.399  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          166 KKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       166 ~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++....+...+......+|+|+|.+|+|||||+..+.....
T Consensus        15 ~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           15 KRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             HHHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            33444444444445678999999999999999999988764

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.47  E-value=0.026  Score=52.81  Aligned_cols=26  Identities=42%  Similarity=0.479  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +..+|.|.|+.|+||||+|+.+.+..
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

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.44  E-value=0.025  Score=53.42  Aligned_cols=25  Identities=32%  Similarity=0.557  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+++|+|+.|+|||||++.+....
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            3589999999999999999998764

>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=94.44  E-value=0.15  Score=51.08  Aligned_cols=88  Identities=17%  Similarity=0.222  Sum_probs=47.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH--HHHHHHHHhhCCCCC---CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ--KIQGELASDLGMNFD---SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~l~~~i~~~l~~~~~---~~~~~~~~~~~l~  254 (724)
                      ...+++|+|.+|+||||++..++.......  ..+.++... .....  ..+..+.+..+...-   .............
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~--~~v~l~~~d-~~~~~~~~ql~~~~~~~~l~~~~~~~~~~p~~l~~~~l  173 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAAD-TQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVE  173 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTT--CCEEEEECC-SSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEecCC-cccHhHHHHHHHhcccCCeEEEEcCCCCCHHHHHHHHH
Confidence            346899999999999999999998876532  235555443 22221  123344455554321   1111222323333


Q ss_pred             HHHhcCCcEEEEEccc
Q 004895          255 QRLKKEKRVLIILDNI  270 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv  270 (724)
                      ..+...+.=++|+|-.
T Consensus       174 ~~~~~~~~D~viiDtp  189 (295)
T 1ls1_A          174 EKARLEARDLILVDTA  189 (295)
T ss_dssp             HHHHHHTCCEEEEECC
T ss_pred             HHHHhCCCCEEEEeCC
Confidence            3332123447788875

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.44  E-value=0.041  Score=47.76  Aligned_cols=51  Identities=18%  Similarity=0.175  Sum_probs=31.4

Q ss_pred             EEEcCCcccC--CcccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCC
Q 004895          602 TLCLDGWRLE--DIAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNC  653 (724)
Q Consensus       602 ~L~L~~~~l~--~~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~  653 (724)
                      .++-+++.++  .++. +-..+|++|+|++|.|+.+|.+ +..+++|++|+|.+|
T Consensus        12 ~v~Cs~~~L~~~~vP~-~lp~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N   65 (130)
T 3rfe_A           12 LVDCGRRGLTWASLPT-AFPVDTTELVLTGNNLTALPPGLLDALPALRTAHLGAN   65 (130)
T ss_dssp             EEECCSSCCCTTTSCS-CCCTTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSS
T ss_pred             EEEeCCCCCccccCCC-CCCcCCCEEECCCCcCCccChhhhhhccccCEEEecCC
Confidence            5566666665  4221 1223577777777777777665 566777777777764

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.43  E-value=0.037  Score=55.44  Aligned_cols=26  Identities=27%  Similarity=0.307  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|.|.|++|+||||+|+.+....
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            45689999999999999999998764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.42  E-value=0.021  Score=54.01  Aligned_cols=26  Identities=38%  Similarity=0.741  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|.|+|+.|+||||+++.+....
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            34689999999999999999998865

>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=94.41  E-value=0.058  Score=50.29  Aligned_cols=83  Identities=14%  Similarity=0.192  Sum_probs=46.2

Q ss_pred             hhcCCCCceEEEcCCC-cCC-----CCCccccCCCCCcEEEcCCcccCCc------ccccCCCCCcEEEccCCcCcc---
Q 004895          570 FFEGTEELKVLDFTGI-RFS-----PLPSSLGRLINLQTLCLDGWRLEDI------AIVGQLKKLEILSLRGAEIKQ---  634 (724)
Q Consensus       570 ~~~~l~~L~~L~l~~~-~~~-----~lp~~i~~l~~L~~L~L~~~~l~~~------~~~~~l~~L~~L~l~~~~i~~---  634 (724)
                      .+.+-+.|+.|+|+++ .+.     .+-..+..-.+|+.|+|++|.+.+.      ..+..=..|++|+|++|.|..   
T Consensus        36 ll~~n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga  115 (197)
T 1pgv_A           36 LREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELL  115 (197)
T ss_dssp             HHTTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHH
T ss_pred             HHhcCCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHH
Confidence            3445566777777764 554     1233444556677777777776541      233344556777777766652   


Q ss_pred             --cchhhhcCCCCCeEccCC
Q 004895          635 --LPLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       635 --lp~~i~~l~~L~~L~l~~  652 (724)
                        +-..+..-+.|++|+|++
T Consensus       116 ~ala~aL~~N~tL~~L~L~n  135 (197)
T 1pgv_A          116 ARLLRSTLVTQSIVEFKADN  135 (197)
T ss_dssp             HHHHHHTTTTCCCSEEECCC
T ss_pred             HHHHHHHhhCCceeEEECCC
Confidence              222334445566666654

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=94.40  E-value=0.028  Score=53.59  Aligned_cols=28  Identities=29%  Similarity=0.363  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+.++|.|.|++|+||||.|+.+++.+.
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~g   54 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKFH   54 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHHC
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHC
Confidence            3567999999999999999999998774

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=94.38  E-value=0.024  Score=61.35  Aligned_cols=44  Identities=11%  Similarity=0.138  Sum_probs=35.4

Q ss_pred             cccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|+++.++.+...+..+.  -|.|+|++|+|||+||+.+++...
T Consensus        23 ~ivGq~~~i~~l~~al~~~~--~VLL~GpPGtGKT~LAraLa~~l~   66 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGE--SVFLLGPPGIAKSLIARRLKFAFQ   66 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTC--EEEEECCSSSSHHHHHHHGGGGBS
T ss_pred             hhHHHHHHHHHHHHHHhcCC--eeEeecCchHHHHHHHHHHHHHHh
Confidence            46788888888877765433  678999999999999999988653

>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=94.35  E-value=0.021  Score=53.02  Aligned_cols=25  Identities=28%  Similarity=0.429  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|+|++|+||||+|+.+.....
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALG   27 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcC
Confidence            3689999999999999999988764

>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=94.35  E-value=0.029  Score=52.08  Aligned_cols=25  Identities=36%  Similarity=0.414  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ....|.|+|+.|+||||+++.+.+.
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

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.35  E-value=0.027  Score=52.63  Aligned_cols=25  Identities=28%  Similarity=0.297  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|.|+.|+||||+|+.+.+..
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            3579999999999999999998765

>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=94.34  E-value=0.22  Score=49.93  Aligned_cols=88  Identities=24%  Similarity=0.265  Sum_probs=49.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCCCC---CchhHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNFDS---NDLIYHRAKQLCQR  256 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~~~---~~~~~~~~~~l~~~  256 (724)
                      ..+++++|.+|+||||++..++.......  ..+.++...-. +...+.++...+..+.+.-.   ............+.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g--~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~~  175 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKG--FKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVEK  175 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTT--CCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHHH
Confidence            56899999999999999999998876532  23556654322 22223344455555543211   11122333344444


Q ss_pred             HhcCCcEEEEEccc
Q 004895          257 LKKEKRVLIILDNI  270 (724)
Q Consensus       257 l~~~kr~LlVlDdv  270 (724)
                      +....-=++|+|-.
T Consensus       176 ~~~~~~D~ViIDTp  189 (297)
T 1j8m_F          176 FLSEKMEIIIVDTA  189 (297)
T ss_dssp             HHHTTCSEEEEECC
T ss_pred             HHhCCCCEEEEeCC
Confidence            43222237777865

>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=94.34  E-value=0.028  Score=51.91  Aligned_cols=25  Identities=48%  Similarity=0.616  Sum_probs=22.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++|+|+.|+|||||++.++.....
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i   26 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            5889999999999999999988753

>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=94.29  E-value=0.025  Score=52.74  Aligned_cols=22  Identities=36%  Similarity=0.572  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .+++|+|+.|+|||||++.+..
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            4789999999999999999975

>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=94.28  E-value=0.026  Score=54.26  Aligned_cols=25  Identities=36%  Similarity=0.550  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|+|+|+.|+||||+|+.+.....
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g   30 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQ   30 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            5899999999999999999988653

>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=94.26  E-value=0.19  Score=50.55  Aligned_cols=88  Identities=22%  Similarity=0.291  Sum_probs=48.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH--HHHHHHHHhhCCCC----CCCchhHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ--KIQGELASDLGMNF----DSNDLIYHRAKQL  253 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~l~~~i~~~l~~~~----~~~~~~~~~~~~l  253 (724)
                      ...++.|+|++|+||||++..++.......  ..+.++.. +.+...  +-+...++..+...    ............+
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g--~kV~lv~~-D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al  179 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAA-DTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAV  179 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEE-CTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcC--CEEEEEcc-ccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            456999999999999999999998876531  23555544 233322  22334455554332    1111011112233


Q ss_pred             HHHHhcCCcEEEEEcccc
Q 004895          254 CQRLKKEKRVLIILDNIW  271 (724)
Q Consensus       254 ~~~l~~~kr~LlVlDdv~  271 (724)
                      ...+.. +.-++|+|-.-
T Consensus       180 ~~a~~~-~~dvvIiDtpg  196 (306)
T 1vma_A          180 AHALAR-NKDVVIIDTAG  196 (306)
T ss_dssp             HHHHHT-TCSEEEEEECC
T ss_pred             HHHHhc-CCCEEEEECCC
Confidence            333433 34478888653

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.26  E-value=0.029  Score=53.03  Aligned_cols=25  Identities=36%  Similarity=0.405  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+++|+|+.|+||||+++.+....
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            4589999999999999999998755

>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=94.25  E-value=0.043  Score=57.47  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+.++|++|+|||++|+.+++..
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~~l   96 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAKHL   96 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHh
Confidence            3468899999999999999999876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.24  E-value=0.38  Score=51.87  Aligned_cols=38  Identities=29%  Similarity=0.353  Sum_probs=27.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      ...+|+|+|.+|+||||++..++.....+ .. .+..|+.
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~-G~-kVllVd~  137 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRK-GW-KTCLICA  137 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHT-TC-CEEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC-CC-eEEEEec
Confidence            45699999999999999999999887643 22 2444544

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.23  E-value=0.031  Score=53.11  Aligned_cols=27  Identities=37%  Similarity=0.532  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+|+|+|+.|+|||||++.+.....
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~~~~   31 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALARTLG   31 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHG
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHhC
Confidence            446899999999999999999988764

>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=0.032  Score=52.65  Aligned_cols=26  Identities=31%  Similarity=0.442  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|+|.|+.|+||||+|+.+.+..
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            45689999999999999999998764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.21  E-value=0.072  Score=51.90  Aligned_cols=49  Identities=22%  Similarity=0.263  Sum_probs=32.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      -.++.|.|.+|+|||+||.+++.....+. -..++|++..  .+..++...+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~-~~~v~~~s~E--~~~~~~~~~~   78 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEY-GEPGVFVTLE--ERARDLRREM   78 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS--SCHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCceeeccc--CCHHHHHHHH
Confidence            45899999999999999999776532221 2346666654  3455555444

>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=94.21  E-value=0.031  Score=54.69  Aligned_cols=27  Identities=33%  Similarity=0.356  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +..+|+|+|+.|+|||||++.+++...
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~lg   52 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNFG   52 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            356999999999999999999997763

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.20  E-value=0.075  Score=46.05  Aligned_cols=53  Identities=19%  Similarity=0.354  Sum_probs=34.7

Q ss_pred             EEEcCCCcCC--CCCccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCc
Q 004895          579 VLDFTGIRFS--PLPSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIK  633 (724)
Q Consensus       579 ~L~l~~~~~~--~lp~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~  633 (724)
                      +++.++++++  .+|..+.  .+|++|+|++|.|+.+  ..+..+++|++|+|++|.+.
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--VDTTELVLTGNNLTALPPGLLDALPALRTAHLGANPWR   68 (130)
T ss_dssp             EEECCSSCCCTTTSCSCCC--TTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSCCB
T ss_pred             EEEeCCCCCccccCCCCCC--cCCCEEECCCCcCCccChhhhhhccccCEEEecCCCee
Confidence            5666666666  6665432  3577777777777763  34667777777777777543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.18  E-value=0.03  Score=51.95  Aligned_cols=24  Identities=25%  Similarity=0.389  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..|.|.|+.|+||||+|+.+.+..
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478999999999999999998765

>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=94.17  E-value=0.026  Score=51.65  Aligned_cols=25  Identities=28%  Similarity=0.392  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|.|+.|+||||+|+.+.+...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg   27 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALG   27 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhC
Confidence            4689999999999999999988764

>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=94.16  E-value=0.029  Score=52.78  Aligned_cols=26  Identities=31%  Similarity=0.411  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .+..+|+|+|+.|+||||+|+.+...
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            45678999999999999999999874

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=94.16  E-value=0.029  Score=52.60  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|+|.|+.|+||||+|+.+.+...
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~   37 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYG   37 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            35899999999999999999998763

>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=94.12  E-value=0.036  Score=52.19  Aligned_cols=26  Identities=23%  Similarity=0.226  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|.|+|+.|+||||+|+.+.+...
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~   45 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLG   45 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999988763

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=94.11  E-value=0.033  Score=52.82  Aligned_cols=26  Identities=19%  Similarity=0.326  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+|.|.|+.|+||||+|+.+.+....
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~   30 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIEL   30 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            57999999999999999999998754

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=94.04  E-value=0.021  Score=59.00  Aligned_cols=111  Identities=12%  Similarity=0.074  Sum_probs=59.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH--HHHHHHHHhhCCCCCCCchhHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ--KIQGELASDLGMNFDSNDLIYHRAKQLCQRL  257 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l  257 (724)
                      ...+++|+|+.|+|||||.+.+.......  ....+ +++.+.....  .. ..++.+.......    ......+...|
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~--~~~~i-~t~ed~~e~~~~~~-~~~v~q~~~~~~~----~~~~~~La~aL  193 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNT--KYHHI-LTIEDPIEFVHESK-KCLVNQREVHRDT----LGFSEALRSAL  193 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHH--CCCEE-EEEESSCCSCCCCS-SSEEEEEEBTTTB----SCHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCC--CCcEE-EEccCcHHhhhhcc-ccceeeeeecccc----CCHHHHHHHHh
Confidence            44599999999999999999998876542  11222 2333221110  00 0000000000011    11233566666


Q ss_pred             hcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEecccchh
Q 004895          258 KKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL  310 (724)
Q Consensus       258 ~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~  310 (724)
                      .. .+=+|++|+.-+.+.++.+...           ...|..|++|+-..+.+
T Consensus       194 ~~-~PdvillDEp~d~e~~~~~~~~-----------~~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          194 RE-DPDIILVGEMRDLETIRLALTA-----------AETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             TS-CCSEEEESCCCSHHHHHHHHHH-----------HHTTCEEEEEESCSSHH
T ss_pred             hh-CcCEEecCCCCCHHHHHHHHHH-----------HhcCCEEEEEEccChHH
Confidence            64 6778899999765554433221           22355688888877653

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.04  E-value=0.028  Score=52.95  Aligned_cols=26  Identities=27%  Similarity=0.424  Sum_probs=22.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++++|+|+.|+|||||++.+.....
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            35789999999999999999988653

>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=94.04  E-value=0.029  Score=53.01  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .+|+|+|+.|+||||+++.+..
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            3799999999999999999987

>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=94.03  E-value=0.065  Score=52.20  Aligned_cols=27  Identities=22%  Similarity=0.103  Sum_probs=23.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+|.|.|++|+||||+|+.+.+..
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            356689999999999999999998766

>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=94.02  E-value=0.033  Score=55.02  Aligned_cols=26  Identities=38%  Similarity=0.611  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|.|+|++|+||||+|+.+.....
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~   29 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILS   29 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            46899999999999999999998764

>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=94.02  E-value=0.088  Score=48.83  Aligned_cols=115  Identities=19%  Similarity=0.178  Sum_probs=60.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec---CCChHHHHHHHHHhhC-------C--CCCCCchh--
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK---NPDAQKIQGELASDLG-------M--NFDSNDLI--  246 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~---~~~~~~l~~~i~~~l~-------~--~~~~~~~~--  246 (724)
                      ...|.|++..|.||||.|--.+-+.... .+ .+.++..-+   ..+..+    +++.++       .  .+......  
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~-G~-rV~~vQF~Kg~~~~gE~~----~l~~L~v~~~~~g~gf~~~~~~~~~~  101 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH-GK-NVGVVQFIKGTWPNGERN----LLEPHGVEFQVMATGFTWETQNREAD  101 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT-TC-CEEEEESSCCSSCCHHHH----HHGGGTCEEEECCTTCCCCGGGHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC-CC-eEEEEEeeCCCCCccHHH----HHHhCCcEEEEcccccccCCCCcHHH
Confidence            3466677777799999999998887643 22 344554332   222333    344442       1  11111101  


Q ss_pred             ----HHHHHHHHHHHhcCCcEEEEEcccccccc-----ccccccccCCCCcCCCCCCCCCcEEEEEecccch
Q 004895          247 ----YHRAKQLCQRLKKEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDL  309 (724)
Q Consensus       247 ----~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v  309 (724)
                          ........+.+..++-=|||||++-....     .+.+...+..        ......||+|+|...-
T Consensus       102 ~~~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~--------Rp~~~~vIlTGr~ap~  165 (196)
T 1g5t_A          102 TAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNA--------RPGHQTVIITGRGCHR  165 (196)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHT--------SCTTCEEEEECSSCCH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHh--------CcCCCEEEEECCCCcH
Confidence                11223344444444555999999954322     2222222222        3456679999999753

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.01  E-value=0.051  Score=55.09  Aligned_cols=44  Identities=20%  Similarity=0.286  Sum_probs=30.5

Q ss_pred             cchHHHHHHHHHHhc-C---CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          163 NSRKKIFQDVIEALK-D---DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~-~---~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +|....+..+...+. .   ....+|+|.|+.|+||||||+.+.....
T Consensus        70 ~~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           70 VTARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             HHHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             hcchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344444444443333 2   2355999999999999999999987764

>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=94.00  E-value=0.036  Score=51.82  Aligned_cols=27  Identities=19%  Similarity=0.315  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..++++|+|+.|+|||||++.+.....
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            456899999999999999999987653

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=93.96  E-value=0.36  Score=49.62  Aligned_cols=51  Identities=24%  Similarity=0.253  Sum_probs=35.2

Q ss_pred             HHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe-EEEEEEecC
Q 004895          171 DVIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK-VVMAEITKN  222 (724)
Q Consensus       171 ~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~  222 (724)
                      +.++.+.. .+-..++|+|.+|+|||+|+..+.+....+ +-+. ++++-+.+.
T Consensus       164 raID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~-~~dv~~V~~lIGER  216 (427)
T 3l0o_A          164 RLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAEN-HPDTIRIILLIDER  216 (427)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHHHHHH-CTTSEEEEEECSCC
T ss_pred             hhhhhcccccCCceEEEecCCCCChhHHHHHHHHHHhhc-CCCeEEEEEEeccC
Confidence            45566552 445688999999999999999999876542 2232 345666544

>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=93.96  E-value=0.029  Score=52.05  Aligned_cols=25  Identities=32%  Similarity=0.473  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.|.|+||.|+|||||++.+.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            3578999999999999999987653

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.94  E-value=0.036  Score=50.35  Aligned_cols=24  Identities=21%  Similarity=0.241  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|.|+.|+||||+|+.+.+...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~   25 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLN   25 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            689999999999999999988764

>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=93.94  E-value=0.044  Score=55.31  Aligned_cols=28  Identities=32%  Similarity=0.521  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +..+++|+|++|+||||+++.++.....
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~  128 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQN  128 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            4569999999999999999999988765

>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=93.92  E-value=0.035  Score=51.74  Aligned_cols=26  Identities=31%  Similarity=0.331  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|+|.|+.|+||||+|+.+.+...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~   31 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFG   31 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999988653

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.88  E-value=0.027  Score=51.61  Aligned_cols=22  Identities=32%  Similarity=0.592  Sum_probs=19.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQI  201 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v  201 (724)
                      .-.+++|+|+.|+|||||++.+
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~   29 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKH   29 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            3468999999999999999964

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=93.86  E-value=0.025  Score=52.27  Aligned_cols=26  Identities=31%  Similarity=0.345  Sum_probs=18.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|.|.|+.|+||||+|+.+.+...
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~   30 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLP   30 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            45899999999999999999987653

>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=93.86  E-value=0.04  Score=52.77  Aligned_cols=26  Identities=19%  Similarity=0.204  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|.|+.|+||||+|+.+++...
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~   29 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFH   29 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcC
Confidence            45799999999999999999988763

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.86  E-value=0.038  Score=51.54  Aligned_cols=25  Identities=32%  Similarity=0.526  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|+|.|+.|+||||+|+.+.+....
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~   26 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQ   26 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            6899999999999999999997753

>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=93.85  E-value=0.043  Score=55.66  Aligned_cols=41  Identities=20%  Similarity=0.323  Sum_probs=32.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      ++.+||+|.|-||+||||.+..++.-.....  ..+.-|++..
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~aLA~~G--kkVllID~Dp   86 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSAAFSILG--KRVLQIGCDP   86 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEEESS
T ss_pred             CCceEEEEECCCccCHHHHHHHHHHHHHHCC--CeEEEEecCC
Confidence            4678999999999999999999998886532  2366677653

>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=93.79  E-value=0.7  Score=49.38  Aligned_cols=42  Identities=31%  Similarity=0.392  Sum_probs=30.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ...+++|+|+.|+|||||++.++......   .+.+++...+.+.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~---~G~V~l~g~D~~r  333 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTFR  333 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEECCCTTC
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhc---CCeEEEecCcccc
Confidence            35699999999999999999999887643   3344554334443

>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=93.79  E-value=0.036  Score=52.46  Aligned_cols=25  Identities=48%  Similarity=0.706  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ...+|+|+|+.|+||||+|+.+...
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            3468999999999999999998764

>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=93.78  E-value=0.073  Score=53.91  Aligned_cols=42  Identities=24%  Similarity=0.256  Sum_probs=29.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      ....+|+|+|+.|+|||||++.+..-......-..+.++.-.
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~gll~~~~G~~~v~~v~qd  129 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTD  129 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHHTSTTCCCEEEEEGG
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHhhccccCCCCeEEEEecC
Confidence            345699999999999999999999877542111235555543

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=93.77  E-value=0.058  Score=50.34  Aligned_cols=38  Identities=21%  Similarity=0.283  Sum_probs=27.7

Q ss_pred             HHHHHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          169 FQDVIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       169 ~~~l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +..+..++.. ++...+.|+|++|+||||+|..+++...
T Consensus        45 ~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~   83 (212)
T 1tue_A           45 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   83 (212)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3444444432 2234799999999999999999998764

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=93.77  E-value=0.043  Score=52.05  Aligned_cols=32  Identities=22%  Similarity=0.230  Sum_probs=26.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK  213 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~  213 (724)
                      ..+|+|.|+.|+||||+|+.+.+.... .+++.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~-~~~~~   41 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKN-NNVEV   41 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHH-TTCCE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH-cCCcE
Confidence            458999999999999999999998764 34554

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.76  E-value=0.047  Score=53.59  Aligned_cols=27  Identities=30%  Similarity=0.320  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+|.|+|++|+||||+|+.+.....
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcC
Confidence            356899999999999999999987653

>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=93.76  E-value=0.045  Score=52.01  Aligned_cols=32  Identities=16%  Similarity=0.218  Sum_probs=26.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK  213 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~  213 (724)
                      ..+|+|.|+.|+||||+|+.+.+.... .+++.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~-~~~~v   40 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCA-AGHRA   40 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH-TTCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH-cCCcE
Confidence            468999999999999999999998764 34444

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.73  E-value=0.22  Score=53.28  Aligned_cols=52  Identities=13%  Similarity=0.070  Sum_probs=37.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -.++.|.|.+|+||||||..++....... =..++|++..  -+..++...++..
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~~~-g~~vl~~slE--~~~~~l~~R~~~~  251 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAALKE-GVGVGIYSLE--MPAAQLTLRMMCS  251 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESS--SCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHhC-CCeEEEEECC--CCHHHHHHHHHHH
Confidence            45899999999999999999998875421 1347777654  4566777666543

>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=93.73  E-value=0.038  Score=52.87  Aligned_cols=111  Identities=12%  Similarity=0.069  Sum_probs=60.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      .-.++.|+|..|+||||++..+.++.....  ..++.+......  . -...+++.++........  .....+.+.+..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g--~kVli~~~~~d~--r-~~~~i~srlG~~~~~~~~--~~~~~i~~~i~~   83 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYAD--VKYLVFKPKIDT--R-SIRNIQSRTGTSLPSVEV--ESAPEILNYIMS   83 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTT--CCEEEEEECCCG--G-GCSSCCCCCCCSSCCEEE--SSTHHHHHHHHS
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcC--CEEEEEEeccCc--h-HHHHHHHhcCCCcccccc--CCHHHHHHHHHH
Confidence            446889999999999999999998886532  234444433221  1 112445555544322110  011223333332


Q ss_pred             ----CCcEEEEEcccccc--ccccccccccCCCCcCCCCCCCCCcEEEEEecccc
Q 004895          260 ----EKRVLIILDNIWTK--LELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD  308 (724)
Q Consensus       260 ----~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~  308 (724)
                          ++.-+||+|.+...  +.++.+. .+          ...+..||+|-+..+
T Consensus        84 ~~~~~~~dvViIDEaQ~l~~~~ve~l~-~L----------~~~gi~Vil~Gl~~d  127 (223)
T 2b8t_A           84 NSFNDETKVIGIDEVQFFDDRICEVAN-IL----------AENGFVVIISGLDKN  127 (223)
T ss_dssp             TTSCTTCCEEEECSGGGSCTHHHHHHH-HH----------HHTTCEEEEECCSBC
T ss_pred             HhhCCCCCEEEEecCccCcHHHHHHHH-HH----------HhCCCeEEEEecccc
Confidence                33459999999643  1222221 11          113677888888654

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.72  E-value=0.037  Score=50.63  Aligned_cols=27  Identities=30%  Similarity=0.482  Sum_probs=24.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ++++|+|..|+|||||++.+.......
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~~~   29 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILRER   29 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhhc
Confidence            589999999999999999999887654

>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=93.70  E-value=0.036  Score=52.57  Aligned_cols=27  Identities=22%  Similarity=0.401  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|+|||||++.+..-..
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            345899999999999999999987653

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.66  E-value=0.042  Score=52.40  Aligned_cols=23  Identities=35%  Similarity=0.460  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.|.|+.|+||||+|+.+.+..
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            57899999999999999998876

>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=93.64  E-value=0.34  Score=51.00  Aligned_cols=57  Identities=18%  Similarity=0.230  Sum_probs=36.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHH--HHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQK--IQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~--l~~~i~~~l~~~  239 (724)
                      ...++.|+|++|+||||++..++.......  ..+..+.. +.+....  .+....+..+.+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g--~~Vllvd~-D~~r~aa~~qL~~~~~~~gv~  155 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKG--RRPLLVAA-DTQRPAAREQLRLLGEKVGVP  155 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTT--CCEEEEEC-CSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcC--CeEEEeec-cccCchhHHHHHHhcccCCcc
Confidence            356899999999999999999999886532  23455544 3333322  234444555543

>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=0.036  Score=52.38  Aligned_cols=22  Identities=36%  Similarity=0.558  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .+|+|+|+.|+||||+++.+..
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            4799999999999999999975

>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=93.63  E-value=0.045  Score=51.14  Aligned_cols=27  Identities=30%  Similarity=0.486  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+|+|+|+.|+||||+|+.+.+..
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHHhc
Confidence            356799999999999999999998763

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.63  E-value=0.043  Score=53.88  Aligned_cols=27  Identities=37%  Similarity=0.466  Sum_probs=23.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+|+|+|+.|+||||+++.+.+...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg   52 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLN   52 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcC
Confidence            446999999999999999999997763

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.61  E-value=0.04  Score=52.84  Aligned_cols=26  Identities=19%  Similarity=0.149  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|.|+.|+||||+|+.+++...
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~   30 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQ   30 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998764

>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=93.61  E-value=0.025  Score=53.77  Aligned_cols=25  Identities=32%  Similarity=0.609  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +|+|.|+.|+||||+|+.+......
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            7899999999999999999988754

>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=93.56  E-value=0.042  Score=53.90  Aligned_cols=28  Identities=25%  Similarity=0.386  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+|+|.|+.|+||||+|+.+.....
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3556899999999999999999988654

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.56  E-value=0.042  Score=52.88  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...|.|.|+.|+||||+|+.+.+..
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

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.53  E-value=0.045  Score=53.40  Aligned_cols=27  Identities=30%  Similarity=0.442  Sum_probs=23.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+|+|.|+.|+|||||++.+....
T Consensus        23 ~~g~iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           23 MRPFLIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             CCSEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            345699999999999999999998865

>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=93.46  E-value=0.046  Score=49.23  Aligned_cols=27  Identities=30%  Similarity=0.431  Sum_probs=24.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..-.+++|+|+.|.|||||++.++.-.
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            445699999999999999999999876

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.41  E-value=0.04  Score=52.71  Aligned_cols=26  Identities=35%  Similarity=0.712  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+....
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34589999999999999999998755

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.34  E-value=0.31  Score=52.25  Aligned_cols=50  Identities=24%  Similarity=0.299  Sum_probs=36.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      -.++.|.|.+|+||||||..++....... =..++|++..  .+..++...++
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~E--~s~~~l~~r~~  252 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSLE--MSAQQLVMRML  252 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEESS--SCHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEECC--CCHHHHHHHHH
Confidence            45899999999999999999998876431 1247777654  34556666654

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.32  E-value=0.047  Score=50.85  Aligned_cols=25  Identities=32%  Similarity=0.458  Sum_probs=22.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+++|+|+.|+|||||++.++....
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhcc
Confidence            3689999999999999999998875

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.28  E-value=0.054  Score=60.59  Aligned_cols=49  Identities=16%  Similarity=0.165  Sum_probs=39.8

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.....++|.+..++.+...+..+  ..+.|+|++|+||||||+.++....
T Consensus        37 p~~l~~i~G~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           37 EKLIDQVIGQEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             SSHHHHCCSCHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             ccccceEECchhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhccCC
Confidence            344567889998888887777654  4789999999999999999998654

>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=93.25  E-value=0.061  Score=51.08  Aligned_cols=28  Identities=25%  Similarity=0.401  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+|.|+|+.|+||||+++.+.....
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3456899999999999999999998876

>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=93.24  E-value=0.051  Score=51.79  Aligned_cols=23  Identities=26%  Similarity=0.390  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|+|.|++|+||||+|+.+.+..
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

>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=93.24  E-value=0.056  Score=51.12  Aligned_cols=24  Identities=38%  Similarity=0.427  Sum_probs=21.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +|.|.|++|+||||.|+.+++.+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g   25 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKG   25 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            688999999999999999998764

>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=93.23  E-value=0.06  Score=57.04  Aligned_cols=46  Identities=26%  Similarity=0.265  Sum_probs=35.0

Q ss_pred             cccchHHHHHHHHHHhcC--------------CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          161 IFNSRKKIFQDVIEALKD--------------DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~~--------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|.++.++.+..++..              ...+-|.++|++|+||||+|+.++....
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~   75 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   75 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcC
Confidence            467888877777655521              1345688999999999999999998774

>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=93.19  E-value=0.055  Score=51.70  Aligned_cols=27  Identities=22%  Similarity=0.322  Sum_probs=23.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|+|||||++.+.....
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            346899999999999999999988654

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=93.16  E-value=0.45  Score=62.16  Aligned_cols=88  Identities=16%  Similarity=0.220  Sum_probs=51.8

Q ss_pred             HHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC--CchhHHH
Q 004895          172 VIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS--NDLIYHR  249 (724)
Q Consensus       172 l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~--~~~~~~~  249 (724)
                      +++.+...+. -|.++|++|+|||+++..+.....   .+ ..+.++.|...+...++..+-..+......  ..     
T Consensus      1296 ll~~ll~~~~-pvLL~GptGtGKT~li~~~L~~l~---~~-~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~----- 1365 (3245)
T 3vkg_A         1296 VLHAWLSEHR-PLILCGPPGSGKTMTLTSTLRAFP---DF-EVVSLNFSSATTPELLLKTFDHHCEYKRTPSGET----- 1365 (3245)
T ss_dssp             HHHHHHHTTC-CCEEESSTTSSHHHHHHHHGGGCT---TE-EEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCE-----
T ss_pred             HHHHHHHCCC-cEEEECCCCCCHHHHHHHHHHhCC---CC-ceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCc-----
Confidence            3444333333 356899999999999877654331   11 256788888888888877775444211110  00     


Q ss_pred             HHHHHHHHhcCCcEEEEEccccc
Q 004895          250 AKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       250 ~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                         +..-...+++.++++||+.-
T Consensus      1366 ---~~~p~~~Gk~~VlFiDDiNm 1385 (3245)
T 3vkg_A         1366 ---VLRPTQLGKWLVVFCDEINL 1385 (3245)
T ss_dssp             ---EEEESSTTCEEEEEETTTTC
T ss_pred             ---ccCCCcCCceEEEEecccCC
Confidence               00000026789999999953

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=93.15  E-value=0.15  Score=49.16  Aligned_cols=36  Identities=22%  Similarity=0.446  Sum_probs=28.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      ...|.|.|+.|+||||+++.+.+.... .++..+...
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~~-~~~~~~~~~   62 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQQ-NGIDHITRT   62 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHHH-TTCCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh-cCCCeeeee
Confidence            458999999999999999999998875 345534433

>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=93.14  E-value=0.11  Score=47.67  Aligned_cols=27  Identities=26%  Similarity=0.525  Sum_probs=24.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+++.|+|+.|+|||||+..+......
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~~   32 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALCA   32 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhccc
Confidence            578999999999999999999987654

>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=50.82  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|+|.|+.|+||||+++.+.+..
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            3589999999999999999998765

>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=93.11  E-value=0.058  Score=51.90  Aligned_cols=26  Identities=23%  Similarity=0.442  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|+|.|++|+||||+|+.+.....
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg   34 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALG   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45899999999999999999988763

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.09  E-value=0.069  Score=53.81  Aligned_cols=28  Identities=32%  Similarity=0.509  Sum_probs=24.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+++|+|+.|+||||+++.++.....
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  126 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  126 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3469999999999999999999988764

>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=93.01  E-value=0.13  Score=53.30  Aligned_cols=39  Identities=26%  Similarity=0.514  Sum_probs=30.3

Q ss_pred             HHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          169 FQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       169 ~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+.+.+.  ..+..+|+|+|.+|+|||||+..+......
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~~l~~  105 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIE  105 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            344454444  456789999999999999999999887754

>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=92.98  E-value=0.07  Score=49.11  Aligned_cols=27  Identities=22%  Similarity=0.332  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+|+|+|+.|+||||+++.+......
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~   31 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVC   31 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            458899999999999999999987654

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.95  E-value=0.17  Score=48.07  Aligned_cols=52  Identities=17%  Similarity=0.183  Sum_probs=33.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ..|.|.|+.|+||||+++.+.+..... .+..+.+..-.....+.+.+++++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc-CCCcceeeeCCCCCHHHHHHHHHHh
Confidence            478999999999999999999988764 4433333322222223444455544

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.92  E-value=0.059  Score=52.30  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .. .+++|+|+.|+|||||++.++--.
T Consensus        23 ~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           23 GR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             CS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            45 799999999999999999987543

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=92.87  E-value=0.059  Score=51.47  Aligned_cols=24  Identities=29%  Similarity=0.320  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..|.|.|++|+||||+|+.+.+..
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            478999999999999999999876

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=92.87  E-value=0.055  Score=52.82  Aligned_cols=26  Identities=35%  Similarity=0.362  Sum_probs=23.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+|+|+|+.|+||||+++.+.....
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg   73 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLG   73 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            35899999999999999999998764

>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=92.84  E-value=0.067  Score=50.47  Aligned_cols=24  Identities=21%  Similarity=0.447  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +|+|.|+.|+||||+|+.+.....
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg   27 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALG   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcC
Confidence            899999999999999999988764

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.82  E-value=0.059  Score=54.87  Aligned_cols=25  Identities=32%  Similarity=0.388  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|+|.|+.|+||||||..++....
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            4899999999999999999988653

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=92.80  E-value=0.42  Score=50.97  Aligned_cols=50  Identities=18%  Similarity=0.249  Sum_probs=36.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      -.++.|.|.+|+||||||.+++.....++  ..++|++...  +..++...++.
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~g--~~vl~fSlEm--s~~ql~~R~~~  246 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEM--GKKENIKRLIV  246 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHTT--CEEEEECSSS--CTTHHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHcC--CEEEEEECCC--CHHHHHHHHHH
Confidence            45899999999999999999998876531  3477776543  44455555554

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=92.79  E-value=0.086  Score=55.85  Aligned_cols=101  Identities=19%  Similarity=0.176  Sum_probs=60.0

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhccC--CCeEEEEEEecCC-ChHHHHHHHHHhhCC--------C
Q 004895          172 VIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV--FDKVVMAEITKNP-DAQKIQGELASDLGM--------N  239 (724)
Q Consensus       172 l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~-~~~~l~~~i~~~l~~--------~  239 (724)
                      .++.|.. .+-..++|.|.+|+|||+|+.+++++....+.  =+.++++-+.+.. ...++.+++...=..        .
T Consensus       142 ~ID~l~pigrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~t  221 (469)
T 2c61_A          142 TIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNL  221 (469)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEE
T ss_pred             eeeeeeccccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEEC
Confidence            4455541 23446788999999999999999988754221  1356777777654 345666666543111        1


Q ss_pred             CCCCchh----HHHHHHHHHHHh--cCCcEEEEEccccc
Q 004895          240 FDSNDLI----YHRAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       240 ~~~~~~~----~~~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                      .+++...    ....-.+.+++.  +++++|+++||+-.
T Consensus       222 sd~p~~~r~~~~~~a~tiAEyfrdd~G~dVLl~~DsltR  260 (469)
T 2c61_A          222 ADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITN  260 (469)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCHHH
Confidence            1222111    112233455555  48999999999844

>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=92.77  E-value=0.078  Score=51.22  Aligned_cols=26  Identities=27%  Similarity=0.199  Sum_probs=23.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|.|+.|+||||+|+.+.+...
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~   41 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFC   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45799999999999999999998764

>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=92.75  E-value=0.068  Score=50.87  Aligned_cols=23  Identities=26%  Similarity=0.176  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.|.|+.|+||||+|+.+.+..
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

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.75  E-value=0.069  Score=51.23  Aligned_cols=23  Identities=26%  Similarity=0.268  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.|.|+.|+||||+|+.+.+..
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

>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=92.74  E-value=0.071  Score=50.86  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      ..+|+|.|+.|+||||+++.+..
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            35899999999999999999975

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.62  E-value=0.28  Score=61.20  Aligned_cols=86  Identities=19%  Similarity=0.219  Sum_probs=56.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~  254 (724)
                      .-+++.|+|++|+||||||.+++.......  ..++|++.....+..     .++.++.+.+     ......+....+.
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~~a~~G--~~vlyis~E~s~~~~-----~a~~lGvd~~~L~I~~~~~~e~il~~~~  454 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  454 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTT--CCEEEECTTSCCCHH-----HHHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHhcC--CeEEEEEcCCCHHHH-----HHHHcCCCHHHeEEeCCCCHHHHHHHHH
Confidence            446999999999999999999998876432  358888877766643     2566665432     1121333333333


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ......+.-+||+|-+..
T Consensus       455 ~lv~~~~~~lIVIDSL~a  472 (2050)
T 3cmu_A          455 ALARSGAVDVIVVDSVAA  472 (2050)
T ss_dssp             HHHHHTCCSEEEESCGGG
T ss_pred             HHHHhcCCcEEEECCHHH
Confidence            333345567999999854

>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=92.60  E-value=0.069  Score=53.31  Aligned_cols=23  Identities=26%  Similarity=0.732  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIA  202 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~  202 (724)
                      ...+|+|+|+.|+||||+|+.+.
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            45689999999999999999998

>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=92.57  E-value=0.2  Score=50.28  Aligned_cols=39  Identities=33%  Similarity=0.266  Sum_probs=29.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      .-.+++|+|++|+|||||++.++........ ..++|++.
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G-~~v~~~~~   72 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAMG-KKVGLAML   72 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHHHHHTSC-CCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHHcC-CeEEEEeC
Confidence            3458999999999999999999988765311 14666654

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=92.55  E-value=0.28  Score=60.43  Aligned_cols=86  Identities=20%  Similarity=0.242  Sum_probs=54.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCC-----CCchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFD-----SNDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~-----~~~~~~~~~~~l~  254 (724)
                      .-.++.|.|++|+||||||.+++.......  ..++|++.......  +   +++.++...+     ......+....+.
T Consensus       731 ~G~lVlI~G~PG~GKTtLal~lA~~aa~~g--~~VlyiS~Ees~~q--l---~A~~lGvd~~~L~i~~~~~leei~~~l~  803 (1706)
T 3cmw_A          731 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDP--I---YARKLGVDIDNLLCSQPDTGEQALEICD  803 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEECTTSCCCH--H---HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCceEEEECCCCCCcHHHHHHHHHHHHHcC--CCeEEEeccchHHH--H---HHHHcCCChhheEEecCCcHHHHHHHHH
Confidence            346899999999999999999998876432  25788877665543  2   2566664321     1111333344443


Q ss_pred             HHHhcCCcEEEEEccccc
Q 004895          255 QRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~~  272 (724)
                      ......+.-+||+|.+..
T Consensus       804 ~lv~~~~~~lVVIDsLq~  821 (1706)
T 3cmw_A          804 ALARSGAVDVIVVDSVAA  821 (1706)
T ss_dssp             HHHHHTCCSEEEESCSTT
T ss_pred             HHHHccCCCEEEEechhh
Confidence            333345667999999854

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=92.52  E-value=0.045  Score=52.88  Aligned_cols=25  Identities=32%  Similarity=0.383  Sum_probs=16.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH-HHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIA-KQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~-~~~  205 (724)
                      -.+++|+|+.|+|||||++.+. ...
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            4589999999999999999998 654

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=92.47  E-value=0.11  Score=54.73  Aligned_cols=101  Identities=18%  Similarity=0.200  Sum_probs=58.6

Q ss_pred             HHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhc--------cCCC-eEEEEEEecCC-ChHHHHHHHHHh--hC-
Q 004895          172 VIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMED--------NVFD-KVVMAEITKNP-DAQKIQGELASD--LG-  237 (724)
Q Consensus       172 l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~--------~~F~-~~~wv~vs~~~-~~~~l~~~i~~~--l~-  237 (724)
                      .++.|. =.+-..++|.|..|+|||+|+.++++.....        .+-+ .++++-+.+.. ...++.+++.+.  +. 
T Consensus       137 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~r  216 (464)
T 3gqb_B          137 TIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSR  216 (464)
T ss_dssp             HHHTTSCCBTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGG
T ss_pred             eeecccccccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccc
Confidence            444444 1233467899999999999999998876431        1222 46677777654 345555555432  11 


Q ss_pred             -----CCCCCCchhH----HHHHHHHHHHh--cCCcEEEEEccccc
Q 004895          238 -----MNFDSNDLIY----HRAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       238 -----~~~~~~~~~~----~~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                           ...+++....    ...-.+.+++.  .++++|+++||+-.
T Consensus       217 tvvv~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlTr  262 (464)
T 3gqb_B          217 SVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTN  262 (464)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHHH
T ss_pred             eEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence                 0112222111    12234556665  37999999999854

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=92.46  E-value=0.093  Score=54.08  Aligned_cols=28  Identities=32%  Similarity=0.509  Sum_probs=24.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...+++|+|+.|+||||+++.++.....
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~  183 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKN  183 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccc
Confidence            3469999999999999999999998764

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=92.46  E-value=0.18  Score=48.10  Aligned_cols=30  Identities=30%  Similarity=0.332  Sum_probs=25.7

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ......|.|.|+.|+||||+++.+.+....
T Consensus        18 ~~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           18 GPGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             -CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            345668999999999999999999998865

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.43  E-value=0.075  Score=53.72  Aligned_cols=24  Identities=29%  Similarity=0.332  Sum_probs=21.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+|.|+|+.|+||||||+.+++..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            489999999999999999998765

>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=92.41  E-value=0.077  Score=53.78  Aligned_cols=28  Identities=25%  Similarity=0.317  Sum_probs=24.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ....+|+|+|+.|+|||||++.+.....
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3456999999999999999999988764

>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=92.41  E-value=0.068  Score=51.75  Aligned_cols=26  Identities=23%  Similarity=0.374  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+.--.
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            44589999999999999999987544

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.41  E-value=0.058  Score=51.78  Aligned_cols=26  Identities=27%  Similarity=0.391  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34589999999999999999987543

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=92.38  E-value=0.11  Score=54.61  Aligned_cols=101  Identities=21%  Similarity=0.193  Sum_probs=58.7

Q ss_pred             HHHHhcC-CCccEEEEEcCCCCcHHHHHHHHHHHHhhc-cCCC-eEEEEEEecCC-ChHHHHHHHHHh--hC------CC
Q 004895          172 VIEALKD-DKLNIIGVCGMGGVGKTTLVKQIAKQVMED-NVFD-KVVMAEITKNP-DAQKIQGELASD--LG------MN  239 (724)
Q Consensus       172 l~~~L~~-~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~-~~~wv~vs~~~-~~~~l~~~i~~~--l~------~~  239 (724)
                      .++.|.. .+-..++|.|..|+|||+|+.++++..... .+-+ .++++-+.+.. ...++.+++.+.  +.      ..
T Consensus       141 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~at  220 (465)
T 3vr4_D          141 AIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNL  220 (465)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEE
T ss_pred             EEecccccccCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEEC
Confidence            4444441 233457899999999999999998876431 1112 46777777654 345566655442  11      01


Q ss_pred             CCCCchhH----HHHHHHHHHHh--cCCcEEEEEccccc
Q 004895          240 FDSNDLIY----HRAKQLCQRLK--KEKRVLIILDNIWT  272 (724)
Q Consensus       240 ~~~~~~~~----~~~~~l~~~l~--~~kr~LlVlDdv~~  272 (724)
                      .+++....    ...-.+.+++.  .++++||++||+-.
T Consensus       221 sd~p~~~r~~a~~~a~tiAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          221 ANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence            12221111    11234556665  37999999999954

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.36  E-value=0.056  Score=51.19  Aligned_cols=24  Identities=38%  Similarity=0.267  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -.+++|+|+.|+|||||++.++--
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            348999999999999999999876

>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=92.29  E-value=0.25  Score=53.14  Aligned_cols=44  Identities=32%  Similarity=0.524  Sum_probs=33.8

Q ss_pred             chHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          164 SRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +..+.+..+...+.+++ +.+.|.|.+|+||||++..+.......
T Consensus        29 ~Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           29 GQKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             HHHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            45555666666665433 489999999999999999999988654

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.28  E-value=0.1  Score=52.97  Aligned_cols=38  Identities=37%  Similarity=0.496  Sum_probs=29.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      ...+|+|+|++|+||||++..++.......  ..+.++..
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g--~kVllid~  141 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELG--YKVLIAAA  141 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTT--CCEEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeC
Confidence            456999999999999999999998876532  23555543

>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=92.26  E-value=0.085  Score=52.83  Aligned_cols=25  Identities=28%  Similarity=0.449  Sum_probs=22.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++|.|+|+.|+||||||..++...
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            3589999999999999999998754

>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=92.15  E-value=0.1  Score=52.15  Aligned_cols=26  Identities=27%  Similarity=0.255  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..++|.|+|+.|+||||||..+++..
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            34689999999999999999998764

>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=92.13  E-value=0.11  Score=51.19  Aligned_cols=27  Identities=30%  Similarity=0.409  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...++.+.|.||+||||++..++....
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            356888999999999999999998776

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=92.12  E-value=0.055  Score=54.26  Aligned_cols=27  Identities=30%  Similarity=0.422  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +..+|+|.|+.|+||||+|+.+.+...
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg   30 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFR   30 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHh
Confidence            456899999999999999999988654

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.11  E-value=0.17  Score=49.77  Aligned_cols=29  Identities=28%  Similarity=0.445  Sum_probs=24.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..-.+++|+|+.|+|||||++.+......
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~~   51 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYINQ   51 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCCC
Confidence            34569999999999999999999887654

>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=92.04  E-value=0.16  Score=48.81  Aligned_cols=28  Identities=25%  Similarity=0.430  Sum_probs=24.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ....|.|.|+.|+||||+++.+.+....
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            3468999999999999999999998864

>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=92.03  E-value=0.08  Score=51.31  Aligned_cols=27  Identities=22%  Similarity=0.436  Sum_probs=22.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|+|||||++.++.-..
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   56 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEMD   56 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCSE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            445899999999999999999976543

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=92.01  E-value=0.12  Score=48.12  Aligned_cols=83  Identities=10%  Similarity=0.048  Sum_probs=58.2

Q ss_pred             hhcCCCCceEEEcCCCcCC-----CCCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcC---c--
Q 004895          570 FFEGTEELKVLDFTGIRFS-----PLPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEI---K--  633 (724)
Q Consensus       570 ~~~~l~~L~~L~l~~~~~~-----~lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i---~--  633 (724)
                      .+..-..|+.|+|++|.+.     .+-..+..-..|++|+|++|.|..  .    ..+..=..|++|+|++|..   .  
T Consensus        65 aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga~ala~aL~~N~tL~~L~L~n~~~~~ig~~  144 (197)
T 1pgv_A           65 AACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQ  144 (197)
T ss_dssp             HHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHH
T ss_pred             HHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHHHHHHHHHhhCCceeEEECCCCcCcCcCHH
Confidence            3556678999999999887     234455566789999999999876  1    4455566799999987533   2  


Q ss_pred             ---ccchhhhcCCCCCeEccCC
Q 004895          634 ---QLPLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       634 ---~lp~~i~~l~~L~~L~l~~  652 (724)
                         .+-..+..-+.|..|+++.
T Consensus       145 g~~~ia~aL~~N~tL~~L~l~~  166 (197)
T 1pgv_A          145 VEMDMMMAIEENESLLRVGISF  166 (197)
T ss_dssp             HHHHHHHHHHHCSSCCEEECCC
T ss_pred             HHHHHHHHHHhCCCcCeEeccC
Confidence               1233445556777777765

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=91.96  E-value=0.57  Score=50.96  Aligned_cols=52  Identities=23%  Similarity=0.136  Sum_probs=37.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      -.++.|.|.+|+||||||.+++....... =..++|++...  +..++...++..
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~~a~~~-g~~vl~~s~E~--s~~~l~~r~~~~  293 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQWGTAM-GKKVGLAMLEE--SVEETAEDLIGL  293 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHHHTTTS-CCCEEEEESSS--CHHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHHHHHhc-CCcEEEEeccC--CHHHHHHHHHHH
Confidence            45889999999999999999998876431 12477776643  566777766543

>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=91.93  E-value=0.087  Score=51.53  Aligned_cols=25  Identities=36%  Similarity=0.456  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-.+++|+|+.|+|||||++.++--
T Consensus        28 ~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           28 KGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3458999999999999999999864

>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=91.90  E-value=0.073  Score=52.77  Aligned_cols=26  Identities=27%  Similarity=0.474  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+.--.
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            34589999999999999999987543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=91.86  E-value=0.084  Score=53.54  Aligned_cols=25  Identities=24%  Similarity=0.422  Sum_probs=22.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..+|.|+|+.|+||||||..+++..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHC
Confidence            4589999999999999999998654

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=91.86  E-value=0.084  Score=52.02  Aligned_cols=26  Identities=27%  Similarity=0.423  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44689999999999999999987543

>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=91.81  E-value=0.078  Score=51.52  Aligned_cols=26  Identities=38%  Similarity=0.526  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||.+.++--.
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34589999999999999999987543

>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=91.77  E-value=0.096  Score=48.73  Aligned_cols=25  Identities=28%  Similarity=0.476  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.|+|+|..|+|||||.+.+....
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            3478999999999999999998754

>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=91.72  E-value=0.068  Score=50.84  Aligned_cols=25  Identities=40%  Similarity=0.643  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -.+++|+|+.|+|||||++.++--.
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            3589999999999999999986543

>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=91.72  E-value=0.079  Score=52.30  Aligned_cols=26  Identities=23%  Similarity=0.502  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+.--.
T Consensus        36 ~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            34589999999999999999987644

>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=91.72  E-value=0.081  Score=50.99  Aligned_cols=27  Identities=30%  Similarity=0.503  Sum_probs=22.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|+|||||.+.++.-..
T Consensus        33 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           33 RGQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            345899999999999999999976543

>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=91.70  E-value=0.081  Score=52.01  Aligned_cols=26  Identities=31%  Similarity=0.440  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||.+.++--.
T Consensus        32 ~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           32 KGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34589999999999999999987544

>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=91.64  E-value=0.11  Score=51.39  Aligned_cols=25  Identities=28%  Similarity=0.424  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-.+++|+|+.|+|||||++.++--
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            4468999999999999999999874

>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=91.64  E-value=0.092  Score=51.69  Aligned_cols=26  Identities=23%  Similarity=0.359  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44699999999999999999987543

>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=91.59  E-value=0.084  Score=51.48  Aligned_cols=26  Identities=38%  Similarity=0.615  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
T Consensus        34 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           34 QGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34589999999999999999987644

>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=91.53  E-value=0.12  Score=51.95  Aligned_cols=27  Identities=22%  Similarity=0.321  Sum_probs=23.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..-.+++|+|+.|.|||||++.+..-.
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            445699999999999999999998876

>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=91.51  E-value=0.1  Score=52.63  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .+|.|.|++|+||||+|+.+.+.
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            47899999999999999999874

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=91.45  E-value=0.14  Score=49.54  Aligned_cols=26  Identities=38%  Similarity=0.428  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+|+|+|+.|+||||+++.+....
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            45689999999999999999998765

>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=91.43  E-value=0.31  Score=46.15  Aligned_cols=32  Identities=22%  Similarity=0.232  Sum_probs=26.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK  213 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~  213 (724)
                      ...|.|.|+.|+||||+++.+.+..... .+..
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~~~-~~~v   37 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLRER-GIEV   37 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHTT-TCCE
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHHHc-CCCc
Confidence            3578999999999999999999988753 3443

>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=91.43  E-value=0.099  Score=50.88  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44689999999999999999987543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.42  E-value=0.23  Score=47.15  Aligned_cols=37  Identities=22%  Similarity=0.203  Sum_probs=27.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      .|.+.|.||+||||+|..++.....+ .++ +..+.+..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~-G~~-V~v~d~D~   44 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQ-GVR-VMAGVVET   44 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-TCC-EEEEECCC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC-CCC-EEEEEeCC
Confidence            47789999999999999999988654 333 44455443

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=91.40  E-value=1  Score=48.54  Aligned_cols=58  Identities=29%  Similarity=0.264  Sum_probs=39.8

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHH
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGEL  232 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i  232 (724)
                      +.++.|. -.+-..++|.|..|+|||+|+.++.+..    +-+.++++-+.+.. ...++++++
T Consensus       221 rvID~l~PigrGqr~~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER~~Ev~e~~~~~  280 (600)
T 3vr4_A          221 RVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGERGNEMTDVVNEF  280 (600)
T ss_dssp             HHHHHHSCCBTTCEEEEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEECHHHHHHHHHHT
T ss_pred             hhhhccCCccCCCEEeeecCCCccHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            3455554 2345689999999999999999998763    23568888888763 334444443

>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=91.39  E-value=0.1  Score=51.16  Aligned_cols=26  Identities=35%  Similarity=0.566  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44599999999999999999987543

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=91.34  E-value=0.42  Score=58.90  Aligned_cols=85  Identities=19%  Similarity=0.200  Sum_probs=60.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      +-++|-|+|+.|+||||||.++.......  =..++|++.....+..     .++.+|.+.+.     ++..++....+.
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~~~~~--g~~~~~i~~e~~~~~~-----~~~~~Gv~~~~l~~~~p~~~e~~l~~~~ 1502 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAAAQRE--GKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD 1502 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT--TCCEEEECTTSCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHhc--CCeEEEEecCCCCCHH-----HHHHcCCCHHHeEEeCCCcHHHHHHHHH
Confidence            34799999999999999999999776433  3458899887777654     37888876432     221334444444


Q ss_pred             HHHhcCCcEEEEEcccc
Q 004895          255 QRLKKEKRVLIILDNIW  271 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~  271 (724)
                      ..++.+..-++|+|-|-
T Consensus      1503 ~~~~s~~~~~vvvDsv~ 1519 (1706)
T 3cmw_A         1503 ALARSGAVDVIVVDSVA 1519 (1706)
T ss_dssp             HHHHHTCCSEEEESCST
T ss_pred             HHHHcCCCCEEEEccHH
Confidence            55556777899999983

>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=91.33  E-value=0.1  Score=51.94  Aligned_cols=27  Identities=30%  Similarity=0.411  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.++.|+|++|+|||||+..++....
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            345899999999999999999987554

>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=91.30  E-value=0.094  Score=51.18  Aligned_cols=26  Identities=31%  Similarity=0.489  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
T Consensus        25 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34589999999999999999987544

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=91.28  E-value=0.11  Score=51.22  Aligned_cols=26  Identities=23%  Similarity=0.316  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+..-.
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            44589999999999999999997543

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.24  E-value=0.11  Score=51.53  Aligned_cols=26  Identities=19%  Similarity=0.325  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44689999999999999999987654

>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=91.20  E-value=0.12  Score=48.28  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -.|+|+|..|+|||||.+.+...
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            46889999999999999999875

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.18  E-value=0.098  Score=51.22  Aligned_cols=26  Identities=35%  Similarity=0.487  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||.+.++.-.
T Consensus        30 ~Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           30 KGDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34589999999999999999987654

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=91.17  E-value=0.69  Score=49.71  Aligned_cols=58  Identities=22%  Similarity=0.235  Sum_probs=40.3

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC-hHHHHHHH
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD-AQKIQGEL  232 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~l~~~i  232 (724)
                      +.++.|. -.+-..++|.|..|+|||+|++.+++..    +-+.++++-+.+..+ ..++.+++
T Consensus       216 rvID~l~PigkGqr~~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          216 RVIDTFFPQAKGGTAAIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             HHHHHHSCEETTCEEEECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             chhhccCCcccCCeEEeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            3455554 2344588999999999999999987653    235678888887654 44555554

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=91.16  E-value=0.13  Score=45.79  Aligned_cols=23  Identities=26%  Similarity=0.502  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      +.|.|+|.+|+|||||+..+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999864

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.11  E-value=0.11  Score=51.24  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
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            44589999999999999999987543

>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=91.10  E-value=0.23  Score=48.53  Aligned_cols=37  Identities=27%  Similarity=0.262  Sum_probs=28.6

Q ss_pred             HHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          169 FQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       169 ~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ...+..|+..  ++...+.++|++|+|||.+|..+++..
T Consensus        90 ~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           90 ASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            4456666653  334579999999999999999998854

>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=91.08  E-value=0.093  Score=55.64  Aligned_cols=28  Identities=18%  Similarity=0.392  Sum_probs=23.8

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .....+|.|+|++|+||||+|+.+....
T Consensus       255 ~~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          255 SPNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CSSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            3456799999999999999999987654

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=91.08  E-value=0.25  Score=45.66  Aligned_cols=25  Identities=24%  Similarity=0.292  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ....|+|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4458899999999999999998764

>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=91.06  E-value=0.13  Score=46.49  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      ..|+|+|.+|+|||||...+..
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999999999975

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.06  E-value=0.1  Score=51.93  Aligned_cols=26  Identities=31%  Similarity=0.365  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++--.
T Consensus        46 ~Ge~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           46 KGDKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34589999999999999999987644

>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=91.02  E-value=0.13  Score=53.41  Aligned_cols=25  Identities=36%  Similarity=0.589  Sum_probs=22.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|+|.|+.|+||||||..++....
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             cEEEEECcchhhHHHHHHHHHHHCC
Confidence            5889999999999999999998764

>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=90.92  E-value=0.24  Score=53.45  Aligned_cols=45  Identities=11%  Similarity=-0.007  Sum_probs=33.9

Q ss_pred             cchHHHHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          163 NSRKKIFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       163 ~gR~~~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..|.+..+.+.+...  .....+|.+.|+.|+||||+|+.+.+....
T Consensus       375 f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          375 FSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             TSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             ccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            356666556666542  234568999999999999999999999863

>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=90.89  E-value=0.1  Score=55.44  Aligned_cols=37  Identities=27%  Similarity=0.446  Sum_probs=28.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEE
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEI  219 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~v  219 (724)
                      ..+|.|+|.+|+||||++..++.....++ . .++.++.
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G-~-kVllv~~  135 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRG-L-KPALIAA  135 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHH-C-CEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcC-C-eEEEEec
Confidence            46899999999999999999998876432 2 2445544

>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=90.79  E-value=0.15  Score=52.98  Aligned_cols=27  Identities=26%  Similarity=0.118  Sum_probs=23.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+++|+|+.|+|||||++.++...
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            455699999999999999999999754

>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=90.74  E-value=0.12  Score=47.65  Aligned_cols=21  Identities=43%  Similarity=0.624  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|+|+|.+|+|||||++.+..
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999999876

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.69  E-value=0.16  Score=49.33  Aligned_cols=26  Identities=31%  Similarity=0.342  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...|.|.|..|+||||+++.+.+...
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            35799999999999999999998763

>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=90.68  E-value=0.1  Score=48.37  Aligned_cols=25  Identities=20%  Similarity=0.210  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -..|.|.|+.|+||||||..+....
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            3578999999999999999998754

>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=90.59  E-value=0.14  Score=45.74  Aligned_cols=23  Identities=39%  Similarity=0.609  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.++|.+|+|||||+..+....
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            47899999999999999998653

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=90.53  E-value=0.38  Score=49.33  Aligned_cols=46  Identities=30%  Similarity=0.421  Sum_probs=33.8

Q ss_pred             cCCCccEEEEEcCCCCcHHHHHHHHHHHHh--hccCCCeEEEEEEecCCC
Q 004895          177 KDDKLNIIGVCGMGGVGKTTLVKQIAKQVM--EDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       177 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~  224 (724)
                      .+...+++.+.|.||+||||+|..++....  ..  =..++-|+.....+
T Consensus        14 ~~~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~--g~~vllid~D~~~~   61 (348)
T 3io3_A           14 QHDSLKWIFVGGKGGVGKTTTSSSVAVQLALAQP--NEQFLLISTDPAHN   61 (348)
T ss_dssp             TCTTCSEEEEECSTTSSHHHHHHHHHHHHHHHCT--TSCEEEEECCSSCH
T ss_pred             cCCCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcC--CCeEEEEECCCCCC
Confidence            345668999999999999999999998876  32  13466666654433

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=90.47  E-value=0.15  Score=50.48  Aligned_cols=25  Identities=40%  Similarity=0.557  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++|+|+.|+|||||.+.++.....
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~~   28 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQVS   28 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCCC
Confidence            5789999999999999999987643

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=90.46  E-value=0.2  Score=46.23  Aligned_cols=26  Identities=19%  Similarity=0.066  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .++.|+|+.|+||||++..++.+...
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~   29 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKL   29 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            47889999999999999877777654

>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=90.44  E-value=0.15  Score=45.76  Aligned_cols=23  Identities=30%  Similarity=0.527  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      --|.|+|.+|+|||||+..+...
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            35789999999999999999864

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=90.37  E-value=0.13  Score=50.66  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -.+++|+|+.|+|||||++.++--
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl   53 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGL   53 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999988643

>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=90.27  E-value=0.17  Score=47.59  Aligned_cols=27  Identities=30%  Similarity=0.321  Sum_probs=20.9

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ..+.-.|+|+|.+|+|||||...+...
T Consensus        27 ~~~~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           27 QGQAIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             ---CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cCCeEEEEEECcCCCCHHHHHHHHHhC
Confidence            344457889999999999999988864

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=90.26  E-value=0.33  Score=46.45  Aligned_cols=27  Identities=30%  Similarity=0.429  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ...|.|.|+.|+||||+++.+++....
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~~l~~   51 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCDRLQE   51 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            458999999999999999999998865

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.26  E-value=0.19  Score=49.56  Aligned_cols=39  Identities=15%  Similarity=0.399  Sum_probs=30.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      ++|+|.|-||+||||+|..++......+  ..++-|+....
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~la~~G--~~VlliD~D~q   40 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSGLHAMG--KTIMVVGCDPK   40 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTT--CCEEEEEECTT
T ss_pred             cEEEEecCCCCcHHHHHHHHHHHHHHCC--CcEEEEcCCCC
Confidence            5788899999999999999999887432  24677776543

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=90.14  E-value=0.47  Score=44.30  Aligned_cols=26  Identities=27%  Similarity=0.471  Sum_probs=23.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .|+|-|.-|+||||.++.+++.....
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~L~~~   27 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQYLEKR   27 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            47888999999999999999998764

>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=90.12  E-value=0.2  Score=52.69  Aligned_cols=25  Identities=20%  Similarity=0.396  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ...+++|+|+.|+|||||.+.+...
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhCC
Confidence            4569999999999999999999873

>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=90.02  E-value=0.17  Score=46.75  Aligned_cols=23  Identities=39%  Similarity=0.609  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.|+|.+|+|||||+..+....
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            57899999999999999998653

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=89.95  E-value=0.18  Score=46.48  Aligned_cols=23  Identities=26%  Similarity=0.422  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ..|+|+|.+|+|||||...+...
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=89.94  E-value=0.18  Score=51.78  Aligned_cols=26  Identities=35%  Similarity=0.423  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||.+.++--.
T Consensus        29 ~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           29 PGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCchHHHHHHHHhcCC
Confidence            34589999999999999999987644

>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=89.89  E-value=0.12  Score=49.67  Aligned_cols=25  Identities=28%  Similarity=0.280  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ...+|+|.|+.|+||||+++.+...
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            4469999999999999999998764

>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=89.89  E-value=0.23  Score=49.63  Aligned_cols=40  Identities=23%  Similarity=0.446  Sum_probs=30.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      .++|+|.|-||+||||+|..++......+  ..++-|+....
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~~La~~G--~rVlliD~D~q   41 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVAALAEMG--KKVMIVGCDPK   41 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHTT--CCEEEEEECSS
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHHHHHHCC--CeEEEEecCCC
Confidence            36888899999999999999999886532  24666766543

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=89.85  E-value=0.2  Score=47.91  Aligned_cols=26  Identities=23%  Similarity=0.180  Sum_probs=22.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...++|.|++|+||||+|+.+.+...
T Consensus         8 ~~~~~~~G~pGsGKsT~a~~L~~~~g   33 (230)
T 3gmt_A            8 HMRLILLGAPGAGKGTQANFIKEKFG   33 (230)
T ss_dssp             -CEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             ccceeeECCCCCCHHHHHHHHHHHhC
Confidence            45789999999999999999998774

>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=89.83  E-value=0.22  Score=47.24  Aligned_cols=27  Identities=22%  Similarity=0.265  Sum_probs=22.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .....|.|+|.+|+|||||+..+....
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345678999999999999999998754

>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=89.81  E-value=0.2  Score=44.87  Aligned_cols=22  Identities=27%  Similarity=0.418  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |+|+|.+|+|||||...+....
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            7899999999999999998654

>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=89.80  E-value=0.16  Score=50.64  Aligned_cols=26  Identities=31%  Similarity=0.548  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.++.-.
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            44689999999999999999997654

---

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	724
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	3e-32
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	7e-09
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	1e-08
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	6e-05
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	0.001
d1jl5a_	353	c.10.2.6 (A:) Leucine rich effector protein YopM {	3e-06
d1z7xw1	460	c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (	5e-06
d2astb2	284	c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p1	7e-06
d1okkd2	207	c.37.1.10 (D:97-303) GTPase domain of the signal r	1e-05
d1koha1	162	c.10.2.3 (A:201-362) mRNA export factor tap {Human	2e-05
d1h6ta2	210	c.10.2.1 (A:31-240) Internalin B {Listeria monocyt	3e-04
d1dcea3	124	c.10.2.2 (A:444-567) Rab geranylgeranyltransferase	4e-04
d1m9la_	198	c.10.3.1 (A:) Outer arm dynein light chain 1 {Gree	7e-04
d1ogqa_	313	c.10.2.8 (A:) Polygalacturonase inhibiting protein	0.001
d1h6ua2	227	c.10.2.1 (A:36-262) Internalin H {Listeria monocyt	0.001
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	0.001
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	0.001
d1xwdc1	242	c.10.2.7 (C:18-259) Follicle-stimulating hormone r	0.002
d1ls1a2	207	c.37.1.10 (A:89-295) GTPase domain of the signal s	0.002
d1xjca_	165	c.37.1.10 (A:) Molybdopterin-guanine dinucleotide	0.003

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  124 bits (311), Expect = 3e-32
 Identities = 36/271 (13%), Positives = 74/271 (27%), Gaps = 35/271 (12%)

Query: 165 RKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIA--KQVMEDNVFDKVVMAEI 219
           R+     VI+ L    D     + + G  G GK+ +  Q       +    +D +V  + 
Sbjct: 25  REYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKD 84

Query: 220 TKNPDAQKIQGELA---------SDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNI 270
           +                        L      +       + +C  L      L + D++
Sbjct: 85  SGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDV 144

Query: 271 WTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEA 330
             +              E  +     R   ++T+R  ++      + +   + +L  +E 
Sbjct: 145 VQE--------------ETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDEC 190

Query: 331 LQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALNKLTSS 390
               E              +  + +    G P  L     + + K+        NKL S 
Sbjct: 191 YDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESR 250

Query: 391 NLREIHGMDADVYSPIKLSYDFLDDEAKSLF 421
            L  +  +          SY  L    +   
Sbjct: 251 GLVGVECI-------TPYSYKSLAMALQRCV 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 = 56.2 bits (134), Expect = 7e-09
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 597 LINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSL 656
           L NL  L L    + DI+ V  L KL+ L     ++  +   +  LT +  L   +   +
Sbjct: 306 LKNLTYLTLYFNNISDISPVSSLTKLQRLFFANNKVSDVS-SLANLTNINWLSAGHN-QI 363

Query: 657 VVIAPNVISKLSRLEELYMGD 677
             + P  ++ L+R+ +L + D
Sbjct: 364 SDLTP--LANLTRITQLGLND 382

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]} Length = 384

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

 Score = 55.4 bits (132), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP 636
           L  L       S +   +  L  LQ L     ++ D++ +  L  +  LS    +I  L 
Sbjct: 309 LTYLTLYFNNISDISP-VSSLTKLQRLFFANNKVSDVSSLANLTNINWLSAGHNQISDLT 367

Query: 637 LQIGQLTRLQLLDLSN 652
             +  LTR+  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 = 43.5 bits (101), Expect = 6e-05
 Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 4/86 (4%)

Query: 597 LINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSL 656
           L       L    + D      L ++  L      IK +   +  L  L  ++ SN   L
Sbjct: 21  LAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNN-QL 78

Query: 657 VVIAPNVISKLSRLEELYMGDSFSQW 682
             I P  +  L++L ++ M ++    
Sbjct: 79  TDITP--LKNLTKLVDILMNNNQIAD 102

>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 = 39.2 bits (90), Expect = 0.001
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 591 PSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDL 650
             S   L  + TL  D   ++ I  V  L  L  ++    ++  +   +  LT+L  + +
Sbjct: 37  TVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDIT-PLKNLTKLVDILM 95

Query: 651 SNC 653
           +N 
Sbjct: 96  NNN 98

>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 = 47.9 bits (112), Expect = 3e-06
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 5/82 (6%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEIL 625
                 +    L+ L+ +  +   LP+       L+ L      L ++      + L+ L
Sbjct: 275 EIRSLCDLPPSLEELNVSNNKLIELPALPP---RLERLIASFNHLAEVP--ELPQNLKQL 329

Query: 626 SLRGAEIKQLPLQIGQLTRLQL 647
            +    +++ P     +  L++
Sbjct: 330 HVEYNPLREFPDIPESVEDLRM 351

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]} Length = 460

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (110), Expect = 5e-06
 Identities = 11/97 (11%), Positives = 38/97 (39%), Gaps = 12/97 (12%)

Query: 598 INLQTLCLDGWRLED---IAIVGQLKKLEILSLRGAEI-----KQLPLQIGQLTRLQLLD 649
           +++Q+L +    L D     ++  L++ +++ L    +     K +   +     L  L+
Sbjct: 2   LDIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELN 61

Query: 650 LSNC----SSLVVIAPNVISKLSRLEELYMGDSFSQW 682
           L +       +  +   + +   ++++L + +     
Sbjct: 62  LRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTG 98

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]} Length = 284

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (107), Expect = 7e-06
 Identities = 24/123 (19%), Positives = 44/123 (35%), Gaps = 27/123 (21%)

Query: 580 LDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQI 639
           LD TG    P     GRL++   +                          + + Q   + 
Sbjct: 5   LDLTGKNLHP--DVTGRLLSQGVI--------------------AFRCPRSFMDQPLAEH 42

Query: 640 GQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGL 699
               R+Q +DLSN    V     ++S+ S+L+ L +     +  ++      +LA+   L
Sbjct: 43  FSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSL-----EGLRLSDPIVNTLAKNSNL 97

Query: 700 SKL 702
            +L
Sbjct: 98  VRL 100

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]} Length = 207

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]

 Score = 44.7 bits (105), Expect = 1e-05
 Identities = 31/163 (19%), Positives = 53/163 (32%), Gaps = 19/163 (11%)

Query: 178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVM-AEITKNPDAQKIQGELASDL 236
           + K  ++ V G+ GVGKTT + ++ +         KV+  A  T          E    L
Sbjct: 3   EPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLG--KKVMFCAGDTFRAAGGTQLSEWGKRL 60

Query: 237 GMNF---DSNDLIYHRAKQLCQRLKKEKRVLIILD---NIWTKLELDKIGIPYGDVDEKD 290
            +              A    Q +K     L+ +D    + TK  L +          K 
Sbjct: 61  SIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKA 120

Query: 291 KNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQL 333
             ++P+             L +D  + +     A    EA+ L
Sbjct: 121 DPEEPKEV----------WLVLDAVTGQNGLEQAKKFHEAVGL 153

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]} Length = 162

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (101), Expect = 2e-05
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 1/87 (1%)

Query: 590 LPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLD 649
           L   + +  +     LD   L     +       +L+ R +    L +    +  L  L+
Sbjct: 12  LKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSSMAATLRIIEENIPELLSLN 71

Query: 650 LSNCS-SLVVIAPNVISKLSRLEELYM 675
           LSN     +    +++ K   L+ L +
Sbjct: 72  LSNNRLYRLDDMSSIVQKAPNLKILNL 98

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]} Length = 210

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]

 Score = 40.4 bits (93), Expect = 3e-04
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 597 LINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSN 652
           L  L TL L+  ++ DI  +  L KL+ L L    I  L   +  L  L +L+L +
Sbjct: 155 LTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLR-ALAGLKNLDVLELFS 209

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 124

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 29/128 (22%), Positives = 47/128 (36%), Gaps = 5/128 (3%)

Query: 578 KVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLP 636
           +VL       + L   L +L+ +  L L   RL      +  L+ LE+L      ++ + 
Sbjct: 1   RVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD 59

Query: 637 LQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAEL 696
             +  L RLQ L L N       A   +    RL  L +    +   + EG        L
Sbjct: 60  -GVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNL--QGNSLCQEEGIQERLAEML 116

Query: 697 KGLSKLTT 704
             +S + T
Sbjct: 117 PSVSSILT 124

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Length = 198

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]

 Score = 39.3 bits (90), Expect = 7e-04
 Identities = 11/52 (21%), Positives = 24/52 (46%), Gaps = 2/52 (3%)

Query: 576 ELKVLDFTGI--RFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEIL 625
           E + ++  G+      + ++L  L   + L L    +E I+ +  ++ L IL
Sbjct: 24  EAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRIL 75

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]} Length = 313

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

 Score = 39.7 bits (91), Expect = 0.001
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 589 PLPSSLGRLINLQTLCLDGWRLE-DIAIVGQLKKLEILSLRG 629
            LP  L +L  L +L +    L  +I   G L++ ++ +   
Sbjct: 259 TLPQGLTQLKFLHSLNVSFNNLCGEIPQGGNLQRFDVSAYAN 300

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]} Length = 227

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

 Score = 38.9 bits (89), Expect = 0.001
 Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 569 HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLR 628
                  +L  L     + S +   L  L NL  + L   ++ D++ +     L I++L 
Sbjct: 167 TPLANLSKLTTLKADDNKISDISP-LASLPNLIEVHLKNNQISDVSPLANTSNLFIVTLT 225

>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 = 39.3 bits (90), Expect = 0.001
 Identities = 22/134 (16%), Positives = 51/134 (38%), Gaps = 6/134 (4%)

Query: 566 ISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDGWRLEDI--AIVGQLKKL 622
           I D  F+  + L  L     + S + P +   L+ L+ L L   +L+++   +   L++L
Sbjct: 46  IKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQEL 105

Query: 623 EILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQW 682
            +      ++++          +  L  +   S  +        + +L  + +  + +  
Sbjct: 106 RVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIE-NGAFQGMKKLSYIRI--ADTNI 162

Query: 683 DKVEGGSNASLAEL 696
             +  G   SL EL
Sbjct: 163 TTIPQGLPPSLTEL 176

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

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]

 Score = 38.2 bits (87), Expect = 0.001
 Identities = 21/207 (10%), Positives = 64/207 (30%), Gaps = 17/207 (8%)

Query: 166 KKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEIT 220
           +  F+ ++ + +  +  + + +  + G+G   L+  +++ ++                  
Sbjct: 8   RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQL 67

Query: 221 KNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIG 280
                      LA + G N    D +    ++L +  +     ++ + +           
Sbjct: 68  MQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL----TDA 123

Query: 281 IPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGE 340
                +   ++        +      R L  +  +  ++ ++    E+ A+    + V  
Sbjct: 124 AANALLKTLEEPPAETWFFLATREPERLLATL-RSRCRLHYLAPPPEQYAVTWLSREVTM 182

Query: 341 STKASDFRPLAEEIVGKCGGLP-VALS 366
           S  A          +    G P  AL+
Sbjct: 183 SQDA------LLAALRLSAGSPGAALA 203

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 242

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]

 Score = 38.0 bits (86), Expect = 0.002
 Identities = 9/41 (21%), Positives = 12/41 (29%), Gaps = 1/41 (2%)

Query: 617 GQLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLDLSNCSSL 656
                  IL +    I  LP      L +L+     N   L
Sbjct: 198 HGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKL 238

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]} Length = 207

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]

 Score = 37.8 bits (87), Expect = 0.002
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 4/96 (4%)

Query: 179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ---KIQGELASD 235
              N+  + G+ G GKTT   ++A           +++A  T+ P A+   ++ GE    
Sbjct: 8   KDRNLWFLVGLQGSGKTTTAAKLALYYKGKG-RRPLLVAADTQRPAAREQLRLLGEKVGV 66

Query: 236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIW 271
             +     +      +++ ++ + E R LI++D   
Sbjct: 67  PVLEVMDGESPESIRRRVEEKARLEARDLILVDTAG 102

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]} Length = 165

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]

 Score = 37.1 bits (85), Expect = 0.003
 Identities = 18/111 (16%), Positives = 36/111 (32%), Gaps = 2/111 (1%)

Query: 181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNF 240
           +N+  V G    GKTTL+++     + +      V         A+    +  S      
Sbjct: 1   MNVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVKHHGHGGEPARPEGVD--SVRHERA 58

Query: 241 DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDK 291
            +          L   L++    L  +  ++  L LD + +     +   K
Sbjct: 59  GAVATAVEGDGLLQLHLRRPLWRLDDVLALYAPLRLDLVLVEGYKQERHPK 109

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	724
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.61
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.55
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.54
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.53
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.51
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.47
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.43
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.43
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.43
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.42
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.42
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.41
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.37
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.36
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.34
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.31
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.3
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.28
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.26
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.24
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.19
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.18
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.18
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.12
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.11
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.04
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.99
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.98
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.98
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.95
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.9
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.81
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.79
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.77
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.77
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.73
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.7
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.68
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.67
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.61
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.59
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.56
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.54
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.51
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.49
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.41
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.4
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.38
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.31
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.3
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.29
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.23
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.07
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.06
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.03
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.02
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.84
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.7
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.67
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.5
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.25
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.85
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.81
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.78
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.78
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.68
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.63
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.58
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.55
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.53
d1okkd2	207	GTPase domain of the signal recognition particle r	96.52
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.51
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.49
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.46
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.45
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.44
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.43
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.4
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.35
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.35
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.35
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.31
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.26
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.24
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.19
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.17
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.13
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.12
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.06
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.03
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.01
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.97
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.92
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.9
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.88
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.81
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.79
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.78
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.75
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.71
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	95.6
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.6
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.55
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.53
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.46
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.46
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.42
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.39
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.2
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.2
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.17
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.15
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.12
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.11
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.03
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.02
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.97
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.76
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.73
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.67
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.56
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.56
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.44
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.38
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.37
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	94.37
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.36
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.36
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.25
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.24
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.17
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	94.12
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	93.86
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	93.71
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.65
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.45
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.4
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	93.3
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	93.16
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.15
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.08
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.01
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	92.98
d1g2912	240	Maltose transport protein MalK, N-terminal domain	92.85
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.82
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.74
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.73
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.68
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.64
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	92.63
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.59
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	92.52
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.39
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	92.39
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	92.37
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	92.32
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	92.3
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	92.18
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.12
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	92.11
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	92.06
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.01
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	91.99
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.96
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	91.95
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.93
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.9
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.86
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	91.8
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	91.72
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.65
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	91.6
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	91.48
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.4
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.4
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.34
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.27
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	91.23
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	91.23
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.19
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	90.99
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	90.84
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	90.77
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	90.77
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.71
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	90.7
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	90.69
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.67
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	90.67
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.66
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	90.58
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.56
d1nrjb_	209	Signal recognition particle receptor beta-subunit	90.54
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	90.52
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	90.52
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.49
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	90.47
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	90.42
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	90.38
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	90.33
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	90.25
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	90.2
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	90.18
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	90.18
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	90.06
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	90.05
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	90.0
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	89.96
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	89.95
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.95
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	89.88
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	89.82
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	89.73
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	89.63
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	89.59
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	89.51
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	89.51
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	89.49
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	89.4
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	89.37
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.36
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	89.35
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	89.31
d2fh5b1	207	Signal recognition particle receptor beta-subunit	89.22
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	89.21
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	89.18
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	88.97
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	88.88
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	88.79
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	88.74
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	88.62
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	88.62
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	88.61
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	88.52
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	88.51
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	88.43
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.34
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	88.13
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.1
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	87.99
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	87.89
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	87.84
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	87.82
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	87.72
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	87.68
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	87.5
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	87.3
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	87.05
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	86.75
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	86.67
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	86.31
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	86.28
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	86.24
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.95
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	85.91
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	85.13
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	84.92
d1tuea_	205	Replication protein E1 helicase domain {Human papi	84.85
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	84.24
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	84.2
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	83.73
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	83.53
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	82.59
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	82.36
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	82.25
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	81.2
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	80.9
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	80.86
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	80.75
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.08

>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=9e-41  Score=337.46  Aligned_cols=244  Identities=14%  Similarity=0.098  Sum_probs=193.5

Q ss_pred             ccccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHHh--hccCCCeEEEEEEecCCChHHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQVM--EDNVFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      ..++||+.++++|+++|.   +...++|+|+||||+||||||+++|++..  ...+|++++|+++++.++...+...+..
T Consensus        20 ~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~   99 (277)
T d2a5yb3          20 MTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDI   99 (277)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHH
T ss_pred             CceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHH
Confidence            446699999999999985   45678999999999999999999999854  5678999999999999987777666544


Q ss_pred             hh---CCCC------CCCchhHHHHHHHHHHHhcCCcEEEEEccccccccccccccccCCCCcCCCCCCCCCcEEEEEec
Q 004895          235 DL---GMNF------DSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLELDKIGIPYGDVDEKDKNDDPRRCTIILTSR  305 (724)
Q Consensus       235 ~l---~~~~------~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR  305 (724)
                      .+   +...      ............+......++|+|+||||||+..+|+.+              ...||+||||||
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~--------------~~~~srilvTTR  165 (277)
T d2a5yb3         100 LLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWA--------------QELRLRCLVTTR  165 (277)
T ss_dssp             HHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHH--------------HHTTCEEEEEES
T ss_pred             HHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhh--------------cccCceEEEEee
Confidence            33   2211      111111222222333333478999999999999888755              335789999999


Q ss_pred             ccchhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHHHHHhcCCCHHHHHHHHH
Q 004895          306 SRDLLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTVANALKNKSPAIWKDALN  385 (724)
Q Consensus       306 ~~~v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~~~~l~~~~~~~w~~~~~  385 (724)
                      +..++.........|++++|+.+|||+||.++++.....+..++++++|+++|+|+||||+++|+.|+.++.+.|.+..+
T Consensus       166 ~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~  245 (277)
T d2a5yb3         166 DVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNN  245 (277)
T ss_dssp             BGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHH
T ss_pred             hHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHH
Confidence            99987543444578999999999999999999886655566678999999999999999999999999999999999888


Q ss_pred             HHhcCccccccCCCcccchhhHhhhhhcHHHHHHHHHhh
Q 004895          386 KLTSSNLREIHGMDADVYSPIKLSYDFLDDEAKSLFLLC  424 (724)
Q Consensus       386 ~l~~~~~~~~~~~~~~i~~~l~~sy~~L~~~~k~cf~~~  424 (724)
                      .+...       ...++..++.+||++||+++|.||.++
T Consensus       246 ~L~~~-------~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         246 KLESR-------GLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HHHHH-------CSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             HHhcC-------cHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            87643       345689999999999999999999874

>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=3.1e-15  Score=148.98  Aligned_cols=173  Identities=19%  Similarity=0.192  Sum_probs=121.2

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTL  603 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L  603 (724)
                      +.++++|.+++|.+..++..  ..+++|+.|.+  ..+....++.  +..+++|++|++++|++...|..+..+.+|++|
T Consensus        30 p~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L--~~N~l~~l~~--~~~l~~L~~L~Ls~N~l~~~~~~~~~l~~L~~L  105 (266)
T d1p9ag_          30 PKDTTILHLSENLLYTFSLATLMPYTRLTQLNL--DRAELTKLQV--DGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVL  105 (266)
T ss_dssp             CTTCCEEECTTSCCSEEEGGGGTTCTTCCEEEC--TTSCCCEEEC--CSCCTTCCEEECCSSCCSSCCCCTTTCTTCCEE
T ss_pred             CcCCCEEECcCCcCCCcCHHHhhcccccccccc--cccccccccc--ccccccccccccccccccccccccccccccccc
Confidence            45677888888877776532  36777888887  2333444442  456778888888888887777777788888888


Q ss_pred             EcCCcccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCC
Q 004895          604 CLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFS  680 (724)
Q Consensus       604 ~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~  680 (724)
                      ++++|.+..  ...+..+.+|++|++++|.++.+|.. +..+++|+.|++++ +.+..+++..++.+++|++|++++|.+
T Consensus       106 ~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~l~~l~~~~~~~l~~l~~l~l~~-N~l~~~~~~~~~~l~~L~~L~Ls~N~L  184 (266)
T d1p9ag_         106 DVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLAN-NNLTELPAGLLNGLENLDTLLLQENSL  184 (266)
T ss_dssp             ECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTT-SCCSCCCTTTTTTCTTCCEEECCSSCC
T ss_pred             cccccccceeeccccccccccccccccccccceeccccccccccchhccccc-ccccccCccccccccccceeecccCCC
Confidence            888887666  35567777888888888888777655 45677888888887 466777777777888888888887643


Q ss_pred             ccccccCCccchHHhhcCCCCCcEEEeecccc
Q 004895          681 QWDKVEGGSNASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       681 ~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ..      .+.   .+..+++|+.|++++|.+
T Consensus       185 ~~------lp~---~~~~~~~L~~L~L~~Np~  207 (266)
T d1p9ag_         185 YT------IPK---GFFGSHLLPFAFLHGNPW  207 (266)
T ss_dssp             CC------CCT---TTTTTCCCSEEECCSCCB
T ss_pred             cc------cCh---hHCCCCCCCEEEecCCCC
Confidence            21      222   233466788888887764

>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=99.55  E-value=6.7e-14  Score=133.71  Aligned_cols=165  Identities=25%  Similarity=0.340  Sum_probs=137.1

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ...++++.+.++.+..++....+++|++|.+.  .+....+++  +.++++|++|++++|+++.+| .++.+++|++|++
T Consensus        45 L~~L~~L~l~~~~i~~l~~l~~l~~L~~L~L~--~n~i~~l~~--~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l  119 (210)
T d1h6ta2          45 LNSIDQIIANNSDIKSVQGIQYLPNVTKLFLN--GNKLTDIKP--LANLKNLGWLFLDENKVKDLS-SLKDLKKLKSLSL  119 (210)
T ss_dssp             HHTCCEEECTTSCCCCCTTGGGCTTCCEEECC--SSCCCCCGG--GTTCTTCCEEECCSSCCCCGG-GGTTCTTCCEEEC
T ss_pred             hcCccEEECcCCCCCCchhHhhCCCCCEEeCC--CccccCccc--cccCccccccccccccccccc-ccccccccccccc
Confidence            45789999999999888776679999999993  334445553  678999999999999999887 5889999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|.+..++.+..+++|+++++++|.++..+ .+.++++|+++++++| .+..+++  ++++++|++|++++|.     +
T Consensus       120 ~~~~~~~~~~l~~l~~l~~l~~~~n~l~~~~-~~~~l~~L~~l~l~~n-~l~~i~~--l~~l~~L~~L~Ls~N~-----i  190 (210)
T d1h6ta2         120 EHNGISDINGLVHLPQLESLYLGNNKITDIT-VLSRLTKLDTLSLEDN-QISDIVP--LAGLTKLQNLYLSKNH-----I  190 (210)
T ss_dssp             TTSCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGGGCTTCSEEECCSS-CCCCCGG--GTTCTTCCEEECCSSC-----C
T ss_pred             ccccccccccccccccccccccccccccccc-cccccccccccccccc-ccccccc--ccCCCCCCEEECCCCC-----C
Confidence            9999888888999999999999999988754 5788999999999995 5666654  7899999999999874     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeec
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDV  709 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~  709 (724)
                      +     .+..+.+|++|+.|+|++
T Consensus       191 ~-----~l~~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         191 S-----DLRALAGLKNLDVLELFS  209 (210)
T ss_dssp             C-----BCGGGTTCTTCSEEEEEE
T ss_pred             C-----CChhhcCCCCCCEEEccC
Confidence            2     234578889999999874

>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=99.54  E-value=3.2e-14  Score=141.52  Aligned_cols=181  Identities=21%  Similarity=0.249  Sum_probs=149.4

Q ss_pred             CceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCC
Q 004895          528 GPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDG  607 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~  607 (724)
                      ....++-++++++.+|..+. ++++.|++  +.+....++...|.++++|+.|++++|.++.+|. ++.+++|++|+|++
T Consensus        11 ~~~~v~C~~~~L~~iP~~lp-~~l~~L~L--s~N~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~~-~~~l~~L~~L~Ls~   86 (266)
T d1p9ag_          11 SHLEVNCDKRNLTALPPDLP-KDTTILHL--SENLLYTFSLATLMPYTRLTQLNLDRAELTKLQV-DGTLPVLGTLDLSH   86 (266)
T ss_dssp             TCCEEECTTSCCSSCCSCCC-TTCCEEEC--TTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEEC-CSCCTTCCEEECCS
T ss_pred             CCeEEEccCCCCCeeCcCcC-cCCCEEEC--cCCcCCCcCHHHhhcccccccccccccccccccc-cccccccccccccc
Confidence            34456777788888886442 68999999  5556677888889999999999999999998874 57899999999999


Q ss_pred             cccCC-cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          608 WRLED-IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       608 ~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      |.++. +..+..+++|++|++++|.+..++. .+..+.+|++|++.+ +.+..+++..+..+++|+.|++++|..     
T Consensus        87 N~l~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~-n~l~~l~~~~~~~l~~l~~l~l~~N~l-----  160 (266)
T d1p9ag_          87 NQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKG-NELKTLPPGLLTPTPKLEKLSLANNNL-----  160 (266)
T ss_dssp             SCCSSCCCCTTTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTT-SCCCCCCTTTTTTCTTCCEEECTTSCC-----
T ss_pred             ccccccccccccccccccccccccccceeeccccccccccccccccc-cccceeccccccccccchhcccccccc-----
Confidence            99988 6788999999999999998887754 477889999999998 577888888888999999999999743     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeeccccccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRIWSL  721 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~~~~  721 (724)
                      .+..+   ..+..+++|+.|++++|.++.+|..++.
T Consensus       161 ~~~~~---~~~~~l~~L~~L~Ls~N~L~~lp~~~~~  193 (266)
T d1p9ag_         161 TELPA---GLLNGLENLDTLLLQENSLYTIPKGFFG  193 (266)
T ss_dssp             SCCCT---TTTTTCTTCCEEECCSSCCCCCCTTTTT
T ss_pred             cccCc---cccccccccceeecccCCCcccChhHCC
Confidence            22112   3456788999999999999999987653

>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=99.53  E-value=1.1e-13  Score=130.89  Aligned_cols=144  Identities=19%  Similarity=0.251  Sum_probs=92.7

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|.+.++.+..+.....+++|++|.+.  ++....+++  +.++++|+.|++++|.+..+|. ++.+.+|++|++
T Consensus        39 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          39 LDQVTTLQADRLGIKSIDGVEYLNNLTQINFS--NNQLTDITP--LKNLTKLVDILMNNNQIADITP-LANLTNLTGLTL  113 (199)
T ss_dssp             HTTCCEEECTTSCCCCCTTGGGCTTCCEEECC--SSCCCCCGG--GTTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             hcCCCEEECCCCCCCCccccccCCCcCcCccc--cccccCccc--ccCCcccccccccccccccccc-cccccccccccc
Confidence            35777777777777666554556777777772  223333333  5666777777777776666653 666777777777


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCC
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      ++|.+.....+..+++|+.|++++|.+..+| .+..+++|+.|++.+| .+..+++  ++++++|++|++++|
T Consensus       114 ~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~-~l~~~~~L~~L~l~~n-~l~~l~~--l~~l~~L~~L~ls~N  182 (199)
T d2omxa2         114 FNNQITDIDPLKNLTNLNRLELSSNTISDIS-ALSGLTSLQQLNFSSN-QVTDLKP--LANLTTLERLDISSN  182 (199)
T ss_dssp             CSSCCCCCGGGTTCTTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSS-CCCCCGG--GTTCTTCCEEECCSS
T ss_pred             cccccccccccchhhhhHHhhhhhhhhcccc-cccccccccccccccc-cccCCcc--ccCCCCCCEEECCCC
Confidence            7766666556666777777777777666554 3666677777777663 4555543  567777777777665

>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=99.51  E-value=1.2e-13  Score=130.65  Aligned_cols=171  Identities=20%  Similarity=0.281  Sum_probs=134.5

Q ss_pred             eccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC
Q 004895          533 SLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED  612 (724)
Q Consensus       533 ~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~  612 (724)
                      .+..+++.......++++++.|.+..  +....+.  .+..+++|++|++++|+++.++. ++++++|++|++++|.+..
T Consensus        24 ~l~~~~~~~~~~~~~l~~l~~L~l~~--~~i~~l~--~l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n~~~~   98 (199)
T d2omxa2          24 VLGKTNVTDTVSQTDLDQVTTLQADR--LGIKSID--GVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIAD   98 (199)
T ss_dssp             HTTCSSTTSEECHHHHTTCCEEECTT--SCCCCCT--TGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCC
T ss_pred             HhCCCCCCCccCHHHhcCCCEEECCC--CCCCCcc--ccccCCCcCcCccccccccCccc-ccCCccccccccccccccc
Confidence            34445554444344678999999933  3333333  26789999999999999998875 8999999999999999988


Q ss_pred             cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccch
Q 004895          613 IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNAS  692 (724)
Q Consensus       613 ~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~  692 (724)
                      ++.+.++++|++|++++|.+..++ .+..+++|+.|++++| .+..++  .+..+++|+.|++.+|.     +++     
T Consensus        99 ~~~l~~l~~L~~L~l~~~~~~~~~-~~~~l~~L~~L~l~~n-~l~~~~--~l~~~~~L~~L~l~~n~-----l~~-----  164 (199)
T d2omxa2          99 ITPLANLTNLTGLTLFNNQITDID-PLKNLTNLNRLELSSN-TISDIS--ALSGLTSLQQLNFSSNQ-----VTD-----  164 (199)
T ss_dssp             CGGGTTCTTCSEEECCSSCCCCCG-GGTTCTTCSEEECCSS-CCCCCG--GGTTCTTCSEEECCSSC-----CCC-----
T ss_pred             cccccccccccccccccccccccc-ccchhhhhHHhhhhhh-hhcccc--ccccccccccccccccc-----ccC-----
Confidence            778999999999999999887764 4888999999999995 466554  37899999999999864     221     


Q ss_pred             HHhhcCCCCCcEEEeecccccccccccccC
Q 004895          693 LAELKGLSKLTTLEIDVRDAEMLRRIWSLG  722 (724)
Q Consensus       693 l~~L~~L~~L~~L~l~~n~~~~lp~~~~~~  722 (724)
                      +..+.++++|+.|++++|.++.+|....+.
T Consensus       165 l~~l~~l~~L~~L~ls~N~i~~i~~l~~L~  194 (199)
T d2omxa2         165 LKPLANLTTLERLDISSNKVSDISVLAKLT  194 (199)
T ss_dssp             CGGGTTCTTCCEEECCSSCCCCCGGGGGCT
T ss_pred             CccccCCCCCCEEECCCCCCCCCccccCCC
Confidence            234778999999999999998887654443

>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=99.47  E-value=3.4e-13  Score=128.65  Aligned_cols=156  Identities=26%  Similarity=0.364  Sum_probs=126.9

Q ss_pred             cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEE
Q 004895          547 ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILS  626 (724)
Q Consensus       547 ~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~  626 (724)
                      ++.+|+.|.+  ..+....+..  +..+++|+.|++++|.++.+|. ++.+++|++|++++|.++.++.++.+++|++|+
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~  118 (210)
T d1h6ta2          44 ELNSIDQIIA--NNSDIKSVQG--IQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVKDLSSLKDLKKLKSLS  118 (210)
T ss_dssp             HHHTCCEEEC--TTSCCCCCTT--GGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCGGGGTTCTTCCEEE
T ss_pred             HhcCccEEEC--cCCCCCCchh--HhhCCCCCEEeCCCccccCccc-cccCccccccccccccccccccccccccccccc
Confidence            5678888888  3333344432  6789999999999999998874 789999999999999999988899999999999


Q ss_pred             ccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEE
Q 004895          627 LRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLE  706 (724)
Q Consensus       627 l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~  706 (724)
                      +++|.+..++ .+..+++|+.+++++| .+...+  .+..+++|+++++++|..     .     .+..+.++++|+.|+
T Consensus       119 l~~~~~~~~~-~l~~l~~l~~l~~~~n-~l~~~~--~~~~l~~L~~l~l~~n~l-----~-----~i~~l~~l~~L~~L~  184 (210)
T d1h6ta2         119 LEHNGISDIN-GLVHLPQLESLYLGNN-KITDIT--VLSRLTKLDTLSLEDNQI-----S-----DIVPLAGLTKLQNLY  184 (210)
T ss_dssp             CTTSCCCCCG-GGGGCTTCCEEECCSS-CCCCCG--GGGGCTTCSEEECCSSCC-----C-----CCGGGTTCTTCCEEE
T ss_pred             cccccccccc-cccccccccccccccc-cccccc--cccccccccccccccccc-----c-----ccccccCCCCCCEEE
Confidence            9999888775 5889999999999884 555543  368999999999998642     2     123478899999999


Q ss_pred             eeccccccccccccc
Q 004895          707 IDVRDAEMLRRIWSL  721 (724)
Q Consensus       707 l~~n~~~~lp~~~~~  721 (724)
                      +++|.++.+|....+
T Consensus       185 Ls~N~i~~l~~l~~l  199 (210)
T d1h6ta2         185 LSKNHISDLRALAGL  199 (210)
T ss_dssp             CCSSCCCBCGGGTTC
T ss_pred             CCCCCCCCChhhcCC
Confidence            999999988854433

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.43  E-value=2e-12  Score=124.91  Aligned_cols=174  Identities=18%  Similarity=0.285  Sum_probs=132.3

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++.+++.++++..++....+++|+.|.+.  .+....+.+  +..++.|+++++++|.++.++ .++.+++|+++.+
T Consensus        40 l~~L~~L~l~~~~i~~l~~l~~l~~L~~L~ls--~n~i~~~~~--l~~l~~l~~l~~~~n~~~~i~-~l~~l~~L~~l~l  114 (227)
T d1h6ua2          40 LDGITTLSAFGTGVTTIEGVQYLNNLIGLELK--DNQITDLAP--LKNLTKITELELSGNPLKNVS-AIAGLQSIKTLDL  114 (227)
T ss_dssp             HHTCCEEECTTSCCCCCTTGGGCTTCCEEECC--SSCCCCCGG--GTTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEEC
T ss_pred             cCCcCEEECCCCCCCcchhHhcCCCCcEeecC--Cceeecccc--ccccccccccccccccccccc-ccccccccccccc
Confidence            46889999999999888766689999999993  333444433  788999999999999888775 5788999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      ++|....+..+...+.+..+.++++.+...+ .+..+++|++|++++| .+...++  ++++++|++|++++|.     +
T Consensus       115 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~L~~L~l~~n-~~~~~~~--l~~l~~L~~L~Ls~n~-----l  185 (227)
T d1h6ua2         115 TSTQITDVTPLAGLSNLQVLYLDLNQITNIS-PLAGLTNLQYLSIGNA-QVSDLTP--LANLSKLTTLKADDNK-----I  185 (227)
T ss_dssp             TTSCCCCCGGGTTCTTCCEEECCSSCCCCCG-GGGGCTTCCEEECCSS-CCCCCGG--GTTCTTCCEEECCSSC-----C
T ss_pred             ccccccccchhccccchhhhhchhhhhchhh-hhcccccccccccccc-ccccchh--hcccccceecccCCCc-----c
Confidence            9988777777777888888888888776543 3677788888888874 3444433  7888888888888763     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      +     .+..+.++++|+.|++++|+++.+|..
T Consensus       186 ~-----~l~~l~~l~~L~~L~Ls~N~lt~i~~l  213 (227)
T d1h6ua2         186 S-----DISPLASLPNLIEVHLKNNQISDVSPL  213 (227)
T ss_dssp             C-----CCGGGGGCTTCCEEECTTSCCCBCGGG
T ss_pred             C-----CChhhcCCCCCCEEECcCCcCCCCccc
Confidence            2     123466778888888888888777753

>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=99.43  E-value=6.8e-13  Score=133.17  Aligned_cols=179  Identities=22%  Similarity=0.270  Sum_probs=126.7

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecc-----------------------cccccccchhhhcCCCCceEE
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAK-----------------------YDSTLQISDHFFEGTEELKVL  580 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~-----------------------~~~~~~~~~~~~~~l~~L~~L  580 (724)
                      +..++.|++++|.++.++..  ..+++|+.|.+..+                       .+....+++..|.++++|++|
T Consensus        31 p~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L  110 (284)
T d1ozna_          31 PAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTL  110 (284)
T ss_dssp             CTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEE
T ss_pred             CCCCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccccccccchhhcccccCCEE
Confidence            55677888888888777643  36777777777321                       111223445567778888888


Q ss_pred             EcCCCcCCCCC-ccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCCCCCC
Q 004895          581 DFTGIRFSPLP-SSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSNCSSL  656 (724)
Q Consensus       581 ~l~~~~~~~lp-~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~~~~l  656 (724)
                      ++++|.+..++ ..+..+.+|+++++++|.++.+  ..+..+.+|++|++++|.++.+|. .+..+++|+++++++ +.+
T Consensus       111 ~l~~n~~~~~~~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~l~~l~~~~f~~l~~L~~l~l~~-N~l  189 (284)
T d1ozna_         111 HLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSLDRLLLHQ-NRV  189 (284)
T ss_dssp             ECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS-SCC
T ss_pred             ecCCcccccccccccchhcccchhhhccccccccChhHhccccchhhcccccCcccccchhhhccccccchhhhhh-ccc
Confidence            88888877553 4566777888888888888773  457778888888888888887754 467788888888888 456


Q ss_pred             cccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccc
Q 004895          657 VVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE  713 (724)
Q Consensus       657 ~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~  713 (724)
                      ..+++..+..+++|++|++++|..     .+..+   ..+.++++|+.|++++|.+.
T Consensus       190 ~~i~~~~f~~l~~L~~L~l~~N~i-----~~~~~---~~~~~~~~L~~L~l~~N~l~  238 (284)
T d1ozna_         190 AHVHPHAFRDLGRLMTLYLFANNL-----SALPT---EALAPLRALQYLRLNDNPWV  238 (284)
T ss_dssp             CEECTTTTTTCTTCCEEECCSSCC-----SCCCH---HHHTTCTTCCEEECCSSCEE
T ss_pred             cccChhHhhhhhhccccccccccc-----ccccc---cccccccccCEEEecCCCCC
Confidence            667677788888888888887642     22222   34567778888888888764

>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=99.43  E-value=1e-12  Score=133.29  Aligned_cols=65  Identities=18%  Similarity=0.241  Sum_probs=49.2

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCc
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPS  592 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~  592 (724)
                      +.++++|++++|.++.++..  ..+++|++|.+  ..+....+++..|.+++.|+.|++++|+++.+|.
T Consensus        30 ~~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l--~~n~~~~i~~~~f~~l~~L~~L~l~~n~l~~l~~   96 (305)
T d1xkua_          30 PPDTALLDLQNNKITEIKDGDFKNLKNLHTLIL--INNKISKISPGAFAPLVKLERLYLSKNQLKELPE   96 (305)
T ss_dssp             CTTCCEEECCSSCCCCBCTTTTTTCTTCCEEEC--CSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCS
T ss_pred             CCCCCEEECcCCcCCCcChhHhhcccccccccc--ccccccccchhhhhCCCccCEecccCCccCcCcc
Confidence            56789999999999888753  36889999988  3444556666778888888888888886655543

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=2.7e-13  Score=123.18  Aligned_cols=132  Identities=16%  Similarity=0.196  Sum_probs=101.9

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhh-hcCCCCCeEc
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQI-GQLTRLQLLD  649 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i-~~l~~L~~L~  649 (724)
                      |.+...||.|+|++|+|+.+|..+..+.+|++|+|++|.++.++.+..+++|++|++++|.++.+|..+ ..+++|++|+
T Consensus        14 ~~n~~~lr~L~L~~n~I~~i~~~~~~l~~L~~L~Ls~N~i~~l~~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L~~L~   93 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNNRICRIGEGLDQALPDLTELI   93 (162)
T ss_dssp             EECTTSCEEEECTTSCCCSCCCGGGGTTCCSEEECCSSCCCEECCCCCCSSCCEEECCSSCCCEECSCHHHHCTTCCEEE
T ss_pred             ccCcCcCcEEECCCCCCCccCccccccccCCEEECCCCCCCccCCcccCcchhhhhcccccccCCCccccccccccccce
Confidence            456778999999999999988777888999999999999988878899999999999999999887764 5789999999


Q ss_pred             cCCCCCCcccCh-HHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEee
Q 004895          650 LSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID  708 (724)
Q Consensus       650 l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~  708 (724)
                      +++| .+..++. ..+..+++|++|++.+|....     ........+..+++|+.||-+
T Consensus        94 L~~N-~i~~~~~l~~l~~l~~L~~L~l~~N~i~~-----~~~~r~~~i~~lp~L~~LD~~  147 (162)
T d1a9na_          94 LTNN-SLVELGDLDPLASLKSLTYLCILRNPVTN-----KKHYRLYVIYKVPQVRVLDFQ  147 (162)
T ss_dssp             CCSC-CCCCGGGGGGGGGCTTCCEEECCSSGGGG-----STTHHHHHHHHCTTCSEETTE
T ss_pred             eccc-cccccccccccccccccchhhcCCCcccc-----ccchHHHHHHHCCCcCeeCCC
Confidence            9984 5555543 347889999999999874321     111112235567788888743

>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=99.42  E-value=5.4e-13  Score=115.11  Aligned_cols=99  Identities=25%  Similarity=0.290  Sum_probs=79.6

Q ss_pred             eEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC-cccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCC
Q 004895          578 KVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED-IAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSL  656 (724)
Q Consensus       578 ~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~-~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l  656 (724)
                      |+|++++|.++.+|. ++.+.+|++|++++|.++. |+.++.+++|++|++++|.++.+| ++..+++|++|++++ +.+
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 RVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCN-NRL   77 (124)
T ss_dssp             SEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCS-SCC
T ss_pred             CEEEcCCCCCCCCcc-cccCCCCCEEECCCCccCcchhhhhhhhcccccccccccccccC-ccccccccCeEECCC-Ccc
Confidence            678888888888764 7888888888888888888 467888888888888888888886 488888888888888 456


Q ss_pred             cccCh-HHhhCCCCCcEEEccCCC
Q 004895          657 VVIAP-NVISKLSRLEELYMGDSF  679 (724)
Q Consensus       657 ~~~~~-~~i~~l~~L~~L~l~~~~  679 (724)
                      ..++. ..++.+++|++|++++|.
T Consensus        78 ~~~~~~~~l~~~~~L~~L~l~~N~  101 (124)
T d1dcea3          78 QQSAAIQPLVSCPRLVLLNLQGNS  101 (124)
T ss_dssp             CSSSTTGGGGGCTTCCEEECTTSG
T ss_pred             CCCCCchhhcCCCCCCEEECCCCc
Confidence            65543 457788888888888864

>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=99.41  E-value=1.5e-12  Score=130.69  Aligned_cols=149  Identities=21%  Similarity=0.270  Sum_probs=120.5

Q ss_pred             CceEEecc-CCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCC-ccccCCCCCcEE
Q 004895          528 GPIAISLP-YRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLP-SSLGRLINLQTL  603 (724)
Q Consensus       528 ~~~~l~l~-~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp-~~i~~l~~L~~L  603 (724)
                      ...++.+. .+.+..++..  ..+++|++|.+  ..+....++...+..+..|+.+++++|.++.+| ..+..+.+|++|
T Consensus        81 ~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L~l--~~n~~~~~~~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L  158 (284)
T d1ozna_          81 LLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL--DRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHL  158 (284)
T ss_dssp             TCCEEECCSCTTCCCCCTTTTTTCTTCCEEEC--TTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEE
T ss_pred             cccccccccccccccccchhhcccccCCEEec--CCcccccccccccchhcccchhhhccccccccChhHhccccchhhc
Confidence            44444433 3344444322  25789999998  344455666667888999999999999999886 467889999999


Q ss_pred             EcCCcccCC--cccccCCCCCcEEEccCCcCccc-chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          604 CLDGWRLED--IAIVGQLKKLEILSLRGAEIKQL-PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       604 ~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~l-p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++++|.++.  +..+.++++|+++++++|.+..+ |..+..+++|++|++++ +.+..+++..++.+++|++|++++|.
T Consensus       159 ~l~~N~l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~-N~i~~~~~~~~~~~~~L~~L~l~~N~  236 (284)
T d1ozna_         159 FLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFA-NNLSALPTEALAPLRALQYLRLNDNP  236 (284)
T ss_dssp             ECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS-SCCSCCCHHHHTTCTTCCEEECCSSC
T ss_pred             ccccCcccccchhhhccccccchhhhhhccccccChhHhhhhhhcccccccc-cccccccccccccccccCEEEecCCC
Confidence            999999987  36788999999999999999866 67799999999999999 56788998889999999999999974

>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=99.37  E-value=1.7e-12  Score=111.88  Aligned_cols=102  Identities=26%  Similarity=0.318  Sum_probs=84.0

Q ss_pred             hcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccc--hhhhcCCCCCeE
Q 004895          571 FEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLP--LQIGQLTRLQLL  648 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp--~~i~~l~~L~~L  648 (724)
                      +.++++|+.|++++|.+..+|+.++.+.+|++|++++|.++.++.++.+++|++|++++|.++.+|  ..+..+++|++|
T Consensus        16 l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N~i~~l~~~~~l~~L~~L~l~~N~i~~~~~~~~l~~~~~L~~L   95 (124)
T d1dcea3          16 LEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLL   95 (124)
T ss_dssp             GGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGGGTTCSSCCEEECCSSCCCSSSTTGGGGGCTTCCEE
T ss_pred             cccCCCCCEEECCCCccCcchhhhhhhhcccccccccccccccCccccccccCeEECCCCccCCCCCchhhcCCCCCCEE
Confidence            567888999999999999999889999999999999999998878999999999999999998776  358889999999


Q ss_pred             ccCCCCCCcc---cChHHhhCCCCCcEE
Q 004895          649 DLSNCSSLVV---IAPNVISKLSRLEEL  673 (724)
Q Consensus       649 ~l~~~~~l~~---~~~~~i~~l~~L~~L  673 (724)
                      ++++| .+..   .+...+..+++|+.|
T Consensus        96 ~l~~N-~i~~~~~~~~~l~~~lp~L~~L  122 (124)
T d1dcea3          96 NLQGN-SLCQEEGIQERLAEMLPSVSSI  122 (124)
T ss_dssp             ECTTS-GGGGSSSCTTHHHHHCTTCSEE
T ss_pred             ECCCC-cCCcCccHHHHHHHHCcCcceE
Confidence            99984 3433   334445567777765

>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=99.36  E-value=1.4e-12  Score=132.78  Aligned_cols=182  Identities=18%  Similarity=0.205  Sum_probs=110.5

Q ss_pred             cCceEEeccCCCcc---cCCCcc-cCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC-CCccccCCCCCc
Q 004895          527 KGPIAISLPYRDIQ---ELPERL-ECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP-LPSSLGRLINLQ  601 (724)
Q Consensus       527 ~~~~~l~l~~~~~~---~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~-lp~~i~~l~~L~  601 (724)
                      .+++.|++.++.+.   .+|..+ .+++|++|++.+.+.....+|.. |.++++|++|++++|++.. .|..+..+.+|+
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~-i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~  128 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPA-IAKLTQLHYLYITHTNVSGAIPDFLSQIKTLV  128 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGG-GGGCTTCSEEEEEEECCEEECCGGGGGCTTCC
T ss_pred             EEEEEEECCCCCCCCCCCCChHHhcCccccccccccccccccccccc-cccccccchhhhccccccccccccccchhhhc
Confidence            35777788777665   344433 67888888883323333345544 6778888888888887774 345566777777


Q ss_pred             EEEcCCcccCC--cccccCCCCCcEEEccCCcCc-ccchhhhcCCCC-CeEccCCCC-----------------------
Q 004895          602 TLCLDGWRLED--IAIVGQLKKLEILSLRGAEIK-QLPLQIGQLTRL-QLLDLSNCS-----------------------  654 (724)
Q Consensus       602 ~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~-~lp~~i~~l~~L-~~L~l~~~~-----------------------  654 (724)
                      ++++++|.+..  |..++.+++|+++++++|.+. .+|..+..+.++ +.+++++|.                       
T Consensus       129 ~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~~~l~l~~~~  208 (313)
T d1ogqa_         129 TLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNM  208 (313)
T ss_dssp             EEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCSEEECCSSE
T ss_pred             ccccccccccccCchhhccCcccceeeccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            77777776544  466777777777777777665 556666655554 444443311                       


Q ss_pred             -----------------------CCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccc
Q 004895          655 -----------------------SLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRD  711 (724)
Q Consensus       655 -----------------------~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~  711 (724)
                                             .+...++ .++.+++|+.|++++|.     +++..|   ..+.+|++|+.|++++|.
T Consensus       209 ~~~~~~~~~~~~~~l~~l~~~~~~l~~~~~-~~~~~~~L~~L~Ls~N~-----l~g~iP---~~l~~L~~L~~L~Ls~N~  279 (313)
T d1ogqa_         209 LEGDASVLFGSDKNTQKIHLAKNSLAFDLG-KVGLSKNLNGLDLRNNR-----IYGTLP---QGLTQLKFLHSLNVSFNN  279 (313)
T ss_dssp             EEECCGGGCCTTSCCSEEECCSSEECCBGG-GCCCCTTCCEEECCSSC-----CEECCC---GGGGGCTTCCEEECCSSE
T ss_pred             cccccccccccccccccccccccccccccc-ccccccccccccCccCe-----ecccCC---hHHhCCCCCCEEECcCCc
Confidence                                   1111122 24455555555555532     333333   345667789999999988


Q ss_pred             cc-ccccc
Q 004895          712 AE-MLRRI  718 (724)
Q Consensus       712 ~~-~lp~~  718 (724)
                      ++ .+|..
T Consensus       280 l~g~iP~~  287 (313)
T d1ogqa_         280 LCGEIPQG  287 (313)
T ss_dssp             EEEECCCS
T ss_pred             ccccCCCc
Confidence            76 56653

>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=99.34  E-value=9.4e-12  Score=130.30  Aligned_cols=166  Identities=22%  Similarity=0.306  Sum_probs=108.0

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++.+++.+|.+..++....+++|+.|.+.  .+....+++  +..+++|+.|+++++.+..+++ +..+..++++.+
T Consensus       218 ~~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~--~n~l~~~~~--~~~~~~L~~L~l~~~~l~~~~~-~~~~~~l~~l~~  292 (384)
T d2omza2         218 LTNLDELSLNGNQLKDIGTLASLTNLTDLDLA--NNQISNLAP--LSGLTKLTELKLGANQISNISP-LAGLTALTNLEL  292 (384)
T ss_dssp             CTTCCEEECCSSCCCCCGGGGGCTTCSEEECC--SSCCCCCGG--GTTCTTCSEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             cCCCCEEECCCCCCCCcchhhcccccchhccc--cCccCCCCc--ccccccCCEeeccCcccCCCCc-cccccccccccc
Confidence            35666777777766666554566777777662  222333332  5566777777777777766553 566677777777


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      +.|.++.+..+..++++++|++++|.++.++. +..+++|++|++++| .++.++  .++.|++|++|++++|.     +
T Consensus       293 ~~n~l~~~~~~~~~~~l~~L~ls~n~l~~l~~-l~~l~~L~~L~L~~n-~l~~l~--~l~~l~~L~~L~l~~N~-----l  363 (384)
T d2omza2         293 NENQLEDISPISNLKNLTYLTLYFNNISDISP-VSSLTKLQRLFFANN-KVSDVS--SLANLTNINWLSAGHNQ-----I  363 (384)
T ss_dssp             CSSCCSCCGGGGGCTTCSEEECCSSCCSCCGG-GGGCTTCCEEECCSS-CCCCCG--GGGGCTTCCEEECCSSC-----C
T ss_pred             cccccccccccchhcccCeEECCCCCCCCCcc-cccCCCCCEEECCCC-CCCCCh--hHcCCCCCCEEECCCCc-----C
Confidence            77777776667777777777777777776653 677777777777774 455543  26777777777777653     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeecc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVR  710 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n  710 (724)
                      ++     +..+.++++|+.|+|+.|
T Consensus       364 ~~-----l~~l~~l~~L~~L~L~~N  383 (384)
T d2omza2         364 SD-----LTPLANLTRITQLGLNDQ  383 (384)
T ss_dssp             CB-----CGGGTTCTTCSEEECCCE
T ss_pred             CC-----ChhhccCCCCCEeeCCCC
Confidence            21     123566777777777765

>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=99.31  E-value=3.1e-11  Score=116.37  Aligned_cols=165  Identities=22%  Similarity=0.338  Sum_probs=135.3

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+++++.+++|.+..++....+++++.+.+.  .+....++  .+.+++.|+.++++++....++ .+.....+.++.+
T Consensus        62 l~~L~~L~ls~n~i~~~~~l~~l~~l~~l~~~--~n~~~~i~--~l~~l~~L~~l~l~~~~~~~~~-~~~~~~~~~~l~~  136 (227)
T d1h6ua2          62 LNNLIGLELKDNQITDLAPLKNLTKITELELS--GNPLKNVS--AIAGLQSIKTLDLTSTQITDVT-PLAGLSNLQVLYL  136 (227)
T ss_dssp             CTTCCEEECCSSCCCCCGGGTTCCSCCEEECC--SCCCSCCG--GGTTCTTCCEEECTTSCCCCCG-GGTTCTTCCEEEC
T ss_pred             CCCCcEeecCCceeeccccccccccccccccc--cccccccc--cccccccccccccccccccccc-hhccccchhhhhc
Confidence            57999999999999888777789999999983  33333443  3778999999999999887654 3677889999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      +++.+.....+..+++|++|++++|.+...+. +.++++|+.|++++| .+..+++  ++++++|++|++++|.     +
T Consensus       137 ~~~~~~~~~~~~~~~~L~~L~l~~n~~~~~~~-l~~l~~L~~L~Ls~n-~l~~l~~--l~~l~~L~~L~Ls~N~-----l  207 (227)
T d1h6ua2         137 DLNQITNISPLAGLTNLQYLSIGNAQVSDLTP-LANLSKLTTLKADDN-KISDISP--LASLPNLIEVHLKNNQ-----I  207 (227)
T ss_dssp             CSSCCCCCGGGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSS-CCCCCGG--GGGCTTCCEEECTTSC-----C
T ss_pred             hhhhhchhhhhccccccccccccccccccchh-hcccccceecccCCC-ccCCChh--hcCCCCCCEEECcCCc-----C
Confidence            99998887778899999999999998887654 889999999999995 6777754  7999999999999974     2


Q ss_pred             cCCccchHHhhcCCCCCcEEEeec
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDV  709 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~  709 (724)
                      +     .+..+.++++|+.|+++.
T Consensus       208 t-----~i~~l~~l~~L~~L~lsn  226 (227)
T d1h6ua2         208 S-----DVSPLANTSNLFIVTLTN  226 (227)
T ss_dssp             C-----BCGGGTTCTTCCEEEEEE
T ss_pred             C-----CCcccccCCCCCEEEeeC
Confidence            2     123478899999999873

>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=99.30  E-value=2.9e-11  Score=126.52  Aligned_cols=174  Identities=20%  Similarity=0.264  Sum_probs=143.9

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..+...+.+.++.+..++....+++|+.|.+.  .+....++  .+..++.|+.|++++|.+..+++ ++.+++|++|++
T Consensus       196 l~~~~~l~l~~n~i~~~~~~~~~~~L~~L~l~--~n~l~~~~--~l~~l~~L~~L~l~~n~l~~~~~-~~~~~~L~~L~l  270 (384)
T d2omza2         196 LTNLESLIATNNQISDITPLGILTNLDELSLN--GNQLKDIG--TLASLTNLTDLDLANNQISNLAP-LSGLTKLTELKL  270 (384)
T ss_dssp             CTTCSEEECCSSCCCCCGGGGGCTTCCEEECC--SSCCCCCG--GGGGCTTCSEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             ccccceeeccCCccCCCCcccccCCCCEEECC--CCCCCCcc--hhhcccccchhccccCccCCCCc-ccccccCCEeec
Confidence            45778888998888887766678899999993  33344443  37789999999999999998764 788999999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccc
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKV  685 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~  685 (724)
                      +++.++..+.+..+..++.+++..|.++.++ .+..++++++|++++| .+..+++  +..+++|++|++++|..     
T Consensus       271 ~~~~l~~~~~~~~~~~l~~l~~~~n~l~~~~-~~~~~~~l~~L~ls~n-~l~~l~~--l~~l~~L~~L~L~~n~l-----  341 (384)
T d2omza2         271 GANQISNISPLAGLTALTNLELNENQLEDIS-PISNLKNLTYLTLYFN-NISDISP--VSSLTKLQRLFFANNKV-----  341 (384)
T ss_dssp             CSSCCCCCGGGTTCTTCSEEECCSSCCSCCG-GGGGCTTCSEEECCSS-CCSCCGG--GGGCTTCCEEECCSSCC-----
T ss_pred             cCcccCCCCcccccccccccccccccccccc-ccchhcccCeEECCCC-CCCCCcc--cccCCCCCEEECCCCCC-----
Confidence            9999998778899999999999999988765 4889999999999995 6777754  78999999999999742     


Q ss_pred             cCCccchHHhhcCCCCCcEEEeecccccccccc
Q 004895          686 EGGSNASLAELKGLSKLTTLEIDVRDAEMLRRI  718 (724)
Q Consensus       686 ~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~~  718 (724)
                      +     .+..+.++++|+.|++++|.++.++..
T Consensus       342 ~-----~l~~l~~l~~L~~L~l~~N~l~~l~~l  369 (384)
T d2omza2         342 S-----DVSSLANLTNINWLSAGHNQISDLTPL  369 (384)
T ss_dssp             C-----CCGGGGGCTTCCEEECCSSCCCBCGGG
T ss_pred             C-----CChhHcCCCCCCEEECCCCcCCCChhh
Confidence            2     123577889999999999999888753

>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=99.28  E-value=2.2e-12  Score=117.09  Aligned_cols=125  Identities=18%  Similarity=0.176  Sum_probs=91.1

Q ss_pred             ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCc-c-cccCCCCCc
Q 004895          546 LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDI-A-IVGQLKKLE  623 (724)
Q Consensus       546 ~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~-~-~~~~l~~L~  623 (724)
                      ..+.++|.|++  .++....++ ..+..+++|++|++++|.+..++ .++.+++|++|++++|.++.+ + .+..+++|+
T Consensus        15 ~n~~~lr~L~L--~~n~I~~i~-~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L~   90 (162)
T d1a9na_          15 TNAVRDRELDL--RGYKIPVIE-NLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNRICRIGEGLDQALPDLT   90 (162)
T ss_dssp             ECTTSCEEEEC--TTSCCCSCC-CGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSCCCEECSCHHHHCTTCC
T ss_pred             cCcCcCcEEEC--CCCCCCccC-ccccccccCCEEECCCCCCCccC-CcccCcchhhhhcccccccCCCccccccccccc
Confidence            34455666666  233333443 34567788899999999888774 478888999999999988873 3 356788999


Q ss_pred             EEEccCCcCcccch--hhhcCCCCCeEccCCCCCCcccC---hHHhhCCCCCcEEEc
Q 004895          624 ILSLRGAEIKQLPL--QIGQLTRLQLLDLSNCSSLVVIA---PNVISKLSRLEELYM  675 (724)
Q Consensus       624 ~L~l~~~~i~~lp~--~i~~l~~L~~L~l~~~~~l~~~~---~~~i~~l~~L~~L~l  675 (724)
                      +|++++|.++.++.  .+..+++|++|++++| .+...|   +..+..+++|+.|+.
T Consensus        91 ~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~~N-~i~~~~~~r~~~i~~lp~L~~LD~  146 (162)
T d1a9na_          91 ELILTNNSLVELGDLDPLASLKSLTYLCILRN-PVTNKKHYRLYVIYKVPQVRVLDF  146 (162)
T ss_dssp             EEECCSCCCCCGGGGGGGGGCTTCCEEECCSS-GGGGSTTHHHHHHHHCTTCSEETT
T ss_pred             cceeccccccccccccccccccccchhhcCCC-ccccccchHHHHHHHCCCcCeeCC
Confidence            99999998887764  5778899999999885 445554   235788899998874

>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=99.26  E-value=8.3e-12  Score=117.02  Aligned_cols=122  Identities=17%  Similarity=0.182  Sum_probs=100.4

Q ss_pred             cEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC-C-CccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEc
Q 004895          552 KLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP-L-PSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSL  627 (724)
Q Consensus       552 r~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~-l-p~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l  627 (724)
                      +++.+  +......+|.+.   .+.++.|+|++|.|+. + +..+..+.+|++|+|++|.+..  +..+..+++|++|++
T Consensus        11 ~~v~C--s~~~L~~iP~~l---p~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~L   85 (192)
T d1w8aa_          11 TTVDC--TGRGLKEIPRDI---PLHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQL   85 (192)
T ss_dssp             TEEEC--TTSCCSSCCSCC---CTTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEEC
T ss_pred             CEEEE--eCCCcCccCCCC---CCCCCEEEeCCCCCcccccccccCCCceEeeeeccccccccccccccccccccceeee
Confidence            34444  344455677653   2679999999999974 4 4567889999999999999887  367889999999999


Q ss_pred             cCCcCcccchh-hhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          628 RGAEIKQLPLQ-IGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       628 ~~~~i~~lp~~-i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      ++|.++.+|+. +.++++|++|+|++ +.+..+++..+..+++|++|++++|.
T Consensus        86 s~N~l~~l~~~~F~~l~~L~~L~L~~-N~l~~i~~~~f~~l~~L~~l~L~~N~  137 (192)
T d1w8aa_          86 GENKIKEISNKMFLGLHQLKTLNLYD-NQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CSCCCCEECSSSSTTCTTCCEEECCS-SCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             ccccccccCHHHHhCCCcccccccCC-ccccccCHHHhcCCcccccccccccc
Confidence            99999998765 78899999999999 67889998888999999999999874

>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=99.24  E-value=9e-12  Score=126.69  Aligned_cols=174  Identities=16%  Similarity=0.184  Sum_probs=113.2

Q ss_pred             ccCceEEeccC-CCcc-cCCCcc-cCCCccEEEEecccccccccchh------------------------hhcCCCCce
Q 004895          526 QKGPIAISLPY-RDIQ-ELPERL-ECPQLKLFLLFAKYDSTLQISDH------------------------FFEGTEELK  578 (724)
Q Consensus       526 ~~~~~~l~l~~-~~~~-~~~~~~-~~~~Lr~L~l~~~~~~~~~~~~~------------------------~~~~l~~L~  578 (724)
                      ...+++|++++ |.+. .+|..+ .+++|++|++..+  ....++..                        .+.+++.|+
T Consensus        75 L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N--~l~~~~~~~~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~  152 (313)
T d1ogqa_          75 LPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHT--NVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLPNLV  152 (313)
T ss_dssp             CTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEE--CCEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCC
T ss_pred             Cccccccccccccccccccccccccccccchhhhccc--cccccccccccchhhhcccccccccccccCchhhccCcccc
Confidence            45677777764 4553 565443 5677777777322  22222222                        345555566


Q ss_pred             EEEcCCCcCC-CCCccccCCCCC-cEEEcCCcccCC-------------------------cccccCCCCCcEEEccCCc
Q 004895          579 VLDFTGIRFS-PLPSSLGRLINL-QTLCLDGWRLED-------------------------IAIVGQLKKLEILSLRGAE  631 (724)
Q Consensus       579 ~L~l~~~~~~-~lp~~i~~l~~L-~~L~L~~~~l~~-------------------------~~~~~~l~~L~~L~l~~~~  631 (724)
                      .+++++|.+. .+|..++.+..+ +++.+++|.++.                         +..++.+.+|++|++++|.
T Consensus       153 ~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~~~l~l~~~~~~~~~~~~~~~~~~l~~l~~~~~~  232 (313)
T d1ogqa_         153 GITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNS  232 (313)
T ss_dssp             EEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCSEEECCSSEEEECCGGGCCTTSCCSEEECCSSE
T ss_pred             eeeccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            6666655555 455555555543 555555444321                         1234567788888888888


Q ss_pred             CcccchhhhcCCCCCeEccCCCCCCc-ccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecc
Q 004895          632 IKQLPLQIGQLTRLQLLDLSNCSSLV-VIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVR  710 (724)
Q Consensus       632 i~~lp~~i~~l~~L~~L~l~~~~~l~-~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n  710 (724)
                      +...|+.++.+++|++|++++| .+. .+|. .+++|++|++|++++|.     ++|..|    ++.+|++|+.+++++|
T Consensus       233 l~~~~~~~~~~~~L~~L~Ls~N-~l~g~iP~-~l~~L~~L~~L~Ls~N~-----l~g~iP----~~~~L~~L~~l~l~~N  301 (313)
T d1ogqa_         233 LAFDLGKVGLSKNLNGLDLRNN-RIYGTLPQ-GLTQLKFLHSLNVSFNN-----LCGEIP----QGGNLQRFDVSAYANN  301 (313)
T ss_dssp             ECCBGGGCCCCTTCCEEECCSS-CCEECCCG-GGGGCTTCCEEECCSSE-----EEEECC----CSTTGGGSCGGGTCSS
T ss_pred             ccccccccccccccccccCccC-eecccCCh-HHhCCCCCCEEECcCCc-----ccccCC----CcccCCCCCHHHhCCC
Confidence            8766778899999999999995 555 5554 58999999999999963     444333    3467788999999999


Q ss_pred             cc
Q 004895          711 DA  712 (724)
Q Consensus       711 ~~  712 (724)
                      +.
T Consensus       302 ~~  303 (313)
T d1ogqa_         302 KC  303 (313)
T ss_dssp             SE
T ss_pred             cc
Confidence            73

>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=99.19  E-value=1.7e-10  Score=116.53  Aligned_cols=147  Identities=16%  Similarity=0.202  Sum_probs=113.6

Q ss_pred             hhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCC--cccccCCCCCcEEEccCCcCcccc-hhhhcCCC
Q 004895          568 DHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLED--IAIVGQLKKLEILSLRGAEIKQLP-LQIGQLTR  644 (724)
Q Consensus       568 ~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp-~~i~~l~~  644 (724)
                      ...|.+++.|+++++++|.+..+|..+  +.+|++|++++|....  +..+..++++++|++++|.++.+| ..+..+++
T Consensus       143 ~~~~~~l~~L~~l~l~~n~l~~l~~~~--~~~L~~L~l~~n~~~~~~~~~~~~~~~l~~L~~s~n~l~~~~~~~~~~l~~  220 (305)
T d1xkua_         143 NGAFQGMKKLSYIRIADTNITTIPQGL--PPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPH  220 (305)
T ss_dssp             TTGGGGCTTCCEEECCSSCCCSCCSSC--CTTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSCCCEECTTTGGGSTT
T ss_pred             ccccccccccCccccccCCccccCccc--CCccCEEECCCCcCCCCChhHhhcccccccccccccccccccccccccccc
Confidence            345778899999999999999888654  6789999999998766  477899999999999999999874 45888999


Q ss_pred             CCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccc--ccccccc
Q 004895          645 LQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAE--MLRRIWS  720 (724)
Q Consensus       645 L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~--~lp~~~~  720 (724)
                      |+.|+|++| .++.+|. .+..+++|++|++++|.+..  +....-...+.+..+.+|+.|++++|.++  .++...|
T Consensus       221 L~~L~L~~N-~L~~lp~-~l~~l~~L~~L~Ls~N~i~~--i~~~~f~~~~~~~~~~~L~~L~L~~N~~~~~~~~~~~f  294 (305)
T d1xkua_         221 LRELHLNNN-KLVKVPG-GLADHKYIQVVYLHNNNISA--IGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTF  294 (305)
T ss_dssp             CCEEECCSS-CCSSCCT-TTTTCSSCCEEECCSSCCCC--CCTTSSSCSSCCTTSCCCSEEECCSSSSCGGGSCGGGG
T ss_pred             ceeeecccc-ccccccc-ccccccCCCEEECCCCccCc--cChhhccCcchhcccCCCCEEECCCCcCccCcCCHhHh
Confidence            999999995 6788875 58999999999999975322  11111112234556788999999999875  3444443

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.18  E-value=2.6e-10  Score=113.43  Aligned_cols=196  Identities=18%  Similarity=0.204  Sum_probs=113.7

Q ss_pred             cccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-----CChHHHHHH
Q 004895          157 KDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-----PDAQKIQGE  231 (724)
Q Consensus       157 ~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~l~~~  231 (724)
                      ...+.|+||++++++|.+.    ..+++.|+|++|+|||+|++++.++...     ...|+.+...     .....+...
T Consensus         9 ~~~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~~~-----~~~~i~~~~~~~~~~~~~~~~~~~   79 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINELNL-----PYIYLDLRKFEERNYISYKDFLLE   79 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHHTC-----CEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             CChhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHCCC-----CeEEEEeccccccccccHHHHHHH
Confidence            3468899999999998764    4568999999999999999999887643     2456655422     223444433


Q ss_pred             HHHhhC--------------CCC-----------CCCchhHHHHHHHHHHH--hcCCcEEEEEcccccccccc------c
Q 004895          232 LASDLG--------------MNF-----------DSNDLIYHRAKQLCQRL--KKEKRVLIILDNIWTKLELD------K  278 (724)
Q Consensus       232 i~~~l~--------------~~~-----------~~~~~~~~~~~~l~~~l--~~~kr~LlVlDdv~~~~~~~------~  278 (724)
                      +.....              ...           ............+.+.+  ..++++++|+|++.......      .
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          80 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHH
Confidence            333210              000           00000001112222222  23678999999985432211      1


Q ss_pred             cccccCCCCcCCCCCCCCCcEEEEEecccchhh-h----------hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCc
Q 004895          279 IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLC-I----------DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDF  347 (724)
Q Consensus       279 l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~-~----------~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l  347 (724)
                      +.... .        .......+++.+...... .          .......+.|.+++.+++.+++.+.+....-..+ 
T Consensus       160 l~~~~-~--------~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~~~-  229 (283)
T d2fnaa2         160 LAYAY-D--------NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFK-  229 (283)
T ss_dssp             HHHHH-H--------HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCC-
T ss_pred             HHHHH-H--------hhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCCHH-
Confidence            11110 0        223344555544432210 0          0112356889999999999999887642222211 


Q ss_pred             hhHHHHHHHHhCCchhHHHHHHHHhc
Q 004895          348 RPLAEEIVGKCGGLPVALSTVANALK  373 (724)
Q Consensus       348 ~~~~~~I~~~c~GlPLai~~~~~~l~  373 (724)
                        ..++|++.++|+|..+..++..+.
T Consensus       230 --~~~~i~~~~~G~P~~L~~~~~~~~  253 (283)
T d2fnaa2         230 --DYEVVYEKIGGIPGWLTYFGFIYL  253 (283)
T ss_dssp             --CHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             --HHHHHHHHhCCCHHHHHHHHHHHH
Confidence              257999999999999999887664

>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=99.18  E-value=2.5e-11  Score=113.66  Aligned_cols=122  Identities=19%  Similarity=0.258  Sum_probs=102.4

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEeccccccc-ccchhhhcCCCCceEEEcCCCcCCCC-CccccCCCCCcEEEcCC
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTL-QISDHFFEGTEELKVLDFTGIRFSPL-PSSLGRLINLQTLCLDG  607 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~-~~~~~~~~~l~~L~~L~l~~~~~~~l-p~~i~~l~~L~~L~L~~  607 (724)
                      +.+..+++++..+|..+ .++++.|.+  +.+... .++...|.++++|+.|++++|.+..+ +..+..+.+|++|+|++
T Consensus        11 ~~v~Cs~~~L~~iP~~l-p~~l~~L~L--s~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~   87 (192)
T d1w8aa_          11 TTVDCTGRGLKEIPRDI-PLHTTELLL--NDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGE   87 (192)
T ss_dssp             TEEECTTSCCSSCCSCC-CTTCSEEEC--CSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS
T ss_pred             CEEEEeCCCcCccCCCC-CCCCCEEEe--CCCCCcccccccccCCCceEeeeeccccccccccccccccccccceeeecc
Confidence            35777888888888755 368999999  334443 46667789999999999999999965 56788899999999999


Q ss_pred             cccCC--cccccCCCCCcEEEccCCcCcccchh-hhcCCCCCeEccCCCC
Q 004895          608 WRLED--IAIVGQLKKLEILSLRGAEIKQLPLQ-IGQLTRLQLLDLSNCS  654 (724)
Q Consensus       608 ~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~~-i~~l~~L~~L~l~~~~  654 (724)
                      |.++.  +..|.++++|++|+|++|.|+.+|++ +..+++|++|+|+++.
T Consensus        88 N~l~~l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~  137 (192)
T d1w8aa_          88 NKIKEISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCCCEECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             ccccccCHHHHhCCCcccccccCCccccccCHHHhcCCcccccccccccc
Confidence            99998  35689999999999999999999776 7899999999999854

>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=99.12  E-value=2.5e-12  Score=120.96  Aligned_cols=135  Identities=22%  Similarity=0.269  Sum_probs=93.5

Q ss_pred             hhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCccc-ccCCCCCcEEEccCCcCcccchhhhcCCCCCe
Q 004895          569 HFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAI-VGQLKKLEILSLRGAEIKQLPLQIGQLTRLQL  647 (724)
Q Consensus       569 ~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~-~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~  647 (724)
                      ..+..+++|+.|++++|.++.++ .+..+++|++|+|++|.++.++. ...+++|++|++++|.++.++ .+..+++|++
T Consensus        42 ~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N~i~~l~-~~~~l~~L~~  119 (198)
T d1m9la_          42 ATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLS-GIEKLVNLRV  119 (198)
T ss_dssp             HHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEEECCCHH-HHHHHHHSSE
T ss_pred             hHHhcccccceeECcccCCCCcc-cccCCccccChhhcccccccccccccccccccccccccccccccc-cccccccccc
Confidence            34677888888888888888875 58888888899988888877433 445567888888888888774 4788888888


Q ss_pred             EccCCCCCCcccCh-HHhhCCCCCcEEEccCCCCccccccCCccc--hHHhhcCCCCCcEEE
Q 004895          648 LDLSNCSSLVVIAP-NVISKLSRLEELYMGDSFSQWDKVEGGSNA--SLAELKGLSKLTTLE  706 (724)
Q Consensus       648 L~l~~~~~l~~~~~-~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~--~l~~L~~L~~L~~L~  706 (724)
                      |++++ +.+..++. ..+..|++|+.|++++|.............  ...-+..+++|+.||
T Consensus       120 L~L~~-N~i~~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~~~~r~~vi~~lp~L~~LD  180 (198)
T d1m9la_         120 LYMSN-NKITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLD  180 (198)
T ss_dssp             EEESE-EECCCHHHHHHHTTTTTCSEEEECSSHHHHHHCTTTTHHHHHHHHHHHCSSCCEES
T ss_pred             ccccc-chhccccccccccCCCccceeecCCCccccCcccccchhhHHHHHHHHCCCcCEeC
Confidence            88888 45555542 357888889999888864321101000000  011255677888876

>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=99.11  E-value=2.4e-12  Score=121.02  Aligned_cols=129  Identities=22%  Similarity=0.257  Sum_probs=104.4

Q ss_pred             ceEEEcCCC--cCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCC
Q 004895          577 LKVLDFTGI--RFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCS  654 (724)
Q Consensus       577 L~~L~l~~~--~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~  654 (724)
                      +..+++.+.  .+..+|.+++.+.+|++|+|++|.++.++.+..+++|++|++++|.++.+|.....+++|++|++++| 
T Consensus        25 ~~~~~l~~~~~~i~~l~~sl~~L~~L~~L~Ls~n~I~~i~~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N-  103 (198)
T d1m9la_          25 AEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYN-  103 (198)
T ss_dssp             CSCEECCBCCTTCCCCHHHHHHTTTCCEEECSEEEESCCCCHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEE-
T ss_pred             cceeeeecccCchhhhhhHHhcccccceeECcccCCCCcccccCCccccChhhcccccccccccccccccccccccccc-
Confidence            344455443  35678889999999999999999999988899999999999999999999877777789999999994 


Q ss_pred             CCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeeccccccc
Q 004895          655 SLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVRDAEML  715 (724)
Q Consensus       655 ~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n~~~~l  715 (724)
                      .++.++  .+..+++|++|++++|.+     +.  ...+..+..+++|+.|++++|.+...
T Consensus       104 ~i~~l~--~~~~l~~L~~L~L~~N~i-----~~--~~~~~~l~~l~~L~~L~L~~N~l~~~  155 (198)
T d1m9la_         104 QIASLS--GIEKLVNLRVLYMSNNKI-----TN--WGEIDKLAALDKLEDLLLAGNPLYND  155 (198)
T ss_dssp             ECCCHH--HHHHHHHSSEEEESEEEC-----CC--HHHHHHHTTTTTCSEEEECSSHHHHH
T ss_pred             cccccc--cccccccccccccccchh-----cc--ccccccccCCCccceeecCCCccccC
Confidence            677664  378999999999998642     21  12356788999999999999976443

>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=99.04  E-value=1.3e-10  Score=115.96  Aligned_cols=176  Identities=20%  Similarity=0.219  Sum_probs=94.8

Q ss_pred             ccCceEEeccCCCccc--CCC-cccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCC-cCC--CCCccccCCCC
Q 004895          526 QKGPIAISLPYRDIQE--LPE-RLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGI-RFS--PLPSSLGRLIN  599 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~--~~~-~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~-~~~--~lp~~i~~l~~  599 (724)
                      +.++++++++++.+..  +.. ...+++|+.|.+.++  .........+.++++|+.|++++| .++  .+..-...+++
T Consensus        45 ~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~--~l~~~~~~~l~~~~~L~~L~Ls~c~~itd~~l~~l~~~~~~  122 (284)
T d2astb2          45 PFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGL--RLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSR  122 (284)
T ss_dssp             CBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTC--BCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTT
T ss_pred             CCCCCEEECCCCccCHHHHHHHHHhCCCccccccccc--CCCcHHHHHHhcCCCCcCccccccccccccccchhhHHHHh
Confidence            3466777776655422  211 125677777777222  222112233556677777777765 343  12222345667


Q ss_pred             CcEEEcCCcc-cCC--c-ccccC-CCCCcEEEccCC--cCc--ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCC
Q 004895          600 LQTLCLDGWR-LED--I-AIVGQ-LKKLEILSLRGA--EIK--QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRL  670 (724)
Q Consensus       600 L~~L~L~~~~-l~~--~-~~~~~-l~~L~~L~l~~~--~i~--~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L  670 (724)
                      |++|++++|. +++  . ..+.. .++|+.|+++++  .++  .++.-..++++|++|++++|..++......++++++|
T Consensus       123 L~~L~ls~c~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~~~l~~~~~L  202 (284)
T d2astb2         123 LDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYL  202 (284)
T ss_dssp             CCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTC
T ss_pred             ccccccccccccccccchhhhcccccccchhhhcccccccccccccccccccccccccccccccCCCchhhhhhcccCcC
Confidence            7777777763 433  1 22332 356777777764  233  2333345567777777777665554444446667777


Q ss_pred             cEEEccCCCCccccccCCccchHHhhcCCCCCcEEEeecc
Q 004895          671 EELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEIDVR  710 (724)
Q Consensus       671 ~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~~n  710 (724)
                      ++|++++|..    ++   ...+..+.++++|+.|+++++
T Consensus       203 ~~L~L~~C~~----i~---~~~l~~L~~~~~L~~L~l~~~  235 (284)
T d2astb2         203 QHLSLSRCYD----II---PETLLELGEIPTLKTLQVFGI  235 (284)
T ss_dssp             CEEECTTCTT----CC---GGGGGGGGGCTTCCEEECTTS
T ss_pred             CEEECCCCCC----CC---hHHHHHHhcCCCCCEEeeeCC
Confidence            7777766531    11   233445566667777776654

>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=98.99  E-value=6.2e-10  Score=108.15  Aligned_cols=152  Identities=17%  Similarity=0.165  Sum_probs=84.9

Q ss_pred             ccCceEEeccCCCcccCCCc--ccCCCccEEEEecccccccccchhhhcCCCCceEEEcCC-CcCCC-CCccccCCCCCc
Q 004895          526 QKGPIAISLPYRDIQELPER--LECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTG-IRFSP-LPSSLGRLINLQ  601 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~--~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~-~~~~~-lp~~i~~l~~L~  601 (724)
                      +.+++.|++++|.+..++..  .++++|+.|.+.. +.....++...|.+++.++.+++.. +.+.. .|..+.++++|+
T Consensus        28 ~~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~-n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~  106 (242)
T d1xwdc1          28 PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQ-NDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQ  106 (242)
T ss_dssp             CSCCSEEEEESCCCCEECTTTTTTCTTCCEEEEES-CTTCCEECSSSEESCTTCCEEEEECCTTCCEECTTSEECCTTCC
T ss_pred             CCCCCEEECcCCcCCccChhHhhccchhhhhhhcc-ccccceeecccccccccccccccccccccccccccccccccccc
Confidence            45788888888888877653  3688888888832 2222334455566777777776643 44443 344566777777


Q ss_pred             EEEcCCcccCCccc---ccCCC-------------------------CCcEEEccCCcCcccchhhhcCCCCCeEccCCC
Q 004895          602 TLCLDGWRLEDIAI---VGQLK-------------------------KLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNC  653 (724)
Q Consensus       602 ~L~L~~~~l~~~~~---~~~l~-------------------------~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~  653 (724)
                      +|++++|.+..++.   +..+.                         .+++|++++|.++.++....+..++..+....+
T Consensus       107 ~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~~~~~~l~~L~l~~n~l~~i~~~~~~~~~l~~~~~l~~  186 (242)
T d1xwdc1         107 YLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDN  186 (242)
T ss_dssp             EEEEESCCCCSCCCCTTTCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCCCEECTTTTTTCCEEEEECTTC
T ss_pred             ccccchhhhcccccccccccccccccccccccccccccccccccccccceeeecccccccccccccccchhhhccccccc
Confidence            77777776554222   22222                         344455555555544444444444444433333


Q ss_pred             CCCcccChHHhhCCCCCcEEEccCC
Q 004895          654 SSLVVIAPNVISKLSRLEELYMGDS  678 (724)
Q Consensus       654 ~~l~~~~~~~i~~l~~L~~L~l~~~  678 (724)
                      +.++.+|+..+.++++|++|++++|
T Consensus       187 n~l~~l~~~~f~~l~~L~~L~Ls~N  211 (242)
T d1xwdc1         187 NNLEELPNDVFHGASGPVILDISRT  211 (242)
T ss_dssp             TTCCCCCTTTTTTSCCCSEEECTTS
T ss_pred             cccccccHHHhcCCCCCCEEECCCC
Confidence            4445554444455555555555553

>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=98.98  E-value=1.7e-09  Score=103.64  Aligned_cols=186  Identities=14%  Similarity=0.140  Sum_probs=118.1

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      |.....++|.++.+++|..++.++..+.+.++|++|+||||+|+.+++....+..-..++-++.+...+...+...+...
T Consensus        11 P~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~   90 (224)
T d1sxjb2          11 PQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHF   90 (224)
T ss_dssp             CSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccccccccccccccccCCceehhhHHHHH
Confidence            45567889999999999999988877778899999999999999999887543111124445555554444433222222


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhhh
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLCI  312 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~~  312 (724)
                      ........               ..+.-++|+|++.....  ...+...+..        ....++++++|.... +...
T Consensus        91 ~~~~~~~~---------------~~~~kviiiDe~d~~~~~~~~~ll~~~e~--------~~~~~~~i~~~~~~~~i~~~  147 (224)
T d1sxjb2          91 AQKKLHLP---------------PGKHKIVILDEADSMTAGAQQALRRTMEL--------YSNSTRFAFACNQSNKIIEP  147 (224)
T ss_dssp             HHBCCCCC---------------TTCCEEEEEESGGGSCHHHHHTTHHHHHH--------TTTTEEEEEEESCGGGSCHH
T ss_pred             HHhhccCC---------------CcceEEEEEecccccchhHHHHHhhhccc--------cccceeeeeccCchhhhhhH
Confidence            11111100               13557899999976532  2222222222        344566666666543 3222


Q ss_pred             hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          313 DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       313 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      -......+++.+++.++....+.+.+....-.-+ .+....|++.|+|.+.-+
T Consensus       148 l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i~-~~~l~~I~~~s~Gd~R~a  199 (224)
T d1sxjb2         148 LQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYT-NDGLEAIIFTAEGDMRQA  199 (224)
T ss_dssp             HHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCBC-HHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhhhcccchhhhHHHHHHHHHhcccCCC-HHHHHHHHHHcCCcHHHH
Confidence            2345678999999999999999887753222111 467889999999987643

>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=98.98  E-value=1.3e-09  Score=105.77  Aligned_cols=187  Identities=19%  Similarity=0.175  Sum_probs=127.5

Q ss_pred             eEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCC-C-CccccCCCCCcEEEcCC
Q 004895          530 IAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSP-L-PSSLGRLINLQTLCLDG  607 (724)
Q Consensus       530 ~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~-l-p~~i~~l~~L~~L~L~~  607 (724)
                      +.+..++.+++.+|..+ .+++++|++  +.+....++...|.++++|++|++++|.+.. + +..+..+.++++|.+..
T Consensus        11 ~~i~c~~~~l~~iP~~l-~~~l~~L~L--s~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~   87 (242)
T d1xwdc1          11 RVFLCQESKVTEIPSDL-PRNAIELRF--VLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEK   87 (242)
T ss_dssp             SEEEEESCSCSSCCSCS-CSCCSEEEE--ESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEEC
T ss_pred             CEEEEeCCCCCCcCCCC-CCCCCEEEC--cCCcCCccChhHhhccchhhhhhhccccccceeeccccccccccccccccc
Confidence            34556667778887644 258999999  4455677888889999999999999999874 3 44678899999998765


Q ss_pred             -cccCC--cccccCCCCCcEEEccCCcCcccch--hhhcCCCCCeEccCCCCCCcccChHHhhCCC-CCcEEEccCCCCc
Q 004895          608 -WRLED--IAIVGQLKKLEILSLRGAEIKQLPL--QIGQLTRLQLLDLSNCSSLVVIAPNVISKLS-RLEELYMGDSFSQ  681 (724)
Q Consensus       608 -~~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~--~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~-~L~~L~l~~~~~~  681 (724)
                       +.+..  +..+..+++|++|++++|.+...|.  .+..+..|..+...+ ..+..+++..+..++ .++.|++.+|...
T Consensus        88 ~n~l~~~~~~~~~~l~~L~~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n-~~l~~i~~~~~~~~~~~l~~L~l~~n~l~  166 (242)
T d1xwdc1          88 ANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDN-INIHTIERNSFVGLSFESVILWLNKNGIQ  166 (242)
T ss_dssp             CTTCCEECTTSEECCTTCCEEEEESCCCCSCCCCTTTCBSSCEEEEEESC-TTCCEECTTSSTTSBSSCEEEECCSSCCC
T ss_pred             cccccccccccccccccccccccchhhhcccccccccccccccccccccc-cccccccccccccccccceeeeccccccc
Confidence             45655  4668999999999999998886654  233344444444443 455566555555554 6777777665422


Q ss_pred             ccc---ccC--------Ccc---chH--HhhcCCCCCcEEEeecccccccccccc
Q 004895          682 WDK---VEG--------GSN---ASL--AELKGLSKLTTLEIDVRDAEMLRRIWS  720 (724)
Q Consensus       682 ~~~---~~~--------~~~---~~l--~~L~~L~~L~~L~l~~n~~~~lp~~~~  720 (724)
                      ...   +..        ...   ..+  ..+.++++|+.|++++|+++.+|...+
T Consensus       167 ~i~~~~~~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~  221 (242)
T d1xwdc1         167 EIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGL  221 (242)
T ss_dssp             EECTTTTTTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSCCCCCCSSSC
T ss_pred             ccccccccchhhhccccccccccccccHHHhcCCCCCCEEECCCCcCCccCHHHH
Confidence            100   000        000   011  225778999999999999999987654

>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=98.95  E-value=3.6e-10  Score=112.66  Aligned_cols=153  Identities=18%  Similarity=0.181  Sum_probs=110.9

Q ss_pred             ccCceEEeccCCCccc--CCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCc-CC--CCCccccC-CCC
Q 004895          526 QKGPIAISLPYRDIQE--LPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIR-FS--PLPSSLGR-LIN  599 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~--~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~-~~--~lp~~i~~-l~~  599 (724)
                      ..++++|++.++.+..  +.....+++|+.|.+.++..-........+.++++|+.|++++|. ++  .++..+.. .++
T Consensus        70 c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c~~itd~~l~~l~~~~~~L~~L~ls~c~~~~~~~~~~~~~~~~~~  149 (284)
T d2astb2          70 CSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSET  149 (284)
T ss_dssp             BCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTT
T ss_pred             CCCcccccccccCCCcHHHHHHhcCCCCcCccccccccccccccchhhHHHHhccccccccccccccccchhhhcccccc
Confidence            5789999999887643  222236899999999432222212223345678999999999974 43  23333433 468


Q ss_pred             CcEEEcCCcc--cCC--cc-cccCCCCCcEEEccCC-cCc-ccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcE
Q 004895          600 LQTLCLDGWR--LED--IA-IVGQLKKLEILSLRGA-EIK-QLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEE  672 (724)
Q Consensus       600 L~~L~L~~~~--l~~--~~-~~~~l~~L~~L~l~~~-~i~-~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~  672 (724)
                      |+.|+++++.  ++.  +. ...++++|++|++++| .++ ..+..+.++++|++|++++|+.++......++++++|++
T Consensus       150 L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~  229 (284)
T d2astb2         150 ITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKT  229 (284)
T ss_dssp             CCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCE
T ss_pred             cchhhhcccccccccccccccccccccccccccccccCCCchhhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCE
Confidence            9999999863  444  33 3467899999999997 576 566778999999999999998776554455889999999


Q ss_pred             EEccCC
Q 004895          673 LYMGDS  678 (724)
Q Consensus       673 L~l~~~  678 (724)
                      |++.+|
T Consensus       230 L~l~~~  235 (284)
T d2astb2         230 LQVFGI  235 (284)
T ss_dssp             EECTTS
T ss_pred             EeeeCC
Confidence            999886

>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=98.90  E-value=6.4e-09  Score=99.68  Aligned_cols=182  Identities=12%  Similarity=0.135  Sum_probs=113.2

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      |.....++|.++.++.|..++..+..+.+.++|++|+||||+|+.+++..........+.-.+.+...+.......+...
T Consensus        10 P~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~   89 (227)
T d1sxjc2          10 PETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDF   89 (227)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhc
Confidence            45567899999999999999987777778899999999999999999986543221223333333333332221111111


Q ss_pred             hCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc--ccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhhh
Q 004895          236 LGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE--LDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLCI  312 (724)
Q Consensus       236 l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~--~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~~  312 (724)
                      ...                ..+..++..++|+|++.....  -..+...+..        ....++++++|.... +...
T Consensus        90 ~~~----------------~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~--------~~~~~~~~~~~~~~~~i~~~  145 (227)
T d1sxjc2          90 AST----------------RQIFSKGFKLIILDEADAMTNAAQNALRRVIER--------YTKNTRFCVLANYAHKLTPA  145 (227)
T ss_dssp             HHB----------------CCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSCHH
T ss_pred             ccc----------------ccccCCCeEEEEEeccccchhhHHHHHHHHhhh--------cccceeeccccCcHHHhHHH
Confidence            000                001123456899999976532  1222222222        345677777776543 2222


Q ss_pred             hcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCch
Q 004895          313 DMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLP  362 (724)
Q Consensus       313 ~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlP  362 (724)
                      -......+.+.+++.++...++.+.+....-.-+ .+....|++.++|..
T Consensus       146 i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i~-~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         146 LLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLS-PNAEKALIELSNGDM  194 (227)
T ss_dssp             HHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCBC-HHHHHHHHHHHTTCH
T ss_pred             HHHHHhhhccccccccccccccccccccccccCC-HHHHHHHHHHcCCcH
Confidence            2345678999999999999999988754322211 466789999999975

>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=98.81  E-value=1.1e-08  Score=98.60  Aligned_cols=193  Identities=12%  Similarity=0.100  Sum_probs=115.5

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc-CCCeEEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN-VFDKVVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|+++.++.+..++.....+.+.++|++|+||||+|+.+++...... .......++.+.......+...+-.
T Consensus         8 P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (237)
T d1sxjd2           8 PKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKN   87 (237)
T ss_dssp             CSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHH
Confidence            444567889999999999999877777788999999999999999998853211 1233445555555554433322222


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLC  311 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~  311 (724)
                      .......... .     .........+.-++|+|++....  .+..+...+..        ....+++++|+.... +..
T Consensus        88 ~~~~~~~~~~-~-----~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~--------~~~~~~~i~~~~~~~~~~~  153 (237)
T d1sxjd2          88 FARLTVSKPS-K-----HDLENYPCPPYKIIILDEADSMTADAQSALRRTMET--------YSGVTRFCLICNYVTRIID  153 (237)
T ss_dssp             HHHSCCCCCC-T-----THHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSCH
T ss_pred             Hhhhhhhhhh-H-----HHHhhccccCceEEEEecccccCHHHHHHHhhcccc--------ccccccccccccccccccc
Confidence            1111111111 0     01111122344579999997652  22222111111        334556666665533 221


Q ss_pred             hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          312 IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       312 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      .-......+++.+++.++...++.+.+....-.- -.+..+.|++.++|.+.
T Consensus       154 ~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~i-~~~~l~~ia~~s~gd~R  204 (237)
T d1sxjd2         154 PLASQCSKFRFKALDASNAIDRLRFISEQENVKC-DDGVLERILDISAGDLR  204 (237)
T ss_dssp             HHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCC-CHHHHHHHHHHTSSCHH
T ss_pred             cccchhhhhccccccccccchhhhhhhhhhcCcC-CHHHHHHHHHHcCCCHH
Confidence            1123346899999999999999998875432221 25678899999988653

>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=98.79  E-value=1e-08  Score=91.58  Aligned_cols=101  Identities=19%  Similarity=0.141  Sum_probs=67.3

Q ss_pred             ceEEEcCCCcCCCCCccccCCCCCcEEEcCCc-ccCC--cccccCCCCCcEEEccCCcCcccch-hhhcCCCCCeEccCC
Q 004895          577 LKVLDFTGIRFSPLPSSLGRLINLQTLCLDGW-RLED--IAIVGQLKKLEILSLRGAEIKQLPL-QIGQLTRLQLLDLSN  652 (724)
Q Consensus       577 L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~-~l~~--~~~~~~l~~L~~L~l~~~~i~~lp~-~i~~l~~L~~L~l~~  652 (724)
                      ...++.+++.+.+.|..+..+.+|++|++.++ .++.  +..|.++++|+.|++++|+|+.+++ .+..+++|++|+|++
T Consensus        10 ~~~l~c~~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~   89 (156)
T d2ifga3          10 SSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSF   89 (156)
T ss_dssp             SSCEECCSSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCS
T ss_pred             CCeEEecCCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCcccccccccccccceeccC
Confidence            34466666666666777777777777777655 3665  2457777777777777777777743 367777777777777


Q ss_pred             CCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          653 CSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       653 ~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                       +.++.+|+..+.. .+|+.|++++|.
T Consensus        90 -N~l~~l~~~~~~~-~~l~~L~L~~Np  114 (156)
T d2ifga3          90 -NALESLSWKTVQG-LSLQELVLSGNP  114 (156)
T ss_dssp             -SCCSCCCSTTTCS-CCCCEEECCSSC
T ss_pred             -CCCcccChhhhcc-ccccccccCCCc
Confidence             4566676654433 357777777754

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.77  E-value=1.2e-08  Score=97.98  Aligned_cols=183  Identities=12%  Similarity=0.096  Sum_probs=109.7

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCe-EEEEEEecCCChHHHHHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDK-VVMAEITKNPDAQKIQGELAS  234 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~l~~~i~~  234 (724)
                      |.....++|.++.+++|..|+..+..+.+.++|++|+||||+|+.+++..... .++. .+-++.+...+...+...+..
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~-~~~~~~~e~n~s~~~~~~~~~~~~~~   98 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKE   98 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGG-GHHHHEEEEETTCHHHHHTTHHHHHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhc-ccCCCeeEEecCcccchhHHHHHHHH
Confidence            44567789999999999999988888889999999999999999999976431 1221 233333321111111111111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEeccc-chhh
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSR-DLLC  311 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~-~v~~  311 (724)
                      ...                .......++.++++||+....  .+..+...+..        ......+|.||... .+..
T Consensus        99 ~~~----------------~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~--------~~~~~~~i~~~n~~~~i~~  154 (231)
T d1iqpa2          99 FAR----------------TKPIGGASFKIIFLDEADALTQDAQQALRRTMEM--------FSSNVRFILSCNYSSKIIE  154 (231)
T ss_dssp             HHH----------------SCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHH--------TTTTEEEEEEESCGGGSCH
T ss_pred             HHh----------------hhhccCCCceEEeehhhhhcchhHHHHHhhhccc--------CCcceEEEeccCChhhchH
Confidence            000                000112467899999997542  22222222211        22334555555443 3322


Q ss_pred             hhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          312 IDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       312 ~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      .-......+.+.+.+.++....+.+.+....-. --.+..+.|++.|+|...-
T Consensus       155 ~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~-i~~~~l~~I~~~~~gdiR~  206 (231)
T d1iqpa2         155 PIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE-LTEEGLQAILYIAEGDMRR  206 (231)
T ss_dssp             HHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE-ECHHHHHHHHHHHTTCHHH
T ss_pred             hHhCccccccccccchhhHHHHHHHHHHHhCCC-CCHHHHHHHHHHcCCCHHH
Confidence            223344689999999999999998887533221 1146778999999997643

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.77  E-value=1.6e-07  Score=90.32  Aligned_cols=186  Identities=13%  Similarity=0.200  Sum_probs=113.5

Q ss_pred             CcccccccchHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-------------------eEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-------------------KVV  215 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-------------------~~~  215 (724)
                      |.....++|.++.++.|..++..++. ..+.|+|+.|+||||+|+.+++........+                   .++
T Consensus         8 P~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   87 (239)
T d1njfa_           8 PQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI   87 (239)
T ss_dssp             CSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTTEE
T ss_pred             CCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCeEE
Confidence            34467889999999999999876554 5688999999999999999988764321111                   122


Q ss_pred             EEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCC
Q 004895          216 MAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKND  293 (724)
Q Consensus       216 wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~  293 (724)
                      .++.+....... .+.+.+.+....                 ..++..++|||+++...  ..+.+...+..        
T Consensus        88 ~~~~~~~~~i~~-ir~~~~~~~~~~-----------------~~~~~kviiIde~d~l~~~~q~~Llk~lE~--------  141 (239)
T d1njfa_          88 EIDAASRTKVED-TRDLLDNVQYAP-----------------ARGRFKVYLIDEVHMLSRHSFNALLKTLEE--------  141 (239)
T ss_dssp             EEETTCSSSHHH-HHHHHHSCCCSC-----------------SSSSSEEEEEETGGGSCHHHHHHHHHHHHS--------
T ss_pred             EecchhcCCHHH-HHHHHHHHHhcc-----------------ccCCCEEEEEECcccCCHHHHHHHHHHHhc--------
Confidence            232222222221 122222221110                 02456799999997753  12223222222        


Q ss_pred             CCCCcEEEEEecccch-hhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh-HHHHH
Q 004895          294 DPRRCTIILTSRSRDL-LCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV-ALSTV  368 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~v-~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL-ai~~~  368 (724)
                      ....+++|++|.+..- ...-......+.+.+++.++..+.+...+......- -++....|++.++|.+- |+..+
T Consensus       142 ~~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~-~~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         142 PPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH-EPRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             CCTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB-CHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             CCCCeEEEEEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhccCC-CHHHHHHHHHHcCCCHHHHHHHH
Confidence            3455677777765442 222234457899999999999998888775322221 24678899999999885 45443

>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=98.73  E-value=6.6e-07  Score=87.70  Aligned_cols=190  Identities=13%  Similarity=0.183  Sum_probs=115.3

Q ss_pred             ccccchHHHHHHHHHHhc------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALK------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELA  233 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~  233 (724)
                      ..++||+.+++++.++|.      ....+.+.|+|++|+||||+|+.+++.......+ ..+|+..............+.
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTA-RFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCC-EEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCC-cEEEecchhhhhhhhhhhhhH
Confidence            357899999999998885      2345789999999999999999999998653322 356777777778888888888


Q ss_pred             HhhCCCCCCCc-hhHHHHHHHHHHHh-cCCcEEEEEcccccccc-----ccccccccCCCCcCCCCCCCCCcEEEEEecc
Q 004895          234 SDLGMNFDSND-LIYHRAKQLCQRLK-KEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKNDDPRRCTIILTSRS  306 (724)
Q Consensus       234 ~~l~~~~~~~~-~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~  306 (724)
                      ...+....... ........+.+.+. ......+++|+++....     ...+......       .......+|.++..
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~-------~~~~~~~~i~~~~~  167 (276)
T d1fnna2          95 RSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADK-------LGAFRIALVIVGHN  167 (276)
T ss_dssp             HHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHH-------HSSCCEEEEEEESS
T ss_pred             HhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhhhHHHHHhcccc-------ccccceEEeecCCc
Confidence            88776543322 12333344444443 24567788888766421     1111111110       02223345555554


Q ss_pred             cchhh------hhcCCCceEecCCCCHHHHHHHHHHHhCCC-CCCCCchhHHHHHHHH
Q 004895          307 RDLLC------IDMNSQKMFWIDALSEEEALQLFEKIVGES-TKASDFRPLAEEIVGK  357 (724)
Q Consensus       307 ~~v~~------~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~l~~~~~~I~~~  357 (724)
                      .....      ........+.+.+.+.++.++++.+++... .....-++..+.|++.
T Consensus       168 ~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~  225 (276)
T d1fnna2         168 DAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADI  225 (276)
T ss_dssp             THHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHH
T ss_pred             hhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHH
Confidence            33210      011123568899999999999998876421 1111123445556554

>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=98.70  E-value=5.9e-08  Score=99.14  Aligned_cols=175  Identities=19%  Similarity=0.217  Sum_probs=120.1

Q ss_pred             ccCceEEeccCCCcccCCCcccCCCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEc
Q 004895          526 QKGPIAISLPYRDIQELPERLECPQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCL  605 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L  605 (724)
                      ..++++|++++++++.+|..  .++|++|.+  +.+....+|.    .+.+|+.|++++|+++.++.-   ...|++|++
T Consensus        37 ~~~l~~LdLs~~~L~~lp~~--~~~L~~L~L--s~N~l~~lp~----~~~~L~~L~l~~n~l~~l~~l---p~~L~~L~L  105 (353)
T d1jl5a_          37 DRQAHELELNNLGLSSLPEL--PPHLESLVA--SCNSLTELPE----LPQSLKSLLVDNNNLKALSDL---PPLLEYLGV  105 (353)
T ss_dssp             HHTCSEEECTTSCCSCCCSC--CTTCSEEEC--CSSCCSSCCC----CCTTCCEEECCSSCCSCCCSC---CTTCCEEEC
T ss_pred             HcCCCEEEeCCCCCCCCCCC--CCCCCEEEC--CCCCCccccc----chhhhhhhhhhhcccchhhhh---ccccccccc
Confidence            35788999999999988863  578999999  3445556664    256899999999998877642   246999999


Q ss_pred             CCcccCCcccccCCCCCcEEEccCCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCcccc-
Q 004895          606 DGWRLEDIAIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDK-  684 (724)
Q Consensus       606 ~~~~l~~~~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~-  684 (724)
                      ++|.+..++.++.+++|++|+++++.+...|..+   ..+..+.+..+.. ...  ..++.++.++.|++..|...... 
T Consensus       106 ~~n~l~~lp~~~~l~~L~~L~l~~~~~~~~~~~~---~~l~~l~~~~~~~-~~~--~~l~~l~~l~~L~l~~n~~~~~~~  179 (353)
T d1jl5a_         106 SNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLP---PSLEFIAAGNNQL-EEL--PELQNLPFLTAIYADNNSLKKLPD  179 (353)
T ss_dssp             CSSCCSSCCCCTTCTTCCEEECCSSCCSCCCCCC---TTCCEEECCSSCC-SSC--CCCTTCTTCCEEECCSSCCSSCCC
T ss_pred             cccccccccchhhhccceeecccccccccccccc---ccccchhhccccc-ccc--ccccccccceeccccccccccccc
Confidence            9999988777889999999999999888776543   4455666655322 111  22567788888887765421110 


Q ss_pred             c---------cCCccchHHhhcCCCCCcEEEeeccccccccc
Q 004895          685 V---------EGGSNASLAELKGLSKLTTLEIDVRDAEMLRR  717 (724)
Q Consensus       685 ~---------~~~~~~~l~~L~~L~~L~~L~l~~n~~~~lp~  717 (724)
                      .         .......+..+..++.|+.++++.|....+|.
T Consensus       180 ~~~~~~~l~~~~~~~~~~~~~~~l~~L~~l~l~~n~~~~~~~  221 (353)
T d1jl5a_         180 LPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPD  221 (353)
T ss_dssp             CCTTCCEEECCSSCCSSCCCCTTCTTCCEEECCSSCCSSCCS
T ss_pred             cccccccccccccccccccccccccccccccccccccccccc
Confidence            0         00111123345567788888888887665553

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.68  E-value=1.4e-07  Score=90.78  Aligned_cols=156  Identities=21%  Similarity=0.317  Sum_probs=100.7

Q ss_pred             ccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEE-EEecCCChHHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMA-EITKNPDAQKIQGELAS  234 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv-~vs~~~~~~~l~~~i~~  234 (724)
                      +.++||++++++++..|....-.-+.+||++|+|||+++..+++......-    .+..+|. +++.          ++.
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~----------lia   87 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS----------LLA   87 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------C
T ss_pred             CcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech----------Hhc
Confidence            457899999999999998666667779999999999999999998654321    2334443 3221          111


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc----------cccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL----------ELDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~----------~~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                        |.+.. .. -++....+...+...++.++++|++....          +...+..|.-         ....-++|.||
T Consensus        88 --g~~~~-g~-~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L---------~rg~i~vIgat  154 (268)
T d1r6bx2          88 --GTKYR-GD-FEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLL---------SSGKIRVIGST  154 (268)
T ss_dssp             --CCCCS-SC-HHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCS---------SSCCCEEEEEE
T ss_pred             --cCccc-hh-HHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHH---------hCCCCeEEEeC
Confidence              11111 11 34455566666666677999999986542          1122222221         34567888888


Q ss_pred             cccchhhh------hcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          305 RSRDLLCI------DMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       305 R~~~v~~~------~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      ........      .....+.+.+++.+.+++.+++....
T Consensus       155 T~eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         155 TYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            87654311      12335689999999999999997754

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.67  E-value=6.3e-08  Score=94.11  Aligned_cols=194  Identities=10%  Similarity=0.104  Sum_probs=103.4

Q ss_pred             CcccccccchHHHHHHHHHHhcCC-CccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEEEEEecC--------
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKDD-KLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVMAEITKN--------  222 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~~-~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~--------  222 (724)
                      |.....++|+++..+.|..++... ..+-+.|+|++|+||||+|+.+++......    .++...|...+..        
T Consensus         7 P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (252)
T d1sxje2           7 PKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVS   86 (252)
T ss_dssp             CCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------------------CCEE
T ss_pred             CCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhhhhhcc
Confidence            445677899999998888887643 345577999999999999999999753211    1111212111110        


Q ss_pred             -------------CChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCC
Q 004895          223 -------------PDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVD  287 (724)
Q Consensus       223 -------------~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~  287 (724)
                                   ......................      ..-... ...+.-++|+|++....  .+..+...+..  
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~-~~~~~~iiiide~d~l~~~~~~~l~~~~e~--  157 (252)
T d1sxje2          87 SPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDF------QDSKDG-LAHRYKCVIINEANSLTKDAQAALRRTMEK--  157 (252)
T ss_dssp             CSSEEEECCC----CCHHHHHHHHHHHTTTTC-------------------CCEEEEEECTTSSCHHHHHHHHHHHHH--
T ss_pred             CCccceeeecccccCCcceeeehhhhhhhhhhhhh------hhcccc-cCCCceEEEeccccccccccchhhhccccc--
Confidence                         0011111111111111000000      000000 11345689999987642  22222222222  


Q ss_pred             cCCCCCCCCCcEEEEEecccc-hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          288 EKDKNDDPRRCTIILTSRSRD-LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       288 ~~~~~~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                            ....+++|+||.+.. +...-......+++.+++.++..+++.+.+.........++..+.|++.+.|.+..
T Consensus       158 ------~~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~~~~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         158 ------YSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRV  229 (252)
T ss_dssp             ------STTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEECCSHHHHHHHHHHTTCHHH
T ss_pred             ------ccccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCCCCCcHHHHHHHHHHcCCcHHH
Confidence                  344567777776554 21111223468899999999999999877643222222246778999999998754

>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=98.61  E-value=6.4e-08  Score=86.25  Aligned_cols=83  Identities=24%  Similarity=0.178  Sum_probs=57.4

Q ss_pred             hcCCCCceEEEcCCC-cCCCCC-ccccCCCCCcEEEcCCcccCCc--ccccCCCCCcEEEccCCcCcccchhhhcCCCCC
Q 004895          571 FEGTEELKVLDFTGI-RFSPLP-SSLGRLINLQTLCLDGWRLEDI--AIVGQLKKLEILSLRGAEIKQLPLQIGQLTRLQ  646 (724)
Q Consensus       571 ~~~l~~L~~L~l~~~-~~~~lp-~~i~~l~~L~~L~L~~~~l~~~--~~~~~l~~L~~L~l~~~~i~~lp~~i~~l~~L~  646 (724)
                      +.++++|+.|+++++ .++.++ ..|..+.+|+.|+|++|.++.+  ..+..+++|++|+|++|.++++|.++....+|+
T Consensus        27 l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~~~l~  106 (156)
T d2ifga3          27 LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQ  106 (156)
T ss_dssp             SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCC
T ss_pred             ccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCcccccccccccccceeccCCCCcccChhhhcccccc
Confidence            455666777777554 366554 3567777777777777777662  457777777777777777777777766556777


Q ss_pred             eEccCCC
Q 004895          647 LLDLSNC  653 (724)
Q Consensus       647 ~L~l~~~  653 (724)
                      +|+|++|
T Consensus       107 ~L~L~~N  113 (156)
T d2ifga3         107 ELVLSGN  113 (156)
T ss_dssp             EEECCSS
T ss_pred             ccccCCC
Confidence            8877774

>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=98.59  E-value=1.3e-07  Score=92.02  Aligned_cols=187  Identities=10%  Similarity=0.021  Sum_probs=107.6

Q ss_pred             CcccccccchHHHHHHHHHHhcC-----------------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          156 MKDYNIFNSRKKIFQDVIEALKD-----------------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~~-----------------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      |.....++|.++.+++|.+++..                 ...+.+.++|++|+||||+|+.+++....     .+++++
T Consensus        10 P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~-----~~~~~~   84 (253)
T d1sxja2          10 PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGY-----DILEQN   84 (253)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTC-----EEEEEC
T ss_pred             CCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHh-----hhhccc
Confidence            34467788999999999888742                 23468999999999999999999987642     255666


Q ss_pred             EecCCChHHHHHHHHHhh-CCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc-----ccccccccCCCCcCCCC
Q 004895          219 ITKNPDAQKIQGELASDL-GMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE-----LDKIGIPYGDVDEKDKN  292 (724)
Q Consensus       219 vs~~~~~~~l~~~i~~~l-~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~-----~~~l~~~~~~~~~~~~~  292 (724)
                      .+...+...+.. ..... ...........    ........++..++++|++.....     +..+....         
T Consensus        85 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~---------  150 (253)
T d1sxja2          85 ASDVRSKTLLNA-GVKNALDNMSVVGYFKH----NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFC---------  150 (253)
T ss_dssp             TTSCCCHHHHHH-TGGGGTTBCCSTTTTTC--------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHH---------
T ss_pred             cccchhhHHHHH-HHHHHhhcchhhhhhhh----hhhcccccccceEEEeeeccccccchhhhhHHHhhhh---------
Confidence            666555444322 22222 11100000000    000011235678999999875422     11111110         


Q ss_pred             CCCCCcEEEEEecccc--hhhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          293 DDPRRCTIILTSRSRD--LLCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       293 ~~~~~s~ilvTtR~~~--v~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                       ......+++|+....  ...........+++.+.+.++....+...+......-+ ++...+|++.++|...
T Consensus       151 -~~~~~~ii~i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~-~~~l~~i~~~s~GDiR  221 (253)
T d1sxja2         151 -RKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD-PNVIDRLIQTTRGDIR  221 (253)
T ss_dssp             -HHCSSCEEEEESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC-TTHHHHHHHHTTTCHH
T ss_pred             -cccccccccccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCCC-HHHHHHHHHhCCCcHH
Confidence             011223444443222  21222344568999999999999998887642211111 2467899999999773

>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=98.56  E-value=1.4e-07  Score=85.51  Aligned_cols=152  Identities=16%  Similarity=0.234  Sum_probs=92.7

Q ss_pred             ccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEE-EEEecCCChHHHHHHHHH
Q 004895          160 NIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVM-AEITKNPDAQKIQGELAS  234 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~w-v~vs~~~~~~~l~~~i~~  234 (724)
                      +..+||++++++++..|....-.-+.++|.+|+|||+++..++++.....    .-+..+| ++++          .++.
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~----------~LiA   91 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG----------ALVA   91 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH----------HHHT
T ss_pred             CCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHH----------HHhc
Confidence            45679999999999999866666778999999999999999999876422    1233444 3322          1221


Q ss_pred             hhCCCCCCCchhHHHHHHHHHHHh-cCCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEEEEe
Q 004895          235 DLGMNFDSNDLIYHRAKQLCQRLK-KEKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTIILTS  304 (724)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~ilvTt  304 (724)
                      ...  .  ...-++....+.+.+. ...+.+|++||+.....         ...+..|.-         ....-++|.||
T Consensus        92 g~~--~--rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L---------~rg~l~~Igat  158 (195)
T d1jbka_          92 GAK--Y--RGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPAL---------ARGELHCVGAT  158 (195)
T ss_dssp             TTC--S--HHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHH---------HTTSCCEEEEE
T ss_pred             cCC--c--cHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHH---------hCCCceEEecC
Confidence            111  0  0012333444555543 34579999999966421         111111111         22445688777


Q ss_pred             cccchh------hhhcCCCceEecCCCCHHHHHHHH
Q 004895          305 RSRDLL------CIDMNSQKMFWIDALSEEEALQLF  334 (724)
Q Consensus       305 R~~~v~------~~~~~~~~~~~l~~L~~~e~~~Lf  334 (724)
                      ......      .......+.+.+++.+.+++..++
T Consensus       159 T~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         159 TLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             CHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             CHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHh
Confidence            765532      112344578999999999887653

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.54  E-value=3.6e-06  Score=82.69  Aligned_cols=199  Identities=19%  Similarity=0.164  Sum_probs=115.4

Q ss_pred             cccccchHHHHHHHHHHhc----CC----C-ccEEEEEcCCCCcHHHHHHHHHHHHhhc----cCCCeEEEEEEecCCCh
Q 004895          159 YNIFNSRKKIFQDVIEALK----DD----K-LNIIGVCGMGGVGKTTLVKQIAKQVMED----NVFDKVVMAEITKNPDA  225 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~----~~----~-~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~  225 (724)
                      +..+.||+.+++.|.+.+.    .+    . ..++.|+|++|+|||++++.+++.....    .......++.+......
T Consensus        15 P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~   94 (287)
T d1w5sa2          15 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNL   94 (287)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccch
Confidence            3567899999999988763    11    1 2245678999999999999999986431    11234667777777788


Q ss_pred             HHHHHHHHHhhCCCCCCCc-hhHHHHHHHHHHHh-cCCcEEEEEccccccccc-----------cccccccCCCCcCCCC
Q 004895          226 QKIQGELASDLGMNFDSND-LIYHRAKQLCQRLK-KEKRVLIILDNIWTKLEL-----------DKIGIPYGDVDEKDKN  292 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~-~~~~~~~~l~~~l~-~~kr~LlVlDdv~~~~~~-----------~~l~~~~~~~~~~~~~  292 (724)
                      ......+...++....... ........+..... .+...++++|.+.....-           ..+...+..      .
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~------~  168 (287)
T d1w5sa2          95 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPS------R  168 (287)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCC------T
T ss_pred             hhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcch------h
Confidence            8888888888776543321 12223333333332 346678888887543211           111000110      0


Q ss_pred             CCCCCcE-EEEEecccchh-------hhhcCCCceEecCCCCHHHHHHHHHHHhCCC-CCCCCchhHHHHHHHHh-----
Q 004895          293 DDPRRCT-IILTSRSRDLL-------CIDMNSQKMFWIDALSEEEALQLFEKIVGES-TKASDFRPLAEEIVGKC-----  358 (724)
Q Consensus       293 ~~~~~s~-ilvTtR~~~v~-------~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~-~~~~~l~~~~~~I~~~c-----  358 (724)
                      ....... |++++......       .........+.+++++.++..+++..++... ....--++..+.|+++.     
T Consensus       169 ~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~  248 (287)
T d1w5sa2         169 DGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKG  248 (287)
T ss_dssp             TSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGT
T ss_pred             hcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHHHHHHhcccc
Confidence            0222333 44444333211       1112334688999999999999999887421 11111245667777765     


Q ss_pred             -CCchh
Q 004895          359 -GGLPV  363 (724)
Q Consensus       359 -~GlPL  363 (724)
                       .|.|-
T Consensus       249 ~~gd~R  254 (287)
T d1w5sa2         249 GDGSAR  254 (287)
T ss_dssp             SCCCHH
T ss_pred             CCCCHH
Confidence             56663

>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=98.51  E-value=4.9e-07  Score=92.07  Aligned_cols=142  Identities=22%  Similarity=0.248  Sum_probs=95.0

Q ss_pred             CCccEEEEecccccccccchhhhcCCCCceEEEcCCCcCCCCCccccCCCCCcEEEcCCcccCCcccccCCCCCcEEEcc
Q 004895          549 PQLKLFLLFAKYDSTLQISDHFFEGTEELKVLDFTGIRFSPLPSSLGRLINLQTLCLDGWRLEDIAIVGQLKKLEILSLR  628 (724)
Q Consensus       549 ~~Lr~L~l~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~lp~~i~~l~~L~~L~L~~~~l~~~~~~~~l~~L~~L~l~  628 (724)
                      .+++.|++  +......+|+    ..++|+.|++++|+++++|..+   .+|+.|++++|.++.++.+  .++|++|+++
T Consensus        38 ~~l~~LdL--s~~~L~~lp~----~~~~L~~L~Ls~N~l~~lp~~~---~~L~~L~l~~n~l~~l~~l--p~~L~~L~L~  106 (353)
T d1jl5a_          38 RQAHELEL--NNLGLSSLPE----LPPHLESLVASCNSLTELPELP---QSLKSLLVDNNNLKALSDL--PPLLEYLGVS  106 (353)
T ss_dssp             HTCSEEEC--TTSCCSCCCS----CCTTCSEEECCSSCCSSCCCCC---TTCCEEECCSSCCSCCCSC--CTTCCEEECC
T ss_pred             cCCCEEEe--CCCCCCCCCC----CCCCCCEEECCCCCCcccccch---hhhhhhhhhhcccchhhhh--cccccccccc
Confidence            35778887  3334445663    2567899999999999888654   4688888888887764432  2468999999


Q ss_pred             CCcCcccchhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCCCccccccCCccchHHhhcCCCCCcEEEee
Q 004895          629 GAEIKQLPLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSFSQWDKVEGGSNASLAELKGLSKLTTLEID  708 (724)
Q Consensus       629 ~~~i~~lp~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l~~L~~L~~L~~L~l~  708 (724)
                      +|.+..+|. ++++++|++|++++| .+...+.    ....+..+.+..+...          ....+..++.++.|.+.
T Consensus       107 ~n~l~~lp~-~~~l~~L~~L~l~~~-~~~~~~~----~~~~l~~l~~~~~~~~----------~~~~l~~l~~l~~L~l~  170 (353)
T d1jl5a_         107 NNQLEKLPE-LQNSSFLKIIDVDNN-SLKKLPD----LPPSLEFIAAGNNQLE----------ELPELQNLPFLTAIYAD  170 (353)
T ss_dssp             SSCCSSCCC-CTTCTTCCEEECCSS-CCSCCCC----CCTTCCEEECCSSCCS----------SCCCCTTCTTCCEEECC
T ss_pred             ccccccccc-hhhhccceeeccccc-ccccccc----ccccccchhhcccccc----------ccccccccccceecccc
Confidence            998888885 678899999999884 3444432    2455666666543211          12234566777788877


Q ss_pred             ccccccccc
Q 004895          709 VRDAEMLRR  717 (724)
Q Consensus       709 ~n~~~~lp~  717 (724)
                      .|....++.
T Consensus       171 ~n~~~~~~~  179 (353)
T d1jl5a_         171 NNSLKKLPD  179 (353)
T ss_dssp             SSCCSSCCC
T ss_pred             ccccccccc
Confidence            776655443

>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=98.49  E-value=5.7e-06  Score=79.03  Aligned_cols=182  Identities=16%  Similarity=0.188  Sum_probs=102.2

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      |.....++|.++.+++|..++.     ....+-+.++|++|+||||+|+.+++.....     .+.++.+......++. 
T Consensus         5 P~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~-----~~~~~~~~~~~~~~~~-   78 (238)
T d1in4a2           5 PKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTN-----IHVTSGPVLVKQGDMA-   78 (238)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHH-
T ss_pred             CCcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhccCCC-----cccccCcccccHHHHH-
Confidence            4456788999999999888875     2335567899999999999999999887432     2334433333322221 


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------ccccc--cccCC-CCcCCCCCCCCCc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDKIG--IPYGD-VDEKDKNDDPRRC  298 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~l~--~~~~~-~~~~~~~~~~~~s  298 (724)
                      .++.                     .  .+++..+++|++.....         .+...  ..... .............
T Consensus        79 ~~~~---------------------~--~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (238)
T d1in4a2          79 AILT---------------------S--LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPF  135 (238)
T ss_dssp             HHHH---------------------H--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCC
T ss_pred             HHHH---------------------h--hccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCe
Confidence            1111                     1  13446667776654321         00000  00000 0000000012234


Q ss_pred             EEEEEecccc-hh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHH
Q 004895          299 TIILTSRSRD-LL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALST  367 (724)
Q Consensus       299 ~ilvTtR~~~-v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~  367 (724)
                      .+|.+|.... .. .........+.+++.+.++...++...+...... .-++....|++.++|.+-.+..
T Consensus       136 ~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~~~~l~~i~~~s~gd~R~ai~  205 (238)
T d1in4a2         136 TLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVE-IEDAAAEMIAKRSRGTPRIAIR  205 (238)
T ss_dssp             EEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCC-BCHHHHHHHHHTSTTCHHHHHH
T ss_pred             EEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccch-hhHHHHHHHHHhCCCCHHHHHH
Confidence            4555555443 22 1222334567899999999999998877533222 2256788999999998776643

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.41  E-value=1.7e-05  Score=75.67  Aligned_cols=183  Identities=18%  Similarity=0.140  Sum_probs=101.1

Q ss_pred             CcccccccchHHHHHHHHHHhc-----CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          156 MKDYNIFNSRKKIFQDVIEALK-----DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       156 ~~~~~~~~gR~~~~~~l~~~L~-----~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      |.....++|.++.+++|..++.     ....+-+.++|++|+||||+|+.+++.....     ..+++.+..........
T Consensus         5 P~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~-----~~~~~~~~~~~~~~~~~   79 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN-----LRVTSGPAIEKPGDLAA   79 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC-----EEEEETTTCCSHHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC-----eEeccCCccccchhhHH
Confidence            3446778999988888877764     2345667799999999999999999877432     34444333322222211


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------ccc----cccccCCCCcCCCCCCCCC
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------LDK----IGIPYGDVDEKDKNDDPRR  297 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~~~----l~~~~~~~~~~~~~~~~~~  297 (724)
                      .+...+                       +.+.++++|++.....         .+.    ....... .........+.
T Consensus        80 ~~~~~~-----------------------~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~-~~~~~~~~~~~  135 (239)
T d1ixsb2          80 ILANSL-----------------------EEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGP-AARTIRLELPR  135 (239)
T ss_dssp             HHHTTC-----------------------CTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTT-CCCEEEEECCC
T ss_pred             HHHhhc-----------------------cCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccch-hhhhcccCCCC
Confidence            111111                       2234556676644310         000    0000000 00000001223


Q ss_pred             cEEEEEe-cccchh-hhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHHHHH
Q 004895          298 CTIILTS-RSRDLL-CIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVALSTV  368 (724)
Q Consensus       298 s~ilvTt-R~~~v~-~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~~  368 (724)
                      ..++.+| +..... .........+.+...+.++...++.+.+...... .-.+....|++.+.|.+-.+..+
T Consensus       136 ~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~-~~~~~l~~ia~~s~gd~R~a~~~  207 (239)
T d1ixsb2         136 FTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR-ITEEAALEIGRRSRGTMRVAKRL  207 (239)
T ss_dssp             CEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCC-BCHHHHHHHHHHTTSSHHHHHHH
T ss_pred             EEEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCc-cchHHHHHHHHHcCCCHHHHHHH
Confidence            3344444 332221 2223445688899999999999988877533322 22568899999999988665433

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.40  E-value=4.3e-06  Score=77.85  Aligned_cols=180  Identities=11%  Similarity=0.132  Sum_probs=103.0

Q ss_pred             hHHHHHHHHHHhcCCCc-cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCC----
Q 004895          165 RKKIFQDVIEALKDDKL-NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMN----  239 (724)
Q Consensus       165 R~~~~~~l~~~L~~~~~-~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~----  239 (724)
                      .++..+++.+.+..++. ..+.++|+.|+||||+|+.+++..-......       ........-...+.......    
T Consensus         7 ~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~-------~~~~~~~~~~~~i~~~~~~~~~~~   79 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQG-------HKSCGHCRGCQLMQAGTHPDYYTL   79 (207)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBT-------TBCCSCSHHHHHHHHTCCTTEEEE
T ss_pred             cHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccc-------cccccccchhhhhhhccccccchh
Confidence            45567788888776664 4689999999999999999998763210000       00000000011111111000    


Q ss_pred             ---CCCCchhHHHHHHHHHHHh----cCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-h
Q 004895          240 ---FDSNDLIYHRAKQLCQRLK----KEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-L  309 (724)
Q Consensus       240 ---~~~~~~~~~~~~~l~~~l~----~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v  309 (724)
                         ........+.+..+.+.+.    .+++-++|+||++...  ....+...+..        ....+++|+||++.. +
T Consensus        80 ~~~~~~~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEe--------p~~~~~fIl~t~~~~~l  151 (207)
T d1a5ta2          80 APEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEE--------PPAETWFFLATREPERL  151 (207)
T ss_dssp             CCCTTCSSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTS--------CCTTEEEEEEESCGGGS
T ss_pred             hhhhcccccccchhhHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHh--------hcccceeeeeecChhhh
Confidence               0000111122233333322    2466799999997753  23333333332        445678887777754 3


Q ss_pred             hhhhcCCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhHH
Q 004895          310 LCIDMNSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVAL  365 (724)
Q Consensus       310 ~~~~~~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  365 (724)
                      ...-.+....+.+.+++.++....+.+...-      -++.+..|++.++|.|-.+
T Consensus       152 l~tI~SRc~~i~~~~~~~~~~~~~L~~~~~~------~~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         152 LATLRSRCRLHYLAPPPEQYAVTWLSREVTM------SQDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             CHHHHTTSEEEECCCCCHHHHHHHHHHHCCC------CHHHHHHHHHHTTTCHHHH
T ss_pred             hhhhcceeEEEecCCCCHHHHHHHHHHcCCC------CHHHHHHHHHHcCCCHHHH
Confidence            3222344578999999999999988765421      1466888999999998654

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.38  E-value=6.9e-06  Score=78.46  Aligned_cols=177  Identities=16%  Similarity=0.169  Sum_probs=99.4

Q ss_pred             ccccccchHHHHHHHHHH---hcC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh
Q 004895          158 DYNIFNSRKKIFQDVIEA---LKD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA  225 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~---L~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  225 (724)
                      ....++|-++.+++|.+.   +..         ...+-+.++|++|+|||++|+.+++.....     .+.++.+     
T Consensus         7 ~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~-----~~~i~~~-----   76 (247)
T d1ixza_           7 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVP-----FITASGS-----   76 (247)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCC-----EEEEEHH-----
T ss_pred             cHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCC-----EEEEEhH-----
Confidence            345677877766655443   221         234578999999999999999999876421     3334332     


Q ss_pred             HHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------------ccccccccCCCCcC
Q 004895          226 QKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------------LDKIGIPYGDVDEK  289 (724)
Q Consensus       226 ~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------------~~~l~~~~~~~~~~  289 (724)
                       ++.    ..    ....  ....+..+++......+++|++||++....                +..+...+..    
T Consensus        77 -~l~----~~----~~g~--~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~----  141 (247)
T d1ixza_          77 -DFV----EM----FVGV--GAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDG----  141 (247)
T ss_dssp             -HHH----HS----CTTH--HHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHT----
T ss_pred             -Hhh----hc----cccH--HHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhC----
Confidence             221    11    0011  223344555555556789999999964310                1111111100    


Q ss_pred             CCCCCCCCcEEEEEecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          290 DKNDDPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       290 ~~~~~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                        .....+.-||.||..........    .-...+.+++.+.++-.++|+..........+.  ....+++.|.|+.-
T Consensus       142 --~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~--~~~~la~~t~g~s~  215 (247)
T d1ixza_         142 --FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV--DLALLAKRTPGFVG  215 (247)
T ss_dssp             --CCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTC--CHHHHHHTCTTCCH
T ss_pred             --CCCCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCcccc--CHHHHHHHCCCCCH
Confidence              01223343445666544321111    234588999999999999999888643322221  24678888888643

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.31  E-value=1.5e-05  Score=76.44  Aligned_cols=176  Identities=16%  Similarity=0.135  Sum_probs=102.0

Q ss_pred             cccccchHHHHHHHHHH---hc---------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          159 YNIFNSRKKIFQDVIEA---LK---------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~---L~---------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ...+.|-++.+++|.+.   +.         ....+.+.++|++|+|||++|+.+++.....     .+.++.+.-.+  
T Consensus        11 ~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~-----~~~i~~~~l~~--   83 (256)
T d1lv7a_          11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP-----FFTISGSDFVE--   83 (256)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCC-----EEEECSCSSTT--
T ss_pred             HHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCC-----EEEEEhHHhhh--
Confidence            45677877777666543   32         1235678899999999999999999877432     23333332211  


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc----------------ccccccccCCCCcCC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE----------------LDKIGIPYGDVDEKD  290 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~----------------~~~l~~~~~~~~~~~  290 (724)
                                  .....  .......+.+......+++|++||++....                +..+...+.      
T Consensus        84 ------------~~~g~--~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d------  143 (256)
T d1lv7a_          84 ------------MFVGV--GASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMD------  143 (256)
T ss_dssp             ------------SCCCC--CHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHH------
T ss_pred             ------------cchhH--HHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhh------
Confidence                        11111  122344555555556789999999964210                011111110      


Q ss_pred             CCCCCCCcEEEEEecccchhhhh-c---CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          291 KNDDPRRCTIILTSRSRDLLCID-M---NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       291 ~~~~~~~s~ilvTtR~~~v~~~~-~---~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      ......+.-||.||......... .   .-...+.+++.+.++-.++|+.........++  .....+++.+.|+.-
T Consensus       144 ~~~~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~--~~~~~la~~t~G~s~  218 (256)
T d1lv7a_         144 GFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPD--IDAAIIARGTPGFSG  218 (256)
T ss_dssp             TCCSSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTT--CCHHHHHHTCTTCCH
T ss_pred             CCCCCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcc--cCHHHHHHhCCCCCH
Confidence            00133345566677765432111 1   23468899999999999999888754332222  224678888888653

>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=98.30  E-value=4.7e-07  Score=92.27  Aligned_cols=182  Identities=14%  Similarity=0.131  Sum_probs=119.8

Q ss_pred             cCceEEeccCCCcccC-----CCc-ccCCCccEEEEeccccccc---cc--------chhhhcCCCCceEEEcCCCcCC-
Q 004895          527 KGPIAISLPYRDIQEL-----PER-LECPQLKLFLLFAKYDSTL---QI--------SDHFFEGTEELKVLDFTGIRFS-  588 (724)
Q Consensus       527 ~~~~~l~l~~~~~~~~-----~~~-~~~~~Lr~L~l~~~~~~~~---~~--------~~~~~~~l~~L~~L~l~~~~~~-  588 (724)
                      .+++.+++.+|.+...     ... ..+++|+.|.+..+.....   .+        ........+.|+.++++++.+. 
T Consensus        93 ~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~l~~n~i~~  172 (344)
T d2ca6a1          93 PKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLEN  172 (344)
T ss_dssp             TTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTG
T ss_pred             CCcccccccccccccccccchhhhhcccccchheecccccccccccccccccccccccccccccCcccceeecccccccc
Confidence            5688888887776432     111 1567888888843221110   00        0011246788999999998876 


Q ss_pred             ----CCCccccCCCCCcEEEcCCcccCCc-------ccccCCCCCcEEEccCCcCc-----ccchhhhcCCCCCeEccCC
Q 004895          589 ----PLPSSLGRLINLQTLCLDGWRLEDI-------AIVGQLKKLEILSLRGAEIK-----QLPLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       589 ----~lp~~i~~l~~L~~L~L~~~~l~~~-------~~~~~l~~L~~L~l~~~~i~-----~lp~~i~~l~~L~~L~l~~  652 (724)
                          .+...+....+|++|+|++|.+...       ..+..+++|++|++++|.++     .+...+..+++|++|++++
T Consensus       173 ~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~  252 (344)
T d2ca6a1         173 GSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLND  252 (344)
T ss_dssp             GGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTT
T ss_pred             cccccccchhhhhhhhcccccccccccccccccchhhhhcchhhhcccccccccccccccccccccccccccchhhhhhc
Confidence                2344566788999999999987651       34778899999999999875     2556678899999999999


Q ss_pred             CCCCcccCh----HHhhC--CCCCcEEEccCCCCccccccCCccchH-Hhhc-CCCCCcEEEeecccccc
Q 004895          653 CSSLVVIAP----NVISK--LSRLEELYMGDSFSQWDKVEGGSNASL-AELK-GLSKLTTLEIDVRDAEM  714 (724)
Q Consensus       653 ~~~l~~~~~----~~i~~--l~~L~~L~l~~~~~~~~~~~~~~~~~l-~~L~-~L~~L~~L~l~~n~~~~  714 (724)
                      |. +.....    ..+..  .++|++|++++|.....     ....+ ..+. ++++|+.|++++|.+..
T Consensus       253 n~-i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~i~~~-----~~~~l~~~l~~~~~~L~~L~l~~N~~~~  316 (344)
T d2ca6a1         253 CL-LSARGAAAVVDAFSKLENIGLQTLRLQYNEIELD-----AVRTLKTVIDEKMPDLLFLELNGNRFSE  316 (344)
T ss_dssp             CC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHH-----HHHHHHHHHHHHCTTCCEEECTTSBSCT
T ss_pred             Cc-cCchhhHHHHHHhhhccCCCCCEEECCCCcCChH-----HHHHHHHHHHccCCCCCEEECCCCcCCC
Confidence            64 443211    22333  36799999998743211     11112 2232 57789999999998754

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.29  E-value=1.8e-06  Score=87.96  Aligned_cols=157  Identities=17%  Similarity=0.241  Sum_probs=91.4

Q ss_pred             cccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc----CCCeEEE-EEEecCCChHHHHHHHH
Q 004895          159 YNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN----VFDKVVM-AEITKNPDAQKIQGELA  233 (724)
Q Consensus       159 ~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~w-v~vs~~~~~~~l~~~i~  233 (724)
                      .++++||+++++++++.|....-.-+.+||++|+|||+++..++++.....    -.+..+| ++++.          ++
T Consensus        21 ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~----------l~   90 (387)
T d1qvra2          21 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS----------LL   90 (387)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC--------------
T ss_pred             CCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh----------hh
Confidence            345779999999999999755445567889999999999988888764432    2234444 44332          11


Q ss_pred             HhhCCCCCCCchhHHHHHHHHHHHhc-CCcEEEEEcccccccc---------ccccccccCCCCcCCCCCCCCCcEEEEE
Q 004895          234 SDLGMNFDSNDLIYHRAKQLCQRLKK-EKRVLIILDNIWTKLE---------LDKIGIPYGDVDEKDKNDDPRRCTIILT  303 (724)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~l~~~l~~-~kr~LlVlDdv~~~~~---------~~~l~~~~~~~~~~~~~~~~~~s~ilvT  303 (724)
                      ...+  ..+ . -.+....+...+.. ..+++|++|++.....         ...+..|.-         ....-++|.|
T Consensus        91 ag~~--~~g-~-~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L---------~rg~~~~I~~  157 (387)
T d1qvra2          91 AGAK--YRG-E-FEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL---------ARGELRLIGA  157 (387)
T ss_dssp             ----------C-HHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH---------HTTCCCEEEE
T ss_pred             cccC--cch-h-HHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHH---------hCCCcceeee
Confidence            1111  111 1 23344445555543 3479999999976521         111111111         2234567777


Q ss_pred             ecccchhh-----hhcCCCceEecCCCCHHHHHHHHHHHh
Q 004895          304 SRSRDLLC-----IDMNSQKMFWIDALSEEEALQLFEKIV  338 (724)
Q Consensus       304 tR~~~v~~-----~~~~~~~~~~l~~L~~~e~~~Lf~~~~  338 (724)
                      |.......     ......+.+.+++.+.+++..++....
T Consensus       158 tT~~ey~~~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         158 TTLDEYREIEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             ECHHHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             cCHHHHHHhcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence            77654421     113446789999999999999998765

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.23  E-value=1e-05  Score=78.03  Aligned_cols=175  Identities=10%  Similarity=0.099  Sum_probs=101.1

Q ss_pred             ccccchHHHHHHHHHHh----cC---------CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          160 NIFNSRKKIFQDVIEAL----KD---------DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       160 ~~~~gR~~~~~~l~~~L----~~---------~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ..+.|-+..+++|.+.+    ..         ...+-+.++|++|+|||++|+.+++.....     .+.++.+.     
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~-----~~~i~~~~-----   73 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAF-----FFLINGPE-----   73 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCE-----EEEECHHH-----
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCe-----EEEEEchh-----
Confidence            45667777777776653    21         235678999999999999999999876432     23333221     


Q ss_pred             HHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccccc---------c----cccccccCCCCcCCCCC
Q 004895          227 KIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTKLE---------L----DKIGIPYGDVDEKDKND  293 (724)
Q Consensus       227 ~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~~~---------~----~~l~~~~~~~~~~~~~~  293 (724)
                               +.......  .......+.......++++|++||++....         .    ..+.....      ...
T Consensus        74 ---------l~~~~~g~--~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~------~~~  136 (258)
T d1e32a2          74 ---------IMSKLAGE--SESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMD------GLK  136 (258)
T ss_dssp             ---------HTTSCTTH--HHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHH------TCC
T ss_pred             ---------hccccccc--HHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccc------ccc
Confidence                     11111111  122333444444446789999999976410         0    01100000      011


Q ss_pred             CCCCcEEEEEecccchhhhhc----CCCceEecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchh
Q 004895          294 DPRRCTIILTSRSRDLLCIDM----NSQKMFWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPV  363 (724)
Q Consensus       294 ~~~~s~ilvTtR~~~v~~~~~----~~~~~~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  363 (724)
                      ...+.-||.||..........    .....+.++..+.++-.++|+.........++.  ....|++.+.|+--
T Consensus       137 ~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~--~~~~la~~t~G~s~  208 (258)
T d1e32a2         137 QRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDV--DLEQVANETHGHVG  208 (258)
T ss_dssp             CSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTC--CHHHHHHHCTTCCH
T ss_pred             ccCCccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCccccccc--chhhhhhcccCCCH
Confidence            344555677887664321111    244688999999999999998877543322322  14688999988643

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.07  E-value=3.1e-05  Score=72.00  Aligned_cols=149  Identities=14%  Similarity=0.148  Sum_probs=86.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      ..+.|+|+.|+|||.|++.+++....+  ...+++++..      ++...+...+...         ......+.+.  .
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~--~~~~~~~~~~------~~~~~~~~~~~~~---------~~~~~~~~~~--~   97 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKR--GYRVIYSSAD------DFAQAMVEHLKKG---------TINEFRNMYK--S   97 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHT--TCCEEEEEHH------HHHHHHHHHHHHT---------CHHHHHHHHH--T
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccC--ccceEEechH------HHHHHHHHHHHcc---------chhhHHHHHh--h
Confidence            347899999999999999999998754  3356666543      4444444443211         1223344444  3


Q ss_pred             cEEEEEcccccc---ccccc-cccccCCCCcCCCCCCCCCcEEEEEecccchh--------hhhcCCCceEecCCCCHHH
Q 004895          262 RVLIILDNIWTK---LELDK-IGIPYGDVDEKDKNDDPRRCTIILTSRSRDLL--------CIDMNSQKMFWIDALSEEE  329 (724)
Q Consensus       262 r~LlVlDdv~~~---~~~~~-l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~--------~~~~~~~~~~~l~~L~~~e  329 (724)
                      --+|++||+...   ..|+. +...+...       ...|..||+||+.....        .........+.++ .++++
T Consensus        98 ~dll~iDDi~~i~~~~~~~~~lf~lin~~-------~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~  169 (213)
T d1l8qa2          98 VDLLLLDDVQFLSGKERTQIEFFHIFNTL-------YLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKT  169 (213)
T ss_dssp             CSEEEEECGGGGTTCHHHHHHHHHHHHHH-------HHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHH
T ss_pred             ccchhhhhhhhhcCchHHHHHHHHHHHHH-------hhccceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHH
Confidence            469999999755   23432 11111110       23577899999976431        1112344577785 47777


Q ss_pred             HHHHHHHHhCCCCCCCCchhHHHHHHHHh
Q 004895          330 ALQLFEKIVGESTKASDFRPLAEEIVGKC  358 (724)
Q Consensus       330 ~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c  358 (724)
                      -.+++++.+....-. --+++..-|++.+
T Consensus       170 ~~~iL~~~a~~rgl~-l~~~v~~yl~~~~  197 (213)
T d1l8qa2         170 RFKIIKEKLKEFNLE-LRKEVIDYLLENT  197 (213)
T ss_dssp             HHHHHHHHHHHTTCC-CCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCC-CCHHHHHHHHHhc
Confidence            788888877422211 1134555555554

>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=1.6e-06  Score=88.06  Aligned_cols=182  Identities=16%  Similarity=0.192  Sum_probs=109.3

Q ss_pred             ccCceEEeccCCCcccCCC------------cccCCCccEEEEeccccccc--ccchhhhcCCCCceEEEcCCCcCCC--
Q 004895          526 QKGPIAISLPYRDIQELPE------------RLECPQLKLFLLFAKYDSTL--QISDHFFEGTEELKVLDFTGIRFSP--  589 (724)
Q Consensus       526 ~~~~~~l~l~~~~~~~~~~------------~~~~~~Lr~L~l~~~~~~~~--~~~~~~~~~l~~L~~L~l~~~~~~~--  589 (724)
                      .+.++.+.+.++.......            ...+++|+.|.+..+.....  ......+...++|+.|++++|.+..  
T Consensus        58 ~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~  137 (344)
T d2ca6a1          58 KKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQA  137 (344)
T ss_dssp             CTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHH
T ss_pred             CCCCCEEECCCCcccccccccchHHHHHHHHHhhCCCcccccccccccccccccchhhhhcccccchheecccccccccc
Confidence            4567777776554322211            11467788888732221111  1112235567788888888887641  


Q ss_pred             ---CCc---------cccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCcc------cchhhhcCCCC
Q 004895          590 ---LPS---------SLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQ------LPLQIGQLTRL  645 (724)
Q Consensus       590 ---lp~---------~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~------lp~~i~~l~~L  645 (724)
                         +..         .......|++|.+++|.+..  .    ..+...++|++|++++|.+..      +...+..+++|
T Consensus       138 ~~~l~~~l~~~~~~~~~~~~~~L~~l~l~~n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L  217 (344)
T d2ca6a1         138 GAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQEL  217 (344)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTC
T ss_pred             cccccccccccccccccccCcccceeecccccccccccccccchhhhhhhhcccccccccccccccccchhhhhcchhhh
Confidence               000         11245678888888887664  1    345677889999999998763      23446778899


Q ss_pred             CeEccCCCCCCccc----ChHHhhCCCCCcEEEccCCCCccccccCCccchH-HhhcC--CCCCcEEEeeccccc
Q 004895          646 QLLDLSNCSSLVVI----APNVISKLSRLEELYMGDSFSQWDKVEGGSNASL-AELKG--LSKLTTLEIDVRDAE  713 (724)
Q Consensus       646 ~~L~l~~~~~l~~~----~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~~~~l-~~L~~--L~~L~~L~l~~n~~~  713 (724)
                      ++|++++|. +...    ....+..+++|++|++++|....     .....+ ..+..  .+.|+.|++++|.++
T Consensus       218 ~~L~Ls~N~-i~~~g~~~L~~~l~~~~~L~~L~Ls~n~i~~-----~g~~~l~~~l~~~~~~~L~~L~ls~N~i~  286 (344)
T d2ca6a1         218 KVLDLQDNT-FTHLGSSALAIALKSWPNLRELGLNDCLLSA-----RGAAAVVDAFSKLENIGLQTLRLQYNEIE  286 (344)
T ss_dssp             CEEECCSSC-CHHHHHHHHHHHGGGCTTCCEEECTTCCCCH-----HHHHHHHHHHHTCSSCCCCEEECCSSCCB
T ss_pred             ccccccccc-ccccccccccccccccccchhhhhhcCccCc-----hhhHHHHHHhhhccCCCCCEEECCCCcCC
Confidence            999998853 3321    12346788899999998874321     111112 22333  357899999999864

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.03  E-value=1.6e-05  Score=76.82  Aligned_cols=156  Identities=15%  Similarity=0.197  Sum_probs=86.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKK  259 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~  259 (724)
                      ..+-|.++|++|+|||+||+.+++.....       ++.++    ..++    ..    .....  .......+......
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~~~~~~-------~~~~~----~~~l----~~----~~~~~--~~~~l~~~f~~A~~   98 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIANECQAN-------FISIK----GPEL----LT----MWFGE--SEANVREIFDKARQ   98 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHHHTTCE-------EEEEC----HHHH----HT----SCTTT--HHHHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCcchhHHHHHHHHhCCc-------EEEEE----HHHh----hh----ccccc--hHHHHHHHHHHHHh
Confidence            34678899999999999999999887532       22222    1111    11    11111  12233444444444


Q ss_pred             CCcEEEEEcccccccc--------c--------cccccccCCCCcCCCCCCCCCcEEEEEecccchhhhhc----CCCce
Q 004895          260 EKRVLIILDNIWTKLE--------L--------DKIGIPYGDVDEKDKNDDPRRCTIILTSRSRDLLCIDM----NSQKM  319 (724)
Q Consensus       260 ~kr~LlVlDdv~~~~~--------~--------~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~v~~~~~----~~~~~  319 (724)
                      ..+++|+|||++....        .        ..+...+.      ......+.-||.||....-.....    .....
T Consensus        99 ~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~------~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~  172 (265)
T d1r7ra3          99 AAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMD------GMSTKKNVFIIGATNRPDIIDPAILRPGRLDQL  172 (265)
T ss_dssp             TCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------------CCEEEECCBSCTTTSCGGGSSTTSEEE
T ss_pred             cCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhh------CcCCCCCEEEEEeCCCchhCCHHHhCCCCccEE
Confidence            6789999999974311        0        11111111      111233456777777665321111    23468


Q ss_pred             EecCCCCHHHHHHHHHHHhCCCCCCCCchhHHHHHHHHhCCchhH
Q 004895          320 FWIDALSEEEALQLFEKIVGESTKASDFRPLAEEIVGKCGGLPVA  364 (724)
Q Consensus       320 ~~l~~L~~~e~~~Lf~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  364 (724)
                      ++++..+.++-.++|+..........+.  ...+|++++.|+..+
T Consensus       173 i~~~~p~~~~R~~il~~~l~~~~~~~~~--~l~~la~~t~g~s~~  215 (265)
T d1r7ra3         173 IYIPLPDEKSRVAILKANLRKSPVAKDV--DLEFLAKMTNGFSGA  215 (265)
T ss_dssp             EECCCCCCHHHHHHHHHHTTCC----CC--CCHHHHHHHCSSCCH
T ss_pred             EEecchHHHHHHHHHHHHhccCCchhhh--hHHHHHhcCCCCCHH
Confidence            9999999999999998876532222211  135788888886643

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=98.02  E-value=0.00012  Score=69.61  Aligned_cols=92  Identities=16%  Similarity=0.113  Sum_probs=52.9

Q ss_pred             cccchHHHHHHHHHHhc----------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK----------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQG  230 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~----------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~  230 (724)
                      +++|..+.++.+++...          ....+-|.++|++|+|||++|+.+++....  +   .+.++.+....      
T Consensus        10 ~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~--~---~~~i~~~~~~~------   78 (246)
T d1d2na_          10 GIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNF--P---FIKICSPDKMI------   78 (246)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTC--S---EEEEECGGGCT------
T ss_pred             CCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcccc--c---ccccccccccc------
Confidence            45565555555444332          123456889999999999999999987643  1   23344332110      


Q ss_pred             HHHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEccccc
Q 004895          231 ELASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWT  272 (724)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~  272 (724)
                            +  .. ..........+++...+..+++|++|+++.
T Consensus        79 ------g--~~-~~~~~~~i~~if~~A~~~~p~il~iDEid~  111 (246)
T d1d2na_          79 ------G--FS-ETAKCQAMKKIFDDAYKSQLSCVVVDDIER  111 (246)
T ss_dssp             ------T--CC-HHHHHHHHHHHHHHHHTSSEEEEEECCHHH
T ss_pred             ------c--cc-ccchhhhhhhhhhhhhhcccceeehhhhhh
Confidence                  0  00 000112233444444556789999999964

>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=97.84  E-value=1.3e-06  Score=78.06  Aligned_cols=61  Identities=23%  Similarity=0.263  Sum_probs=30.5

Q ss_pred             CCCCCcEEEccCCcCccc---chhhhcCCCCCeEccCCCCCCcccChHHhhCCCCCcEEEccCCC
Q 004895          618 QLKKLEILSLRGAEIKQL---PLQIGQLTRLQLLDLSNCSSLVVIAPNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       618 ~l~~L~~L~l~~~~i~~l---p~~i~~l~~L~~L~l~~~~~l~~~~~~~i~~l~~L~~L~l~~~~  679 (724)
                      .+++|++|++++|.|+.+   +..+..+++|+.|++++ +.++.++.-......+|+.|++.+|.
T Consensus        63 ~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~-N~i~~l~~l~~l~~~~L~~L~L~~Np  126 (162)
T d1koha1          63 NIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSG-NELKSERELDKIKGLKLEELWLDGNS  126 (162)
T ss_dssp             HCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTT-SCCCCGGGHHHHTTCCCSSCCCTTST
T ss_pred             hCCCCCEeeCCCccccCCchhHHHHhhCCccccccccc-CccccchhhhhhhccccceeecCCCC
Confidence            455555555555555543   23344555666666655 34444443222233445555555543

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.70  E-value=2.7e-06  Score=75.98  Aligned_cols=65  Identities=29%  Similarity=0.280  Sum_probs=35.0

Q ss_pred             hhhcCCCCceEEEcCCCcCCCCC---ccccCCCCCcEEEcCCcccCCccccc--CCCCCcEEEccCCcCc
Q 004895          569 HFFEGTEELKVLDFTGIRFSPLP---SSLGRLINLQTLCLDGWRLEDIAIVG--QLKKLEILSLRGAEIK  633 (724)
Q Consensus       569 ~~~~~l~~L~~L~l~~~~~~~lp---~~i~~l~~L~~L~L~~~~l~~~~~~~--~l~~L~~L~l~~~~i~  633 (724)
                      ..+..++.|++|++++|+++.++   ..+..+++|++|+|++|.++.++.+.  ...+|+.|++++|.+.
T Consensus        59 ~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~  128 (162)
T d1koha1          59 IIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLS  128 (162)
T ss_dssp             HHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTS
T ss_pred             HHHHhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCCcC
Confidence            34456677777777777776543   23445566666666666655532211  1224555555555443

>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=97.67  E-value=3.8e-06  Score=88.47  Aligned_cols=106  Identities=13%  Similarity=0.087  Sum_probs=55.6

Q ss_pred             CceEEeccCCCcccC--CC-cccCCCccEEEEeccccccc--ccchhhhcCCCCceEEEcCCCcCCC-----CCcccc-C
Q 004895          528 GPIAISLPYRDIQEL--PE-RLECPQLKLFLLFAKYDSTL--QISDHFFEGTEELKVLDFTGIRFSP-----LPSSLG-R  596 (724)
Q Consensus       528 ~~~~l~l~~~~~~~~--~~-~~~~~~Lr~L~l~~~~~~~~--~~~~~~~~~l~~L~~L~l~~~~~~~-----lp~~i~-~  596 (724)
                      +++.|+++.+++...  .. ...++++++|.+..+.-...  ......+..+++|+.|||++|.+..     +...+. .
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~   82 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTP   82 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCST
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhcC
Confidence            455666766666432  11 12456677777733221110  1112234566677777777776641     112221 1


Q ss_pred             CCCCcEEEcCCcccCCc------ccccCCCCCcEEEccCCcCc
Q 004895          597 LINLQTLCLDGWRLEDI------AIVGQLKKLEILSLRGAEIK  633 (724)
Q Consensus       597 l~~L~~L~L~~~~l~~~------~~~~~l~~L~~L~l~~~~i~  633 (724)
                      ..+|++|+|++|.+++.      ..+..+++|++|++++|.++
T Consensus        83 ~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~i~  125 (460)
T d1z7xw1          83 SCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLG  125 (460)
T ss_dssp             TCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCH
T ss_pred             CCCCCEEECCCCCccccccccccchhhccccccccccccccch
Confidence            23577777777766541      34556667777777777655

>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=97.50  E-value=2.3e-05  Score=82.29  Aligned_cols=103  Identities=24%  Similarity=0.332  Sum_probs=75.6

Q ss_pred             CceEEEcCCCcCCC--CCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCcc-----cchhhh-c
Q 004895          576 ELKVLDFTGIRFSP--LPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQ-----LPLQIG-Q  641 (724)
Q Consensus       576 ~L~~L~l~~~~~~~--lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~-----lp~~i~-~  641 (724)
                      .|+.||+++++++.  +..-+..+++++.|+|++|.++.  .    ..+..+++|++|||++|.++.     +...+. .
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~   82 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTP   82 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCST
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhcC
Confidence            58899999999983  34446678899999999998875  1    346788999999999998863     222222 2


Q ss_pred             CCCCCeEccCCCCCCcccC----hHHhhCCCCCcEEEccCCC
Q 004895          642 LTRLQLLDLSNCSSLVVIA----PNVISKLSRLEELYMGDSF  679 (724)
Q Consensus       642 l~~L~~L~l~~~~~l~~~~----~~~i~~l~~L~~L~l~~~~  679 (724)
                      ..+|++|++++|. ++...    +..+..+++|++|++++|.
T Consensus        83 ~~~L~~L~L~~n~-it~~~~~~l~~~l~~~~~L~~L~L~~N~  123 (460)
T d1z7xw1          83 SCKIQKLSLQNCC-LTGAGCGVLSSTLRTLPTLQELHLSDNL  123 (460)
T ss_dssp             TCCCCEEECTTSC-CBGGGHHHHHHHTTSCTTCCEEECCSSB
T ss_pred             CCCCCEEECCCCC-ccccccccccchhhcccccccccccccc
Confidence            3579999999964 44321    3346788999999998864

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.25  E-value=0.0012  Score=60.05  Aligned_cols=130  Identities=12%  Similarity=0.071  Sum_probs=75.8

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh--ccCCCeEEEEEEec-CCChHHHHHHHHHhhCCCCCCCch
Q 004895          169 FQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME--DNVFDKVVMAEITK-NPDAQKIQGELASDLGMNFDSNDL  245 (724)
Q Consensus       169 ~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~~~~~~  245 (724)
                      ++.+..++..+..+.+.++|++|+||||+|..+.+....  ..|.| ++++...+ ..+++++ +++.+.+.....    
T Consensus         3 ~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~~~~----   76 (198)
T d2gnoa2           3 LETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSPE----   76 (198)
T ss_dssp             HHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCCS----
T ss_pred             HHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhhCcc----
Confidence            444555566677889999999999999999999987643  23334 44444322 2244444 335444433221    


Q ss_pred             hHHHHHHHHHHHhcCCcEEEEEccccccc--cccccccccCCCCcCCCCCCCCCcEEEEEecccc-hhhhhcCCCceEec
Q 004895          246 IYHRAKQLCQRLKKEKRVLIILDNIWTKL--ELDKIGIPYGDVDEKDKNDDPRRCTIILTSRSRD-LLCIDMNSQKMFWI  322 (724)
Q Consensus       246 ~~~~~~~l~~~l~~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~~~~~~~~~~~s~ilvTtR~~~-v~~~~~~~~~~~~l  322 (724)
                                   .+++-++|+|+++...  ..+.+...+..        ...++.+|++|.+.. +...-.+....+.+
T Consensus        77 -------------~~~~KviIId~ad~l~~~aqNaLLK~LEE--------Pp~~t~fiLit~~~~~ll~TI~SRC~~i~~  135 (198)
T d2gnoa2          77 -------------LYTRKYVIVHDCERMTQQAANAFLKALEE--------PPEYAVIVLNTRRWHYLLPTIKSRVFRVVV  135 (198)
T ss_dssp             -------------SSSSEEEEETTGGGBCHHHHHHTHHHHHS--------CCTTEEEEEEESCGGGSCHHHHTTSEEEEC
T ss_pred             -------------cCCCEEEEEeCccccchhhhhHHHHHHhC--------CCCCceeeeccCChhhCHHHHhcceEEEeC
Confidence                         1455699999997653  34444333333        345666666666544 33322344456776


Q ss_pred             CCC
Q 004895          323 DAL  325 (724)
Q Consensus       323 ~~L  325 (724)
                      .+.
T Consensus       136 ~~p  138 (198)
T d2gnoa2         136 NVP  138 (198)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            643

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.85  E-value=0.00057  Score=60.53  Aligned_cols=80  Identities=14%  Similarity=0.194  Sum_probs=38.9

Q ss_pred             CCCCceEEEcCCC-cCC-----CCCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCcc-----c
Q 004895          573 GTEELKVLDFTGI-RFS-----PLPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQ-----L  635 (724)
Q Consensus       573 ~l~~L~~L~l~~~-~~~-----~lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~-----l  635 (724)
                      +.+.|+.|+|+++ .+.     .+-..+....+|++|+|++|.+..  .    ..+...+.|++|++++|.++.     +
T Consensus        13 n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l   92 (167)
T d1pgva_          13 DDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARL   92 (167)
T ss_dssp             TCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHH
T ss_pred             CCCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHH
Confidence            4455666666553 233     122234445556666666665543  1    233344556666666655542     1


Q ss_pred             chhhhcCCCCCeEccCC
Q 004895          636 PLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       636 p~~i~~l~~L~~L~l~~  652 (724)
                      -..+...+.|++|++++
T Consensus        93 ~~aL~~n~sL~~L~l~~  109 (167)
T d1pgva_          93 LRSTLVTQSIVEFKADN  109 (167)
T ss_dssp             HHHTTTTCCCSEEECCC
T ss_pred             HHHHHhCCcCCEEECCC
Confidence            22344445555555554

>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=96.81  E-value=0.00085  Score=65.93  Aligned_cols=104  Identities=19%  Similarity=0.319  Sum_probs=56.6

Q ss_pred             ccchHHHHHHHHHHhc-------CC--CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK-------DD--KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGEL  232 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~-------~~--~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i  232 (724)
                      ++|.++.++.+...+.       ++  ...++.++|+.|+|||.+|+.+++.....  -...+-++.+...+...+    
T Consensus        25 v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~--~~~~~~~~~~~~~~~~~~----   98 (315)
T d1qvra3          25 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT--EEAMIRIDMTEYMEKHAV----   98 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS--GGGEEEECTTTCCSSGGG----
T ss_pred             EeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC--CcceEEEeccccccchhh----
Confidence            4577777777766543       11  23478899999999999999999986311  122344444443332211    


Q ss_pred             HHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          233 ASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      .+-+|.+..-.  .......+.+.+.+....+++||+++..
T Consensus        99 ~~L~g~~~gyv--G~~~~~~l~~~~~~~p~~Vvl~DEieK~  137 (315)
T d1qvra3          99 SRLIGAPPGYV--GYEEGGQLTEAVRRRPYSVILFDEIEKA  137 (315)
T ss_dssp             GGC----------------CHHHHHHHCSSEEEEESSGGGS
T ss_pred             hhhcCCCCCCc--CcccCChHHHHHHhCCCcEEEEehHhhc
Confidence            11112111100  0001123445555556799999999865

>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=96.78  E-value=0.00042  Score=61.37  Aligned_cols=28  Identities=25%  Similarity=0.503  Sum_probs=25.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .+|++|+|+.|+|||||++++.+....+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            4799999999999999999999987653

>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=96.78  E-value=0.00056  Score=61.17  Aligned_cols=38  Identities=13%  Similarity=0.066  Sum_probs=29.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAE  218 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  218 (724)
                      +..+|.|+|++|+||||+|+.++...... +++...++.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~~L~~~-~~~~~~~~~   42 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQVTLNQQ-GGRSVSLLL   42 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHH-CSSCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhc-CCCchhhhh
Confidence            34689999999999999999999988653 455555553

>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=96.68  E-value=0.0055  Score=55.59  Aligned_cols=59  Identities=24%  Similarity=0.251  Sum_probs=41.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCCh--HHHHHHHHHhhCCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDA--QKIQGELASDLGMNF  240 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~--~~l~~~i~~~l~~~~  240 (724)
                      ....||.++|+.|+||||.+.+++.....+   ...+.+-..+.+..  .+-++...+.++.+.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~   67 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTFRAAAVEQLQVWGQRNNIPV   67 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEECCCTTCHHHHHHHHHHHHHTTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccccchhhhhhhhhhcCCcc
Confidence            456899999999999999888888877632   23344444455554  455677778887764

>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=96.63  E-value=0.0026  Score=62.42  Aligned_cols=102  Identities=18%  Similarity=0.258  Sum_probs=59.8

Q ss_pred             cccchHHHHHHHHHHhc---------CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          161 IFNSRKKIFQDVIEALK---------DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       161 ~~~gR~~~~~~l~~~L~---------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++|.++.++.+...+.         +....++.++|+.|+|||.||+.+++-..     ...+-++++.-.+...    
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~-----~~~i~~d~s~~~~~~~----   93 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG-----IELLRFDMSEYMERHT----   93 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHT-----CEEEEEEGGGCSSSSC----
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhcc-----CCeeEeccccccchhh----
Confidence            35688888888776653         12345888999999999999999998753     3345555554322111    


Q ss_pred             HHHhhCCCCCCCchhHHHHHHHHHHHhcCCcEEEEEcccccc
Q 004895          232 LASDLGMNFDSNDLIYHRAKQLCQRLKKEKRVLIILDNIWTK  273 (724)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~l~~~l~~~kr~LlVlDdv~~~  273 (724)
                      +.+-++......  .......+...+......+++||+++..
T Consensus        94 ~~~l~g~~~gy~--g~~~~~~l~~~~~~~~~~vvl~DeieKa  133 (315)
T d1r6bx3          94 VSRLIGAPPGYV--GFDQGGLLTDAVIKHPHAVLLLDEIEKA  133 (315)
T ss_dssp             CSSSCCCCSCSH--HHHHTTHHHHHHHHCSSEEEEEETGGGS
T ss_pred             hhhhcccCCCcc--ccccCChhhHHHHhCccchhhhcccccc
Confidence            011122221111  1111122344444567789999999765

>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=96.58  E-value=0.0053  Score=58.14  Aligned_cols=85  Identities=16%  Similarity=0.208  Sum_probs=57.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      .-+++-|+|+.|+||||||.+++.......  ..++|++....++.+.     ++++|.+.+.     ....++..+.+.
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~  131 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIAD  131 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHH
Confidence            457999999999999999988887765443  3589999988888653     5666765332     111233333332


Q ss_pred             HHHhcCCcEEEEEcccc
Q 004895          255 QRLKKEKRVLIILDNIW  271 (724)
Q Consensus       255 ~~l~~~kr~LlVlDdv~  271 (724)
                      .....++.-|||+|.+-
T Consensus       132 ~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         132 MLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             HHHHTTCEEEEEEECST
T ss_pred             HHHhcCCCCEEEEeccc
Confidence            23334567899999983

>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=96.55  E-value=0.00054  Score=61.65  Aligned_cols=26  Identities=23%  Similarity=0.362  Sum_probs=23.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++.|+|.|+.|+||||||+.+++...
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~   32 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFN   32 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            57899999999999999999998653

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.53  E-value=0.0014  Score=57.98  Aligned_cols=83  Identities=11%  Similarity=0.048  Sum_probs=60.2

Q ss_pred             hhcCCCCceEEEcCCCcCC-----CCCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcCccc---
Q 004895          570 FFEGTEELKVLDFTGIRFS-----PLPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEIKQL---  635 (724)
Q Consensus       570 ~~~~l~~L~~L~l~~~~~~-----~lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i~~l---  635 (724)
                      .+...+.|+.|++++|.+.     .+...+...+.|++|+|++|.+..  .    ..+..-++|++|++++|.+..+   
T Consensus        39 ~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~~aL~~n~sL~~L~l~~n~~~~~g~~  118 (167)
T d1pgva_          39 AACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQ  118 (167)
T ss_dssp             HHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCCSSCCCCHH
T ss_pred             HHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHHHHHHHhCCcCCEEECCCCcCCCccHH
Confidence            3566788999999999886     233455667889999999999876  2    4577778899999998865543   


Q ss_pred             -----chhhhcCCCCCeEccCC
Q 004895          636 -----PLQIGQLTRLQLLDLSN  652 (724)
Q Consensus       636 -----p~~i~~l~~L~~L~l~~  652 (724)
                           ...+...+.|+.|+++.
T Consensus       119 ~~~~l~~~L~~n~sL~~l~l~~  140 (167)
T d1pgva_         119 VEMDMMMAIEENESLLRVGISF  140 (167)
T ss_dssp             HHHHHHHHHHHCSSCCEEECCC
T ss_pred             HHHHHHHHHHhCCCccEeeCcC
Confidence                 33344556666666654

>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=96.52  E-value=0.0063  Score=55.14  Aligned_cols=60  Identities=22%  Similarity=0.269  Sum_probs=43.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec-CCChHHHHHHHHHhhCCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK-NPDAQKIQGELASDLGMNF  240 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~~~~~l~~~i~~~l~~~~  240 (724)
                      ++.+||.++|+.|+||||.+.+++...... . ..+..+++.. .....+-++..++.++.+.
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~~-g-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   64 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQNL-G-KKVMFCAGDTFRAAGGTQLSEWGKRLSIPV   64 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHTT-T-CCEEEECCCCSSTTHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-C-CcEEEEEeccccccchhhHhhcccccCceE
Confidence            456899999999999999988888877643 2 3467776643 2455566778888887764

>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=96.51  E-value=0.00052  Score=60.31  Aligned_cols=25  Identities=36%  Similarity=0.444  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.|.|+|++|+||||+|+.++....
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~   27 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLN   27 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688899999999999999998763

>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=96.49  E-value=0.0046  Score=58.66  Aligned_cols=84  Identities=21%  Similarity=0.254  Sum_probs=58.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLC  254 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~  254 (724)
                      .-+++-|+|++|+||||||.+++.......  ..++|++....++.+     +++.+|.+.+.     ....++..+ +.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~-~~  127 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALE-IM  127 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHH-HH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHH-HH
Confidence            456999999999999999999988875432  348999998888874     67788876432     111233333 33


Q ss_pred             HHH-hcCCcEEEEEcccc
Q 004895          255 QRL-KKEKRVLIILDNIW  271 (724)
Q Consensus       255 ~~l-~~~kr~LlVlDdv~  271 (724)
                      +.+ ..+..-|+|+|-+-
T Consensus       128 ~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         128 ELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             HHHHTTTCCSEEEEECTT
T ss_pred             HHHHhcCCCcEEEEeccc
Confidence            444 33456689999884

>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=96.46  E-value=0.00076  Score=58.45  Aligned_cols=24  Identities=29%  Similarity=0.414  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++|.|+|++|+||||+|+.+....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            478899999999999999886543

>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=96.45  E-value=0.0017  Score=58.77  Aligned_cols=30  Identities=30%  Similarity=0.502  Sum_probs=26.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+.-+|+|.|++|+||||||+.+.+....
T Consensus        19 ~~~~~iIgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          19 TAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            445568999999999999999999988775

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.44  E-value=0.0016  Score=57.41  Aligned_cols=62  Identities=13%  Similarity=0.215  Sum_probs=28.4

Q ss_pred             hcCCCCceEEEcCC-CcCC-----CCCccccCCCCCcEEEcCCcccCC--c----ccccCCCCCcEEEccCCcC
Q 004895          571 FEGTEELKVLDFTG-IRFS-----PLPSSLGRLINLQTLCLDGWRLED--I----AIVGQLKKLEILSLRGAEI  632 (724)
Q Consensus       571 ~~~l~~L~~L~l~~-~~~~-----~lp~~i~~l~~L~~L~L~~~~l~~--~----~~~~~l~~L~~L~l~~~~i  632 (724)
                      ..+.+.|+.|++++ +.++     .+-..+...++|+.|+|++|.+..  .    ..+...++|+.|++++|.+
T Consensus        13 ~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~   86 (166)
T d1io0a_          13 QNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFI   86 (166)
T ss_dssp             HTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCC
T ss_pred             HhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccc
Confidence            33445566666554 2333     122233345555555555555443  1    2233444555555555443

>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=96.43  E-value=0.00079  Score=60.38  Aligned_cols=27  Identities=30%  Similarity=0.433  Sum_probs=24.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      +.|.|+|++|+|||||+++++......
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            468999999999999999999998654

>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=96.40  E-value=0.001  Score=60.51  Aligned_cols=28  Identities=32%  Similarity=0.399  Sum_probs=25.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+++.+|.|+|++|+||||+|+.+++..
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4567899999999999999999999876

>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=96.35  E-value=0.00093  Score=59.20  Aligned_cols=24  Identities=38%  Similarity=0.587  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++|.|+|++|+||||+|+.+....
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            579999999999999999998754

>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=96.35  E-value=0.00085  Score=59.42  Aligned_cols=25  Identities=44%  Similarity=0.458  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.|.|+|++|+||||+|+.+++...
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l~   29 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKSG   29 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHC
Confidence            4578999999999999999998763

>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=96.35  E-value=0.0061  Score=55.32  Aligned_cols=57  Identities=19%  Similarity=0.240  Sum_probs=39.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC--hHHHHHHHHHhhCCC
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD--AQKIQGELASDLGMN  239 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~--~~~l~~~i~~~l~~~  239 (724)
                      +.+|+.++|+.|+||||.+.+++.....+ . ..+..+++ +.+.  ..+-++...+.++.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~~~-g-~kV~lit~-Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYKGK-G-RRPLLVAA-DTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT-T-CCEEEEEC-CSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHC-C-CcEEEEec-ccccchHHHHHHHHHHhcCCc
Confidence            45799999999999999988888887643 2 23555554 3333  345566777777765

>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=96.31  E-value=0.014  Score=52.93  Aligned_cols=60  Identities=25%  Similarity=0.324  Sum_probs=42.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNF  240 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~  240 (724)
                      ....||.++|+.|+||||.+.+++.....++  ..+..+++... ....+-++..++.++.+.
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~--~kV~lit~Dt~R~gA~eQL~~~a~~l~i~~   69 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEG--KSVVLAAADTFRAAAIEQLKIWGERVGATV   69 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTT--CCEEEEEECTTCHHHHHHHHHHHHHHTCEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CceEEEeecccccchhHHHHHHhhhcCccc
Confidence            4567999999999999998888888775432  34666766432 234455677777777653

>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=96.26  E-value=0.0081  Score=56.79  Aligned_cols=84  Identities=19%  Similarity=0.230  Sum_probs=56.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCC-----CchhHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDS-----NDLIYHRAKQLCQ  255 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~-----~~~~~~~~~~l~~  255 (724)
                      -+++-|+|++|+||||||-+++.......  ..++|++....++..     .++.+|.+.+.     ....++..+.+..
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~  126 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICDA  126 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHHH
Confidence            46999999999999999999998876542  348999988888763     46677765321     1112333333333


Q ss_pred             HHhcCCcEEEEEcccc
Q 004895          256 RLKKEKRVLIILDNIW  271 (724)
Q Consensus       256 ~l~~~kr~LlVlDdv~  271 (724)
                      ....++.-|+|+|-+-
T Consensus       127 l~~~~~~~liViDSi~  142 (263)
T d1u94a1         127 LARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHTCCSEEEEECGG
T ss_pred             HHhcCCCCEEEEECcc
Confidence            3333445688999883

>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=96.24  E-value=0.01  Score=53.83  Aligned_cols=60  Identities=23%  Similarity=0.297  Sum_probs=36.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC-CChHHHHHHHHHhhCCCC
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN-PDAQKIQGELASDLGMNF  240 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~~~~~l~~~i~~~l~~~~  240 (724)
                      ....||.++|+.|+||||.+.+++...+.+ .. .+..|++... ....+-++..++.++.+.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~~~-g~-kV~lit~Dt~R~ga~eQL~~~a~~l~v~~   70 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYKKK-GF-KVGLVGADVYRPAALEQLQQLGQQIGVPV   70 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHHHT-TC-CEEEEECCCSSHHHHHHHHHHHHHHTCCE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CC-ceEEEEeeccccchhHHHHHhccccCcce
Confidence            457899999999999999888888877643 22 3666665422 223344566677777653

>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=96.19  E-value=0.0033  Score=59.09  Aligned_cols=40  Identities=25%  Similarity=0.342  Sum_probs=32.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      .-+++.|+|.+|+|||+||.+++.....  +...++|++...
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~--~~~~~~~is~e~   64 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACA--NKERAILFAYEE   64 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHT--TTCCEEEEESSS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHH--hccccceeeccC
Confidence            4569999999999999999999998653  356688887654

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.17  E-value=0.0017  Score=57.39  Aligned_cols=28  Identities=25%  Similarity=0.479  Sum_probs=24.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ...+++.|.|++|+||||+|+.+.....
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4568999999999999999999998763

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.13  E-value=0.0022  Score=56.45  Aligned_cols=27  Identities=30%  Similarity=0.446  Sum_probs=24.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ++++|+|..|+|||||+.++....+.+
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHhC
Confidence            689999999999999999999998764

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.12  E-value=0.0033  Score=55.28  Aligned_cols=115  Identities=10%  Similarity=0.057  Sum_probs=77.8

Q ss_pred             cCCCCCcEEEcCCc-ccCC--c----ccccCCCCCcEEEccCCcCc-----ccchhhhcCCCCCeEccCCCCCCccc---
Q 004895          595 GRLINLQTLCLDGW-RLED--I----AIVGQLKKLEILSLRGAEIK-----QLPLQIGQLTRLQLLDLSNCSSLVVI---  659 (724)
Q Consensus       595 ~~l~~L~~L~L~~~-~l~~--~----~~~~~l~~L~~L~l~~~~i~-----~lp~~i~~l~~L~~L~l~~~~~l~~~---  659 (724)
                      .+.++|++|+|+++ .++.  .    ..+...++|++|++++|.++     .+-..+...++|+.|++.+|..-...   
T Consensus        14 ~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~~g~~~   93 (166)
T d1io0a_          14 NNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGILA   93 (166)
T ss_dssp             TTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHHH
T ss_pred             hcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccchhHHH
Confidence            46689999999984 5654  1    45678899999999999876     23345677899999999986432111   


Q ss_pred             ChHHhhCCCCCcEEEccCCCCccccccCCc-cchHHhhcCCCCCcEEEeecccc
Q 004895          660 APNVISKLSRLEELYMGDSFSQWDKVEGGS-NASLAELKGLSKLTTLEIDVRDA  712 (724)
Q Consensus       660 ~~~~i~~l~~L~~L~l~~~~~~~~~~~~~~-~~~l~~L~~L~~L~~L~l~~n~~  712 (724)
                      ....+...++|+.++++.+.   +.+.... ......+...++|++|+++++..
T Consensus        94 l~~~l~~~~~L~~l~L~l~~---n~i~~~~~~~La~~L~~n~~L~~L~l~~~~~  144 (166)
T d1io0a_          94 LVEALQSNTSLIELRIDNQS---QPLGNNVEMEIANMLEKNTTLLKFGYHFTQQ  144 (166)
T ss_dssp             HHHGGGGCSSCCEEECCCCS---SCCCHHHHHHHHHHHHHCSSCCEEECCCSSH
T ss_pred             HHHHHHhCccccEEeeccCC---CcCcHHHHHHHHHHHHhCCCcCEEeCcCCCC
Confidence            12346778899988886532   1121111 11233466788999999988764

>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=96.06  E-value=0.0016  Score=59.14  Aligned_cols=27  Identities=33%  Similarity=0.484  Sum_probs=24.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +..+||.|.|++|+||||+|+.+++.+
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            567899999999999999999998866

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.03  E-value=0.002  Score=58.31  Aligned_cols=27  Identities=22%  Similarity=0.332  Sum_probs=24.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+|.++|++|+||||+|+.+......
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            458889999999999999999998764

>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=96.01  E-value=0.002  Score=57.71  Aligned_cols=27  Identities=26%  Similarity=0.438  Sum_probs=24.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ++|+|.|+.|+||||+++.+.+.....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            689999999999999999999987653

>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=95.97  E-value=0.0019  Score=56.62  Aligned_cols=23  Identities=39%  Similarity=0.559  Sum_probs=21.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      |.|+||+|+||||+|+.+++...
T Consensus         3 I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            67889999999999999999884

>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=95.93  E-value=0.0024  Score=56.44  Aligned_cols=27  Identities=33%  Similarity=0.397  Sum_probs=23.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ++...|.|.|++|+||||+|+.+++..
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            345578999999999999999999865

>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=95.92  E-value=0.0022  Score=56.76  Aligned_cols=26  Identities=19%  Similarity=0.287  Sum_probs=23.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .++|.|.|++|+||||+|+.+++...
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~   28 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcC
Confidence            46899999999999999999988764

>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=95.90  E-value=0.0018  Score=57.08  Aligned_cols=23  Identities=30%  Similarity=0.510  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      |.++||+|+||||+++.+++...
T Consensus         4 IvliG~~G~GKSTig~~La~~l~   26 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALG   26 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHhC
Confidence            45669999999999999998875

>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=95.88  E-value=0.0032  Score=61.65  Aligned_cols=45  Identities=27%  Similarity=0.291  Sum_probs=34.3

Q ss_pred             ccchHHHHHHHHHHhc--------------CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          162 FNSRKKIFQDVIEALK--------------DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~--------------~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++|.++.++.+...+.              ....+.+.++||+|+|||.||+.+++...
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~   74 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLAN   74 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccc
Confidence            5688888877765441              11346777999999999999999998763

>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=95.81  E-value=0.012  Score=55.47  Aligned_cols=102  Identities=21%  Similarity=0.310  Sum_probs=63.2

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCC-ChHHHHHHHHHhh--CCC-------
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNP-DAQKIQGELASDL--GMN-------  239 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~l~~~i~~~l--~~~-------  239 (724)
                      +.++.+. -.+-+.++|.|..|+|||+|+..+.+.... .+=+.++++-+.+.. ...++.+++.+.-  ...       
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~~~-~~~~v~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~tv  135 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAK-AHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVA  135 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHHTT-TCSSEEEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCEE
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHHHh-hCCCeEEEEEeccChHHHHHHHHHHHhcCccccccccceEE
Confidence            3455554 233456999999999999999999987543 234567888887664 3556666666531  100       


Q ss_pred             -----CCCCchh----HHHHHHHHHHHh--cCCcEEEEEcccccc
Q 004895          240 -----FDSNDLI----YHRAKQLCQRLK--KEKRVLIILDNIWTK  273 (724)
Q Consensus       240 -----~~~~~~~----~~~~~~l~~~l~--~~kr~LlVlDdv~~~  273 (724)
                           .++....    ...+-.+.+++.  +++++|+++||+...
T Consensus       136 vv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~  180 (276)
T d2jdid3         136 LVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRF  180 (276)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHH
Confidence                 1111111    112234556665  378999999998543

>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=95.79  E-value=0.0027  Score=58.25  Aligned_cols=27  Identities=22%  Similarity=0.330  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +.+|.++|.+|+||||+|+++++....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            357899999999999999999987754

>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=95.78  E-value=0.0039  Score=59.61  Aligned_cols=27  Identities=26%  Similarity=0.283  Sum_probs=23.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..+.|.++|++|+||||||+.+++...
T Consensus        31 ~P~~ilL~GpPGtGKT~la~~la~~~~   57 (273)
T d1gvnb_          31 SPTAFLLGGQPGSGKTSLRSAIFEETQ   57 (273)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHHHTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            456788999999999999999998774

>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=95.75  E-value=0.0024  Score=56.52  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.++|++|+||||+|+.+++...
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg   27 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALG   27 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhC
Confidence            466889999999999999998875

>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=95.71  E-value=0.0031  Score=56.01  Aligned_cols=25  Identities=48%  Similarity=0.616  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      -|+|+|+.|+|||||++.+......
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            3789999999999999999998764

>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=0.0032  Score=55.70  Aligned_cols=25  Identities=20%  Similarity=0.428  Sum_probs=21.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      +...+|.++|++|+||||+|+....
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999997754

>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=95.60  E-value=0.0034  Score=58.07  Aligned_cols=42  Identities=31%  Similarity=0.350  Sum_probs=32.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      .+||+|.||+|+||||+|+.+++++.-.         ++    +..+++++++..
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~~~gl~---------~i----StGdLlR~~a~~   44 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAEALQWH---------LL----DSGAIYRVLALA   44 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHTCE---------EE----EHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCc---------EE----CHHHHHHHHHHH
Confidence            4699999999999999999999988531         22    345777776643

>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=95.55  E-value=0.0027  Score=56.20  Aligned_cols=25  Identities=32%  Similarity=0.454  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-++|.|.|++|+||||+|+.+.+.
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~   27 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANL   27 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999999998654

>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=95.53  E-value=0.0038  Score=56.38  Aligned_cols=24  Identities=29%  Similarity=0.342  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+|.|.|++|+||||.|+.+++..
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            589999999999999999999876

>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=95.46  E-value=0.017  Score=54.71  Aligned_cols=100  Identities=21%  Similarity=0.201  Sum_probs=56.6

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCC-----CCCCc
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMN-----FDSND  244 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~-----~~~~~  244 (724)
                      ++++.+. -.+-+.++|.|..|+|||+|+..+.+..... +-++++.+.+-+.. .++ ..++.+.....     .+++.
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~~-~~~~v~~~~~iger-~~e-v~~~~~~~~~~vv~~t~d~~~  108 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN-HPDCVLMVLLIDER-PEE-VTEMQRLVKGEVVASTFDEPA  108 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHHH-CTTSEEEEEEEEEC-HHH-HHHHHHHCSSEEEEEETTSCH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhhc-CCCeEEEEEeecee-HHH-HHhHHhhcceEEEeccCCCch
Confidence            4666665 2445689999999999999999999987653 34555544333221 112 22333332211     11111


Q ss_pred             hh----HHHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          245 LI----YHRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       245 ~~----~~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ..    ...+-.+.+++. +++.+|+++||+-..
T Consensus       109 ~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsltr~  142 (289)
T d1xpua3         109 SRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRL  142 (289)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTCEEEEEESCHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhccCceeecCcHHHH
Confidence            11    112233444443 478999999999543

>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=95.46  E-value=0.0085  Score=57.52  Aligned_cols=52  Identities=23%  Similarity=0.397  Sum_probs=39.5

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          169 FQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       169 ~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      +..+.+.+.....+||.+.|-||+||||+|..++.....++  ..++-|+....
T Consensus         8 ~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~G--~rVllvD~Dp~   59 (279)
T d1ihua2           8 LSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADMG--FDVHLTTSDPA   59 (279)
T ss_dssp             HHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESCCC
T ss_pred             HHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--CcEEEEeCCCC
Confidence            44566666678889999999999999999999988876543  23666665533

>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=95.42  E-value=0.0087  Score=54.58  Aligned_cols=30  Identities=23%  Similarity=0.403  Sum_probs=26.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ..+..+|.+.|++|+||||+|+.+......
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~~   50 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLVR   50 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            566779999999999999999999987643

>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=95.39  E-value=0.0048  Score=55.31  Aligned_cols=26  Identities=31%  Similarity=0.468  Sum_probs=23.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ++|.|.|+.|+||||+++.+......
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            57899999999999999999998865

>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=95.20  E-value=0.026  Score=54.49  Aligned_cols=71  Identities=14%  Similarity=0.329  Sum_probs=43.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhhCCCCCCCchhHHHHHHHHHHHhcCC
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDLGMNFDSNDLIYHRAKQLCQRLKKEK  261 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l~~~~~~~~~~~~~~~~l~~~l~~~k  261 (724)
                      .++.++|++|+|||.||+.++.....+..|   +-+..++-.+              .....  .+.....+++..++  
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~~~~~~---~~~~~~~~~~--------------~~~G~--~e~~~~~~f~~a~~--  182 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALGGKDKY---ATVRFGEPLS--------------GYNTD--FNVFVDDIARAMLQ--  182 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHHTTSCC---EEEEBSCSST--------------TCBCC--HHHHHHHHHHHHHH--
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhcCCCCe---EEEEhhHhhh--------------cccch--HHHHHHHHHHHHhh--
Confidence            456678999999999999999987533223   1233333221              11111  23344555555543  


Q ss_pred             cEEEEEcccccc
Q 004895          262 RVLIILDNIWTK  273 (724)
Q Consensus       262 r~LlVlDdv~~~  273 (724)
                      +++|++|.++..
T Consensus       183 ~~ilf~DEid~~  194 (321)
T d1w44a_         183 HRVIVIDSLKNV  194 (321)
T ss_dssp             CSEEEEECCTTT
T ss_pred             ccEEEeehhhhh
Confidence            579999999654

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.20  E-value=0.024  Score=52.84  Aligned_cols=49  Identities=14%  Similarity=0.067  Sum_probs=34.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccC----CCeEEEEEEecCCChHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNV----FDKVVMAEITKNPDAQKI  228 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~l  228 (724)
                      .-+++.|+|++|+||||||.+++........    -..++|++....++....
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   85 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRL   85 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGGGG
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHHHH
Confidence            4569999999999999999998765432211    245788887776664433

>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=95.17  E-value=0.014  Score=56.88  Aligned_cols=57  Identities=19%  Similarity=0.339  Sum_probs=38.6

Q ss_pred             HHHHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC
Q 004895          168 IFQDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD  224 (724)
Q Consensus       168 ~~~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  224 (724)
                      ....+++.+.  .++..+|+|.|++|+|||||...+........+=-.++=++.+..++
T Consensus        36 ~~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~~   94 (323)
T d2qm8a1          36 AVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRT   94 (323)
T ss_dssp             HHHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGSS
T ss_pred             HHHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHHH
Confidence            3445555543  46778999999999999999999998776533222345555554443

>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=95.15  E-value=0.015  Score=56.83  Aligned_cols=62  Identities=18%  Similarity=0.339  Sum_probs=35.0

Q ss_pred             HHHHHHhc--CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHH
Q 004895          170 QDVIEALK--DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGE  231 (724)
Q Consensus       170 ~~l~~~L~--~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~  231 (724)
                      .++++.+.  .++..+|+|+|++|+|||||...+......+.+=-.++=++.+..++-..++.+
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgd  104 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGD  104 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-----------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccc
Confidence            34444443  456889999999999999999999988876432112333443444444444443

>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=95.12  E-value=0.0057  Score=54.97  Aligned_cols=26  Identities=19%  Similarity=0.149  Sum_probs=22.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +..|.|.|++|+||||+|+.+++...
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~   28 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQ   28 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHC
Confidence            34578999999999999999988774

>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=95.11  E-value=0.0054  Score=56.30  Aligned_cols=27  Identities=26%  Similarity=0.405  Sum_probs=23.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +-||+|.|..|+||||+|+.+.+....
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            348999999999999999999988754

>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=95.03  E-value=0.0064  Score=56.17  Aligned_cols=40  Identities=25%  Similarity=0.198  Sum_probs=30.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASD  235 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~  235 (724)
                      +|+|-|++|+||||+|+.++..+.-.       ++      +..++++.++..
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~lg~~-------~i------stGdl~R~~a~~   44 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDFGFT-------YL------DTGAMYRAATYM   44 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHHCCE-------EE------EHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCc-------EE------CHHHHHHHHHHH
Confidence            68899999999999999999988531       22      345777776644

>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=95.02  E-value=0.0064  Score=54.89  Aligned_cols=26  Identities=38%  Similarity=0.431  Sum_probs=23.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +.++|.|.|++|+||||+|+.+++..
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            45799999999999999999998865

>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=94.97  E-value=0.0066  Score=54.00  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .|.|.|++|+||||+|+.+++..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37799999999999999998876

>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=94.76  E-value=0.0088  Score=53.27  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|.|++|+||||+|+.+++...
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g   25 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYG   25 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            477999999999999999998873

>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=94.73  E-value=0.009  Score=53.61  Aligned_cols=26  Identities=31%  Similarity=0.460  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +.-.|.|.|++|+||||+|+.+++.+
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHH
Confidence            34467788999999999999999865

>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=94.67  E-value=0.0087  Score=53.21  Aligned_cols=24  Identities=25%  Similarity=0.301  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|.|++|+||||+|+.+++...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g   25 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLG   25 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHC
Confidence            477899999999999999998873

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=94.56  E-value=0.009  Score=59.07  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=34.3

Q ss_pred             ccccccchHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          158 DYNIFNSRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       158 ~~~~~~gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      +...++|.+..+..|.-.....+..-+.++|.+|+||||||+.+..-
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~i   51 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAAL   51 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHh
Confidence            45677899887776553333223345789999999999999999864

>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=94.56  E-value=0.01  Score=52.84  Aligned_cols=25  Identities=24%  Similarity=0.514  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ++|.|+|+.|+|||||++.+.++..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4788999999999999999987653

>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=94.44  E-value=0.012  Score=56.21  Aligned_cols=38  Identities=16%  Similarity=0.336  Sum_probs=30.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEec
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITK  221 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~  221 (724)
                      +.|+|+|-||+||||+|..++...... .+ .++-|++..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~-G~-rVllID~D~   39 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAM-GK-TIMVVGCDP   39 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTT-TC-CEEEEEECT
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhC-CC-cEEEEecCC
Confidence            679999999999999999999998754 23 466676653

>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=94.38  E-value=0.028  Score=54.07  Aligned_cols=47  Identities=21%  Similarity=0.339  Sum_probs=35.4

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChH
Q 004895          178 DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       178 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  226 (724)
                      ++..++|.+.|-||+||||+|..++.....++  ..+.-|+.....++.
T Consensus         5 ~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G--~rVLlvD~Dp~~~l~   51 (296)
T d1ihua1           5 QNIPPYLFFTGKGGVGKTSISCATAIRLAEQG--KRVLLVSTDPASNVG   51 (296)
T ss_dssp             SSCCSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEECCTTCCHH
T ss_pred             CCCCeEEEEECCCcChHHHHHHHHHHHHHHCC--CCEEEEeCCCCCCHH
Confidence            45678999999999999999999999887643  236677765444443

>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=94.37  E-value=0.011  Score=52.43  Aligned_cols=24  Identities=21%  Similarity=0.289  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|.|++|+||||+|+.+++...
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~g   27 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERFH   27 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            355779999999999999998763

>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=94.37  E-value=0.01  Score=53.28  Aligned_cols=23  Identities=30%  Similarity=0.546  Sum_probs=20.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      |.|+|+.|+|||||++.+.+...
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHhCC
Confidence            67999999999999999988764

>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=94.36  E-value=0.079  Score=50.79  Aligned_cols=27  Identities=26%  Similarity=0.332  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..-+|+|.|..|+||||+|+.+.....
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHh
Confidence            456999999999999999999998875

>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=94.36  E-value=0.069  Score=50.54  Aligned_cols=79  Identities=18%  Similarity=0.034  Sum_probs=45.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCC-eEEEEEEecCCChHHHHHHHHHhhCCC------CCCCchhHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFD-KVVMAEITKNPDAQKIQGELASDLGMN------FDSNDLIYHRAKQL  253 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~l~~~i~~~l~~~------~~~~~~~~~~~~~l  253 (724)
                      .-+|+|.|..|+||||||..+......+..+. .++-++..+-+-..+-...+.+.....      ..+.+.+.......
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~~~~~pl~~~RG~PgThD~~ll~~~  106 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQFKNNKLLQGRGLPGTHDMKLLQEV  106 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHHTTTCGGGSSSCSTTSBCHHHHHHH
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCCCCHHHHHHHhhhccccccceecCCCcchhHHHHHHH
Confidence            44899999999999999999988765532222 355555544332222234444443211      11222245566666


Q ss_pred             HHHHhc
Q 004895          254 CQRLKK  259 (724)
Q Consensus       254 ~~~l~~  259 (724)
                      ...|.+
T Consensus       107 l~~l~~  112 (286)
T d1odfa_         107 LNTIFN  112 (286)
T ss_dssp             HHHHTC
T ss_pred             HHHHHh
Confidence            666654

>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=94.25  E-value=0.015  Score=51.98  Aligned_cols=25  Identities=28%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +.++| |+|++|+||||+|+.+++..
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            34555 78999999999999999876

>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=94.24  E-value=0.012  Score=52.09  Aligned_cols=24  Identities=25%  Similarity=0.120  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .|.|.|++|+||||.|+.+++...
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~   25 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYG   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            367899999999999999998763

>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=94.17  E-value=0.028  Score=51.06  Aligned_cols=27  Identities=19%  Similarity=0.363  Sum_probs=24.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ..|+|.|+.|+||||+++.+.+....+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~~L~~~   30 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVEALCAA   30 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            578899999999999999999988764

>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=94.12  E-value=0.013  Score=52.36  Aligned_cols=24  Identities=33%  Similarity=0.488  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -|.|+|+.|+|||||++.+.++..
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCC
Confidence            478999999999999999988764

>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=93.86  E-value=0.017  Score=51.03  Aligned_cols=25  Identities=16%  Similarity=0.327  Sum_probs=22.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +.|.|+||.|+|||||++.+..+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCC
Confidence            5789999999999999999987654

>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=93.71  E-value=0.021  Score=53.25  Aligned_cols=25  Identities=32%  Similarity=0.539  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ||+|+|+.|+|||||...+.+....
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~   26 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLED   26 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh
Confidence            7899999999999999999876643

>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=93.65  E-value=0.018  Score=51.62  Aligned_cols=22  Identities=36%  Similarity=0.508  Sum_probs=19.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIA  202 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~  202 (724)
                      +-+|+|+|+.|+||||+|..+-
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4589999999999999999773

>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=93.45  E-value=0.14  Score=46.96  Aligned_cols=40  Identities=20%  Similarity=0.092  Sum_probs=27.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      .-.++.|.|.+|+|||+||.+++....... -..++|++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~-~~~~~~~s~e   64 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEF-DEPGVFVTFE   64 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH-CCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCccccccc
Confidence            456899999999999999987655433221 2236666554

>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=93.40  E-value=0.024  Score=54.57  Aligned_cols=40  Identities=23%  Similarity=0.384  Sum_probs=30.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKN  222 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  222 (724)
                      .+.|+|.|-||+||||+|..++...... .. .++-|++...
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~~LA~~-G~-rVLlID~DpQ   41 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVAALAEM-GK-KVMIVGCDPK   41 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHHHT-TC-CEEEEEECSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHHHHC-CC-CEEEEecCCC
Confidence            3578899999999999999999888653 22 3777777543

>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=93.30  E-value=0.059  Score=50.25  Aligned_cols=48  Identities=23%  Similarity=0.243  Sum_probs=35.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc----cCCCeEEEEEEecCCChHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED----NVFDKVVMAEITKNPDAQK  227 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~~  227 (724)
                      .-+++.|+|++|+||||||.+++......    .....++|+......+...
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPER   86 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHH
Confidence            34699999999999999999998875422    1234578887776666543

>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=93.16  E-value=0.016  Score=54.96  Aligned_cols=28  Identities=29%  Similarity=0.412  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +.+||+|.|..|+||||+|+.+.+....
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~i~~~   30 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQIFRR   30 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            5679999999999999999999887764

>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=93.15  E-value=0.026  Score=51.06  Aligned_cols=25  Identities=24%  Similarity=0.386  Sum_probs=22.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+|.|+||+|+|||||.+.+.....
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4788999999999999999988753

>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=93.08  E-value=0.037  Score=50.06  Aligned_cols=26  Identities=31%  Similarity=0.581  Sum_probs=23.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      .|+|-|+-|+||||+++.+.+....+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            58899999999999999999988654

>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=93.01  E-value=0.08  Score=47.88  Aligned_cols=35  Identities=23%  Similarity=0.326  Sum_probs=27.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      +.|+|-|+.|+||||+++.+.+..... .+..+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~-g~~~~~~~   37 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQL-GIRDMVFT   37 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhC-CCCeEEEe
Confidence            468899999999999999999988653 34444443

>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=92.98  E-value=0.017  Score=51.94  Aligned_cols=27  Identities=26%  Similarity=0.239  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+.-+|+|-|..|+||||+|+.+.+..
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGGT
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            345589999999999999999986544

>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=92.85  E-value=0.027  Score=51.98  Aligned_cols=26  Identities=31%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|+|||||++.++--.
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34599999999999999999987543

>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=92.82  E-value=0.029  Score=48.06  Aligned_cols=22  Identities=27%  Similarity=0.418  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|.+|+|||||...+..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            6799999999999999987764

>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=92.74  E-value=0.05  Score=53.84  Aligned_cols=26  Identities=31%  Similarity=0.410  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ....+..+||.|+|||.||+.++...
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcceeeeCCCCccHHHHHHHHHhhc
Confidence            34568889999999999999998764

>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=92.73  E-value=0.02  Score=51.55  Aligned_cols=27  Identities=41%  Similarity=0.618  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +-.+++|+|+.|+|||||.+.++.-.+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcccc
Confidence            345899999999999999999976543

>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=92.68  E-value=0.23  Score=46.78  Aligned_cols=52  Identities=27%  Similarity=0.228  Sum_probs=36.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCChHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPDAQKIQGELASDL  236 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~l~~~i~~~l  236 (724)
                      .++.|.|.+|+||||++.+++.+......+ .+++++.  ..+..++...++...
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~--E~~~~~~~~r~~~~~   87 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAML--EESVEETAEDLIGLH   87 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEES--SSCHHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeee--ccchhhHHhHHHHHh
Confidence            488899999999999999998776443222 3555544  345666666666544

>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=92.64  E-value=0.069  Score=52.74  Aligned_cols=29  Identities=24%  Similarity=0.061  Sum_probs=25.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +..+.+.++||+|+|||++|..+++....
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~~~  180 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELCGG  180 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            45578999999999999999999998753

>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=92.63  E-value=0.029  Score=51.39  Aligned_cols=35  Identities=20%  Similarity=0.260  Sum_probs=25.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEE
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMA  217 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv  217 (724)
                      +-.+++|+|+.|+|||||++.+.--...   -.+.+++
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl~~p---~sG~I~~   64 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCLDKP---TEGEVYI   64 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSCC---SEEEEEE
T ss_pred             CCCEEEEECCCCCCcchhhHhccCCCCC---CcceeEE
Confidence            4459999999999999999987654322   2345555

>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=92.59  E-value=0.035  Score=50.88  Aligned_cols=26  Identities=31%  Similarity=0.423  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|+|||||.+.++--.
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            44599999999999999999886644

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=92.52  E-value=0.11  Score=48.83  Aligned_cols=91  Identities=15%  Similarity=0.142  Sum_probs=51.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEecCCC-hHHHHHHHHHh--hCC------CCCCCch----hH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEITKNPD-AQKIQGELASD--LGM------NFDSNDL----IY  247 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~l~~~i~~~--l~~------~~~~~~~----~~  247 (724)
                      -..++|+|..|+|||+|+........  .+-+.++++-+.+... ..++..++.+.  +..      ..++...    ..
T Consensus        67 GQr~~Ifg~~g~GKt~l~~~~~~~~~--~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~  144 (276)
T d1fx0a3          67 GQRELIIGDRQTGKTAVATDTILNQQ--GQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAP  144 (276)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHTCC--TTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHH
T ss_pred             CceEeeccCCCCChHHHHHHHHhhhc--ccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHH
Confidence            34578999999999999988655433  2345667777766532 23333333322  100      0111110    11


Q ss_pred             HHHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          248 HRAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       248 ~~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                      ..+-.+.+++. +++++|+++||+-..
T Consensus       145 ~~a~tiAEyfrd~G~~Vlll~Dsltr~  171 (276)
T d1fx0a3         145 YTGAALAEYFMYRERHTLIIYDDLSKQ  171 (276)
T ss_dssp             HHHHHHHHHHHHTTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHcCCceeEEeeccHHH
Confidence            22333444443 378999999998543

>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=92.39  E-value=0.038  Score=51.35  Aligned_cols=27  Identities=30%  Similarity=0.316  Sum_probs=23.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +++.|+|-|+-|+||||+++.+.+...
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~l~   27 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHh
Confidence            357899999999999999999998764

>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=92.39  E-value=0.064  Score=49.28  Aligned_cols=37  Identities=27%  Similarity=0.421  Sum_probs=30.3

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          182 NIIGVC-GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       182 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      +||+|+ |-||+||||+|..++......  -..++.|++.
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~la~~--g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVALAQL--GHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHHHHHT--TCCEEEEECC
T ss_pred             EEEEEECCCCCChHHHHHHHHHHHHHhC--CCCEEEEeCC
Confidence            688887 899999999999999988753  2358888775

>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=92.37  E-value=0.033  Score=51.63  Aligned_cols=26  Identities=38%  Similarity=0.615  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-..++|+|+.|.|||||++.+..-.
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            34589999999999999999997654

>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=92.32  E-value=0.04  Score=50.72  Aligned_cols=26  Identities=31%  Similarity=0.358  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|.|||||.+.+.--.
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            44589999999999999999887644

>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=92.30  E-value=0.033  Score=51.38  Aligned_cols=26  Identities=35%  Similarity=0.507  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|+|||||++.++--.
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            34699999999999999999986644

>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=92.18  E-value=0.037  Score=50.88  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .+++|+|+.|+|||||++.++--.+
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEECCCCChHHHHHHHHHcCCC
Confidence            4888999999999999999987543

>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=92.12  E-value=0.039  Score=51.55  Aligned_cols=26  Identities=23%  Similarity=0.392  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+..-.
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            44689999999999999999996544

>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=92.11  E-value=0.065  Score=49.89  Aligned_cols=43  Identities=21%  Similarity=0.365  Sum_probs=32.1

Q ss_pred             ccchHHHHHHHHHHhc---CCCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          162 FNSRKKIFQDVIEALK---DDKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       162 ~~gR~~~~~~l~~~L~---~~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |||....++++.+.+.   ..+.+ |.|.|..|+|||++|+.+.+.-
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~~p-vlI~Ge~GtGK~~~A~~ih~~s   47 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAECP-VLITGESGVGKEVVARLIHKLS   47 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCCSC-EEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEecCHHHHHHHHHHHHHhCCCCC-EEEECCCCcCHHHHHHHHHHhc
Confidence            6777777777766654   33444 5788999999999999997643

>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=92.06  E-value=0.24  Score=45.49  Aligned_cols=56  Identities=18%  Similarity=0.217  Sum_probs=37.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhccC--------------CCeEEEEEEecCCChHHHHHHHHHhhC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMEDNV--------------FDKVVMAEITKNPDAQKIQGELASDLG  237 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--------------F~~~~wv~vs~~~~~~~l~~~i~~~l~  237 (724)
                      -.++.|.|.+|+|||++|.+++........              ...++|++.....+. .....+...+.
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~e~~~~~-~~~~~~~~~~~  103 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRP-ERIMQMAEHAG  103 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCH-HHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEEecCCcCH-HHHHHHHhhcc
Confidence            469999999999999999999987643211              123678876555543 33344444443

>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=92.01  E-value=0.044  Score=48.97  Aligned_cols=25  Identities=24%  Similarity=0.494  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      ++.+.|+|+|.+|+|||||...+.+
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcC
Confidence            4567899999999999999999975

>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=91.99  E-value=0.033  Score=52.16  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-.+++|+|+.|+|||||++.+.--
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            4469999999999999999998643

>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=91.96  E-value=0.088  Score=47.81  Aligned_cols=28  Identities=25%  Similarity=0.332  Sum_probs=24.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +-..|+|-|+-|+||||+++.+.+....
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L~~   29 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKLQP   29 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHTTT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            3468999999999999999999988754

>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=91.95  E-value=0.032  Score=50.99  Aligned_cols=26  Identities=27%  Similarity=0.259  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|+|||||++.+.--.
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            44599999999999999999997644

>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=91.93  E-value=0.044  Score=51.11  Aligned_cols=27  Identities=19%  Similarity=0.310  Sum_probs=22.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      ..-.+++|+|+.|+|||||++.+..-.
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            345699999999999999999987644

>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=91.90  E-value=0.042  Score=47.44  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|+|+|.+|+|||||.+.+..+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37899999999999999987653

>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=91.86  E-value=0.044  Score=50.77  Aligned_cols=26  Identities=27%  Similarity=0.402  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-..++|+|+.|+|||||++.+..-.
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            45689999999999999999997644

>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=91.80  E-value=0.047  Score=51.89  Aligned_cols=27  Identities=30%  Similarity=0.465  Sum_probs=23.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      +-.+++|+|+.|+|||||++.+.-...
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            456899999999999999999986553

>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=91.72  E-value=0.12  Score=48.03  Aligned_cols=47  Identities=15%  Similarity=0.138  Sum_probs=34.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh----ccCCCeEEEEEEecCCChH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME----DNVFDKVVMAEITKNPDAQ  226 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~----~~~F~~~~wv~vs~~~~~~  226 (724)
                      .-+++.|+|++|+|||++|.+++.....    ...+..+.|+.....+...
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPD   86 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHH
Confidence            4469999999999999999999886532    1234567888776665543

>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=91.65  E-value=0.039  Score=50.23  Aligned_cols=27  Identities=22%  Similarity=0.171  Sum_probs=23.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      -+++.|.|++|+|||+||.+++.....
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~~~~   49 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVTCQL   49 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTS
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            469999999999999999999887543

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.60  E-value=0.14  Score=48.19  Aligned_cols=103  Identities=14%  Similarity=0.129  Sum_probs=54.9

Q ss_pred             HHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHhhcc-CC----C-eEEEEEEecCCC-hHHHHHHHHHhhCC----
Q 004895          171 DVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVMEDN-VF----D-KVVMAEITKNPD-AQKIQGELASDLGM----  238 (724)
Q Consensus       171 ~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F----~-~~~wv~vs~~~~-~~~l~~~i~~~l~~----  238 (724)
                      +.++.+. =.+-+.++|.|.+|+|||+|+..+........ .-    . .++++-+.+... ..++...+...-..    
T Consensus        57 raID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tv  136 (285)
T d2jdia3          57 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTI  136 (285)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEE
T ss_pred             eEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceE
Confidence            3455554 23345688999999999999988877643211 11    1 245555555432 34444444432111    


Q ss_pred             ----CCCCCchhHH----HHHHHHHHHh-cCCcEEEEEcccccc
Q 004895          239 ----NFDSNDLIYH----RAKQLCQRLK-KEKRVLIILDNIWTK  273 (724)
Q Consensus       239 ----~~~~~~~~~~----~~~~l~~~l~-~~kr~LlVlDdv~~~  273 (724)
                          ..++......    .+-.+.+++. +++++|+++||+-..
T Consensus       137 vv~~ts~~~~~~r~~~~~~a~tiAEyfrd~G~~VLll~Dsltr~  180 (285)
T d2jdia3         137 VVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQ  180 (285)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcChHHH
Confidence                1122211111    1122334443 479999999998543

>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=91.48  E-value=0.05  Score=47.04  Aligned_cols=21  Identities=33%  Similarity=0.654  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>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=91.40  E-value=0.051  Score=46.98  Aligned_cols=22  Identities=36%  Similarity=0.348  Sum_probs=19.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||||+..+.+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999998753

>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=91.40  E-value=0.13  Score=43.62  Aligned_cols=29  Identities=28%  Similarity=0.345  Sum_probs=25.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhhc
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~  208 (724)
                      ...+|.+.|.=|+||||+++.+++.....
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            44589999999999999999999987653

>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=91.34  E-value=0.052  Score=47.42  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999998765

>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=91.27  E-value=0.056  Score=48.94  Aligned_cols=19  Identities=32%  Similarity=0.534  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQI  201 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v  201 (724)
                      +|+|+|+.|+||||+|+.+
T Consensus         5 iIgitG~igSGKStv~~~l   23 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAF   23 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHH
Confidence            8999999999999999865

>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=91.23  E-value=0.071  Score=46.74  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=20.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .+..-|.|+|.+|+|||||...+..
T Consensus        11 ~k~~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          11 KKTGKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhC
Confidence            3445678999999999999988754

>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=91.23  E-value=0.055  Score=46.88  Aligned_cols=23  Identities=30%  Similarity=0.397  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|+..+.++.
T Consensus         6 KivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37799999999999999988753

>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=91.19  E-value=0.028  Score=52.16  Aligned_cols=25  Identities=24%  Similarity=0.360  Sum_probs=22.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+.|+|-|+.|+||||+|+.+.+..
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            4689999999999999999987755

>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=90.99  E-value=0.054  Score=49.62  Aligned_cols=25  Identities=32%  Similarity=0.555  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .++|..|.|+-|.|||||.+++.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            5789999999999999999888763

>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=90.84  E-value=0.047  Score=50.31  Aligned_cols=26  Identities=35%  Similarity=0.455  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|+|||||++.+.--.
T Consensus        30 ~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          30 NGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            34699999999999999999997643

>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=90.77  E-value=0.054  Score=50.00  Aligned_cols=26  Identities=35%  Similarity=0.566  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .-.+++|+|+.|.|||||.+.+.--.
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            44699999999999999999887654

>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=90.77  E-value=0.06  Score=48.58  Aligned_cols=20  Identities=40%  Similarity=0.596  Sum_probs=18.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQI  201 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v  201 (724)
                      -+|+|+|..|+||||+|+.+
T Consensus         3 ~iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            47999999999999999866

>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=90.71  E-value=0.058  Score=46.57  Aligned_cols=21  Identities=29%  Similarity=0.474  Sum_probs=18.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|.|+|.+|+|||||...+..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~   24 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNG   24 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            367999999999999998754

>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=90.70  E-value=0.066  Score=46.53  Aligned_cols=21  Identities=33%  Similarity=0.463  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||...+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999988765

>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=90.69  E-value=0.062  Score=49.65  Aligned_cols=26  Identities=38%  Similarity=0.526  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-.+++|+|+.|.|||||.+.+.--.
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34599999999999999999987654

>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=90.67  E-value=0.064  Score=46.69  Aligned_cols=23  Identities=39%  Similarity=0.602  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||||.+.+.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37799999999999999988743

>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=90.67  E-value=0.065  Score=46.24  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|.+|+|||+|++.+.+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999988653

>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=90.66  E-value=0.12  Score=52.43  Aligned_cols=26  Identities=35%  Similarity=0.452  Sum_probs=22.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +-|.++||.|+|||.||+.++....+
T Consensus        50 sNILliGPTGvGKTlLAr~LAk~l~V   75 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIARRLAKLANA   75 (443)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTC
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHhCC
Confidence            46889999999999999999987643

>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=90.58  E-value=0.068  Score=46.30  Aligned_cols=22  Identities=36%  Similarity=0.499  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|.|+|.+|+|||+|+..+...
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999998764

>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=90.56  E-value=0.098  Score=45.54  Aligned_cols=34  Identities=18%  Similarity=0.341  Sum_probs=24.5

Q ss_pred             HHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          170 QDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       170 ~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ..+..++..... -|.|+|.+|+|||||..++...
T Consensus         5 ~~~~~~~~~k~~-kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           5 TRIWRLFNHQEH-KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHHTTSCE-EEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHHhCCCeE-EEEEECCCCCCHHHHHHHHhcC
Confidence            345555444444 5679999999999999987654

>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=90.54  E-value=0.073  Score=47.92  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      +.|+|+|.+|+|||||...+.+.
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            57899999999999999999764

>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=90.52  E-value=0.069  Score=46.40  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||||+..+.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            36899999999999999988654

>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=90.52  E-value=0.069  Score=46.25  Aligned_cols=22  Identities=23%  Similarity=0.475  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|.+|+|||||...+.++.
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999998754

>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=90.49  E-value=0.09  Score=48.34  Aligned_cols=37  Identities=30%  Similarity=0.504  Sum_probs=29.7

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHHHHHhhccCCCeEEEEEEe
Q 004895          182 NIIGVC-GMGGVGKTTLVKQIAKQVMEDNVFDKVVMAEIT  220 (724)
Q Consensus       182 ~vi~I~-G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~vs  220 (724)
                      +||+|+ +-||+||||+|..++......+  ..++-++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g--~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRG--RKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTT--CCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCC--CCEEEEeCC
Confidence            589998 7899999999999999887532  347777764

>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=90.47  E-value=0.07  Score=46.18  Aligned_cols=23  Identities=39%  Similarity=0.559  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|+.++.++.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~~   27 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            37799999999999999998753

>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=90.42  E-value=0.071  Score=46.24  Aligned_cols=22  Identities=32%  Similarity=0.599  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||+|...+.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5789999999999999998754

>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=90.38  E-value=0.061  Score=46.82  Aligned_cols=21  Identities=48%  Similarity=0.819  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||||...+..+
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999988764

>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=90.33  E-value=0.061  Score=50.25  Aligned_cols=27  Identities=30%  Similarity=0.406  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      .-.+++|+|+.|.|||||++.+.--.+
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCCc
Confidence            345899999999999999999976543

>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=90.25  E-value=0.073  Score=46.45  Aligned_cols=23  Identities=39%  Similarity=0.548  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|+..+.+..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47799999999999999987643

>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=90.20  E-value=0.076  Score=46.33  Aligned_cols=22  Identities=32%  Similarity=0.526  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999998764

>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=90.18  E-value=0.078  Score=46.07  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .|+|+|.+|+|||||...+...
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            5899999999999999998743

>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=90.18  E-value=0.075  Score=45.92  Aligned_cols=21  Identities=33%  Similarity=0.539  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998764

>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=90.06  E-value=0.067  Score=46.43  Aligned_cols=21  Identities=29%  Similarity=0.461  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||+|++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            679999999999999988654

>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=90.05  E-value=0.081  Score=45.19  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|+++|.+|+|||||+..+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999987763

>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=90.00  E-value=0.078  Score=46.09  Aligned_cols=23  Identities=39%  Similarity=0.544  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|...+..+.
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37799999999999999987753

>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=89.96  E-value=0.08  Score=46.17  Aligned_cols=21  Identities=33%  Similarity=0.528  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||+..+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>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=89.95  E-value=0.08  Score=45.78  Aligned_cols=23  Identities=30%  Similarity=0.468  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-|.|+|..|+|||||...+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45789999999999999998764

>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=89.95  E-value=0.083  Score=46.15  Aligned_cols=22  Identities=27%  Similarity=0.555  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|.|+|..|+|||||+..+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998764

>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=89.88  E-value=0.085  Score=45.64  Aligned_cols=22  Identities=41%  Similarity=0.679  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||+|+..+....
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6799999999999999987754

>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=89.82  E-value=0.079  Score=46.77  Aligned_cols=21  Identities=33%  Similarity=0.479  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||||+..+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            679999999999999988653

>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=89.73  E-value=0.086  Score=45.55  Aligned_cols=22  Identities=41%  Similarity=0.668  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||||+..+.+..
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7899999999999999988753

>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=89.63  E-value=0.078  Score=46.27  Aligned_cols=21  Identities=48%  Similarity=0.624  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|.++|.+|+|||||...+..
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999998754

>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=89.59  E-value=0.067  Score=49.18  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      .-.+++|+|+.|.|||||.+.+.-
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            345999999999999999988865

>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=89.51  E-value=0.09  Score=45.97  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|+..+.+..
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            46789999999999999887653

>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=89.51  E-value=0.094  Score=45.49  Aligned_cols=22  Identities=32%  Similarity=0.468  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|.|+|.+|+|||+|+.++.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988764

>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=89.49  E-value=0.094  Score=45.45  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|..|+|||+|+..+.+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999988754

>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=89.40  E-value=0.095  Score=46.39  Aligned_cols=22  Identities=36%  Similarity=0.477  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|-+|+|||+|.+++..+.
T Consensus         5 ivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            6799999999999999876554

>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=89.37  E-value=0.084  Score=46.13  Aligned_cols=24  Identities=33%  Similarity=0.552  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      +..|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            567899999999999999999864

>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=89.36  E-value=0.093  Score=46.74  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.|+|.+|+|||||+..+.+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHhhCC
Confidence            7799999999999999988653

>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=89.35  E-value=0.063  Score=50.04  Aligned_cols=25  Identities=36%  Similarity=0.559  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-..++|+|+.|+|||||++.+..-
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhc
Confidence            4468999999999999999988653

>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=89.31  E-value=0.11  Score=48.15  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .+|+|+|..|+||||+|+.+.+..
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC
Confidence            589999999999999999987643

>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=89.22  E-value=0.11  Score=46.78  Aligned_cols=24  Identities=21%  Similarity=0.264  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      +-|+|+|.+|+|||||..++....
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            358999999999999999998753

>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=89.21  E-value=0.1  Score=44.91  Aligned_cols=21  Identities=38%  Similarity=0.507  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||..++...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            668999999999999988654

>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=89.18  E-value=0.1  Score=45.93  Aligned_cols=22  Identities=36%  Similarity=0.416  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|.|+|.+|+|||+|..++..+
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998764

>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=88.97  E-value=0.11  Score=45.83  Aligned_cols=21  Identities=38%  Similarity=0.616  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>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=88.88  E-value=0.11  Score=45.36  Aligned_cols=24  Identities=25%  Similarity=0.466  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ...|+|+|.+|+|||||...+...
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999998864

>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=88.79  E-value=0.11  Score=45.88  Aligned_cols=23  Identities=39%  Similarity=0.449  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||+|...+.++.
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            37899999999999999987653

>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=88.74  E-value=0.11  Score=45.13  Aligned_cols=21  Identities=33%  Similarity=0.635  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||||+..+.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999988764

>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=88.62  E-value=0.082  Score=46.38  Aligned_cols=20  Identities=25%  Similarity=0.677  Sum_probs=18.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~  203 (724)
                      |+|+|.+|+|||||...+..
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999998864

>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=88.62  E-value=0.11  Score=45.16  Aligned_cols=21  Identities=38%  Similarity=0.490  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|.++|.+|+|||+|+..+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367999999999999998864

>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=88.61  E-value=0.12  Score=44.74  Aligned_cols=23  Identities=35%  Similarity=0.488  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|.+|+|||||+..+.+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~~~   28 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999987643

>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=88.52  E-value=0.15  Score=46.08  Aligned_cols=27  Identities=22%  Similarity=0.156  Sum_probs=24.0

Q ss_pred             cEEEEEcCC-CCcHHHHHHHHHHHHhhc
Q 004895          182 NIIGVCGMG-GVGKTTLVKQIAKQVMED  208 (724)
Q Consensus       182 ~vi~I~G~g-GiGKTtLa~~v~~~~~~~  208 (724)
                      +.+.|.|-| |+||||++..++.....+
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~   29 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA   29 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC
Confidence            467899998 999999999999998764

>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=88.51  E-value=0.12  Score=45.11  Aligned_cols=22  Identities=32%  Similarity=0.570  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||||...+.+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7799999999999999987643

>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=88.43  E-value=0.12  Score=45.30  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|..|+|||+|++.+.+..
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999888753

>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=88.34  E-value=0.11  Score=46.28  Aligned_cols=19  Identities=42%  Similarity=0.606  Sum_probs=17.3

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQI  201 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v  201 (724)
                      -|.|+|.+|+|||||..++
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3679999999999999988

>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=88.13  E-value=0.13  Score=44.47  Aligned_cols=22  Identities=41%  Similarity=0.673  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|..|+|||||+..+.++.
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5688999999999999998753

>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=88.10  E-value=0.13  Score=45.57  Aligned_cols=21  Identities=33%  Similarity=0.512  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.++|.+|+|||+|..++...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999988554

>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=87.99  E-value=0.17  Score=47.58  Aligned_cols=26  Identities=31%  Similarity=0.478  Sum_probs=22.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      .+..|+|.+|+||||||.+++.....
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~ia~   55 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQIAG   55 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHHc
Confidence            57889999999999999999877543

>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=87.89  E-value=0.098  Score=46.07  Aligned_cols=21  Identities=33%  Similarity=0.645  Sum_probs=18.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|+|+|.+|+|||||...+..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999998754

>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=87.84  E-value=0.07  Score=46.41  Aligned_cols=22  Identities=41%  Similarity=0.558  Sum_probs=17.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||+|...+.+..
T Consensus         6 i~vvG~~~vGKTsli~~~~~~~   27 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTGE   27 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC---
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999876653

>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=87.82  E-value=0.12  Score=45.19  Aligned_cols=22  Identities=32%  Similarity=0.496  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998753

>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=87.72  E-value=0.14  Score=45.37  Aligned_cols=22  Identities=36%  Similarity=0.422  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |.++|.+|+|||+|+..+.+..
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999887643

>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=87.68  E-value=0.15  Score=44.57  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.++|.+|+|||||...+.+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            46899999999999999887754

>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=87.50  E-value=0.24  Score=44.68  Aligned_cols=32  Identities=34%  Similarity=0.578  Sum_probs=23.5

Q ss_pred             HHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHH
Q 004895          169 FQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       169 ~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      ++.|.++|.   -+...++|..|+|||||...+..
T Consensus        86 ~~~L~~~l~---~kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          86 IEELKEYLK---GKISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             HHHHHHHHS---SSEEEEECSTTSSHHHHHHHHST
T ss_pred             HhhHHHHhc---CCeEEEECCCCCCHHHHHHhhcc
Confidence            345555553   24678999999999999998754

>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=87.30  E-value=0.15  Score=43.55  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|+|+|.+|+|||||..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999988754

>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=87.05  E-value=0.18  Score=43.76  Aligned_cols=24  Identities=25%  Similarity=0.448  Sum_probs=19.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      ..+ |.++|.+|+|||||...+.+.
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            344 669999999999999988654

>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=86.75  E-value=0.11  Score=45.52  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=18.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIA  202 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~  202 (724)
                      ---|.++|.+|+|||||..++.
T Consensus        17 ~~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          17 ELRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTC
T ss_pred             eEEEEEECCCCCCHHHHHHHHh
Confidence            3356699999999999998764

>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=86.67  E-value=0.17  Score=43.91  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-|.|.|.+|+||||+|..+..+
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            46789999999999999987764

>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=86.31  E-value=0.29  Score=47.97  Aligned_cols=42  Identities=19%  Similarity=0.162  Sum_probs=28.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhhc-cCCCeEEEEEEecC
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVMED-NVFDKVVMAEITKN  222 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~  222 (724)
                      .++..|.|++|.||||++..+....... ..-...+.++....
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTg  205 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTG  205 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSH
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcH
Confidence            4689999999999999988776654322 11233566665443

>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=86.28  E-value=0.2  Score=45.54  Aligned_cols=21  Identities=38%  Similarity=0.520  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      -|.++|.+|+|||||.+++..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            578999999999999998754

>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=86.24  E-value=0.11  Score=45.22  Aligned_cols=21  Identities=29%  Similarity=0.491  Sum_probs=8.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~  204 (724)
                      |.|+|.+|+|||||+..+..+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877754

>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=85.95  E-value=0.13  Score=44.97  Aligned_cols=25  Identities=16%  Similarity=0.312  Sum_probs=20.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHHH
Q 004895          179 DKLNIIGVCGMGGVGKTTLVKQIAK  203 (724)
Q Consensus       179 ~~~~vi~I~G~gGiGKTtLa~~v~~  203 (724)
                      ++...|+|+|.+++|||||..++..
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhC
Confidence            3456799999999999999988743

>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=85.91  E-value=0.19  Score=43.98  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      -|+|+|..|+|||||...+...
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999988754

>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=85.13  E-value=0.22  Score=42.89  Aligned_cols=23  Identities=22%  Similarity=0.358  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-|.|.|..|+||||+|..+..+
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            46789999999999999887765

>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=84.92  E-value=0.19  Score=43.60  Aligned_cols=23  Identities=17%  Similarity=0.309  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 004895          182 NIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .-|.|.|++|+||||+|..+..+
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            45789999999999999988753

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=84.85  E-value=0.39  Score=42.18  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=30.2

Q ss_pred             HHHHHHHHhc-CCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          168 IFQDVIEALK-DDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       168 ~~~~l~~~L~-~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      -+..+..+|. .++...+.++|+++.|||++|..+.+-..
T Consensus        39 Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          39 FLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             HHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            3455555554 35668999999999999999999888763

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=84.24  E-value=0.25  Score=46.33  Aligned_cols=28  Identities=29%  Similarity=0.304  Sum_probs=24.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          180 KLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       180 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +.|-|+|+|.+|.|||||+..+......
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~~~g~   32 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILYYTGR   32 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHHHHTS
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHHhcCc
Confidence            4678999999999999999999876543

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {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: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=84.20  E-value=3.7  Score=36.79  Aligned_cols=44  Identities=20%  Similarity=0.237  Sum_probs=36.8

Q ss_pred             chHHHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          164 SRKKIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       164 gR~~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      ......+++.+.+..+......|.|..|+|||-++-......-.
T Consensus        59 ~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~  102 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD  102 (233)
T ss_dssp             HHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH
Confidence            46677788888888888888899999999999999988877654

>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=83.73  E-value=0.11  Score=44.34  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=19.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 004895          184 IGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       184 i~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      |+++|.+|+|||||...+....
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            7899999999999999998654

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {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: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=83.53  E-value=0.31  Score=46.97  Aligned_cols=23  Identities=43%  Similarity=0.647  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 004895          183 IIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      -|.|+|..|+||||+.+.+....
T Consensus       168 nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGS
T ss_pred             CEEEEeeccccchHHHHHHhhhc
Confidence            37889999999999999887654

>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=82.59  E-value=0.61  Score=43.23  Aligned_cols=37  Identities=32%  Similarity=0.437  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcC--CCccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          168 IFQDVIEALKD--DKLNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       168 ~~~~l~~~L~~--~~~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .+.++...+.+  ...--|+|+|..|+|||||...+..+
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            34444444442  23346779999999999999999864

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=82.36  E-value=0.37  Score=44.90  Aligned_cols=24  Identities=29%  Similarity=0.558  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQ  204 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~  204 (724)
                      .|-|+|+|..|.|||||+..+...
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHHHH
Confidence            467999999999999999998654

>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=82.25  E-value=0.42  Score=43.47  Aligned_cols=25  Identities=36%  Similarity=0.420  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHH
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQV  205 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~  205 (724)
                      .++|+|+|..+.|||||+..+....
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHhhc
Confidence            4679999999999999999887654

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=80.90  E-value=0.82  Score=43.25  Aligned_cols=39  Identities=21%  Similarity=0.171  Sum_probs=23.2

Q ss_pred             cEEEEEcCCCCcHHHHHH-HHHHHHhhc-cCCCeEEEEEEe
Q 004895          182 NIIGVCGMGGVGKTTLVK-QIAKQVMED-NVFDKVVMAEIT  220 (724)
Q Consensus       182 ~vi~I~G~gGiGKTtLa~-~v~~~~~~~-~~F~~~~wv~vs  220 (724)
                      ..+.|.|.+|+||||.+. .+.+-.+.. .....++.++.+
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~t   55 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFT   55 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESS
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCc
Confidence            346788999999997654 443333221 122456666654

>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=80.86  E-value=0.35  Score=46.69  Aligned_cols=27  Identities=26%  Similarity=0.295  Sum_probs=22.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHHHHHhh
Q 004895          181 LNIIGVCGMGGVGKTTLVKQIAKQVME  207 (724)
Q Consensus       181 ~~vi~I~G~gGiGKTtLa~~v~~~~~~  207 (724)
                      +-.|.|-|+-|+||||+++.+.+....
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             eEEEEEECCccCCHHHHHHHHHHHhcc
Confidence            346788999999999999999987653

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

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: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=80.75  E-value=0.76  Score=45.66  Aligned_cols=39  Identities=21%  Similarity=0.156  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhcCCCccEEEEEcCCCCcHHHHHHHHHHHHh
Q 004895          167 KIFQDVIEALKDDKLNIIGVCGMGGVGKTTLVKQIAKQVM  206 (724)
Q Consensus       167 ~~~~~l~~~L~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~  206 (724)
                      ..++.+.++ ......+|.|.|+.|.||||....+.+...
T Consensus       145 ~~~~~l~~l-~~~~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         145 HNHDNFRRL-IKRPHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             HHHHHHHHH-HTSSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             HHHHHHHHH-HhhhhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            344444444 455678999999999999999999988763

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=80.08  E-value=0.74  Score=44.00  Aligned_cols=39  Identities=21%  Similarity=0.199  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHH-HHHHHhhc-cCCCeEEEEEEec
Q 004895          183 IIGVCGMGGVGKTTLVKQ-IAKQVMED-NVFDKVVMAEITK  221 (724)
Q Consensus       183 vi~I~G~gGiGKTtLa~~-v~~~~~~~-~~F~~~~wv~vs~  221 (724)
                      .+.|.|.+|+||||.+.+ +++-.... ...+.++.++.+.
T Consensus        26 ~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~   66 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTN   66 (318)
T ss_dssp             CEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSH
T ss_pred             CEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccH
Confidence            366889999999976654 33333221 1224466665443